Merge pull request #1870 from AMICI-dev/release_0.13.0

Release 0.13.0

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -8,9 +8,9 @@ on:
   pull_request:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml
-      - python/amici/ode_export.py
-      - python/amici/sbml_import.py
-      - python/amici/import_utils.py
+      - python/sdist/amici/ode_export.py
+      - python/sdist/amici/sbml_import.py
+      - python/sdist/amici/import_utils.py
       - scripts/run-SBMLTestsuite.sh
       - tests/testSBMLSuite.py
       - tests/conftest.py

.github/workflows/test_valgrind.yml

@@ -1,4 +1,4 @@
-name: C++ Tests
+name: Valgrind tests
 on:
   push:
     branches:
@@ -12,15 +12,15 @@ on:
     - cron:  '48 4 * * *'
 
 jobs:
-  valgrind:
-    name: Tests Valgrind
+  valgrind_cpp:
+    name: Valgrind C++
 
     # TODO: prepare image with more deps preinstalled
     runs-on: ubuntu-22.04
 
     strategy:
       matrix:
-        python-version: [ "3.8" ]
+        python-version: [ "3.9" ]
 
     env:
       ENABLE_AMICI_DEBUGGING: "TRUE"
@@ -57,6 +57,46 @@ jobs:
       run: |
         scripts/run-valgrind-cpp.sh
 
+  valgrind_python:
+    name: Valgrind Python
+
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [ "3.9" ]
+
+    env:
+      ENABLE_AMICI_DEBUGGING: "TRUE"
+
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    # install amici dependencies
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            g++ \
+            libatlas-base-dev \
+            libboost-serialization-dev \
+            libhdf5-serial-dev \
+            python3-venv \
+            swig \
+            valgrind \
+            libboost-math-dev
+
+    - name: Build AMICI
+      run: |
+        scripts/buildAll.sh
+
     - name: Install python package
       run: |
         scripts/installAmiciSource.sh

CHANGELOG.md

@@ -2,6 +2,18 @@
 
 ## v0.X Series
 
+### v0.13.0 (2022-10-04)
+
+* Fixed extraction of common subexpressions
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1865
+* Added function to convert `ReturnData::status` flags to string
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1864
+
+And further contributions by @dweindl, @FFroehlich
+
+**Full Changelog**:
+https://github.com/AMICI-dev/AMICI/compare/v0.12.0...v0.13.0
+
 ### v0.12.0 (2022-08-26)
 
 Features:
@@ -14,6 +26,7 @@ Features:
 * Option to extract common subexpressions
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1852,
   https://github.com/AMICI-dev/AMICI/pull/1856
+  **not available in this release, use v0.13.0**
 * Parallelize matrix simplification
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1778
 * Validate PEtab problems before attempting import
@@ -32,7 +45,7 @@ Fixes:
 And further contributions by @dilpath, @dweindl, @FFroehlich
 
 **Full Changelog**:
-https://github.com/AMICI-dev/AMICI/compare/v0.11.32...v0.11.33
+https://github.com/AMICI-dev/AMICI/compare/v0.11.32...v0.12.0
 
 ### v0.11.32 (2022-07-15)
 

include/amici/amici.h

@@ -132,6 +132,15 @@ std::vector<std::unique_ptr<ReturnData>>
 runAmiciSimulations(Solver const &solver, const std::vector<ExpData *> &edatas,
                     Model const &model, bool failfast, int num_threads);
 
+
+/**
+ * @brief Get the string representation of the given simulation status code
+ * (see ReturnData::status).
+ * @param return_code
+ * @return Name of the variable representing this status code.
+ */
+std::string simulation_status_to_str(int status);
+
 } // namespace amici
 
 #endif /* amici_h */

include/amici/defines.h

@@ -60,7 +60,10 @@ constexpr double pi = M_PI;
 
 constexpr int AMICI_ONEOUTPUT=                 5;
 
-/* Return codes */
+// Return codes
+//
+// NOTE: When adding / removing / renaming return codes,
+//       please update simulation_status_to_str_map in amici.h
 constexpr int AMICI_RECOVERABLE_ERROR=         1;
 constexpr int AMICI_UNRECOVERABLE_ERROR=     -10;
 constexpr int AMICI_TOO_MUCH_WORK=            -1;

pytest.ini

@@ -1,6 +1,6 @@
 [pytest]
 
-addopts = -vv
+addopts = -vv --strict-markers
 
 filterwarnings =
     # hundreds of SBML <=5.17 warnings