Merge branch 'develop' into telemetry

.all-contributorsrc

@@ -970,6 +970,18 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "MarcBerliner",
+      "name": "Marc Berliner",
+      "avatar_url": "https://avatars.githubusercontent.com/u/34451391?v=4",
+      "profile": "http://marcberliner.com",
+      "contributions": [
+        "code",
+        "doc",
+        "infra",
+        "maintenance"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.gitignore

@@ -64,6 +64,7 @@ coverage.xml
 htmlcov/
 
 # virtual environment
+.venv
 env/
 venv/
 venv3.5/

README.md

@@ -15,7 +15,7 @@
 [![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/pybamm-team/PyBaMM/badge)](https://scorecard.dev/viewer/?uri=github.com/pybamm-team/PyBaMM)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-91-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-92-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>

all_contributors.md

@@ -122,6 +122,9 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/pipliggins"><img src="https://avatars.githubusercontent.com/u/55396775?v=4?s=100" width="100px;" alt="Pip Liggins"/><br /><sub><b>Pip Liggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=pipliggins" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=pipliggins" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/medha-14"><img src="https://avatars.githubusercontent.com/u/143182673?v=4?s=100" width="100px;" alt="Medha Bhardwaj"/><br /><sub><b>Medha Bhardwaj</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=medha-14" title="Code">💻</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="http://marcberliner.com"><img src="https://avatars.githubusercontent.com/u/34451391?v=4?s=100" width="100px;" alt="Marc Berliner"/><br /><sub><b>Marc Berliner</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=MarcBerliner" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=MarcBerliner" title="Documentation">📖</a> <a href="#infra-MarcBerliner" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-MarcBerliner" title="Maintenance">🚧</a></td>
+    </tr>
   </tbody>
 </table>
 

src/pybamm/CITATIONS.bib

@@ -291,7 +291,7 @@ @article{Hindmarsh2005
 @misc{jax2018,
   author = {James Bradbury and Roy Frostig and Peter Hawkins and Matthew James Johnson and Chris Leary and Dougal Maclaurin and Skye Wanderman-Milne},
   title = {{JAX: composable transformations of Python+NumPy programs}},
-  url = {http://github.com/google/jax},
+  url = {http://github.com/jax-ml/jax},
   version = {0.2.5},
   year = {2018},
 }

src/pybamm/solvers/jax_bdf_solver.py

@@ -28,7 +28,7 @@
     MIN_FACTOR = 0.2
     MAX_FACTOR = 10
 
-    # https://github.com/google/jax/issues/4572#issuecomment-709809897
+    # https://github.com/jax-ml/jax/issues/4572#issuecomment-709809897
     def some_hash_function(x):
         return hash(str(x))
 
@@ -711,7 +711,7 @@ def block_fun(i, j, Ai, Aj):
         return onp.block(blocks)
 
     # NOTE: the code below (except the docstring on jax_bdf_integrate and other minor
-    # edits), has been modified from the JAX library at https://github.com/google/jax.
+    # edits), has been modified from the JAX library at https://github.com/jax-ml/jax.
     # The main difference is the addition of support for semi-explicit dae index 1
     # problems via the addition of a mass matrix.
     # This is under an Apache license, a short form of which is given here:

src/pybamm/solvers/jax_solver.py

@@ -46,7 +46,7 @@ class JaxSolver(pybamm.BaseSolver):
     extra_options : dict, optional
         Any options to pass to the solver.
         Please consult `JAX documentation
-        <https://github.com/google/jax/blob/master/jax/experimental/ode.py>`_
+        <https://github.com/jax-ml/jax/blob/master/jax/experimental/ode.py>`_
         for details.
     """
 
@@ -263,8 +263,8 @@ async def solve_model_async(inputs_v):
         # sparse matrix support in JAX resulting in high memory usage, or a bug
         # in the BDF solver.
         #
-        # This issue on guthub appears related:
-        # https://github.com/google/jax/discussions/13930
+        # This issue on GitHub appears related:
+        # https://github.com/jax-ml/jax/discussions/13930
         #
         #     # Split input list based on the number of available xla devices
         #     device_count = jax.local_device_count()