Merge pull request #57 from RangamaniLabUCSD/dokken/deprecated_unused…

…_functions Add deprecation notice
RangamaniLabUCSD · Mar 1, 2023 · 7575ae8 · 7575ae8
2 parents 49bcfc3 + d4bb91a
commit 7575ae8
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diff --git a/docs/_pythonapi/stubs.common.rst b/docs/_pythonapi/stubs.common.rst
@@ -19,8 +19,7 @@
       convert_xml_to_hdf5
       cube_condition
       data_path
-      empty_sbmodel
-      face_topology
+      facet_topology
       find_steady_state
       insert_dataframe_col
       interp_limit_dy
@@ -33,7 +32,6 @@
       read_hdf5
       read_sbmodel
       round_to_n
-      sbmodel_from_locals
       stubs_expressions
       sub
       submesh_dof_to_mesh_dof

diff --git a/examples/example1/example1.ipynb b/examples/example1/example1.ipynb
@@ -25,27 +25,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "cc398816",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Authorization required, but no authorization protocol specified\n",
-      "Authorization required, but no authorization protocol specified\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "\n",
     "import dolfin as d\n",
     "import sympy as sym\n",
     "\n",
     "from stubs import unit, config, common, mesh, model\n",
-    "from stubs.model_assembly import Compartment, Parameter, Reaction, Species"
+    "from stubs.model_assembly import Compartment, Parameter, Reaction, Species, sbmodel_from_locals"
    ]
   },
   {
@@ -59,7 +50,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "4f4023cf",
    "metadata": {},
    "outputs": [],
@@ -87,7 +78,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "09079b17",
    "metadata": {},
    "outputs": [],
@@ -164,7 +155,7 @@
     "    # =============================================================================================\n",
     "    # Gather all parameters, species, compartments and reactions\n",
     "    # =============================================================================================\n",
-    "    return common.sbmodel_from_locals(locals().values())"
+    "    return sbmodel_from_locals(locals().values())"
    ]
   },
   {
@@ -178,48 +169,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "fe56e162",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[32m[2023-01-20 time=02:35:42] Creating dolfin object for space-dependent initial condition R1\u001b[0m \u001b[97m\u001b[0m\n",
-      "\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!\u001b[0m \u001b[31m[2023-01-20 time=02:35:42] Warning! Pre-integrating parameter j1pulse. Make sure that expressions j1pulse appears in have no other time-dependent variables.\u001b[0m \u001b[35m!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\n",
-      "\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!\u001b[0m \u001b[31m[2023-01-20 time=02:35:42] Warning! Pre-integrating parameter j1pulse. Make sure that expressions j1pulse appears in have no other time-dependent variables.\u001b[0m \u001b[35m!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\u001b[35m!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\u001b[0m\n",
-      "\n",
-      "\u001b[32m[2023-01-20 time=02:35:42] Time-dependent parameter j1pulse evaluated from expression.\u001b[0m \u001b[97m\u001b[0m\n",
-      "HDF5 mesh, \"parent_mesh\", successfully loaded from file: mesh/DemoCuboidsMesh.h5!\n",
-      "Object `config.solver.update` not found.\n"
-     ]
-    },
-    {
-     "ename": "AttributeError",
-     "evalue": "'SolverConfig' object has no attribute 'update'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[4], line 25\u001b[0m\n\u001b[1;32m     23\u001b[0m model \u001b[39m=\u001b[39m model\u001b[39m.\u001b[39mModel(pc, sc, cc, rc, config, parent_mesh)\n\u001b[1;32m     24\u001b[0m get_ipython()\u001b[39m.\u001b[39mrun_line_magic(\u001b[39m'\u001b[39m\u001b[39mpinfo\u001b[39m\u001b[39m'\u001b[39m, \u001b[39m'\u001b[39m\u001b[39mconfig.solver.update\u001b[39m\u001b[39m'\u001b[39m)\n\u001b[0;32m---> 25\u001b[0m config\u001b[39m.\u001b[39;49msolver\u001b[39m.\u001b[39;49mupdate(\n\u001b[1;32m     26\u001b[0m     {\n\u001b[1;32m     27\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mfinal_t\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m1\u001b[39m,\n\u001b[1;32m     28\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39minitial_dt\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m0.01\u001b[39m,\n\u001b[1;32m     29\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mtime_precision\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m6\u001b[39m,\n\u001b[1;32m     30\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39muse_snes\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39mTrue\u001b[39;00m,\n\u001b[1;32m     31\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mprint_assembly\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39mFalse\u001b[39;00m,\n\u001b[1;32m     32\u001b[0m     }\n\u001b[1;32m     33\u001b[0m )\n\u001b[1;32m     35\u001b[0m model\u001b[39m.\u001b[39minitialize(initialize_solver\u001b[39m=\u001b[39m\u001b[39mFalse\u001b[39;00m)\n\u001b[1;32m     36\u001b[0m model\u001b[39m.\u001b[39minitialize_discrete_variational_problem_and_solver()\n",
-      "\u001b[0;31mAttributeError\u001b[0m: 'SolverConfig' object has no attribute 'update'"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "\n",
     "pc, sc, cc, rc = make_model()\n",
     "\n",
     "# =============================================================================================\n",
@@ -281,7 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b54d28ca",
+   "id": "644b1304",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -294,7 +248,7 @@
    "notebook_metadata_filter": "-all"
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

diff --git a/examples/example2/example2.ipynb b/examples/example2/example2.ipynb
@@ -33,7 +33,7 @@
     "import numpy as np\n",
     "\n",
     "from stubs import unit, config, common, mesh, model\n",
-    "from stubs.model_assembly import Compartment, Parameter, Reaction, Species"
+    "from stubs.model_assembly import Compartment, Parameter, Reaction, Species, sbmodel_from_locals"
    ]
   },
   {
@@ -113,7 +113,7 @@
     "    # =============================================================================================\n",
     "    # Gather all parameters, species, compartments and reactions\n",
     "    # =============================================================================================\n",
-    "    return common.sbmodel_from_locals(locals().values())"
+    "    return sbmodel_from_locals(locals().values())"
    ]
   },
   {
@@ -187,6 +187,14 @@
     "        if modelCur.t >= modelCur.final_t:\n",
     "            break"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4fe15da8",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/examples/misc/rabona/test_different_step_size_err.py b/examples/misc/rabona/test_different_step_size_err.py
@@ -17,7 +17,7 @@
 
 errors = []
 for dt in [0.012, 0.01, 0.008, 0.006, 0.004, 0.002]:
-    pc, sc, cc, rc = stubs.common.read_sbmodel('model.sbmodel')
+    pc, sc, cc, rc = stubs.model_assembly.read_sbmodel('model.sbmodel')
 
     # Define solvers
     mps = stubs.solvers.MultiphysicsSolver('iterative')

diff --git a/stubs/__init__.py b/stubs/__init__.py
@@ -12,5 +12,5 @@
     "common",
     "mesh",
     "unit",
-    "post_process"
+    "post_process",
 ]