tau-fibrils-yolo 0.0.3__tar.gz → 0.0.4__tar.gz

{tau_fibrils_yolo-0.0.3 → tau_fibrils_yolo-0.0.4}/.github/workflows/release.yml

@@ -63,20 +63,27 @@ jobs:
           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/pyapp-latest/Cargo.toml
+        run: cargo build --release --manifest-path pyapp-latest/Cargo.toml
 
       - name: Archive Windows executable
         shell: bash
-        working-directory: pyapp/pyapp-latest/target/release
+        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
+          tar -czvf ../../../executable-windows.tar.gz $EXECUTABLE_NAME
 
       - name: Upload artifact
         uses: actions/upload-artifact@v2

{tau_fibrils_yolo-0.0.3/src/tau_fibrils_yolo.egg-info → tau_fibrils_yolo-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tau-fibrils-yolo
-Version: 0.0.3
+Version: 0.0.4
 Summary: YoloV8 model for the detection of Tau fibrils in Cryo-EM images.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: BSD 3-Clause License

tau_fibrils_yolo-0.0.4/src/tau_fibrils_yolo/__init__.py

@@ -0,0 +1,8 @@
+from tau_fibrils_yolo._widget import YoloDetectorWidget
+from tau_fibrils_yolo.predict import FibrilsDetector
+
+from ._version import version as __version__
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"

{tau_fibrils_yolo-0.0.3 → tau_fibrils_yolo-0.0.4}/src/tau_fibrils_yolo/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.3'
-__version_tuple__ = version_tuple = (0, 0, 3)
+__version__ = version = '0.0.4'
+__version_tuple__ = version_tuple = (0, 0, 4)

{tau_fibrils_yolo-0.0.3 → tau_fibrils_yolo-0.0.4/src/tau_fibrils_yolo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tau-fibrils-yolo
-Version: 0.0.3
+Version: 0.0.4
 Summary: YoloV8 model for the detection of Tau fibrils in Cryo-EM images.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: BSD 3-Clause License

tau_fibrils_yolo-0.0.4/src/tau_fibrils_yolo.egg-info/SOURCES.txt

@@ -0,0 +1,24 @@
+.gitignore
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+.github/workflows/release.yml
+assets/icon.png
+assets/screenshot.png
+scripts/train.py
+src/tau_fibrils_yolo/__init__.py
+src/tau_fibrils_yolo/__main__.py
+src/tau_fibrils_yolo/_version.py
+src/tau_fibrils_yolo/_widget.py
+src/tau_fibrils_yolo/cli.py
+src/tau_fibrils_yolo/crossover_distance.py
+src/tau_fibrils_yolo/napari.yaml
+src/tau_fibrils_yolo/postprocess.py
+src/tau_fibrils_yolo/predict.py
+src/tau_fibrils_yolo.egg-info/PKG-INFO
+src/tau_fibrils_yolo.egg-info/SOURCES.txt
+src/tau_fibrils_yolo.egg-info/dependency_links.txt
+src/tau_fibrils_yolo.egg-info/entry_points.txt
+src/tau_fibrils_yolo.egg-info/requires.txt
+src/tau_fibrils_yolo.egg-info/top_level.txt

tau_fibrils_yolo-0.0.3/pyapp/build.py

@@ -1,48 +0,0 @@
-"""
-Packages the depalma-napari-omero project into a single exectuable with PyApp.
-"""
-import os
-import shutil
-import subprocess
-from pathlib import Path
-
-from depalma_napari_omero import __version__, __name__
-
-script_directory = Path(__file__).parent
-
-# Set environment variables
-os.environ['PYAPP_PROJECT_NAME'] = __name__
-os.environ['PYAPP_PROJECT_VERSION'] = __version__
-os.environ['PYAPP_PYTHON_VERSION'] = "3.9"
-os.environ['PYAPP_EXEC_SCRIPT'] = str((script_directory.parent / 'src' / __name__ / '__main__.py').resolve())
-if os.name == 'nt':
-    print("Building for Windows.")
-    extension = '.exe'  # Windows
-    platform = 'w64'
-    os.environ['PYAPP_PROJECT_DEPENDENCY_FILE'] = str((script_directory / 'requirements.w64.txt').resolve())
-else:
-    print("Building for Linux / MacOS.")
-    extension = ''  # Linux and MacOS
-    platform = 'u64'
-    os.environ['PYAPP_PROJECT_DEPENDENCY_FILE'] = str((script_directory / 'requirements.txt').resolve())
-
-# Print them
-print(f"{os.environ['PYAPP_PROJECT_NAME']=}")
-print(f"{os.environ['PYAPP_PROJECT_VERSION']=}")
-print(f"{os.environ['PYAPP_PYTHON_VERSION']=}")
-print(f"{os.environ['PYAPP_EXEC_SCRIPT']=}")
-print(f"{os.environ['PYAPP_PROJECT_DEPENDENCY_FILE']=}")
-
-# Change directory and run cargo build
-os.chdir(str(script_directory / 'pyapp-latest'))
-subprocess.run(['cargo', 'build', '--release'], capture_output=True, text=True)
-os.chdir(str(script_directory))
-
-source_path = str((script_directory / 'pyapp-latest' / 'target' / 'release' / f'pyapp{extension}').resolve())
-destination_path = str((script_directory.parent / 'release' / f'{__name__}_{platform}_{__version__}{extension}').resolve())
-
-if os.path.exists(source_path):
-    shutil.copy(source_path, destination_path)
-    print(f"Copied {source_path} to {destination_path}")
-else:
-    print(f"{source_path} does not exist")

