Moving to src layout (pybamm-team#4311)

* Moving to src layout Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * Applying require changes according to src path Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * using src/pybamm Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * changing path of pybamm.root_dir() Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * style: pre-commit fixes * changing path to src/pybamm in CMakeLists.txt Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * fixing RTD failure Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * using pybamm.__path__[0] Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> * style: pre-commit fixes * Update noxfile.py Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com> * Fix notebook paths --------- Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> Co-authored-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com> Co-authored-by: Arjun Verma <arjunverma.oc@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
kratman · Aug 8, 2024 · f49189c · f49189c
1 parent fe6230d
commit f49189c
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Showing 357 changed files with 93 additions and 97 deletions.
diff --git a/.gitignore b/.gitignore
@@ -14,8 +14,8 @@
 !requirements*
 !LICENSE.txt
 !CMakeLists.txt
-!pybamm/CITATIONS.bib
-!pybamm/input/**/*.csv
+!src/pybamm/CITATIONS.bib
+!src/pybamm/input/**/*.csv
 !tests/unit/test_parameters/*.csv
 !benchmarks/benchmark_images/*.png
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -48,8 +48,8 @@ set(IDAKLU_EXPR_CASADI_SOURCE_FILES "")
 if(${PYBAMM_IDAKLU_EXPR_CASADI} STREQUAL "ON" )
   add_compile_definitions(CASADI_ENABLE)
   set(IDAKLU_EXPR_CASADI_SOURCE_FILES
-    pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.cpp
-    pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.hpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.cpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.hpp
   )
 endif()
 
@@ -65,43 +65,43 @@ if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
   add_compile_definitions(IREE_ENABLE)
   # Source file list
   set(IDAKLU_EXPR_IREE_SOURCE_FILES
-    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.cpp
-    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.hpp
-    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.cpp
-    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.hpp
-    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.cpp
-    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.hpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.cpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.hpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.cpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.hpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.cpp
+    src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.hpp
   )
 endif()
 
 # The complete (all dependencies) sources list should be mirrored in setup.py
 pybind11_add_module(idaklu
   # pybind11 interface
-  pybamm/solvers/c_solvers/idaklu.cpp
+  src/pybamm/solvers/c_solvers/idaklu.cpp
   # IDAKLU solver (SUNDIALS)
-  pybamm/solvers/c_solvers/idaklu/idaklu_solver.hpp
-  pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.cpp
-  pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.hpp
-  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.inl
-  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.hpp
-  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.cpp
-  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.hpp
-  pybamm/solvers/c_solvers/idaklu/sundials_functions.inl
-  pybamm/solvers/c_solvers/idaklu/sundials_functions.hpp
-  pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp
-  pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp
-  pybamm/solvers/c_solvers/idaklu/common.hpp
-  pybamm/solvers/c_solvers/idaklu/python.hpp
-  pybamm/solvers/c_solvers/idaklu/python.cpp
-  pybamm/solvers/c_solvers/idaklu/Solution.cpp
-  pybamm/solvers/c_solvers/idaklu/Solution.hpp
-  pybamm/solvers/c_solvers/idaklu/Options.hpp
-  pybamm/solvers/c_solvers/idaklu/Options.cpp
+  src/pybamm/solvers/c_solvers/idaklu/idaklu_solver.hpp
+  src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.cpp
+  src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.hpp
+  src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.inl
+  src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.hpp
+  src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.cpp
+  src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.hpp
+  src/pybamm/solvers/c_solvers/idaklu/sundials_functions.inl
+  src/pybamm/solvers/c_solvers/idaklu/sundials_functions.hpp
+  src/pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp
+  src/pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp
+  src/pybamm/solvers/c_solvers/idaklu/common.hpp
+  src/pybamm/solvers/c_solvers/idaklu/python.hpp
+  src/pybamm/solvers/c_solvers/idaklu/python.cpp
+  src/pybamm/solvers/c_solvers/idaklu/Solution.cpp
+  src/pybamm/solvers/c_solvers/idaklu/Solution.hpp
+  src/pybamm/solvers/c_solvers/idaklu/Options.hpp
+  src/pybamm/solvers/c_solvers/idaklu/Options.cpp
   # IDAKLU expressions / function evaluation [abstract]
-  pybamm/solvers/c_solvers/idaklu/Expressions/Expressions.hpp
-  pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp
-  pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp
-  pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp
+  src/pybamm/solvers/c_solvers/idaklu/Expressions/Expressions.hpp
+  src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp
+  src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp
+  src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp
   # IDAKLU expressions - concrete implementations
   ${IDAKLU_EXPR_CASADI_SOURCE_FILES}
   ${IDAKLU_EXPR_IREE_SOURCE_FILES}

