Migration to juliacall

.github/CODEOWNERS

@@ -1,7 +1,7 @@
 # see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
 
 # default owners = active maintainers
-* @Doresic @PaulJonasJost @vwiela
+* @Doresic @PaulJonasJost @MoR1chter
 
 # Examples
 /doc/example/censored_data.ipynb @Doresic
@@ -35,22 +35,22 @@
 /pypesto/optimize/ @PaulJonasJost
 /pypesto/petab/ @dweindl @FFroehlich
 /pypesto/predict/ @dilpath
-/pypesto/problem/ @PaulJonasJost @vwiela
+/pypesto/problem/ @PaulJonasJost @MoR1chter
 /pypesto/profile/ @PaulJonasJost @Doresic
 /pypesto/result/ @PaulJonasJost
-/pypesto/sample/ @dilpath @arrjon
+/pypesto/sample/ @dilpath @arrjon @vwiela
 /pypesto/select/ @dilpath
 /pypesto/startpoint/ @PaulJonasJost
 /pypesto/store/ @PaulJonasJost
-/pypesto/visualize/ @stephanmg
+/pypesto/visualize/ @Doresic
 
 # Tests
-/test/base/ @PaulJonasJost @vwiela
+/test/base/ @PaulJonasJost @MoR1chter
 /test/doc/ @PaulJonasJost
 /test/hierarchical/ @dweindl @Doresic
 /test/julia/ @PaulJonasJost @vwiela
 /test/optimize/ @PaulJonasJost
 /test/petab/ @dweindl @FFroehlich
 /test/profile/ @PaulJonasJost @Doresic
-/test/sample/ @dilpath @arrjon
+/test/sample/ @dilpath @arrjon @vwiela
 /test/select/ @dilpath

.github/workflows/ci.yml

@@ -55,7 +55,7 @@ jobs:
         CXX: clang++
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
@@ -91,7 +91,7 @@ jobs:
       run: ulimit -n 65536 65536 && tox -e base
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
@@ -163,7 +163,7 @@ jobs:
         CXX: clang++
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
@@ -174,11 +174,6 @@ jobs:
       matrix:
         python-version: ['3.11', '3.13']
 
-    # needed to allow julia-actions/cache to delete old caches that it has created
-    permissions:
-      actions: write
-      contents: read
-
     steps:
     - name: Check out repository
       uses: actions/checkout@v6
@@ -196,25 +191,15 @@ jobs:
           .tox/
         key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
-    - name: Install julia
-      uses: julia-actions/setup-julia@v2
-      with:
-        version: 1.11
-
     - name: Install dependencies
       run: .github/workflows/install_deps.sh
 
-    - name: Install PEtabJL dependencies
-      run: >
-        julia -e 'using Pkg; Pkg.add("PEtab");
-        Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")'
-
     - name: Run tests
       timeout-minutes: 25
       run: tox -e julia
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
@@ -250,7 +235,7 @@ jobs:
       run: tox -e optimize
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
@@ -286,7 +271,7 @@ jobs:
       run: tox -e hierarchical
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
@@ -322,7 +307,7 @@ jobs:
       run: tox -e select
 
     - name: Coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml

.github/workflows/deploy.yml

@@ -11,6 +11,13 @@ jobs:
       matrix:
         python-version: ['3.12']
 
+    environment:
+      name: PyPI
+      url: https://pypi.org/p/pypesto
+
+    permissions:
+      id-token: write
+
     steps:
     - name: Check out repository
       uses: actions/checkout@v6
@@ -25,15 +32,14 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies
+    - name: dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        python -m pip install -U build
 
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Build distribution
+      run:
+        python -m build
+
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

doc/example/getting_started.ipynb

@@ -92,7 +92,9 @@
      "name": "#%% md\n"
     }
    },
-   "source": "Define lower and upper parameter bounds and create an optimization problem."
+   "source": [
+    "Define lower and upper parameter bounds and create an optimization problem."
+   ]
   },
   {
    "cell_type": "code",
@@ -632,7 +634,7 @@
    "outputs": [],
    "source": [
     "# adapt x_labels.\n",
-    "x_labels = [f\"Log10({name})\" for name in problem.x_names]\n",
+    "x_labels = [f\"Log({name})\" for name in problem.x_names]\n",
     "\n",
     "ax = visualize.profiles(result, x_labels=x_labels, show_bounds=True)\n",
     "# visualize optimal parameter values\n",
@@ -650,6 +652,22 @@
     ")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The 2D profile visualization shows joint parameter paths across all profile pairs. Diagonal plots show 1D profiles (likelihood ratio vs. parameter value). Off-diagonal plots show how each non-profiled parameter moves while another is profiled, with color indicating the likelihood ratio.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig, axes = pypesto.visualize.visualize_2d_profile(result)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -675,7 +693,7 @@
     "    result, confidence_level=0.95, show_bounds=True\n",
     ")\n",
     "\n",
-    "ax.set_xlabel(\"Log10(Parameter value)\");"
+    "ax.set_xlabel(\"Log(Parameter value)\");"
    ]
   },
   {
@@ -695,7 +713,7 @@
     "    result, confidence_levels=[0.99, 0.95, 0.9]\n",
     ")\n",
     "\n",
-    "ax.set_xlabel(\"Log10(Parameter value)\");"
+    "ax.set_xlabel(\"Log(Parameter value)\");"
    ]
   },
   {

