pywarper 0.1.0__tar.gz

pywarper-0.1.0/.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install SuiteSparse (required by scikit-sparse)
+      run: |
+          sudo apt-get update
+          sudo apt-get install -y libsuitesparse-dev
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install .[scikit-sparse]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

pywarper-0.1.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

pywarper-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache
+
+# Distribution / packaging
+build/
+dist/
+*.egg-info/
+*.egg
+
+# Environments
+.env
+.venv
+env/
+venv/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# macOS
+.DS_Store
+
+# Editor directories and files
+.idea/
+.vscode/
+*.swp
+*.swo
+
+dev/

pywarper-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pywarper
+Version: 0.1.0
+Summary: Conformal mapping-based warping of neuronal arbor morphologies.
+Requires-Python: >=3.9.0
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pygridfit>=0.1.4
+Requires-Dist: scipy>=1.13.1
+Requires-Dist: watermark>=2.5.0
+Provides-Extra: dev
+Requires-Dist: maturin; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: twine; extra == 'dev'
+Provides-Extra: scikit-sparse
+Requires-Dist: pygridfit[scikit-sparse]>=0.1.4; extra == 'scikit-sparse'
+Requires-Dist: scikit-sparse>=0.4.15; extra == 'scikit-sparse'
+Description-Content-Type: text/markdown
+
+# pywarper
+
+`pywarper` is a Python package for conformal mapping-based warping of neuronal arbor morphologies, based on the [MATLAB implementations](https://github.com/uygarsumbul/rgc) (Sümbül, et al. 2014). 
+
+## Installation
+
+```bash
+git clone https://github.com/berenslab/pywarper.git
+pip install -e pywarper
+```
+
+By default, `pywarper` uses `scipy.sparse.linalg.spsolve` to solve sparse matrices, which can be slow. For faster performance, you can manually install [scikit-sparse](https://github.com/scikit-sparse/scikit-sparse), as it requires additional dependencies:
+
+```bash
+# mac
+brew install suite-sparse
+
+# debian
+sudo apt-get install libsuitesparse-dev
+
+pip install -e pywarper[scikit-sparse]
+```
+
+## Usage
+
+See the [example](https://github.com/berenslab/pywarper/blob/main/notebooks/example.ipynb) notebook for usage. 

pywarper-0.1.0/README.md

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+# pywarper
+
+`pywarper` is a Python package for conformal mapping-based warping of neuronal arbor morphologies, based on the [MATLAB implementations](https://github.com/uygarsumbul/rgc) (Sümbül, et al. 2014). 
+
+## Installation
+
+```bash
+git clone https://github.com/berenslab/pywarper.git
+pip install -e pywarper
+```
+
+By default, `pywarper` uses `scipy.sparse.linalg.spsolve` to solve sparse matrices, which can be slow. For faster performance, you can manually install [scikit-sparse](https://github.com/scikit-sparse/scikit-sparse), as it requires additional dependencies:
+
+```bash
+# mac
+brew install suite-sparse
+
+# debian
+sudo apt-get install libsuitesparse-dev
+
+pip install -e pywarper[scikit-sparse]
+```
+
+## Usage
+
+See the [example](https://github.com/berenslab/pywarper/blob/main/notebooks/example.ipynb) notebook for usage.