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -38,7 +38,7 @@ We use [GIT](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedi
 2. Create a [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) of this repo (ideally on your own [fork](https://help.github.com/articles/fork-a-repo/)), where all changes will be made
 3. Download the source code onto your local system, by [cloning](https://help.github.com/articles/cloning-a-repository/) the repository (or your fork of the repository).
 4. [Install](https://docs.pybamm.org/en/latest/source/user_guide/installation/install-from-source.html) PyBaMM with the developer options.
-5. [Test](#testing) if your installation worked, using the test script: `$ python run-tests.py --unit`.
+5. [Test](#testing) if your installation worked, using pytest: `$ pytest -m unit`.
 
 You now have everything you need to start making changes!
 
@@ -405,7 +405,7 @@ pybamm.print_citations()
 
 to the end of a script will print all citations that were used by that script. This will print BibTeX information to the terminal; passing a filename to `print_citations` will print the BibTeX information to the specified file instead.
 
-When you contribute code to PyBaMM, you can add your own papers that you would like to be cited if that code is used. First, add the BibTeX for your paper to [CITATIONS.bib](https://github.com/pybamm-team/PyBaMM/blob/develop/pybamm/CITATIONS.bib). Then, add the line
+When you contribute code to PyBaMM, you can add your own papers that you would like to be cited if that code is used. First, add the BibTeX for your paper to [CITATIONS.bib](https://github.com/pybamm-team/PyBaMM/blob/develop/src/pybamm/CITATIONS.bib). Then, add the line
 
 ```python3
 pybamm.citations.register("your_paper_bibtex_identifier")

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,4 @@
-graft pybamm
+graft src
 include CITATION.cff
 prune tests
 

diff --git a/README.md b/README.md
@@ -161,7 +161,7 @@ We would be grateful if you could also cite the relevant papers. These will chan
 pybamm.print_citations()
 ```
 
-to the end of your script. This will print BibTeX information to the terminal; passing a filename to `print_citations` will print the BibTeX information to the specified file instead. A list of all citations can also be found in the [citations file](https://github.com/pybamm-team/PyBaMM/blob/develop/pybamm/CITATIONS.bib). In particular, PyBaMM relies heavily on [CasADi](https://web.casadi.org/publications/).
+to the end of your script. This will print BibTeX information to the terminal; passing a filename to `print_citations` will print the BibTeX information to the specified file instead. A list of all citations can also be found in the [citations file](https://github.com/pybamm-team/PyBaMM/blob/develop/src/pybamm/CITATIONS.bib). In particular, PyBaMM relies heavily on [CasADi](https://web.casadi.org/publications/).
 See [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#citations) for information on how to add your own citations when you contribute.
 
 ## 🛠️ Contributing to PyBaMM

diff --git a/docs/conf.py b/docs/conf.py
@@ -288,7 +288,7 @@
 
 # -- sphinxcontrib-bibtex configuration --------------------------------------
 
-bibtex_bibfiles = ["../pybamm/CITATIONS.bib"]
+bibtex_bibfiles = ["../src/pybamm/CITATIONS.bib"]
 bibtex_style = "unsrt"
 bibtex_footbibliography_header = """.. rubric:: References"""
 bibtex_reference_style = "author_year"

