Merge branch 'develop' into ExpData_clear_observations

.github/actions/install-macos-dependencies/action.yml

@@ -0,0 +1,31 @@
+name: Install AMICI dependencies for MacOS
+description: Install AMICI dependencies for MacOS
+
+runs:
+  using: "composite"
+  steps:
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # AMICI repository root
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+      shell: bash
+
+    # BioNetGen path
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # CMake hints
+    # Ensure CMake is using the python version that we will use for the python tests later on
+    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+      shell: bash
+
+    # install amici dependencies
+    - name: homebrew
+      run: brew install hdf5 swig gcc libomp boost
+      shell: bash

.github/workflows/test_python_cplusplus.yml

@@ -218,8 +218,8 @@ jobs:
 
     # TODO: Include notebooks in coverage report
 
-  osx:
-    name: Tests OSX
+  macos_cpp_py:
+    name: Tests MacOS C++/Python
     runs-on: macos-latest
 
     steps:
@@ -231,16 +231,11 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
-    # Ensure CMake is using the python version that we will use for the python tests later on
-    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
-    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
-    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
 
-    # install amici dependencies
     - name: homebrew
-      run: brew install hdf5 swig gcc cppcheck libomp boost
+      run: brew install cppcheck
 
     - name: Build AMICI
       run: scripts/buildAll.sh
@@ -254,8 +249,47 @@ jobs:
     - name: cppcheck
       run: scripts/run-cppcheck.sh
 
-    - name: Python tests
-      run: scripts/run-python-tests.sh
-
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          test_pregenerated_models.py \
+          test_splines_short.py \
+          test_misc.py
+
+
+  macos_python:
+    name: Tests MacOS Python
+    runs-on: macos-latest
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
+
+    - name: Install python package
+      run: |
+        pip show numpy > /dev/null || python3 -m pip install numpy
+        scripts/installAmiciSource.sh
+
+    - name: Check OpenMP support
+      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+
+    - name: Get BioNetGen
+      run: scripts/buildBNGL.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          --ignore=test_pregenerated_models.py \
+          --ignore=test_splines_short.py \
+          --ignore=test_misc.py

.pre-commit-config.yaml

@@ -1,12 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -16,15 +10,21 @@ repos:
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-    - id: black-jupyter
-      # It is recommended to specify the latest version of Python
-      # supported by your project here, or alternatively use
-      # pre-commit's default_language_version, see
-      # https://pre-commit.com/#top_level-default_language_version
-      language_version: python3.11
-      args: ["--line-length", "79"]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - python/sdist/pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - python/sdist/pyproject.toml
 
 exclude: '^(ThirdParty|models)/'

documentation/conf.py

@@ -5,7 +5,6 @@
 # This file does only contain a selection of the most common options. For a
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/stable/config
-
 import os
 import re
 import subprocess
@@ -18,6 +17,7 @@
 import exhale_multiproject_monkeypatch
 import mock
 import pandas as pd
+import sphinx
 import sympy as sp
 from exhale import configs as exhale_configs
 from sphinx.transforms.post_transforms import ReferencesResolver

include/amici/edata.h

@@ -14,24 +14,24 @@ class ReturnData;
 
 /**
  * @brief ExpData carries all information about experimental or
- * condition-specific data
+ * condition-specific data.
  */
 class ExpData : public SimulationParameters {
 
   public:
     /**
-     * @brief default constructor
+     * @brief Default constructor.
      */
     ExpData() = default;
 
     /**
-     * @brief Copy constructor, needs to be declared to be generated in
-     * swig
+     * @brief Copy constructor.
      */
+    // needs to be declared to be wrapped by SWIG
     ExpData(ExpData const&) = default;
 
     /**
-     * @brief constructor that only initializes dimensions
+     * @brief Constructor that only initializes dimensions.
      *
      * @param nytrue Number of observables
      * @param nztrue Number of event outputs
@@ -154,6 +154,16 @@ class ExpData : public SimulationParameters {
     /**
      * @brief Set output timepoints.
      *
+     * If the number of timepoint increases, this will grow the
+     * observation/sigma matrices and fill new entries with NaN.
+     * If the number of timepoints decreases, this will shrink the
+     * observation/sigma matrices.
+     *
+     * Note that the mapping from timepoints to measurements will not be
+     * preserved. E.g., say there are measurements at t = 2, and this
+     * function is called with [1, 2], then the old measurements will belong to
+     * t = 1.
+     *
      * @param ts timepoints
      */
     void setTimepoints(std::vector<realtype> const& ts);
@@ -225,7 +235,7 @@ class ExpData : public SimulationParameters {
     void setObservedDataStdDev(std::vector<realtype> const& observedDataStdDev);
 
     /**
-     * @brief Set indentical standard deviation for all measurements.
+     * @brief Set identical standard deviation for all measurements.
      *
      * @param stdDev standard deviation (dimension: scalar)
      */
@@ -278,26 +288,23 @@ class ExpData : public SimulationParameters {
     realtype const* getObservedDataStdDevPtr(int it) const;
 
     /**
-     * @brief set function that copies observed event data from input to
-     * ExpData::observedEvents
+     * @brief Set observed event data.
      *
      * @param observedEvents observed data (dimension: nmaxevent x nztrue,
      * row-major)
      */
     void setObservedEvents(std::vector<realtype> const& observedEvents);
 
