tau-fibrils-yolo 0.0.1__tar.gz → 0.0.2__tar.gz

{tau_fibrils_yolo-0.0.1/src/tau_fibrils_yolo.egg-info → tau_fibrils_yolo-0.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tau-fibrils-yolo
-Version: 0.0.1
+Version: 0.0.2
 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-0.0.2/pyapp/build.py

@@ -0,0 +1,48 @@
+"""
+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-0.0.2/pyapp/pyapp-latest/.cargo/config.toml

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

tau_fibrils_yolo-0.0.2/pyapp/pyapp-latest/.gitattributes

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

tau_fibrils_yolo-0.0.2/pyapp/pyapp-latest/.github/FUNDING.yml

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

tau_fibrils_yolo-0.0.2/pyapp/pyapp-latest/.github/dependabot.yml

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

tau_fibrils_yolo-0.0.2/pyapp/pyapp-latest/.github/workflows/dependabot-auto-merge.yml

@@ -0,0 +1,26 @@
+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-0.0.2/pyapp/pyapp-latest/.github/workflows/docs-dev.yml

@@ -0,0 +1,22 @@
+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-0.0.2/pyapp/pyapp-latest/.github/workflows/docs-latest.yml

@@ -0,0 +1,19 @@
+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-0.0.2/pyapp/pyapp-latest/.github/workflows/docs.yml

@@ -0,0 +1,81 @@
+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-0.0.2/pyapp/pyapp-latest/.github/workflows/publish.yml

@@ -0,0 +1,39 @@
+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-0.0.2/pyapp/pyapp-latest/.github/workflows/test.yml

@@ -0,0 +1,116 @@
+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-0.0.2/pyapp/pyapp-latest/.gitignore

@@ -0,0 +1,20 @@
+# 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-0.0.2/pyapp/pyapp-latest/.linkcheckerrc

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

tau_fibrils_yolo-0.0.2/pyapp/pyapp-latest/.rustfmt.toml

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