Merge pull request #40 from jag1g13/clean-build

Clean up CI and fix dependencies on macOS

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.6, 3.7, 3.8]
-        os: [ubuntu-latest, macos-11.0]
+        os: [ubuntu-latest, macos-latest]
 
     runs-on: ${{ matrix.os }}
 
@@ -27,33 +27,28 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install pre-install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install poetry wheel
-        poetry config virtualenvs.in-project true
-
-    - name: Cache venv
-      uses: actions/cache@v2
-      with:
-        path: .venv
-        key: ${{ matrix.os }}-${{ matrix.python-version }}-venv-${{ hashFiles('poetry.lock') }}
+    - name: Install Poetry
+      uses: snok/install-poetry@v1.1.1
 
-    - name: Install project dependencies
+    - name: Install project and dependencies
       run: |
-        poetry install --no-root --extras docs --extras test
+        poetry install
 
     - name: Test with pytest
       run: |
-        make test
+        poetry run pytest --cov=pycgtool --cov-report=
+
+    - name: Lint with flake8 - stop build if fails
+      run: |
+        poetry run prospector --strictness veryhigh --test-warnings --tool pyflakes
 
-    - name: Lint with flake8 and prospector
+    - name: Full lint - don't stop build
       run: |
-        make lint
+        poetry run prospector --strictness veryhigh --test-warnings --member-warnings --max-line-length 120 --zero-exit
 
     - name: Test that docs build
       run: |
-        make docs
+        SPHINXBUILD="poetry run sphinx-build" make -C docs html
 
     - name: Check that test coverage is above 80%
       run: |

pyproject.toml

@@ -15,7 +15,7 @@ keywords = [
 ]
 
 classifiers = [
-    "Development Status :: 2 - Pre-Alpha",
+    "Development Status :: 3 - Alpha",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Chemistry",
@@ -28,16 +28,14 @@ pycgtool = "pycgtool.__main__:main"
 [tool.poetry.dependencies]
 python = "^3.6"
 wheel = "^0.35.1"
-numpy = "^1.19.1"
+numpy = [
+    { version = "^1.19.1", python = "<3.7" },  # Support for Python 3.6 was dropped in 1.20
+    { version = "^1.20.0", python = ">=3.7" }  # But 1.20 should resolve issue with MDTraj on macOS
+]
 cython = "^0.29.21"
-mdtraj = "^1.9.4"
+mdtraj = "^1.9.5"
 rich = "^9.2.0"
 
-# Optional extras to enable additional functionality
-sphinx-autoapi = { version = "^1.5.0", optional = true }
-sphinx-rtd-theme = { version = "^0.5.0", optional = true }
-sphinx = { version = "^3.2.1", optional = true }
-
 [tool.poetry.dev-dependencies]
 prospector = "^1.3.0"
 pytest = "^6.0.1"
@@ -45,10 +43,10 @@ pytest-cov = "^2.10.1"
 yapf = "^0.30.0"
 vulture = "^2.1"
 rstcheck = "^3.3.1"
-
-[tool.poetry.extras]
-docs = ["sphinx", "sphinx-autoapi", "sphinx-rtd-theme"]
-test = ["pytest", "pytest-cov", "prospector", "flake8"]
+flake8 = "^3.8.4"
+Sphinx = "^3.4.3"
+sphinx-autoapi = "^1.5.1"
+sphinx-rtd-theme = "^0.5.1"
 
 [build-system]
 requires = ["poetry>=0.12"]