diff --git a/docs/source/examples/notebooks/models/SPM.ipynb b/docs/source/examples/notebooks/models/SPM.ipynb
@@ -124,8 +124,7 @@
     "variable = list(model.rhs.keys())[1]\n",
     "equation = list(model.rhs.values())[1]\n",
     "print(\"rhs equation for variable '\", variable, \"' is:\")\n",
-    "path = \"docs/source/examples/notebooks/models/\"\n",
-    "equation.visualise(path + \"spm1.png\")"
+    "equation.visualise(\"spm1.png\")"
    ]
   },
   {
@@ -383,7 +382,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.concatenated_rhs.children[1].visualise(path + \"spm2.png\")"
+    "model.concatenated_rhs.children[1].visualise(\"spm2.png\")"
    ]
   },
   {

diff --git a/examples/scripts/drive_cycle.py b/examples/scripts/drive_cycle.py
@@ -3,9 +3,7 @@
 #
 import pybamm
 import pandas as pd
-import os
 
-os.chdir(pybamm.__path__[0] + "/..")
 
 pybamm.set_logging_level("INFO")
 

diff --git a/examples/scripts/experiment_drive_cycle.py b/examples/scripts/experiment_drive_cycle.py
@@ -3,9 +3,7 @@
 #
 import pybamm
 import pandas as pd
-import os
 
-os.chdir(pybamm.__path__[0] + "/..")
 
 pybamm.set_logging_level("INFO")
 

diff --git a/noxfile.py b/noxfile.py
@@ -180,7 +180,7 @@ def run_doctests(session):
         "-m",
         "pytest",
         "--doctest-plus",
-        "pybamm",
+        "src",
     )
 
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -169,13 +169,12 @@ pybamm = [
     "*.md",
     "*.csv",
     "*.py",
-    "pybamm/CITATIONS.bib",
-    "pybamm/plotting/mplstyle",
+    "src/pybamm/CITATIONS.bib",
+    "src/pybamm/plotting/mplstyle",
 ]
 
 [tool.setuptools.packages.find]
-include = ["pybamm", "pybamm.*"]
-
+where = ["src"]
 [tool.ruff]
 extend-include = ["*.ipynb"]
 extend-exclude = ["__init__.py"]
@@ -264,7 +263,7 @@ log_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 log_date_format = "%Y-%m-%d %H:%M:%S"
 
 [tool.coverage.run]
-source = ["pybamm"]
+source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
 [tool.repo-review]

diff --git a/scripts/update_version.py b/scripts/update_version.py
@@ -24,7 +24,9 @@ def update_version():
     )
 
     # pybamm/version.py
-    with open(os.path.join(pybamm.root_dir(), "pybamm", "version.py"), "r+") as file:
+    with open(
+        os.path.join(pybamm.root_dir(), "src", "pybamm", "version.py"), "r+"
+    ) as file:
         output = file.read()
         replace_version = re.sub(
             '(?<=__version__ = ")(.+)(?=")', release_version, output

diff --git a/setup.py b/setup.py
@@ -295,40 +295,40 @@ def compile_KLU():
     name="pybamm.solvers.idaklu",
     # The sources list should mirror the list in CMakeLists.txt
     sources=[
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Expressions.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSparsity.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.cpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEBaseFunction.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunction.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.cpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.cpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.cpp",
-        "pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.hpp",
-        "pybamm/solvers/c_solvers/idaklu/idaklu_solver.hpp",
-        "pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.cpp",
-        "pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.hpp",
-        "pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.inl",
-        "pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.hpp",
-        "pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.cpp",
-        "pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.hpp",
-        "pybamm/solvers/c_solvers/idaklu/sundials_functions.inl",
-        "pybamm/solvers/c_solvers/idaklu/sundials_functions.hpp",
-        "pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp",
-        "pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp",
-        "pybamm/solvers/c_solvers/idaklu/common.hpp",
-        "pybamm/solvers/c_solvers/idaklu/python.hpp",
-        "pybamm/solvers/c_solvers/idaklu/python.cpp",
-        "pybamm/solvers/c_solvers/idaklu/Solution.cpp",
-        "pybamm/solvers/c_solvers/idaklu/Solution.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Options.hpp",
-        "pybamm/solvers/c_solvers/idaklu/Options.cpp",
-        "pybamm/solvers/c_solvers/idaklu.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Expressions.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSparsity.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEBaseFunction.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunction.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/idaklu_solver.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.inl",
+        "src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/sundials_functions.inl",
+        "src/pybamm/solvers/c_solvers/idaklu/sundials_functions.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/common.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/python.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/python.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Solution.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Solution.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Options.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/Options.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu.cpp",
     ],
 )
 ext_modules = [idaklu_ext] if compile_KLU() else []

