More CI (mypy, coverage), setup pre-commit, formatting (#24)

* add pre-commit config file

* clang format tweaks

* run black

* ci: add mypy gha workflow

* add pre-commit note in README

* fix mypy gha job

* fix trailing whitespace

* configure mypy

* use micromamba gha for tests

* fix tests gha

* typo

* enable coverage

* try fix codecov upload

* add coverage badge in README

Author: benbovy

.clang-format

@@ -1,10 +1,17 @@
 ---
 Language:        Cpp
 BasedOnStyle:  Google
+ColumnLimit: 100
 TabWidth: 4
 IndentWidth: 4
 PointerAlignment: Left
 ReferenceAlignment: Pointer
 IndentAccessModifiers: false
 AccessModifierOffset: -4
+BinPackArguments: false
+BinPackParameters: false
+ExperimentalAutoDetectBinPacking: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortLambdasOnASingleLine: Inline
 ...

.github/workflows/lint.yaml

@@ -0,0 +1,39 @@
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: Lint
+
+jobs:
+  lint:
+    name: mypy
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@v15
+        with:
+          environment-file: ci/environment.yml
+          environment-name: spherely-dev
+          extra-specs: |
+            python=3.11
+
+      - name: Build and install spherely
+        run: |
+          python -m pip install . -v --no-build-isolation
+
+      - name: Install mypy
+        run: |
+          python -m pip install 'mypy<0.990'
+
+      - name: Run mypy
+        run: |
+          python -m mypy --install-types --non-interactive

.github/workflows/run-tests.yaml

@@ -10,6 +10,9 @@ jobs:
   test:
     name: ${{ matrix.os }}, ${{ matrix.python-version }}, ${{ matrix.env }}
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
@@ -36,41 +39,20 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v3
 
-      - name: Setup mambaforge
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: spherely-dev
-          use-mamba: true
-          python-version: ${{ matrix.python-version }}
-          environment-file: ${{ matrix.env }}
-
       - name: Get Date
         id: get-date
-        shell: bash -l {0}
         # cache will last one day
         run: echo "::set-output name=today::$(/bin/date -u '+%Y%m%d')"
 
-      - name: Cache environment
-        uses: actions/cache@v2
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
-          path: ${{ env.CONDA }}/envs
-          key: ${{ runner.os }}-{{ matrix.python-version }}-conda-${{ hashFiles( matrix.env ) }}-${{ steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER }}
-        env:
-          # Increase this value to reset cache if ci/environment.yml has not changed
-          CACHE_NUMBER: 0
-        id: conda-cache
-
-      - name: Update environment
-        run: mamba env update -n spherely-dev -f ${{ matrix.env }}
-        if: steps.conda-cache.outputs.cache-hit != 'true'
-
-      - name: Conda info
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
+          environment-file: ${{ matrix.env }}
+          environment-name: spherely-dev
+          cache-env: true
+          cache-env-key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ hashFiles( matrix.env) }}"
+          extra-specs: |
+            python=${{ matrix.python-version }}
 
       - name: Fetch s2geography
         uses: actions/checkout@v3
@@ -80,11 +62,9 @@ jobs:
           path: deps/s2geography
           fetch-depth: 0
         if: |
-          matrix.dev == true &&
-          steps.conda-cache.outputs.cache-hit != 'true'
+          matrix.dev == true
 
       - name: Configure, build & install s2geography (unix)
-        shell: bash -l {0}
         run: |
           cd deps/s2geography
           cmake -S . -B build \
@@ -96,11 +76,9 @@ jobs:
           cmake --install build
         if: |
           matrix.dev == true &&
-          (steps.conda-cache.outputs.cache-hit != 'true' &&
-          (runner.os == 'Linux' || runner.os == 'macOS'))
+          (runner.os == 'Linux' || runner.os == 'macOS')
 
       - name: Configure, build & install s2geography (win)
-        shell: bash -l {0}
         run: |
           cd deps/s2geography
           cmake -S . -B build \
@@ -111,15 +89,27 @@ jobs:
           cmake --build build --config Release
           cmake --install build
         if: |
-          matrix.dev == true &&
-          (steps.conda-cache.outputs.cache-hit != 'true' &&
-          runner.os == 'Windows')
+          matrix.dev == true && runner.os == 'Windows'
 
