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Move amici.petab to amici.importers.petab
and all petab v1 functionality to amici.importers.petab.v1.
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‎.github/workflows/test_petab_sciml.yml‎

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

‎doc/examples/example_errors.ipynb‎

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

‎doc/examples/example_jax/ExampleJax.ipynb‎

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

‎doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb‎

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

‎doc/examples/example_petab/petab.ipynb‎

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

‎doc/examples/example_petab/petab_v2.ipynb‎

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

‎doc/python_modules.rst‎

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@@ -17,16 +17,16 @@ AMICI Python API
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amici.importers.pysb
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amici.importers.bngl
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amici.importers.antimony
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amici.petab
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amici.petab.conditions
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amici.petab.import_helpers
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amici.petab.parameter_mapping
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amici.petab.petab_import
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amici.petab.petab_importer
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amici.petab.pysb_import
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amici.petab.sbml_import
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amici.petab.simulations
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amici.petab.simulator
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amici.importers.petab
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amici.importers.petab.v1
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amici.importers.petab.v1.conditions
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amici.importers.petab.v1.import_helpers
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amici.importers.petab.v1.parameter_mapping
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amici.importers.petab.v1.petab_import
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amici.importers.petab.v1.pysb_import
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amici.importers.petab.v1.sbml_import
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amici.importers.petab.v1.simulations
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amici.importers.petab.v1.simulator
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amici.jax
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amici.exporters.sundials.de_export
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amici.de_model

‎python/sdist/amici/adapters/fiddy.py‎

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from petab.v1.C import LIN, LOG, LOG10
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import amici
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import amici.petab.simulations
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from amici.petab.conditions import create_edatas
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from amici.petab.parameter_mapping import create_parameter_mapping
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from amici.petab.simulations import LLH, SLLH
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import amici.importers.petab.v1.simulations
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from amici.importers.petab import LLH, SLLH
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from amici.importers.petab.v1.conditions import create_edatas
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from amici.importers.petab.v1.parameter_mapping import create_parameter_mapping
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from .. import ReturnData, SensitivityOrder
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if TYPE_CHECKING:
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from amici.petab.petab_importer import PetabSimulator
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from amici.importers.petab import PetabSimulator
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__all__ = [
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"run_simulation_to_cached_functions",
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free_parameter_ids = list(petab_problem.parameter_df.index)
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328328
if simulate_petab is None:
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simulate_petab = amici.petab.simulations.simulate_petab
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simulate_petab = amici.importers.petab.v1.simulations.simulate_petab
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edatas = None
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if precreate_edatas:

‎python/sdist/amici/importers/petab/__init__.py‎

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"""
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PEtab import related code.
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This submodule contains all functionality related to importing PEtab problems.
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For importing and simulating
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`PEtab v2 <https://petab.readthedocs.io/en/latest/v2/documentation_data_format.html#>`__
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problems, the relevant classes are:
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10+
* :class:`PetabImporter`: Import a PEtab problem as an AMICI model.
11+
* :class:`PetabSimulator`: Simulate PEtab problems with AMICI.
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* :class:`ExperimentManager`: Create :class:`amici.ExpData` objects for PEtab
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experiments.
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See :doc:`/examples/example_petab/petab_v2` for example usage.
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Note that the PEtab v2 API is still under development and may change in future
17+
releases.
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The PEtab legacy v1 import functionality is still available under
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:mod:`amici.importers.petab.v1`.
21+
Note that this functionality will be deprecated once the PEtab v2 import is
22+
stable.
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Most PEtab v1 problems can be also imported using the PEtab v2 import by
24+
passing a :class:`petab.v1.Problem` instance to the PEtab v2 import functions.
25+
"""
26+
27+
from ._petab_importer import * # noqa: F403, F401

python/sdist/amici/petab/cli/import_petab.py renamed to python/sdist/amici/importers/petab/_cli/import_petab.py

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import argparse
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import petab.v1 as petab
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from ..petab_import import import_model_sbml
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from amici.importers.petab.v1.petab_import import import_model_sbml
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def _parse_cli_args():

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