New ci (#48)

Co-authored-by: dmaljovec <daniel.maljovec@recursionpharma.com>

.coveragerc

@@ -1,5 +1,12 @@
+[paths]
+source =
+    topopy/
+    /Users/runner/work/topopy/topopy/topopy/
+    /home/runner/work/topopy/topopy/topopy/
+    D:\a\topopy\topopy\topopy\
+
 [run]
 branch = True
 omit =
     topopy/tests/*
-    topopy/topology.py
+    topopy/topology.py

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 88
+extend-ignore = E203

.github/workflows/publish.yaml

@@ -0,0 +1,72 @@
+name: Release
+on:
+  workflow_run:
+    workflows: ["Test"]
+    branches: [main]
+    types:
+      - completed
+jobs:
+  push_tag:
+    name: Push Tag
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v3
+      - name: Push tag
+        id: tag_version
+        uses: mathieudutour/github-tag-action@v6.1
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+  build_wheels:
+    needs: push_tag
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, windows-2019, macOS-11]
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.11.2
+
+      - name: Build wheels
+        run: |
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          make
+          python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  publish:
+    needs: build_wheels
+    name: Publish Wheels and Source Distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v3
+      - uses: actions/download-artifact@v3
+        with:
+          path: ./wheelhouse
+      - name: Build source distribution
+        run: |
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          make
+          python setup.py sdist -d wheelhouse
+      - run: |
+          mv artifact/*.whl ./
+          rm -rf artifact
+        working-directory: ./wheelhouse
+      - name: Publish wheels to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages_dir: wheelhouse/

.github/workflows/quality.yaml

@@ -0,0 +1,18 @@
+name: Quality
+on: [push]
+jobs:
+  tests:
+    name: Quality
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+      - name: update pip
+        run: |
+          pip install -U wheel
+          pip install -U setuptools
+          python -m pip install -U pip
+      - run: pip install tox
+      - run: tox -e style

.github/workflows/test.yaml

@@ -0,0 +1,46 @@
+name: Test
+on: [push]
+jobs:
+  tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        minor_version: [7, 8, 9, 10, 11]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: 3.${{ matrix.minor_version }}
+      - name: update pip
+        run: |
+          pip install -U wheel
+          pip install -U setuptools
+          python -m pip install -U pip
+      - run: pip install tox
+      - run: make
+      - run: tox -e py3${{ matrix.minor_version }}
+      - uses: actions/upload-artifact@v3
+        with:
+          name: coverage.${{ matrix.os }}.py3${{ matrix.minor_version }}
+          path: ./.coverage.py3${{ matrix.minor_version }}
+  coverage:
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/download-artifact@v3
+        with:
+          path: .
+      - run: pip install coverage
+      - run: |
+          coverage combine coverage*/
+          coverage report --fail-under=95
+          coverage lcov
+      - name: publish coverage to Coveralls
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./coverage.lcov

.gitignore

@@ -22,4 +22,4 @@ topopy.egg-info/*
 
 .ipynb_checkpoints
 docs/_build
-
+.python-version

.pre-commit-config.yaml

@@ -1,6 +1,74 @@
+# https://pre-commit.com/hooks.html
+
+exclude: ^(docs/|.tox)
+default_language_version:
+  python: python3
 repos:
--   repo: https://github.com/ambv/black
-    rev: stable
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
     hooks:
-    - id: black
-      language_version: python2.7
+      - id: check-added-large-files # Prevent giant files from being committed
+      - id: check-ast # Simply check whether the files parse as valid python.
+      - id: check-byte-order-marker # forbid files which have a UTF-8 byte-order marker
+      - id: check-builtin-literals # Require literal syntax when initializing empty or zero Python builtin types.
+      - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems
+      - id: check-docstring-first # Checks a common error of defining a docstring after code.
+      - id: check-executables-have-shebangs # Ensures that (non-binary) executables have a shebang.
+      - id: check-json # This hook checks json files for parseable syntax.
+      - id: check-shebang-scripts-are-executable # Ensures that (non-binary) files with a shebang are executable.
+      - id: pretty-format-json # This hook sets a standard for formatting JSON files.
+        args: ['--autofix']
+      - id: check-merge-conflict # Check for files that contain merge conflict strings.
+      - id: check-symlinks # Checks for symlinks which do not point to anything.
+      - id: check-toml # This hook checks toml files for parseable syntax.
+      - id: check-vcs-permalinks # Ensures that links to vcs websites are permalinks.
+      - id: check-xml # This hook checks xml files for parseable syntax.
+      - id: check-yaml # This hook checks yaml files for parseable syntax.
+      - id: debug-statements # Check for debugger imports and py37+ `breakpoint()` calls in python source.
+      - id: destroyed-symlinks # Detects symlinks which are changed to regular files with a content of a path which that symlink was pointing to.
+      - id: detect-private-key # Detects the presence of private keys
+      - id: end-of-file-fixer # Ensures that a file is either empty, or ends with one newline.
+      - id: fix-byte-order-marker # removes UTF-8 byte order marker
+      - id: mixed-line-ending # Replaces or checks mixed line ending
+      - id: sort-simple-yaml # Sorts simple YAML files which consist only of top-level keys, preserving comments and blocks.
+      - id: trailing-whitespace # This hook trims trailing whitespace.
+  - repo: local
+    hooks:
+      - id: flake8
+        name: flake8
+        entry: "flake8 --config ./.flake8"
+        language: system # will not create a separate virtualenv for the hook and will run it in whatever environment you happen to be in when you run git commit or pre-commit run
+        types: [python] # trigger for commits changing Python files
+        require_serial: true # use require_serial so that script is only called once per commit
+      - id: isort
+        name: isort
+        entry: "isort --settings-path=pyproject.toml"
+        language: system
+        types: [python]
+        require_serial: true
+      - id: black
+        name: black
+        entry: "black ."
+        language: system
+        types: [python]
+        require_serial: true
+      - id: mypy
+        name: mypy
+        entry: "mypy --config-file=pyproject.toml"
+        language: system
+        types: [python]
+        require_serial: true
+      # - id: bandit
+      #   name: bandit
+      #   entry: "bandit -r -c pyproject.toml ."
+      #   language: system
+      #   types: [python]
+        # require_serial: true
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: python-check-blanket-noqa # Enforce that noqa annotations always occur with specific codes. Sample annotations: # noqa: F401, # noqa: F401,W203
+      # - id: python-check-blanket-type-ignore # Enforce that # type: ignore annotations always occur with specific codes. Sample annotations: # type: ignore[attr-defined], # type: ignore[attr-defined, name-defined]
+      - id: python-check-mock-methods # Prevent common mistakes of assert mck.not_called(), assert mck.called_once_with(...) and mck.assert_called.
+      - id: python-use-type-annotations # Enforce that python3.6+ type annotations are used instead of type comments
+      - id: text-unicode-replacement-char # Forbid files which have a UTF-8 Unicode replacement character

