Merge pull request #2077 from AMICI-dev/release_0.17.1

Release 0.17.1

Author: dweindl

.github/workflows/test_install.yml

@@ -50,8 +50,8 @@ jobs:
       run: |
         scripts/installAmiciArchive.sh
 
-  sdist:
-    name: sdist Install
+  sdist_ubuntu:
+    name: sdist Install Ubuntu
 
     runs-on: ubuntu-22.04
 
@@ -92,3 +92,45 @@ jobs:
     - name: Test import
       run: |
         python -m amici
+
+
+  sdist_macos:
+    name: sdist Install macos
+
+    runs-on: macos-latest
+
+    strategy:
+      matrix:
+        python-version: [3.9]
+
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+
+    # install amici dependencies
+    - name: homebrew
+      run: |
+        brew install hdf5 swig gcc cppcheck libomp boost \
+          && brew ls -v boost \
+          && brew ls -v libomp \
+          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.81.0_1/lib/" >> $GITHUB_ENV \
+          && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV
+
+    - name: Create AMICI sdist
+      run: |
+        scripts/buildSdist.sh
+
+    - name: Install python sdist
+      run: |
+        pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
+
+    - name: Test import
+      run: |
+        python -m amici

CHANGELOG.md

@@ -2,6 +2,15 @@
 
 ## v0.X Series
 
+### v0.17.1 (2023-05-10)
+
+This release fixes two bugs:
+
+* One bug introduced in v0.17.0, that causes an `ImportError`
+  on macOS (https://github.com/AMICI-dev/AMICI/issues/2075).
+* An AttributeError in petab_import_pysb with petab>=0.2.0
+  https://github.com/AMICI-dev/AMICI/pull/2079
+
 ### v0.17.0 (2023-05-09)
 
 AMICI v0.17.0 requires Python>=3.9 and a C++17 compatible compiler

ThirdParty/sundials/cmake/tpl/FindKLU.cmake

@@ -35,7 +35,9 @@ if(WIN32)
   set(CMAKE_FIND_LIBRARY_PREFIXES lib ${CMAKE_FIND_LIBRARY_PREFIXES})
   set(CMAKE_FIND_LIBRARY_SUFFIXES d.lib ${CMAKE_FIND_LIBRARY_SUFFIXES})
 elseif(APPLE)
-  set(CMAKE_FIND_LIBRARY_SUFFIXES d.a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+    # AMICI
+    # set(CMAKE_FIND_LIBRARY_SUFFIXES d.a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+    set(CMAKE_FIND_LIBRARY_SUFFIXES .a d.a ${CMAKE_FIND_LIBRARY_SUFFIXES})
 else()
   set(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
 endif()

python/sdist/amici/petab_import_pysb.py

@@ -9,16 +9,16 @@
 import os
 from itertools import chain
 from pathlib import Path
-from typing import Dict, Iterable, Optional, Tuple, Union
+from typing import Dict, Iterable, Optional, Union
 
-import libsbml
 import petab
 import pysb
 import sympy as sp
 from petab.C import (CONDITION_FILES, CONDITION_NAME, FORMAT_VERSION,
                      MEASUREMENT_FILES, NOISE_FORMULA, OBSERVABLE_FILES,
                      OBSERVABLE_FORMULA, PARAMETER_FILE, SBML_FILES,
                      VISUALIZATION_FILES)
+from petab.models.sbml_model import SbmlModel
 
 from .logging import get_logger, log_execution_time, set_log_level
 
@@ -56,7 +56,7 @@ def __init__(self, pysb_model: 'pysb.Model' = None, *args, **kwargs):
         self._add_observation_model()
 
         if self.pysb_model is not None:
-            self.sbml_document, self.sbml_model = \
+            self.model = \
                 create_dummy_sbml(
                     self.pysb_model,
                     observable_ids=self.observable_df.index.values
@@ -252,17 +252,16 @@ def from_yaml(yaml_config: Union[Dict, Path, str],
 def create_dummy_sbml(
         pysb_model: 'pysb.Model',
         observable_ids: Optional[Iterable[str]] = None
-) -> Tuple['libsbml.Model', 'libsbml.SBMLDocument']:
+) -> SbmlModel:
     """Create SBML dummy model for to use PySB models with PEtab.
 
     Model must at least contain PEtab problem parameter and noise parameters
     for observables.
 
     :param pysb_model: PySB model
     :param observable_ids: Observable IDs
-    :return: A dummy SBML model and document.
+    :return: A dummy petab SBML model.
     """
-
     import libsbml
 
     document = libsbml.SBMLDocument(3, 1)
@@ -305,7 +304,7 @@ def create_dummy_sbml(
         s.setCompartment('dummy_compartment')
         s.setConstant(False)
 
-    return document, dummy_sbml_model
+    return SbmlModel(sbml_model=dummy_sbml_model, sbml_document=document)
 
 
 @log_execution_time('Importing PEtab model', logger)

python/sdist/setup.cfg

@@ -44,7 +44,7 @@ include_package_data = True
 zip_safe = False
 
 [options.extras_require]
-petab = petab>=0.1.27
+petab = petab>=0.2.0
 pysb = pysb>=1.13.1
 test =
     pytest

version.txt

@@ -1 +1 @@
-0.17.0
+0.17.1