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.cargo/config.toml

@@ -1,2 +0,0 @@
-[target.'cfg(all(windows, target_env = "msvc"))']
-rustflags = ["-C", "target-feature=+crt-static"]

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.gitattributes

@@ -1,2 +0,0 @@
-# Auto detect text files and perform LF normalization
-* text=auto eol=lf

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/FUNDING.yml

@@ -1,4 +0,0 @@
-github:
-- ofek
-custom:
-- https://ofek.dev/donate/

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/dependabot.yml

@@ -1,11 +0,0 @@
-version: 2
-updates:
-- package-ecosystem: github-actions
-  directory: /
-  schedule:
-    interval: monthly
-
-- package-ecosystem: cargo
-  directory: /
-  schedule:
-    interval: monthly

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/workflows/dependabot-auto-merge.yml

@@ -1,26 +0,0 @@
-name: Dependabot auto-merge
-
-on: pull_request
-
-permissions:
-  contents: write
-  pull-requests: write
-
-jobs:
-  enable:
-    if: ${{ github.actor == 'dependabot[bot]' }}
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Dependabot metadata
-      id: metadata
-      uses: dependabot/fetch-metadata@v2
-      with:
-        github-token: "${{ secrets.GITHUB_TOKEN }}"
-
-    - name: Enable auto-merge for Dependabot PRs
-      if: ${{contains(steps.metadata.outputs.dependency-names, 'my-dependency') && steps.metadata.outputs.update-type == 'version-update:semver-patch'}}
-      run: gh pr merge --auto --merge "$PR_URL"
-      env:
-        PR_URL: ${{github.event.pull_request.html_url}}
-        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/workflows/docs-dev.yml

@@ -1,22 +0,0 @@
-name: Docs dev
-
-on:
-  push:
-    branches:
-    - master
-  pull_request:
-    branches:
-    - master
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.sha }}
-  cancel-in-progress: true
-
-jobs:
-  docs:
-    uses: ./.github/workflows/docs.yml
-    with:
-      version: dev
-      publish: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
-    permissions:
-      contents: write

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/workflows/docs-latest.yml

@@ -1,19 +0,0 @@
-name: Docs latest
-
-on:
-  push:
-    tags:
-    - v*
-  workflow_dispatch:
-
-concurrency:
-  group: docs-deploy
-
-jobs:
-  docs:
-    uses: ./.github/workflows/docs.yml
-    with:
-      version: latest
-      publish: true
-    permissions:
-      contents: write

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/workflows/docs.yml

@@ -1,81 +0,0 @@
-name: docs
-
-on:
-  workflow_call:
-    inputs:
-      version:
-        required: true
-        type: string
-      publish:
-        required: true
-        type: boolean
-
-defaults:
-  run:
-    shell: bash
-
-env:
-  PYTHONUNBUFFERED: '1'
-  FORCE_COLOR: '1'
-  STABLE_PYTHON_VERSION: "3.11"
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
-      with:
-        # Fetch all history for applying timestamps to every page
-        fetch-depth: 0
-
-    - name: Set up Python ${{ env.STABLE_PYTHON_VERSION }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ env.STABLE_PYTHON_VERSION }}
-
-    - name: Install Hatch
-      run: pip install hatch
-
-    - name: Configure Git for GitHub Actions bot
-      run: |-
-        git config --local user.name 'github-actions[bot]'
-        git config --local user.email 'github-actions[bot]@users.noreply.github.com'
-
-    - name: Build documentation
-      run: hatch run docs:build-check
-
-    - name: Commit documentation
-      run: hatch run docs:ci-build ${{ inputs.version }}
-
-    - name: Create archive
-      run: git archive --prefix site/ -o site.tar.gz gh-pages
-
-    - name: Upload site
-      uses: actions/upload-artifact@v4
-      with:
-        name: site
-        path: site.tar.gz
-
-  publish:
-    if: ${{ inputs.publish }}
-    needs:
-    - build
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Download site
-      uses: actions/download-artifact@v4
-      with:
-        name: site
-
-    - name: Unpack archive
-      run: tar -xzf site.tar.gz
-
-    - name: Publish site
-      uses: peaceiris/actions-gh-pages@v4
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: site
-        commit_message: ${{ github.event.head_commit.message }}

