👷Add CI infrastructure files to run notebooks

action.yml

@@ -25,6 +25,9 @@ outputs:
   example-list:
     description: "List of all possible example names to be used in a workflow matrix."
     value: ${{ steps.example-run.outputs.example-list }}
+  notebook-path:
+    description: "Path to evaluated notebook after running the example"
+    value: ${{ steps.example-notebook-run.outputs.notebook-path }}
 
 runs:
   using: "composite"
@@ -62,7 +65,7 @@ runs:
         echo "::endgroup::"
       shell: bash
 
-    - name: Run example
+    - name: Run example scripts
       id: example-run
       run: |
         echo "::group:: Running ${{ inputs.example_name }}"
@@ -78,6 +81,21 @@ runs:
         echo "::endgroup::"
       shell: bash
 
+    - name: Run example notebooks
+      id: example-notebook-run
+      run: |
+        echo "::group:: Running ${{ inputs.example_name }}"
+        if [ '${{ inputs.set_example_list }}' = 'false' ]
+        then
+          python pyglotaran-examples/scripts/run_examples_notebooks.py ${{ inputs.example_name }} 2>&1
+        else
+          pip install yaargh papermill
+          python pyglotaran-examples/scripts/run_examples_notebooks.py set-gha-example-list-output
+        fi
+
+        echo "::endgroup::"
+      shell: bash
+
     - name: Save Examples commit sha
       if: inputs.set_example_list == 'false'
       run: |

pyglotaran_examples/.github/requirements_ci.txt

@@ -0,0 +1,7 @@
+
+pyglotaran>=0.3.0
+jupyterlab>=3.0.0
+matplotlib>=3.3.0
+
+yaargh>=0.28.0
+papermill>=2.3.4

