Fix pre-commit configuration

Relevant changes are only in .pre-commit-config.yaml * run black on notebooks via pre-commit * set proper line width (pyproject.toml is not used if we are running things from the repo root) * compatible line width for black + isort * fix json error in binder/overview.ipynb * re-blacken everything
AMICI-dev · Aug 30, 2023 · f7cbca4 · f7cbca4
1 parent 556fba4
commit f7cbca4
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
   hooks:
     - id: isort
       name: isort (python)
-      args: ["--profile", "black", "--filter-files"]
+      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -17,16 +17,14 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 23.7.0
   hooks:
-    - id: black
+    - id: black-jupyter
       # It is recommended to specify the latest version of Python
       # supported by your project here, or alternatively use
       # pre-commit's default_language_version, see
       # https://pre-commit.com/#top_level-default_language_version
       language_version: python3.11
       args: ["--line-length", "79"]
-    - id: black-jupyter
-      language_version: python3.11
 
 exclude: '^(ThirdParty|models)/'
diff --git a/binder/overview.ipynb b/binder/overview.ipynb
@@ -34,7 +34,8 @@
     "\n",
     "* [Interfacing JAX](../python/examples/example_jax/ExampleJax.ipynb)\n",
     "\n",
-    "  Provides guidance on how to combine AMICI with differential programming frameworks such as JAX.\n"
+    "  Provides guidance on how to combine AMICI with differential programming frameworks such as JAX.\n",
+    "\n",
     "* [Efficient spline interpolation](../python/examples/example_splines/ExampleSplines.ipynb)\n",
     "\n",
     "  Shows how to add annotated spline formulas to existing SBML models in order to speed up AMICI's model import.\n",

diff --git a/documentation/ExampleJax.ipynb b/documentation/ExampleJax.ipynb
@@ -645,7 +645,9 @@
     "\n",
     "def amici_hcb_sllh(parameters: jnp.array):\n",
     "    sllh = amici_hcb_base(parameters)[\"sllh\"]\n",
-    "    return jnp.asarray(tuple(sllh[par_id] for par_id in petab_problem.x_free_ids))"
+    "    return jnp.asarray(\n",
+    "        tuple(sllh[par_id] for par_id in petab_problem.x_free_ids)\n",
+    "    )"
    ]
   },
   {
@@ -769,7 +771,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "llh_jax, sllh_jax = jax_objective_with_parameter_transform(petab_problem.x_nominal_free)"
+    "llh_jax, sllh_jax = jax_objective_with_parameter_transform(\n",
+    "    petab_problem.x_nominal_free\n",
+    ")"
    ]
   },
   {
@@ -791,7 +795,9 @@
     "# TODO remove me as soon as sllh in simulate_petab is fixed\n",
     "sllh = {\n",
     "    name: value / (np.log(10) * par_value)\n",
-    "    for (name, value), par_value in zip(r[\"sllh\"].items(), petab_problem.x_nominal_free)\n",
+    "    for (name, value), par_value in zip(\n",
+    "        r[\"sllh\"].items(), petab_problem.x_nominal_free\n",
+    "    )\n",
     "}"
    ]
   },
@@ -942,7 +948,9 @@
    "outputs": [],
    "source": [
     "jax.config.update(\"jax_enable_x64\", True)\n",
-    "llh_jax, sllh_jax = jax_objective_with_parameter_transform(petab_problem.x_nominal_free)"
+    "llh_jax, sllh_jax = jax_objective_with_parameter_transform(\n",
+    "    petab_problem.x_nominal_free\n",
+    ")"
    ]
   },
   {

diff --git a/documentation/conf.py b/documentation/conf.py
@@ -52,7 +52,9 @@ def my_exhale_generate_doxygen(doxygen_input):
     DomainDirectiveFactory as breathe_DomainDirectiveFactory,
 )
 
-old_breathe_DomainDirectiveFactory_create = breathe_DomainDirectiveFactory.create
+old_breathe_DomainDirectiveFactory_create = (
+    breathe_DomainDirectiveFactory.create
+)
 
 
 def my_breathe_DomainDirectiveFactory_create(domain: str, args):
@@ -67,7 +69,9 @@ def my_breathe_DomainDirectiveFactory_create(domain: str, args):
     return cls(domain + ":" + name, *args[1:])
 
