pyfmaps 1.1.0__tar.gz → 1.2.0__tar.gz

pyfmaps-1.2.0/.github/workflows/documentation.yml

@@ -0,0 +1,51 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+  workflow_dispatch:
+  release:
+
+jobs:
+  build_documentation:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # setuptools_scm needs tags to compute the version
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+        cache: "pip"
+
+    - name: Install package (with dependencies for docs)
+      run: |
+        pip install --upgrade pip
+        pip install -r requirements_docs.txt
+        pip install .
+
+    - name: Build HTML
+      run: |
+        sphinx-build -b html docs/source/ docs/_build/html
+
+    - name: upload artifact
+      uses: actions/upload-artifact@v4
+      with:
+        path:
+          docs/_build/html/
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      if: github.ref == 'refs/heads/master'
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/_build/html
+        force_orphan: true

pyfmaps-1.2.0/.github/workflows/lint.yml

@@ -0,0 +1,24 @@
+name: lint
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: ruff
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v1
+        with:
+          version: 0.15.22
+          args: check --output-format=github
+      - uses: astral-sh/ruff-action@v1
+        with:
+          version: 0.15.22
+          args: format --check

pyfmaps-1.2.0/.github/workflows/test_and_deploy.yml

@@ -0,0 +1,82 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - master
+      - main
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [windows-latest, ubuntu-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # setuptools_scm needs full history + tags for the version
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest-cov
+          pip install .
+
+      # this runs the platform-specific tests
+      - name: Run tests
+        shell: bash -l {0}
+        run: pytest -v --cov=./ --cov-report=xml
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v4
+
+  deploy:
+    # Runs on a pushed v* tag: builds, publishes to PyPI via Trusted Publishing
+    # (no API token needed), and creates a GitHub Release with generated notes.
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      id-token: write # OIDC token for PyPI Trusted Publishing
+      contents: write # create the GitHub Release
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # setuptools_scm needs the tag to compute the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build distributions
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build .
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: dist/*

pyfmaps-1.2.0/.gitignore

@@ -0,0 +1,104 @@
+docs/build
+docs/source/generated/*
+docs/make.bat
+docs/Makefile
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# data
+/data
+
+# STRESS outputs
+*.pdf
+*.vtp
+*.mat
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py
+
+# scratch / local test notebooks
+small_test.ipynb
+
+# Dask
+dask-worker-space/
+

pyfmaps-1.2.0/.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+# Install with: pip install pre-commit && pre-commit install
+# Run on all files: pre-commit run --all-files
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.22
+    hooks:
+      # Lint (with autofix), then format.
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

{pyfmaps-1.1.0 → pyfmaps-1.2.0}/MANIFEST.in

@@ -1,7 +1,5 @@
 include LICENSE
 include README.md
 
-include data/*
-
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

{pyfmaps-1.1.0/pyfmaps.egg-info → pyfmaps-1.2.0}/PKG-INFO

@@ -1,34 +1,70 @@
 Metadata-Version: 2.4
 Name: pyfmaps
-Version: 1.1.0
+Version: 1.2.0
 Summary: Python bindings for functional maps
 Author: Robin Magnet
 License: MIT License
+        
+        Copyright (c) 2020 Robin Magnet
+        
+        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, andor sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of 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.
 Project-URL: Bug Tracker, https://github.com/RobinMagnet/pyFM/issues
-Project-URL: Documentation, https://github.com/RobinMagnet/pyFM/blob/master/example_notebook.ipynb
+Project-URL: Documentation, https://robinmagnet.github.io/pyFM/
 Project-URL: Source Code, https://github.com/RobinMagnet/pyFM
 Project-URL: User Support, https://github.com/RobinMagnet/pyFM/issues
-Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Software Development :: Testing
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: scipy
-Requires-Dist: potpourri3d
+Requires-Dist: potpourri3d>=1.3
 Requires-Dist: robust_laplacian
 Requires-Dist: tqdm
 Requires-Dist: scikit-learn
+Provides-Extra: dev
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: myst_parser>=0.13; extra == "docs"
+Requires-Dist: sphinx>=4.0; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-gallery; extra == "docs"
+Requires-Dist: sphinx-math-dollar; extra == "docs"
 Dynamic: license-file
 
