Test petab/develop

.github/workflows/test_benchmark_collection_models.yml

@@ -52,6 +52,10 @@ jobs:
         AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
+    - run: |
+        python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
+        &&  python3 -m pip install -U sympy
+
     # retrieve test models
     - name: Download and test benchmark collection
       run: |

.github/workflows/test_petab_test_suite.yml

@@ -58,7 +58,7 @@ jobs:
       - name: Install petab
         run: |
           source ./venv/bin/activate \
-            && pip3 install wheel pytest shyaml pytest-cov pysb
+            && pip3 install wheel pytest shyaml pytest-cov pysb>=1.16
 
       # retrieve test models
       - name: Download and install PEtab test suite
@@ -68,11 +68,18 @@ jobs:
             && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
+      - name: Install petab
+        run: |
+          source ./venv/bin/activate \
+            && python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
+            && python3 -m pip install sympy>=1.12.1
+
+
       - name: Run PEtab-related unit tests
         run: |
           source ./venv/bin/activate \
             && pytest --cov-report=xml:coverage.xml \
-              --cov=./ python/tests/test_*petab*.py python/tests/petab/
+              --cov=./ python/tests/test_*petab*.py python/tests/petab_/
 
       # run test models
       - name: Run PEtab test suite

documentation/python_installation.rst

@@ -360,16 +360,19 @@ environment variables:
 |                            | Default: ``ON``                  |                                 |
 +----------------------------+----------------------------------+---------------------------------+
 
-Installation under Anaconda
----------------------------
+Installation under conda
+------------------------
 
-To use an Anaconda installation of Python
-`https://www.anaconda.com/distribution/ <https://www.anaconda.com/distribution/>`_,
-Python>=3.7), proceed as follows:
+There is no amici conda recipe available yet. However, you can install AMICI
+using pip in a conda environment.
 
-Since Anaconda provides own versions of some packages which might not
-work with AMICI (in particular the ``gcc`` compiler), create a minimal
-virtual environment via:
+.. note::
+
+   It is possible, but we currently don't recommend using conda for installing
+   AMICI, as it commonly leads to conflicts with system installations of
+   libraries and compilers.
+
+Create a minimal conda environment via:
 
 .. code-block:: bash
 
@@ -415,7 +418,7 @@ Now, you are ready to use AMICI in the virtual environment.
 
 .. note::
 
-   **Anaconda on Mac**
+   **conda on Mac**
 
    If the above installation does not work for you, try installing AMICI via:
 
@@ -437,6 +440,9 @@ Now, you are ready to use AMICI in the virtual environment.
 
    (For further discussion see https://github.com/AMICI-dev/AMICI/issues/357)
 
+Known issues:
+
+* ``CMAKE_AR-NOTFOUND: not found``: Try ``conda install binutils``.
 
 Optional Boost support
 ----------------------

pytest.ini

@@ -3,6 +3,7 @@
 addopts = -vv --strict-markers
 
 filterwarnings =
+    # warnings are errors
     error
     # amici
     ignore:Conservation laws for non-constant species in models with RateRules are currently not supported and will be turned off.:UserWarning
@@ -13,7 +14,6 @@ filterwarnings =
     ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning
     # pysb warnings
     ignore:the imp module is deprecated in favour of importlib.*:DeprecationWarning:pysb\.core
-    ignore:Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working.*:DeprecationWarning:pysb\.core
     ignore:Model.initial_conditions will be removed in a future version. Instead, you can get a list of Initial objects with Model.initials.:DeprecationWarning:pysb\.core
     # https://github.com/pytest-dev/pytest-xdist/issues/825#issuecomment-1292283870
     ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning

python/sdist/amici/petab/cli/import_petab.py

@@ -3,7 +3,7 @@
 import petab
 
 from ..petab_import import import_model_sbml
-from petab.models.sbml_model import SbmlModel
+from petab.v1.models.sbml_model import SbmlModel
 
 
 def _parse_cli_args():

python/sdist/amici/petab/conditions.py

@@ -9,9 +9,9 @@
 import amici
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 from amici import AmiciModel
-from petab.C import (
+from petab.v1.C import (
     MEASUREMENT,
     NOISE_PARAMETERS,
     OBSERVABLE_ID,

python/sdist/amici/petab/import_helpers.py

@@ -11,9 +11,9 @@
 
 import amici
 import pandas as pd
-import petab
+import petab.v1 as petab
 import sympy as sp
-from petab.C import (
+from petab.v1.C import (
     CONDITION_NAME,
     ESTIMATE,
     NOISE_DISTRIBUTION,
@@ -22,7 +22,7 @@
     OBSERVABLE_NAME,
     OBSERVABLE_TRANSFORMATION,
 )
-from petab.parameters import get_valid_parameters_for_parameter_table
+from petab.v1.parameters import get_valid_parameters_for_parameter_table
 from sympy.abc import _clash
 
 logger = logging.getLogger(__name__)

python/sdist/amici/petab/parameter_mapping.py

@@ -27,17 +27,17 @@
 import amici
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 import sympy as sp
 from amici.sbml_import import get_species_initial
-from petab.C import *  # noqa: F403
-from petab.C import (
+from petab.v1.C import *  # noqa: F403
+from petab.v1.C import (
     LIN,
     PARAMETER_SCALE,
     PREEQUILIBRATION_CONDITION_ID,
     SIMULATION_CONDITION_ID,
 )
-from petab.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
+from petab.v1.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
 from sympy.abc import _clash
 
 from .. import AmiciModel

python/sdist/amici/petab/petab_import.py

@@ -12,8 +12,8 @@
 from warnings import warn
 
 import amici
-import petab
-from petab.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
+import petab.v1 as petab
+from petab.v1.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
 
 from ..logging import get_logger
 from .import_helpers import _can_import_model, _create_model_name, check_model

python/sdist/amici/petab/petab_problem.py

@@ -4,8 +4,8 @@
 
 import amici
 import pandas as pd
-import petab
-from petab.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID
+import petab.v1 as petab
+from petab.v1.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID
 
 from .conditions import create_edatas, fill_in_parameters
 from .parameter_mapping import create_parameter_mapping

python/sdist/amici/petab/pysb_import.py

@@ -9,12 +9,12 @@
 import re
 from pathlib import Path
 
-import petab
+import petab.v1 as petab
 import pysb
 import pysb.bng
 import sympy as sp
-from petab.C import CONDITION_NAME, NOISE_FORMULA, OBSERVABLE_FORMULA
-from petab.models.pysb_model import PySBModel
+from petab.v1.C import CONDITION_NAME, NOISE_FORMULA, OBSERVABLE_FORMULA
+from petab.v1.models.pysb_model import PySBModel
 
 from ..logging import get_logger, log_execution_time, set_log_level
 from . import PREEQ_INDICATOR_ID

python/sdist/amici/petab/sbml_import.py

@@ -8,11 +8,11 @@
 
 import amici
 import libsbml
-import petab
+import petab.v1 as petab
 import sympy as sp
 from _collections import OrderedDict
 from amici.logging import log_execution_time, set_log_level
-from petab.models import MODEL_TYPE_SBML
+from petab.v1.models import MODEL_TYPE_SBML
 from sympy.abc import _clash
 
 from . import PREEQ_INDICATOR_ID
@@ -90,7 +90,7 @@ def import_model_sbml(
     :return:
         The created :class:`amici.sbml_import.SbmlImporter` instance.
     """
-    from petab.models.sbml_model import SbmlModel
+    from petab.v1.models.sbml_model import SbmlModel
 
     set_log_level(logger, verbose)
 

python/sdist/amici/petab/simulations.py

@@ -12,8 +12,8 @@
 import amici
 import numpy as np
 import pandas as pd
-import petab
-from petab.C import *  # noqa: F403
+import petab.v1 as petab
+from petab.v1.C import *  # noqa: F403
 
 from .. import AmiciExpData, AmiciModel
 from ..logging import get_logger, log_execution_time

python/sdist/amici/petab/simulator.py

@@ -14,7 +14,7 @@
 from collections.abc import Callable
 
 import pandas as pd
-import petab
+import petab.v1 as petab
 from amici import AmiciModel, SensitivityMethod_none
 
 from .petab_import import import_petab_problem

python/sdist/amici/petab/util.py

@@ -5,10 +5,10 @@
 
 import libsbml
 import pandas as pd
-import petab
-from petab.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID
-from petab.mapping import resolve_mapping
-from petab.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
+import petab.v1 as petab
+from petab.v1.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID
+from petab.v1.mapping import resolve_mapping
+from petab.v1.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
 
 if TYPE_CHECKING:
     pysb = None

python/tests/test_petab_import.py

@@ -5,7 +5,7 @@
 import pytest
 from amici.testing import TemporaryDirectoryWinSafe, skip_on_valgrind
 
-petab = pytest.importorskip("petab", reason="Missing petab")
+petab = pytest.importorskip("petab.v1", reason="Missing petab")
 
 
 @pytest.fixture
@@ -76,7 +76,7 @@ def test_get_fixed_parameters(get_fixed_parameters_model):
     from amici.petab.sbml_import import (
         _get_fixed_parameters_sbml as get_fixed_parameters,
     )
-    from petab.models.sbml_model import SbmlModel
+    from petab.v1.models.sbml_model import SbmlModel
 
     sbml_doc, sbml_model = get_fixed_parameters_model
     condition_df = petab.get_condition_df(
@@ -117,7 +117,7 @@ def test_get_fixed_parameters(get_fixed_parameters_model):
 @skip_on_valgrind
 def test_default_output_parameters(simple_sbml_model):
     from amici.petab.petab_import import import_model
-    from petab.models.sbml_model import SbmlModel
+    from petab.v1.models.sbml_model import SbmlModel
 
     sbml_doc, sbml_model = simple_sbml_model
     condition_df = petab.get_condition_df(

python/tests/test_petab_objective.py

@@ -6,7 +6,7 @@
 import amici
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 import pytest
 from amici.petab.petab_import import import_petab_problem
 from amici.petab.simulations import SLLH, simulate_petab

python/tests/test_petab_simulate.py

@@ -3,7 +3,7 @@
 import tempfile
 from pathlib import Path
 
-import petab
+import petab.v1 as petab
 import petabtests
 import pytest
 from amici.petab.simulator import PetabSimulator

tests/benchmark-models/test_petab_model.py

@@ -15,7 +15,7 @@
 import amici
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 import yaml
 from amici.logging import get_logger
 from amici.petab.simulations import (
@@ -24,7 +24,7 @@
     rdatas_to_measurement_df,
     simulate_petab,
 )
-from petab.visualize import plot_problem
+from petab.v1.visualize import plot_problem
 
 logger = get_logger(f"amici.{__name__}", logging.WARNING)
 

tests/petab_test_suite/test_petab_suite.py

@@ -6,7 +6,7 @@
 
 import amici
 import pandas as pd
-import petab
+import petab.v1 as petab
 import petabtests
 import pytest
 from _pytest.outcomes import Skipped