Merge branch 'develop' into 330_truncated

Author: dweindl

doc/conf.py

@@ -47,6 +47,7 @@
 ]
 
 intersphinx_mapping = {
+    "petab": ("https://petab.readthedocs.io/en/latest/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
     "numpy": ("https://numpy.org/devdocs/", None),
     "sympy": ("https://docs.sympy.org/latest/", None),
@@ -62,6 +63,7 @@
 exclude_patterns = [
     "build/doctrees",
     "build/html",
+    "build/jupyter_execute",
     "**.ipynb_checkpoints",
     "logo/LICENSE.md",
 ]
@@ -71,10 +73,10 @@
 autosummary_generate = True
 
 autodoc_default_options = {
-    "members": None,
+    "members": True,
     "imported-members": ["petab"],
-    "inherited-members": None,
-    "show-inheritance": None,
+    "show-inheritance": True,
+    "undoc-members": True,
 }
 
 # For some reason causes sphinx import errors otherwise

doc/development.rst

@@ -24,3 +24,67 @@ Python compatibility
 --------------------
 
 We follow `numpy's Python support policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_.
+
+Release process
+---------------
+
+1. Update the version number in ``petab/version.py``.
+
+2. Update the changelog in ``doc/CHANGELOG.md``.
+   The update content can be generated automatically:
+   draft a new dummy GitHub release with a dummy tag and the ``develop``
+   branch, then click :guilabel:`Generate release notes`.
+
+3. Create a pull request with the to-be-released changes to the main branch
+   (usually from ``develop``).
+
+4. Once the pull request is merged, create a new release on GitHub.
+   Make sure to set the tag to the version number prefixed with 'v'
+   (e.g., ``v1.0.0``), and the release title to ``libpetab-python $RELEASE_TAG``
+   (e.g., ``libpetab-python v1.0.0``).
+
+5. Check that the release is now available on PyPI.
+   The upload to PyPI is performed automatically by a GitHub Actions workflow,
+   which may take a few minutes to complete.
+
+6. Merge the main branch back into the `develop` branch.
+
+Style guide
+-----------
+
+Code style
+~~~~~~~~~~
+
+We use pre-commit with ruff to enforce code style. To install pre-commit and
+the pre-commit hooks, run:
+
+.. code-block:: bash
+
+    pip install pre-commit
+    pre-commit install
+
+To run the pre-commit checks manually on all, not just the modified files, run:
+
+.. code-block:: bash
+
+    pre-commit run --all-files
+
+Documentation style
+~~~~~~~~~~~~~~~~~~~
+
+We use `Sphinx <https://www.sphinx-doc.org/>`_ to generate the documentation.
+The documentation is written in `reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_.
+
+We use the `sphinx docstring-style <https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html>`__ for new code.
+The ``:param [ParamName]:`` and ``:return:`` statements are important when
+applicable.
+Manual type annotations (``:type  [ParamName]:``) are redundant and should be
+avoided.
+
+To build the documentation, run:
+
+.. code-block:: bash
+
+    cd doc
+    make html
+    # then open `build/html/index.html` in a browser

doc/modules.rst

@@ -16,6 +16,7 @@ API Reference
    petab.v1.core
    petab.v1.distributions
    petab.v1.lint
+   petab.v1.math
    petab.v1.measurements
    petab.v1.models
    petab.v1.observables
@@ -31,6 +32,7 @@ API Reference
    petab.v1.yaml
    petab.v2
    petab.v2.C
+   petab.v2.core
    petab.v2.experiments
    petab.v2.lint
    petab.v2.models

petab/v1/lint.py

@@ -53,6 +53,9 @@
     "observable_table_has_nontrivial_noise_formula",
 ]
 
+#: Regular expression pattern for valid PEtab IDs
+_petab_id_pattern = re.compile(r"^[a-zA-Z_]\w*$")
+
 
 def _check_df(df: pd.DataFrame, req_cols: Iterable, name: str) -> None:
     """Check if given columns are present in DataFrame
@@ -903,21 +906,6 @@ def lint_problem(problem: "petab.Problem") -> bool:
     else:
         logger.warning("Model not available. Skipping.")
 
