Merge branch 'main' into claude/issue-540-fix-3c75eb

Author: dweindl

.gitignore

@@ -117,3 +117,6 @@ doc/_static/README.rst
 
 # BNGL corpus fixtures are fetched on demand (tests/v1/fetch_bngl_corpus.py)
 tests/v1/bngl_corpus/*.bngl
+
+# CI resolves the latest dependency versions
+uv.lock

CHANGELOG.md

@@ -1,5 +1,69 @@
 # PEtab changelog
 
+## 0.10 series
+
+### 0.10.0 (unreleased)
+
+**Breaking changes**
+* Removed the deprecated top-level aliases for `petab.v1` (deprecated since
+  0.4.0). Accessing `petab.<name>` or importing `petab.<module>` for anything
+  other than `petab.v1`, `petab.v2`, `petab.ENV_NUM_THREADS` and
+  `petab.__version__` now raises `AttributeError` / `ModuleNotFoundError`.
+  Use `petab.v1.<name>` instead, e.g., `import petab.v1 as petab`.
+  `import petab` no longer imports `petab.v1`.
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/538)
+* `petab.v2.Parameter` has a new `name` field for the `parameterName` column,
+  which was previously stored as an extra attribute `parameterName`.
+  `BaseTable` subclasses now implement `_to_df` instead of `to_df`.
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/543)
+
+**Fixes**
+* `get_model_for_condition` no longer turns rate-rule targets that are
+  overridden in the condition table into constants
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/520)
+* Raise a clear error for a PEtab YAML file with an empty `problems` section
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/521)
+* Several fixes to the v1-to-v2 converter (`petab1to2`): keep
+  pre-equilibration for conditions that set nothing, order placeholders by
+  index instead of lexicographically, rescale noise and priors when
+  converting `log10` to `log`, and fix the conversion of `logNormal`,
+  `logLaplace` and `parameterScaleUniform` priors
+  (by @FFroehlich in
+  https://github.com/PEtab-dev/libpetab-python/pull/532,
+  https://github.com/PEtab-dev/libpetab-python/pull/533,
+  https://github.com/PEtab-dev/libpetab-python/pull/535, and
+  https://github.com/PEtab-dev/libpetab-python/pull/536)
+* `petab_math_str` now produces valid PEtab math expressions for boolean
+  operators, (in)equality, `min`/`max`, powers with negative bases, and
+  `pi`/`e`, and prints floats without loss of precision. PEtab v2 condition
+  and measurement tables now write expressions in PEtab syntax
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/545)
+* `petab.v2.ProblemConfig.to_yaml` no longer writes empty optional entries
+  (`condition_files`, `experiment_files`, `mapping_files`, `extensions`)
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/547)
+* `to_df` no longer fails for empty v2 parameter, observable and measurement
+  tables
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/543)
+* `petab1to2` no longer writes condition tables without any
+  condition-specific changes
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/554)
+* `petab.v2.ConditionTable.from_df` no longer stores the condition ID on
+  each `Change`, which caused renamed conditions to be written with their
+  old ID
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/551)
+
+**Features**
+* `petab1to2` and `petab_files_1to2` can skip validation via `validate=False`
+  (by @FFroehlich in https://github.com/PEtab-dev/libpetab-python/pull/534)
+* Added `petab.v2.C.PROBLEM_CONFIG_REQUIRED_KEYS` and
+  `petab.v2.C.PROBLEM_CONFIG_OPTIONAL_KEYS`
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/547)
+* PEtab v2 tables can omit empty columns or columns at their default values
+  via `to_df(columns=...)`, `to_tsv(columns=...)` and
+  `Problem.to_files(columns=...)`, or globally via `petab.v2.set_options` and
+  `petab.v2.option_context`
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/543)
+
 ## 0.9 series
 
 ### 0.9.0

README.md

@@ -39,11 +39,11 @@ be:
     entrypoints to be available as a shell command from anywhere, called
     `petablint`
 
-  - [petab.create_parameter_df](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.parameters.html#petab.parameters.create_parameter_df)
+  - [petab.v1.create_parameter_df](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.v1.parameters.html#petab.v1.parameters.create_parameter_df)
     to create the parameter table, once you have set up the model,
     condition table, observable table and measurement table
 
-  - [petab.create_combine_archive](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.core.html#petab.core.create_combine_archive)
+  - [petab.v1.create_combine_archive](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.v1.core.html#petab.v1.core.create_combine_archive)
     to create a [COMBINE Archive](https://combinearchive.org/index/) from PEtab
     files
 

doc/example/example_visualization.ipynb

@@ -26,10 +26,10 @@
     "from pathlib import Path\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
-    "from petab.visualize import plot_problem\n",
     "\n",
-    "import petab\n",
-    "from petab import Problem\n",
+    "import petab.v1 as petab\n",
+    "from petab.v1 import Problem\n",
+    "from petab.v1.visualize import plot_problem\n",
     "\n",
     "example_dir_fujita = Path(\"example_Fujita\")\n",
     "petab_yaml_fujita = example_dir_fujita / \"Fujita.yaml\"\n",
@@ -62,7 +62,7 @@
    "source": [
     "### Plotting measurements\n",
     "\n",
-    "For the most basic visualization, we can use the [plot_problem()](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.visualize.html#petab.visualize.plot_problem) function."
+    "For the most basic visualization, we can use the [plot_problem()](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.v1.visualize.html#petab.v1.visualize.plot_problem) function."
    ]
   },
   {

doc/modules.rst

@@ -38,4 +38,5 @@ API Reference
    petab.v2.extensions
    petab.v2.lint
    petab.v2.models
+   petab.v2.options
    petab.v2.petab1to2

petab/__init__.py

@@ -10,72 +10,15 @@
 """
 
 import importlib
-import sys
-from functools import partial
-from pathlib import Path
-from warnings import warn
+
+from .version import __version__  # noqa: F401
 
