Adding support for Python 3.10 and updating test infrastructure (#63)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/cpp.yml

@@ -1,10 +1,17 @@
 name: C++
-
 on:
   push:
-    branches: [main]
+    branches:
+      - main
+    tags:
+      - "*"
+    paths-ignore:
+      - "docs/**"
   pull_request:
-    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
 
 jobs:
   build:

.github/workflows/python.yml

@@ -1,114 +1,74 @@
 name: Python
 on:
   push:
-    branches: [main]
+    branches:
+      - main
+    tags:
+      - "*"
+    paths-ignore:
+      - "docs/**"
   pull_request:
-    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
+  tests:
+    runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9"]
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9"]
+        extras: ["core", "jax", "pymc3"]
+        include:
+          - python-version: "3.10"
+            extras: "core"
+
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout
+        uses: actions/checkout@v2
         with:
-          submodules: true
           fetch-depth: 0
-      - name: Set up Python ${{ matrix.python-version }}
+          submodules: true
+
+      - name: Setup Python
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: ilammy/msvc-dev-cmd@v1
-      - name: Install dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install -e ".[test]"
-        env:
-          DISTUTILS_USE_SDK: 1
-          MSSdk: 1
-      - name: Run the unit tests
-        run: python -m pytest --cov celerite2 python/test
-      - name: Coveralls
-        if: startsWith(matrix.os, 'ubuntu')
-        uses: AndreMiras/coveralls-python-action@v20201129
-        with:
-          parallel: true
-          flag-name: Unit Tests
 
-  theano:
-    runs-on: "ubuntu-latest"
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          submodules: true
-          fetch-depth: 0
-      - name: Set up Python
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: 3.8
-          auto-update-conda: true
       - name: Install dependencies
-        shell: bash -l {0}
         run: |
-          conda install -q numpy scipy theano mkl-service
           python -m pip install -U pip
-          python -m pip install --use-feature=2020-resolver -e ".[test,theano]"
-      - name: Get theano compiledir
-        id: compiledir
-        shell: bash -l {0}
-        run: |
-          python -c "import theano; print('::set-output name=compiledir::' + theano.config.compiledir.split('/')[-1])"
-      - name: "Cache ~/.theano"
-        uses: actions/cache@v2
-        with:
-          path: ~/.theano
-          key: theano-${{ steps.compiledir.outputs.compiledir }}-${{ hashFiles('python/test/theano/*.py') }}
-          restore-keys: |
-            theano-${{ steps.compiledir.outputs.compiledir }}-
-            theano-
-      - name: Run the unit tests
-        shell: bash -l {0}
-        run: python -m pytest --cov celerite2 python/test/theano
-      - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@v20201129
-        with:
-          parallel: true
-          flag-name: Unit Tests
+          python -m pip install -U coveralls coverage[toml] tox tox-gh-actions pybind11
 
-  jax:
-    runs-on: "ubuntu-latest"
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          submodules: true
-          fetch-depth: 0
-      - name: Set up Python
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: 3.8
-          auto-update-conda: true
-      - name: Install dependencies
-        shell: bash -l {0}
+      - name: Run tests
+        run: python -m tox
+        env:
+          EXTRAS: ${{ matrix.extras }}
+
+      - name: Combine and upload coverage
         run: |
-          python -m pip install -U pip
-          python -m pip install --use-feature=2020-resolver -e ".[test,jax]"
-      - name: Run the unit tests
-        shell: bash -l {0}
-        run: python -m pytest --cov celerite2 python/test/jax
-      - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@v20201129
-        with:
-          parallel: true
-          flag-name: Unit Tests
+          python -m coverage combine
+          python -m coverage xml -i
+          python -m coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_PARALLEL: true
+          COVERALLS_FLAG_NAME: py${{ matrix.python-version }}-${{ matrix.extras }}
 
   coverage:
-    needs: [build, theano, jax]
+    needs: tests
     runs-on: ubuntu-latest
     steps:
-      - name: Coveralls Finished
-        uses: AndreMiras/coveralls-python-action@v20201129
+      - name: Setup Python
+        uses: actions/setup-python@v2
         with:
-          parallel-finished: true
+          python-version: "3.9"
+      - name: Finish coverage collection
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U coveralls
+          python -m coveralls --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tutorials.yml

@@ -9,6 +9,10 @@ on:
     types:
       - published
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   notebooks:
     name: "Build the notebooks for the docs"
@@ -27,6 +31,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install -U pip
+          python -m pip install "numpy<1.22"
           python -m pip install ".[tutorials]"
 
       - name: Get theano compiledir

.github/workflows/wheels.yml

@@ -14,14 +14,11 @@ jobs:
         with:
           submodules: true
           fetch-depth: 0
-      - uses: ilammy/msvc-dev-cmd@v1
-      - uses: joerick/cibuildwheel@v1.9.0
+      - uses: pypa/cibuildwheel@v2.3.1
         env:
-          CIBW_BUILD: "cp3?-*"
-          CIBW_SKIP: "cp35-* *-win32 *-manylinux_i686"
+          CIBW_SKIP: "pp* *-win32 *-manylinux_i686 *-musllinux*"
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-          DISTUTILS_USE_SDK: 1
-          MSSdk: 1
+          CIBW_ARCHS_MACOS: "x86_64 universal2 arm64"
       - uses: actions/upload-artifact@v2
         with:
           path: ./wheelhouse/*.whl

.gitignore

@@ -35,3 +35,6 @@ dist
 .envrc
 .coverage
 *.ipynb
+.coverage*
+.eggs
+.tox

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=40.6.0", "wheel", "setuptools_scm", "numpy>=1.13.0", "pybind11>=2.4"]
+requires = ["setuptools>=40.6.0", "wheel", "setuptools_scm", "oldest-supported-numpy", "pybind11>=2.4"]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
@@ -28,5 +28,27 @@ use_parentheses = true
 known_third_party = ["numpy"]
 
 [tool.pytest.ini_options]
-norecursedirs = "python/test/*"
 addopts = "-v"
+
+[tool.coverage.run]
+parallel = true
+branch = true
+source = ["celerite2"]
+omit = [
+  "*_test.py",
+  "*__init__*",
+  "*/celerite2/celerite2_version.py",
+]
+
+[tool.coverage.paths]
+source = ["python", "*/site-packages"]
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+  "raise NotImplementedError",
+  "except ImportError",
+  "pragma: no cover",
+  "def R_op",
+  "if verbose"
+]