From 316d94dc9266188939b221dd17e7d59304ae58f3 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Wed, 15 Nov 2023 12:37:12 +0100
Subject: [PATCH 1/8] Easier access to timepoints via ExpDataView (#2193)

ExpDataView provides convenient access to measurements and the like as numpy
arrays. However, accessing the associated timepoints is currently only
possible via `ExpDataView(...)._swigptr.ts_` which returns an
amici.amici.DoubleVector. That's awkward.

Now:

```python
amici.ExpDataView(amici.ExpData(1, 2, 3, [4, 5, 6])).ts
Out[3]: array([4., 5., 6.])
```

Resolves #2191
---
 python/sdist/amici/numpy.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index d9b34b6447..7a917d6c98 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -343,6 +343,7 @@ class ExpDataView(SwigPtrView):
     """
 
     _field_names = [
+        "ts",
         "observedData",
         "observedDataStdDev",
         "observedEvents",
@@ -363,7 +364,9 @@ def __init__(self, edata: Union[ExpDataPtr, ExpData]):
                 f"Unsupported pointer {type(edata)}, must be"
                 f"amici.ExpDataPtr!"
             )
-        self._field_dimensions = {  # observables
+        self._field_dimensions = {
+            "ts": [edata.nt()],
+            # observables
             "observedData": [edata.nt(), edata.nytrue()],
             "observedDataStdDev": [edata.nt(), edata.nytrue()],
             # event observables
@@ -378,6 +381,7 @@ def __init__(self, edata: Union[ExpDataPtr, ExpData]):
                 len(edata.fixedParametersPreequilibration)
             ],
         }
+        edata.ts = edata.ts_
         edata.observedData = edata.getObservedData()
         edata.observedDataStdDev = edata.getObservedDataStdDev()
         edata.observedEvents = edata.getObservedEvents()

From eccdc1f31362fb47319df9cc87891e9f3d3f0804 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Wed, 15 Nov 2023 14:38:01 +0100
Subject: [PATCH 2/8] Nicer __repr__ for ReturnDataView (#2192)

Previously:

```
<ReturnDataView(<amici.amici.ReturnData; proxy of <Swig Object of type 'amici::ReturnData *' at 0x7f794a9ef8d0> >)>
```

Now:

```
<ReturnDataView(id='ctrl+basal_preeq', status=AMICI_SUCCESS)>
```
---
 python/sdist/amici/numpy.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index 7a917d6c98..03786dc262 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -297,6 +297,10 @@ def __getitem__(
 
         return super().__getitem__(item)
 
+    def __repr__(self):
+        status = amici.simulation_status_to_str(self._swigptr.status)
+        return f"<{self.__class__.__name__}(id={self._swigptr.id!r}, status={status})>"
+
     def by_id(
         self, entity_id: str, field: str = None, model: Model = None
     ) -> np.array:

From 187362a93fc397548ebe9f524d48a3de6dda116e Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Wed, 15 Nov 2023 17:13:35 +0100
Subject: [PATCH 3/8] Fix ExpData equality operator for Python (#2194)

Wasn't automatically handled by swig for unclear reasons. Works now. Fixes #2190.
---
 python/tests/test_swig_interface.py | 9 +++++++++
 swig/edata.i                        | 3 +++
 2 files changed, 12 insertions(+)

diff --git a/python/tests/test_swig_interface.py b/python/tests/test_swig_interface.py
index b1afa0b76b..8c895eb852 100644
--- a/python/tests/test_swig_interface.py
+++ b/python/tests/test_swig_interface.py
@@ -442,3 +442,12 @@ def test_edata_repr():
             assert expected_str in repr(e)
     # avoid double delete!!
     edata_ptr.release()
+
+
+def test_edata_equality_operator():
+    e1 = amici.ExpData(1, 2, 3, [3])
+    e2 = amici.ExpData(1, 2, 3, [3])
+    assert e1 == e2
+    # check that comparison with other types works
+    # this is not implemented by swig by default
+    assert e1 != 1
diff --git a/swig/edata.i b/swig/edata.i
index 59dcb4fa8a..5dd46c95ee 100644
--- a/swig/edata.i
+++ b/swig/edata.i
@@ -74,6 +74,9 @@ def _edata_repr(self: "ExpData"):
 %pythoncode %{
 def __repr__(self):
     return _edata_repr(self)
+
+def __eq__(self, other):
+    return other.__class__ == self.__class__ and __eq__(self, other)
 %}
 };
 %extend std::unique_ptr<amici::ExpData> {

