flagserpy 0.1.0__tar.gz

flagserpy-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,76 @@
+name: Build package on different OSs and Python versions
+
+on : [push, pull_request]
+
+jobs:
+
+  build_package:
+    name: Build ${{ github.event.repository.name }} on ${{ matrix.os }} for Python-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+          - os: macos-latest
+            path: ~/Library/Caches/pip
+          - os: windows-latest
+            path: ~\AppData\Local\pip\Cache
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v5
+        name: Install Python-${{ matrix.python-version }}
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Activating Python cache
+        uses: actions/cache@v4
+        id: cache_python
+        continue-on-error: true
+        with:
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Build ${{ github.event.repository.name }}
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[doc,tests]"
+
+      - name: Install and run flake8 on Mac
+        if: ${{ runner.os == 'macOS' }}
+        run: |
+          flake8
+
+      - name: Run test on Mac with coverage generated
+        if: ${{ runner.os == 'macOS' }}
+        run: |
+          pytest flagserpy/tests --cov flagserpy --cov-report xml
+
+      - name: Run test on Linux and Windows with no coverage generated
+        if: ${{ runner.os != 'macOS' }}
+        run: |
+          python -m pytest flagserpy/tests --no-cov --no-coverage-upload
+
+      - name: Build sphinx doc on Linux
+        if: ${{ runner.os == 'Linux' }}
+        run: |
+          cd doc
+          python -m pip install -r requirements.txt
+          sphinx-build -b html . build
+
+      - name: Upload built documentation and coverage as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: ArtifactsCI-${{ matrix.os }}-${{ matrix.python-version }}
+          if-no-files-found: ignore
+          path: |
+            doc/build
+            coverage.xml
+            htmlcov

flagserpy-0.1.0/.github/workflows/wheels.yml

@@ -0,0 +1,174 @@
+name: Build and Publish
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - "v*"
+
+concurrency:
+  group: build-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.1.0
+        env:
+          # Most cibuildwheel options (build, skip, macos archs) live in
+          # [tool.cibuildwheel] in pyproject.toml. Only platform-specific
+          # bits that don't fit cleanly there are set here.
+          CIBW_BEFORE_BUILD_WINDOWS: sed -i $'s/\r$//' README.rst && python -m pip install delvewheel
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -vv -w {dest_dir} {wheel}"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: ./dist/*.tar.gz
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    needs:
+      - build_wheels
+      - build_sdist
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/flagserpy
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all wheel artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Publish distributions to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    needs:
+      - publish-to-testpypi
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/flagserpy
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all wheel artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Publish distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Sign and publish GitHub Release
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    needs:
+      - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - name: Download all wheel artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Sign distributions with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes ""
+
+      - name: Upload distributions and signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

flagserpy-0.1.0/.gitignore

@@ -0,0 +1,129 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+docs/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.pytest_cache/
+test-output.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/build/
+doc/generated/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# Emacs
+*~
+
+# macOS
+*.DS_Store
+
+# IDEs
+.idea/*
+.vscode/*
+
+# scikit-build-core editable.mode = "inplace" build artifacts
+.cmake/
+.ninja_deps
+.ninja_log
+.skbuild-info.json
+CMakeCache.txt
+CMakeFiles/
+CMakeInit.txt
+build.ninja
+cmake_install.cmake
+flagserpy/modules/

flagserpy-0.1.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "flagser"]
+	path = flagser
+	url = https://github.com/luetge/flagser.git

flagserpy-0.1.0/.tools/git-pre-commit

@@ -0,0 +1,8 @@
+#!/bin/sh
+
+branch="$(git rev-parse --abbrev-ref HEAD)"
+
+if [ "$branch" = "master" ]; then
+  echo "You can't commit directly to master branch"
+  exit 1
+fi