     /**
-     * @brief set function that copies observed event data for specific event
-     * observable
+     * @brief Set observed event data for specific event observable.
      *
      * @param observedEvents observed data (dimension: nmaxevent)
      * @param iz observed event data index
      */
     void setObservedEvents(std::vector<realtype> const& observedEvents, int iz);
 
     /**
-     * @brief get function that checks whether event data at specified indices
-     * has been set
+     * @brief Check whether event data at specified indices has been set.
      *
      * @param ie event index
      * @param iz event observable index
@@ -306,42 +313,38 @@ class ExpData : public SimulationParameters {
     bool isSetObservedEvents(int ie, int iz) const;
 
     /**
-     * @brief get function that copies data from ExpData::mz to output
+     * @brief Get observed event data.
      *
      * @return observed event data
      */
     std::vector<realtype> const& getObservedEvents() const;
 
     /**
-     * @brief get function that returns a pointer to observed data at ieth
-     * occurrence
+     * @brief Get pointer to observed data at ie-th occurrence.
      *
      * @param ie event occurrence
      *
-     * @return pointer to observed event data at ieth occurrence
+     * @return pointer to observed event data at ie-th occurrence
      */
     realtype const* getObservedEventsPtr(int ie) const;
 
     /**
-     * @brief set function that copies data from input to
-     * ExpData::observedEventsStdDev
+     * @brief Set standard deviation of observed event data.
      *
      * @param observedEventsStdDev standard deviation of observed event data
      */
     void
     setObservedEventsStdDev(std::vector<realtype> const& observedEventsStdDev);
 
     /**
-     * @brief set function that sets all ExpData::observedDataStdDev to the
-     * input value
+     * @brief Set standard deviation of observed event data.
      *
      * @param stdDev standard deviation (dimension: scalar)
      */
     void setObservedEventsStdDev(realtype stdDev);
 
     /**
-     * @brief set function that copies standard deviation of observed data for
-     * specific observable
+     * @brief Set standard deviation of observed data for a specific observable.
      *
      * @param observedEventsStdDev standard deviation of observed data
      * (dimension: nmaxevent)
@@ -352,17 +355,16 @@ class ExpData : public SimulationParameters {
     );
 
     /**
-     * @brief set function that sets all standard deviation of a specific
-     * observable to the input value
+     * @brief Set all standard deviations of a specific event-observable.
      *
      * @param stdDev standard deviation (dimension: scalar)
      * @param iz observed data index
      */
     void setObservedEventsStdDev(realtype stdDev, int iz);
 
     /**
-     * @brief get function that checks whether standard deviation of even data
-     * at specified indices has been set
+     * @brief Check whether standard deviation of event data
+     * at specified indices has been set.
      *
      * @param ie event index
      * @param iz event observable index
@@ -371,16 +373,15 @@ class ExpData : public SimulationParameters {
     bool isSetObservedEventsStdDev(int ie, int iz) const;
 
     /**
-     * @brief get function that copies data from ExpData::observedEventsStdDev
-     * to output
+     * @brief Get standard deviation of observed event data.
      *
      * @return standard deviation of observed event data
      */
     std::vector<realtype> const& getObservedEventsStdDev() const;
 
     /**
-     * @brief get function that returns a pointer to standard deviation of
-     * observed event data at ie-th occurrence
+     * @brief Get pointer to standard deviation of
+     * observed event data at ie-th occurrence.
      *
      * @param ie event occurrence
      *

include/amici/logging.h

@@ -83,7 +83,7 @@ struct LogItem {
         , message(message){};
 
     /** Severity level */
-    LogSeverity severity;
+    LogSeverity severity = LogSeverity::error;
 
     /** Short identifier for the logged event */
     std::string identifier;

include/amici/model.h

@@ -1437,7 +1437,7 @@ class Model : public AbstractModel, public ModelDimensions {
     std::vector<int> const& getReinitializationStateIdxs() const;
 
     /** Flag indicating Matlab- or Python-based model generation */
-    bool pythonGenerated;
+    bool pythonGenerated = false;
 
     /**
      * @brief getter for dxdotdp (matlab generated)
@@ -2020,7 +2020,11 @@ class Model : public AbstractModel, public ModelDimensions {
      * Indicates whether the result of every call to `Model::f*` should be
      * checked for finiteness
      */
+#ifdef NDEBUG
     bool always_check_finite_{false};
+#else
+    bool always_check_finite_{true};
+#endif
 
     /** indicates whether sigma residuals are to be added for every datapoint */
     bool sigma_res_{false};

include/amici/simulation_parameters.h

@@ -35,6 +35,11 @@ class SimulationParameters {
               this->parameters.size(), ParameterScaling::none
           )) {}
 
+#ifndef SWIGPYTHON
+    /*
+     * include/amici/simulation_parameters.h:71: Warning 509: Overloaded method amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >) effectively ignored,
+     * include/amici/simulation_parameters.h:54: Warning 509: as it is shadowed by amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< int,std::allocator< int > >).
+     */
     /**
      * @brief Constructor
      * @param fixedParameters Model constants
@@ -69,6 +74,7 @@ class SimulationParameters {
               this->parameters.size(), ParameterScaling::none
           ))
         , ts_(std::move(timepoints)) {}
+#endif
 
     /**
      * @brief Set reinitialization of all states based on model constants for