Merge pull request #1874 from Saransh-cpp/make-colab-books-work

Make `PyBaMM` importable in `Linux` systems if `jax` is already installed
pybamm-team · Dec 29, 2021 · 660c5d2 · 660c5d2
2 parents ccf5be7 + ceb47d0
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diff --git a/.github/release_checklist.md b/.github/release_checklist.md
@@ -4,4 +4,4 @@
   - `CITATION.cff`
   - `vcpkg.json`
 - Update CHANGELOG.md with a summary of the release
-- Update jax and jaxlib to latest version in `pybamm.util.install_jax` and fix any bugs that arise
+- Update jax and jaxlib to latest version in `pybamm.util` and fix any bugs that arise
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 ## Bug fixes
 
+-   `PyBaMM` is now importable in `Linux` systems where `jax` is already installed ([#1874](https://github.com/pybamm-team/PyBaMM/pull/1874))
 -   Simulations with drive cycles now support `initial_soc` ([#1842](https://github.com/pybamm-team/PyBaMM/pull/1842))
 -   Fixed bug in expression tree simplification ([#1831](https://github.com/pybamm-team/PyBaMM/pull/1831))
 -   Solid tortuosity is now correctly calculated with Bruggeman coefficient of the respective electrode ([#1773](https://github.com/pybamm-team/PyBaMM/pull/1773))
@@ -37,7 +38,7 @@
 -   The `chemistry` keyword argument in `ParameterValues` has been deprecated. Use `ParameterValues(chem)` instead of `ParameterValues(chemistry=chem)` ([#1822](https://github.com/pybamm-team/PyBaMM/pull/1822))
 -   Raise error when trying to convert an `Interpolant` with the "pchip" interpolator to CasADI ([#1791](https://github.com/pybamm-team/PyBaMM/pull/1791))
 -   Raise error if `Concatenation` is used directly with `Variable` objects (`concatenation` should be used instead) ([#1789](https://github.com/pybamm-team/PyBaMM/pull/1789))
--   Made jax, jaxlib and the PyBaMM JaxSolver optional ([#1767](https://github.com/pybamm-team/PyBaMM/pull/1767))
+-   Made jax, jaxlib and the PyBaMM JaxSolver optional ([#1767](https://github.com/pybamm-team/PyBaMM/pull/1767), [#1803](https://github.com/pybamm-team/PyBaMM/pull/1803))
 
 # [v21.10](https://github.com/pybamm-team/PyBaMM/tree/v21.10) - 2021-10-31
 

diff --git a/examples/notebooks/Creating Models/1-an-ode-model.ipynb b/examples/notebooks/Creating Models/1-an-ode-model.ipynb
@@ -296,7 +296,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -310,7 +310,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/Creating Models/2-a-pde-model.ipynb b/examples/notebooks/Creating Models/2-a-pde-model.ipynb
@@ -340,7 +340,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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    "base_numbering": 1,

diff --git a/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb b/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb
@@ -362,7 +362,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb b/examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb
@@ -422,7 +422,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/Creating Models/5-half-cell-model.ipynb b/examples/notebooks/Creating Models/5-half-cell-model.ipynb
@@ -648,7 +648,7 @@
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    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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    "base_numbering": 1,

diff --git a/examples/notebooks/Creating Models/6-a-simple-SEI-model.ipynb b/examples/notebooks/Creating Models/6-a-simple-SEI-model.ipynb
@@ -728,7 +728,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -742,7 +742,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/Getting Started/Tutorial 1 - How to run a model.ipynb b/examples/notebooks/Getting Started/Tutorial 1 - How to run a model.ipynb
@@ -264,7 +264,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -278,7 +278,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 2 - Compare models.ipynb b/examples/notebooks/Getting Started/Tutorial 2 - Compare models.ipynb
@@ -158,7 +158,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -172,7 +172,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
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  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 3 - Basic plotting.ipynb b/examples/notebooks/Getting Started/Tutorial 3 - Basic plotting.ipynb
@@ -1072,7 +1072,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

diff --git a/examples/notebooks/Getting Started/Tutorial 4 - Setting parameter values.ipynb b/examples/notebooks/Getting Started/Tutorial 4 - Setting parameter values.ipynb
@@ -728,7 +728,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/Getting Started/Tutorial 5 - Run experiments.ipynb b/examples/notebooks/Getting Started/Tutorial 5 - Run experiments.ipynb
@@ -213,7 +213,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -227,7 +227,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.0"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/examples/notebooks/Getting Started/Tutorial 6 - Managing simulation outputs.ipynb b/examples/notebooks/Getting Started/Tutorial 6 - Managing simulation outputs.ipynb
@@ -436,7 +436,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -450,7 +450,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/Getting Started/Tutorial 7 - Model options.ipynb b/examples/notebooks/Getting Started/Tutorial 7 - Model options.ipynb
@@ -149,7 +149,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -163,7 +163,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
   }
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  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 8 - Solver options.ipynb b/examples/notebooks/Getting Started/Tutorial 8 - Solver options.ipynb
@@ -149,7 +149,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -163,7 +163,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Getting Started/Tutorial 9 - Changing the mesh.ipynb b/examples/notebooks/Getting Started/Tutorial 9 - Changing the mesh.ipynb
@@ -325,7 +325,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/batch_study.ipynb b/examples/notebooks/batch_study.ipynb
@@ -639,7 +639,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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    "base_numbering": 1,

diff --git a/examples/notebooks/change-settings.ipynb b/examples/notebooks/change-settings.ipynb
@@ -671,7 +671,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -685,7 +685,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/customize-quick-plot.ipynb b/examples/notebooks/customize-quick-plot.ipynb
@@ -31,7 +31,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install pybamm -q\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",
@@ -228,7 +228,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -242,7 +242,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.9.0"
   },
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diff --git a/examples/notebooks/expression_tree/broadcasts.ipynb b/examples/notebooks/expression_tree/broadcasts.ipynb
@@ -290,7 +290,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/examples/notebooks/expression_tree/expression-tree.ipynb b/examples/notebooks/expression_tree/expression-tree.ipynb
@@ -255,9 +255,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "PyBaMM development (env)",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "pybamm-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -269,9 +269,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/examples/notebooks/initialize-model-with-solution.ipynb b/examples/notebooks/initialize-model-with-solution.ipynb
@@ -30,7 +30,7 @@
     }
    ],
    "source": [
-    "%pip install pybamm -q\n",
+    "%pip install pybamm -q    # install PyBaMM if it is not installed\n",
     "\n",
     "import pybamm\n",
     "import pandas as pd\n",
@@ -312,7 +312,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -326,7 +326,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.0"
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    "base_numbering": 1,

diff --git a/examples/notebooks/models/DFN-with-particle-size-distributions.ipynb b/examples/notebooks/models/DFN-with-particle-size-distributions.ipynb
@@ -487,7 +487,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/models/DFN.ipynb b/examples/notebooks/models/DFN.ipynb
@@ -283,7 +283,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -297,7 +297,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.0"
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diff --git a/examples/notebooks/models/MPM.ipynb b/examples/notebooks/models/MPM.ipynb
@@ -973,7 +973,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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    "base_numbering": 1,

diff --git a/examples/notebooks/models/SPM.ipynb b/examples/notebooks/models/SPM.ipynb
@@ -1199,7 +1199,7 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
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