Move amici.petab to amici.importers.petab

.github/workflows/test_petab_sciml.yml

@@ -56,7 +56,7 @@ jobs:
       - name: Install python package
         run: scripts/installAmiciSource.sh
 
-      - name: Install petab
+      - name: Install Python dependencies
         run: |
           source ./venv/bin/activate \
             && pip3 install wheel pytest shyaml pytest-cov
@@ -65,14 +65,16 @@ jobs:
       - name: Download and install PEtab SciML
         run: |
           source ./venv/bin/activate \
-            && python -m pip install git+https://github.com/petab-dev/petab_sciml.git@main#subdirectory=src/python \
-
+            && python -m pip install git+https://github.com/petab-dev/petab_sciml.git@main#subdirectory=src/python
 
       - name: Install petab
+        # FIXME: Currently, an older version of petab that is required for
+        #  these tests, because petab-sciml is currently a mix of petab v1
+        #  and v2 functionality.
         run: |
           source ./venv/bin/activate \
             && python3 -m pip uninstall -y petab \
-            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@sciml \
+            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@sciml
 
       - name: Run PEtab SciML testsuite
         run: |

binder/overview.ipynb

@@ -39,10 +39,7 @@
     "* [Efficient spline interpolation](../doc/examples/example_splines/ExampleSplines.ipynb)\n",
     "\n",
     "  Shows how to add annotated spline formulas to existing SBML models to speed up AMICI's model import.\n",
-    "\n",
-    "* [A real-world application of splines](../doc/examples/example_splines_swameye/ExampleSplinesSwameye2003.ipynb)\n",
-    "\n",
-    "  An illustration of how to apply AMICI's spline functionalities to parameter estimation for a reaction network.\n"
+    "\n"
    ]
   }
  ],

doc/examples/example_errors.ipynb

@@ -11,11 +11,10 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1863901917703506",
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": null,
    "source": [
     "%matplotlib inline\n",
     "import os\n",
@@ -34,8 +33,12 @@
     "    run_simulation,\n",
     "    simulation_status_to_str,\n",
     ")\n",
-    "from amici.petab.petab_import import import_petab_problem\n",
-    "from amici.petab.simulations import EDATAS, RDATAS, simulate_petab\n",
+    "from amici.importers.petab.v1 import (\n",
+    "    EDATAS,\n",
+    "    RDATAS,\n",
+    "    import_petab_problem,\n",
+    "    simulate_petab,\n",
+    ")\n",
     "from amici.plotting import plot_jacobian, plot_state_trajectories\n",
     "from petab.v1.sbml import get_sbml_model\n",
     "\n",
@@ -48,7 +51,8 @@
     "        import benchmark_models_petab\n",
     "    except ModuleNotFoundError:\n",
     "        print(\"** Please restart the kernel. **\")"
-   ]
+   ],
+   "id": "b9e6cb8843da8bc3"
   },
   {
    "cell_type": "markdown",

doc/examples/example_jax/ExampleJax.ipynb

@@ -274,23 +274,16 @@
    ]
   },
   {
+   "metadata": {},
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "6ada3fb8",
-   "metadata": {
-    "ExecuteTime": {
-     "start_time": "2024-10-18T20:36:51.765461Z"
-    },
-    "jupyter": {
-     "is_executing": true
-    }
-   },
    "outputs": [],
+   "execution_count": null,
    "source": [
-    "from amici.petab.petab_import import import_petab_problem\n",
+    "from amici.importers.petab.v1 import import_petab_problem\n",
     "\n",
     "amici_model = import_petab_problem(petab_problem, compile_=True, verbose=False)"
-   ]
+   ],
+   "id": "4c510f3e65879888"
   },
   {
    "cell_type": "markdown",
@@ -311,14 +304,13 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "72053647",
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": null,
    "source": [
     "import amici\n",
-    "from amici.petab.simulations import simulate_petab\n",
+    "from amici.importers.petab.v1 import simulate_petab\n",
     "\n",
     "amici_solver = amici_model.create_solver()\n",
     "amici_solver.set_sensitivity_order(amici.SensitivityOrder.first)\n",
@@ -336,7 +328,8 @@
     "        tuple(ret[\"sllh\"][par_id] for par_id in petab_problem.x_free_ids)\n",
     "    )\n",
     "    return llh, sllh"
-   ]
+   ],
+   "id": "beb890bd2f3d0880"
   },
   {
    "cell_type": "markdown",

doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb

@@ -32,7 +32,7 @@
    "outputs": [],
    "source": [
     "import petab.v1 as petab\n",
-    "from amici.petab.petab_import import import_petab_problem\n",
+    "from amici.importers.petab.v1 import import_petab_problem\n",
     "\n",
     "# Define the model name and YAML file location\n",
     "model_name = \"Boehm_JProteomeRes2014\"\n",
@@ -566,7 +566,7 @@
    "outputs": [],
    "source": [
     "import amici\n",
-    "from amici.petab import simulate_petab\n",
+    "from amici.importers.petab.v1 import simulate_petab\n",
     "\n",
     "# Import the PEtab problem as a standard AMICI model\n",
     "amici_model = import_petab_problem(\n",

doc/examples/example_petab/petab.ipynb

@@ -12,16 +12,18 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": null,
    "source": [
     "import petab\n",
     "from amici import run_simulation\n",
-    "from amici.petab.petab_import import import_petab_problem\n",
-    "from amici.petab.petab_problem import PetabProblem\n",
-    "from amici.petab.simulations import simulate_petab\n",
+    "from amici.importers.petab.v1 import (\n",
+    "    import_petab_problem,\n",
+    "    simulate_petab,\n",
+    ")\n",
+    "from amici.importers.petab.v1.petab_problem import PetabProblem\n",
     "from amici.plotting import plot_state_trajectories"
    ]
   },

doc/examples/example_petab/petab_v2.ipynb

@@ -13,22 +13,19 @@
    ]
   },
   {
+   "metadata": {},
    "cell_type": "code",
-   "id": "initial_id",
-   "metadata": {
-    "collapsed": true
-   },
+   "outputs": [],
+   "execution_count": null,
    "source": [
     "import logging\n",
     "\n",
     "import amici\n",
-    "from amici.petab.petab_importer import *\n",
-    "from amici.petab.simulations import RDATAS\n",
+    "from amici.importers.petab import *\n",
     "from amici.plotting import *\n",
     "from petab.v2 import Problem"
    ],
-   "outputs": [],
-   "execution_count": null
+   "id": "419616ae233de558"
   },
   {
    "cell_type": "markdown",

doc/examples/example_splines/ExampleSplines.ipynb

@@ -6,7 +6,9 @@
    "source": [
     "# AMICI Python example \"splines\"\n",
     "\n",
-    "This is an example showing how to add spline assignment rules to a pre-existing SBML model."
+    "This is an example showing how to add spline assignment rules to a pre-existing SBML model.\n",
+    "\n",
+    "A full application example of using splines to parametrize time-dependent unknown inputs followed by parameter estimation with pypesto can be found in the [pypesto documentation](https://pypesto.readthedocs.io/en/latest/example.html#application-examples)."
    ]
   },
   {