From 1726f437b9e1a0819e4f2667dc6e0015d05c563f Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Wed, 15 Nov 2023 19:31:40 +0100
Subject: [PATCH 4/8] Enable deepcopy for ExpData(View) (#2196)

Fixes a bug in `SwigPtrView.__deepcopy__` which did not produce a deep copy.

Add `SwigPtrView.__eq__` to allow for comparison. The view objects are considered equal if the underlying viewed objects are equal.

Fixes #2189.
---
 python/sdist/amici/numpy.py         | 18 +++++++++++++++++-
 python/tests/test_swig_interface.py | 19 +++++++++++++++++++
 swig/edata.i                        |  5 +++++
 3 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index 03786dc262..b84e52cc2b 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -137,7 +137,8 @@ def __deepcopy__(self, memo):
 
         :returns: SwigPtrView deep copy
         """
-        other = SwigPtrView(self._swigptr)
+        # We assume we have a copy-ctor for the swigptr object
+        other = self.__class__(copy.deepcopy(self._swigptr))
         other._field_names = copy.deepcopy(self._field_names)
         other._field_dimensions = copy.deepcopy(self._field_dimensions)
         other._cache = copy.deepcopy(self._cache)
@@ -151,6 +152,18 @@ def __repr__(self):
         """
         return f"<{self.__class__.__name__}({self._swigptr})>"
 
+    def __eq__(self, other):
+        """
+        Equality check
+
+        :param other: other object
+
+        :returns: whether other object is equal to this object
+        """
+        if not isinstance(other, self.__class__):
+            return False
+        return self._swigptr == other._swigptr
+
 
 class ReturnDataView(SwigPtrView):
     """
@@ -344,6 +357,9 @@ class ExpDataView(SwigPtrView):
     """
     Interface class for C++ Exp Data objects that avoids possibly costly
     copies of member data.
+
+    NOTE: This currently assumes that the underlying :class:`ExpData`
+    does not change after instantiating an :class:`ExpDataView`.
     """
 
     _field_names = [
diff --git a/python/tests/test_swig_interface.py b/python/tests/test_swig_interface.py
index 8c895eb852..a746552b55 100644
--- a/python/tests/test_swig_interface.py
+++ b/python/tests/test_swig_interface.py
@@ -7,6 +7,7 @@
 import numbers
 
 import amici
+import numpy as np
 
 
 def test_version_number(pysb_example_presimulation_module):
@@ -451,3 +452,21 @@ def test_edata_equality_operator():
     # check that comparison with other types works
     # this is not implemented by swig by default
     assert e1 != 1
+
+
+def test_expdata_and_expdataview_are_deepcopyable():
+    edata1 = amici.ExpData(3, 2, 3, range(4))
+    edata1.setObservedData(np.zeros((3, 4)).flatten())
+
+    # ExpData
+    edata2 = copy.deepcopy(edata1)
+    assert edata1 == edata2
+    assert edata1.this != edata2.this
+    edata2.setTimepoints([0])
+    assert edata1 != edata2
+
+    # ExpDataView
+    ev1 = amici.ExpDataView(edata1)
+    ev2 = copy.deepcopy(ev1)
+    assert ev2._swigptr.this != ev1._swigptr.this
+    assert ev1 == ev2
diff --git a/swig/edata.i b/swig/edata.i
index 5dd46c95ee..f2f7d0da8a 100644
--- a/swig/edata.i
+++ b/swig/edata.i
@@ -77,6 +77,11 @@ def __repr__(self):
 
 def __eq__(self, other):
     return other.__class__ == self.__class__ and __eq__(self, other)
+
+def __deepcopy__(self, memo):
+    # invoke copy constructor
+    return type(self)(self)
+
 %}
 };
 %extend std::unique_ptr<amici::ExpData> {