 
-breathe_DomainDirectiveFactory.create = my_breathe_DomainDirectiveFactory_create
+breathe_DomainDirectiveFactory.create = (
+    my_breathe_DomainDirectiveFactory_create
+)
 
 
 # END Monkeypatch breathe
@@ -102,7 +106,9 @@ def install_doxygen():
     subprocess.run(cmd, shell=True, check=True)
     assert os.path.islink(os.path.join(some_dir_on_path, "doxygen"))
     # verify it's available
-    res = subprocess.run(["doxygen", "--version"], check=False, capture_output=True)
+    res = subprocess.run(
+        ["doxygen", "--version"], check=False, capture_output=True
+    )
     print(res.stdout.decode(), res.stderr.decode())
     assert version in res.stdout.decode()
 
@@ -294,7 +300,9 @@ def install_doxygen():
     "verboseBuild": True,
 }
 
-mtocpp_filter = os.path.join(amici_dir, "matlab", "mtoc", "config", "mtocpp_filter.sh")
+mtocpp_filter = os.path.join(
+    amici_dir, "matlab", "mtoc", "config", "mtocpp_filter.sh"
+)
 exhale_projects_args = {
     "AMICI_CPP": {
         "exhaleDoxygenStdin": "\n".join(

diff --git a/documentation/recreate_reference_list.py b/documentation/recreate_reference_list.py
@@ -42,7 +42,10 @@ def get_sub_bibliography(year, by_year, bibfile):
 
     entries = ",".join(["@" + x for x in by_year[year]])
     stdin_input = (
-        "---\n" f"bibliography: {bibfile}\n" f'nocite: "{entries}"\n...\n' f"# {year}"
+        "---\n"
+        f"bibliography: {bibfile}\n"
+        f'nocite: "{entries}"\n...\n'
+        f"# {year}"
     )
 
     out = subprocess.run(
@@ -67,7 +70,8 @@ def main():
     with open(outfile, "w") as f:
         f.write("# References\n\n")
         f.write(
-            "List of publications using AMICI. " f"Total number is {num_total}.\n\n"
+            "List of publications using AMICI. "
+            f"Total number is {num_total}.\n\n"
         )
         f.write(
             "If you applied AMICI in your work and your publication is "

diff --git a/python/benchmark/benchmark_pysb.py b/python/benchmark/benchmark_pysb.py
@@ -33,7 +33,9 @@
 
     with amici.add_path(os.path.dirname(pysb.examples.__file__)):
         with amici.add_path(
-            os.path.join(os.path.dirname(__file__), "..", "tests", "pysb_test_models")
+            os.path.join(
+                os.path.dirname(__file__), "..", "tests", "pysb_test_models"
+            )
         ):
             pysb.SelfExporter.cleanup()  # reset pysb
             pysb.SelfExporter.do_export = True
@@ -52,9 +54,9 @@
                 integrator_options={"rtol": rtol, "atol": atol},
             )
             time_pysb = (
-                timeit.Timer("pysb_simres = sim.run()", globals={"sim": sim}).timeit(
-                    number=N_REPEATS
-                )
+                timeit.Timer(
+                    "pysb_simres = sim.run()", globals={"sim": sim}
+                ).timeit(number=N_REPEATS)
                 / N_REPEATS
             )
 
@@ -76,7 +78,9 @@
                 observables=list(pysb_model.observables.keys()),
             )
 
-            amici_model_module = amici.import_model_module(pysb_model.name, outdir)
+            amici_model_module = amici.import_model_module(
+                pysb_model.name, outdir
+            )
 
             model_pysb = amici_model_module.getModel()
 

