Merge pull request #266 from dweindl/release_0.3.0

Release 0.3.0

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]

.github/workflows/ci_tests.yml

@@ -2,6 +2,7 @@ name: CI
 
 on:
   push:
+  pull_request:
   workflow_dispatch:
   schedule:
     - cron:  '48 4 * * *'
@@ -11,7 +12,7 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.10", "3.12"]
     runs-on: ${{ matrix.platform }}
 
     steps:

.pre-commit-config.yaml

@@ -1,12 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -16,13 +10,19 @@ repos:
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-    - id: black-jupyter
-      # It is recommended to specify the latest version of Python
-      # supported by your project here, or alternatively use
-      # pre-commit's default_language_version, see
-      # https://pre-commit.com/#top_level-default_language_version
-      language_version: python3.11
-      args: ["--line-length", "79"]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - pyproject.toml

.readthedocs.yaml

@@ -10,7 +10,7 @@ sphinx:
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.9"
+    python: "3.10"
 
 python:
    install:

CHANGELOG.md

@@ -1,5 +1,29 @@
 # PEtab changelog
 
+## 0.3 series
+
+### 0.3.0
+
+**This release requires `python>=3.10`**
+
+**Features**
+* Visualization: Make line plot lines configurable via
+  `petab.visualize.plotter.measurement_line_kwargs and
+  `petab.visualize.plotter.simulation_line_kwargs`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/254
+* Validator: check that `datasetId`s referenced in visualization tables exists
+  in measurement tables
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/255
+
+**Fixes**
+* Drop an index if it's reset
+  by @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/262
+
+## New Contributors
+* @PaulJonasJost made their first contribution in https://github.com/PEtab-dev/libpetab-python/pull/250
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.2.9...v0.3.0
+
 ## 0.2 series
 
 ### 0.2.9

README.md

@@ -22,7 +22,7 @@ and the easiest way to install it is running
 
     pip3 install petab
 
-It will require Python>=3.9 to run. (We are following the
+It will require Python>=3.10 to run. (We are following the
 [numpy Python support policy](https://numpy.org/neps/nep-0029-deprecation_policy.html)).
 
 Development versions of the PEtab library can be installed using
@@ -57,7 +57,7 @@ Examples for PEtab Python library usage:
 
 ## Getting help
 
-If you have any question or problems with this package, feel free to post them
+If you have any questions or problems with this package, feel free to post them
 at our GitHub [issue tracker](https://github.com/PEtab-dev/libpetab-python/issues/).
 
 ## Contributing

doc/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "libpetab-python"
-copyright = "2018-2023, the PEtab developers"
+copyright = "2018-2024, the PEtab developers"
 author = "PEtab developers"
 
 # The full version, including alpha/beta/rc tags
@@ -29,7 +29,7 @@
 # -- Custom pre-build --------------------------------------------------------
 
 
-subprocess.run(["python", "md2rst.py"])
+subprocess.run([sys.executable, "md2rst.py"])  # noqa: S603
 
 # -- General configuration ---------------------------------------------------
 
@@ -74,7 +74,6 @@
     "members": None,
     "imported-members": ["petab"],
     "inherited-members": None,
-    "private-members": None,
     "show-inheritance": None,
 }
 

petab/calculate.py

@@ -7,11 +7,11 @@
 import numpy as np
 import pandas as pd
 import sympy
-from sympy.abc import _clash
 
 import petab
 
 from .C import *
+from .math import sympify_petab
 
 __all__ = [
     "calculate_residuals",
@@ -157,7 +157,7 @@ def get_symbolic_noise_formulas(observable_df) -> Dict[str, sympy.Expr]:
         if NOISE_FORMULA not in observable_df.columns:
             noise_formula = None
         else:
-            noise_formula = sympy.sympify(row.noiseFormula, locals=_clash)
+            noise_formula = sympify_petab(row.noiseFormula)
         noise_formulas[observable_id] = noise_formula
     return noise_formulas
 
