Merge branch 'develop' into install_odes

.all-contributorsrc

@@ -442,7 +442,7 @@
       "login": "wigging",
       "name": "Gavin Wiggins",
       "avatar_url": "https://avatars.githubusercontent.com/u/6828967?v=4",
-      "profile": "https://wigging.me",
+      "profile": "https://gavinw.me",
       "contributions": [
         "bug",
         "code"
@@ -708,6 +708,15 @@
       "contributions": [
         "infra"
       ]
+    },
+    {
+      "login": "Agnik7",
+      "name": "Agnik Bakshi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/77234005?v=4",
+      "profile": "https://github.com/Agnik7",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/release_reminder.md

@@ -1,5 +1,6 @@
 ---
 title: Create {{ date | date('YY.MM') }} (final or rc0) release
+labels: priority:high
 ---
 Quarterly reminder to create a -
 

.github/wheel_failure.md

@@ -0,0 +1,6 @@
+---
+title: Fortnightly build for wheels failed
+labels: priority:high, bug
+---
+
+The build is failing with the following logs - {{ env.LOGS }}

.github/workflows/docker.yml

@@ -0,0 +1,75 @@
+name: Build & Push Docker Images
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+    - develop
+
+jobs:
+  pre_job:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+            username: ${{ secrets.DOCKERHUB_USERNAME }}
+            password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: List built images
+        run: docker images
+
+      - name: Build and Push Docker Image (Without Solvers)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:latest
+          push: true
+
+      - name: Build and Push Docker Image (With JAX Solver)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:jax
+          push: true
+          build-args: |
+            JAX=true
+
+      - name: Build and Push Docker Image (With ODES & DAE Solver)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:odes
+          push: true
+          build-args: |
+            ODES=true
+
+      - name: Build and Push Docker Image (With IDAKLU Solver)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:idaklu
+          push: true
+          build-args: |
+            IDAKLU=true
+
+      - name: Build and Push Docker Image (With All Solvers)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:latest
+          push: true
+          build-args: |
+            ALL=true

.github/workflows/publish_pypi.yml

@@ -3,6 +3,9 @@ name: Build and publish package to PyPI
 on:
   release:
     types: [published]
+  schedule:
+    # Run at 10 am UTC on day-of-month 1 and 15.
+    - cron: "0 10 1,15 * *"
   workflow_dispatch:
     inputs:
       target:
@@ -151,6 +154,7 @@ jobs:
           if-no-files-found: error
 
   publish_pypi:
+    if: github.event_name != 'schedule'
     name: Upload package to PyPI
     needs: [build_wheels, build_windows_wheels, build_sdist]
     runs-on: ubuntu-latest
@@ -164,9 +168,7 @@ jobs:
           mv windows_wheels/* wheels/* sdist/* files/
 
       - name: Publish on PyPI
-        if: |
-          github.event.inputs.target == 'pypi' ||
-          (github.event_name == 'push' && github.ref == 'refs/heads/main')
+        if: github.event.inputs.target == 'pypi' || github.event_name == 'release'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
@@ -181,3 +183,17 @@ jobs:
           password: ${{ secrets.TESTPYPI_TOKEN }}
           packages-dir: files/
           repository-url: https://test.pypi.org/legacy/
+
+  open_failure_issue:
+    needs: [build_windows_wheels, build_wheels, build_sdist]
+    name: Open an issue if build fails
+    if: ${{ always() && contains(needs.*.result, 'failure') }}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: JasonEtco/create-an-issue@v2
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        LOGS: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+      with:
+        filename: .github/wheel_failure.md

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
          additional_dependencies: [black==22.12.0]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
         - id: check-added-large-files
         - id: check-case-conflict

CONTRIBUTING.md

@@ -44,7 +44,7 @@ You now have everything you need to start making changes!
 