pyglotaran_examples/.github/workflows/integration_test.yml

@@ -0,0 +1,199 @@
+name: "Run Examples"
+
+on:
+  push:
+    tags:
+      - v**
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      pyglotaran_branch:
+        description: "pyglotaran branch/tag to run the examples against"
+        required: true
+        default: "main"
+      pyglotaran_examples_branch:
+        description: "pyglotaran-examples branch/tag to use"
+        required: true
+        default: "main"
+
+jobs:
+  create-example-list:
+    name: Create Example List
+    runs-on: ubuntu-latest
+    outputs:
+      example-list: ${{ steps.create-example-list.outputs.example-list }}
+    steps:
+      - name: Cloning pyglotaran-examples
+        if: ${{ github.event.inputs.pyglotaran_examples_branch }} == ""
+        uses: actions/checkout@v4
+        with:
+          path: pyglotaran-examples
+      - name: Set example list output
+        id: create-example-list
+        uses: ./pyglotaran-examples
+        with:
+          example_name: set example list
+          set_example_list: true
+
+  run-examples:
+    name: "Run Example: "
+    runs-on: ubuntu-latest
+    needs: [create-example-list]
+    strategy:
+      matrix:
+        example_name: ${{fromJson(needs.create-example-list.outputs.example-list)}}
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          repository: "glotaran/pyglotaran"
+          # If not provided (push and pull_request event) it uses the main branch
+          ref: ${{ github.event.inputs.pyglotaran_branch != '' && github.event.inputs.pyglotaran_branch || 'main'}}
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install pyglotaran
+        run: |
+          pip install wheel
+          pip install .
+      - name: Cloning pyglotaran-examples
+        if: ${{ github.event.inputs.pyglotaran_examples_branch }} == ""
+        uses: actions/checkout@v4
+        with:
+          path: pyglotaran-examples
+      - id: example-run
+        uses: ./pyglotaran-examples
+        with:
+          example_name: ${{ matrix.example_name }}
+          examples_branch: ${{ github.event.inputs.pyglotaran_examples_branch }}
+
+      - name: Upload Example Plots Artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: example-notebooks-${{ matrix.example_name }}
+          path: ${{ steps.example-run.outputs.notebook-path }}
+
+      - name: Upload Example Results
+        uses: actions/upload-artifact@v4
+        with:
+          name: example-results-${{ matrix.example_name }}
+          path: ~/pyglotaran_examples_results
+
+  collect-artifacts:
+    if: always()
+    name: "Collect artifacts and reupload as bundel"
+    runs-on: ubuntu-latest
+    needs: [run-examples]
+    steps:
+      - name: Download Notebooks Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: example-notebooks
+          pattern: example-notebooks-*
+          merge-multiple: true
+
+      - name: Upload Example Notebooks Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: example-notebooks
+          path: example-notebooks
+          overwrite: true
+
+      - name: Delete Intermediate Notebooks artifacts
+        uses: GeekyEggo/delete-artifact@v5
+        with:
+          name: example-notebooks-*
+
+      - name: Download Result Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: example-results
+          pattern: example-results-*
+          merge-multiple: true
+
+      - name: Upload Example Result Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: example-results
+          path: example-results
+          overwrite: true
+
+      - name: Delete Intermediate Result artifacts
+        uses: GeekyEggo/delete-artifact@v5
+        with:
+          name: example-results-*
+
+  compare-results:
+    name: Compare Results
+    runs-on: ubuntu-latest
+    needs: [collect-artifacts]
+    steps:
+      - name: Checkout compare results
+        uses: actions/checkout@v4
+        with:
+          repository: "glotaran/pyglotaran-examples"
+          ref: comparison-results
+          path: comparison-results
+
+      - name: Download result artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: example-results
+          path: comparison-results-current
+
+      - name: Show used versions for result creation
+        run: |
+          echo "::group:: ✔️ Compare-Results"
+          echo "✔️ pyglotaran-examples commit: $(< comparison-results/example_commit_sha.txt)"
+          echo "✔️ pyglotaran commit: $(< comparison-results/pyglotaran_commit_sha.txt)"
+          echo "::endgroup::"
+          echo "::group:: ♻️ Current-Results"
+          echo "♻️ pyglotaran-examples commit: $(< comparison-results-current/example_commit_sha.txt)"
+          echo "::endgroup::"
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Run result validator
+        uses: glotaran/pyglotaran-validation@main
+        with:
+          validation_name: pyglotaran-examples
+
+  create-release:
+    name: "🚀 Create release assets and tag comparison-results branch"
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    needs: [compare-results]
+    steps:
+      - name: ⏬ Checkout compare results
+        uses: actions/checkout@v4
+        with:
+          repository: "glotaran/pyglotaran-examples"
+          ref: comparison-results
+
+      - name: Get tag name
+        id: tag
+        uses: devops-actions/[email protected]
+
+      - name: 📦 Create release asset
+        run: zip -r comparison-results-${{steps.tag.outputs.tag}}.zip . -x ".git/*"
+
+      - name: 🚀⬆️ Upload Release Asset
+        uses: softprops/action-gh-release@v1
+        with:
+          files: comparison-results-${{steps.tag.outputs.tag}}.zip
+          generate_release_notes: true
+          append_body: true
+
+      - name: 📦 Create comparison-results tag
+        run: |
+          git config user.email '41898282+github-actions[bot]@users.noreply.github.com'
+          git config user.name 'github-actions[bot]'
+          NEW_VERSION="comparison-results-${{steps.tag.outputs.tag}}"
+          git tag -a $NEW_VERSION -m "Comparison results used with release ${{steps.tag.outputs.tag}}"
+          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
+          git push origin $NEW_VERSION

