Merge pull request #183 from PEtab-dev/release_0.1.30

Release 0.1.30

Author: dweindl

.ci_pip_reqs.txt

@@ -39,17 +39,14 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        pip install -r .ci_pip_reqs.txt
-        pip install .[reports,combine,tests]
+        pip install -r requirements-dev.txt
 
-    - name: Run flake8
-      run: |
-        python -m flake8
+    - name: Quality tests
+      run: tox -e quality
       if: matrix.platform == 'ubuntu-latest'
 
-    - name: Run tests
-      run: |
-        pytest --cov --cov-report=xml tests
+    - name: Unit tests
+      run: tox -e unit
 
     - name: Coverage
       uses: codecov/codecov-action@v1

.github/workflows/ci_tests.yml

@@ -2,6 +2,32 @@
 
 ## 0.1 series
 
+### 0.1.30
+
+Various smaller fixes:
+
+* Vis: Handle missing data more gracefully by @dweindl
+  in https://github.com/PEtab-dev/libpetab-python/pull/175
+* Fix test dependencies: scipy by @dweindl
+  in https://github.com/PEtab-dev/libpetab-python/pull/177
+* Add `petab.Problem.__str__` by @dweindl
+  in https://github.com/PEtab-dev/libpetab-python/pull/178
+* Fix deprecated tight layout matplotlib by @yannikschaelte
+  in https://github.com/PEtab-dev/libpetab-python/pull/180
+* Move tests to tox by @yannikschaelte
+  in https://github.com/PEtab-dev/libpetab-python/pull/182
+* Update deprecated functions in tests by @yannikschaelte
+  in https://github.com/PEtab-dev/libpetab-python/pull/181
+* Use petab identifier for combine archives by @fbergmann
+  in https://github.com/PEtab-dev/libpetab-python/pull/179
+
+New Contributors
+* @fbergmann made their first contribution
+  in https://github.com/PEtab-dev/libpetab-python/pull/179
+
+**Full Changelog**:
+https://github.com/PEtab-dev/libpetab-python/compare/v0.1.29...v0.1.30
+
 ### 0.1.29
 
 Features:

CHANGELOG.md

@@ -396,7 +396,7 @@ def _add_file_metadata(location: str, description: str = ""):
     archive.addFile(
         str(yaml_file),
         os.path.basename(yaml_file),
-        libcombine.KnownFormats.lookupFormat("yaml"),
+        "http://identifiers.org/combine.specifications/petab.version-1",
         True
     )
     _add_file_metadata(location=os.path.basename(yaml_file),

petab/core.py

@@ -104,6 +104,31 @@ def __setattr__(self, name, value):
         else:
             super().__setattr__(name, value)
 
+    def __str__(self):
+        model = f"with model ({self.model})" if self.model else "without model"
+        conditions = f"{self.condition_df.shape[0]} conditions" \
+            if self.condition_df is not None else "without conditions table"
+
+        observables = f"{self.observable_df.shape[0]} observables" \
+            if self.observable_df is not None else "without observables table"
+
+        measurements = f"{self.measurement_df.shape[0]} measurements" \
+            if self.measurement_df is not None \
+            else "without measurements table"
+
+        if self.parameter_df is not None:
+            num_estimated_parameters = sum(self.parameter_df[ESTIMATE] == 1) \
+                if ESTIMATE in self.parameter_df \
+                else self.parameter_df.shape[0]
+            parameters = f"{num_estimated_parameters} estimated parameters"
+        else:
+            parameters = "without parameter_df table"
+
+        return (
+            f"PEtab Problem {model}, {conditions}, {observables}, "
+            f"{measurements}, {parameters}"
+        )
+
     @staticmethod
     def from_files(
             sbml_file: Union[str, Path] = None,
@@ -386,7 +411,7 @@ def to_files(
         visualization tables, they will be merged and written to a single file.
 
