Automatic packaging and CI test updates (#386)

* Reorganizing the requirements locations

* WIP: Trying out composite Github actions

* Incorporating composite Github action in CI suite

* Make CI run on all PRs

* Bug: Requirements files were switched

* Moving jsonschema to requirements

* Installing only the necessary requirements in CI

* Adding pytest to type-checking required packages

* Complementing the CI test description

* WIP: Test version check

* WIP: Check new version validity

* WIP: Test version validity [fail 1]

* WIP: Test version check [fail 2]

* Bring version back

* Trigger new workflow run

* WIP: Test stable version validity [fail 3]

* WIP: Test stable version validity [pass]

* Finish version checker tests

* Adding full test workflow

* Make full tests run on push only

* Centralizing the different packages

* Add packaging script

* WIP: Test publish workflow

* Test: Trigger 'publish' workflow

* WIP: 2nd 'publish' workflow test

* WIP: 3rd 'publish' workflow test

* Finish the 'publish' workflow

* Documenting the Release procedure

* Review comments + Details on merge commit messages

* Adding review suggestions

.github/scripts/package.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+# Exit if something fails
+set -e
+
+# Find and change to the repository directory
+repo_dir=$(git rev-parse --show-toplevel)
+cd "${repo_dir}"
+
+# Removing existing files in /dist
+rm -rf dist
+
+packages=$(cat packages.txt)
+# Build the pulser packages
+for pkg in $packages
+do
+  echo "Packaging $pkg"
+  python $pkg/setup.py -q bdist_wheel -d "../dist"
+  rm -r $pkg/build
+done
+
+# Build the pulser metapackage
+python setup.py -q bdist_wheel -d "dist"
+rm -r build
+
+echo "Built wheels:"
+ls dist

.github/workflows/ci.yml

@@ -12,83 +12,59 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out Pulser
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v3
+      - name: Pulser + flake8 install
+        uses: ./.github/workflows/pulser-setup
         with:
-          python-version: 3.8
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e ./pulser-core -e ./pulser-simulation
-          pip install -r requirements.txt
+          extra-packages: flake8
       - name: Lint with flake8
         run: flake8
   black:
     runs-on: ubuntu-latest
     steps:
       - name: Check out Pulser
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v3
+      - name: Pulser + black install
+        uses: ./.github/workflows/pulser-setup
         with:
-          python-version: 3.8
-      - name: Install black
-        run: |
-          python -m pip install --upgrade pip
-          pip install black
-          pip install 'black[jupyter]'
+          extra-packages: black
       - name: Check formatting with black
         run: black --check --diff .
   isort:
     runs-on: ubuntu-latest
     steps:
       - name: Check out Pulser
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v3
+      - name: Pulser + isort install
+        uses: ./.github/workflows/pulser-setup
         with:
-          python-version: 3.8
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e ./pulser-core -e ./pulser-simulation
-          pip install -r requirements.txt
+          extra-packages: isort
       - name: Check import sorting with isort
         run: isort --check-only --diff .
   typing:
     runs-on: ubuntu-latest
     steps:
       - name: Check out Pulser
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v3
+      - name: Pulser + mypy install
+        uses: ./.github/workflows/pulser-setup
         with:
-          python-version: 3.8
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e ./pulser-core -e ./pulser-simulation
-          pip install -r requirements.txt
+          extra-packages: '''mypy\|pytest'''
       - name: Type check with mypy
         run: mypy
   test:
-    runs-on: ${{ matrix.os }}
+    if: github.event_name != 'push'
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: ['3.7', '3.9']
     steps:
       - name: Check out Pulser
-        uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v3
+      - name: Pulser + pytest install
+        uses: ./.github/workflows/pulser-setup
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e ./pulser-core -e ./pulser-simulation
-          pip install -r requirements.txt
+          extra-packages: pytest
       - name: Run the unit tests & generate coverage report
         run: pytest --cov --cov-fail-under=100

.github/workflows/publish.yml

@@ -0,0 +1,79 @@
+name: Upload Release Package to PyPI
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out Pulser
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.ref }}
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+      - name: Build packages
+        shell: bash
+        run: ./.github/scripts/package.sh
+      - name: Publish to TestPyPI
+        env:
+          TWINE_USERNAME: ${{ secrets.TESTPYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.TESTPYPI_PASSWORD }}
+        run: twine upload --repository testpypi dist/*
+      - name: Install from TestPyPI
+        timeout-minutes: 5
+        shell: bash
+        run: |
+          version="$(head -1 VERSION.txt)"
+          until pip install -i https://test.pypi.org/simple/ pulser==$version --extra-index-url https://pypi.org/simple
+          do
+            echo "Failed to install from TestPyPI, will wait for upload and retry."
+            sleep 30
+          done
+      - name: Test the installation
+        # Installs pytest from dev_requirements.txt (in case it has a version specifier)
+        run: |
+          grep -e pytest dev_requirements.txt | sed 's/ //g' | xargs pip install
+          pytest
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: twine upload dist/*
+
+  check-release:
+    needs: deploy
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+    steps:
+      - name: Check out Pulser
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.ref }}
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Pulser from PyPI
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          pip install pulser
+      - name: Test the installation
+        shell: bash
+        run: |
+          version="$(head -1 VERSION.txt)"
+          python -c "import pulser; assert pulser.__version__ == '$version'"
+          grep -e pytest dev_requirements.txt | sed 's/ //g' | xargs pip install
+          pytest

