🩹🚇 Adapt to changed outputs in pyglotaran-examples GHA (#274)

* 🚧 Add back pinned requirements file
* 🚇 Adjust CI workflows to use staging branches
* 🩹🧪 Fix tests as far as possible
* 🧹 Fix  pre-commit issues (x2)

.github/workflows/integration-tests.yml

@@ -18,10 +18,11 @@ jobs:
     steps:
       - name: Set example list output
         id: create-example-list
-        uses: glotaran/pyglotaran-examples@main
+        uses: glotaran/pyglotaran-examples@staging_rewrite
         with:
           example_name: set example list
           set_example_list: true
+          examples_branch: staging_rewrite
 
   run-examples:
     name: "Run Example: "
@@ -41,14 +42,16 @@ jobs:
       - name: Install pyglotaran-extras
         run: |
           pip install wheel
+          python -m pip install git+https://github.com/glotaran/pyglotaran@staging
           pip install .
 
       - name: ${{ matrix.example_name }}
         id: example-run
-        uses: glotaran/pyglotaran-examples@main
+        uses: glotaran/pyglotaran-examples@staging_rewrite
         with:
           example_name: ${{ matrix.example_name }}
           install_extras: false
+          examples_branch: staging_rewrite
 
       - name: Upload Example Plots Artifact
         uses: actions/upload-artifact@v4
@@ -57,6 +60,7 @@ jobs:
           path: ${{ steps.example-run.outputs.notebook-path }}
 
   collect-artifacts:
+    if: always()
     name: "Collect artifacts and reupload as bundel"
     runs-on: ubuntu-latest
     needs: [run-examples]

.github/workflows/test.yml

@@ -108,6 +108,7 @@ jobs:
         run: |
           python -m pip install -U pip wheel
           python -m pip install -r requirements_pinned.txt
+          python -m pip install git+https://github.com/glotaran/pyglotaran@staging
           python -m pip install -U -e ".[test]"
 
       - name: Run tests
@@ -122,32 +123,32 @@ jobs:
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-  test-pyglotaran-dev:
-    name: Test pyglotaran dev
-    runs-on: ubuntu-latest
-    needs: [pre-commit, docs]
+      # test-pyglotaran-dev:
+      #   name: Test pyglotaran dev
+      #   runs-on: ubuntu-latest
+      #   needs: [pre-commit, docs]
 
-    steps:
-      - name: Check out repo
-        uses: actions/checkout@v4
+      #   steps:
+      #     - name: Check out repo
+      #       uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
+      #     - name: Set up Python 3.10
+      #       uses: actions/setup-python@v5
+      #       with:
+      #         python-version: "3.10"
 
-      - name: Install dependencies
-        run: |
-          python -m pip install -U pip wheel
-          python -m pip install -r requirements_pinned.txt
-          python -m pip install -U -e ".[test]"
-          python -m pip install git+https://github.com/glotaran/pyglotaran
+      #     - name: Install dependencies
+      #       run: |
+      #         python -m pip install -U pip wheel
+      #         python -m pip install -r requirements_pinned.txt
+      #         python -m pip install -U -e ".[test]"
+      #         python -m pip install git+https://github.com/glotaran/pyglotaran
 
-      - name: Show installed dependencies
-        run: pip freeze
+      #     - name: Show installed dependencies
+      #       run: pip freeze
 
-      - name: Run tests
-        run: python -m pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
+      #     - name: Run tests
+      #       run: python -m pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
 
       - name: Codecov Upload
         continue-on-error: true
@@ -197,7 +198,10 @@ jobs:
     name: Deploy to PyPi
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-    needs: [test, test-pyglotaran-dev, test-min-versions]
+    needs:
+      - test
+      # - test-pyglotaran-dev
+      - test-min-versions
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:

.pre-commit-config.yaml

@@ -115,7 +115,7 @@ repos:
           - "--allow-init-docstring=True"
           - "--skip-checking-short-docstrings=False"
         name: "flake8 lint docstrings"
-        exclude: "^(docs/|tests?/|pyglotaran_extras/compat)"
+        exclude: "^(docs/|tests?/|pyglotaran_extras/compat/)"
         additional_dependencies: [pydoclint==0.3.8]
 
