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Make PyBaMM importable in Linux systems if jax is already installed #1874

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merged 10 commits into from
Dec 29, 2021
Merged

Make PyBaMM importable in Linux systems if jax is already installed #1874

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8786b29
Uninstall jax before installing PyBaMM in notebooks
Saransh-cpp Dec 27, 2021
4a2a201
Add `--yes` flag while uninstalling `jax`
Saransh-cpp Dec 27, 2021
b448299
Add a new function to check jax and jaxlib versions
Saransh-cpp Dec 27, 2021
1d2fa8e
Update the error message
Saransh-cpp Dec 27, 2021
09c6e23
Rename function, add documentation and test
Saransh-cpp Dec 28, 2021
ce4ef19
flake8
Saransh-cpp Dec 28, 2021
73d10f3
Fix tests + revert notebook changes
Saransh-cpp Dec 28, 2021
bc62937
Update CHANGELOG.md
Saransh-cpp Dec 28, 2021
80bc629
Create global variables for jax and jaxlib versions
Saransh-cpp Dec 28, 2021
ceb47d0
coverage
Saransh-cpp Dec 28, 2021
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5 changes: 3 additions & 2 deletions examples/notebooks/Creating Models/1-an-ode-model.ipynb
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Expand Up @@ -37,6 +37,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -296,7 +297,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -310,7 +311,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.10"
"version": "3.9.0"
}
},
"nbformat": 4,
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3 changes: 2 additions & 1 deletion examples/notebooks/Creating Models/2-a-pde-model.ipynb
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Expand Up @@ -39,6 +39,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -340,7 +341,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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3 changes: 2 additions & 1 deletion examples/notebooks/Creating Models/3-negative-particle-problem.ipynb
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Expand Up @@ -62,6 +62,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -362,7 +363,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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3 changes: 2 additions & 1 deletion examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb
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Expand Up @@ -57,6 +57,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -422,7 +423,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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3 changes: 2 additions & 1 deletion examples/notebooks/Creating Models/5-half-cell-model.ipynb
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Expand Up @@ -68,6 +68,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -648,7 +649,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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5 changes: 3 additions & 2 deletions examples/notebooks/Creating Models/6-a-simple-SEI-model.ipynb
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Expand Up @@ -188,6 +188,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -728,7 +729,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -742,7 +743,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.10"
"version": "3.9.0"
}
},
"nbformat": 4,
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5 changes: 3 additions & 2 deletions examples/notebooks/Getting Started/Tutorial 1 - How to run a model.ipynb
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Expand Up @@ -32,6 +32,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm"
]
Expand Down Expand Up @@ -264,7 +265,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -278,7 +279,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.0"
}
},
"nbformat": 4,
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5 changes: 3 additions & 2 deletions examples/notebooks/Getting Started/Tutorial 2 - Compare models.ipynb
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Expand Up @@ -30,6 +30,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm"
]
Expand Down Expand Up @@ -158,7 +159,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -172,7 +173,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.0"
}
},
"nbformat": 4,
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3 changes: 2 additions & 1 deletion examples/notebooks/Getting Started/Tutorial 3 - Basic plotting.ipynb
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Expand Up @@ -47,6 +47,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import matplotlib.pyplot as plt\n",
Expand Down Expand Up @@ -1072,7 +1073,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
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3 changes: 2 additions & 1 deletion examples/notebooks/Getting Started/Tutorial 4 - Setting parameter values.ipynb
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Expand Up @@ -28,6 +28,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import os\n",
Expand Down Expand Up @@ -728,7 +729,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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5 changes: 3 additions & 2 deletions examples/notebooks/Getting Started/Tutorial 5 - Run experiments.ipynb
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Expand Up @@ -28,6 +28,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm"
]
Expand Down Expand Up @@ -213,7 +214,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -227,7 +228,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.8"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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5 changes: 3 additions & 2 deletions examples/notebooks/Getting Started/Tutorial 6 - Managing simulation outputs.ipynb
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Expand Up @@ -40,6 +40,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"model = pybamm.lithium_ion.SPMe()\n",
Expand Down Expand Up @@ -436,7 +437,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -450,7 +451,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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5 changes: 3 additions & 2 deletions examples/notebooks/Getting Started/Tutorial 7 - Model options.ipynb
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Expand Up @@ -23,6 +23,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm"
]
Expand Down Expand Up @@ -149,7 +150,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -163,7 +164,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.0"
}
},
"nbformat": 4,
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5 changes: 3 additions & 2 deletions examples/notebooks/Getting Started/Tutorial 8 - Solver options.ipynb
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Expand Up @@ -27,6 +27,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm"
]
Expand Down Expand Up @@ -149,7 +150,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -163,7 +164,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.0"
}
},
"nbformat": 4,
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3 changes: 2 additions & 1 deletion examples/notebooks/Getting Started/Tutorial 9 - Changing the mesh.ipynb
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Expand Up @@ -27,6 +27,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm"
]
Expand Down Expand Up @@ -325,7 +326,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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3 changes: 2 additions & 1 deletion examples/notebooks/batch_study.ipynb
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Expand Up @@ -31,6 +31,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"\n",
Expand Down Expand Up @@ -639,7 +640,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
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5 changes: 3 additions & 2 deletions examples/notebooks/change-settings.ipynb
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Expand Up @@ -39,6 +39,7 @@
}
],
"source": [
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"import numpy as np\n",
Expand Down Expand Up @@ -671,7 +672,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -685,7 +686,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.0"
}
},
"nbformat": 4,
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7 changes: 4 additions & 3 deletions examples/notebooks/customize-quick-plot.ipynb
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Expand Up @@ -31,7 +31,8 @@
"metadata": {},
"outputs": [],
"source": [
"%pip install pybamm -q\n",
"%pip uninstall --yes jax # uninstall jax if it is installed (Google Colab)\n",
"%pip install pybamm -q # install PyBaMM if it is not installed\n",
"import pybamm\n",
"\n",
"models = [pybamm.lithium_ion.SPM(), pybamm.lithium_ion.SPMe(), pybamm.lithium_ion.DFN()]\n",
Expand Down Expand Up @@ -228,7 +229,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -242,7 +243,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.9.0"
},
"toc": {
"base_numbering": 1,
Expand Down
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