Merge pull request #211 from PEtab-dev/0.2.2

Release 0.2.2

Author: dweindl

.github/workflows/deploy.yml

@@ -7,6 +7,11 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/sbmlmath
+    permissions:
+      id-token: write
 
     steps:
     - name: Check out repository
@@ -15,14 +20,12 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: 3.11
-    - name: Install dependencies
+
+    - name: Install dependencies / build sdist
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        pip install setuptools wheel build
+        python -m build -s
+
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## 0.2 series
 
+### 0.2.2
+
+* Fixed IndexError with numpy 1.25.0 by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/209
+* Made `SbmlModel.from_file(..., model_id)` optional by @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/207
+
 ### 0.2.1
 
 Fixes:

petab/models/sbml_model.py

@@ -59,7 +59,7 @@ def __setstate__(self, state):
         self.__dict__.update(state)
 
     @staticmethod
-    def from_file(filepath_or_buffer, model_id: str):
+    def from_file(filepath_or_buffer, model_id: str = None):
         sbml_reader, sbml_document, sbml_model = get_sbml_model(
             filepath_or_buffer)
         return SbmlModel(

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = '0.2.1'
+__version__ = '0.2.2'

petab/visualize/plotter.py

@@ -116,6 +116,8 @@ def generate_lineplot(
             if plotTypeData == REPLICATE:
                 replicates = np.stack(
                     measurements_to_plot.data_to_plot.repl.values)
+                if replicates.ndim == 1:
+                    replicates = np.expand_dims(replicates, axis=1)
 
                 # plot first replicate
                 p = ax.plot(
@@ -544,6 +546,8 @@ def _line_plot_at_t_inf(
                 p = None
                 if plotTypeData == REPLICATE:
                     replicates = measurements_data_to_plot_inf.repl
+                    if replicates.ndim == 0:
+                        replicates = np.expand_dims(replicates, axis=0)
 
                     # plot first replicate
                     p = ax_inf.plot(
@@ -587,6 +591,8 @@ def _line_plot_at_t_inf(
 
             if plotTypeData == REPLICATE:
                 replicates = simulations_data_to_plot_inf.repl
+                if replicates.ndim == 0:
+                    replicates = np.expand_dims(replicates, axis=0)
 
                 # plot first replicate
                 p = ax_inf.plot(

pytest.ini

@@ -1,3 +1,4 @@
 [pytest]
 filterwarnings =
+    error
     ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning

tests/test_deprecated.py

@@ -23,8 +23,11 @@ def test_problem_with_sbml_model():
             parameter_df=parameter_df,
         )
 
-    _, condition_model = petab.get_model_for_condition(
-        petab_problem, "condition_1")
+    with pytest.warns(UserWarning,
+                      match="An SBML rule was removed to set the component "
+                            "species_2 to a constant value."):
+        _, condition_model = petab.get_model_for_condition(
+            petab_problem, "condition_1")
 
     check_model(condition_model)
 

tests/test_model_pysb.py

@@ -1,9 +1,19 @@
 """Test related to petab.models.model_pysb"""
 import pysb
+import pytest
+
 from petab.models.pysb_model import PySBModel, parse_species_name, \
     pattern_from_string
 
 
+@pytest.fixture(scope="function")
+def uses_pysb():
+    """Cleanup PySB auto-exported symbols before and after test"""
+    pysb.SelfExporter.cleanup()
+    yield ()
+    pysb.SelfExporter.cleanup()
+
+
 def test_parse_species_name():
     assert parse_species_name("cyclin(Y='U', b=None)") \
            == [("cyclin", None, {'Y': 'U', 'b': None})]
@@ -32,7 +42,7 @@ def test_parse_species_name():
     # TODO: MultiState
 
 
-def test_pysb_model():
+def test_pysb_model(uses_pysb):
     model = pysb.Model()
     pysb.Compartment("c1")
     pysb.Monomer("A")
@@ -58,7 +68,7 @@ def test_pysb_model():
     assert petab_model.is_state_variable("A(s='a')") is False
 
 
-def test_pattern_parsing():
+def test_pattern_parsing(uses_pysb):
     model = pysb.Model()
     c1 = pysb.Compartment("c1")
     A = pysb.Monomer("A")

tests/test_sbml.py

@@ -1,7 +1,8 @@
-import sys
 import os
+import sys
 
 import pandas as pd
+import pytest
 
 sys.path.append(os.getcwd())
 import petab  # noqa: E402
@@ -88,7 +89,12 @@ def test_get_condition_specific_models():
     )
 
     # create SBML model for condition with parameters updated from problem
-    _, condition_model = petab.get_model_for_condition(
-        petab_problem, "condition_1")
+    with pytest.warns(
+            UserWarning,
+            match="An SBML rule was removed to set the "
+                  "component species_2 to a constant value."
+    ):
+        _, condition_model = petab.get_model_for_condition(
+            petab_problem, "condition_1")
 
     check_model(condition_model)

tests/test_visualization.py

@@ -19,6 +19,13 @@
 EXAMPLE_DIR = Path(__file__).parents[1] / "doc" / "example"
 