.github/workflows/pulser-setup/action.yml

@@ -0,0 +1,31 @@
+name: Pulser setup
+description: "Sets up Python and installs Pulser."
+inputs:
+  python-version:
+    description: Python version
+    required: false
+    default: '3.9'
+  extra-packages:
+    description: Extra packages to install (give to grep)
+    required: false
+    default: ''
+runs:
+  using: 'composite'
+  steps: 
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python-version }}
+        cache: 'pip'
+    - name: Install Pulser
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ./pulser-core -e ./pulser-simulation
+    - name: Install extra packages from the dev requirements
+      if: "${{ inputs.extra-packages != '' }}"
+      shell: bash
+      run: |
+        grep -e ${{ inputs.extra-packages }} dev_requirements.txt \
+          | sed 's/ //g' \
+          | xargs pip install

.github/workflows/test.yml

@@ -0,0 +1,25 @@
+name: test
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+jobs:
+  full-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+    steps:
+      - name: Check out Pulser
+        uses: actions/checkout@v3
+      - name: Pulser + pytest setup
+        uses: ./.github/workflows/pulser-setup
+        with:
+          python-version: ${{ matrix.python-version }}
+          extra-packages: pytest
+      - name: Run the unit tests & generate coverage report
+        run: pytest --cov --cov-fail-under=100

.github/workflows/version.yml

@@ -0,0 +1,48 @@
+name: version
+
+on:
+  pull_request:
+    paths:
+      - 'VERSION.txt'
+
+jobs:
+  validate-version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out base branch
+        uses: actions/checkout@v3
+        with:
+          ref:  ${{ github.event.pull_request.base.ref }}
+      - name: Get old version
+        run: |
+          old_version="$(head -1 VERSION.txt)"
+          echo "Old version: $old_version"
+          echo "old_version=$old_version" >> $GITHUB_ENV
+      - name: Check out head branch
+        uses: actions/checkout@v3
+      - name: Get new version 
+        run: |
+          new_version="$(head -1 VERSION.txt)"
+          echo "New version: $new_version"
+          echo "new_version=$new_version" >> $GITHUB_ENV
+      - name: Compare versions
+        run: dpkg --compare-versions "${{ env.old_version }}" lt "${{ env.new_version }}"
+      - name: Check stable version validity
+        if: github.event.pull_request.base.ref == 'master'
+        run: |
+          pattern=^\(0\|[1-9]\d*\)\.\(0\|[1-9]\d*\)\.\(0\|[1-9]\d*\)$
+          if [[ ${{ env.new_version }} =~ $pattern ]]; then
+            echo "New version is valid."; exit 0
+          else
+            echo "New version is invalid."; exit 1
+          fi
+      - name: Check development version validity
+        if: github.event.pull_request.base.ref != 'master'
+        run: |
+          pattern=^\(0\|[1-9]\d*\)\.\(0\|[1-9]\d*\)dev\(0\|[1-9]\d*\)$
+          if [[ ${{ env.new_version }} =~ $pattern ]]; then
+            echo "New version is valid."; exit 0
+          else
+            echo "New version is invalid."; exit 1
+          fi
+

.readthedocs.yml

@@ -18,6 +18,6 @@ sphinx:
 python:
    install:
      - requirements: docs/requirements.txt
-     - requirements: requirements.txt
+     - requirements: dev_requirements.txt
      - requirements: pulser-core/rtd_requirements.txt
      - requirements: pulser-simulation/rtd_requirements.txt

CONTRIBUTING.md

@@ -70,7 +70,7 @@ Here are the steps you should follow to make your contribution:
 We enforce some continuous integration standards in order to maintain the quality of Pulser's code. Make sure you follow them, otherwise your pull requests will be blocked until you fix them. To check if your changes pass all CI tests before you make the PR, you'll need additional packages, which you can install by running
 
 ```shell
-pip install -r requirements.txt
+pip install -r dev_requirements.txt
 ```
 
 - **Tests**: We use [`pytest`](https://docs.pytest.org/en/latest/) to run unit tests on our code. If your changes break existing tests, you'll have to update these tests accordingly. Additionally, we aim for 100% coverage over our code. Try to cover all the new lines of code with simple tests, which should be placed in the `Pulser/pulser/tests` folder. To run all tests and check coverage, run:

MANIFEST.in

@@ -1,4 +1,3 @@
 include README.md
-include requirements.txt
 include LICENSE
 include VERSION.txt

README.md

@@ -55,7 +55,7 @@ your installation will change accordingly.
 To run the tutorials or the test suite locally, after installation first run the following to install the development requirements:
 
 ```bash
-pip install -r requirements.txt
+pip install -r dev_requirements.txt
 ```
 
 Then, you can do the following to run the test suite and report test coverage:

VERSION.txt

@@ -1 +1 @@
-0.6.0.dev
+0.7dev0

dev_requirements.txt

@@ -0,0 +1,17 @@
+# tests
+black
+black[jupyter]
+flake8
+flake8-docstrings
+isort
+mypy == 0.921
+pytest
+pytest-cov
+
+# CI
+pre-commit
+
+# tutorials
+notebook
+python-igraph
+scikit-optimize

docs/source/installation.rst

@@ -42,4 +42,4 @@ your installation will change accordingly.
 If you want to install the development requirements, stay inside the same ``Pulser``
 directory and follow up by running: ::
 
-  pip install -r requirements.txt
+  pip install -r dev_requirements.txt

packages.txt

@@ -0,0 +1,2 @@
+pulser-core
+pulser-simulation

pulser-core/requirements.txt

@@ -0,0 +1,6 @@
+jsonschema == 4.4.0
+matplotlib
+numpy >= 1.20
+scipy
+backports.cached-property; python_version == '3.7'
+typing-extensions; python_version == '3.7'