Merge branch 'develop' into fix_1422

documentation/python_interface.rst

@@ -31,10 +31,25 @@ the semantic
 `SBML Test Suite <https:/sbmlteam/sbml-test-suite/>`_
 (`current status <https:/AMICI-dev/AMICI/actions>`_).
 
-The following SBML test tags are supported
+The following SBML test suite tags are currently supported
 (i.e., at least one test case with the respective test passes;
 `tag descriptions <https:/sbmlteam/sbml-test-suite/blob/master/docs/tags-documentation/all-tags.txt>`_):
 
+**Component tags:**
+
+* AssignmentRule
+* Compartment
+* CSymbolAvogadro
+* CSymbolTime
+* FunctionDefinition
+* InitialAssignment
+* Parameter
+* RateRule
+* Reaction
+* Species
+
+**Test tags:**
+
 * 0D-Compartment
 * Amount
 * AssignedConstantStoichiometry
@@ -66,8 +81,6 @@ for details and progress):
 - Events (currently Matlab-only) (`#757 <https:/AMICI-dev/AMICI/issues/757>`_)
 - Algebraic rules (`#760 <https:/AMICI-dev/AMICI/issues/760>`_)
 
-contributions are welcome.
-
 However, the following features are unlikely to be supported:
 
 - any SBML extensions
@@ -105,7 +118,7 @@ Importing plain ODEs
 
 The AMICI Python interface does not currently support direct import of ODEs.
 However, it is straightforward to encode them as RateRules in an SBML model.
-The `yaml2sbml <https:/martamatos/yaml2sbml>`_ package may come in
+The `yaml2sbml <https:/yaml2sbml-dev/yaml2sbml>`_ package may come in
 handy, as it facilitates generating SBML models from a YAML-based specification
 of an ODE model. Besides the SBML model it can also create
 `PEtab <https:/PEtab-dev/PEtab>`_ files.
@@ -140,21 +153,27 @@ OpenMP support for parallelized simulation for multiple experimental conditions
 AMICI can be built with OpenMP support, which allows to parallelize model
 simulations for multiple experimental conditions.
 
-On Linux and OSX this is enabled by default. This can be verified using::
+On Linux and OSX this is enabled by default. This can be verified using:
 
- import amici
- amici.compiledWithOpenMP()
+.. code-block:: python
+
+ import amici
+ amici.compiledWithOpenMP()
 
 If not already enabled by default, you can enable OpenMP support by setting
 the environment variables ``AMICI_CXXFLAGS`` and ``AMICI_LDFLAGS`` to the
 correct OpenMP flags of your compiler and linker, respectively. This has to be
 done for both AMICI package installation *and* model compilation. When using
-``gcc`` on Linux, this would be::
+``gcc`` on Linux, this would be:
+
+.. code-block:: bash
+
+ # on your shell:
+ AMICI_CXXFLAGS=-fopenmp AMICI_LDFLAGS=-fopenmp pip3 install amici
 
- # on your shell:
- AMICI_CXXFLAGS=-fopenmp AMICI_LDFLAGS=-fopenmp pip3 install amici
+.. code-block:: python
 
-  # in python, before model compilation:
-  import os
-  os.environ['AMICI_CXXFLAGS'] = '-fopenmp'
-  os.environ['AMICI_LDFLAGS'] = '-fopenmp'
+ # in python, before model compilation:
+ import os
+ os.environ['AMICI_CXXFLAGS'] = '-fopenmp'
+ os.environ['AMICI_LDFLAGS'] = '-fopenmp'

tests/conftest.py

@@ -75,13 +75,21 @@ def pytest_sessionfinish(session, exitstatus):
 
 def write_passed_tags(passed_ids, out=sys.stdout):
  """Write tags of passed SBML semantic test cases"""
- passed_tags = set()
+ passed_component_tags = set()
+ passed_test_tags = set()
+
  from testSBMLSuite import get_tags_for_test
  for test_id in passed_ids:
- passed_tags |= get_tags_for_test(test_id)
-
- out.write("At least one test with the following tags has passed:\n")
- out.write(' ' + '\n '.join(passed_tags))
+ cur_component_tags, cur_test_tags = get_tags_for_test(test_id)
+ passed_component_tags |= cur_component_tags
+ passed_test_tags |= cur_test_tags
+
+ out.write("\nAt least one test with the following component tags has "
+ "passed:\n")
+ out.write(' ' + '\n '.join(sorted(passed_component_tags)))
+ out.write("\n\nAt least one test with the following test tags has "
+ "passed:\n")
+ out.write(' ' + '\n '.join(sorted(passed_test_tags)))
 
 
 def pytest_runtest_logreport(report: "TestReport") -> None:

tests/testSBMLSuite.py

@@ -19,6 +19,7 @@
 import re
 import shutil
 import sys
+from typing import Tuple, Set
 
 import amici
 import libsbml as sbml
@@ -307,16 +308,28 @@ def format_test_id(test_id) -> str:
  return test_str
 
 
-def get_tags_for_test(test_id):
- """Get sbml test suite tags for the given test ID"""
+def get_tags_for_test(test_id) -> Tuple[Set[str], Set[str]]:
+ """Get sbml test suite tags for the given test ID
+
+ Returns:
+ Tuple of set of strings for componentTags and testTags
+ """
 
  current_test_path = os.path.join(TEST_PATH, test_id)
  info_file = os.path.join(current_test_path, f'{test_id}-model.m')
  with open(info_file) as f:
+ component_tags = set()
+ test_tags = set()
  for line in f:
  if line.startswith('testTags:'):
- res = set(re.split(r'[ ,:]', line[len('testTags:'):].strip()))
- res.discard('')
- return res
- print(f"No testTags found for test case {test_id}.")
- return set()
+ test_tags = set(
+ re.split(r'[ ,:]', line[len('testTags:'):].strip()))
+ test_tags.discard('')
+ if line.startswith('componentTags:'):
+ component_tags = set(
+ re.split(r'[ ,:]', line[len('componentTags:'):].strip()))
+ component_tags.discard('')
+ if test_tags and component_tags:
+ return component_tags, test_tags
+ print(f"No componentTags or testTags found for test case {test_id}.")
+ return component_tags, test_tags