Merge pull request #1258 from pybamm-team/release-0.3.0

Fix graphviz version for windows

.github/workflows/test_on_push.yml

@@ -56,7 +56,7 @@ jobs:
         
     - name: Install Windows system dependencies
       if: matrix.os == 'windows-latest'
-      run: choco install graphviz
+      run: choco install graphviz --version=2.38.0.20190211
 
     - name: Install standard python dependencies
       run: |

pybamm/CITATIONS.txt

@@ -36,6 +36,17 @@
   note = {\href{ http://dx.doi.org/10.1149/1.2221597}{doi: 10.1149/1.2221597}},
 }
 
+@Article{harris2020array,
+  title={Array programming with NumPy},
+  author={Harris, Charles R and Millman, K Jarrod and van der Walt, St{'e}fan J and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J and others},
+  journal={Nature},
+  volume={585},
+  number={7825},
+  pages={357--362},
+  year={2020},
+  publisher={Nature Publishing Group}
+}
+
 @techreport{hindmarsh2000pvode,
   title={The {PVODE} and {IDA} algorithms},
   author={Hindmarsh, AC},
@@ -55,6 +66,14 @@
   publisher={ACM New York, NY, USA}
 }
 
+@software{jax2018github,
+  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 {P}ython+{N}um{P}y programs},
+  url = {http://github.com/google/jax},
+  version = {0.2.5},
+  year = {2018},
+}
+
 @article{kim2011multi,
   title={Multi-domain modeling of lithium-ion batteries encompassing multi-physics in varied length scales},
   author={Kim, Gi-Heon and Smith, Kandler and Lee, Kyu-Jin and Santhanagopalan, Shriram and Pesaran, Ahmad},

pybamm/citations.py

@@ -29,8 +29,9 @@ def _reset(self):
         "Reset citations to default only (only for testing purposes)"
         # Initialize empty papers to cite
         self._papers_to_cite = set()
-        # Register the PyBaMM paper
+        # Register the PyBaMM paper and the numpy paper
         self.register("sulzer2020python")
+        self.register("harris2020array")
 
     def read_citations(self):
         "Read the citations text file"

pybamm/solvers/jax_solver.py

@@ -60,6 +60,7 @@ def __init__(
         self.extra_options = extra_options or {}
         self.name = "JAX solver ({})".format(method)
         self._cached_solves = dict()
+        pybamm.citations.register("jax2018github")
 
     def get_solve(self, model, t_eval):
         """

tests/unit/test_citations.py

@@ -3,15 +3,16 @@
 #
 import pybamm
 import unittest
+from platform import system
 
 
 class TestCitations(unittest.TestCase):
     def test_citations(self):
         citations = pybamm.citations
-        citations._reset()
         # Default papers should be in both _all_citations dict and in the papers to cite
         self.assertIn("sulzer2020python", citations._all_citations.keys())
         self.assertIn("sulzer2020python", citations._papers_to_cite)
+        self.assertIn("harris2020array", citations._papers_to_cite)
         # Non-default papers should only be in the _all_citations dict
         self.assertIn("sulzer2019physical", citations._all_citations.keys())
         self.assertNotIn("sulzer2019physical", citations._papers_to_cite)
@@ -180,6 +181,14 @@ def test_solver_citations(self):
             pybamm.IDAKLUSolver()
             self.assertIn("hindmarsh2005sundials", citations._papers_to_cite)
 
+    @unittest.skipIf(system() == "Windows", "JAX not supported on windows")
+    def test_jax_citations(self):
+        citations = pybamm.citations
+        citations._reset()
+        self.assertNotIn("jax2018github", citations._papers_to_cite)
+        pybamm.JaxSolver()
+        self.assertIn("jax2018github", citations._papers_to_cite)
+
 
 if __name__ == "__main__":
     print("Add -v for more debug output")