diff --git a/python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb b/python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb
@@ -61,7 +61,9 @@
    "source": [
     "from IPython.display import Image\n",
     "\n",
-    "fig = Image(filename=(\"../../../documentation/gfx/steadystate_solver_workflow.png\"))\n",
+    "fig = Image(\n",
+    "    filename=(\"../../../documentation/gfx/steadystate_solver_workflow.png\")\n",
+    ")\n",
     "fig"
    ]
   },
@@ -252,7 +254,9 @@
     ")\n",
     "model_reduced = model_reduced_module.getModel()\n",
     "\n",
-    "model_module = amici.import_model_module(model_name, os.path.abspath(model_output_dir))\n",
+    "model_module = amici.import_model_module(\n",
+    "    model_name, os.path.abspath(model_output_dir)\n",
+    ")\n",
     "model = model_module.getModel()\n",
     "\n",
     "\n",
@@ -431,7 +435,9 @@
     "solver.setMaxSteps(100)\n",
     "rdata = amici.runAmiciSimulation(model, solver)\n",
     "print(\"Status of postequilibration:\", rdata[\"posteq_status\"])\n",
-    "print(\"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"])"
+    "print(\n",
+    "    \"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"]\n",
+    ")"
    ]
   },
   {
@@ -470,7 +476,8 @@
     "\n",
     "print(\"Status of postequilibration:\", rdata_reduced[\"posteq_status\"])\n",
     "print(\n",
-    "    \"Number of steps employed in postequilibration:\", rdata_reduced[\"posteq_numsteps\"]\n",
+    "    \"Number of steps employed in postequilibration:\",\n",
+    "    rdata_reduced[\"posteq_numsteps\"],\n",
     ")"
    ]
   },
@@ -542,7 +549,9 @@
     "rdata = amici.runAmiciSimulation(model, solver)\n",
     "\n",
     "print(\"Status of postequilibration:\", rdata[\"posteq_status\"])\n",
-    "print(\"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"])\n",
+    "print(\n",
+    "    \"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"]\n",
+    ")\n",
     "print(\"Computed state sensitivities:\")\n",
     "print(rdata[\"sx\"][0, :, :])"
    ]
@@ -585,15 +594,19 @@
    "source": [
     "# Call simulation with singular Jacobian and newtonOnly mode (will fail)\n",
     "model.setTimepoints(np.full(1, np.inf))\n",
-    "model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.newtonOnly)\n",
+    "model.setSteadyStateSensitivityMode(\n",
+    "    amici.SteadyStateSensitivityMode.newtonOnly\n",
+    ")\n",
     "solver = model.getSolver()\n",
     "solver.setSensitivityMethod(amici.SensitivityMethod.forward)\n",
     "solver.setSensitivityOrder(amici.SensitivityOrder.first)\n",
     "solver.setMaxSteps(10000)\n",
     "rdata = amici.runAmiciSimulation(model, solver)\n",
     "\n",
     "print(\"Status of postequilibration:\", rdata[\"posteq_status\"])\n",
-    "print(\"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"])\n",
+    "print(\n",
+    "    \"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"]\n",
+    ")\n",
     "print(\"Computed state sensitivities:\")\n",
     "print(rdata[\"sx\"][0, :, :])"
    ]
@@ -621,7 +634,9 @@
    "source": [
     "# Call postequilibration by setting an infinity timepoint\n",
     "model_reduced.setTimepoints(np.full(1, np.inf))\n",
-    "model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.newtonOnly)\n",
+    "model.setSteadyStateSensitivityMode(\n",
+    "    amici.SteadyStateSensitivityMode.newtonOnly\n",
+    ")\n",
     "solver_reduced = model_reduced.getSolver()\n",
     "solver_reduced.setNewtonMaxSteps(10)\n",
     "solver_reduced.setSensitivityMethod(amici.SensitivityMethod.forward)\n",
@@ -631,7 +646,8 @@
     "\n",
     "print(\"Status of postequilibration:\", rdata_reduced[\"posteq_status\"])\n",
     "print(\n",
-    "    \"Number of steps employed in postequilibration:\", rdata_reduced[\"posteq_numsteps\"]\n",
+    "    \"Number of steps employed in postequilibration:\",\n",
+    "    rdata_reduced[\"posteq_numsteps\"],\n",
     ")\n",
     "print(\"Computed state sensitivities:\")\n",
     "print(rdata_reduced[\"sx\"][0, :, :])"
@@ -687,7 +703,9 @@
     "edata.setObservedData([1.8] * 2)\n",
     "edata.fixedParameters = np.array([3.0, 5.0])\n",
     "\n",
-    "model_reduced.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.newtonOnly)\n",