 ENV_NUM_THREADS = "PETAB_NUM_THREADS"
 __all__ = ["ENV_NUM_THREADS"]
 
 
 def __getattr__(name):
-    if attr := globals().get(name):
-        return attr
-    if name == "v1":
-        return importlib.import_module("petab.v1")
-    if name == "v2":
-        return importlib.import_module("petab.v2")
-    if name not in (
-        "__path__",
-        "__all__",
-        "__wrapped__",
-        # accessed under pytest
-        "_pytestfixturefunction",
-        "__test__",
-        "__bases__",
-    ):
-        warn(
-            f"Accessing `petab.{name}` is deprecated and will be removed in "
-            f"the next major release. Please use `petab.v1.{name}` instead.",
-            DeprecationWarning,
-            stacklevel=3,
-        )
-    return getattr(importlib.import_module("petab.v1"), name)
-
-
-def _v1getattr(name, module):
-    if name not in ("__path__", "__all__", "__wrapped__"):
-        warn(
-            f"Accessing `petab.{name}` is deprecated and will be removed in "
-            f"the next major release. Please use `petab.v1.{name}` instead.",
-            DeprecationWarning,
-            stacklevel=3,
-        )
-    try:
-        return module.__dict__[name]
-    except KeyError:
-        raise AttributeError(name) from None
-
-
-# Create dummy modules for all old modules
-v1_root = Path(__file__).resolve().parent / "v1"
-v1_objects = [f.relative_to(v1_root) for f in v1_root.rglob("*")]
-for v1_object in v1_objects:
-    if "__pycache__" in str(v1_object):
-        continue
-    if v1_object.suffix not in ["", ".py"]:
-        continue
-    if not (v1_root / v1_object).exists():
-        raise ValueError(v1_root / v1_object)
-    v1_object_parts = [*v1_object.parts[:-1], v1_object.stem]
-    module_name = ".".join(["petab", *v1_object_parts])
-
-    try:
-        real_module = importlib.import_module(
-            f"petab.v1.{'.'.join(v1_object_parts)}"
-        )
-        real_module.__getattr__ = partial(_v1getattr, module=real_module)
-        sys.modules[module_name] = real_module
-    except ModuleNotFoundError:
-        pass
+    """Lazily import the `petab.v1` and `petab.v2` subpackages."""
+    if name in ("v1", "v2"):
+        return importlib.import_module(f"petab.{name}")
+    raise AttributeError(f"module 'petab' has no attribute '{name}'")

petab/v1/composite_problem.py

@@ -15,7 +15,7 @@ class CompositeProblem:
 
     Attributes:
         problems:
-            List of :py:class:`petab.Problem` s
+            List of :py:class:`petab.v1.Problem` s
         parameter_df:
             PEtab parameter DataFrame
     """

petab/v1/core.py

@@ -185,7 +185,7 @@ def get_hyperparameter_replacement_id(
 
 
 def get_flattened_id_mappings(
-    petab_problem: "petab.problem.Problem",
+    petab_problem: "petab.v1.problem.Problem",
 ) -> dict[str, dict[str, str]]:
     """Get mapping from unflattened to flattened observable IDs.
 
@@ -240,7 +240,7 @@ def get_flattened_id_mappings(
 
 
 def flatten_timepoint_specific_output_overrides(
-    petab_problem: "petab.problem.Problem",
+    petab_problem: "petab.v1.problem.Problem",
 ) -> None:
     """Flatten timepoint-specific output parameter overrides.
 
@@ -322,7 +322,7 @@ def flatten_timepoint_specific_output_overrides(
 
 def unflatten_simulation_df(
     simulation_df: pd.DataFrame,
-    petab_problem: "petab.problem.Problem",
+    petab_problem: "petab.v1.problem.Problem",
 ) -> pd.DataFrame:
     """Unflatten simulations from a flattened PEtab problem.
 

petab/v1/lint.py

@@ -1172,7 +1172,7 @@ def assert_measurements_numeric(
     )
     if not all_measurements_are_numeric:
         raise AssertionError(
-            "Some values in the `petab.C.MEASUREMENT` column of the PEtab "
+            "Some values in the `petab.v1.C.MEASUREMENT` column of the PEtab "
             "measurements table are not numeric."
         )
 

petab/v1/math/SympyVisitor.py

@@ -73,7 +73,7 @@ class MathVisitorSympy(PetabMathExprParserVisitor):
     Converts PEtab math expressions to sympy expressions.
 
     Most users will not need to interact with this class directly, but rather
-    use :func:`petab.math.sympify_petab`.
+    use :func:`petab.v1.math.sympify_petab`.
 
     Evaluation of any sub-expressions currently relies on sympy's defaults.