   - repo: https://github.com/codespell-project/codespell

pyglotaran_extras/compat/convert_result_dataset.py

@@ -40,6 +40,7 @@ def _adjust_estimations_to_spectra(ds: xr.Dataset, *, cleanup: bool = False) ->
 
 
 def _adjust_activation_to_irf(ds: xr.Dataset, *, cleanup: bool = False) -> None:
+    """Adjust the activation to the corresponding IRF."""
     if "gaussian_activation_center" in ds:
         values = ds.gaussian_activation_center.to_numpy().flatten()
         ds["irf_center"] = values[0]

requirements_pinned.txt

@@ -0,0 +1,8 @@
+# Runtime dependencies
+
+cycler==0.12.1
+numpy==1.26.4
+matplotlib==3.9.0
+# pyglotaran==0.8.0
+tabulate==0.9.0
+xarray==2024.5.0

tests/conftest.py

@@ -8,12 +8,10 @@
 import netCDF4  # noqa: F401
 # isort: on
 
-from dataclasses import replace
-
 import pytest
-from glotaran.optimization.optimize import optimize
 from glotaran.testing.simulated_data.parallel_spectral_decay import SCHEME as SCHEME_PAR
 from glotaran.testing.simulated_data.sequential_spectral_decay import SCHEME as SCHEME_SEQ
+from glotaran.testing.simulated_data.shared_decay import PARAMETERS
 
 from pyglotaran_extras.io.setup_case_study import get_script_dir
 
@@ -26,12 +24,10 @@ def wrapped_get_script_dir():
 @pytest.fixture(scope="session")
 def result_parallel_spectral_decay():
     """Test result from ``glotaran.testing.simulated_data.parallel_spectral_decay``."""
-    scheme = replace(SCHEME_PAR, maximum_number_function_evaluations=1)
-    return optimize(scheme)
+    return SCHEME_PAR.optimize(PARAMETERS, maximum_number_function_evaluations=1)
 
 
 @pytest.fixture(scope="session")
 def result_sequential_spectral_decay():
     """Test result from ``glotaran.testing.simulated_data.sequential_spectral_decay``."""
-    scheme = replace(SCHEME_SEQ, maximum_number_function_evaluations=1)
-    return optimize(scheme)
+    return SCHEME_SEQ.optimize(PARAMETERS, maximum_number_function_evaluations=1)

tests/inspect/test_a_matrix.py

@@ -32,7 +32,7 @@ def test_a_matrix_to_html_table(
         encoding="utf8"
     )
     assert a_matrix_to_html_table(
-        result_parallel_spectral_decay.data["dataset_1"].a_matrix_megacomplex_parallel_decay,
+        result_parallel_spectral_decay.data["parallel-decay"].a_matrix_megacomplex_parallel_decay,
         "megacomplex_parallel_decay",
         **kwargs,
     ) == expected.rstrip("\n")
@@ -60,10 +60,10 @@ def test_show_a_matrixes(
     )
 
     result = result_parallel_spectral_decay
-    result.data["dataset_2"] = result_sequential_spectral_decay.data["dataset_1"]
+    result.data["dataset_2"] = result_sequential_spectral_decay.data["sequential-decay"]
     # dummy data for filtering based on a-matrix size
     single_entry_data = result_sequential_spectral_decay.data[
-        "dataset_1"
+        "sequential-decay"
     ].a_matrix_megacomplex_sequential_decay[:1, :1]
     single_entry_data = single_entry_data.rename(
         {
@@ -85,7 +85,7 @@ def test_show_a_matrixes_multiple_a_matrixes_in_dataset(
     ).read_text(encoding="utf8")
 
     single_entry_data = result_sequential_spectral_decay.data[
-        "dataset_1"
+        "sequential-decay"
     ].a_matrix_megacomplex_sequential_decay[:1, :1]
 
     a_matrix_one = single_entry_data.rename(

tests/io/test_load_data.py

@@ -43,7 +43,8 @@ def test_load_data(
     result_sequential_spectral_decay: Result, tmp_path: Path, recwarn: WarningsRecorder
 ):
     """All input_type permutations result in a ``xr.Dataset``."""
-    compare_dataset = result_sequential_spectral_decay.data["dataset_1"]
+    compare_dataset = result_sequential_spectral_decay.data["sequential-decay"]
+    save_path = tmp_path / "result"
 
     from_result = load_data(result_sequential_spectral_decay)
 
@@ -53,9 +54,9 @@ def test_load_data(
 
     run_load_data_test(from_dataset, compare_dataset)
 
-    result_sequential_spectral_decay.save(tmp_path / "result.yml")
+    result_sequential_spectral_decay.save(save_path)
 
-    from_file = load_data(tmp_path / "dataset_1.nc")
+    from_file = load_data(save_path / "data/sequential-decay.nc")
 
     run_load_data_test(from_file, compare_dataset)
 
@@ -69,7 +70,7 @@ def test_load_data(
     assert len(filter_warnings(recwarn)) == 0
 
     # Ensure not to mutate original fixture
-    result_multi_dataset = load_result(tmp_path / "result.yml")
+    result_multi_dataset = load_result(save_path)
     result_multi_dataset.data["dataset_2"] = xr.Dataset({"foo": [1]})
 
     from_result_multi_dataset = load_data(result_multi_dataset)