 
+@pytest.fixture(scope="function")
+def close_fig():
+    """Close all open matplotlib figures"""
+    yield
+    plt.close('all')
+
+
 @pytest.fixture
 def data_file_Fujita():
     return EXAMPLE_DIR / "example_Fujita" / "Fujita_measurementData.tsv"
@@ -88,6 +95,7 @@ def visu_file_Fujita_minimal():
            / "Fujita_visuSpec_mandatory.tsv"
 
 
+@pytest.mark.filterwarnings("ignore:Visualization table is empty")
 @pytest.fixture
 def visu_file_Fujita_empty():
     return EXAMPLE_DIR / "example_Fujita" / "visuSpecs" \
@@ -137,7 +145,8 @@ def simulation_file_Isensee():
 def test_visualization_with_vis_and_sim(data_file_Isensee,
                                         condition_file_Isensee,
                                         vis_spec_file_Isensee,
-                                        simulation_file_Isensee):
+                                        simulation_file_Isensee,
+                                        close_fig):
     validate_visualization_df(
         petab.Problem(
             condition_df=petab.get_condition_df(condition_file_Isensee),
@@ -151,7 +160,8 @@ def test_visualization_with_vis_and_sim(data_file_Isensee,
 def test_visualization_replicates(data_file_Isensee,
                                   condition_file_Isensee,
                                   vis_spec_file_Isensee_replicates,
-                                  simulation_file_Isensee):
+                                  simulation_file_Isensee,
+                                  close_fig):
     plot_with_vis_spec(vis_spec_file_Isensee_replicates,
                        condition_file_Isensee,
                        data_file_Isensee, simulation_file_Isensee)
@@ -160,15 +170,17 @@ def test_visualization_replicates(data_file_Isensee,
 def test_visualization_scatterplot(data_file_Isensee,
                                    condition_file_Isensee,
                                    vis_spec_file_Isensee_scatterplot,
-                                   simulation_file_Isensee):
+                                   simulation_file_Isensee,
+                                   close_fig):
     plot_with_vis_spec(vis_spec_file_Isensee_scatterplot,
                        condition_file_Isensee,
                        data_file_Isensee, simulation_file_Isensee)
 
 
 def test_visualization_small_visu_file_w_datasetid(data_file_Fujita,
                                                    condition_file_Fujita,
-                                                   visu_file_Fujita_small):
+                                                   visu_file_Fujita_small,
+                                                   close_fig):
     """
     Test: visualization specification file only with few columns in
     particular datasetId
@@ -181,7 +193,8 @@ def test_visualization_small_visu_file_w_datasetid(data_file_Fujita,
 def test_visualization_small_visu_file_wo_datasetid(
         data_file_Fujita,
         condition_file_Fujita,
-        visu_file_Fujita_wo_dsid_wo_yvalues):
+        visu_file_Fujita_wo_dsid_wo_yvalues,
+        close_fig):
     """
     Test: visualization specification file only with few columns in
     particular no datasetId column
@@ -194,7 +207,8 @@ def test_visualization_small_visu_file_wo_datasetid(
 def test_visualization_all_obs_with_diff_settings(
         data_file_Fujita,
         condition_file_Fujita,
-        visu_file_Fujita_all_obs_with_diff_settings):
+        visu_file_Fujita_all_obs_with_diff_settings,
+        close_fig):
     """
     Test: visualization specification file only with few columns. In
     particular, no datasetId column and no yValues column, but more than one
@@ -207,7 +221,8 @@ def test_visualization_all_obs_with_diff_settings(
 
 def test_visualization_minimal_visu_file(data_file_Fujita,
                                          condition_file_Fujita,
-                                         visu_file_Fujita_minimal):
+                                         visu_file_Fujita_minimal,
+                                         close_fig):
     """
     Test: visualization specification file only with mandatory column plotId
     (optional columns are optional)
@@ -218,18 +233,21 @@ def test_visualization_minimal_visu_file(data_file_Fujita,
 
 def test_visualization_empty_visu_file(data_file_Fujita,
                                        condition_file_Fujita,
-                                       visu_file_Fujita_empty):
+                                       visu_file_Fujita_empty,
+                                       close_fig):
     """
     Test: Empty visualization specification file should default to routine
     for no file at all
     """
-    plot_with_vis_spec(visu_file_Fujita_empty, condition_file_Fujita,
-                       data_file_Fujita)
+    with pytest.warns(UserWarning, match="Visualization table is empty."):
+        plot_with_vis_spec(visu_file_Fujita_empty, condition_file_Fujita,
+                           data_file_Fujita)
 
 
 def test_visualization_minimal_data_file(data_file_Fujita_minimal,
                                          condition_file_Fujita,
-                                         visu_file_Fujita_wo_dsid_wo_yvalues):
+                                         visu_file_Fujita_wo_dsid_wo_yvalues,
+                                         close_fig):
     """
     Test visualization, with the case: data file only with mandatory columns
     (optional columns are optional)
@@ -240,7 +258,8 @@ def test_visualization_minimal_data_file(data_file_Fujita_minimal,
 
