.github/workflows/python-package.yml

@@ -0,0 +1,177 @@
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+    tags:     [ 'v*' ]     # run when pushing v1.2.3-style tags
+  pull_request:
+    branches: [ master ]
+  release:
+    types: [ created ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.11]
+    name: "lint | Python ${{ matrix.python-version }}"
+    steps:
+    - uses: actions/checkout@v4
+    - 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
+        pip install flake8
+        pip install .
+    - name: Setup flake8 annotations
+      uses: rbialon/flake8-annotations@v1
+    - name: Run flake8
+      run: |
+        flake8 clifford --show-source --statistics
+
+  test:
+    defaults:
+      run:
+        # conda needs this to activate environments properly
+        shell: bash -l {0}
+    needs: lint
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # fastest jobs first
+          - python-version: 3.11
+            name: without JIT
+            disable_jit: 1
+          - python-version: 3.11
+            name: doctests
+            mode: doctests
+          # really slow job next, so it runs in parallel with the others
+          - python-version: 3.11
+            name: slow tests
+            mode: very_slow
+          - python-version: 3.8
+            name: default
+          - python-version: 3.11
+            name: default
+          - python-version: 3.12
+            name: default
+          #- python-version: 3.11
+          #  name: conda
+          #  conda: true
+          - python-version: 3.11
+            name: benchmarks
+            mode: bench
+
+    name: "build | ${{ matrix.name }} | Python ${{matrix.python-version}}"
+    steps:
+    - uses: actions/checkout@v4
+
+    # python / pip
+    - name: Set up Python ${{ matrix.python-version }}
+      if: "!matrix.conda"
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      if: "!matrix.conda"
+      run: |
+        python -m pip install --upgrade pip;
+        pip install . --prefer-binary;
+        # test dependencies
+        pip install --upgrade pytest pytest-cov pytest-benchmark IPython
+
+    # conda
+    - name: Set up Python ${{ matrix.python-version }} (conda)
+      if: matrix.conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies (conda)
+      if: matrix.conda
+      run: |
+        echo $CONDA/bin >> $GITHUB_PATH;
+        conda install \
+          "numpy>=1.17.0" \
+          scipy \
+          pip \
+          IPython \
+          h5py;
+        conda install -c conda-forge sparse;
+        conda install -c numba "numba>=0.45.1";
+        # make sure in conda we do not overwrite dependencies with pip
+        python setup.py develop --no-deps;
+        # test dependencies
+        python -m pip install --upgrade pytest pytest-cov pytest-benchmark;
+
+    - name: Test with pytest
+      env:
+        MODE: ${{ matrix.mode }}
+        NUMBA_DISABLE_JIT: ${{ matrix.disable_jit }}
+      run: |
+        PYTEST_ARGS=();
+        if [[ "${MODE}" == "bench" ]]; then
+          PYTEST_ARGS+=(--benchmark-only);
+        else
+          PYTEST_ARGS+=(--benchmark-skip);
+        fi;
+        if [[ "${MODE}" == "very_slow" ]]; then
+          PYTEST_ARGS+=(-m "veryslow");
+        else
+          PYTEST_ARGS+=(-m "not veryslow");
+        fi;
+        if [[ "${MODE}" == "doctests" ]]; then
+          PYTEST_ARGS+=(--doctest-modules --ignore clifford/test);
+        fi;
+
+        # `python -m` ensures we dispatch to conda if appropriate
+        python -m pytest \
+          --pyargs clifford \
+          "${PYTEST_ARGS[@]}" \
+          --color=yes \
+          -o junit_family=legacy \
+          --junitxml=junit/test-results.xml \
+          --durations=25 \
+          --cov=clifford \
+          --cov-branch;
+    # This only publishes result for the last run right now
+    # - name: Publish Test Report
+    #   uses: mikepenz/action-junit-report@v2
+    #   if: ${{ always() }}
+    #   with:
+    #     report_paths: 'junit/test-results.xml'
+    - uses: codecov/codecov-action@v5
+
+  deploy:
+    needs: test
+    runs-on: ubuntu-latest
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    environment: pypi
+    permissions:
+      # IMPORTANT: this permission is mandatory for Trusted Publishing
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    - name: "Install"
+      run: |
+        python -m pip install --upgrade pip;
+        python -m pip install build
+        python -m build --sdist --wheel --outdir dist/
+    - uses: actions/upload-artifact@v4
+      with:
+        name: dist
+        path: dist
+    - name: Publish to PyPI (tags only)
+      if: startsWith(github.ref, 'refs/tags/v')
+      uses: pypa/gh-action-pypi-publish@release/v1

.mailmap

@@ -0,0 +1,19 @@
+# Prevent git from showing duplicate names with commands like "git shortlog"
+# See the manpage of git-shortlog for details.
+# The syntax is:
+# Name that should be used <email that should be used> Bad name <bad email>
+#
+# You can skip Bad name if it is the same as the one that should be used, and is unique.
+#
+# This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
+# gives no duplicates.
+
+Hugo Hadfield <hadfield.hugo@gmail.com> hugo hadfield <hadfield.hugo@gmail.com>
+Hugo Hadfield <hadfield.hugo@gmail.com> hugohadfield <hadfield.hugo@gmail.com>
+Hugo Hadfield <hadfield.hugo@gmail.com> Hugo <hadfield.hugo@gmail.com>
+
+Alex Arsenovic <alexanderarsenovic@gmail.com> alex arsenovic <alexanderarsenovic@gmail.com>
+Alex Arsenovic <alexanderarsenovic@gmail.com> alex arsenovic <arsenovic@virginia.edu>
+Alex Arsenovic <alexanderarsenovic@gmail.com> arsenovic <alexanderarsenovic@gmail.com>
+
+Robert Kern <robert.kern@gmail.com> root <root@Sacrilege.local>

.readthedocs.yml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -15,7 +21,6 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
   install:
     - method: pip
       path: .

.zenodo.json

@@ -3,11 +3,6 @@
     "id": "BSD-3-Clause"
   }, 
   "creators": [
-    {
-      "affiliation": "810 Labs",
-      "name": "Alex Arsenovic",
-      "orcid": "0000-0002-8599-5873"
-    },
     {
       "affiliation": "University of Cambridge",
       "name": "Hugo Hadfield",
@@ -18,6 +13,11 @@
       "name": "Eric Wieser",
       "orcid": "0000-0003-0412-4978"
     },
+    {
+      "affiliation": "810 Labs",
+      "name": "Alex Arsenovic",
+      "orcid": "0000-0002-8599-5873"
+    },
     {
       "affiliation": "Enthought, Inc.",
       "name": "Robert Kern"