Copier update: misc agent instructions

.config/.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.0.139
+_commit: v0.0.143
 _src_path: gh:LabAutomationAndScreening/copier-base-template.git
 copier_answers_directory: .config
 description: A web app that is hosted within a local intranet. Nuxt frontend, python

.config/pyrefly.toml

@@ -22,7 +22,7 @@ project-includes = [
                     "../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
+disable-project-excludes-heuristics = true # with this being enabled by default, pyrefly thinks 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

.config/ruff.toml

@@ -39,6 +39,9 @@ exclude = [
 line-length = 120
 indent-width = 4
 
+# resolved relative to the cwd where ruff runs (repo root under pre-commit), so this nests the cache under .config
+cache-dir = ".config/.ruff_cache"
+
 target-version = "py312"
 
 [lint]
@@ -66,8 +69,11 @@ 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
+    "SIM103", # Explicit if/else branches let the coverage checker track both paths, unlike evaluating an expression
     "SIM108", # Explicit if/else branches let the coverage checker track both paths, unlike a ternary
+    "SIM110", # Explicit if statements and loops let the coverage checker track both paths, unlike using `any` or `all` with a generator expression
     "SIM114", # Using `or` statements to simplify this would confuse the coverage checker
+    "SIM401", # using dictionary getters to simplify this would inhibit the coverage checker from tracking both paths
     "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

.devcontainer/devcontainer.json

@@ -16,16 +16,16 @@
       "extensions": [
         // basic tooling
         // "eamodio.gitlens@15.5.1",
-        "coderabbit.coderabbit-vscode@0.20.7",
+        "coderabbit.coderabbit-vscode@0.21.0",
         "ms-vscode.live-server@0.5.2025051301",
         "MS-vsliveshare.vsliveshare@1.0.5905",
-        "anthropic.claude-code@2.1.205",
+        "anthropic.claude-code@2.1.211",
 
         // Python
         "ms-python.python@2026.5.2026052901",
-        "meta.pyrefly@1.1.9001",
+        "meta.pyrefly@1.1.9002",
         "ms-vscode-remote.remote-containers@0.414.0",
-        "charliermarsh.ruff@2026.56.0",
+        "charliermarsh.ruff@2026.60.0",
 
         // Misc file formats
         "bierner.markdown-mermaid@1.29.0",
@@ -60,5 +60,5 @@
   "initializeCommand": "sh .devcontainer/initialize-command.sh",
   "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): 7f763b1e # spellchecker:disable-line
+  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): ce58396b # spellchecker:disable-line
 }

.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
 
   # Reformatting (should generally come before any file format or other checks, because reformatting can change things)
   - repo: https://github.com/crate-ci/typos
-    rev: 359573a3ff38f71c93e160f2ace96d118f6ff42e  # frozen: v1
+    rev: 96d9af6217dc2855210655af7e1ff19d23d4e593  # frozen: v1
     hooks:
       - id: typos
         args: [--write-changes, --force-exclude, --config, .config/_typos.toml]
@@ -113,7 +113,7 @@ repos:
           )$
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: 515f543f5718ebfd6ce22e16708bb32c68ff96e1  # frozen: v3.8.3
+    rev: 9337a74165b178ae2c766f60bee7252a0f06f3e8  # frozen: v3.9.5
     hooks:
       - id: prettier
         args: [--config, .config/.prettierrc]
@@ -185,7 +185,7 @@ repos:
       - id: check-case-conflict
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 943377262562a12b57292fc98fabd7dbf81451fe  # frozen: 0.37.2
+    rev: 1a4bb160cab6417b3045e1b37b6b72449243e658  # frozen: 0.37.4
     hooks:
       - id: check-github-workflows
 
@@ -239,7 +239,7 @@ repos:
         description: Runs hadolint to lint Dockerfiles
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 6fec9b7edb08fd9989088709d864a7826dc74e80  # frozen: v0.15.12
+    rev: 2700fd5671c633760d912769c041bfcde2b9a01b  # frozen: v0.15.22
     hooks:
       - id: ruff
         name: ruff-src
@@ -270,7 +270,7 @@ repos:
           )$
 
   - repo: https://github.com/pylint-dev/pylint
-    rev: 88e1ab7545a4af4aea15c305a154c164a95ab842  # frozen: v4.0.5
+    rev: 8a396357098337ba8be714fffdf2d00947a9778c  # frozen: v4.0.6
     hooks:
       - id: pylint
         name: pylint

