Add pre-commit hooks to the repo

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/automatic_testing.yml

@@ -4,10 +4,17 @@
 name: SIMPA tests
 
 on:
+  # run SIMPA tests on pushes to the main or develop branch
   push:
     branches: [ main, develop ]
+  # and on all pull requests to the main or develop branch
   pull_request:
     branches: [ main, develop ]
+  # as well as upon manual triggers through the 'Actions' tab of the Github UI
+  workflow_dispatch:
+  # Additionally, run Friday morning 6AM, so that we can react quickly if things break
+  schedule:
+  - cron: "0 5 * * 5"
 
 jobs:
   build:

.github/workflows/pypi.yml

@@ -0,0 +1,18 @@
+# Uploads the current version of the package to PyPI when commit are pushed to main (including merges via pull requests)
+
+name: Upload to PyPI
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build and publish to pypi
+        uses: JRubics/poetry-publish@v1.16
+        with:
+          pypi_token: ${{ secrets.PYPI_TOKEN }}

.gitlint

@@ -0,0 +1,7 @@
+# Configuration file for gitlint, used via pre-commit
+# Configuration docs: http://jorisroovers.github.io/gitlint/configuration/
+# Default rules: https://github.com/jorisroovers/gitlint/blob/master/docs/rules.md
+
+[general]
+# Ignore certain rules, you can reference them by their id or by their full name
+ignore=title-max-length, title-trailing-punctuation, body-is-missing, body-max-line-length, body-first-line-empty, body-min-length, body-changed-file-mention

.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+default_install_hook_types: [pre-commit, commit-msg]
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks # Uses MIT-License (MIT compatible) 
+    rev: v4.4.0
+    hooks:
+    -   id: check-yaml # checks is yaml file is valid
+    -   id: check-added-large-files # prevents adding large files, above 500kB
+
+-   repo: https://github.com/pre-commit/mirrors-autopep8 # Uses MIT-License (MIT compatible) 
+    rev: v2.0.2  # Use the sha / tag you want to point at
+    hooks:
+    -   id: autopep8 # formats code according to PEP8 standard. Lets commit fail if it needs to reformat code. Config for autopep8 is done in myproject.toml
+
+-   repo: https://github.com/citation-file-format/cff-converter-python # Uses Apache 2.0-License (MIT compatible)
+    rev: "44e8fc9"
+    hooks:
+      - id: validate-cff # validates cff citation files
+
+- repo: https://github.com/Lucas-C/pre-commit-hooks # Uses MIT License (MIT compatible)
+  rev: v1.5.1
+  hooks:
+    - id: insert-license    # Checks if the license header specified at license_header.txt is added in the first lines of each python file. If not, it suggests to insert them.
+      types: [python]
+      args:
+        - --license-filepath
+        - license_header.txt        # defaults to: LICENSE.txt
+
+-   repo: https://github.com/jorisroovers/gitlint # Uses MIT License (MIT compatible)
+    rev:  v0.19.1
+    hooks:
+    -   id: gitlint
+
+-   repo: https://github.com/tcort/markdown-link-check # Uses ISC-License (MIT compatible) 
+    rev: v3.10.3
+    hooks:
+      - id: markdown-link-check # checks if links in markdown files work
+        exclude: docs/
+        types: [markdown]
+
+# toggle comment to perform git config user email check. Note that you have to place the check-email.sh script in your .git/hooks/ folder
+# -   repo: local
+#     hooks:
+#       - id: git-config-email-check # checks if git config user email address is valid according to specified domains in check-email.sh script
+#         name: git-config-email-check
+#         entry: .git/hooks/check-email.sh
+#         language: script

CONTRIBUTING.md

@@ -36,9 +36,10 @@ In general the following steps are involved during a contribution:
 5.	Perform test driven development on feature branch. 
       A new implemented feature / a bug fix should be accompanied by a test. 
       Additionally, all previously existing tests must still pass after the contribution. 
-6.	Once development is finished, create a pull request including your changes. 
+6.    Run pre-commit hooks and make sure all hooks are passing.
+7.	Once development is finished, create a pull request including your changes. 
       For more information on how to create pull request, see GitHub's [about pull requests](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests).
-7.	A member of the core development team will review your pull request and potentially require further changes 
+8.	A member of the core development team will review your pull request and potentially require further changes 
       (see [Contribution review and integration](#contribution-review-and-integration)). 
       Once all remarks have been resolved, your changes will be merged into the develop branch.
 
@@ -86,8 +87,37 @@ In case already existing commits need to be signed off, you can make use of the
 
 `git commit --amend --signoff`
 
+### Install pre-commit hooks
+
+In your SIMPA root directory run `pre-commit install` to set up the pre-commit hooks defined in `.pre-commit-config.yaml`. This will generate pre-commit hooks in `.git/hooks/` and run them for every commit. To run them manually before you commit, call `pre-commit run --all-files`.
+
+<details>
+<summary>Further information on pre-commit hooks</summary>
+
+#### git config user email address checking
+The `git-config-email-check` hook is by default commented out in `pre-commit-config.yaml`. If you want to get a warning when you are not using a specified git config user email address domain, then you might want to comment this hook in. Then you would have to place a file according to the given path, e.g. at `.git/hooks/check-email.sh` with the following content:
+
+```shell
+#!/bin/bash
+PWD=`pwd`
+EMAIL=$(git config user.email)
+if [[ $EMAIL == *"@yourdomain.com"* ]]; then
+  echo "[INFO] Verified email: $EMAIL"
+else
+  echo "[ERROR] Invalid email: $EMAIL => Please configure the company email and retry."
+  echo "Steps:"
+  echo "   cd $PWD"
+  echo '   git config user.email "<user>@yourdomain.com"'
+  echo ""
+  exit 1;
+fi;
+```
+
+Change the domain in lines 4 and 10 according to your specific domain (e.g. corporate email domain) or even whole email address.
+</details>
+
 ### Contribution review and integration
-To ensure correctness and high quality of the submitted code, each contribution will be reviewed by a member of the core development team regarding among others the following aspects:
+To ensure correctness and high quality of the submitted code, each contribution will be checked by pre-commit hooks and reviewed by a member of the core development team regarding among others the following aspects:
 - The code is correct and implements the described feature / fixes the described issue.
 - The code follows the [SIMPA coding style](#coding-style)
 - The code is [documented appropriately](#documenting-your-code)
@@ -104,7 +134,7 @@ We also have a Slack workspace that you can join if you are interested to contri
 
