Repository: Systems-Theory-in-Systems-Biology/EPI (language: python)

Issue:
Improve dependency management
**Is your feature request related to a problem? Please describe.**
Epipy users are forced to install the sbml and the amici library and the corresponding c++ libraries even if they do not need sbml support. This complicates the installation process.

**Describe the solution you'd like**
Make amici an optional dependency for epipy. The installation would/should look like this
`pip install epipy` or `pip install epipy[sbml]` depending on whether sbml support is wanted.
Additionally we could build wheels which include the cpp dependencies: https://davidmontague.xyz/posts/packaging-native-extensions-with-poetry/

**Describe alternatives you've considered**
-

**Additional context**
Are all c++ dependencies for epipy already specified in the installation instructions?



Discussion / hints:
@shoepfl this refers to the [discussion](https://github.com/orgs/Systems-Theory-in-Systems-Biology/discussions/37) you started, doesn't it?

yes exactly, there are also some tips for the amici installation and I like the solution to install the amici dependency optional
I tried to use eulerpi without installing amici but the model class currently depends on amici. 
Therfore, you can currently not effectively infer parameters with eulerpi without previously installing amici. 
Sorry, I accidentally closed this issue.

Fix patch:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0aadd2e6..f181782f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
           path: .venv
           key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
       - name: Install dependencies
-        run: poetry install --no-interaction --with=dev
+        run: poetry install --no-interaction --with=dev --extras=sbml
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       - name: Prepare cpp test
         run: |
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index fd186185..4599b2f5 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -36,7 +36,7 @@ jobs:
           path: .venv
           key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
       - name: Install dependencies
-        run: poetry install --no-interaction --with=dev
+        run: poetry install --no-interaction --with=dev --extras=sbml
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       - name: Publish to PyPI
         env:
diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml
index 8c580898..1462d439 100644
--- a/.github/workflows/sphinx.yml
+++ b/.github/workflows/sphinx.yml
@@ -39,7 +39,7 @@ jobs:
           path: .venv
           key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
       - name: Install dependencies
-        run: poetry install --no-interaction --with=dev
+        run: poetry install --no-interaction --with=dev --extras=sbml
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       - name: Build documentation
         run: |
diff --git a/.gitignore b/.gitignore
index f3926a03..2dcd6dd2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -134,6 +134,4 @@ dmypy.json
 # Project specific
 Data
 Applications
-amici
-swig
-generated_sbml_model
+generated_sbml_models
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 758e39ef..5375eb3b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,7 +23,18 @@ All notable changes to this project will be documented in this file.
 
 ### Changed
 
--Updated the dependencies to the latest possible versions
+### Fixed
+
+## [0.6.0] - 2023-11-02
+
+Breaking changes: SBML support is now only available when install eulerpi with the "sbml" extra!
+
+### Added
+
+### Changed
+
+- Updated the dependencies to the latest possible versions
+- Made the sbml model support optional using the extra `sbml`
 
 ### Fixed
 
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 958406f0..c78af5b6 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -17,12 +17,13 @@ All types of contributions are encouraged and valued. See the [Table of Contents
 
 - [I Have a Question](#i-have-a-question)
 - [I Want To Contribute](#i-want-to-contribute)
+- [How to install the current main branch directly?](#how-to-install-the-current-main-branch-directly)
   - [Reporting Bugs](#reporting-bugs)
   - [Suggesting Enhancements](#suggesting-enhancements)
   - [Your First Code Contribution](#your-first-code-contribution)
   - [Improving The Documentation](#improving-the-documentation)
 - [Styleguides](#styleguides)
-  - [Code styl](#code-styl)
+  - [Code style](#code-style)
   - [Commit Messages](#commit-messages)
 - [Join The Project Team](#join-the-project-team)
 
@@ -47,10 +48,14 @@ We will then take care of the issue as soon as possible.
 When contributing to this project, you must agree that you have authored 100% of the content, that you have the necessary rights to the content and that the content you contribute may be provided under the project license.
 