+    "model_reduced.setSteadyStateSensitivityMode(\n",
+    "    amici.SteadyStateSensitivityMode.newtonOnly\n",
+    ")\n",
     "solver_reduced = model_reduced.getSolver()\n",
     "solver_reduced.setNewtonMaxSteps(10)\n",
     "solver_reduced.setSensitivityMethod(amici.SensitivityMethod.adjoint)\n",
@@ -697,7 +715,8 @@
     "\n",
     "print(\"Status of postequilibration:\", rdata_reduced[\"posteq_status\"])\n",
     "print(\n",
-    "    \"Number of steps employed in postequilibration:\", rdata_reduced[\"posteq_numsteps\"]\n",
+    "    \"Number of steps employed in postequilibration:\",\n",
+    "    rdata_reduced[\"posteq_numsteps\"],\n",
     ")\n",
     "print(\n",
     "    \"Number of backward steps employed in postequilibration:\",\n",
@@ -733,17 +752,22 @@
    ],
    "source": [
     "# Call adjoint postequilibration with model with singular Jacobian\n",
-    "model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.newtonOnly)\n",
+    "model.setSteadyStateSensitivityMode(\n",
+    "    amici.SteadyStateSensitivityMode.newtonOnly\n",
+    ")\n",
     "solver = model.getSolver()\n",
     "solver.setNewtonMaxSteps(10)\n",
     "solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)\n",
     "solver.setSensitivityOrder(amici.SensitivityOrder.first)\n",
     "rdata = amici.runAmiciSimulation(model, solver, edata)\n",
     "\n",
     "print(\"Status of postequilibration:\", rdata[\"posteq_status\"])\n",
-    "print(\"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"])\n",
     "print(\n",
-    "    \"Number of backward steps employed in postequilibration:\", rdata[\"posteq_numstepsB\"]\n",
+    "    \"Number of steps employed in postequilibration:\", rdata[\"posteq_numsteps\"]\n",
+    ")\n",
+    "print(\n",
+    "    \"Number of backward steps employed in postequilibration:\",\n",
+    "    rdata[\"posteq_numstepsB\"],\n",
     ")\n",
     "print(\"Computed gradient:\", rdata[\"sllh\"])"
    ]
@@ -890,7 +914,9 @@
     "edata.setTimepoints(np.array([0.0, 0.1, 1.0]))\n",
     "\n",
     "# create the solver object and run the simulation, singular Jacobian, enforce Newton solver for sensitivities\n",
-    "model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.newtonOnly)\n",
+    "model.setSteadyStateSensitivityMode(\n",
+    "    amici.SteadyStateSensitivityMode.newtonOnly\n",
+    ")\n",
     "solver = model.getSolver()\n",
     "solver.setNewtonMaxSteps(10)\n",
     "solver.setSensitivityMethod(amici.SensitivityMethod.forward)\n",
@@ -1086,7 +1112,9 @@
     "solver_reduced = model_reduced.getSolver()\n",
     "solver_reduced.setNewtonMaxSteps(10)\n",
     "solver_reduced.setSensitivityMethod(amici.SensitivityMethod.adjoint)\n",
-    "solver_reduced.setSensitivityMethodPreequilibration(amici.SensitivityMethod.adjoint)\n",
+    "solver_reduced.setSensitivityMethodPreequilibration(\n",
+    "    amici.SensitivityMethod.adjoint\n",
+    ")\n",
     "solver_reduced.setSensitivityOrder(amici.SensitivityOrder.first)\n",
     "rdata_reduced = amici.runAmiciSimulation(model_reduced, solver_reduced, edata)\n",
     "\n",
@@ -1193,14 +1221,18 @@
     "solver_reduced.setAbsoluteToleranceSteadyState(1e-3)\n",
     "solver_reduced.setRelativeToleranceSteadyStateSensi(1e-2)\n",
     "solver_reduced.setAbsoluteToleranceSteadyStateSensi(1e-3)\n",
-    "rdata_reduced_lax = amici.runAmiciSimulation(model_reduced, solver_reduced, edata)\n",
+    "rdata_reduced_lax = amici.runAmiciSimulation(\n",
+    "    model_reduced, solver_reduced, edata\n",
+    ")\n",
     "\n",
     "# run with strict tolerances\n",
     "solver_reduced.setRelativeToleranceSteadyState(1e-12)\n",
     "solver_reduced.setAbsoluteToleranceSteadyState(1e-16)\n",
     "solver_reduced.setRelativeToleranceSteadyStateSensi(1e-12)\n",
     "solver_reduced.setAbsoluteToleranceSteadyStateSensi(1e-16)\n",
-    "rdata_reduced_strict = amici.runAmiciSimulation(model_reduced, solver_reduced, edata)\n",
+    "rdata_reduced_strict = amici.runAmiciSimulation(\n",
+    "    model_reduced, solver_reduced, edata\n",
+    ")\n",
     "\n",
     "# compare ODE outputs\n",
     "print(\"\\nODE solver steps, which were necessary to reach steady state:\")\n",