flagserpy-0.1.0/CMakeLists.txt

@@ -0,0 +1,71 @@
+cmake_minimum_required(VERSION 3.15)
+project(flagser_pybind LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 14)
+
+find_package(pybind11 CONFIG REQUIRED)
+
+set(BINDINGS_DIR "src")
+
+# When scikit-build-core is invoked in editable.mode = "inplace" the source and
+# binary directories coincide. In that case the compiled modules must land
+# inside the Python package (flagserpy/modules) so that `from .modules.* import ...`
+# works without any wheel-install step. For regular (out-of-tree) builds the
+# normal install(TARGETS ... DESTINATION flagserpy/modules) rules below apply.
+if("${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}"
+   AND DEFINED SKBUILD)
+  set(FLAGSERPY_INPLACE_OUTPUT_DIR
+      "${CMAKE_CURRENT_SOURCE_DIR}/flagserpy/modules")
+  file(MAKE_DIRECTORY "${FLAGSERPY_INPLACE_OUTPUT_DIR}")
+endif()
+
+# flagser
+pybind11_add_module(flagser_pybind "${BINDINGS_DIR}/flagser_bindings.cpp")
+target_compile_definitions(flagser_pybind PRIVATE RETRIEVE_PERSISTENCE=1 MANY_VERTICES=1)
+target_include_directories(flagser_pybind PRIVATE .)
+if(DEFINED FLAGSERPY_INPLACE_OUTPUT_DIR)
+    set_target_properties(flagser_pybind PROPERTIES
+        LIBRARY_OUTPUT_DIRECTORY "${FLAGSERPY_INPLACE_OUTPUT_DIR}$<0:>")
+endif()
+if(MSVC)
+    target_compile_options(flagser_pybind PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)
+    target_compile_options(flagser_pybind PUBLIC $<$<CONFIG:DEBUG>:/O1 /DEBUG:FULL /Zi /Zo>)
+else()
+    target_compile_options(flagser_pybind PUBLIC $<$<CONFIG:RELEASE>: -O3>)
+    target_compile_options(flagser_pybind PUBLIC $<$<CONFIG:DEBUG>: -O2 -ggdb -D_GLIBCXX_DEBUG>)
+endif()
+install(TARGETS flagser_pybind DESTINATION flagserpy/modules)
+
+# flagser with USE_COEFFICIENTS
+pybind11_add_module(flagser_coeff_pybind "${BINDINGS_DIR}/flagser_bindings.cpp")
+target_compile_definitions(flagser_coeff_pybind PRIVATE RETRIEVE_PERSISTENCE=1 USE_COEFFICIENTS=1 MANY_VERTICES=1)
+target_include_directories(flagser_coeff_pybind PRIVATE .)
+if(DEFINED FLAGSERPY_INPLACE_OUTPUT_DIR)
+    set_target_properties(flagser_coeff_pybind PROPERTIES
+        LIBRARY_OUTPUT_DIRECTORY "${FLAGSERPY_INPLACE_OUTPUT_DIR}$<0:>")
+endif()
+if(MSVC)
+    target_compile_options(flagser_coeff_pybind PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)
+    target_compile_options(flagser_coeff_pybind PUBLIC $<$<CONFIG:DEBUG>:/O1 /DEBUG:FULL /Zi /Zo>)
+else()
+    target_compile_options(flagser_coeff_pybind PUBLIC $<$<CONFIG:RELEASE>: -O3>)
+    target_compile_options(flagser_coeff_pybind PUBLIC $<$<CONFIG:DEBUG>: -O2 -ggdb -D_GLIBCXX_DEBUG>)
+endif()
+install(TARGETS flagser_coeff_pybind DESTINATION flagserpy/modules)
+
+# flagser-count
+pybind11_add_module(flagser_count_pybind "${BINDINGS_DIR}/flagser_count_bindings.cpp")
+target_compile_definitions(flagser_count_pybind PRIVATE MANY_VERTICES=1)
+target_include_directories(flagser_count_pybind PRIVATE .)
+if(DEFINED FLAGSERPY_INPLACE_OUTPUT_DIR)
+    set_target_properties(flagser_count_pybind PROPERTIES
+        LIBRARY_OUTPUT_DIRECTORY "${FLAGSERPY_INPLACE_OUTPUT_DIR}$<0:>")
+endif()
+if(MSVC)
+    target_compile_options(flagser_count_pybind PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)
+    target_compile_options(flagser_count_pybind PUBLIC $<$<CONFIG:DEBUG>:/O1 /DEBUG:FULL /Zi /Zo>)
+else()
+    target_compile_options(flagser_count_pybind PUBLIC $<$<CONFIG:RELEASE>: -O3>)
+    target_compile_options(flagser_count_pybind PUBLIC $<$<CONFIG:DEBUG>: -O2 -ggdb -D_GLIBCXX_DEBUG>)
+endif()
+install(TARGETS flagser_count_pybind DESTINATION flagserpy/modules)

flagserpy-0.1.0/CODE_AUTHORS

@@ -0,0 +1,7 @@
+# The following is the list of the code authors of the giotto-learn python
+# package. Where component authors are known, add them here.
+
+Guillaume Tauzin, guillaume.tauzin@epfl.ch
+Julian Burella Pérez, julian.burellaperez@heig-vd.ch
+Umberto Lupo, u.lupo@l2f.ch
+Florian Unger, florian.unger@fau.de

flagserpy-0.1.0/CODE_OF_CONDUCT.rst

@@ -0,0 +1,55 @@
+CONTRIBUTOR CODE OF CONDUCT
+===========================
+(Code of Conduct)
+-----------------
+
+
+Our Pledge
+----------
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* 	Using welcoming and inclusive language;
+* 	Being respectful of differing viewpoints and experiences;
+* 	Gracefully accepting constructive criticism;
+* 	Focusing on what is best for the community;
+* 	Showing empathy towards other community members.
+
+Examples of unacceptable behavior by participants include:
+
+* 	The use of sexualized language or imagery and unwelcome sexual attention or advances;
+* 	Trolling, insulting/derogatory comments, and personal or political attacks;
+* 	Public or private harassment;
+* 	Publishing others’ private information, such as a physical or electronic address, without explicit permission;
+* 	Other conduct which could reasonably be considered inappropriate in a professional setting.
+
+Our Responsibilities
+--------------------
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+Scope
+-----
+
+This Code of Conduct applies within all Giotto’s project spaces, to all content on <www.giotto.ai>, Giotto’s GitHub organization, or any other official Giotto web presence allowing for community interactions, and it also applies when an individual is representing the project or its community in public spaces.
+
+Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at <maintainers@giotto.ai>. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances, Sanctions may include written warnings, expulsions from the project, project sponsored spaces, or project forums, or any other sanction which is deemed appropriate. [The project team] is obligated to maintain confidentiality with regard to the reporter of an incident. If the act is ongoing (such as someone engaging in harassment) or involves a threat to anyone's safety (e.g. threats of violence), the the project team may issue sanctions without notice. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by the project leader.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>, and includes some aspects of the TensorFlow Code of Conduct, available at <https://github.com/tensorflow/tensorflow/blob/master/CODE_OF_CONDUCT.md>