 ## How to install the current main branch directly?
+
 To install the current main branch version you can use git in your conda environment:
-```pip install git+https://github.com/Systems-Theory-in-Systems-Biology/EPI```
+```pip install "eulerpi @ git+https://github.com/Systems-Theory-in-Systems-Biology/EPI@main"```
+or
+```pip install "eulerpi[sbml] @ git+https://github.com/Systems-Theory-in-Systems-Biology/EPI@main"```
+for the sbml model support.
 
-like this you can also install feature-branches.
+Like this you can also install feature-branches.
 Please be aware that these versions are under development and the double-checked versions are published on pypi.
 
 ### Reporting Bugs
diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
index 3f7d6082..b3fa0113 100644
--- a/DEVELOPMENT.md
+++ b/DEVELOPMENT.md
@@ -44,7 +44,7 @@
 - Install eulerpi:
 
   ```bash
-  poetry install --with=dev
+  poetry install --with=dev --extras=sbml
   ```
 
 - Run the tests:
@@ -201,7 +201,7 @@ poetry publish --build
 Test this with
 
 ```bash
-pip install eulerpi
+pip install eulerpi[sbml]
 ```
 
 ## Jax with CUDA
diff --git a/README.md b/README.md
index f9fe60b2..b8531aa1 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,14 @@ The package is available on pypi and can be installed with:
 pip install eulerpi
 ```
 
+or
+
+```bash
+pip install eulerpi[sbml]
+```
+
+for the support of sbml models.
+
 Make sure that you have the following C++ libraries installed
 
 ```bash
diff --git a/docs/requirements.txt b/docs/requirements.txt
index d18f9a83..d4f4abbf 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,2 +1,2 @@
 # Install eulerpi and its dependencies so sphinx can generate the docs.
--e .[dev]
+-e .[dev, amici]
diff --git a/docs/source/MarkdownLinks/todos.rst b/docs/source/MarkdownLinks/todos.rst
deleted file mode 100644
index 44e8e4d7..00000000
--- a/docs/source/MarkdownLinks/todos.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-.. -----
-.. TODOs
-.. -----
-
-.. include:: ../../../TODO.md
-    :parser: myst_parser.sphinx_
diff --git a/docs/source/welcome.rst b/docs/source/welcome.rst
index 97a8990e..13fb44f1 100644
--- a/docs/source/welcome.rst
+++ b/docs/source/welcome.rst
@@ -47,6 +47,14 @@ The package is available on pypi and can be installed with:
    
    pip install eulerpi
 
+or
+
+.. code-block:: bash
+
+    pip install eulerpi[sbml]
+
+for the support of sbml models.
+
 Make sure that you have the following C++ libraries installed:
 
 .. code-block:: bash
diff --git a/eulerpi/core/model.py b/eulerpi/core/model.py
index 35500def..34cbc080 100644
--- a/eulerpi/core/model.py
+++ b/eulerpi/core/model.py
@@ -9,9 +9,20 @@
 import numpy as np
 from jax import jacrev, jit, vmap
 
-import amici
 from eulerpi.jax_extension import value_and_jacrev
 
+amici_available = False
+try:
+    import amici
+
+    amici_available = True
+except ImportError:
+    pass
+
+
+def is_amici_available():
+    return amici_available
+
 
 class Model(ABC):
     """The base class for all models using the EPI algorithm.
@@ -333,10 +344,19 @@ def __init__(
         name: Optional[str] = None,
         **kwargs,
     ) -> None:
+        if not is_amici_available():
+            raise ImportError(
+                "The SBMLModel class requires an AMICI installation. "
+                "Please install AMICI first."
+                "You can do this manually or install eulerpi with the [amici] extra: pip install eulerpi[amici]"
+            )
+
         super().__init__(central_param, param_limits, name, **kwargs)
 
         self.amici_model_name = self.name
-        self.amici_model_dir = "./amici/" + self.amici_model_name
+        self.amici_model_dir = (
+            "./generated_sbml_models/" + self.amici_model_name
+        )
 