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/workflows/publish.yml

@@ -1,39 +0,0 @@
-name: Publish
-
-on:
-  push:
-    tags:
-    - v*
-
-defaults:
-  run:
-    shell: bash
-
-jobs:
-  publish:
-    name: Publish release
-    runs-on: ubuntu-latest
-
-    permissions:
-      contents: write
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
-
-    - name: Publish to crates.io
-      env:
-        CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
-      run: cargo publish
-
-    - name: Create source archives
-      run: |-
-        git archive --prefix pyapp-${{ github.ref_name }}/ -o source.tar.gz HEAD
-        git archive --prefix pyapp-${{ github.ref_name }}/ -o source.zip HEAD
-
-    - name: Add source archives to current release
-      uses: softprops/action-gh-release@v2
-      with:
-        files: |-
-          source.tar.gz
-          source.zip

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.github/workflows/test.yml

@@ -1,116 +0,0 @@
-name: Test
-
-on:
-  push:
-    branches:
-    - master
-  pull_request:
-    branches:
-    - master
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.sha }}
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash
-
-env:
-  STABLE_PYTHON_VERSION: "3.11"
-
-jobs:
-  test:
-    name: ${{ matrix.job.target }} (${{ matrix.job.os }})
-    runs-on: ${{ matrix.job.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        job:
-        # Linux
-        - target: aarch64-unknown-linux-gnu
-          os: ubuntu-22.04
-          cross: true
-        - target: x86_64-unknown-linux-gnu
-          os: ubuntu-22.04
-          cross: true
-          test: true
-          validate: true
-        - target: x86_64-unknown-linux-musl
-          os: ubuntu-22.04
-          cross: true
-        - target: i686-unknown-linux-gnu
-          os: ubuntu-22.04
-          cross: true
-          python_version: "3.11"
-        - target: powerpc64le-unknown-linux-gnu
-          os: ubuntu-22.04
-          cross: true
-        # Windows
-        - target: x86_64-pc-windows-msvc
-          os: windows-2022
-          test: true
-        - target: i686-pc-windows-msvc
-          os: windows-2022
-        # macOS
-        - target: aarch64-apple-darwin
-          os: macos-14
-          test: true
-        - target: x86_64-apple-darwin
-          os: macos-12
-          test: true
-
-    env:
-      CARGO: cargo
-      CARGO_BUILD_TARGET: "${{ matrix.job.target }}"
-      PYAPP_PROJECT_NAME: cowsay
-      PYAPP_PROJECT_VERSION: "5.0.0"
-      PYAPP_PYTHON_VERSION: "${{ matrix.job.python_version }}"
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
-
-    - name: Set up Python ${{ env.STABLE_PYTHON_VERSION }}
-      if: matrix.job.validate
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ env.STABLE_PYTHON_VERSION }}
-
-    - name: Validate
-      if: matrix.job.validate
-      run: python scripts/validate_options.py
-
-    - name: Set up cross compiling
-      if: matrix.job.cross
-      uses: taiki-e/install-action@v2
-      with:
-        tool: cross
-
-    - name: Configure cross compiling
-      if: matrix.job.cross
-      run: echo "CARGO=cross" >> $GITHUB_ENV
-
-    - name: Install Rust toolchain
-      uses: dtolnay/rust-toolchain@stable
-      with:
-        targets: ${{ matrix.job.target }}
-        components: clippy, rustfmt
-
-    - name: Lint
-      run: $CARGO clippy --no-deps
-
-    - name: Format
-      if: matrix.job.validate
-      run: cargo fmt --check
-
-    - name: See dependency tree
-      run: $CARGO tree
-
-    - name: Build
-      if: ${{ !matrix.job.test }}
-      run: $CARGO build
-
-    - name: Test
-      if: matrix.job.test
-      run: cargo run -- Moo Success!

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.gitignore

@@ -1,20 +0,0 @@
-# Generated by Cargo
-# will have compiled files and executables
-debug/
-target/
-
-# These are backup files generated by rustfmt
-**/*.rs.bk
-
-# MSVC Windows builds of rustc generate these, which store debugging information
-*.pdb
-
-# Added by cargo
-/target
-
-# Documentation
-/.cache/
-/site/
-
-# Editor configs
-.vscode/

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.linkcheckerrc

@@ -1,2 +0,0 @@
-# https://linkchecker.github.io/linkchecker/man/linkcheckerrc.html
-[AnchorCheck]

tau_fibrils_yolo-0.0.3/pyapp/pyapp-latest/.rustfmt.toml

@@ -1,3 +0,0 @@
-# https://rust-lang.github.io/rustfmt/
-edition = "2021"
-reorder_imports = true