requirements.txt

@@ -1,3 +1,4 @@
 -r .github/requirements_ci.txt
 
+yaargh
 git+https://github.com/glotaran/pyglotaran-extras.git

scripts/run_examples_notebooks.py

@@ -0,0 +1,145 @@
+from __future__ import annotations
+
+import json
+import os
+import warnings
+from pathlib import Path
+
+import papermill as pm
+import yaargh
+
+REPO_ROOT = Path(__file__).parent.parent
+EXAMPLES_FOLDER = REPO_ROOT / "pyglotaran_examples"
+
+
+def github_format_warning(message, category, filename, lineno, line=None):
+    return f"::warning file={filename},line={lineno}::{category.__name__}: {message}\n"
+
+
+def run_notebook(notebook_path: Path) -> Path:
+    """Run notebook to update results."""
+    print("\n", "#" * 80, sep="")
+    print("#", f"RUNNING: {notebook_path.name.upper()}".center(78), "#", sep="")
+    print("#" * 80, "\n")
+    if "GITHUB_OUTPUT" in os.environ:
+        warnings.formatwarning = github_format_warning
+        gh_output = Path(os.getenv("GITHUB_OUTPUT", ""))
+        with gh_output.open("a", encoding="utf8") as f:
+            f.writelines([f"notebook-path={notebook_path.as_posix()}"])
+        print(f"Setting notebook-path output to {notebook_path.as_posix()}")
+    pm.execute_notebook(notebook_path, notebook_path, cwd=notebook_path.parent)
+
+
+def fluorescence():
+    """Run study_fluorescence/global_and_target_analysis.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "study_fluorescence/global_and_target_analysis.ipynb")
+
+
+def transient_absorption():
+    """Runs study_transient_absorption/target_analysis.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "study_transient_absorption/target_analysis.ipynb")
+
+
+def transient_absorption_two_datasets():
+    """Runs study_transient_absorption/two_dataset_analysis.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "study_transient_absorption/two_dataset_analysis.ipynb")
+
+
+def spectral_constraints():
+    """Runs ex_spectral_constraints/ex_spectral_constraints.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "ex_spectral_constraints/ex_spectral_constraints.ipynb")
+
+
+def spectral_guidance():
+    """Runs ex_spectral_guidance/ex_spectral_guidance.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "ex_spectral_guidance/ex_spectral_guidance.ipynb")
+
+
+def two_datasets():
+    """Runs ex_two_datasets/ex_two_datasets.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "ex_two_datasets/ex_two_datasets.ipynb")
+
+
+def sim_3d_disp():
+    """Runs test/simultaneous_analysis_3d_disp/sim_analysis_script_3d_disp.ipynb"""
+    return run_notebook(
+        EXAMPLES_FOLDER / "test/simultaneous_analysis_3d_disp/sim_analysis_script_3d_disp.ipynb"
+    )
+
+
+def sim_3d_nodisp():
+    """Runs test/simultaneous_analysis_3d_nodisp/simultaneous_analysis_3d_nodisp.ipynb"""
+    return run_notebook(
+        EXAMPLES_FOLDER
+        / "test/simultaneous_analysis_3d_nodisp/simultaneous_analysis_3d_nodisp.ipynb"
+    )
+
+
+def sim_3d_weight():
+    """Runs test/simultaneous_analysis_3d_weight/simultaneous_analysis_3d_weight.ipynb"""
+    return run_notebook(
+        EXAMPLES_FOLDER
+        / "test/simultaneous_analysis_3d_weight/simultaneous_analysis_3d_weight.ipynb"
+    )
+
+
+def sim_6d_disp():
+    """Runs test/simultaneous_analysis_6d_disp/simultaneous_analysis_6d_disp.ipynb"""
+    return run_notebook(
+        EXAMPLES_FOLDER / "test/simultaneous_analysis_6d_disp/simultaneous_analysis_6d_disp.ipynb"
+    )
+
+
+def doas_beta():
+    """Runs ex_doas_beta/ex_doas_beta.ipynb"""
+    return run_notebook(EXAMPLES_FOLDER / "ex_doas_beta/ex_doas_beta.ipynb")
+
+
+all_funcs = [
+    # fluorescence,
+    # transient_absorption,
+    # transient_absorption_two_datasets,
+    spectral_constraints,
+    # spectral_guidance,
+    # two_datasets,
+    sim_3d_disp,
+    # sim_3d_nodisp,
+    # sim_3d_weight,
+    # sim_6d_disp,
+    doas_beta,
+]
+
+
+def run_all():
+    """Runs all examples."""
+    errors = {}
+    for func in all_funcs:
+        try:
+            func()
+        except Exception as err:
+            errors[func.__name__] = err
+    if errors:
+        for func_name, err in errors.items():
+            print("\n", "#" * 80, sep="")
+            print("#", f"Error running: {func_name.upper()}".center(78), "#", sep="")
+            print("#" * 80, "\n")
+            print(err)
+        print("Failed to run the following examples:")
+        for func_name in errors:
+            print(func_name)
+
+
+def set_gha_example_list_output():
+    """Export a list of all examples to an output github in github actions."""
+    example_names = [func.__name__.replace("_", "-") for func in all_funcs]
+    gh_output = Path(os.getenv("GITHUB_OUTPUT", ""))
+    with gh_output.open("a", encoding="utf8") as f:
+        f.writelines([f"example-list={json.dumps(example_names)}"])
+
+
+parser = yaargh.ArghParser()
+parser.add_commands([*all_funcs, run_all, set_gha_example_list_output])
+
+
+if __name__ == "__main__":
+    parser.dispatch()