         # Generate python code
         if not skip_creation:
diff --git a/eulerpi/examples/sbml/sbml_caffeine_model.py b/eulerpi/examples/sbml/sbml_caffeine_model.py
index 2b4251ba..d688c6b5 100644
--- a/eulerpi/examples/sbml/sbml_caffeine_model.py
+++ b/eulerpi/examples/sbml/sbml_caffeine_model.py
@@ -1,4 +1,4 @@
-import importlib
+from importlib.resources import as_file, files
 
 import numpy as np
 
@@ -16,20 +16,19 @@ def __init__(
         param_limits: np.ndarray = PARAM_LIMITS,
         **kwargs,
     ) -> None:
-        sbml_file = importlib.resources.path(
-            "eulerpi.examples.sbml", "Caffeine_2Wks_Exponential_decay.xml"
-        )
         param_ids = ["A", "B"]
         timepoints = np.array([0.5, 1.0])
-
-        super().__init__(
-            sbml_file,
-            central_param,
-            param_limits,
-            timepoints,
-            param_ids,
-            **kwargs,
-        )
+        sbml_files = files(package="eulerpi.examples.sbml")
+        sbml_file_name = "Caffeine_2Wks_Exponential_decay.xml"
+        with as_file(sbml_files.joinpath(sbml_file_name)) as sbml_file:
+            super().__init__(
+                sbml_file,
+                central_param,
+                param_limits,
+                timepoints,
+                param_ids,
+                **kwargs,
+            )
 
     def generate_artificial_params(self, num_samples: int) -> np.ndarray:
         diff0 = 0.2
diff --git a/eulerpi/examples/sbml/sbml_menten_model.py b/eulerpi/examples/sbml/sbml_menten_model.py
index e7567e62..758d882f 100644
--- a/eulerpi/examples/sbml/sbml_menten_model.py
+++ b/eulerpi/examples/sbml/sbml_menten_model.py
@@ -1,4 +1,4 @@
-import importlib
+from importlib.resources import as_file, files
 
 import numpy as np
 
@@ -21,22 +21,21 @@ def __init__(
         param_limits: np.ndarray = PARAM_LIMITS,
         **kwargs,
     ) -> None:
-        sbml_file = importlib.resources.path(
-            "eulerpi.examples.sbml", "sbml_menten_model.xml"
-        )
         timepoints = np.array([0.5, 1.0])
         param_ids = ["Km", "kcat"]
         state_ids = ["s1"]
-
-        super().__init__(
-            sbml_file,
-            central_param,
-            param_limits,
-            timepoints,
-            param_ids,
-            state_ids,
-            **kwargs,
-        )
+        sbml_files = files(package="eulerpi.examples.sbml")
+        sbml_file_name = "sbml_menten_model.xml"
+        with as_file(sbml_files.joinpath(sbml_file_name)) as sbml_file:
+            super().__init__(
+                sbml_file,
+                central_param,
+                param_limits,
+                timepoints,
+                param_ids,
+                state_ids,
+                **kwargs,
+            )
 
     def generate_artificial_params(self, num_samples: int) -> np.ndarray:
         diff0 = 5.0
diff --git a/poetry.lock b/poetry.lock
index 97327c1d..38c834b8 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -15,7 +15,7 @@ files = [
 name = "amici"
 version = "0.16.1"
 description = "Advanced multi-language Interface to CVODES and IDAS"
-optional = false
+optional = true
 python-versions = ">=3.8"
 files = [
     {file = "amici-0.16.1.tar.gz", hash = "sha256:aec799184cc96fcbda075ab2a4599890ab42474145e064cc57da995e38a49b28"},
@@ -65,46 +65,39 @@ files = [
 
