Feature/mx-1347 link cruft template (#61)

# Added - cruft template link # Changes - harmonized boilerplate
robert-koch-institut · Jan 17, 2024 · c456e8d · c456e8d
1 parent 00e095a
commit c456e8d
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diff --git a/.cruft.json b/.cruft.json
@@ -0,0 +1,14 @@
+{
+  "checkout": null,
+  "commit": "fb8fdbbc28f15d99939d22915b49348150d1d534",
+  "context": {
+    "cookiecutter": {
+      "project_name": "common",
+      "short_summary": "Common library for MEx python projects.",
+      "long_summary": "The `mex-common` library is a software development toolkit that is used by multiple components within the MEx project. It contains utilities for building pipelines like a common commandline interface, logging and configuration setup. It also provides common auxiliary connectors that can be used to fetch data from external services and a re-usable implementation of the MEx metadata schema as pydantic models.",
+      "_template": "https://github.com/robert-koch-institut/mex-template"
+    }
+  },
+  "directory": null,
+  "template": "https://github.com/robert-koch-institut/mex-template"
+}
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,28 +1,20 @@
-# Ticket Number
-<!--- Number of the ticket of this PR. -->
+# PR Context
+<!-- Additional info for the reviewer -->
 
-# Uncovered Acceptance Criteria
-<!--- Acceptance criteria that you did not cover and why you did not cover them. -->
-
-# Open Questions
-<!--- Questions that you have. -->
+# Added
+<!-- New features and interfaces -->
 
 # Changes
+<!-- Changes in existing functionality -->
 
-## Added
-<!--- For new features. -->
-
-## Changes
-<!--- For changes in existing functionality. -->
-
-## Deprecated
-<!--- For soon-to-be removed features. -->
+# Deprecated
+<!-- Soon-to-be removed features -->
 
-## Removed
-<!--- For now removed features. -->
+# Removed
+<!-- Definitely removed features -->
 
-## Fixed
-<!--- For any bug fixes. -->
+# Fixed
+<!-- Fixed bugs -->
 
-## Security
-<!--- In case of fixed vulnerabilities. --> 
+# Security
+<!-- Fixed vulnerabilities -->
diff --git a/.github/workflows/cookiecutter.yml b/.github/workflows/cookiecutter.yml
@@ -0,0 +1,42 @@
+name: Cookiecutter
+
+on:
+  push:
+    branches: ["main"]
+  workflow_dispatch:
+
+env:
+  PIP_NO_OPTION: on
+  PIP_NO_CLEAN: on
+  PIP_PREFER_BINARY: on
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+
+      - name: Cache requirements
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-requirements
+        with:
+          path: ~/.cache/pip
+          key: ${{ env.cache-name }}-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ env.cache-name }}-
+
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install requirements
+        run: make setup
+
+      - name: Check template
+        run: cruft check
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -45,7 +45,7 @@ jobs:
           cache-name: cache-poetry
         with:
           path: ~/.cache/pip
-          key: ${{ env.cache-name }}-${{ hashFiles('**/poetry.lock') }}
+          key: ${{ env.cache-name }}-${{ hashFiles('poetry.lock') }}
           restore-keys: |
             ${{ env.cache-name }}-
 

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -29,6 +29,16 @@ jobs:
           restore-keys: |
             ${{ env.cache-name }}-
 
+      - name: Cache poetry
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-poetry
+        with:
+          path: ~/.cache/pip
+          key: ${{ env.cache-name }}-${{ hashFiles('poetry.lock') }}
+          restore-keys: |
+            ${{ env.cache-name }}-
+
       - name: Setup python
         uses: actions/setup-python@v4
         with:

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -35,7 +35,7 @@ jobs:
           cache-name: cache-poetry
         with:
           path: ~/.cache/pip
-          key: ${{ env.cache-name }}-${{ hashFiles('**/poetry.lock') }}
+          key: ${{ env.cache-name }}-${{ hashFiles('poetry.lock') }}
           restore-keys: |
             ${{ env.cache-name }}-
 

diff --git a/.gitignore b/.gitignore
@@ -34,7 +34,7 @@ MANIFEST
 pip-log.txt
 pip-delete-this-directory.txt
 