 ### B. Writing your code
 
-6. PyBaMM is developed in [Python](https://en.wikipedia.org/wiki/Python_(programming_language)), and makes heavy use of [NumPy](https://en.wikipedia.org/wiki/NumPy) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](http://blog.hackerearth.com/how-can-r-users-learn-python-for-data-science)).
+6. PyBaMM is developed in [Python](https://en.wikipedia.org/wiki/Python_(programming_language)), and makes heavy use of [NumPy](https://en.wikipedia.org/wiki/NumPy) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](https://www.rebeccabarter.com/blog/2023-09-11-from_r_to_python)).
 7. Make sure to follow our [coding style guidelines](#coding-style-guidelines).
 8. Commit your changes to your branch with [useful, descriptive commit messages](https://chris.beams.io/posts/git-commit/): Remember these are publicly visible and should still make sense a few months ahead in time. While developing, you can keep using the GitHub issue you're working on as a place for discussion. [Refer to your commits](https://stackoverflow.com/questions/8910271/how-can-i-reference-a-commit-in-an-issue-comment-on-github) when discussing specific lines of code.
 9. If you want to add a dependency on another library, or re-use code you found somewhere else, have a look at [these guidelines](#dependencies-and-reusing-code).
@@ -185,7 +185,7 @@ You may also test multiple notebooks this way. Passing the path to a folder will
 nox -s examples -- docs/source/examples/notebooks/models/
 ```
 
-You may also use an appropriate [glob pattern](https://www.malikbrowne.com/blog/a-beginners-guide-glob-patterns) to run all notebooks matching a particular folder or name pattern.
+You may also use an appropriate [glob pattern](https://docs.python.org/3/library/glob.html) to run all notebooks matching a particular folder or name pattern.
 
 To edit the structure and how the Jupyter notebooks get rendered in the Sphinx documentation (using `nbsphinx`), install [Pandoc](https://pandoc.org/installing.html) on your system, either using `conda` (through the `conda-forge` channel)
 

README.md

@@ -14,7 +14,7 @@
 [![code style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-64-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-65-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -233,7 +233,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/chuckliu1979"><img src="https://avatars.githubusercontent.com/u/13491954?v=4?s=100" width="100px;" alt="Chuck Liu"/><br /><sub><b>Chuck Liu</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achuckliu1979" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=chuckliu1979" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/partben"><img src="https://avatars.githubusercontent.com/u/88316576?v=4?s=100" width="100px;" alt="partben"/><br /><sub><b>partben</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=partben" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://wigging.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt="Gavin Wiggins"/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://gavinw.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt="Gavin Wiggins"/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/dion-w"><img src="https://avatars.githubusercontent.com/u/91852142?v=4?s=100" width="100px;" alt="Dion Wilde"/><br /><sub><b>Dion Wilde</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Adion-w" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=dion-w" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.ehtec.co"><img src="https://avatars.githubusercontent.com/u/48386220?v=4?s=100" width="100px;" alt="Elias Hohl"/><br /><sub><b>Elias Hohl</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=ehtec" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/KAschad"><img src="https://avatars.githubusercontent.com/u/93784399?v=4?s=100" width="100px;" alt="KAschad"/><br /><sub><b>KAschad</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AKAschad" title="Bug reports">🐛</a></td>
@@ -268,6 +268,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://aitorres.com"><img src="https://avatars.githubusercontent.com/u/26191851?v=4?s=100" width="100px;" alt="Andrés Ignacio Torres"/><br /><sub><b>Andrés Ignacio Torres</b></sub></a><br /><a href="#infra-aitorres" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Agnik7"><img src="https://avatars.githubusercontent.com/u/77234005?v=4?s=100" width="100px;" alt="Agnik Bakshi"/><br /><sub><b>Agnik Bakshi</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=Agnik7" title="Documentation">📖</a></td>
     </tr>
   </tbody>
 </table>

docs/conf.py

@@ -155,6 +155,10 @@
     # add Algolia to the persistent navbar, this removes the default search icon
     "navbar_persistent": "algolia-searchbox",
     "use_edit_page_button": True,
+    "analytics": {
+        "plausible_analytics_domain": "docs.pybamm.org",
+        "plausible_analytics_url": "https://plausible.io/js/script.js",
+    },
     "pygment_light_style": "xcode",
     "pygment_dark_style": "monokai",
     "footer_start": [

tests/unit/test_batch_study.py

@@ -5,6 +5,7 @@
 import os
 import pybamm
 import unittest
+from tempfile import TemporaryDirectory
 
 spm = pybamm.lithium_ion.SPM()
 spm_uniform = pybamm.lithium_ion.SPM({"particle": "uniform profile"})
@@ -90,21 +91,19 @@ def test_solve(self):
             self.assertIn(output_experiment, experiments_list)
 
     def test_create_gif(self):
-        bs = pybamm.BatchStudy({"spm": pybamm.lithium_ion.SPM()})
-        bs.solve([0, 10])
+        with TemporaryDirectory() as dir_name:
+            bs = pybamm.BatchStudy({"spm": pybamm.lithium_ion.SPM()})