From 48b8629ca9c78571d9fae1ea3ad13994da899f78 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Wed, 15 Nov 2023 21:35:01 +0100
Subject: [PATCH 5/8] Allow subsetting simulation conditions in simulate_petab
 (#2199)

simulate_petab was mainly intended to simulate all conditions at once,
but the `simulation_conditions` argument provides also an easy way to
simulate only a subset of conditions. However, this currently fails,
because the full parameter mapping is used an then wrong conditions
are assigned.

This is fixed here. Also it saved a minuscule amount of time.
---
 python/sdist/amici/petab_objective.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/sdist/amici/petab_objective.py b/python/sdist/amici/petab_objective.py
index 87409ee446..e3111d3b68 100644
--- a/python/sdist/amici/petab_objective.py
+++ b/python/sdist/amici/petab_objective.py
@@ -516,6 +516,7 @@ def create_parameter_mapping(
             observable_df=petab_problem.observable_df,
             mapping_df=petab_problem.mapping_df,
             model=petab_problem.model,
+            simulation_conditions=simulation_conditions,
             **dict(
                 default_parameter_mapping_kwargs, **parameter_mapping_kwargs
             ),

From 17f85fb5b88aec529ddca2ee94c5c40cf4b50183 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Thu, 16 Nov 2023 08:38:05 +0100
Subject: [PATCH 6/8] GHA: Modularize actions (apt dependencies, sonar tools)
 (#2197)

* GHA: Test composite actions

* ..

* sonar
---
 .../install-apt-dependencies/action.yml       | 16 +++++++++++
 .github/actions/setup-sonar-tools/action.yml  | 26 ++++++++++++++++++
 .../test_benchmark_collection_models.yml      |  7 ++---
 .github/workflows/test_install.yml            | 23 +++++-----------
 .github/workflows/test_performance.yml        |  8 +++---
 .github/workflows/test_petab_test_suite.yml   |  8 +++---
 .github/workflows/test_python_cplusplus.yml   | 27 ++++---------------
 .github/workflows/test_python_ver_matrix.yml  | 11 ++------
 .../test_sbml_semantic_test_suite.yml         |  8 +++---
 .github/workflows/test_valgrind.yml           | 22 ++++++---------
 10 files changed, 76 insertions(+), 80 deletions(-)
 create mode 100644 .github/actions/install-apt-dependencies/action.yml
 create mode 100644 .github/actions/setup-sonar-tools/action.yml

diff --git a/.github/actions/install-apt-dependencies/action.yml b/.github/actions/install-apt-dependencies/action.yml
new file mode 100644
index 0000000000..0474e5befa
--- /dev/null
+++ b/.github/actions/install-apt-dependencies/action.yml
@@ -0,0 +1,16 @@
+name: Install apt dependencies
+description: Install apt dependencies for the AMICI Python package
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              g++ \
+              libatlas-base-dev \
+              libboost-chrono-dev \
+              libboost-math-dev \
+              libboost-serialization-dev \
+              libhdf5-serial-dev \
+              swig
+      shell: bash
diff --git a/.github/actions/setup-sonar-tools/action.yml b/.github/actions/setup-sonar-tools/action.yml
new file mode 100644
index 0000000000..d791c120bf
--- /dev/null
+++ b/.github/actions/setup-sonar-tools/action.yml
@@ -0,0 +1,26 @@
+name: Set up Sonar tools
+description: Download and install sonar-scanner and build-wrapper
+runs:
+  using: "composite"
+  steps:
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
+      shell: bash
+    - run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Install sonarcloud tools
+      run: |
+        sudo apt-get install nodejs curl unzip \
+        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
+          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
+        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
+        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
+          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
+        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+      shell: bash
diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
index 9cfa50ea2a..e5d13946e7 100644
--- a/.github/workflows/test_benchmark_collection_models.yml
+++ b/.github/workflows/test_benchmark_collection_models.yml
@@ -37,11 +37,8 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig libatlas-base-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
 
diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
index 6721008599..0ad1ec0a14 100644
--- a/.github/workflows/test_install.yml
+++ b/.github/workflows/test_install.yml
@@ -22,17 +22,14 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - name: apt
       run: |
         sudo apt-get update \
           && sudo apt-get install -y \
-            cmake \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
-            swig
+            cmake
 
     - name: Build suitesparse
       run: |
@@ -70,16 +67,8 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
-            swig
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     - name: Create AMICI sdist
       run: |
diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
index 871421ffd0..de9dd686d9 100644
--- a/.github/workflows/test_performance.yml
+++ b/.github/workflows/test_performance.yml
@@ -35,11 +35,9 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig libatlas-base-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - run: pip3 install petab shyaml build
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
index 70acd254df..26a4ac7a26 100644
--- a/.github/workflows/test_petab_test_suite.yml
+++ b/.github/workflows/test_petab_test_suite.yml
@@ -34,14 +34,14 @@ jobs:
         with:
           fetch-depth: 20
 
+      - name: Install apt dependencies
+        uses: ./.github/actions/install-apt-dependencies
+
       # install dependencies
       - name: apt
         run: |
           sudo apt-get update \
-            && sudo apt-get install -y \
-            swig \
-            libatlas-base-dev \
-            python3-venv
+            && sudo apt-get install -y python3-venv
 
       - name: Build BNGL
         run: |
diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
index 44eeec8acb..546b297712 100644
--- a/.github/workflows/test_python_cplusplus.yml
+++ b/.github/workflows/test_python_cplusplus.yml
@@ -35,23 +35,11 @@ jobs:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
     - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
-    # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
-    - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
-    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
-    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
-    - run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
-
-    # TODO: add to ci image
-    - name: Install sonarcloud tools
-      run: |
-        sudo apt-get install nodejs curl unzip \
-        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
-          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
-        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
-        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
-          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
-        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+    - name: Set up Sonar tools
+      uses: ./.github/actions/setup-sonar-tools
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     # install amici dependencies
     - name: apt
@@ -60,12 +48,7 @@ jobs:
           && sudo apt-get install -y \
             cmake \
             g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libboost-chrono-dev \
-            libhdf5-serial-dev \
             python3-venv \
-            swig \
             lcov \
             libboost-math-dev
 
diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
index 59dcf91041..73aba014cd 100644
--- a/.github/workflows/test_python_ver_matrix.yml
+++ b/.github/workflows/test_python_ver_matrix.yml
@@ -41,15 +41,8 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-          swig \
-          libatlas-base-dev \
-          libhdf5-serial-dev \
-          libboost-math-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     # install AMICI
     - name: Build BNGL
diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
index 68bfaed8e3..0fde56b8f9 100644
--- a/.github/workflows/test_sbml_semantic_test_suite.yml
+++ b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -40,10 +40,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig4.0 libatlas-base-dev
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh ${{ matrix.cases }}
 
diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
index 1138e663c0..7b513f28dd 100644
--- a/.github/workflows/test_valgrind.yml
+++ b/.github/workflows/test_valgrind.yml
@@ -34,20 +34,17 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     # 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
+            valgrind
 
     - name: Build AMICI
       run: |
@@ -78,20 +75,17 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     # 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
+            valgrind
 
     - name: Build AMICI
       run: |

From acf526a40fa842db6a707b1280ec4d4fb4f095e5 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Thu, 16 Nov 2023 08:39:37 +0100
Subject: [PATCH 7/8] GHA: Clean up custom doxygen (#2201)