pypesto/hierarchical/inner_calculator_collector.py

@@ -475,7 +475,7 @@ def __call__(
                     "Cannot use least squares solver with"
                     "parameter dependent sigma! Support can be "
                     "enabled via "
-                    "amici_model.setAddSigmaResiduals()."
+                    "amici_model.set_add_sigma_residuals()."
                 )
             self._known_least_squares_safe = True  # don't check this again
 

pypesto/hierarchical/ordinal/solver.py

@@ -236,7 +236,7 @@ def calculate_gradients(
         par_sim_ids:
             Ids of outer simulation parameters, includes fixed parameters.
         par_edata_indices:
-            Indices of parameters from `amici_model.getParameterIds()` that are needed for
+            Indices of parameters from `amici_model.get_free_parameter_ids()` that are needed for
             sensitivity calculation. Comes from `edata.plist` for each condition.
         snllh:
             A zero-initialized vector of the same length as ``par_opt_ids`` to store the

pypesto/objective/amici/amici.py

@@ -139,7 +139,7 @@ def __init__(
             derivatives.
         amici_reporting:
             Determines which quantities will be computed by AMICI,
-            see ``amici.Solver.setReturnDataReportingMode``. Set to ``None``
+            see ``amici.Solver.set_return_data_reporting_mode``. Set to ``None``
             to compute only the minimum required information.
         """
         import amici

pypesto/objective/amici/amici_calculator.py

@@ -137,7 +137,7 @@ def __call__(
                     "Cannot use least squares solver with"
                     "parameter dependent sigma! Support can be "
                     "enabled via "
-                    "amici_model.setAddSigmaResiduals()."
+                    "amici_model.set_add_sigma_residuals()."
                 )
             self._known_least_squares_safe = True  # don't check this again
 

pypesto/objective/julia/base.py

@@ -1,7 +1,14 @@
-"""Interface to Julia via pyjulia."""
+"""Interface to Julia via juliacall."""
 
 from collections.abc import Callable
 
+# Import juliacall early to avoid conflicts with other libraries (especially numpy)
+# See: https://juliapy.github.io/PythonCall.jl/dev/faq/
+try:
+    from juliacall import Main as jl  # noqa: F401
+except ImportError:
+    jl = None
+
 import numpy as np
 
 from ..function import Objective
@@ -27,10 +34,10 @@ def _read_source(module_name: str, source_file: str) -> None:
     module_name: Julia module name.
     source_file: Qualified Julia source file.
     """
-    from julia import Main
+    from juliacall import Main as jl
 
-    if not hasattr(Main, module_name):
-        Main.include(source_file)
+    if not hasattr(jl, module_name):
+        jl.include(source_file)
 
 
 class JuliaObjective(Objective):
@@ -40,45 +47,18 @@ class JuliaObjective(Objective):
     It expects the corresponding Julia objects to be defined in a
     `source_file` within a `module`.
 
-    We use the PyJulia package to access Julia from inside Python.
-    It can be installed via `pip install pypesto[julia]`, however requires
-    additional Julia dependencies to be installed via:
+    We use the juliacall package (part of PythonCall.jl) to access Julia
+    from inside Python. It can be installed via `pip install pypesto[julia]`.
 
-    >>> python -c "import julia; julia.install()"
+    juliacall automatically manages the Julia installation and configuration,
+    so no additional setup steps are required beyond pip installation.
 
     For further information, see
-    https://pyjulia.readthedocs.io/en/latest/installation.html.
-
-    There are some known problems, e.g. with statically linked Python
-    interpreters, see
-    https://pyjulia.readthedocs.io/en/latest/troubleshooting.html
-    for details.
-    Possible solutions are to pass ``compiled_modules=False`` to the Julia
-    constructor early in your code:
-
-    >>> from julia.api import Julia
-    >>> jl = Julia(compiled_modules=False)
-
-    This however slows down loading and using Julia packages, especially for
-    large ones.
-    An alternative is to use the ``python-jl`` command shipped with PyJulia:
-
-    >>> python-jl MY_SCRIPT.py
-
-    This basically launches a Python interpreter inside Julia.
-    When using Jupyter notebooks, this wrapper can be installed as an
-    additional kernel via:
-
-    >>> python -m ipykernel install --name python-jl [--prefix=/path/to/python/env]
-
-    And changing the first argument in
-    ``/path/to/python/env/share/jupyter/kernels/python-jl/kernel.json``
-    to ``python-jl``.
+    https://juliapy.github.io/PythonCall.jl/stable/juliacall/
 
-    Model simulations are eagerly converted to Python objects
-    (specifically, `numpy.ndarray` and `pandas.DataFrame`).
-    This can introduce overhead and could be avoided by an alternative
-    lazy implementation.
+    Model simulations are efficiently handled with minimal overhead.
+    By default, juliacall wraps mutable objects instead of copying them,
+    providing better performance than PyJulia.
 
     Parameters
     ----------
@@ -103,10 +83,10 @@ def __init__(
     ):
         # lazy imports
         try:
-            from julia import Main  # noqa: F401
+            from juliacall import Main as jl  # noqa: F401
         except ImportError:
             raise ImportError(
-                "Install PyJulia, e.g. via `pip install pypesto[julia]`, "
+                "Install juliacall, e.g. via `pip install pypesto[julia]`, "
                 "and see the class documentation",
             ) from None
 
@@ -133,10 +113,10 @@ def get(self, name: str, as_array: bool = False) -> Callable | None:
 
         Use this function to access any variable from the Julia module.
         """
-        from julia import Main
+        from juliacall import Main as jl
 
         if name is not None:
-            ret = getattr(getattr(Main, self.module), name, None)
+            ret = getattr(getattr(jl, self.module), name, None)
             if as_array:
                 ret = _as_array(ret)
             return ret