Added pooch registries for data files (pybamm-team#4098)

* added pooch * removed getpath() * added data_loader to notebooks and scripts * removed data files in the registry * added docs and implemented code review suggestions * added example notebook, unit tests and edited changelog * fixed pouch cell notebook * Apply suggestions from code review Co-authored-by: Agriya Khetarpal <[email protected]> * style: pre-commit fixes * added more test coverage, fixed notebook and code review suggestions * added bib references * fixed doctest and script test errors * fixed codacy warnings * using sockets for checking network * code review suggestions along with notebook update * Apply suggestions from code review Co-authored-by: Eric G. Kratz <[email protected]> * fixed RUF015 * changed link referenced and fixed lychee warning * changed the data files link under input/ to pybamm-data repo --------- Co-authored-by: Agriya Khetarpal <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ferran Brosa Planella <[email protected]> Co-authored-by: Arjun Verma <[email protected]> Co-authored-by: Eric G. Kratz <[email protected]>
js1tr3 · Aug 12, 2024 · 64f1bb1 · 64f1bb1
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diff --git a/.lycheeignore b/.lycheeignore
@@ -1,6 +1,8 @@
 # a list of links/files to be ignored by lychee link checker (see workflow file)
 https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v%7BSUITESPARSE_VERSION%7D.tar.gz
 https://github.com/LLNL/sundials/releases/download/v%7BSUNDIALS_VERSION%7D/sundials-%7BSUNDIALS_VERSION%7D.tar.gz
+https://mac.r-project.org/openmp/openmp-%7BOPENMP_VERSION%7D-darwin20-Release.tar.gz
+https://github.com/pybamm-team/pybamm-data/releases/download/%7Bself.version%7D
 
 # Errors in docs/source/user_guide/getting_started.md
 file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/api_docs

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,7 @@
 
 ## Breaking changes
 
+- Removed data files under `pybamm/input` and released them in a separate repository upstream at [pybamm-data](https://github.com/pybamm-team/pybamm-data/releases/tag/v1.0.0). Note that data files under `pybamm/input/parameters` have not been removed. ([#4098](https://github.com/pybamm-team/PyBaMM/pull/4098))
 - Removed `check_model` argument from `Simulation.solve`. To change the `check_model` option, use `Simulation(..., discretisation_kwargs={"check_model": False})`. ([#4020](https://github.com/pybamm-team/PyBaMM/pull/4020))
 - Removed multiple Docker images. Here on, a single Docker image tagged `pybamm/pybamm:latest` will be provided with both solvers (`IDAKLU` and `JAX`) pre-installed. ([#3992](https://github.com/pybamm-team/PyBaMM/pull/3992))
 - Removed support for Python 3.8 ([#3961](https://github.com/pybamm-team/PyBaMM/pull/3961))

diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -30,3 +30,4 @@ For a high-level introduction to PyBaMM, see the :ref:`user guide <user_guide>`
    callbacks
    citations
    batch_study
+   pybamm_data
diff --git a/docs/source/api/pybamm_data.rst b/docs/source/api/pybamm_data.rst
@@ -0,0 +1,7 @@
+PyBaMM Data
+===========
+
+.. autoclass:: pybamm.DataLoader
+  :members:
+
+.. footbibliography::
diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
@@ -127,3 +127,4 @@ The notebooks are organised into subfolders, and can be viewed in the galleries
     notebooks/change-settings.ipynb
     notebooks/initialize-model-with-solution.ipynb
     notebooks/solution-data-and-processed-variables.ipynb
+    notebooks/pybamm_data.ipynb
diff --git a/docs/source/examples/notebooks/initialize-model-with-solution.ipynb b/docs/source/examples/notebooks/initialize-model-with-solution.ipynb
@@ -23,10 +23,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[33mWARNING: You are using pip version 21.0.1; however, version 21.1 is available.\n",
-      "You should consider upgrading via the '/Users/vsulzer/Documents/Energy_storage/PyBaMM/.tox/dev/bin/python -m pip install --upgrade pip' command.\u001b[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "An NVIDIA GPU may be present on this machine, but a CUDA-enabled jaxlib is not installed. Falling back to cpu.\n"
+     ]
     }
    ],
    "source": [
@@ -76,8 +81,9 @@
    "outputs": [],
    "source": [
     "# import drive cycle from file\n",
+    "data_loader = pybamm.DataLoader()\n",
     "drive_cycle = pd.read_csv(\n",
-    "    \"pybamm/input/drive_cycles/US06.csv\", comment=\"#\", header=None\n",
+    "    f\"{data_loader.get_data(\"US06.csv\")}\", comment=\"#\", header=None\n",
     ").to_numpy()\n",
     "# create interpolant\n",
     "param = model.default_parameter_values\n",
@@ -160,7 +166,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7ad44c260ec446e0bd04a2f7dfbf8c65",
+       "model_id": "cd7fa37499ed49a7a8fa691a0ad9ffa6",
        "version_major": 2,
        "version_minor": 0
       },
@@ -174,7 +180,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x1447078e0>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x71a9e17ab080>"
       ]
      },
      "execution_count": 6,
@@ -241,7 +247,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "aaf63750ed354d1987703fd2fdde83af",
+       "model_id": "22c047080ebe4a14a664affed4e97ba1",
        "version_major": 2,
        "version_minor": 0
       },
@@ -255,7 +261,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x10437c370>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x71a9d02dac30>"
       ]
      },
      "execution_count": 8,
@@ -329,7 +335,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.12.3"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/docs/source/examples/notebooks/models/Validating_mechanical_models_Enertech_DFN.ipynb b/docs/source/examples/notebooks/models/Validating_mechanical_models_Enertech_DFN.ipynb
diff --git a/docs/source/examples/notebooks/models/compare-comsol-discharge-curve.ipynb b/docs/source/examples/notebooks/models/compare-comsol-discharge-curve.ipynb
diff --git a/docs/source/examples/notebooks/models/compare-ecker-data.ipynb b/docs/source/examples/notebooks/models/compare-ecker-data.ipynb
diff --git a/docs/source/examples/notebooks/models/pouch-cell-model.ipynb b/docs/source/examples/notebooks/models/pouch-cell-model.ipynb
diff --git a/docs/source/examples/notebooks/models/saving_models.ipynb b/docs/source/examples/notebooks/models/saving_models.ipynb
@@ -354,7 +354,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -368,10 +368,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
-  },
-  "orig_nbformat": 4
+   "version": "3.12.3"
+  }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/docs/source/examples/notebooks/parameterization/change-input-current.ipynb b/docs/source/examples/notebooks/parameterization/change-input-current.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "# Changing the input current when solving PyBaMM models\n",
     "\n",
-    "This notebook shows you how to change the input current when solving PyBaMM models. It also explains how to load in current data from a file, and how to add a user-defined current function. For more examples of different drive cycles see [here](https://github.com/pybamm-team/PyBaMM/tree/develop/pybamm/input/drive_cycles).\n",
+    "This notebook shows you how to change the input current when solving PyBaMM models. It also explains how to load in current data from a file, and how to add a user-defined current function. For more examples of different drive cycles see [here](https://github.com/pybamm-team/pybamm-data/releases/tag/v1.0.0).\n",
     "\n",
     "### Table of Contents\n",
     "1. Constant current\n",
@@ -38,6 +38,13 @@
      "text": [
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "An NVIDIA GPU may be present on this machine, but a CUDA-enabled jaxlib is not installed. Falling back to cpu.\n"
+     ]
     }
    ],
    "source": [
@@ -76,7 +83,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "aef64b871f1346a4b42c722c7eecfe38",
+       "model_id": "174048e3ccf74930a39a249dc0723975",
        "version_major": 2,
        "version_minor": 0
       },
@@ -86,6 +93,16 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x79ada1f321e0>"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -110,13 +127,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6447d4f706374208b5cbd283577b5da5",
+       "model_id": "bd1dbdfee61f4e518c3534b44e0ce879",
        "version_major": 2,
        "version_minor": 0
       },
@@ -126,6 +143,16 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x79ae443f29f0>"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -148,17 +175,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Downloading file 'US06.csv' from 'https://github.com/pybamm-team/pybamm-data/releases/download/v1.0.0/US06.csv' to '/home/santa/.cache/pybamm'.\n"
+     ]
+    }
+   ],
    "source": [
     "import pandas as pd  # needed to read the csv data file\n",
     "\n",
     "model = pybamm.lithium_ion.DFN()\n",
     "\n",
     "# import drive cycle from file\n",
+    "data_loader = pybamm.DataLoader()\n",
     "drive_cycle = pd.read_csv(\n",
-    "    \"pybamm/input/drive_cycles/US06.csv\", comment=\"#\", header=None\n",
+    "    f\"{data_loader.get_data(\"US06.csv\")}\", comment=\"#\", header=None\n",
     ").to_numpy()\n",
     "\n",
     "# load parameter values\n",
@@ -185,13 +221,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "84f87c3d21644c20bafdac8e9b69247d",
+       "model_id": "513c59118a6144a8a205510aaa9e9527",
        "version_major": 2,
        "version_minor": 0
       },
@@ -201,6 +237,16 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x79ad7d74c620>"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -233,7 +279,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -258,7 +304,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -283,13 +329,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6c06d938eca0491d88cdcbb29c59cd2a",
+       "model_id": "40a6ad712e184ba1a161932440d7a99d",
        "version_major": 2,
        "version_minor": 0
       },
@@ -299,6 +345,16 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x79ad73fea6c0>"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -352,7 +408,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.13 ('conda_jl')",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -366,7 +422,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.12.3"
   },
   "toc": {
    "base_numbering": 1,
@@ -388,5 +444,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }