🚀 Update to version v0.2.0

predict-idlab · Nov 4, 2024 · c83a740 · c83a740
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diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,52 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    # run a code a code scan at the beginning of every work week
+    - cron: '00 00 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: 'ubuntu-latest'
+    timeout-minutes: 360
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -9,6 +9,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: false
+
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
       - uses: actions/setup-python@v4
         with:
           python-version: '3.11'
@@ -18,7 +33,7 @@ jobs:
       - name: Install Dependencies
         run: |
           pip install -U .
-          pdm sync -d --only-keep -G doc
+          pdm sync -d
       - name: Sphinx build
         run: pdm run doc
       - name: Deploy to GitHub Pages

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -2,8 +2,9 @@ name: Tests
 
 on:
   push:
-    branches: [main]
+    branches: '**'
   pull_request:
+    branches: '**'
 
 jobs:
   build:
@@ -14,16 +15,33 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: false
+
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
       - name: Set up Python ${{ matrix.python-version }}
         uses: pdm-project/setup-pdm@v3
         with:
           python-version: ${{ matrix.python-version }}
           cache: true
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade tox .
-      - name: Test with tox
+          apt-get update && apt-get install ffmpeg libsm6 libxext6  -y
+          pip install -U .
+          pdm sync -d
+      - name: Test with pytest
         run: |
-          tox --version
-          pyversion="${{ matrix.python-version }}"
-          tox -e py${pyversion/./}
+          pdm run test --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
diff --git a/.gitignore b/.gitignore
@@ -29,10 +29,11 @@ test_notebooks
 .idea
 .vscode
 tags
+junit
 
 # Unittest and coverage
 htmlcov/*
-.coverage
+.coverage*
 .tox
 junit.xml
 coverage.xml
@@ -47,4 +48,12 @@ wheel/*
 docs/_build/*
 cover/*
 MANIFEST
-.pdm-python
+.pdm-python
+
+# example files
+examples/configs/*
+examples/datasets/*
+examples/lightning_logs/*
+examples/lightning_models/*
+examples/main.py
+*model_checkpoints/*
diff --git a/LICENSE b/LICENSE
@@ -1,30 +1,9 @@
-IMEC license
+MIT License
 
-Copyright (c) Jef Jonkers
-2023 Ghent University and IMEC vzw with offices at Technologiepark 15,  9052 Ghent, Belgium - Email: [email protected].
-Belgium - Contact info: http://predict.idlab.ugent.be
+Copyright (c) 2024 Jef Jonkers
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software for non-commercial educational and research use, including without
-limitation the rights to use, copy, modify, merge, publish, distribute and/or
-sublicense copies of the Software, and to permit persons to whom the Software
-is furnished to do so, subject to the following conditions:
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 
-1. The above copyright notice and this permission notice shall be included in
-   all copies of the Software.
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
-2. Permission is restricted to non-commercial educational and research use:
-   the use of the Software is allowed for teaching purposes and academic
-   research. Usage by non-academic parties is allowed in a strict research
-   environment only. The use of the results of the research for commercial
-   purposes or inclusion in commercial activities requires the permission of
-   Ghent University and IMEC vzw.
-
-3. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-   IN THE SOFTWARE.
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
@@ -1,11 +1,19 @@
 <p align="center">
     <a href="https://predict-idlab.github.io/landmarker">
-        <img alt="landmarker" src="/docs/_static/images/logo.svg" width="66%">
+        <img alt="landmarker" src="https://raw.githubusercontent.com/predict-idlab/landmarker/main/docs/_static/images/logo.svg" width="66%">
     </a>
 </p>
 
+[![PyPI Latest Release](https://img.shields.io/pypi/v/landmarker.svg)](https://pypi.org/project/landmarker/)
+[![support-version](https://img.shields.io/badge/python-3.10%20%7C%203.11-blue)](https://pypi.org/project/landmarker/)
+[![codecov](https://img.shields.io/codecov/c/github/predict-idlab/landmarker?logo=codecov)](https://codecov.io/gh/predict-idlab/landmarker)
+[![CodeQL](https://github.com/predict-idlab/landmarker/actions/workflows/codeql.yml/badge.svg)](https://github.com/predict-idlab/landmarker/actions/workflows/codeql.yml)
+[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?)](http://makeapullrequest.com)
+[![Documentation](https://github.com/predict-idlab/landmarker/actions/workflows/documentation.yml/badge.svg)](https://predict-idlab.github.io/landmarker/)
+[![Testing](https://github.com/predict-idlab/landmarker/actions/workflows/tests.yml/badge.svg)](https://github.com/predict-idlab/landmarker/actions/workflows/tests.yml)
 
-Landmarker is a [PyTorch](https://pytorch.org/)-based toolkit for (anatomical) landmark detection in images. It is designed to be easy to use and to provide a flexible framework for state-of-the-art landmark detection algorithms for small and large datasets. Landmarker was developed for landmark detection in medical images. However, it can be used for any type of landmark detection problem.
+
+Landmarker is a [PyTorch](https://pytorch.org/)-based toolkit for (anatomical) landmark localization in 2D/3D images. It is designed to be easy to use and to provide a flexible framework for state-of-the-art landmark localization algorithms for small and large datasets. Landmarker was developed for landmark detection in medical images. However, it can be used for any type of landmark localization problem.
 
 ## 🛠️ Installation
 
@@ -20,13 +28,11 @@ Technical documentation is available at [documentation](https://predict-idlab.gi
 Examples and tutorials are available at [examples](https://predict-idlab.github.io/landmarker/examples/index.html)
 
 ## ✨ Features
-- **Modular**: Landmarker is designed to be modular. It is easy to add new models, datasets, and loss functions.
-- **Flexible**: Landmarker provides a flexible framework for landmark detection. It is easy to customize the training and evaluation process.
-- **Easy to use**: Landmarker is easy to use. It provides a simple API for training and evaluation.
+- **Modular**: Landmarker is designed to be modular. Almost all components can be used independently.
+- **Flexible**: Landmarker provides a flexible framework for landmark detection, allowing you to easily customize your model, loss function, and data loaders.
 - **State-of-the-art**: Landmarker provides state-of-the-art landmark detection models and loss functions.
 
 ## 📈 Future Work
-- Extension to 3D landmark detection.
 - Extension to landmark detection in videos.
 - Add uncertainty estimation.
 - ...
@@ -41,10 +47,10 @@ If you use Landmarker in your research, please cite the following paper:
 SCIENTIFIC PAPER UNDER REVIEW
 
 ## 📝 License
-Landmark is licensed under the IMEC [license](LICENSE).
+Landmark is licensed under the MIT [license](LICENSE).
 
 ---
 
 <p align="center">
 👤 <i>Jef Jonkers</i>
-</p>
+</p>
diff --git a/docs/index.md b/docs/index.md
@@ -48,10 +48,6 @@ reference/visualize
 
 # Landmarker
 
-:::::{caution}
-🚧 Still under construction. 🚧
-:::::
-
 **Version**: {{ version }}
 
 **Useful links**: