tau-fibrils-yolo 0.0.5__tar.gz → 0.0.6__tar.gz

tau_fibrils_yolo-0.0.6/.github/workflows/release.yml

@@ -0,0 +1,126 @@
+# name: Publish, Build and Release
+
+# on:
+#   push:
+#     branches:
+#       - main
+#     tags:
+#       - "v*"
+#   pull_request:
+#     branches:
+#       - main
+#   workflow_dispatch:
+
+# permissions:
+#   contents: write
+
+# jobs:
+#   deploy:
+#     runs-on: ubuntu-latest
+#     if: contains(github.ref, 'tags')
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Set up Python
+#         uses: actions/setup-python@v4
+#         with:
+#           python-version: "3.9"
+#       - name: Install dependencies
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install -U setuptools setuptools_scm wheel twine build
+#       - name: Build and publish
+#         env:
+#           TWINE_USERNAME: __token__
+#           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+#         run: |
+#           git tag
+#           python -m build .
+#           twine upload dist/*
+
+#   build:
+#     needs: deploy
+#     runs-on: ${{ matrix.os }}
+#     strategy:
+#       matrix:
+#         os: [windows-latest]
+
+#     env:
+#       PYAPP_PROJECT_NAME: 'tau_fibrils_yolo'
+
+#     steps:
+#       - name: Checkout code
+#         uses: actions/checkout@v2
+      
+#       - name: Install Rust
+#         uses: actions-rs/toolchain@v1
+#         with:
+#           toolchain: stable
+#           override: true
+
+#       - name: Extract PyPi package version
+#         shell: bash
+#         run: |
+#           VERSION=${{ github.ref_name }}
+#           VERSION=${VERSION#v}
+#           echo "VERSION=$VERSION" >> $GITHUB_ENV
+      
+#       - name: Download PyApp
+#         shell: bash
+#         run: |
+#           curl https://github.com/ofek/pyapp/releases/latest/download/source.tar.gz -Lo pyapp-source.tar.gz
+#           tar -xzf pyapp-source.tar.gz
+#           mv pyapp-v* pyapp-latest
+
+#       - name: Build executable for Windows
+#         env:
+#           PYAPP_PROJECT_VERSION: ${{ env.VERSION }}
+#           PYAPP_PYTHON_VERSION: '3.9'
+#         run: cargo build --release --manifest-path pyapp-latest/Cargo.toml
+
+#       - name: Archive Windows executable
+#         shell: bash
+#         working-directory: pyapp-latest/target/release
+#         run: |
+#           EXECUTABLE_NAME=${{ env.PYAPP_PROJECT_NAME }}_${{ runner.os }}_${{ env.VERSION }}.exe
+#           mv pyapp.exe $EXECUTABLE_NAME
+#           tar -czvf ../../../executable-windows.tar.gz $EXECUTABLE_NAME
+
+#       - name: Upload artifact
+#         uses: actions/upload-artifact@v2
+#         with:
+#           name: executable-${{ runner.os }}
+#           path: executable-*.tar.gz
+
+#   release:
+#     needs: build
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: Checkout code
+#         uses: actions/checkout@v2
+
+#       - name: Download Windows artifact
+#         uses: actions/download-artifact@v2
+#         with:
+#           name: executable-Windows
+#           path: .
+
+#       - name: Create Release
+#         id: create_release
+#         uses: actions/create-release@v1
+#         env:
+#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#         with:
+#           tag_name: ${{ github.ref_name }}
+#           release_name: Release ${{ github.ref_name }}
+#           draft: false
+#           prerelease: false
+
+#       - name: Upload Windows executable to release
+#         uses: actions/upload-release-asset@v1
+#         env:
+#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#         with:
+#           upload_url: ${{ steps.create_release.outputs.upload_url }}
+#           asset_path: ./executable-windows.tar.gz
+#           asset_name: executable-windows.tar.gz
+#           asset_content_type: application/gzip

tau_fibrils_yolo-0.0.5/.github/workflows/release.yml → tau_fibrils_yolo-0.0.6/.github/workflows/release_multiplatform.yml

@@ -42,7 +42,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-latest]
+        os: [windows-latest, ubuntu-latest, macos-latest]
 
     env:
       PYAPP_PROJECT_NAME: 'tau_fibrils_yolo'
@@ -71,19 +71,29 @@ jobs:
           tar -xzf pyapp-source.tar.gz
           mv pyapp-v* pyapp-latest
 
