Merge pull request #141 from bhosale2/101_poetry_setup

Poetry setup for PyElastica (#101)

.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

@@ -22,11 +22,13 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v3.1.0
+      - name: Setup Poetry
+        uses: Gr1N/setup-poetry@v7
         with:
-          python-version: "3.x"
+          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.
@@ -36,10 +38,4 @@ jobs:
           # The folder containing your sphinx docs.
           docs-folder: docs/
           # The command used to build your documentation.
-          build-command: make html SPHINXOPTS+="-W --keep-going" #  -n"
-          # Run before the build command, you can use this to install system level dependencies, for example with "apt-get update -y && apt-get install -y perl"
-          pre-build-command: |
-            pwd
-            python --version
-            pip install -r requirements.txt
-            pip install -r docs/requirements.txt
+          build-command: make html #"-W --keep-going" #  -n"

.github/workflows/main.yml

@@ -1,110 +1,112 @@
 # 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') }}
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
           restore-keys: |
             ${{ runner.os }}-pip-
-      - name: Cache pip MacOS
-        uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
+      - name: Install dependencies
+        run: |
+          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!
+      # Run style checks (black and flake8)
+      - name: Run style checks
+        run: |
+          make check-codestyle
+      # Test PyElastica using pytest
+      - name: Run tests
+        run: |
+          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/setup-python@v2.2.2
         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')
+          python-version: ${{ matrix.python-version }}
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+      - name: Set up cache
+        uses: actions/cache@v3
         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: |
             ${{ runner.os }}-pip-
       - name: Install dependencies
         run: |
-          echo update pip
-          python -m pip install --upgrade pip
-          echo update requirments
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          echo update test requirements
-          if [ -f tests/requirements.txt ]; then pip install -r tests/requirements.txt; fi
-    
-      # Runs a single command using the runners shell
-      - name: Welcome message
-        run: echo Hello, world! Welcome PyElastica Build, lets start testing!
-
-      # Formatting test with black and flake8
-      - name: Black and Flake8 formatting tests
+          poetry config virtualenvs.in-project true
+          poetry install
+      - name: Run style checks
         run: |
-          if [[ "${{ 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
+          make check-codestyle
+      # Set environment variables for coverage test.
       # For the coverage test we disable numba jit compilation, since it prevents generating coverage data.
       - name: Set environment variables for coverage test
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.6" ]]; then 
-            echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV
-          fi
-        
-      # Test Pyelastica using pytest
+          echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV
       - name: Test PyElastica using pytest
+        if: startsWith(runner.os, 'macOS')
         run: |
-          if [[ "${{ 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
+          poetry run pytest -c pyproject.toml --cov=elastica --cov-report=xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          token: ${{ secrets.CODECOV_TOKEN }}

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

@@ -13,12 +13,13 @@ jobs:
         uses: actions/setup-python@v3.1.0
         with:
           python-version: "3.x"
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3
       - 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 }}

CONTRIBUTING.md

@@ -33,15 +33,37 @@ The following is a set of guidelines for contributing to PyElastica. These are m
 
 ## Before I get started
 
-### Installation and packages
+### Setup development environment
+
+Below are steps of how to setup development environment. We mainly use `poetry` to manage 
+the project, although most of the important commands will be provided in `Makefile`.
+
+1. Clone!
 
 First **create the fork repository and clone** to your local machine.
-We provide [requirements.txt](requirements.txt) to include all the dependencies.
+
+2. Virtual python workspace: `conda`, `pyenv`, or `venv`.
+
+We recommend using python version above 3.8.0.
+
+```bash
+conda create --name pyelastica-dev
+conda activate pyelastica-dev
+conda install python==3.8
+```
+
+3. Setup [`poetry`](https://python-poetry.org) and `dependencies`!
+
 ```bash
-$ pip install -r requirements.txt
+make poetry-download
+make install
 ```
 
-> **Note:** Make sure that **PyElastica** is not installed using pip.
+If you are planning to contribute on documentation, extra dependencies can be installed 
+using `poetry install -E docs`. The detail instruction is included 
+[here](/~https://github.com/GazzolaLab/PyElastica/blob/master/docs/README.md).
+
+4. Now your working environment is set!
 
 ### Project workflow
 
@@ -116,7 +138,7 @@ Please follow these steps to have your contribution considered by the maintainer
 	In order to run pytest, run the following line from the top directory:
 
 	`
-	python3 -m pytest
+	make test
 	`
 
 3. After you submit your pull request, verify that all status checks are passing <details><summary>What if the status checks are failing?</summary>If a status check is failing, and you believe that the failure is unrelated to your change, please leave a comment on the pull request explaining why you believe the failure is unrelated. A maintainer will re-run the status check for you. If we conclude that the failure was a false positive, then we will open an issue to track that problem with our status check suite.</details>
@@ -139,17 +161,9 @@ Ask any question about **how to use PyElastica and detail implementation** in th
 
 We use [flake8](https://pypi.org/project/flake8/) and [Black](https://pypi.org/project/black/) for python style.
 
-You can install flake8 using pip:
-
-`pip install flake8==3.8.3`
-
-You can install black using pip:
-
-`pip install black`
-
 In order to format the code:
 
-`make all`
+`make formatting`
 
 > **Note:** Format/refactoring patches that are not anything substantial to the context or functionality will likely be rejected.