CHANGELOG.md

@@ -51,4 +51,4 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 [0.0.4]: https://github.com/olivierlacan/keep-a-changelog/compare/v0.0.3...v0.0.4
 [0.0.3]: https://github.com/olivierlacan/keep-a-changelog/compare/v0.0.2...v0.0.3
 [0.0.2]: https://github.com/olivierlacan/keep-a-changelog/compare/v0.0.1...v0.0.2
-[0.0.1]: https://github.com/olivierlacan/keep-a-changelog/compare/v0.0.0...v0.0.1
+[0.0.1]: https://github.com/olivierlacan/keep-a-changelog/compare/v0.0.0...v0.0.1

MANIFEST.in

@@ -3,4 +3,3 @@ include *.md
 include *.py
 include LICENSE
 include README.rst
-include requirements.txt

MergeTree.cpp

@@ -205,4 +205,3 @@ std::map< std::pair<int, int>, std::vector<int> > MergeTree<T>::AugmentedEdges()
 
 template class MergeTree<double>;
 template class MergeTree<float>;
-

MorseComplex.h

@@ -259,4 +259,4 @@ class MorseComplex
   void ComputeMaximaPersistence();
 };
 
-#endif //MC_H
+#endif //MC_H

README.rst

@@ -5,24 +5,38 @@ topopy
 
 .. image:: https://img.shields.io/pypi/v/topopy.svg
         :target: https://pypi.python.org/pypi/topopy
-        :alt: PyPI
-
-.. image:: https://travis-ci.org/maljovec/topopy.svg?branch=master
-        :target: https://travis-ci.org/maljovec/topopy
-        :alt: Build Status
-
-.. image:: https://coveralls.io/repos/github/maljovec/topopy/badge.svg?branch=master
-        :target: https://coveralls.io/github/maljovec/topopy?branch=master
-        :alt: Coverage Status
-
+        :alt: Latest Version on PyPI
+.. image:: https://img.shields.io/pypi/dm/topopy.svg?label=PyPI%20downloads
+        :target: https://pypi.org/project/topopy/
+        :alt: PyPI downloads
+
+.. image:: https://github.com/maljovec/topopy/actions/workflows/quality.yaml/badge.svg?branch=main
+        :target: https://github.com/maljovec/topopy/actions
+        :alt: Code Quality Test Results
+.. image:: https://github.com/maljovec/topopy/actions/workflows/test.yaml/badge.svg?branch=main
+        :target: https://github.com/maljovec/topopy/actions
+        :alt: Test Suite Results
+
+.. image:: https://www.codefactor.io/repository/github/maljovec/topopy/badge
+        :target: https://www.codefactor.io/repository/github/maljovec/topopy
+        :alt: CodeFactor
+.. image:: https://coveralls.io/repos/github/maljovec/topopy/badge.svg?branch=main
+        :target: https://coveralls.io/github/maljovec/topopy?branch=main
+        :alt: Coveralls
 .. image:: https://readthedocs.org/projects/topopy/badge/?version=latest
         :target: https://topopy.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-
+        :alt: ReadTheDocs
 .. image:: https://pyup.io/repos/github/maljovec/topopy/shield.svg
         :target: https://pyup.io/repos/github/maljovec/topopy/
         :alt: Pyup
 
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+        :target: https://github.com/psf/black
+        :alt: This code is formatted in black
+.. image:: https://img.shields.io/badge/License-BSD_3--Clause-blue.svg
+        :target: https://opensource.org/licenses/BSD-3-Clause
+        :alt: BSD 3-Clause License
+
 .. end_badges
 
 .. logo