 [[package]]
 name = "asttokens"
-version = "2.4.0"
+version = "2.4.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = "*"
 files = [
-    {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"},
-    {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"},
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
 ]
 
 [package.dependencies]
 six = ">=1.12.0"
 
 [package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "babel"
-version = "2.13.0"
+version = "2.13.1"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"},
-    {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"},
+    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
 ]
 
+[package.dependencies]
+setuptools = {version = "*", markers = "python_version >= \"3.12\""}
+
 [package.extras]
 dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
-[[package]]
-name = "backcall"
-version = "0.2.0"
-description = "Specifications for callback functions passed in to an API"
-optional = false
-python-versions = "*"
-files = [
-    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
-    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
-]
-
 [[package]]
 name = "beautifulsoup4"
 version = "4.12.2"
@@ -125,29 +118,29 @@ lxml = ["lxml"]
 
 [[package]]
 name = "black"
-version = "23.10.0"
+version = "23.10.1"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -253,101 +246,101 @@ files = [
 
 [[package]]
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+    {file = "charset_normalizer-3.3.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:ff8fa367d09b717b2a17a052544193ad76cd49979c805768879cb63d9ca50561"},
+    {file = "charset_normalizer-3.3.2-cp39-cp39-win32.whl", hash = "sha256:aed38f6e4fb3f5d6bf81bfa990a07806be9d83cf7bacef998ab1a9bd660a581f"},
+    {file = "charset_normalizer-3.3.2-cp39-cp39-win_amd64.whl", hash = "sha256:b01b88d45a6fcb69667cd6d2f7a9aeb4bf53760d7fc536bf679ec94fe9f3ff3d"},
+    {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"},
 ]
 
 [[package]]
@@ -672,13 +665,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.0.0"
+version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
-    {file = "executing-2.0.0-py2.py3-none-any.whl", hash = "sha256:06df6183df67389625f4e763921c6cf978944721abf3e714000200aab95b0657"},
-    {file = "executing-2.0.0.tar.gz", hash = "sha256:0ff053696fdeef426cda5bd18eacd94f82c91f49823a2e9090124212ceea9b08"},
+    {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"},
+    {file = "executing-2.0.1.tar.gz", hash = "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147"},
 ]
 
 [package.extras]
@@ -686,19 +679,19 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "filelock"
-version = "3.12.4"
+version = "3.13.1"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.12.4-py3-none-any.whl", hash = "sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4"},
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+    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
+    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
-typing = ["typing-extensions (>=4.7.1)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
 name = "flake8"
@@ -831,7 +824,7 @@ files = [
 name = "h5py"
 version = "3.10.0"
 description = "Read and write HDF5 files from Python"
-optional = false
+optional = true
 python-versions = ">=3.8"
 files = [
     {file = "h5py-3.10.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b963fb772964fc1d1563c57e4e2e874022ce11f75ddc6df1a626f42bd49ab99f"},
@@ -887,13 +880,13 @@ lxml = ["lxml"]
 
 [[package]]
 name = "identify"
-version = "2.5.30"
+version = "2.5.31"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.30-py2.py3-none-any.whl", hash = "sha256:afe67f26ae29bab007ec21b03d4114f41316ab9dd15aa8736a167481e108da54"},
-    {file = "identify-2.5.30.tar.gz", hash = "sha256:f302a4256a15c849b91cfcdcec052a8ce914634b2f77ae87dad29cd749f2d88d"},
+    {file = "identify-2.5.31-py2.py3-none-any.whl", hash = "sha256:90199cb9e7bd3c5407a9b7e81b4abec4bb9d249991c79439ec8af740afc6293d"},
+    {file = "identify-2.5.31.tar.gz", hash = "sha256:7736b3c7a28233637e3c36550646fc6389bedd74ae84cb788200cc8e2dd60b75"},
 ]
 