-# Unit test / coverage reports
+# Testing / coverage reports
 htmlcov/
 .tox/
 .nox/
@@ -54,7 +54,7 @@ pytestdebug.log
 *.mo
 *.pot
 
-# Scrapy stuff:
+# Scrapy stuff
 .scrapy
 
 # Sphinx documentation
@@ -75,7 +75,7 @@ ipython_config.py
 # pyenv
 .python-version
 
-# PEP 582; used by e.g. pyflow
+# PEP 582
 __pypackages__/
 
 # Celery stuff

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,12 +3,12 @@ default_language_version:
   python: python3.11
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.1.13
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.1
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -17,6 +17,7 @@ repos:
       - id: pretty-format-json
         name: json
         args: [--autofix]
+        exclude: .cruft.json
       - id: check-yaml
         name: yaml
   - repo: https://github.com/python-poetry/poetry

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- cruft template link
+
 ### Changes
 
+- harmonized boilerplate
+
 ### Deprecated
 
 ### Removed
@@ -43,7 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - tests for `mex.common.types.PathWrapper`
-- method `is_relative` to `mex.common.types.PathWrapper` to check whether the path is 
+- method `is_relative` to `mex.common.types.PathWrapper` to check whether the path is
   relative
 
 ### Changes
@@ -52,7 +56,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- nesting of `mex.common.types.PathWrapper` on instantiation 
+- nesting of `mex.common.types.PathWrapper` on instantiation
 
 ## [0.18.0] - 2023-12-20
 

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Robert Koch-Institut
+Copyright (c) 2024 Robert Koch-Institut
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: all test setup hooks install pytest linter build docs
+.PHONY: all test setup hooks install linter pytest wheel docs
 all: install test
 test: linter pytest
 
@@ -28,7 +28,7 @@ pytest:
 	@ echo running unit tests; \
 	poetry run pytest -m "not integration"; \
 
-build:
+wheel:
 	# build the python package
 	@ echo building wheel; \
 	poetry build --no-interaction --format wheel; \
@@ -37,4 +37,4 @@ docs:
 	# use sphinx to auto-generate html docs from code
 	@ echo generating api docs; \
 	poetry run sphinx-apidoc -f -o docs/source mex; \
-	poetry run sphinx-build -b dirhtml docs docs/dist; \
+	poetry run sphinx-build -aE -b dirhtml docs docs/dist; \
diff --git a/README.md b/README.md
@@ -19,6 +19,10 @@ Via MEx, metadata will be made findable, accessible and shareable, as well as av
 for further research. The goal is to get an overview of what research data is available,
 understand its context, and know what needs to be considered for subsequent use.
 
+RKI cooperated with D4L data4life gGmbH for a pilot phase where the vision of a
+FAIR metadata catalog was explored and concepts and prototypes were developed.
+The partnership has ended with the successful conclusion of the pilot phase.
+
 After an internal launch, the metadata will also be made publicly available and thus be
 available to external researchers as well as the interested (professional) public to
 find research data from the RKI.
@@ -33,15 +37,15 @@ data Findable, Accessible, Interoperable and Reusable.
 ## package
 
 The `mex-common` library is a software development toolkit that is used by multiple
-components within the MEx project. It contains utilities for building pipelines
-like a common commandline interface, logging and configuration setup. It also provides
-common auxiliary connectors that can be used to fetch data from external services and
-a re-usable implementation of the MEx metadata schema as pydantic models.
+components within the MEx project. It contains utilities for building pipelines like a
+common commandline interface, logging and configuration setup. It also provides common
+auxiliary connectors that can be used to fetch data from external services and a
+re-usable implementation of the MEx metadata schema as pydantic models.
 