@@ -322,7 +322,8 @@ def calculate_llh_for_table(
     parameter_df: pd.DataFrame,
 ) -> float:
     """Calculate log-likelihood for one set of tables. For the arguments, see
-    `calculate_llh`."""
+    `calculate_llh`.
+    """
     llhs = []
 
     # matching columns
@@ -335,7 +336,7 @@ def calculate_llh_for_table(
     noise_formulas = get_symbolic_noise_formulas(observable_df)
 
     # iterate over measurements, find corresponding simulations
-    for irow, row in measurement_df.iterrows():
+    for _, row in measurement_df.iterrows():
         measurement = row[MEASUREMENT]
 
         # look up in simulation df

petab/composite_problem.py

@@ -46,7 +46,6 @@ def from_yaml(yaml_config: Union[Dict, str]) -> "CompositeProblem":
         Arguments:
             yaml_config: PEtab configuration as dictionary or YAML file name
         """
-
         if isinstance(yaml_config, str):
             path_prefix = os.path.dirname(yaml_config)
             yaml_config = yaml.load_yaml(yaml_config)

petab/conditions.py

@@ -18,7 +18,7 @@
 
 
 def get_condition_df(
-    condition_file: Union[str, pd.DataFrame, Path, None]
+    condition_file: Union[str, pd.DataFrame, Path, None],
 ) -> pd.DataFrame:
     """Read the provided condition file into a ``pandas.Dataframe``
 
@@ -40,14 +40,17 @@ def get_condition_df(
     )
 
     if not isinstance(condition_file.index, pd.RangeIndex):
-        condition_file.reset_index(inplace=True)
+        condition_file.reset_index(
+            drop=condition_file.index.name != CONDITION_ID,
+            inplace=True,
+        )
 
     try:
         condition_file.set_index([CONDITION_ID], inplace=True)
     except KeyError:
         raise KeyError(
             f"Condition table missing mandatory field {CONDITION_ID}."
-        )
+        ) from None
 
     return condition_file
 
@@ -75,7 +78,6 @@ def create_condition_df(
         A :py:class:`pandas.DataFrame` with empty given rows and columns and
         all nan values
     """
-
     condition_ids = [] if condition_ids is None else list(condition_ids)
 
     data = {CONDITION_ID: condition_ids}

petab/core.py

@@ -72,7 +72,7 @@ def write_simulation_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
 
 
 def get_visualization_df(
-    visualization_file: Union[str, Path, pd.DataFrame, None]
+    visualization_file: Union[str, Path, pd.DataFrame, None],
 ) -> Union[pd.DataFrame, None]:
     """Read PEtab visualization table
 
@@ -102,7 +102,8 @@ def get_visualization_df(
     except pd.errors.EmptyDataError:
         warn(
             "Visualization table is empty. Defaults will be used. "
-            "Refer to the documentation for details."
+            "Refer to the documentation for details.",
+            stacklevel=2,
         )
         vis_spec = pd.DataFrame()
     return vis_spec
@@ -226,9 +227,9 @@ def get_flattened_id_mappings(
 
         mappings[OBSERVABLE_ID][observable_replacement_id] = observable_id
 
-        for field, hyperparameter_type, target in [
-            (NOISE_PARAMETERS, "noiseParameter", NOISE_FORMULA),
-            (OBSERVABLE_PARAMETERS, "observableParameter", OBSERVABLE_FORMULA),
+        for field, hyperparameter_type in [
+            (NOISE_PARAMETERS, "noiseParameter"),
+            (OBSERVABLE_PARAMETERS, "observableParameter"),
         ]:
             if field in measurements:
                 mappings[field][
@@ -357,7 +358,6 @@ def concat_tables(
     Returns:
         The concatenated DataFrames
     """
-
     if isinstance(tables, pd.DataFrame):
         return tables
 