         Arguments:
-            sbml_file: SBML model destination
+            sbml_file: SBML model destination (deprecated)
             model_file: Model destination
             condition_file: Condition table destination
             measurement_file: Measurement table destination

petab/problem.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = '0.1.29'
+__version__ = '0.1.30'

petab/version.py

@@ -95,7 +95,8 @@ def generate_lineplot(
 
         label_base = dataplot.legendEntry
 
-        if measurements_to_plot is not None:
+        if measurements_to_plot is not None \
+                and not measurements_to_plot.data_to_plot.empty:
             # plotting all measurement data
 
             if plotTypeData == REPLICATE:
@@ -361,7 +362,7 @@ def generate_figure(
 
             fig, axes = plt.subplots(num_row, num_col, squeeze=False,
                                      figsize=self.figure.size)
-            fig.set_tight_layout(True)
+            fig.set_layout_engine("tight")
 
             for ax in axes.flat[self.figure.num_subplots:]:
                 ax.remove()
@@ -372,11 +373,15 @@ def generate_figure(
         for subplot in self.figure.subplots:
             if subplot_dir is not None:
                 fig, ax = plt.subplots(figsize=self.figure.size)
-                fig.set_tight_layout(True)
+                fig.set_layout_engine("tight")
             else:
                 ax = axes[subplot.plotId]
 
-            self.generate_subplot(ax, subplot)
+            try:
+                self.generate_subplot(ax, subplot)
+            except Exception as e:
+                raise RuntimeError(
+                    f"Error plotting {getattr(subplot, PLOT_ID)}.") from e
 
             if subplot_dir is not None:
                 # TODO: why this doesn't work?

petab/visualize/plotter.py

@@ -0,0 +1 @@
+tox >= 3.26.0

requirements-dev.txt

@@ -12,13 +12,13 @@ def read(fname):
 def absolute_links(txt):
     """Replace relative petab github links by absolute links."""
 
-    raw_base = "(https://raw.githubusercontent.com/"\
-               "petab-dev/libpetab-python/master/"
-    embedded_base = "(https://github.com/petab-dev/libpetab-python/"\
-                    "tree/master/"
+    raw_base = \
+        "(https://raw.githubusercontent.com/petab-dev/libpetab-python/master/"
+    embedded_base = \
+        "(https://github.com/petab-dev/libpetab-python/tree/master/"
     # iterate over links
-    for var in re.findall(r'\[.*?\]\((?!http).*?\)', txt):
-        if re.match(r'.*?.(png|svg)\)', var):
+    for var in re.findall(r"\[.*?\]\((?!http).*?\)", txt):
+        if re.match(r".*?.(png|svg)\)", var):
             # link to raw file
             rep = var.replace("(", raw_base)
         else:
@@ -30,62 +30,72 @@ def absolute_links(txt):
 
 # Python version check. We need >= 3.6 due to e.g. f-strings
 if sys.version_info < (3, 8, 0):
-    sys.exit('PEtab requires at least Python version 3.8')
+    sys.exit("PEtab requires at least Python version 3.8")
 
 # read version from file
-__version__ = ''
-version_file = os.path.join('petab', 'version.py')
+__version__ = ""
+version_file = os.path.join("petab", "version.py")
 # sets __version__
 exec(read(version_file))  # pylint: disable=W0122 # nosec
 
 ENTRY_POINTS = {
-    'console_scripts': [
-        'petablint = petab.petablint:main',
-        'petab_visualize = petab.visualize.cli:_petab_visualize_main',
+    "console_scripts": [
+        "petablint = petab.petablint:main",
+        "petab_visualize = petab.visualize.cli:_petab_visualize_main",
     ]
 }
 
