Release 0.2.8

Merge pull request #245 from PEtab-dev/release_0.2.8

Author: dweindl

CHANGELOG.md

@@ -2,6 +2,17 @@
 
 ## 0.2 series
 
+### 0.2.8
+
+* Fixed pandas `FutureWarning` in `petab/visualize/lint.py`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/242
+* Added `petab.Problem.n_{estimated,measurements,priors}`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/243
+* Require pyarrow
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/244
+
+* **Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.2.7...v0.2.8
+
 ### 0.2.7
 
 * Fixed a bug in `flatten_timepoint_specific_output_overrides`, which
@@ -178,8 +189,8 @@ Features:
 * Argument forwarding for
   `Problem.get_optimization_to_simulation_parameter_mapping` by @dweindl in
   https://github.com/PEtab-dev/libpetab-python/pull/159
-* Added candidate schema for version 2  by @dweindl in
-  https://github.com/PEtab-dev/libpetab-python/pull/142
+* Added candidate schema for version 2
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/142
 * `get_parameter_df`: Allow any collection of parameter tables by @dweindl in
   https://github.com/PEtab-dev/libpetab-python/pull/153,
   @m-philipps in https://github.com/PEtab-dev/libpetab-python/pull/156,
@@ -435,7 +446,7 @@ Documentation:
 
 * In README, add to the overview table the coverage for the supporting tools,
   and links and usage examples (various commits)
-* Show REAMDE on readthedocs documentation front page (PEtab-dev/PEtab#400)
+* Show README on readthedocs documentation front page (PEtab-dev/PEtab#400)
 * Correct description of observable and noise formulas (PEtab-dev/PEtab#401)
 * Update documentation on optional visualization values (PEtab-dev/PEtab#405, PEtab-dev/PEtab#419)
 

petab/problem.py

@@ -1004,3 +1004,21 @@ def scale_parameters(
             )
             for parameter_id, parameter_value in x_dict.items()
         }
+
+    @property
+    def n_estimated(self) -> int:
+        """The number of estimated parameters."""
+        return len(self.x_free_indices)
+
+    @property
+    def n_measurements(self) -> int:
+        """Number of measurements."""
+        return self.measurement_df[MEASUREMENT].notna().sum()
+
+    @property
+    def n_priors(self) -> int:
+        """Number of priors."""
+        if OBJECTIVE_PRIOR_PARAMETERS not in self.parameter_df:
+            return 0
+
+        return self.parameter_df[OBJECTIVE_PRIOR_PARAMETERS].notna().sum()

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = "0.2.7"
+__version__ = "0.2.8"

petab/visualize/lint.py

@@ -144,7 +144,7 @@ def set_default(column: str, value):
         elif value is not None:
             if isinstance(value, str):
                 vis_df[column] = vis_df[column].astype("object")
-            vis_df[column].fillna(value, inplace=True)
+            vis_df.fillna({column: value}, inplace=True)
 
     set_default(C.PLOT_NAME, "")
     set_default(C.PLOT_TYPE_SIMULATION, C.LINE_PLOT)

setup.py

@@ -63,6 +63,9 @@ def absolute_links(txt):
     install_requires=[
         "numpy>=1.15.1",
         "pandas>=1.2.0",
+        # remove when pandas >= 3, see also
+        # https://github.com/pandas-dev/pandas/issues/54466
+        "pyarrow",
         "python-libsbml>=5.17.0",
         "sympy",
         "colorama",

tests/test_petab.py

@@ -46,6 +46,7 @@ def petab_problem():
     measurement_df = pd.DataFrame(
         data={
             OBSERVABLE_ID: ["obs1", "obs2"],
+            MEASUREMENT: [0.1, 0.2],
             OBSERVABLE_PARAMETERS: ["", "p1;p2"],
             NOISE_PARAMETERS: ["p3;p4", "p5"],
         }
@@ -63,6 +64,7 @@ def petab_problem():
         data={
             PARAMETER_ID: ["dynamicParameter1", "dynamicParameter2"],
             PARAMETER_NAME: ["", "..."],
+            ESTIMATE: [1, 0],
         }
     ).set_index(PARAMETER_ID)
 
@@ -92,13 +94,18 @@ def petab_problem():
         petab.write_observable_df(observable_df, observable_file_name)
 
         with pytest.deprecated_call():
-            yield petab.Problem.from_files(
+            petab_problem = petab.Problem.from_files(
                 sbml_file=sbml_file_name,
                 measurement_file=measurement_file_name,
                 condition_file=condition_file_name,
                 parameter_file=parameter_file_name,
                 observable_files=observable_file_name,
             )
+            assert petab_problem.n_measurements == 2
+            assert petab_problem.n_estimated == 1
+            assert petab_problem.n_priors == 0
+
+            yield petab_problem
 
 
 @pytest.fixture