 ## license
 
-This package is licensed under the [MIT license](/LICENSE). Other components of the
-MEx project will be released under the same license in the future.
+This package is licensed under the [MIT license](/LICENSE). All other software
+components of the MEx project are open-sourced under the same license as well.
 
 ## development
 
@@ -66,11 +70,20 @@ MEx project will be released under the same license in the future.
 - or run manually
   - linter checks via `pre-commit run --all-files`
   - all tests via `poetry run pytest`
+  - just unit tests via `poetry run pytest -m "not integration"`
 
 ### updating dependencies
 
+- update boilerplate files with `cruft update`
 - update global dependencies in `requirements.txt` manually
 - update git hooks with `pre-commit autoupdate`
 - show outdated dependencies with `poetry show --outdated`
 - update dependencies in poetry using `poetry update --lock`
-- update github actions manually in `.github\workflows\default.yml`
+- update github actions manually in `.github/workflows/*.yml`
+
+### creating release
+
+- update version, eg `poetry version minor`
+- commit update `git commit --message "..." pyproject.toml`
+- create a tag `git tag ...`
+- push `git push --follow-tags`
diff --git a/SECURITY.md b/SECURITY.md
@@ -2,13 +2,13 @@
 
 ## Supported Versions
 
-This python package is currently in pre-release state. That means changes can
+This software package is currently in pre-release state. That means changes can
 occur frequently and only the latest released version will be supported with
 security and bug fixes. It is therefore not recommended to use this package in
 productive environments.
 
 ## Reporting a Vulnerability
 
 If you discover a vulnerability, please contact the author team directly via
-[email](pyproject.toml). Pull-requests with proposed solutions are explicitly
+[email](mailto:[email protected]). Pull-requests with proposed solutions are explicitly
 welcomed as well.
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,7 +1,9 @@
 # sphinx configuration
 
-html_theme = "sphinx_book_theme"
 extensions = ["sphinx.ext.napoleon"]
+html_theme = "alabaster"
 napoleon_google_docstring = True
 napoleon_include_init_with_doc = True
 napoleon_include_private_with_doc = True
+project = "mex-common"
+templates_path = ["."]
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,7 +1,10 @@
-mex-common
-==========
+Documentation
+=============
+
+Common library for MEx python projects.
 
 .. toctree::
+    :maxdepth: 2
     :glob:
 
     source/*
diff --git a/docs/layout.html b/docs/layout.html
@@ -0,0 +1,18 @@
+{% extends '!layout.html' %}
+
+{% block footer %}
+    <div class="footer">
+        <a href="https://www.rki.de/DE/Content/Forsch/MEx/MEx_inhalt.html" rel="nofollow">
+            MEx Project
+        </a> |
+        <a href="https://www.rki.de/DE/Service/Impressum/impressum_node.html" rel="nofollow">
+            RKI Imprint
+        </a> |
+        <a href="https://docs.github.com/site-policy/privacy-policies/github-privacy-statement" rel="nofollow">
+            GitHub Privacy
+        </a> |
+        <a href="https://docs.github.com/en/site-policy/privacy-policies/github-cookies" rel="nofollow">
+            GitHub Cookies
+        </a>
+    </div>
+{% endblock %}
diff --git a/mex.bat b/mex.bat
@@ -32,7 +32,7 @@ echo linting all files
 pre-commit run --all-files
 if %errorlevel% neq 0 exit /b %errorlevel%
 
-@REM run the pytest test suite with all unit tests
+@REM run the pytest test suite with unit and integration tests
 echo running all tests
 poetry run pytest
 exit /b %errorlevel%
@@ -41,7 +41,7 @@ exit /b %errorlevel%
 :docs
 @REM use sphinx to auto-generate html docs from code
 echo generating api docs
-poetry run sphinx-apidoc -f -o docs/source mex
+poetry run sphinx-apidoc -f -o docs\source mex
 if %errorlevel% neq 0 exit /b %errorlevel%
-poetry run sphinx-build -b dirhtml docs docs/dist
+poetry run sphinx-build -aE -b dirhtml docs docs\dist
 exit /b %errorlevel%