-      - name: Build executable for Windows
+      - name: Build executable
         env:
           PYAPP_PROJECT_VERSION: ${{ env.VERSION }}
           PYAPP_PYTHON_VERSION: '3.9'
         run: cargo build --release --manifest-path pyapp-latest/Cargo.toml
 
-      - name: Archive Windows executable
+      - name: Archive executable
         shell: bash
         working-directory: pyapp-latest/target/release
         run: |
-          EXECUTABLE_NAME=${{ env.PYAPP_PROJECT_NAME }}_${{ runner.os }}_${{ env.VERSION }}.exe
-          mv pyapp.exe $EXECUTABLE_NAME
-          tar -czvf ../../../executable-windows.tar.gz $EXECUTABLE_NAME
+          if [ "${{ matrix.os }}" == "windows-latest" ]; then
+            EXECUTABLE_NAME=${{ env.PYAPP_PROJECT_NAME }}_${{ runner.os }}_${{ env.VERSION }}.exe
+            mv pyapp.exe $EXECUTABLE_NAME
+            tar -czvf ../../../executable-windows.tar.gz $EXECUTABLE_NAME
+          elif [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
+            EXECUTABLE_NAME=${{ env.PYAPP_PROJECT_NAME }}_${{ runner.os }}_${{ env.VERSION }}
+            mv pyapp $EXECUTABLE_NAME
+            tar -czvf ../../../executable-linux.tar.gz $EXECUTABLE_NAME
+          elif [ "${{ matrix.os }}" == "macos-latest" ]; then
+            EXECUTABLE_NAME=${{ env.PYAPP_PROJECT_NAME }}_${{ runner.os }}_${{ env.VERSION }}
+            mv pyapp $EXECUTABLE_NAME
+            tar -czvf ../../../executable-macos.tar.gz $EXECUTABLE_NAME
+          fi
 
       - name: Upload artifact
         uses: actions/upload-artifact@v2
@@ -104,6 +114,18 @@ jobs:
           name: executable-Windows
           path: .
 
+      - name: Download Linux artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: executable-Linux
+          path: .
+      
+      - name: Download MacOS artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: executable-macOS
+          path: .
+
       - name: Create Release
         id: create_release
         uses: actions/create-release@v1
@@ -124,3 +146,23 @@ jobs:
           asset_path: ./executable-windows.tar.gz
           asset_name: executable-windows.tar.gz
           asset_content_type: application/gzip
+      
+      - name: Upload Linux executable to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./executable-linux.tar.gz
+          asset_name: executable-linux.tar.gz
+          asset_content_type: application/gzip
+      
+      - name: Upload MacOS executable to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./executable-macos.tar.gz
+          asset_name: executable-macos.tar.gz
+          asset_content_type: application/gzip

{tau_fibrils_yolo-0.0.5 → tau_fibrils_yolo-0.0.6}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: tau-fibrils-yolo
-Version: 0.0.5
-Summary: YoloV8 model for the detection of Tau fibrils in Cryo-EM images.
+Version: 0.0.6
+Summary: YoloV8 model for the detection of Tau fibrils in EM images.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE
                                Version 3, 19 November 2007
@@ -690,13 +690,13 @@ Requires-Dist: ultralytics
 Requires-Dist: opencv-contrib-python-headless
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
-# 🧬 Tau Fibrils Yolo - Object detection in Cryo-EM images
+# 🧬 Tau Fibrils Yolo - Object detection in EM images
 
 ![screenshot](assets/screenshot.png)
 
-We provide a [YoloV8](https://docs.ultralytics.com/) model for the detection of oriented bounding boxes (OBBs) of Tau fibrils in Cryo-EM images.
+We provide a [YoloV8](https://docs.ultralytics.com/) model for the detection of oriented bounding boxes (OBBs) of Tau fibrils in EM images.
 
-[[`Installation`](#installation)] [[`Model`](#model)] [[`Usage`](#usage)]
+[[`Installation`](#installation)] [[`Model`](#model)] [[`Usage`](#usage)] [[`Training`](#training)]
 
 This project is part of a collaboration between the [EPFL Center for Imaging](https://imaging.epfl.ch/) and the [Laboratory of Biological Electron Microscopy](https://www.lbem.ch/).
 