-    if problem.measurement_df is not None:
-        logger.info("Checking measurement table...")
-        try:
-            check_measurement_df(problem.measurement_df, problem.observable_df)
-
-            if problem.condition_df is not None:
-                assert_measurement_conditions_present_in_condition_table(
-                    problem.measurement_df, problem.condition_df
-                )
-        except AssertionError as e:
-            logger.error(e)
-            errors_occurred = True
-    else:
-        logger.warning("Measurement table not available. Skipping.")
-
     if problem.condition_df is not None:
         logger.info("Checking condition table...")
         try:
@@ -950,6 +938,21 @@ def lint_problem(problem: "petab.Problem") -> bool:
     else:
         logger.warning("Observable table not available. Skipping.")
 
+    if problem.measurement_df is not None:
+        logger.info("Checking measurement table...")
+        try:
+            check_measurement_df(problem.measurement_df, problem.observable_df)
+
+            if problem.condition_df is not None:
+                assert_measurement_conditions_present_in_condition_table(
+                    problem.measurement_df, problem.condition_df
+                )
+        except AssertionError as e:
+            logger.error(e)
+            errors_occurred = True
+    else:
+        logger.warning("Measurement table not available. Skipping.")
+
     if problem.parameter_df is not None:
         logger.info("Checking parameter table...")
         try:
@@ -1041,10 +1044,13 @@ def assert_model_parameters_in_condition_or_parameter_table(
                 mapping_df[MODEL_ENTITY_ID],
                 strict=True,
             )
-            # mapping table entities mapping to already allowed parameters
-            if to_id in allowed_in_condition_cols
-            # mapping table entities mapping to species
-            or model.is_state_variable(to_id)
+            if not pd.isna(to_id)
+            and (
+                # mapping table entities mapping to already allowed parameters
+                to_id in allowed_in_condition_cols
+                # mapping table entities mapping to species
+                or model.is_state_variable(to_id)
+            )
         }
 
     allowed_in_parameter_table = (
@@ -1186,7 +1192,7 @@ def is_valid_identifier(x: str) -> bool:
     if pd.isna(x):
         return False
 
-    return re.match(r"^[a-zA-Z_]\w*$", x) is not None
+    return _petab_id_pattern.match(x) is not None
 
 
 def check_ids(ids: Iterable[str], kind: str = "") -> None:

petab/v1/math/SympyVisitor.py

@@ -39,8 +39,12 @@
 }
 _unary_funcs = {
     "exp": sp.exp,
-    "log10": lambda x: -sp.oo if x.is_zero is True else sp.log(x, 10),
-    "log2": lambda x: -sp.oo if x.is_zero is True else sp.log(x, 2),
+    "log10": lambda x, evaluate=True: -sp.oo
+    if x.is_zero is True
+    else sp.log(x, 10, evaluate=evaluate),
+    "log2": lambda x, evaluate=True: -sp.oo
+    if x.is_zero is True
+    else sp.log(x, 2, evaluate=evaluate),
     "ln": sp.log,
     "sqrt": sp.sqrt,
     "abs": sp.Abs,
@@ -75,8 +79,14 @@ class MathVisitorSympy(PetabMathExprParserVisitor):
 
     For a general introduction to ANTLR4 visitors, see:
     https://github.com/antlr/antlr4/blob/7d4cea92bc3f7d709f09c3f1ac77c5bbc71a6749/doc/python-target.md
+
+    :param evaluate: Whether to evaluate the expression.
     """
 
+    def __init__(self, evaluate=True):
+        super().__init__()
+        self.evaluate = evaluate
+
     def visitPetabExpression(
         self, ctx: PetabMathExprParser.PetabExpressionContext
     ) -> sp.Expr | sp.Basic:
@@ -101,9 +111,17 @@ def visitMultExpr(
             operand1 = bool2num(self.visit(ctx.getChild(0)))
             operand2 = bool2num(self.visit(ctx.getChild(2)))
             if ctx.ASTERISK():
-                return operand1 * operand2
+                return sp.Mul(operand1, operand2, evaluate=self.evaluate)
             if ctx.SLASH():
-                return operand1 / operand2
+                return (
+                    operand1 / operand2
+                    if self.evaluate
+                    else sp.Mul(
+                        operand1,
+                        sp.Pow(operand2, -1, evaluate=False),
+                        evaluate=False,
+                    )
+                )
 
         raise AssertionError(f"Unexpected expression: {ctx.getText()}")
 