diff --git a/pybamm/CITATIONS.bib → src/pybamm/CITATIONS.bib b/pybamm/CITATIONS.bib → src/pybamm/CITATIONS.bib
diff --git a/pybamm/__init__.py → src/pybamm/__init__.py b/pybamm/__init__.py → src/pybamm/__init__.py
diff --git a/pybamm/batch_study.py → src/pybamm/batch_study.py b/pybamm/batch_study.py → src/pybamm/batch_study.py
diff --git a/pybamm/callbacks.py → src/pybamm/callbacks.py b/pybamm/callbacks.py → src/pybamm/callbacks.py
diff --git a/pybamm/citations.py → src/pybamm/citations.py b/pybamm/citations.py → src/pybamm/citations.py
@@ -68,7 +68,7 @@ def read_citations(self):
         """
         try:
             parse_file = import_optional_dependency("pybtex.database", "parse_file")
-            citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
+            citations_file = os.path.join(pybamm.__path__[0], "CITATIONS.bib")
             bib_data = parse_file(citations_file, bib_format="bibtex")
             for key, entry in bib_data.entries.items():
                 self._add_citation(key, entry)

diff --git a/pybamm/discretisations/__init__.py → src/pybamm/discretisations/__init__.py b/pybamm/discretisations/__init__.py → src/pybamm/discretisations/__init__.py
diff --git a/pybamm/discretisations/discretisation.py → src/pybamm/discretisations/discretisation.py b/pybamm/discretisations/discretisation.py → src/pybamm/discretisations/discretisation.py
diff --git a/pybamm/doc_utils.py → src/pybamm/doc_utils.py b/pybamm/doc_utils.py → src/pybamm/doc_utils.py
diff --git a/pybamm/experiment/__init__.py → src/pybamm/experiment/__init__.py b/pybamm/experiment/__init__.py → src/pybamm/experiment/__init__.py
diff --git a/pybamm/experiment/experiment.py → src/pybamm/experiment/experiment.py b/pybamm/experiment/experiment.py → src/pybamm/experiment/experiment.py
diff --git a/pybamm/experiment/step/__init__.py → src/pybamm/experiment/step/__init__.py b/pybamm/experiment/step/__init__.py → src/pybamm/experiment/step/__init__.py
diff --git a/pybamm/experiment/step/base_step.py → src/pybamm/experiment/step/base_step.py b/pybamm/experiment/step/base_step.py → src/pybamm/experiment/step/base_step.py
diff --git a/pybamm/experiment/step/step_termination.py → ...ybamm/experiment/step/step_termination.py b/pybamm/experiment/step/step_termination.py → ...ybamm/experiment/step/step_termination.py
diff --git a/pybamm/experiment/step/steps.py → src/pybamm/experiment/step/steps.py b/pybamm/experiment/step/steps.py → src/pybamm/experiment/step/steps.py
diff --git a/pybamm/expression_tree/__init__.py → src/pybamm/expression_tree/__init__.py b/pybamm/expression_tree/__init__.py → src/pybamm/expression_tree/__init__.py
diff --git a/pybamm/expression_tree/array.py → src/pybamm/expression_tree/array.py b/pybamm/expression_tree/array.py → src/pybamm/expression_tree/array.py
diff --git a/pybamm/expression_tree/averages.py → src/pybamm/expression_tree/averages.py b/pybamm/expression_tree/averages.py → src/pybamm/expression_tree/averages.py
diff --git a/pybamm/expression_tree/binary_operators.py → ...ybamm/expression_tree/binary_operators.py b/pybamm/expression_tree/binary_operators.py → ...ybamm/expression_tree/binary_operators.py
