Including testing tutorial notebooks in PR unit CI workflow (#127)

* add nbmake and test for notebooks, test on multiple python versions

* install grits from source, fix path to tutorials

* remove str in nb path

* install tutorials dir in setup.py, move tutorials into flowermd

* move tutorials back

* use nbmake in separate line

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove cmeutils install from source

* Put back data dir

* fix CG notebook

* fix param in welding tutorial

* pass python version to mamba, add macos

* create new job for testing tutorials

* remove python 3.9 from tests, change python version in env files

* fix python version arg

* fix input

* remove python 3.12 from env and tests

* comment out sims in surface wetting tutorial

* add on issue comment to yml file

* run through surface wetting sim, comment out sim run cells

* change comment trigger

* try adding branche and paths under issue_comment

* filter only PR comments in pytest workflow

* change the PR comment body condition

* Fix bug in test notebook if condition

* add checks for open PR and reaction to trigger comment

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: marjanalbouye <marjan.albouye73@gmail.com>

.github/workflows/pytest.yml

@@ -14,12 +14,25 @@ on:
       - flowermd/**
       - environment-dev.yml
       - .github/workflows/pytest.yml
-  # Allows workflow to be manually triggered
+  issue_comment:
+    types: [created]
+    branches: [ main ]
+    paths:
+      - flowermd/**
+      - environment-dev.yml
+      - .github/workflows/pytest.yml
+
   workflow_dispatch:
 
 jobs:
   pytest:
-    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+        python-version: ['3.10', '3.11']
+
+    runs-on: ${{ matrix.os }}
 
     steps:
     - name: Check out repository
@@ -29,6 +42,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v2
       with:
         environment-file: environment-dev.yml
+        python-version: ${{ matrix.python-version }}
         miniforge-variant: Mambaforge
         miniforge-version: 4.9.2-4
         use-mamba: true
@@ -46,3 +60,56 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
+
+  test-tutorials:
+    if: ${{ github.event.issue.pull_request && github.event.comment.body== '/testtutorials'}}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Put a reaction to the comment
+      run: gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        NODE_ID: ${{ github.event.comment.node_id }}
+    - name: Check if PR is open
+      run: |
+          STATE=$(gh pr view $PR_NUMBER --repo ${{ github.repository }} --json state --jq .state)
+          if [ "$STATE" != "OPEN" ]; then
+            echo "Cannot build for closed PRs"
+            (
+              echo "**${{ github.workflow }}**"
+              echo "Cannot build Kuby for a closed PR. Use the `latest` version (built for the `master` branch) or create a new PR."
+            ) | \
+            gh pr comment "${PR_NUMBER}" --repo ${{ github.repository }} -F -
+            gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:THUMBS_DOWN}){reaction{content}subject{id}}}"
+            gh api graphql --silent --raw-field query="mutation RemoveReaction {removeReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
+            exit 1
+          fi
+      env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.issue.number }}
+          NODE_ID: ${{ github.event.comment.node_id }}
+    - name: Get PR HEAD Ref
+      id: getRef
+      run: echo "pr_ref=$(gh pr view $PR_NUMBER --repo ${{ github.repository }} --json headRefOid | jq -r '.headRefOid')" >> $GITHUB_OUTPUT
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        PR_NUMBER: ${{ github.event.issue.number }}
+
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Build environment
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        environment-file: environment-dev.yml
+        miniforge-variant: Mambaforge
+        miniforge-version: 4.9.2-4
+        use-mamba: true
+
+    - name: Install package
+      shell: bash -l {0}
+      run: pip install .
+
+    - name: Run pytest on tutorials
+      shell: bash -l {0}
+      run: python -m pytest -rs -v --nbmake tutorials/

environment-dev.yml

@@ -16,7 +16,9 @@ dependencies:
   - py3Dmol
   - pytest
   - pytest-cov
+  - nbmake
   - python >=3.10, <3.12
   - fresnel >=0.13.5
   - cmeutils >=1.1.1
-  - grits >=0.3.0
+  - pip:
+      - git+https://github.com/cmelab/grits.git@main

setup.py

@@ -90,11 +90,11 @@ def run(self):
         "flowermd": [
             "modules/**",
             "library/**",
-            "assets/forcefields/*",
-            "assets/molecule_files/*",
+            "assets/forcefields/**",
+            "assets/molecule_files/**",
             "utils/**",
             "internal/**",
-        ]
+        ],
     },
     install_requires=REQUIRED,
     include_package_data=True,