flagserpy-0.1.0/CONTRIBUTING.rst

@@ -0,0 +1,123 @@
+Contributing guidelines
+=======================
+
+Pull Request Checklist
+----------------------
+
+Before sending your pull requests, make sure you followed this list.
+  - Read the `contributing guidelines <https://github.com/giotto-ai/pyflagser/blob/master/GOVERNANCE.rst>`_.
+  - Read the `code of conduct <https://github.com/giotto-ai/pyflagser/blob/master/CODE_OF_CONDUCT.rst>`_.
+  - Ensure you have signed the `contributor license agreement (CLA) <https://cla-assistant.io/giotto-ai/pyflagser>`_.
+  - Check if the changes are consistent with the guidelines.
+  - Changes are consistent with the Coding Style.
+  - Run Unit Tests.
+
+How to become a contributor and submit your own code
+----------------------------------------------------
+
+Contributor License Agreements
+------------------------------
+
+In order to become a contributor of Giotto, the first step is to sign the
+`contributor license agreement (CLA) <https://cla-assistant.io/giotto-ai/pyflagser>`_.
+**NOTE**: Only original source code from you and other people that have signed
+the CLA can be accepted into the main repository.
+
+Contributing code
+-----------------
+
+If you have improvements to Giotto, do not hesitate to send us pull requests!
+Please follow the Github how to (https://help.github.com/articles/using-pull-requests/).
+The Giotto Team will review your pull requests. Once the pull requests are approved and pass continuous integration checks, the
+Giotto team will work on getting your pull request submitted to our GitHub
+repository. Eventually, your pull request will be merged automatically on GitHub.
+If you want to contribute, start working through the Giotto codebase,
+navigate to the `GitHub issue tab <https://github.com/giotto-ai/pyflagser/issues>`_
+and start looking through interesting issues. These are issues that we believe
+are particularly well suited for outside contributions, often because we
+probably won't get to them right now. If you decide to start on an issue, leave
+a comment so that other people know that you're working on it. If you want to
+help out, but not alone, use the issue comment thread to coordinate.
+
+Contribution guidelines and standards
+-------------------------------------
+
+Before sending your pull request for review, make sure your changes are
+consistent with the guidelines and follow the coding style below.
+
+General guidelines and philosophy for contribution
+--------------------------------------------------
+
+* Include unit tests when you contribute new features, as they help to
+  a) prove that your code works correctly, and
+  b) guard against future breaking changes to lower the maintenance cost.
+* Bug fixes also generally require unit tests, because the presence of bugs
+  usually indicates insufficient test coverage.
+* Keep API compatibility in mind when you change code in core Giotto.
+* Clearly define your exceptions using the utils functions and test the exceptions.
+* When you contribute a new feature to Giotto, the maintenance burden is   
+  (by default) transferred to the Giotto team. This means that the benefit   
+  of the contribution must be compared against the cost of maintaining the   
+  feature.
+
+C++ coding style
+----------------
+
+Changes to Giotto C/C++ code should conform to `Google C++ Style Guide <https://google.github.io/styleguide/cppguide.html>`_.
+Use `clang-tidy` to check your C/C++ changes. To install `clang-tidy` on
+ubuntu:16.04, do:
+
+
+.. code-block:: bash
+
+    apt-get install -y clang-tidy
+
+You can check a C/C++ file by doing:
+
+.. code-block:: bash
+
+    clang-format <my_cc_file> --style=google > /tmp/my_cc_file.ccdiff <my_cc_file> /tmp/my_cc_file.cc
+
+Python coding style
+-------------------
+
+Changes to Giotto Python code should conform to PEP8 directives.
+Use `flake8` to check your Python changes. To install `flake8` just do
+
+.. code-block:: python
+
+    pip install flake8
+
+You can use `flake8` on your python code via the following instructions:
+
+.. code-block:: python
+
+    flake8 name_of_your_script.py
+
+Git pre-commit hook
+-------------------
+We provide a pre-commit git hook to prevent accidental commits to the master branch. To activate, run
+
+.. code-block:: bash
+
+    cd .git/hooks
+    ln -s ../../.tools/git-pre-commit pre-commit
+
+Running unit tests
+------------------
+
+There are two ways to run Giotto unit tests.
+
+1. Using tools and libraries installed directly on your system. The election tool is `pytest`. To install `pytest` just do
+
+.. code-block:: python
+
+    pip install pytest
+
+You can use `pytest` on your python code via the following instructions:
+
+.. code-block:: python
+
+    pytest name_of_your_script.py
+
+2. Using Azure (azure-pipelines.yml) and Giotto's CI scripts.