jinns 1.2.0__tar.gz → 1.3.0__tar.gz

{jinns-1.2.0 → jinns-1.3.0}/.gitlab-ci.yml

@@ -17,10 +17,11 @@ black:
 run_tests:
   stage: tests
   before_script:
-    - pip install --break-system-packages pytest coverage pytest-cov
-    - pwd
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip install pytest coverage pytest-cov
+    - pip install -e .
   script:
-    - pip install --break-system-packages -e .
     - pytest --cov=jinns --ignore=tests/solver_tests/test_NSPipeFlow_x64.py
   coverage: '/TOTAL.*\s+(\d+%)$/'
 
@@ -28,10 +29,13 @@ build_doc:
   stage: build
   needs: [] # don't need to wait for other jobs
   before_script:
-
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip install -e .
+    - pip install -r docs/doc_requirements.txt
   script:
-    - pip install --break-system-packages -e .
-    - pip install --break-system-packages -r docs/doc_requirements.txt
+    - pip list
+    - python -m mkdocstrings_handlers.python.debug
     - mkdocs build
     - mkdocs build  # twice, see https://github.com/patrick-kidger/pytkdocs_tweaks
 

{jinns-1.2.0 → jinns-1.3.0}/.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_stages: [commit]
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
         stages: [commit]
     -   id: end-of-file-fixer
         stages: [commit]
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 25.1.0
     hooks:
     -   id: black
         stages: [commit]

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/ODE/1D_Generalized_Lotka_Volterra.ipynb

@@ -109,16 +109,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "eqx_list = [\n",
-    "    [eqx.nn.Linear, 1, 20],\n",
-    "    [jax.nn.tanh],\n",
-    "    [eqx.nn.Linear, 20, 20],\n",
-    "    [jax.nn.tanh],\n",
-    "    [eqx.nn.Linear, 20, 20],\n",
-    "    [jax.nn.tanh],\n",
-    "    [eqx.nn.Linear, 20, 1],\n",
-    "    [jnp.exp]\n",
-    "]\n",
+    "eqx_list = (\n",
+    "    (eqx.nn.Linear, 1, 20),\n",
+    "    (jax.nn.tanh,),\n",
+    "    (eqx.nn.Linear, 20, 20),\n",
+    "    (jax.nn.tanh,),\n",
+    "    (eqx.nn.Linear, 20, 20),\n",
+    "    (jax.nn.tanh,),\n",
+    "    (eqx.nn.Linear, 20, 1),\n",
+    "    (jnp.exp,)\n",
+    ")\n",
     "key, subkey = random.split(key)"
    ]
   },
@@ -172,7 +172,7 @@
     "init_nn_params_list = []\n",
     "for _ in range(3):\n",
     "    key, subkey = random.split(key)\n",
-    "    u, init_nn_params = jinns.utils.create_PINN(subkey, eqx_list, \"ODE\", 0)\n",
+    "    u, init_nn_params = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"ODE\")\n",
     "    init_nn_params_list.append(init_nn_params)"
    ]
   },

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/ODE/linear_fo_equation.ipynb

@@ -103,18 +103,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "eqx_list = [\n",
-    "    [eqx.nn.Linear, 1, 20],\n",
-    "    [jax.nn.tanh],\n",
-    "    [eqx.nn.Linear, 20, 20],\n",
-    "    [jax.nn.tanh],\n",
-    "    [eqx.nn.Linear, 20, 20],\n",
-    "    [jax.nn.tanh],\n",
-    "    [eqx.nn.Linear, 20, 1],\n",
-    "    # [jnp.exp]\n",
-    "]\n",
+    "eqx_list = (\n",
+    "    (eqx.nn.Linear, 1, 20),\n",
+    "    (jax.nn.tanh,),\n",
+    "    (eqx.nn.Linear, 20, 20),\n",
+    "    (jax.nn.tanh,),\n",
+    "    (eqx.nn.Linear, 20, 20),\n",
+    "    (jax.nn.tanh,),\n",
+    "    (eqx.nn.Linear, 20, 1),\n",
+    "    # (jnp.exp,)\n",
+    ")\n",
     "key, subkey = random.split(key)\n",
-    "u, init_nn_params = jinns.utils.create_PINN(subkey, eqx_list, \"ODE\")"
+    "u, init_nn_params = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"ODE\")"
    ]
   },
   {

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/ODE/systems_biology_informed_neural_network.ipynb

@@ -253,11 +253,10 @@
     "\n",
     "for i, k in enumerate(nn_keys):\n",
     "    key, subkey = random.split(key)\n",
-    "    u_k, init_nn_params_k = jinns.utils.create_PINN(\n",
-    "        subkey,\n",
-    "        eqx_list,\n",
-    "        \"ODE\",\n",
-    "        0,\n",
+    "    u_k, init_nn_params_k = jinns.nn.PINN_MLP.create(\n",
+    "        key=subkey,\n",
+    "        eqx_list=eqx_list,\n",
+    "        eq_type=\"ODE\",\n",
     "        input_transform=feature_transform,\n",
     "        output_transform=partial(output_transform, id_component=i),\n",
     "    )\n",