 def test_visualization_with_dataset_list(data_file_Isensee,
                                          condition_file_Isensee,
-                                         simulation_file_Isensee):
+                                         simulation_file_Isensee,
+                                         close_fig):
     datasets = [['JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
                  'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'],
                 ['JI09_160201_Drg453-452_CycNuc__ctrl',
@@ -257,7 +276,8 @@ def test_visualization_with_dataset_list(data_file_Isensee,
 
 def test_visualization_without_datasets(data_file_Fujita,
                                         condition_file_Fujita,
-                                        simu_file_Fujita):
+                                        simu_file_Fujita,
+                                        close_fig):
 
     sim_cond_id_list = [['model1_data1'], ['model1_data2', 'model1_data3'],
                         ['model1_data4', 'model1_data5'], ['model1_data6']]
@@ -284,7 +304,8 @@ def test_visualization_without_datasets(data_file_Fujita,
 
 
 def test_visualization_only_simulations(condition_file_Fujita,
-                                        simu_file_Fujita):
+                                        simu_file_Fujita,
+                                        close_fig):
 
     sim_cond_id_list = [['model1_data1'], ['model1_data2', 'model1_data3'],
                         ['model1_data4', 'model1_data5'], ['model1_data6']]
@@ -300,7 +321,9 @@ def test_visualization_only_simulations(condition_file_Fujita,
                           plotted_noise=PROVIDED)
 
 
-def test_simple_visualization(data_file_Fujita, condition_file_Fujita):
+def test_simple_visualization(
+        data_file_Fujita, condition_file_Fujita, close_fig
+):
     plot_without_vis_spec(condition_file_Fujita,
                           measurements_df=data_file_Fujita)
     plot_without_vis_spec(condition_file_Fujita,
@@ -311,7 +334,8 @@ def test_simple_visualization(data_file_Fujita, condition_file_Fujita):
 def test_visualization_with__t_inf(data_file_Fujita_t_inf,
                                    simu_file_Fujita_t_inf,
                                    condition_file_Fujita,
-                                   visu_file_Fujita_replicates):
+                                   visu_file_Fujita_replicates,
+                                   close_fig):
     # plot only measurements
     plot_without_vis_spec(condition_file_Fujita,
                           measurements_df=data_file_Fujita_t_inf)
@@ -333,7 +357,8 @@ def test_visualization_with__t_inf(data_file_Fujita_t_inf,
 
 
 def test_save_plots_to_file(data_file_Isensee, condition_file_Isensee,
-                            vis_spec_file_Isensee, simulation_file_Isensee):
+                            vis_spec_file_Isensee, simulation_file_Isensee,
+                            close_fig):
     with TemporaryDirectory() as temp_dir:
         plot_with_vis_spec(vis_spec_file_Isensee, condition_file_Isensee,
                            data_file_Isensee, simulation_file_Isensee,
@@ -349,7 +374,11 @@ def test_save_visu_file(data_file_Isensee,
                                         data_file_Isensee)
         figure, _ = vis_spec_parser.parse_from_id_list()
 
-        figure.save_to_tsv(path.join(temp_dir, "visuSpec.tsv"))
+        with pytest.warns(
+                UserWarning,
+                match="please check that datasetId column corresponds to"
+        ):
+            figure.save_to_tsv(path.join(temp_dir, "visuSpec.tsv"))
 
         datasets = [['JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
                      'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'],
@@ -361,16 +390,20 @@ def test_save_visu_file(data_file_Isensee,
                                         data_file_Isensee)
         figure, _ = vis_spec_parser.parse_from_id_list(datasets,
                                                        group_by='dataset')
-        figure.save_to_tsv(path.join(temp_dir, "visuSpec1.tsv"))
+        with pytest.warns(
+                UserWarning,
+                match="please check that datasetId column corresponds to"
+        ):
+            figure.save_to_tsv(path.join(temp_dir, "visuSpec1.tsv"))
 
 
-def test_residuals_plot(simu_file_Fujita):
+def test_residuals_plot(simu_file_Fujita, close_fig):
     fujita_yaml = EXAMPLE_DIR / "example_Fujita" / "Fujita.yaml"
     fujita_petab_problem = petab.Problem.from_yaml(fujita_yaml)
     plot_residuals_vs_simulation(fujita_petab_problem, simu_file_Fujita)
 
 
-def test_goodness_of_fit_plot(simu_file_Fujita):
+def test_goodness_of_fit_plot(simu_file_Fujita, close_fig):
     fujita_yaml = EXAMPLE_DIR / "example_Fujita" / "Fujita.yaml"
     fujita_petab_problem = petab.Problem.from_yaml(fujita_yaml)
     plot_goodness_of_fit(fujita_petab_problem, simu_file_Fujita)
@@ -389,6 +422,7 @@ def test_cli():
         subprocess.run(args, check=True)
 
 
+@pytest.mark.filterwarnings("ignore:Visualization table is empty")
 @pytest.mark.parametrize(
     "vis_file",
     (