 # pyFM - Python Functional Maps Library

pyfmaps-1.2.0/docs/source/_templates/autosummary/class.rst

@@ -0,0 +1,8 @@
+{{ fullname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :member-order: bysource

pyfmaps-1.2.0/docs/source/_templates/autosummary/module.rst

@@ -0,0 +1,52 @@
+{{ fullname | escape | underline }}
+
+.. automodule:: {{ fullname }}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: {{ _('Modules') }}
+
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

pyfmaps-1.2.0/docs/source/api.rst

@@ -0,0 +1,103 @@
+.. _api_documentation:
+
+API Documentation
+=================
+
+Complete reference for the ``pyFM`` package, generated from the source
+docstrings. Every function, class, and method has its own page — use the tables
+below or the sidebar to navigate.
+
+Core classes
+------------
+
+The high-level objects most users interact with.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   ~pyFM.mesh.TriMesh
+   ~pyFM.functional.FunctionalMapping
+
+Functional Map Network
+----------------------
+
+Consistent map synchronization across a collection of shapes (the ``FMN``
+class and its helpers).
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   ~pyFM.FMN.FMN.FMN
+   ~pyFM.FMN.FMN.CLB_quad_form
+
+Shape signatures
+----------------
+
+Heat and Wave Kernel Signatures.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   pyFM.signatures
+
+Spectral operations
+-------------------
+
+Conversions between pointwise and functional maps, shape difference operators,
+and nearest-neighbour utilities.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   pyFM.spectral
+
+Map refinement
+--------------
+
+ICP and ZoomOut refinement of functional maps.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   pyFM.refine
+
+Evaluation
+----------
+
+Geodesic accuracy, continuity, and coverage metrics for correspondences.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   pyFM.eval
+
+Mesh geometry & I/O
+-------------------
+
+Standalone geometric operators (areas, normals, gradients, geodesics),
+Laplacians, and mesh file readers/writers.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   pyFM.mesh.geometry
+   pyFM.mesh.laplacian
+   pyFM.mesh.file_utils
+
+Optimization internals
+----------------------
+
+Energy terms and gradients used by :class:`~pyFM.functional.FunctionalMapping`.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   pyFM.optimize

pyfmaps-1.2.0/docs/source/conf.py

@@ -0,0 +1,76 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+
+import importlib.metadata
+import pathlib
+import sys
+
+sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "pyfmaps"
+copyright = "2024, Robin Magnet"
+author = "Robin Magnet"
+try:
+    release = importlib.metadata.version("pyfmaps")
+except importlib.metadata.PackageNotFoundError:
+    release = "0.0.0"
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",  # merge type hints into descriptions (after napoleon)
+    "sphinx_math_dollar",
+    "sphinx.ext.mathjax",
+    "sphinx_copybutton",  # copy button on code blocks
+    "myst_parser",
+    "sphinx_design",
+]
+
+# Napoleon (numpydoc parsing)
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_use_param = True
+napoleon_use_rtype = True
+
+# Members are documented on their own per-object pages (numpy-style), so module
+# and class pages only render the module/class docstring + summary tables.
+autodoc_default_options = {"member-order": "bysource"}
+autosummary_generate = True
+# Honour each module's __all__ so only intended public names are documented
+# (default True *ignores* __all__, which would leak imported numpy/tqdm/sklearn names).
+autosummary_ignore_module_all = False
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+source_suffix = [".rst", ".md"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]
+
+
+from sphinx.ext.autodoc import between
+
+
+def setup(app):
+    # Register a sphinx.ext.autodoc.between listener to ignore everything
+    # between lines that contain the word IGNORE
+    app.connect("autodoc-process-docstring", between("^.*IGNORE.*$", exclude=True))
+    return app

pyfmaps-1.2.0/docs/source/examples.md

@@ -0,0 +1,15 @@
+Examples
+========
+
+Runnable example notebooks live in the
+[`examples/` directory](https://github.com/RobinMagnet/pyFM/tree/master/examples)
+of the repository:
+
+- **`mesh_and_matching/basic_functions.ipynb`** — compute a functional map
+  between two meshes and convert it to a point-to-point map.
+- **`mesh_and_matching/matching_with_zoomout.ipynb`** — refine a map with
+  ZoomOut.
+- **`functional_map_network/FMN_base.ipynb`** — consistent maps across a
+  collection of shapes with the Functional Map Network.
+
+Richer example pages with interactive plots are planned for a future release.