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/PDE/1D_non_stationary_Burgers.ipynb

@@ -116,7 +116,7 @@
     "    (eqx.nn.Linear, 32, 1)\n",
     ")\n",
     "key, subkey = random.split(key)\n",
-    "u_pinn, init_nn_params_pinn = jinns.utils.create_PINN(subkey, eqx_list, \"nonstatio_PDE\", 1)"
+    "u_pinn, init_nn_params_pinn = jinns.nn.PINN_MLP(key=subkey, eqx_list=eqx_list, eq_type=\"nonstatio_PDE\")"
    ]
   },
   {
@@ -146,7 +146,7 @@
     "    (eqx.nn.Linear, 128, r)\n",
     ")\n",
     "key, subkey = random.split(key)\n",
-    "u_spinn, init_nn_params_spinn = jinns.utils.create_SPINN(subkey, d, r, eqx_list, \"nonstatio_PDE\")"
+    "u_spinn, init_nn_params_spinn = jinns.nn.SPINN_MLP.create(subkey, d, r, eqx_list, \"nonstatio_PDE\")"
    ]
   },
   {

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/PDE/1D_non_stationary_Fisher_KPP_Bounded_Domain.ipynb

@@ -153,7 +153,7 @@
     "    (jnp.exp,)\n",
     ")\n",
     "key, subkey = random.split(key)\n",
-    "u_pinn, init_nn_params_pinn = jinns.utils.create_PINN(subkey, eqx_list, \"nonstatio_PDE\", 1)"
+    "u_pinn, init_nn_params_pinn = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"nonstatio_PDE\")"
    ]
   },
   {
@@ -184,7 +184,7 @@
     "\n",
     ")\n",
     "key, subkey = random.split(key)\n",
-    "u_spinn, init_nn_params_spinn = jinns.utils.create_SPINN(subkey, d, r, eqx_list, \"nonstatio_PDE\")"
+    "u_spinn, init_nn_params_spinn = jinns.nn.SPINN_MLP.create(subkey, d, r, eqx_list, \"nonstatio_PDE\")"
    ]
   },
   {

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/PDE/2D_Heat_inverse_problem.ipynb

@@ -201,7 +201,7 @@
     ")\n",
     "\n",
     "key, subkey = random.split(key)\n",
-    "u, init_sol_nn_params= jinns.utils.create_PINN(subkey, eqx_list, \"nonstatio_PDE\", 2, slice_solution=jnp.s_[:1])"
+    "u, init_sol_nn_params= jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"nonstatio_PDE\", slice_solution=jnp.s_[:1])"
    ]
   },
   {
@@ -230,7 +230,7 @@
     "# )\n",
     "\n",
     "# key, subkey = random.split(key)\n",
-    "# sol_pinn = jinns.utils.create_PINN(subkey, eqx_list, \"nonstatio_PDE\", 2)\n",
+    "# sol_pinn = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"nonstatio_PDE\")\n",
     "# init_sol_nn_params = sol_pinn.init_params()\n",
     "# eqx_list = (\n",
     "#     (eqx.nn.Linear, 3, 50), # 3 = t + x (2D)\n",
@@ -243,7 +243,7 @@
     "# )\n",
     "\n",
     "# key, subkey = random.split(key)\n",
-    "# a_pinn = jinns.utils.create_PINN(subkey, eqx_list, \"nonstatio_PDE\", 2)\n",
+    "# a_pinn = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"nonstatio_PDE\")\n",
     "# init_a_nn_params = a_pinn.init_params()\n",
     "\n",
     "# from jinns.utils._pinn import PINN\n",

{jinns-1.2.0 → jinns-1.3.0}/Notebooks/PDE/2D_Navier_Stokes_PipeFlow.ipynb

@@ -206,7 +206,7 @@
     "]\n",
     "key, subkey = random.split(key)\n",
     "u_output_transform = lambda pinn_in, pinn_out, params: pinn_out * (R**2 - pinn_in[1] ** 2)\n",
-    "u, u_init_nn_params = jinns.utils.create_PINN(subkey, eqx_list, \"statio_PDE\", 2, output_transform=u_output_transform)\n",
+    "u, u_init_nn_params = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"statio_PDE\", output_transform=u_output_transform)\n",
     "\n",
     "eqx_list = [\n",
     "    [eqx.nn.Linear, 2, 50],\n",
@@ -223,7 +223,7 @@
     "         + (xmax - pinn_in[0]) / (xmax - xmin) * p_in\n",
     "         + (xmin - pinn_in[0]) * (xmax - pinn_in[0]) * pinn_out\n",
     "     )\n",
-    "p, p_init_nn_params = jinns.utils.create_PINN(subkey, eqx_list, \"statio_PDE\", 2, output_transform=p_output_transform)"
+    "p, p_init_nn_params = jinns.nn.PINN_MLP.create(key=subkey, eqx_list=eqx_list, eq_type=\"statio_PDE\", output_transform=p_output_transform)"
    ]
   },
   {