Handle installation and dependencies in one single place.
---
 .github/actions/setup-doxygen/action.yml | 20 ++++++++++++++++++
 .github/workflows/test_doc.yml           | 27 ++++++------------------
 scripts/downloadAndBuildDoxygen.sh       |  9 +++++---
 3 files changed, 32 insertions(+), 24 deletions(-)
 create mode 100644 .github/actions/setup-doxygen/action.yml

diff --git a/.github/actions/setup-doxygen/action.yml b/.github/actions/setup-doxygen/action.yml
new file mode 100644
index 0000000000..f6a62181c1
--- /dev/null
+++ b/.github/actions/setup-doxygen/action.yml
@@ -0,0 +1,20 @@
+name: Set up doxygen
+description: |
+  Download, build, and install doxygen.
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install apt dependencies for doxygen
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              bison \
+              ragel \
+              graphviz \
+              texlive-latex-extra
+      shell: bash
+
+    - name: Download and build doxygen
+      run: sudo scripts/downloadAndBuildDoxygen.sh
+      shell: bash
diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
index 98c023ba79..64dc0b301d 100644
--- a/.github/workflows/test_doc.yml
+++ b/.github/workflows/test_doc.yml
@@ -16,7 +16,6 @@ on:
 jobs:
   doxygen:
     name: Test Doxygen
-
     runs-on: ubuntu-22.04
 
     strategy:
@@ -32,26 +31,14 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-          bison \
-          ragel \
-          graphviz \
-          texlive-latex-extra
-
-    - name: Build doxygen
-      run: |
-        sudo scripts/downloadAndBuildDoxygen.sh
+    - name: Set up doxygen
+      uses: ./.github/actions/setup-doxygen
 
     - name: Run doxygen
-      run: |
-        scripts/run-doxygen.sh
+      run: scripts/run-doxygen.sh
 
   sphinx:
     name: Test Sphinx
-
     runs-on: ubuntu-22.04
 
     strategy:
@@ -70,9 +57,8 @@ jobs:
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
       - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.1.1/install/bin/swig" >> $GITHUB_ENV
 
-      - name: Build doxygen
-        run: |
-          sudo scripts/downloadAndBuildDoxygen.sh
+      - name: Set up doxygen
+        uses: ./.github/actions/setup-doxygen
 
       # install amici dependencies
       - name: apt
@@ -90,5 +76,4 @@ jobs:
           sudo scripts/downloadAndBuildSwig.sh
 
       - name: sphinx
-        run: |
-          scripts/run-sphinx.sh
+        run: scripts/run-sphinx.sh
diff --git a/scripts/downloadAndBuildDoxygen.sh b/scripts/downloadAndBuildDoxygen.sh
index c51c05c599..19d86be5a1 100755
--- a/scripts/downloadAndBuildDoxygen.sh
+++ b/scripts/downloadAndBuildDoxygen.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 # Download and build Doxygen (in case apt or homebrew version is buggy again)
-set -e
+set -euo pipefail
 
 SCRIPT_PATH=$(dirname "$BASH_SOURCE")
 AMICI_PATH=$(cd "$SCRIPT_PATH"/.. && pwd)
@@ -8,8 +8,11 @@ AMICI_PATH=$(cd "$SCRIPT_PATH"/.. && pwd)
 DOXYGEN_DIR="${AMICI_PATH}"/ThirdParty/doxygen
 cd "${AMICI_PATH}"/ThirdParty
 if [[ ! -d ${DOXYGEN_DIR} ]]; then
-  # git clone --depth 1 https://github.com/doxygen/doxygen.git "${DOXYGEN_DIR}"
-  git clone --single-branch --branch Release_1_9_7 --depth 1 https://github.com/doxygen/doxygen.git "${DOXYGEN_DIR}"
+  git clone --single-branch \
+            --branch Release_1_9_7 \
+            --depth 1 \
+            -c advice.detachedHead=false \
+            https://github.com/doxygen/doxygen.git "${DOXYGEN_DIR}"
 fi
 
 cd "${DOXYGEN_DIR}"

From 32730f0bca120e1ac646066047aae26e0b5ab654 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Thu, 16 Nov 2023 08:42:17 +0100
Subject: [PATCH 8/8] GHA: Cleanup custom swig usage (#2200)

* GHA: Cleanup custom swig usage

* Previously the newest swig was downloaded and built, but not used because of a wrong path. Fixed here.
* Make scripts/downloadAndBuildSwig.sh accept a version number argument
* Use composite action to make it more maintainable and avoid issues as fixed above

* ..
---
 .github/actions/setup-swig/action.yml | 20 ++++++++++++++++++++
 .github/workflows/deploy_branch.yml   |  8 +++-----
 .github/workflows/deploy_release.yml  |  8 +++-----
 .github/workflows/test_doc.yml        |  5 +----
 scripts/downloadAndBuildSwig.sh       |  6 ++++--
 5 files changed, 31 insertions(+), 16 deletions(-)
 create mode 100644 .github/actions/setup-swig/action.yml

diff --git a/.github/actions/setup-swig/action.yml b/.github/actions/setup-swig/action.yml
new file mode 100644
index 0000000000..0eb8a04473
--- /dev/null
+++ b/.github/actions/setup-swig/action.yml
@@ -0,0 +1,20 @@
+name: Set up SWIG
+description: |
+  Download and build SWIG and set the SWIG environment variable to the path of
+  the SWIG executable.
+
+inputs:
+  swig_version:
+    description: 'Swig version to build'
+    required: false
+    default: '4.1.1'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Download and build SWIG
+      run: scripts/downloadAndBuildSwig.sh
+      shell: bash
+
+    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-${{ inputs.swig_version }}/install/bin/swig" >> $GITHUB_ENV
+      shell: bash
diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
index 77883907d3..73294286a1 100644
--- a/.github/workflows/deploy_branch.yml
+++ b/.github/workflows/deploy_branch.yml
@@ -21,12 +21,10 @@ jobs:
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Create AMICI sdist
       run: |
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
index ce493533e7..001d0328bf 100644
--- a/.github/workflows/deploy_release.yml
+++ b/.github/workflows/deploy_release.yml
@@ -24,12 +24,10 @@ jobs:
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: sdist
       run: |
diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
index 64dc0b301d..717ec9cc53 100644
--- a/.github/workflows/test_doc.yml
+++ b/.github/workflows/test_doc.yml
@@ -55,7 +55,6 @@ jobs:
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.1.1/install/bin/swig" >> $GITHUB_ENV
 
       - name: Set up doxygen
         uses: ./.github/actions/setup-doxygen
@@ -71,9 +70,7 @@ jobs:
               pandoc \
               python3-venv \
 
-      - name: Build swig
-        run: |
-          sudo scripts/downloadAndBuildSwig.sh
+      - uses: ./.github/actions/setup-swig
 
       - name: sphinx
         run: scripts/run-sphinx.sh
diff --git a/scripts/downloadAndBuildSwig.sh b/scripts/downloadAndBuildSwig.sh
index b7d7f9d865..5fa0896f6c 100755
--- a/scripts/downloadAndBuildSwig.sh
+++ b/scripts/downloadAndBuildSwig.sh
@@ -1,11 +1,13 @@
 #!/usr/bin/env bash
 # Download and build SWIG
-set -e
+#
+# Usage: downloadAndBuildSwig.sh [swig_version]
+set -euo pipefail
 
 SCRIPT_PATH=$(dirname "$BASH_SOURCE")
 AMICI_PATH=$(cd "$SCRIPT_PATH/.." && pwd)
 
-swig_version=4.1.1
+swig_version="${1:-"4.1.1"}"
 SWIG_ARCHIVE="swig-${swig_version}.tar.gz"
 SWIG_URL="http://downloads.sourceforge.net/project/swig/swig/swig-${swig_version}/${SWIG_ARCHIVE}"
 SWIG_DIR="swig-${swig_version}"