 # project metadata
 # noinspection PyUnresolvedReferences
-setup(name='petab',
-      version=__version__,
-      description='Parameter estimation tabular data',
-      long_description=absolute_links(read('README.md')),
-      long_description_content_type="text/markdown",
-      author='The PEtab developers',
-      author_email='[email protected]',
-      url='https://github.com/PEtab-dev/libpetab-python',
-      packages=find_packages(exclude=['doc*', 'test*']),
-      install_requires=['numpy>=1.15.1',
-                        'pandas>=1.2.0',
-                        'matplotlib>=3.5.0',
-                        'python-libsbml>=5.17.0',
-                        'sympy',
-                        'colorama',
-                        'seaborn',
-                        'pyyaml',
-                        'jsonschema',
-                        ],
-      include_package_data=True,
-      python_requires='>=3.8.0',
-      entry_points=ENTRY_POINTS,
-      extras_require={
-          'tests': [
-              'flake8',
-              'pytest',
-              'python-libcombine',
-              'simplesbml'
-          ],
-          'reports': ['Jinja2'],
-          'combine': ['python-libcombine>=0.2.6'],
-          'doc': [
-              'sphinx>=3.5.3, !=5.1.0',
-              'sphinxcontrib-napoleon>=0.7',
-              'sphinx-markdown-tables>=0.0.15',
-              'sphinx-rtd-theme>=0.5.1',
-              'm2r2',
-              'myst-nb>=0.14.0',
-              'ipython>=7.21.0',
-          ]
-      }
-      )
+setup(
+    name="petab",
+    version=__version__,
+    description="Parameter estimation tabular data",
+    long_description=absolute_links(read("README.md")),
+    long_description_content_type="text/markdown",
+    author="The PEtab developers",
+    author_email="[email protected]",
+    url="https://github.com/PEtab-dev/libpetab-python",
+    packages=find_packages(exclude=["doc*", "test*"]),
+    install_requires=[
+        "numpy>=1.15.1",
+        "pandas>=1.2.0",
+        "matplotlib>=3.6.0",
+        "python-libsbml>=5.17.0",
+        "sympy",
+        "colorama",
+        "seaborn",
+        "pyyaml",
+        "jsonschema",
+    ],
+    include_package_data=True,
+    python_requires=">=3.8.0",
+    entry_points=ENTRY_POINTS,
+    extras_require={
+        "tests": [
+            "pytest",
+            "pytest-cov",
+            "simplesbml",
+            "scipy",
+        ],
+        "quality": [
+            "flake8>=3.8.3",
+        ],
+        "reports": [
+            # https://github.com/spatialaudio/nbsphinx/issues/641
+            "Jinja2==3.0.3",
+        ],
+        "combine": [
+            "python-libcombine>=0.2.6",
+        ],
+        "doc": [
+            "sphinx>=3.5.3, !=5.1.0",
+            "sphinxcontrib-napoleon>=0.7",
+            "sphinx-markdown-tables>=0.0.15",
+            "sphinx-rtd-theme>=0.5.1",
+            "m2r2",
+            "myst-nb>=0.14.0",
+            "ipython>=7.21.0",
+        ],
+    },
+)

setup.py

@@ -0,0 +1,58 @@
+"""Check that deprecated functionality raises but still works."""
+import pytest
+import tempfile
+from pathlib import Path
+
+import petab
+
+from .test_sbml import create_test_data, check_model
+from .test_petab import petab_problem  # noqa: F401
+
+
+def test_problem_with_sbml_model():
+    """Test that a problem can be correctly created from sbml model."""
+    # retrieve test data
+    ss_model, condition_df, observable_df, measurement_df, parameter_df = \
+        create_test_data()
+
+    with pytest.deprecated_call():
+        petab_problem = petab.Problem(  # noqa: F811
+            sbml_model=ss_model.model,
+            condition_df=condition_df,
+            measurement_df=measurement_df,
+            parameter_df=parameter_df,
+        )
+
+    _, condition_model = petab.get_model_for_condition(
+        petab_problem, "condition_1")
+
+    check_model(condition_model)
+
+
+def test_to_files_with_sbml_model(petab_problem):  # noqa: F811
+    """Test problem.to_files."""
+    with tempfile.TemporaryDirectory() as outdir:
+        # create target files
+        sbml_file = Path(outdir, "model.xml")
+        condition_file = Path(outdir, "conditions.tsv")
+        measurement_file = Path(outdir, "measurements.tsv")
+        parameter_file = Path(outdir, "parameters.tsv")
+        observable_file = Path(outdir, "observables.tsv")
+
+        # write contents to files
+        with pytest.deprecated_call():
+            petab_problem.to_files(
+                sbml_file=sbml_file,
+                condition_file=condition_file,
+                measurement_file=measurement_file,
+                parameter_file=parameter_file,
+                visualization_file=None,
+                observable_file=observable_file,
+                yaml_file=None,
+            )
+
+        # exemplarily load some
+        parameter_df = petab.get_parameter_df(parameter_file)
+        same_nans = parameter_df.isna() == petab_problem.parameter_df.isna()
+        assert ((parameter_df == petab_problem.parameter_df) | same_nans) \
+            .all().all()