       - name: Build and install spherely
-        shell: bash -l {0}
-        run: python -m pip install . -v --no-build-isolation
+        run: |
+          python -m pip install . -v --no-build-isolation --config-settings cmake.define.SPHERELY_CODE_COVERAGE=ON --config-settings build-dir=_skbuild
 
       - name: Run tests
-        shell: bash -l {0}
         run: |
           pytest . -vv
+
+      - name: Generate coverage report
+        run: |
+          python -m pip install gcovr
+          gcovr --exclude-unreachable-branches --print-summary -x -o coverage.xml
+        if: |
+          runner.os == 'Linux' && matrix.python-version == '3.11' && matrix.dev == false
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          verbose: true
+        if: |
+          runner.os == 'Linux' && matrix.python-version == '3.11' && matrix.dev == false

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: debug-statements
+      - id: mixed-line-ending
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+        args: [--safe, --quiet]
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v15.0.7
+    hooks:
+      - id: clang-format
+        args: [--style=file]
+
+ci:
+  autofix_prs: false

CMakeLists.txt

@@ -7,6 +7,8 @@ project(
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "The C++ standard to build with")
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+option(SPHERELY_CODE_COVERAGE "Enable coverage reporting" OFF)
+
 # Dependencies
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/third_party/cmake")
@@ -25,6 +27,11 @@ set(S2GEOGRAPHY_ROOT_DIR "$ENV{CONDA_PREFIX}")
 find_package(s2 REQUIRED)
 find_package(s2geography REQUIRED)
 
+if(SPHERELY_CODE_COVERAGE)
+  message(STATUS "Building spherely with coverage enabled")
+  add_library(coverage_config INTERFACE)
+endif()
+
 # Compile definitions and flags
 
 if (MSVC)
@@ -72,6 +79,12 @@ endif()
 
 set_target_properties(spherely PROPERTIES CXX_VISIBILITY_PRESET "hidden")
 
+if (SPHERELY_CODE_COVERAGE)
+  target_compile_options(coverage_config INTERFACE -O0 -g --coverage)
+  target_link_options(coverage_config INTERFACE --coverage)
+  target_link_libraries(spherely PUBLIC coverage_config)
+endif()
+
 # Install
 
 install(TARGETS spherely LIBRARY DESTINATION .)

README.md

@@ -2,6 +2,7 @@
 
 ![Tests](https://github.com/benbovy/spherely/actions/workflows/run-tests.yaml/badge.svg)
 [![Docs](https://readthedocs.org/projects/spherely/badge/?version=latest)](https://spherely.readthedocs.io)
+[![Coverage](https://codecov.io/gh/benbovy/spherely/branch/main/graph/badge.svg)](https://app.codecov.io/gh/benbovy/spherely?branch=main)
 
 *Python library for manipulation and analysis of geometric objects on the sphere.*
 
@@ -67,7 +68,17 @@ Run the tests:
 $ pytest . -v
 ```
 
-## Using the latest s2geography
+Spherely also uses [pre-commit](https://pre-commit.com/) for code
+auto-formatting and linting at every commit. After installing it, you can enable
+pre-commit hooks with the following command:
+
+```
+$ pre-commit install
+```
+
+(Note: you can skip the pre-commit checks with `git commit --no-verify`)
+
+## Using the latest s2geography version
 
 If you want to compile spherely against the latest version of s2geography, use:
 

docs/api.rst

@@ -54,4 +54,4 @@ Predicates
    intersects
    contains
    within
-   disjoint   
+   disjoint

pyproject.toml

@@ -27,3 +27,8 @@ Repository = "https://github.com/benbovy/spherely"
 
 [project.optional-dependencies]
 test = ["pytest>=6.0"]
+
+[tool.mypy]
+files = ["tests", "src/spherely.pyi"]
+show_error_codes = true
+warn_unused_ignores = true