Improve template documentation

docker/ci-runner/Dockerfile

-FROM python:3.12
+# This dockerfile is used throughout steps of the CI/CD pipeline
+# It contains dependencies to execute the template and run tests
+FROM python:3.13
 
 RUN python -m pip install --upgrade pip
 RUN python -m pip install --upgrade cookiecutter tox twine

{{cookiecutter.project_slug}}/.gitlab-ci.yml

@@ -2,8 +2,6 @@ default:
   image:
     name: $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG
     pull_policy: always
-  before_script:
-    - python --version # For debugging
   cache:
     paths:
       - .cache/pip
@@ -24,12 +22,13 @@ stages:
 variables:
   PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
 
+# Job templates from Gitlab that scan for security issues or leaked secrets
 include:
   - template: Security/SAST.gitlab-ci.yml
   - template: Security/Dependency-Scanning.gitlab-ci.yml
   - template: Security/Secret-Detection.gitlab-ci.yml
 
-# Prepare image to run ci on
+# Prepare image to run ci on, image will be used in most jobs
 trigger_prepare:
   stage: prepare
   trigger:
@@ -53,16 +52,6 @@ sast:
       pmd-apex, security-code-scan, sobelow, spotbugs
   stage: test
 
-dependency_scanning:
-  # override default before_script, job won't have Python available
-  before_script:
-    - uname
-
-secret_detection:
-  # override default before_script, job won't have Python available
-  before_script:
-    - uname
-
 # Basic setup for all Python versions for which we don't have a base image
 .run_unit_test_version_base:
   before_script:
@@ -71,6 +60,7 @@ secret_detection:
     - python -m pip install --upgrade tox twine
 
 # Run all unit tests for Python versions except the base image
+# The base image is used for the highest Python version
 run_unit_tests:
   extends: .run_unit_test_version_base
   stage: test
@@ -95,6 +85,7 @@ run_unit_tests_coverage:
     paths:
       - htmlcov/*
 
+# Build and packge the project
 package_files:
   stage: package
   artifacts:
@@ -104,6 +95,7 @@ package_files:
   script:
     - tox -e build
 
+# Build the sphinx documentation
 package_docs:
   stage: package
   artifacts:
@@ -113,6 +105,7 @@ package_docs:
   script:
     - tox -e docs
 
+# Build a tiny docker image that contains the minimal dependencies to run this project
 docker_build:
   stage: images
   image: docker:latest
@@ -203,6 +196,7 @@ publish_to_readthedocs:
     - echo "scp docs/* ???"
     - exit 1
 
+# automatically create a release on Gitlab for every tagged commit
 release_job:
   stage: publish
   image: registry.gitlab.com/gitlab-org/release-cli:latest

{{cookiecutter.project_slug}}/.pre-commit-config.yaml

+# run several checks prior to creating a commit or pushing to a remote
+# These can be skipped (but you shouldn't generally as the pipeline will fail)
+# using `git push / commit --no-check`
+# for more information see: https://pre-commit.com/
 default_stages: [ pre-commit, pre-push ]
 default_language_version:
   python: python3

{{cookiecutter.project_slug}}/README.md

@@ -57,5 +57,7 @@ To automatically apply most suggested linting changes execute:
 
 ```tox -e format```
 
+The configuration for linting and tox can be found in `pyproject.toml`
+
 ## License
 This project is licensed under the Apache License Version 2.0

{{cookiecutter.project_slug}}/bin/install-hooks/pre-commit.sh

-#!/bin/bash
-
-if [ ! -f "setup.sh" ]; then
-  echo "pre-commit.sh must be executed with repository root as working directory!"
-  exit 1
-fi
-
-pre-commit install --hook-type pre-push

{{cookiecutter.project_slug}}/docker/ci-runner/Dockerfile

+# This dockerfile is used throughout steps of the CI/CD pipeline
+# It contains dependencies to run tests
 FROM python:3.13
 
 RUN python -m pip install --upgrade pip

{{cookiecutter.project_slug}}/docker/{{cookiecutter.project_slug}}/Dockerfile

+# This dockerfile creates a minimal docker image that can run the project.
+# It can copy the result of `tox -e build` from the host to the container
+# or build from source inside the container.
+# Set `docker build --build-arg BUILD_ENV=copy` to copy from the host, rebuild otherwise
+# contrarily, to the ci image it does not contain any dependencies used for testing.
 ARG BUILD_ENV=no_copy
 
+# Build without copying from host inside docker
 FROM python:3.13 AS build_no_copy
 ADD ../../requirements.txt .
 COPY ../.. /work
-RUN rm -r /work/dist | true
+RUN rm -rf /work/dist
 RUN python -m pip install --user tox
 WORKDIR /work
 RUN python -m tox -e build
 
+# Copy build package from host `dist` directory
 FROM python:3.13 AS build_copy
 COPY dist /work/dist
 
+# Dynamically set `build` from `build_no_copy` or `build_copy` depending on
+# `BUILD_ENV` argument
 FROM build_${BUILD_ENV} AS build
 
+# Copy build stage files into final python slim image and install
 FROM python:3.13-slim
 COPY --from=build /work/dist /dist
 RUN python -m pip install /dist/*.whl

{{cookiecutter.project_slug}}/docs/cleanup.py

@@ -3,6 +3,16 @@
 #  Copyright (C) 2023 ASTRON (Netherlands Institute for Radio Astronomy)
 #  SPDX-License-Identifier: Apache-2.0
 
+"""
+Remove generated source documentation files except for index.rst
+
+If a source file is created, documentation is generated and the source file is later
+removed. The documentation for this source file will persists.
+
+This file ensures generated source documentation files, which are automatically
+generated from source, are removed between every build.
+"""
+
 import os
 
 file_dir = os.path.dirname(os.path.realpath(__file__))

{{cookiecutter.project_slug}}/setup.sh

@@ -4,8 +4,10 @@
 # SPDX-License-Identifier: Apache-2.0
 #
 
-# This file's directory is used to determine the station control directory
-# location.
+# Substitute BASH_SOURCE if unset this is required for simple shells
+# such as the one found in docker or alpine docker images.
+# `#! /usr/bin/env bash` does not actually ensure the sourcing is executed
+# using BASH
 if [ -z ${BASH_SOURCE} ]; then
   BASH_SOURCE=${(%):-%x}
 fi
@@ -24,7 +26,7 @@ source "$VENV_DIR/bin/activate"
 python -m pip install pre-commit
 python -m pip install "tox>=4.21.0"
 
-# Install git pre-commit pre-push hook
-if [ ! -f "${ABSOLUTE_PATH}/.git/hooks/pre-push.legacy" ]; then
-  source "${ABSOLUTE_PATH}/bin/install-hooks/pre-commit.sh"
+# Install git pre-commit pre-push hook if not already installed
+if [ ! -f "${ABSOLUTE_PATH}/.git/hooks/pre-push" ]; then
+  pre-commit install --hook-type pre-push
 fi