@@ -112,9 +130,9 @@ def visitAddExpr(self, ctx: PetabMathExprParser.AddExprContext) -> sp.Expr:
         op1 = bool2num(self.visit(ctx.getChild(0)))
         op2 = bool2num(self.visit(ctx.getChild(2)))
         if ctx.PLUS():
-            return op1 + op2
+            return sp.Add(op1, op2, evaluate=self.evaluate)
         if ctx.MINUS():
-            return op1 - op2
+            return sp.Add(op1, -op2, evaluate=self.evaluate)
 
         raise AssertionError(
             f"Unexpected operator: {ctx.getChild(1).getText()} "
@@ -146,28 +164,32 @@ def visitFunctionCall(
                     f"Unexpected number of arguments: {len(args)} "
                     f"in {ctx.getText()}"
                 )
-            return _trig_funcs[func_name](*args)
+            return _trig_funcs[func_name](*args, evaluate=self.evaluate)
         if func_name in _unary_funcs:
             if len(args) != 1:
                 raise AssertionError(
                     f"Unexpected number of arguments: {len(args)} "
                     f"in {ctx.getText()}"
                 )
-            return _unary_funcs[func_name](*args)
+            return _unary_funcs[func_name](*args, evaluate=self.evaluate)
         if func_name in _binary_funcs:
             if len(args) != 2:
                 raise AssertionError(
                     f"Unexpected number of arguments: {len(args)} "
                     f"in {ctx.getText()}"
                 )
-            return _binary_funcs[func_name](*args)
+            return _binary_funcs[func_name](*args, evaluate=self.evaluate)
         if func_name == "log":
             if len(args) not in [1, 2]:
                 raise AssertionError(
                     f"Unexpected number of arguments: {len(args)} "
                     f"in {ctx.getText()}"
                 )
-            return -sp.oo if args[0].is_zero is True else sp.log(*args)
+            return (
+                -sp.oo
+                if args[0].is_zero is True
+                else sp.log(*args, evaluate=self.evaluate)
+            )
 
         if func_name == "piecewise":
             if (len(args) - 1) % 2 != 0:
@@ -184,7 +206,7 @@ def visitFunctionCall(
                     args[::2], args[1::2], strict=True
                 )
             )
-            return sp.Piecewise(*sp_args)
+            return sp.Piecewise(*sp_args, evaluate=self.evaluate)
 
         raise ValueError(f"Unknown function: {ctx.getText()}")
 
@@ -203,7 +225,7 @@ def visitPowerExpr(
             )
         operand1 = bool2num(self.visit(ctx.getChild(0)))
         operand2 = bool2num(self.visit(ctx.getChild(2)))
-        return sp.Pow(operand1, operand2)
+        return sp.Pow(operand1, operand2, evaluate=self.evaluate)
 
     def visitUnaryExpr(
         self, ctx: PetabMathExprParser.UnaryExprContext
@@ -240,7 +262,7 @@ def visitComparisonExpr(
         if op in ops:
             lhs = bool2num(lhs)
             rhs = bool2num(rhs)
-            return ops[op](lhs, rhs)
+            return ops[op](lhs, rhs, evaluate=self.evaluate)
 
         raise AssertionError(f"Unexpected operator: {op}")
 
@@ -301,4 +323,6 @@ def num2bool(x: sp.Basic | sp.Expr) -> sp.Basic | sp.Expr:
         return sp.false
     if x.is_zero is False:
         return sp.true
+    if isinstance(x, Boolean):
+        return x
     return sp.Piecewise((True, x != 0.0), (False, True))

petab/v1/math/__init__.py

@@ -1,3 +1,4 @@
 """Functions for parsing and evaluating mathematical expressions."""
 
+from .printer import PetabStrPrinter, petab_math_str  # noqa: F401
 from .sympify import sympify_petab  # noqa: F401