Merge pull request #180 from GazzolaLab/update-0.3.0

Update 0.3.0

.coveragerc

@@ -8,7 +8,7 @@ exclude_lines =
     def __repr__
     from
     import
-    
+show_missing = true
 
 [run]
 branch = True
@@ -20,6 +20,7 @@ omit =
     elastica/systems/analytical.py
     # omit deprecation warning message
     elastica/_elastica_numpy.py
+    elastica/_elastica_numba.py
     # omit experimental modules
     elastica/experimental/*
 	setup.py

.github/workflows/ci-sphinx.yml

@@ -0,0 +1,41 @@
+name: CI-sphinx
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the "main" branch
+  pull_request:
+    branches:
+      - 'main'
+      - 'update-*'
+      - 'doc_patch'
+  push:
+    branches: [ 'main', 'doc_patch' ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+      - name: Setup Poetry
+        uses: Gr1N/setup-poetry@v7
+        with:
+          poetry-preview: false
+      - name: Export requirements file for sphinx
+        run: |
+          poetry export -E docs --without-hashes -f requirements.txt --output docs/requirements.txt
+
+      - name: Sphinx Build
+        # You may pin to the exact commit or the version.
+        # uses: ammaraskar/sphinx-action@8b4f60114d7fd1faeba1a712269168508d4750d2
+        uses: ammaraskar/[email protected]
+        with:
+          # The folder containing your sphinx docs.
+          docs-folder: docs/
+          # The command used to build your documentation.
+          build-command: make html #"-W --keep-going" #  -n"

.github/workflows/main.yml

@@ -1,110 +1,107 @@
 # This is a basic workflow to help you get started with Actions
-
 name: CI
 
-# Controls when the action will run. Triggers the workflow on push request
-# events for the master branch, and pull request events for all branches.
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ '**' ]
+# Controls when the action will run.
+on: [push, pull_request]
+# Older settings:
+# Triggers the workflow on push request events for the master branch,
+# and pull request events for all branches.
+#on:
+#  push:
+#    branches: [ master ]
+#  pull_request:
+#    branches: [ '**' ]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ${{ matrix.os }} #ubuntu-latest
-
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
         os: [ubuntu-latest, macos-latest] #, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos
-        python-version: [3.6, 3.7, 3.8]
-
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+          - os: macos-latest
+            path: ~/Library/Caches/pip
+#          - os: windows-latest
+#            path: ~\AppData\Local\pip\Cache
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
-
       # Ref: https://docs.github.com/en/free-pro-team@latest/actions/guides/building-and-testing-python
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v2.2.2
         with:
           python-version: ${{ matrix.python-version }}
-
       # You can test your matrix by printing the current Python version
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-
-      # Cache the pip requirmenets for other tests. If requirements cached use them to speed up the build.
-      # Ref: https://github.com/actions/cache/blob/main/examples.md#python---pip 
-      - name: Cache pip Linux
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'Linux')
+      # Install Poetry and dependencies
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+      - name: Set up cache
+        uses: actions/cache@v3
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-      - name: Cache pip MacOS
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
-        with:
-          path: ~/Library/Caches/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-            
-      - name: Cache pip Windows
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'Windows')
-        with:
-          path: ~\AppData\Local\pip\Cache
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Install dependencies
         run: |
-          echo update pip
-          python -m pip install --upgrade pip
-          echo update requirments
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          echo update test requirements
-          if [ -f tests/requirements.txt ]; then pip install -r tests/requirements.txt; fi
-    
+          poetry config virtualenvs.in-project true
+          poetry install
       # Runs a single command using the runners shell
       - name: Welcome message
         run: echo Hello, world! Welcome PyElastica Build, lets start testing!
-
-      # Formatting test with black and flake8
-      - name: Black and Flake8 formatting tests
+      # Run style checks (black and flake8)
+      - name: Run style checks
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.6" ]]; then 
-            black --version
-            black --check elastica tests
-            flake8 --version
-            flake8 elastica tests 
-          fi
-          
-      # Set environment variables for coverage test. Coverage test is done using python 3.6
-      # For the coverage test we disable numba jit compilation, since it prevents generating coverage data.
-      - name: Set environment variables for coverage test
+          make check-codestyle
+      # Test PyElastica using pytest
+      - name: Run tests
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.6" ]]; then 
-            echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV
-          fi
-        
-      # Test Pyelastica using pytest
+          make test
+  report-coverage:  # Report coverage from python 3.8 and mac-os. May change later
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8"]
+        os: [macos-latest]
+        include:
+          - os: macos-latest
+            path: ~/Library/Caches/pip
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+      - name: Set up cache
+        uses: actions/cache@v3
+        with:
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install dependencies
+        run: |
+          poetry config virtualenvs.in-project true
+          poetry install
+      - name: Run style checks
+        run: |
+          make check-codestyle
       - name: Test PyElastica using pytest
+        if: startsWith(runner.os, 'macOS')
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.6" ]]; then 
-            python3 -m pytest --cov=elastica --cov-report=xml
-            codecov
-          else
-            python3 -m pytest
-          fi
-      - name: Upload coverage reports to Codecov with GitHub Action
-        uses: codecov/codecov-action@v3
+          make test_coverage_xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/publish-to-pypi.yml

@@ -13,12 +13,13 @@ jobs:
         uses: actions/[email protected]
         with:
           python-version: "3.x"
+      - name: Install Poetry
+        uses: snok/[email protected]
       - name: Build
         run: |
-          python setup.py sdist
-          ls dist
+          poetry build
       - name: Publish distribution 📦 to PyPI
         if: startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@master
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+default_language_version:
+  python: python3
+
+default_stages: [commit, push]
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-json
+      - id: check-yaml
+      - id: end-of-file-fixer
+        exclude: LICENSE
+
+  - repo: local
+    hooks:
+      - id: formatting
+        name: formatting
+        entry: make formatting
+        types: [python]
+        language: system

.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools: {python: "3.10"}
+  jobs:
+    pre_create_environment:
+      - asdf plugin add poetry
+      - asdf install poetry latest
+      - asdf global poetry latest
+      - poetry config virtualenvs.create false  # Key
+    post_install:
+      - poetry install -E docs
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  #fail_on_warning: true