@@ -389,7 +389,6 @@ def to_float_if_float(x: Any) -> Any:
     Returns:
         ``x`` as float if possible, otherwise ``x``
     """
-
     try:
         return float(x)
     except (ValueError, TypeError):
@@ -427,19 +426,18 @@ def create_combine_archive(
         email: E-mail address of archive creator
         organization: Organization of archive creator
     """
-
     path_prefix = os.path.dirname(str(yaml_file))
     yaml_config = yaml.load_yaml(yaml_file)
 
     # function-level import, because module-level import interfered with
     # other SWIG interfaces
     try:
         import libcombine
-    except ImportError:
+    except ImportError as err:
         raise ImportError(
             "To use PEtab's COMBINE functionality, libcombine "
             "(python-libcombine) must be installed."
-        )
+        ) from err
 
     def _add_file_metadata(location: str, description: str = ""):
         """Add metadata to the added file"""

petab/lint.py

@@ -10,12 +10,12 @@
 import numpy as np
 import pandas as pd
 import sympy as sp
-from sympy.abc import _clash
 
 import petab
 
 from . import core, measurements, parameters
 from .C import *  # noqa: F403
+from .math import sympify_petab
 from .models import Model
 
 logger = logging.getLogger(__name__)
@@ -105,7 +105,6 @@ def check_condition_df(
     Raises:
         AssertionError: in case of problems
     """
-
     # Check required columns are present
     req_cols = []
     _check_df(df, req_cols, "condition")
@@ -167,7 +166,6 @@ def check_measurement_df(
     Raises:
         AssertionError, ValueError: in case of problems
     """
-
     _check_df(df, MEASUREMENT_DF_REQUIRED_COLS, "measurement")
 
     for column_name in MEASUREMENT_DF_REQUIRED_COLS:
@@ -319,7 +317,7 @@ def check_observable_df(observable_df: pd.DataFrame) -> None:
     for row in observable_df.itertuples():
         obs = getattr(row, OBSERVABLE_FORMULA)
         try:
-            sp.sympify(obs, locals=_clash)
+            sympify_petab(obs)
         except sp.SympifyError as e:
             raise AssertionError(
                 f"Cannot parse expression '{obs}' "
@@ -328,7 +326,7 @@ def check_observable_df(observable_df: pd.DataFrame) -> None:
 
         noise = getattr(row, NOISE_FORMULA)
         try:
-            sympified_noise = sp.sympify(noise, locals=_clash)
+            sympified_noise = sympify_petab(noise)
             if sympified_noise is None or (
                 sympified_noise.is_Number and not sympified_noise.is_finite
             ):
@@ -432,7 +430,6 @@ def assert_measured_observables_defined(
     Raises:
         AssertionError: in case of problems
     """
-
     used_observables = set(measurement_df[OBSERVABLE_ID].values)
     defined_observables = set(observable_df.index.values)
     if undefined_observables := (used_observables - defined_observables):
@@ -453,7 +450,6 @@ def condition_table_is_parameter_free(condition_df: pd.DataFrame) -> bool:
         ``True`` if there are no parameter overrides in the condition table,
         ``False`` otherwise.
     """
-
     return len(petab.get_parametric_overrides(condition_df)) == 0
 
 
@@ -468,7 +464,6 @@ def assert_parameter_id_is_string(parameter_df: pd.DataFrame) -> None:
     Raises:
         AssertionError: in case of problems
     """
-
     for parameter_id in parameter_df:
         if isinstance(parameter_id, str):
             if parameter_id[0].isdigit():
@@ -1088,7 +1083,6 @@ def assert_measurement_conditions_present_in_condition_table(
     Raises:
         AssertionError: in case of problems
     """
-
     used_conditions = set(measurement_df[SIMULATION_CONDITION_ID].values)
     if PREEQUILIBRATION_CONDITION_ID in measurement_df:
         used_conditions |= set(