@@ -795,6 +795,10 @@ folder/
     ├── image_002_results.csv
 ```
 
+## Training
+
+The instructions for training the model can be found [here](./scripts/instructions.md).
+
 ## Issues
 
 If you encounter any problems, please file an issue along with a detailed description.

{tau_fibrils_yolo-0.0.5 → tau_fibrils_yolo-0.0.6}/README.md

@@ -1,11 +1,11 @@
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
-# 🧬 Tau Fibrils Yolo - Object detection in Cryo-EM images
+# 🧬 Tau Fibrils Yolo - Object detection in EM images
 
 ![screenshot](assets/screenshot.png)
 
-We provide a [YoloV8](https://docs.ultralytics.com/) model for the detection of oriented bounding boxes (OBBs) of Tau fibrils in Cryo-EM images.
+We provide a [YoloV8](https://docs.ultralytics.com/) model for the detection of oriented bounding boxes (OBBs) of Tau fibrils in EM images.
 
-[[`Installation`](#installation)] [[`Model`](#model)] [[`Usage`](#usage)]
+[[`Installation`](#installation)] [[`Model`](#model)] [[`Usage`](#usage)] [[`Training`](#training)]
 
 This project is part of a collaboration between the [EPFL Center for Imaging](https://imaging.epfl.ch/) and the [Laboratory of Biological Electron Microscopy](https://www.lbem.ch/).
 
@@ -104,6 +104,10 @@ folder/
     ├── image_002_results.csv
 ```
 
+## Training
+
+The instructions for training the model can be found [here](./scripts/instructions.md).
+
 ## Issues
 
 If you encounter any problems, please file an issue along with a detailed description.

{tau_fibrils_yolo-0.0.5 → tau_fibrils_yolo-0.0.6}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "tau-fibrils-yolo"
 dynamic = ["version"]
-description = "YoloV8 model for the detection of Tau fibrils in Cryo-EM images."
+description = "YoloV8 model for the detection of Tau fibrils in EM images."
 readme = "README.md"
 requires-python = ">=3.9"
 license = {file = "LICENSE"}

{tau_fibrils_yolo-0.0.5 → tau_fibrils_yolo-0.0.6}/src/tau_fibrils_yolo/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5'
-__version_tuple__ = version_tuple = (0, 0, 5)
+__version__ = version = '0.0.6'
+__version_tuple__ = version_tuple = (0, 0, 6)

{tau_fibrils_yolo-0.0.5 → tau_fibrils_yolo-0.0.6}/src/tau_fibrils_yolo.egg-info/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: tau-fibrils-yolo
-Version: 0.0.5
-Summary: YoloV8 model for the detection of Tau fibrils in Cryo-EM images.
+Version: 0.0.6
+Summary: YoloV8 model for the detection of Tau fibrils in EM images.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE
                                Version 3, 19 November 2007
@@ -690,13 +690,13 @@ Requires-Dist: ultralytics
 Requires-Dist: opencv-contrib-python-headless
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
-# 🧬 Tau Fibrils Yolo - Object detection in Cryo-EM images
+# 🧬 Tau Fibrils Yolo - Object detection in EM images
 
 ![screenshot](assets/screenshot.png)
 
-We provide a [YoloV8](https://docs.ultralytics.com/) model for the detection of oriented bounding boxes (OBBs) of Tau fibrils in Cryo-EM images.
+We provide a [YoloV8](https://docs.ultralytics.com/) model for the detection of oriented bounding boxes (OBBs) of Tau fibrils in EM images.
 
-[[`Installation`](#installation)] [[`Model`](#model)] [[`Usage`](#usage)]
+[[`Installation`](#installation)] [[`Model`](#model)] [[`Usage`](#usage)] [[`Training`](#training)]
 
 This project is part of a collaboration between the [EPFL Center for Imaging](https://imaging.epfl.ch/) and the [Laboratory of Biological Electron Microscopy](https://www.lbem.ch/).
 
@@ -795,6 +795,10 @@ folder/
     ├── image_002_results.csv
 ```
 
+## Training
+
+The instructions for training the model can be found [here](./scripts/instructions.md).
+
 ## Issues
 
 If you encounter any problems, please file an issue along with a detailed description.

{tau_fibrils_yolo-0.0.5 → tau_fibrils_yolo-0.0.6}/src/tau_fibrils_yolo.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ MANIFEST.in
 README.md
 pyproject.toml
 .github/workflows/release.yml
+.github/workflows/release_multiplatform.yml
 assets/icon.png
 assets/screenshot.png
 scripts/00_annotate.py