 [package.extras]
@@ -971,13 +964,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.25.2"
+version = "6.26.0"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.25.2-py3-none-any.whl", hash = "sha256:2e2ee359baba19f10251b99415bb39de1e97d04e1fab385646f24f0596510b77"},
-    {file = "ipykernel-6.25.2.tar.gz", hash = "sha256:f468ddd1f17acb48c8ce67fcfa49ba6d46d4f9ac0438c1f441be7c3d1372230b"},
+    {file = "ipykernel-6.26.0-py3-none-any.whl", hash = "sha256:3ba3dc97424b87b31bb46586b5167b3161b32d7820b9201a9e698c71e271602c"},
+    {file = "ipykernel-6.26.0.tar.gz", hash = "sha256:553856658eb8430bbe9653ea041a41bff63e9606fc4628873fc92a6cf3abd404"},
 ]
 
 [package.dependencies]
@@ -1004,25 +997,23 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio"
 
 [[package]]
 name = "ipython"
-version = "8.16.1"
+version = "8.17.2"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "ipython-8.17.2.tar.gz", hash = "sha256:126bb57e1895594bb0d91ea3090bbd39384f6fe87c3d57fd558d0670f50339bb"},
 ]
 
 [package.dependencies]
 appnope = {version = "*", markers = "sys_platform == \"darwin\""}
-backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
 exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
-pickleshare = "*"
 prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
@@ -1030,17 +1021,17 @@ traitlets = ">=5"
 typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
+all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
 notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath", "trio"]
 
 [[package]]
 name = "isort"
@@ -1203,13 +1194,13 @@ files = [
 
 [[package]]
 name = "jupyter-client"
-version = "8.4.0"
+version = "8.5.0"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1226,13 +1217,13 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 
 [[package]]
 name = "jupyter-core"
-version = "5.4.0"
+version = "5.5.0"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1241,7 +1232,7 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
 traitlets = ">=5.3"
 
 [package.extras]
-docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
 test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
@@ -1549,39 +1540,39 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.8.0"
+version = "3.8.1"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1589,13 +1580,12 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
+kiwisolver = ">=1.3.1"
 numpy = ">=1.21,<2"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=7"
 
 [[package]]
 name = "matplotlib-inline"
@@ -1692,7 +1682,7 @@ dev = ["absl-py", "pyink", "pylint (>=2.6.0)", "pytest", "pytest-xdist"]
 name = "mpmath"
 version = "1.3.0"
 description = "Python library for arbitrary-precision floating-point arithmetic"
-optional = false
+optional = true
 python-versions = "*"
 files = [
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@@ -1865,43 +1855,43 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.1.1"
+version = "2.1.2"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
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+    {file = "pandas-2.1.2.tar.gz", hash = "sha256:52897edc2774d2779fbeb6880d2cfb305daa0b1a29c16b91f531a18918a6e0f3"},
 ]
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.22.4", markers = "python_version < \"3.11\""},
-    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
-    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
+    {version = ">=1.22.4,<2", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
+    {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1981,17 +1971,6 @@ files = [
 [package.dependencies]
 ptyprocess = ">=0.5"
 
-[[package]]
-name = "pickleshare"
-version = "0.7.5"
-description = "Tiny 'shelve'-like database with concurrency support"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "pillow"
 version = "10.1.0"
@@ -2063,7 +2042,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 name = "pkgconfig"
 version = "1.5.5"
 description = "Interface Python with pkg-config"
-optional = false
+optional = true
 python-versions = ">=3.3,<4.0"
 files = [
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@@ -2263,13 +2242,13 @@ tomli = {version = "*", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
+    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
 ]
 
