Merge pull request #383 from IMSY-DKFZ/develop

Merge develop into main

.github/release-drafter.yml

@@ -0,0 +1,32 @@
+name-template: 'v$RESOLVED_VERSION 🌈'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+      - 'documentation'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🧰 Maintenance'
+    label: 'chore'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## Changes
+
+  $CHANGES

.github/workflows/automatic_testing.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:

.github/workflows/pypi.yml

@@ -1,20 +1,53 @@
-# Uploads the current version of the package to PyPI when commit are pushed to main (including merges via pull requests)
+# Uploads the current version of the package to PyPI when publishing a release
 
 name: Upload to PyPI
 
 on:
-  push:
-    branches:
-      - main
+  release:
+    types: [published]
 
 jobs:
-  build-and-publish:
+  release-build:
     if: github.repository == 'IMSY-DKFZ/simpa'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Build and publish to pypi
-        uses: JRubics/[email protected]
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    if: github.repository == 'IMSY-DKFZ/simpa'
+    runs-on: ubuntu-latest
+
+    needs:
+      - release-build
+
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+      url: https://pypi.org/project/simpa/
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
         with:
-          pypi_token: ${{ secrets.PYPI_TOKEN }}
-          python_version: '3.10'
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1    

.github/workflows/release-drafter.yml

@@ -0,0 +1,41 @@
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - main
+  # pull_request event is required only for autolabeler
+#  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+#    types: [ opened, reopened, synchronize ]
+  # pull_request_target event is required for autolabeler to support PRs from forks
+  # pull_request_target:
+  #   types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: read
+    runs-on: ubuntu-latest
+    steps:
+      # (Optional) GitHub Enterprise requires GHE_HOST variable set
+      #- name: Set GHE_HOST
+      #  run: |
+      #    echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV
+
+      # Drafts your next Release notes as Pull Requests are merged into "main"
+      - uses: release-drafter/release-drafter@v6
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -15,6 +15,14 @@ docs/objects.inv
 
 simpa_tests/figures
 simpa_tests/figures/*
+simpa_tests/**/figures
+simpa_tests/**/figures/*
+simpa_tests/manual_tests/figures
+simpa_tests/manual_tests/reference_figures
+simpa_tests/manual_tests/manual_tests_*
+
+simpa_examples/benchmarking/*.csv
+simpa_examples/benchmarking/*.txt
 
 path_config.env
 
@@ -143,6 +151,9 @@ dmypy.json
 .idea/*
 /*/.idea/*/
 
+#VSCode
+.vscode/
+
 # numpy files
 *npy
 /.mailmap

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
       types: [python]
       args:
         - --license-filepath
-        - license_header.txt        # defaults to: LICENSE.txt
+        - .pre_commit_configs/license_header.txt        # defaults to: LICENSE.txt
 
 -   repo: https://github.com/jorisroovers/gitlint # Uses MIT License (MIT compatible)
     rev:  v0.19.1
@@ -36,6 +36,19 @@ repos:
       - id: markdown-link-check # checks if links in markdown files work
         exclude: docs/
         types: [markdown]
+        args: 
+           - -c
+           - .pre_commit_configs/link-config.json
+        always_run: true
+
+-   repo: local
+    hooks:
+      - id: build-sphinx-docs
+        name: Build Sphinx documentation
+        entry: make -C docs html # builds the sphinx documentation
+        language: system
+        pass_filenames: false
+        always_run: true
 
 # 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

.pre_commit_configs/link-config.json

@@ -0,0 +1,7 @@
+{
+    "ignorePatterns": [
+        {
+            "pattern": "https://doi.org/10.1117/1.JBO.27.8.083010"
+        }
+    ]
+}

.readthedocs.yaml

@@ -4,19 +4,16 @@ version: 2
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
-  tools: {python: "3.10"}
-  jobs:
-    post_create_environment:
-      - pip install poetry
-    post_install:
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+  tools:
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
   configuration: docs/source/conf.py
   fail_on_warning: false
 
+# Python configuration
 python:
   install:
     - method: pip

CONTRIBUTING.md

@@ -25,23 +25,27 @@ Once you reached out to us, you will be provided with the information on how to
 In general the following steps are involved during a contribution:
 
 ### Contribution process
-1.	Create feature request / bug report on the [SIMPA issues page](https://github.com/IMSY-DKFZ/simpa/issues)
-2.	Discuss potential contribution with core development team
-3.	Fork the [SIMPA repository](https://github.com/IMSY-DKFZ/simpa)
-4.	Create feature branch from develop using the naming convention T<Issue#>_<FeatureName>, 
-      where <Issue#> represent the number github assigned the created issue and <FeatureName> describes 
-      what is being developed in CamelCaseNotation.
-    Examples: `T13_FixSimulatorBug`, `T27_AddNewSimulator`
-
-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.    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).
-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.
+1. Create feature request / bug report on the [SIMPA issues page](https://github.com/IMSY-DKFZ/simpa/issues)
+2. Discuss potential contribution with core development team
+3. Fork the [SIMPA repository](https://github.com/IMSY-DKFZ/simpa)
+4. Make sure that you've installed all the optional dependencies by running `pip install .[docs,profile,testing]` 
+   in the root directory of the repository.
+5. Create feature branch from develop using the naming convention T<Issue#>_<FeatureName>, 
+        where <Issue#> represents the number Github assigned the created issue and <FeatureName> describes 
+        what is being developed in CamelCaseNotation.
+        Examples: `T13_FixSimulatorBug`, `T27_AddNewSimulator`
+6. Perform test driven development on a 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. 
+7. Run pre-commit hooks and make sure all hooks are passing. 
+8. Please also make sure that you benchmark your contributions please use the benchmarking bash script (see [benchmarking.md](docs/source/benchmarking.md) for more details).
+   Please add the results to the PR and compare them to the current develop.
+9. 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).
+10.     If there are conflicts between the simpa develop branch and your branch, you should update your feature branch with the simpa develop branch using a "merge" strategy instead of "rebase". 
+11. 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.
 
 For each contribution, please make sure to consider the following: