Adding pre-commit instructions to the README

.github/workflows/docs.yml

@@ -0,0 +1,49 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - main
+  release:
+
+  pull_request:
+    branches:
+      - main
+
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: build
+          auto-update-conda: true
+
+      - name: install requirements
+        run: >-
+          conda install -n build -c conda-forge 
+          --file requirements/build.txt
+          --file requirements/run.txt
+          --file requirements/docs.txt
+          --quiet --yes
+
+      - name: install the package
+        run: python -m pip install . --no-deps
+
+      - name: build documents
+        run: make -C doc/manual html
+
+      - name: Deploy
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/manual/build/html

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+default_language_version:
+    python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/ambv/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+  - repo: local
+    hooks:
+      - id: prevent-commit-to-main
+        name: Prevent Commit to Main Branch
+        entry: ./prevent_commit_to_main.sh
+        language: script
+        stages: [commit]

README.rst

@@ -150,6 +150,24 @@ rather than copied to a system directory, use ::
 
      python -m pip install -e .
 
+CONTRIBUTING
+------------------------------------------------------------------------
+We welcome contributors from the community.  Please consider posting issues, and taking issues and posting PRs.
+
+To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
+hooks.
+
+1. modify the permissions to executable on the bash script called ``prevent_commit_to_main.sh`` in this directory: ``chmod +x prevent_commit_to_main.sh``
+
+2. install pre-commit in your working environment with ``conda install pre-commit``
+
+3. initialize pre-commit (one time only) ``pre-commit install``
+
+Thereafter your code will be linted by black and isort and checked against flake8 before you can commit.
+If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should
+pass after they are modified).  If the flake8 test fails please see the error messages and fix them manually before
+trying to commit again
+
 
 CONTACTS
 ------------------------------------------------------------------------

doc/make.bat → doc/manual/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/source/conf.py → doc/manual/source/conf.py

@@ -13,7 +13,7 @@
 import sys
 import os
 sys.path.insert(0, os.path.abspath('../..'))
-sys.path.insert(0, os.path.abspath('../../src'))
+sys.path.insert(0, os.path.abspath('../../../src'))
 
 
 # -- Project information -----------------------------------------------------

doc/source/index.rst → doc/manual/source/index.rst

@@ -63,7 +63,7 @@ To get started, please go to :ref:`quick_start`
    release
    package
 
-.. include:: ../../CHANGELOG.rst
+.. include:: ../../../CHANGELOG.rst
 
 Indices
 -------

doc/manual/source/release.rst

@@ -0,0 +1,4 @@
+.. index:: release notes
+
+.. include:: /../../../CHANGELOG.rst
+

prevent_commit_to_main.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+##!"C:\\Program Files\\Git\\usr\\bin\\bash.exe"
+
+branch="$(git rev-parse --abbrev-ref HEAD)"
+
+if [ "$branch" = "main" ]; then
+echo "You are on the main branch. Committing to the main branch is not allowed."
+exit 1
+fi