ci(PythonSemanticRelease): update python semantic release to v8; mino…

…r change to README; added support for py3.11; updated dependencies

.github/workflows/_quality.yaml

@@ -11,6 +11,8 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
       - uses: pre-commit/action@v3.0.0
       - uses: pre-commit-ci/lite-action@v1.0.0
         if: always()
@@ -20,7 +22,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: [ "3.8" , "3.9", "3.10"]
+        python-version: ["3.8" , "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3
@@ -36,25 +38,25 @@ jobs:
         with:
           path: |
             ~/.local
-          key: poetry-1.3.2
+          key: poetry-1.6.1
           restore-keys: |
-            poetry-1.3.2
+            poetry-1.6.1
 
       - name: Cache virtualenv
         uses: actions/cache@v3
         id: virtualenv-cache
         with:
           path: |
             ~/.cache
-          key: virtualenv-${{ hashFiles('**/poetry.lock') }}
+          key: virtualenv-Python${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
           restore-keys: |
-            virtualenv-${{ hashFiles('**/poetry.lock') }}
+            virtualenv-Python${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
       - name: Install and configure Poetry
         if: steps.poetry-cache.outputs.cache-hit != 'true'
-        uses: snok/install-poetry@v1.3
+        uses: snok/install-poetry@v1
         with:
-          version: 1.3.2
+          version: 1.6.1
           virtualenvs-create: true
           virtualenvs-in-project: false
           installer-parallel: true

.github/workflows/_release.yaml

@@ -2,23 +2,36 @@ name: Semantic Release
 
 on:
   workflow_call:
-    secrets:
-      PYPI_PASSWORD:
-        required: true
 
 jobs:
   release:
     runs-on: ubuntu-latest
     concurrency: release
+    permissions:
+      id-token: write
+      contents: write
 
     steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
 
-      - name: Python Semantic Release
-        uses: relekang/python-semantic-release@master
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          repository_username: __token__
-          repository_password: ${{ secrets.PYPI_PASSWORD }}
+    # This action uses Python Semantic Release v8
+    - name: Python Semantic Release
+      id: release
+      uses: python-semantic-release/python-semantic-release@v8.1.1
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      # NOTE: DO NOT wrap the conditional in ${{ }} as it will always evaluate to true.
+      # See https://github.com/actions/runner/issues/1173
+      if: steps.release.outputs.released == 'true'
+
+    - name: Publish package to GitHub Release
+      uses: python-semantic-release/upload-to-gh-release@main
+      if: steps.release.outputs.released == 'true'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        tag: ${{ steps.release.outputs.tag }}

.github/workflows/ci.yaml

@@ -15,8 +15,6 @@ jobs:
   Release:
     needs: Quality
     uses: MedVisBonn/eyepy/.github/workflows/_release.yaml@master
-    secrets:
-      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
 
   Documentation:
     needs: Release

README.md

@@ -6,7 +6,7 @@ Use Python to import, analyse and visualize retinal imaging data.
 ![header_gif](https://user-images.githubusercontent.com/5720058/228815448-4b561246-dac9-4f8f-abde-e0dd5457a72b.gif)
 
 [![Documentation](https://img.shields.io/badge/docs-eyepy-blue)](https://MedVisBonn.github.io/eyepy)
-[![PyPI version](https://badge.fury.io/py/eyepie.svg)](https://badge.fury.io/py/eyepie)
+[![PyPI version](https://badge.fury.io/py/eyepy.svg)](https://badge.fury.io/py/eyepy)
 [![DOI](https://zenodo.org/badge/292547201.svg)](https://zenodo.org/badge/latestdoi/292547201)
 
 
@@ -53,6 +53,7 @@ ev = ep.import_retouch("path/to/volume_folder")
 
 # Related Projects:
 
++ [eyeseg](https://github.com/MedVisBonn/eyeseg): A python package for segmentation of retinal layers and drusen in OCT data.
 + [OCT-Converter](https://github.com/marksgraham/OCT-Converter): Extract raw optical coherence tomography (OCT) and fundus data from proprietary file formats. (.fds/.fda/.e2e/.img/.oct/.dcm)
 + [eyelab](https://github.com/MedVisBonn/eyelab): A GUI for annotation of OCT data based on eyepy
 + Projects by the [Translational Neuroimaging Laboratory](https://github.com/neurodial)

docs/development.md

@@ -0,0 +1,59 @@
+If you want to contribute to eyepy this is a guide on how to do it. We are happy to accept contributions from everyone. If you have any questions, please open an issue or contact us via email.
+
+## Project setup
+In the following the setup of the eyepy project is described, mainly for internal documentation purposes, but feel free to use it as a guide for your own projects.
+
+### Depdency management and packaging
+We use [poetry](https://python-poetry.org/docs/) for dependency management and packaging. Hence when you want to contribute to eyepy you need to install poetry first. Do so as described in the [documentation](https://python-poetry.org/docs/#installation).
+
+You will use Poetry to install the project's dependencies in a virtual environment or run the project's scripts and tests.
+
+Running the tests in the projects virtual environment is as simple as running
+
+```bash
+poetry run pytest
+```
+
+Internally poetry is also used to build the package and deploy it to [PyPI](https://pypi.org/project/eyepie/). This is done via [GitHub Actions] triggered by a push to the master branch.
+
+### Code formatting and linting
+Do not spend your time on code formatting. We use yapf and isort to format the code automatically. You can run them via pre-commit hooks. See the section on [pre-commit hooks](#pre-commit-hooks) for more information.
+
++ Automatic code formatting with [pre-commit] check-yaml, end-of-file-fixer, trailing-whitespace, isort, yapf[google], commitizen
+
++ Quality checks - run pre-commit hooks and pytest via [GitHub Actions] for every pull request and push to master
+
+Deployment for every push to master
++ Use Semantic release for Github releases and PyPI deployment via [GitHub Actions]
++ Build documentation with mkdocs and deploy it to [GitHub Pages] via [GitHub Actions]
+
+### Semantic commit messages
++ Only allow commits with [semantic commit messages] via [commitizen]
++ Automatic increase of version number based on [semantic commit messages] via [commitizen]
+
+
+## Setting up your development environment
+
+### Forking the repository
+
+First, you need to fork the repository. This will create a copy of the repository under your own account. You can do this by clicking on the "Fork" button in the top right corner of the repository page.
+After that, you need to clone your fork to your local machine. You can do this by running the following command in your terminal:
+
+```bash
+git clone https://github.com/[YOUR_USERNAME]/eyepy.git
+```
+
+### Setting up the development environment
+We use poetry for dependency management and building
+
+### Commiting changes
+
+#### Run the tests
+
+#### Run the pre-commit hooks
+
+#### Commitizen for semantic commit messages
+
+### Push to your repository
+
+### Create a pull request

noxfile.py

@@ -0,0 +1,11 @@
+import nox  # type: ignore - nox is not a project dependency. This module is used by the global nox command, not this project
+
+
+@nox.session(python=['3.8', '3.9', '3.10', '3.11'])
+def tests(session):
+    # Install the project dependencies
+    session.install('poetry')
+    session.run('poetry', 'install')
+
+    # Run the tests
+    session.run('pytest', *session.posargs)