 [package.dependencies]
@@ -2301,7 +2280,7 @@ six = ">=1.5"
 name = "python-libsbml"
 version = "5.20.2"
 description = "LibSBML Python API"
-optional = false
+optional = true
 python-versions = "*"
 files = [
     {file = "python_libsbml-5.20.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:11cb3b9a96d3438f6600d2f0900506dc86fcf2c6cadef5d401c8b9886abbb3ae"},
@@ -2687,28 +2666,6 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments
 testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
-[[package]]
-name = "setuptools-scm"
-version = "8.0.4"
-description = "the blessed package to manage your versions by scm tags"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "setuptools-scm-8.0.4.tar.gz", hash = "sha256:b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7"},
-    {file = "setuptools_scm-8.0.4-py3-none-any.whl", hash = "sha256:b47844cd2a84b83b3187a5782c71128c28b4c94cad8bfb871da2784a5cb54c4f"},
-]
-
-[package.dependencies]
-packaging = ">=20"
-setuptools = "*"
-tomli = {version = ">=1", markers = "python_version < \"3.11\""}
-typing-extensions = "*"
-
-[package.extras]
-docs = ["entangled-cli[rich]", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings[python]", "pygments"]
-rich = ["rich"]
-test = ["build", "pytest", "rich", "wheel"]
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -2975,7 +2932,7 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "sympy"
 version = "1.12"
 description = "Computer algebra system (CAS) in Python"
-optional = false
+optional = true
 python-versions = ">=3.8"
 files = [
     {file = "sympy-1.12-py3-none-any.whl", hash = "sha256:c3588cd4295d0c0f603d0f2ae780587e64e2efeedb3521e46b9bb1d08d184fa5"},
@@ -3011,7 +2968,7 @@ files = [
 name = "toposort"
 version = "1.10"
 description = "Implements a topological sort algorithm."
-optional = false
+optional = true
 python-versions = "*"
 files = [
     {file = "toposort-1.10-py3-none-any.whl", hash = "sha256:cbdbc0d0bee4d2695ab2ceec97fe0679e9c10eab4b2a87a9372b929e70563a87"},
@@ -3060,18 +3017,18 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.11.2"
+version = "5.13.0"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "traitlets-5.11.2-py3-none-any.whl", hash = "sha256:98277f247f18b2c5cabaf4af369187754f4fb0e85911d473f72329db8a7f4fae"},
-    {file = "traitlets-5.11.2.tar.gz", hash = "sha256:7564b5bf8d38c40fa45498072bf4dc5e8346eb087bbf1e2ae2d8774f6a0f078e"},
+    {file = "traitlets-5.13.0-py3-none-any.whl", hash = "sha256:baf991e61542da48fe8aef8b779a9ea0aa38d8a54166ee250d5af5ecf4486619"},
+    {file = "traitlets-5.13.0.tar.gz", hash = "sha256:9b232b9430c8f57288c1024b34a8f0251ddcc47268927367a0dd3eeaca40deb5"},
 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.6.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "typeguard"
@@ -3129,13 +3086,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.24.5"
+version = "20.24.6"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"},
-    {file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"},
+    {file = "virtualenv-20.24.6-py3-none-any.whl", hash = "sha256:520d056652454c5098a00c0f073611ccbea4c79089331f60bf9d7ba247bb7381"},
+    {file = "virtualenv-20.24.6.tar.gz", hash = "sha256:02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af"},
 ]
 
 [package.dependencies]
@@ -3149,13 +3106,13 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 
 [[package]]
 name = "wcwidth"
-version = "0.2.8"
+version = "0.2.9"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
 files = [
-    {file = "wcwidth-0.2.8-py2.py3-none-any.whl", hash = "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704"},
-    {file = "wcwidth-0.2.8.tar.gz", hash = "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"},
+    {file = "wcwidth-0.2.9-py2.py3-none-any.whl", hash = "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223"},
+    {file = "wcwidth-0.2.9.tar.gz", hash = "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8"},
 ]
 
