Merge pull request #2 from fmi-faim/update-activation-functions

Rework RDCNet

Author: Tim-Oliver Buchholz

.copier-answers.yml

@@ -1,2 +1,4 @@
 # GitHub syntax highlighting
 pixi.lock linguist-language=YAML
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitattributes

@@ -0,0 +1,72 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build wheel and source distribution
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+
+    environment: release
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch
+
+    - name: Build package
+      run: hatch build
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-artifacts
+        path: dist/*
+        if-no-files-found: error
+
+  publish:
+    name: Publish to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    needs:
+      - build
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - name: Download Python artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: python-artifacts
+          path: dist
+      - name: Add assets to release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+      - name: Publish package distributions to PyPI
+        uses: pypa/[email protected]

.github/workflows/publish.yml

@@ -14,6 +14,7 @@ repos:
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --extend-ignore=E402]
+        exclude: 'src/pytorch_rdc_net/matching.py'
       - id: ruff-format
   - repo: https://github.com/crate-ci/typos
     rev: v1.23.6
@@ -22,13 +23,4 @@ repos:
         files: \.(py|md|rst|yaml|toml)
         # empty to do not write fixes
         args: []
-        exclude: pyproject.toml
-# mypy will force you to type your code ;)
-#   - repo: https://github.com/pre-commit/mirrors-mypy
-#     rev: v1.11.1
-#     hooks:
-#       - id: mypy
-#         language: python
-#         args: [--strict, --ignore-missing-imports]
-#         additional_dependencies: ['types-requests', 'types-PyYAML']
-#         exclude: docs/source/conf.py
+        exclude: 'pyproject.toml|src/pytorch_rdc_net/matching.py'

.pre-commit-config.yaml

@@ -1,19 +1,16 @@
-# Pytorch Rdc-Net
+# PyTorch RDC-Net
 
-## Repository Overview
-The repository uses [pixi](https://pixi.sh) to manage the project dependencies.
-Please follow the installation instructions in [docs/installation.md](docs/installation.md) to get started.
-Once pixi is installed you can run `pixi run build_docs` in the root of the project to build the documentation.
-The documentation is then available offline in `site/index.html`.
+This is a PyTorch implementation of the [RDC-Net](https://github.com/fmi-basel/RDCNet) for instance segmentation of 2D and 3D images. Some demo training scripts can be found [here](https://github.com/fmi-faim/faim_rdcnet).
 
-* `docs`: Contains the source files for the documentation.
-* `infrastructure`: Contains installed tools e.g. pixi.
-* `processed_data`: Contains all processed data which is used for the final results.
-* `raw_data`: Contains the raw data from your experiments.
-* `results`: Contains final results like figures and plots.
-* `runs`: Contains all config files which were used to produce processed data or results.
-* `sandbox`: Contains all experimental code and scripts which are not used for final results.
-* `source`: Contains all scripts which are used to produce processed data and final results.
 
----
-This project was generated with the [faim-ipa-project](https://fmi-faim.github.io/ipa-project-template/) copier template.
+## Citation
+If you find this work useful, please consider citing:
+
+```bibtex
+@inproceedings{ortiz2020,
+  title={RDCNet: Instance segmentation with a minimalist recurrent residual network},
+  author={Ortiz, Raphael and de Medeiros, Gustavo and Peters H.F.M., Antoine and Liberali, Prisca and Rempfler, Markus},
+  booktitle={International Workshop on Machine Learning in Medical Imaging},
+  year={2020},
+}
+```