 ## Coding style
 
-When writing code for SIMPA, please use the [PEP 8](https://www.python.org/dev/peps/pep-0008/) python coding conventions
+When writing code for SIMPA, please use the [PEP 8](https://www.python.org/dev/peps/pep-0008/) python coding conventions (which will be checked with the [autopep8 pre-commit hook](https://github.com/pre-commit/mirrors-autopep8))
 and consider using the following structures in your code in order to make a new
 developer or someone external always know exactly what to expect.
 

README.md

@@ -1,11 +1,14 @@
+<div align="center">
+
+![Logo](docs/source/images/simpa_logo.png?raw=true "Logo")
+
 [![Documentation Status](https://readthedocs.org/projects/simpa/badge/?version=develop)](https://simpa.readthedocs.io/en/develop/?badge=develop)
 ![Build Status](https://github.com/IMSY-DKFZ/simpa/actions/workflows/automatic_testing.yml/badge.svg)
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/IMSY-DKFZ/simpa/blob/main/LICENSE.md)
-
 [![Pypi Badge](https://img.shields.io/pypi/v/simpa)](https://pypi.org/project/simpa/)
 [![PyPI downloads](https://img.shields.io/pypi/dw/simpa?color=gr&label=pypi%20downloads)](https://pypi.org/project/simpa/)
 
-![Logo](docs/source/images/simpa_logo.png?raw=true "Logo")
+</div>
 
 # The toolkit for Simulation and Image Processing for Photonics and Acoustics (SIMPA)
 
@@ -177,7 +180,7 @@ To contribute to SIMPA, please fork the SIMPA github repository and create a pul
 suggested changes. The core developers will then review the suggested changes and integrate these into the code 
 base.
 
-Please make sure that you have included unit tests for your code and that all previous tests still run through.
+Please make sure that you have included unit tests for your code and that all previous tests still run through. Please also run the pre-commit hooks and make sure they are passing.
 
 There is a regular SIMPA status meeting every Friday on even calendar weeks at 10:00 CET/CEST, and you are very welcome to participate and
 raise any issues or suggest new features. If you want to join this meeting, write one of the core developers.

docs/source/clean_up_rst_files.py

@@ -40,7 +40,8 @@
 if os.path.exists(os.path.join(current_dir, "simpa_examples.rst")):
     os.remove(os.path.join(current_dir, "simpa_examples.rst"))
 simpa_examples_rst_file = open(os.path.join(current_dir, "simpa_examples.rst"), "w")
-simpa_examples_rst_file.write("simpa\_examples\n=========================================\n\n.. toctree::\n   :maxdepth: 2\n\n")
+simpa_examples_rst_file.write(
+    "simpa\_examples\n=========================================\n\n.. toctree::\n   :maxdepth: 2\n\n")
 examples = glob.glob(os.path.join(current_dir, "../" + folder_level + "simpa_examples/*.py"))
 for example in examples:
     example_file_name = example.split("/")[-1]
@@ -51,7 +52,8 @@
     if os.path.exists(os.path.join(current_dir, example_file_name_rst)):
         os.remove(os.path.join(current_dir, example_file_name_rst))
     example_rst_file = open(os.path.join(current_dir, example_file_name_rst), "a")
-    example_rst_file.write("{}\n=========================================\n\n.. literalinclude:: ../{}\n   :language: python\n   :lines: 1-\n\n".format(example_file_name, f'../simpa_examples/{example_file_name}.py'))
+    example_rst_file.write("{}\n=========================================\n\n.. literalinclude:: ../{}\n   :language: python\n   :lines: 1-\n\n".format(
+        example_file_name, f'../simpa_examples/{example_file_name}.py'))
     example_rst_file.close()
     simpa_examples_rst_file.writelines("   {}\n".format(example_file_name))
 

docs/source/conf.py

@@ -23,14 +23,14 @@
 
 project = 'SIMPA'
 _copyright = '2020-2021, IMSY (Division of Intelligent Medical Systems), DKFZ, Heidelberg and ' \
-            'Janek Groehl'
+    'Janek Groehl'
 author = 'IMSY (Division of Intelligent Medical Systems), DKFZ, Heidelberg and ' \
          'Janek Groehl'
 
 # The full version
 # SIMPA syntax: RELEASE.MAJOR.MINOR
-with open('../../VERSION', 'r') as readme_file:
-    version = readme_file.read()
+with open('../../pyproject.toml', 'r') as py_project_file:
+    version = py_project_file.readlines()[2].split('\"')[-2]
 
 # -- General configuration ---------------------------------------------------
 

license_header.txt

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021 Division of Intelligent Medical Systems, DKFZ
+SPDX-FileCopyrightText: 2021 Janek Groehl
+SPDX-License-Identifier: MIT