 [[package]]
@@ -3171,13 +3128,13 @@ files = [
 
 [[package]]
 name = "wheel"
-version = "0.41.2"
+version = "0.41.3"
 description = "A built-package format for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"},
-    {file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"},
+    {file = "wheel-0.41.3-py3-none-any.whl", hash = "sha256:488609bc63a29322326e05560731bf7bfea8e48ad646e1f5e40d366607de0942"},
+    {file = "wheel-0.41.3.tar.gz", hash = "sha256:4d4987ce51a49370ea65c0bfd2234e8ce80a12780820d9dc462597a6e60d0841"},
 ]
 
 [package.extras]
@@ -3187,7 +3144,7 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
 name = "wurlitzer"
 version = "3.0.3"
 description = "Capture C-level output in context managers"
-optional = false
+optional = true
 python-versions = ">=3.5"
 files = [
     {file = "wurlitzer-3.0.3-py3-none-any.whl", hash = "sha256:ffcc584109f5ecd5244abfde4534f22140f8735a4890ce1abd90b4e503f5f427"},
@@ -3233,7 +3190,10 @@ files = [
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
+[extras]
+sbml = ["amici"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "<3.13, >=3.9"
-content-hash = "c378dc99233b10fcbd45fb8add18e439b851f0e933266e0f2ca121543e86bbb3"
+content-hash = "4a20c756283ad9e008c77d2c9951d24b6330af734f9505dca72130f3d9a592cd"
diff --git a/pyproject.toml b/pyproject.toml
index edeb021d..ff43115a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,9 +28,12 @@ jaxlib = "^0.4.19"
 tqdm = "^4.66.0"
 seedir = "^0.4.2"
 yfinance = "^0.2.31"
-amici = "^0.16.1"
+amici = { version = "^0.16.1", optional = true }
 scikit-learn = "^1.3.1"
 
+[tool.poetry.extras]
+sbml = ["amici"]
+
 [tool.poetry.group.dev.dependencies]
 pre-commit = "^3.5.0"
 black = "^23.10.0"
@@ -69,8 +72,7 @@ testpaths = [
   "tests",
 ]
 norecursedirs = [
-    "swig",
-    "generated_sbml_model",
+    "generated_sbml_models",
     "Data",
     "Applications",
     "build",


Test patch:
diff --git a/tests/test_examples.py b/tests/test_examples.py
index 69033030..fc886c13 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -8,7 +8,7 @@
 import pytest
 
 from eulerpi.core.inference import InferenceType, inference
-from eulerpi.core.model import Model
+from eulerpi.core.model import Model, is_amici_available
 
 cpp_plant_example = pytest.param(
     ("eulerpi.examples.cpp.cpp_plant", "CppPlant"),
@@ -34,6 +34,22 @@
     ),
 )
 
+menten_example = pytest.param(
+    ("eulerpi.examples.sbml.sbml_menten_model", "MentenSBMLModel"),
+    marks=pytest.mark.skipif(
+        not is_amici_available(),
+        reason="Amici not available, no SBML models can be tested",
+    ),
+)
+
+caffeine_example = pytest.param(
+    ("eulerpi.examples.sbml.sbml_caffeine_model", "CaffeineSBMLModel"),
+    marks=pytest.mark.skipif(
+        not is_amici_available(),
+        reason="Amici not available, no SBML models can be tested",
+    ),
+)
+
 
 def Examples():
     """Provides the list of examples to the parametrized test"""
@@ -53,8 +69,8 @@ def Examples():
         cpp_plant_example,
         ("eulerpi.examples.cpp.python_reference_plants", "ExternalPlant"),
         ("eulerpi.examples.cpp.python_reference_plants", "JaxPlant"),
-        ("eulerpi.examples.sbml.sbml_menten_model", "MentenSBMLModel"),
-        ("eulerpi.examples.sbml.sbml_caffeine_model", "CaffeineSBMLModel"),
+        menten_example,
+        caffeine_example,
     ]:
         yield example