+            bs.solve([0, 10])
 
-        # Create a temporary file name
-        test_stub = "batch_study_test"
-        test_file = f"{test_stub}.gif"
+            # Create a temporary file name
+            test_file = os.path.join(dir_name, "batch_study_test.gif")
 
-        # create a GIF before calling the plot method
-        bs.create_gif(number_of_images=3, duration=1, output_filename=test_file)
+            # create a GIF before calling the plot method
+            bs.create_gif(number_of_images=3, duration=1, output_filename=test_file)
 
-        # create a GIF after calling the plot method
-        bs.plot(testing=True)
-        bs.create_gif(number_of_images=3, duration=1, output_filename=test_file)
-
-        os.remove(test_file)
+            # create a GIF after calling the plot method
+            bs.plot(testing=True)
+            bs.create_gif(number_of_images=3, duration=1, output_filename=test_file)
 
 
 if __name__ == "__main__":

tests/unit/test_expression_tree/test_symbol.py

@@ -4,6 +4,7 @@
 from tests import TestCase
 import os
 import unittest
+from tempfile import TemporaryDirectory
 
 import numpy as np
 from scipy.sparse import csr_matrix, coo_matrix
@@ -386,13 +387,16 @@ def test_symbol_repr(self):
         )
 
     def test_symbol_visualise(self):
-        c = pybamm.Variable("c", "negative electrode")
-        d = pybamm.Variable("d", "negative electrode")
-        sym = pybamm.div(c * pybamm.grad(c)) + (c / d + c - d) ** 5
-        sym.visualise("test_visualize.png")
-        self.assertTrue(os.path.exists("test_visualize.png"))
-        with self.assertRaises(ValueError):
-            sym.visualise("test_visualize")
+        with TemporaryDirectory() as dir_name:
+            test_stub = os.path.join(dir_name, "test_visualize")
+            test_name = f"{test_stub}.png"
+            c = pybamm.Variable("c", "negative electrode")
+            d = pybamm.Variable("d", "negative electrode")
+            sym = pybamm.div(c * pybamm.grad(c)) + (c / d + c - d) ** 5
+            sym.visualise(test_name)
+            self.assertTrue(os.path.exists(test_name))
+            with self.assertRaises(ValueError):
+                sym.visualise(test_stub)
 
     def test_has_spatial_derivatives(self):
         var = pybamm.Variable("var", domain="test")

tests/unit/test_parameters/test_lead_acid_parameters.py

@@ -1,10 +1,11 @@
 #
 # Test for the standard lead acid parameters
 #
+import os
 from tests import TestCase
 import pybamm
 from tests import get_discretisation_for_testing
-
+from tempfile import TemporaryDirectory
 import unittest
 
 
@@ -15,10 +16,11 @@ def test_scipy_constants(self):
         self.assertAlmostEqual(constants.F.evaluate(), 96485, places=0)
 
     def test_print_parameters(self):
-        parameters = pybamm.LeadAcidParameters()
-        parameter_values = pybamm.lead_acid.BaseModel().default_parameter_values
-        output_file = "lead_acid_parameters.txt"
-        parameter_values.print_parameters(parameters, output_file)
+        with TemporaryDirectory() as dir_name:
+            parameters = pybamm.LeadAcidParameters()
+            parameter_values = pybamm.lead_acid.BaseModel().default_parameter_values
+            output_file = os.path.join(dir_name, "lead_acid_parameters.txt")
+            parameter_values.print_parameters(parameters, output_file)
 
     def test_parameters_defaults_lead_acid(self):
         # Load parameters to be tested

tests/unit/test_parameters/test_lithium_ion_parameters.py

@@ -1,19 +1,21 @@
 #
-# Tests lithium ion parameters load and give expected values
+# Tests lithium-ion parameters load and give expected values
 #
+import os
 from tests import TestCase
 import pybamm
-
+from tempfile import TemporaryDirectory
 import unittest
 import numpy as np
 
 
 class TestLithiumIonParameterValues(TestCase):
     def test_print_parameters(self):
-        parameters = pybamm.LithiumIonParameters()
-        parameter_values = pybamm.lithium_ion.BaseModel().default_parameter_values
-        output_file = "lithium_ion_parameters.txt"
-        parameter_values.print_parameters(parameters, output_file)
+        with TemporaryDirectory() as dir_name:
+            parameters = pybamm.LithiumIonParameters()
+            parameter_values = pybamm.lithium_ion.BaseModel().default_parameter_values
+            output_file = os.path.join(dir_name, "lithium_ion_parameters.txt")
+            parameter_values.print_parameters(parameters, output_file)
 
     def test_lithium_ion(self):
         """This test checks that all the parameters are being calculated

tests/unit/test_plotting/test_quick_plot.py

@@ -3,6 +3,7 @@
 import unittest
 from tests import TestCase
 import numpy as np
+from tempfile import TemporaryDirectory
 
 
 class TestQuickPlot(TestCase):
@@ -290,12 +291,13 @@ def test_spm_simulation(self):
         quick_plot.plot(0)
 
         # test creating a GIF
-        test_stub = "spm_sim_test"
-        test_file = f"{test_stub}.gif"
-        quick_plot.create_gif(number_of_images=3, duration=3, output_filename=test_file)
-        assert not os.path.exists(f"{test_stub}*.png")
-        assert os.path.exists(test_file)
-        os.remove(test_file)
+        with TemporaryDirectory() as dir_name:
+            test_stub = os.path.join(dir_name, "spm_sim_test")
+            test_file = f"{test_stub}.gif"
+            quick_plot.create_gif(number_of_images=3, duration=3,
+                                  output_filename=test_file)
+            assert not os.path.exists(f"{test_stub}*.png")
+            assert os.path.exists(test_file)
         pybamm.close_plots()
 
     def test_loqs_spme(self):