AGENTS.md

@@ -9,13 +9,18 @@ This project is a Copier template used to generate applications that are able to
 - Comments should be used very rarely. Code should generally express its intent.
 - Never write a one-line docstring — either the name is sufficient or the behavior warrants a full explanation.
 - Don't sort or remove imports manually — pre-commit handles it.
-- Always include type hints for pyright in Python
-- Respect the pyright rule reportUnusedCallResult; assign unneeded return values to `_`
 - Prefer keyword-only parameters (unless a very clear single-argument function): use `*` in Python signatures and destructured options objects in TypeScript.
 - When disabling a linting rule with an inline directive, provide a comment at the end of the line (or on the line above for tools that don't allow extra text after an inline directive) describing the reasoning for disabling the rule.
 - Avoid telling the type checker what a type is rather than letting it prove it. This includes type assertions (`as SomeType` in TypeScript, `cast()` in Python) and variable annotations that override inference. Prefer approaches that let the type checker verify the type itself: `isinstance`/`instanceof` narrowing, restructuring code so the correct type flows naturally, or using discriminated unions. When there is genuinely no alternative, add a comment explaining why the workaround is necessary and why it is safe.
 - Avoid `||` (TypeScript) or `or` (Python) in `if`/`elif` conditions, and avoid `x in ['a', 'b']`-style membership tests in implementation code — coverage tools treat these as a single branch, silently masking untested paths and producing false 100% branch coverage. Use separate `if`/`elif` branches instead so each condition is independently covered.
 
+### Python
+
+- Always include type hints.
+- Respect the pyrefly unused-call-result check; assign unneeded return values to `_`
+- Prefer explicit `if`/`else` (or a `for` loop with `if`/`return`) over one-line forms that collapse branches: a ternary, `d.get(key, default)`, returning a boolean expression `return b > 5`/`return bool(b)`, or `any()`/`all()` over a generator in place of a loop. `coverage.py` tracks branches as line-to-line arcs, so a single-line expression hides the untaken path.
+- When filtering logic combines multiple `and`-joined guards (e.g. a null check alongside a value check), prefer a loop with explicit `if`/`continue` branches over a single-line comprehension. A compound boolean filter on one line hides individual branches from line coverage — each guard condition should be its own statement so missing test cases are surfaced.
+
 ## Testing
 
 - Always run tests with an explicit path (e.g. uv run pytest tests/unit) — test runners discover all types (unit, integration, E2E...) by default.
@@ -24,7 +29,6 @@ This project is a Copier template used to generate applications that are able to
 - Avoid magic values in comparisons in tests in all languages (like ruff rule PLR2004 specifies). Note: `1` and `0` are not magic numbers (according to PLR2004)
 - Prefer using random values in tests rather than arbitrary ones (e.g. the faker library, uuids, random.randint) when possible. For enums, pick randomly rather than hardcoding one value.
 - Avoid loops in tests — assert each item explicitly so failures pinpoint the exact element. When verifying a condition across all items in a collection, collect the violations into a list and assert it's empty (e.g., assert [x for x in items if bad_condition(x)] == []).
-- When filtering logic combines multiple `and`-joined guards (e.g. a null check alongside a value check), prefer a loop with explicit `if`/`continue` branches over a single-line comprehension. A compound boolean filter on one line hides individual branches from line coverage — each guard condition should be its own statement so missing test cases are surfaced.
 - When a test's final assertion is an absence (e.g., element is `null`, list is empty, modal is closed), include a prior presence assertion confirming the expected state existed before the action that removed it. A test whose only assertion is an absence check can pass vacuously if setup silently failed.
 - When asserting a mock or spy was called with specific arguments, always constrain as tightly as possible. In order of preference: (1) assert called exactly once with those args (`assert_called_once_with` in Python, `toHaveBeenCalledExactlyOnceWith` in Vitest/Jest); (2) if multiple calls are expected, assert the total call count and use a positional or last-call assertion (`nthCalledWith`, `lastCalledWith` / `assert_has_calls` with `call_args_list[n]`); (3) plain "called with at any point" (`toHaveBeenCalledWith`, `assert_called_with`) is a last resort only when neither the call count nor the call order can reasonably be constrained.
 - When asserting an exception is raised, verify the error message includes all key constructor arguments — not just one identifying field. This ensures the error message is fully populated and catches cases where arguments are swapped or missing. In Python: use the `match` parameter in `pytest.raises`. In TypeScript: use a regex or substring in `toThrow`, or catch and assert on error properties individually.
@@ -77,7 +81,7 @@ This project is a Copier template used to generate applications that are able to
 - ❌ Never use `uv run python -c "import ...; print(...)"` or `inspect` to introspect Python source. ✅ Read source files directly or grep for symbols — the code is on disk and can be read without running it.
 - Check .devcontainer/devcontainer.json for tooling versions (Python, Node, etc.) when reasoning about version-specific stdlib or tooling behavior.
 - For frontend tests, run commands via `pnpm` scripts from `frontend/package.json` — never invoke tools directly (not pnpm exec <tool>, npx <tool>, etc.). ✅ pnpm test-unit  ❌ pnpm vitest ... or npx vitest ...
-- For linting and type-checking, prefer `pre-commit run <hook-id>` over invoking tools directly — this matches the permission allow-list and mirrors what CI runs. Key hook IDs: `typescript-check`, `eslint`, `pyright`, `ruff`, `ruff-format`.
+- For linting and type-checking, prefer `pre-commit run <hook-id>` over invoking tools directly — this matches the permission allow-list and mirrors what CI runs. Key hook IDs: `typescript-check`, `eslint`, `pyrefly`, `ruff`, `ruff-format`.
 - Never rely on IDE diagnostics for ruff warnings — the IDE may not respect the project's ruff.toml config. Run `pre-commit run ruff -a` to get accurate results.
 - Never use `pnpm --prefix <path>` or `uv --directory <path>` to target a different directory — these flags break the permission allow-list matcher the same way chained `cd &&` commands do. Instead, rely on the working directory already being correct (the cwd persists between Bash tool calls), or issue a plain `cd <path>` as a separate prior tool call to reposition before running the command.
 - Never use backslash line continuations in shell commands — always write the full command on a single line. Backslashes break the permission allow-list matcher.

extensions/context.py

@@ -113,6 +113,7 @@ def hook(  # noqa: PLR0915 # yes, this is a lot of statements, but it's all just
         context["gha_amazon_ecr_login"] = "v2.1.5"
         context["gha_setup_node"] = "v6.4.0"
         context["gha_action_gh_release"] = "v3.0.0"
+        context["gha_codecov"] = "v7.0.0"
         context["gha_mutex"] = "1ebad517141198e08d47cf72f3c0975316620a65 # v1.0.0-alpha.10"
         context["gha_pypi_publish"] = "v1.14.0"
         context["gha_sleep"] = "v2.0.3"

template/.config/pyrefly.toml

@@ -24,7 +24,7 @@ project-includes = [
 # "../backend" is needed so the tests package (rooted at backend/) resolves relative imports;
 # without it pyrefly infers the import root from this config's dir (.config/) and can't name the test modules
 search-path = ["../backend/src", "../backend"]
-disable-project-excludes-heuristics = true # with this being enabled by default, pyrefly things the src is excluded because it's an editable local install
+disable-project-excludes-heuristics = true # with this being enabled by default, pyrefly thinks 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

template/.config/ruff.toml

@@ -39,6 +39,9 @@ exclude = [
 line-length = 120
 indent-width = 4
 
+# resolved relative to the cwd where ruff runs (repo root under pre-commit), so this nests the cache under .config
+cache-dir = ".config/.ruff_cache"
+
 target-version = "py312"
 
 [lint]
@@ -66,8 +69,11 @@ 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
+    "SIM103", # Explicit if/else branches let the coverage checker track both paths, unlike evaluating an expression
     "SIM108", # Explicit if/else branches let the coverage checker track both paths, unlike a ternary
+    "SIM110", # Explicit if statements and loops let the coverage checker track both paths, unlike using `any` or `all` with a generator expression
     "SIM114", # Using `or` statements to simplify this would confuse the coverage checker
+    "SIM401", # using dictionary getters to simplify this would inhibit the coverage checker from tracking both paths
     "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

template/.devcontainer/devcontainer.json.jinja

@@ -35,16 +35,16 @@
         "-AmazonWebServices.aws-toolkit-vscode", // the AWS CLI feature installs this automatically, but it's causing problems in VS Code{% endraw %}{% endif %}{% raw %}
         // basic tooling
         // "eamodio.gitlens@15.5.1",
-        "coderabbit.coderabbit-vscode@0.20.7",
+        "coderabbit.coderabbit-vscode@0.21.0",
         "ms-vscode.live-server@0.5.2025051301",
         "MS-vsliveshare.vsliveshare@1.0.5905",{% endraw %}{% if install_claude_cli %}{% raw %}
-        "anthropic.claude-code@2.1.205",{% endraw %}{% endif %}{% raw %}{% endraw %}{% if (is_child_of_copier_base_template is defined and is_child_of_copier_base_template is sameas(true)) or (is_child_of_copier_base_template is not defined and template_uses_python is defined and template_uses_python is sameas(true)) %}{% raw %}
+        "anthropic.claude-code@2.1.211",{% endraw %}{% endif %}{% raw %}{% endraw %}{% if (is_child_of_copier_base_template is defined and is_child_of_copier_base_template is sameas(true)) or (is_child_of_copier_base_template is not defined and template_uses_python is defined and template_uses_python is sameas(true)) %}{% raw %}
 
         // Python
         "ms-python.python@2026.5.2026052901",
-        "meta.pyrefly@1.1.9001",
+        "meta.pyrefly@1.1.9002",
         "ms-vscode-remote.remote-containers@0.414.0",
-        "charliermarsh.ruff@2026.56.0",{% endraw %}{% endif %}{% raw %}
+        "charliermarsh.ruff@2026.60.0",{% endraw %}{% endif %}{% raw %}
 {% endraw %}{% if is_child_of_copier_base_template is not defined and template_uses_vuejs is defined and template_uses_vuejs is sameas(true) %}{% raw %}
         // VueJS
         "vue.volar@3.2.5",