Switching to tox for tests

.github/workflows/joss.yml

@@ -4,10 +4,8 @@ on:
   push:
     branches:
       - main
-      - joss
-  pull_request:
-    branches:
-      - main
+    paths:
+      - "joss/**"
 
 jobs:
   joss:

.github/workflows/tests.yml

@@ -4,11 +4,12 @@ on:
   push:
     branches:
       - main
+    tags:
+      - "*"
+    paths-ignore:
+      - "joss/**"
+      - "docs/**"
   pull_request:
-    branches:
-      - main
-  release:
-    types: [published]
 
 jobs:
   tests:
@@ -17,60 +18,77 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9"]
-        pymc-arviz:
-          - '"pymc3~=3.9.0" "arviz<0.11"'
-          - '"pymc3~=3.10.0" "arviz<0.11"'
-          - '"pymc3~=3.11.0"'
-          - '"https://github.com/pymc-devs/pymc3/archive/master.zip"'
+        pymc-version: ["3.9", "3.10", "3.11", "dev"]
+        include:
+          - python-version: "3.8"
+            pymc-version: "3.11"
 
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout
+        uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
-        name: Install Python
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install ${{ matrix.pymc-arviz }}
-          python -m pip install -e .[test]
-          python -m pip install --no-deps starry
-
-      - name: Get compiledir
-        id: compiledir
-        shell: bash -l {0}
-        run: |
-          python -c "from aesara_theano_fallback import aesara; print('::set-output name=compiledir::' + aesara.config.compiledir)"
-
-      - name: Cache compiledir
-        uses: actions/cache@v2
-        with:
-          path: ${{ steps.compiledir.outputs.compiledir }}
-          key: compiledir-${{ steps.compiledir.outputs.compiledir }}-${{ matrix.pymc-arviz }}-${{ github.sha }}
-          restore-keys: |
-            compiledir-${{ steps.compiledir.outputs.compiledir }}-${{ matrix.pymc-arviz }}-
+          python -m pip install -U coveralls coverage[toml] tox tox-gh-actions
 
       - name: Run tests
-        run: python -m pytest --cov=exoplanet -v tests
+        run: python -m tox
+        env:
+          PYMC_VERSION: ${{ matrix.pymc-version }}
 
-      - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@v20201129
-        with:
-          parallel: true
-          flag-name: Unit Tests
+      - name: Combine and upload coverage
+        run: |
+          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 }}-pymc${{ matrix.pymc-version }}
 
   coverage:
-    name: "Merge and upload coverage"
     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 }}
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install tox
+
+      - name: Lint the code
+        run: python -m tox -e lint
 
   build:
     runs-on: ubuntu-latest
@@ -92,7 +110,7 @@ jobs:
           path: dist/*
 
   upload_pypi:
-    needs: [tests, build]
+    needs: [tests, lint, build]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:

.github/workflows/tutorials.yml

@@ -3,12 +3,11 @@ on:
   push:
     branches:
       - main
+    tags:
+      - "*"
+    paths-ignore:
+      - "joss/**"
   pull_request:
-    branches:
-      - main
-  release:
-    types:
-      - published
 
 jobs:
   notebooks:

pyproject.toml

@@ -4,21 +4,6 @@ build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 79
-exclude = '''
-/(
-    \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-  | docs/tutorials
-)/
-'''
 
 [tool.isort]
 skip_glob = ["docs/tutorials/*.py"]
@@ -28,3 +13,29 @@ include_trailing_comma = true
 force_grid_wrap = 0
 use_parentheses = true
 known_third_party = ["astropy", "corner", "jupytext", "matplotlib", "nbconvert", "nbformat", "numpy", "packaging", "pandas", "pkg_resources", "pymc3", "pytest", "requests", "scipy", "setuptools", "sphinx_typlog_theme", "theano"]
+
+[tool.coverage.run]
+parallel = true
+branch = true
+source = ["exoplanet"]
+omit = [
+  "*_test.py",
+  "*__init__*",
+  "*/exoplanet/exoplanet_version.py",
+  "*/exoplanet/orbits/constants.py",
+  "*/exoplanet/light_curves/integrated.py",
+  "*/exoplanet/light_curves/interpolated.py",
+]
+
+[tool.coverage.paths]
+source = ["src", "*/site-packages"]
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+  "raise NotImplementedError",
+  "except ImportError",
+  "pragma: no cover",
+  "def R_op",
+  "if verbose"
+]

pytest.ini

@@ -1,4 +1,5 @@
 [pytest]
+testpaths = "tests"
 addopts =
     -v
 filterwarnings =

setup.py

@@ -34,7 +34,7 @@
     "test": [
         "scipy",
         "pytest",
-        "pytest-cov>=2.6.1",
+        "coverage[toml]",
         "pytest-env",
         "batman-package",
     ],

tox.ini

@@ -0,0 +1,33 @@
+[tox]
+envlist = py{38,39}-pymc{39,310,311,dev},lint
+
+[gh-actions]
+python =
+    3.8: py38
+    3.9: py39
+
+[gh-actions:env]
+PYMC_VERSION =
+    3.9: pymc39
+    3.10: pymc310
+    3.11: pymc311
+    dev: pymcdev
+
+[testenv]
+passenv = GITHUB_*
+deps =
+    pymc{39,310}: arviz<0.11
+    pymc39: pymc3~=3.9.0
+    pymc310: pymc3~=3.10.0
+    pymc311: pymc3~=3.11.0
+    pymcdev: https://github.com/pymc-devs/pymc3/archive/v3.zip
+extras = test
+commands =
+    pip freeze
+    python -m coverage run -m pytest -v {posargs}
+
+[testenv:lint]
+skip_install = true
+deps = pre-commit
+commands =
+    pre-commit run --all-files