diff --git a/pybamm/expression_tree/broadcasts.py → src/pybamm/expression_tree/broadcasts.py b/pybamm/expression_tree/broadcasts.py → src/pybamm/expression_tree/broadcasts.py
diff --git a/pybamm/expression_tree/concatenations.py → src/pybamm/expression_tree/concatenations.py b/pybamm/expression_tree/concatenations.py → src/pybamm/expression_tree/concatenations.py
diff --git a/pybamm/expression_tree/exceptions.py → src/pybamm/expression_tree/exceptions.py b/pybamm/expression_tree/exceptions.py → src/pybamm/expression_tree/exceptions.py
diff --git a/pybamm/expression_tree/functions.py → src/pybamm/expression_tree/functions.py b/pybamm/expression_tree/functions.py → src/pybamm/expression_tree/functions.py
diff --git a/...m/expression_tree/independent_variable.py → ...m/expression_tree/independent_variable.py b/...m/expression_tree/independent_variable.py → ...m/expression_tree/independent_variable.py
diff --git a/pybamm/expression_tree/input_parameter.py → ...pybamm/expression_tree/input_parameter.py b/pybamm/expression_tree/input_parameter.py → ...pybamm/expression_tree/input_parameter.py
diff --git a/pybamm/expression_tree/interpolant.py → src/pybamm/expression_tree/interpolant.py b/pybamm/expression_tree/interpolant.py → src/pybamm/expression_tree/interpolant.py
diff --git a/pybamm/expression_tree/matrix.py → src/pybamm/expression_tree/matrix.py b/pybamm/expression_tree/matrix.py → src/pybamm/expression_tree/matrix.py
diff --git a/...mm/expression_tree/operations/__init__.py → ...mm/expression_tree/operations/__init__.py b/...mm/expression_tree/operations/__init__.py → ...mm/expression_tree/operations/__init__.py
diff --git a/...sion_tree/operations/convert_to_casadi.py → ...sion_tree/operations/convert_to_casadi.py b/...sion_tree/operations/convert_to_casadi.py → ...sion_tree/operations/convert_to_casadi.py
diff --git a/...ession_tree/operations/evaluate_python.py → ...ession_tree/operations/evaluate_python.py b/...ession_tree/operations/evaluate_python.py → ...ession_tree/operations/evaluate_python.py
diff --git a/...mm/expression_tree/operations/jacobian.py → ...mm/expression_tree/operations/jacobian.py b/...mm/expression_tree/operations/jacobian.py → ...mm/expression_tree/operations/jacobian.py
diff --git a/...mm/expression_tree/operations/latexify.py → ...mm/expression_tree/operations/latexify.py b/...mm/expression_tree/operations/latexify.py → ...mm/expression_tree/operations/latexify.py
diff --git a/...m/expression_tree/operations/serialise.py → ...m/expression_tree/operations/serialise.py b/...m/expression_tree/operations/serialise.py → ...m/expression_tree/operations/serialise.py
diff --git a/...ression_tree/operations/unpack_symbols.py → ...ression_tree/operations/unpack_symbols.py b/...ression_tree/operations/unpack_symbols.py → ...ression_tree/operations/unpack_symbols.py
diff --git a/pybamm/expression_tree/parameter.py → src/pybamm/expression_tree/parameter.py b/pybamm/expression_tree/parameter.py → src/pybamm/expression_tree/parameter.py
diff --git a/pybamm/expression_tree/printing/__init__.py → ...bamm/expression_tree/printing/__init__.py b/pybamm/expression_tree/printing/__init__.py → ...bamm/expression_tree/printing/__init__.py
diff --git a/...mm/expression_tree/printing/print_name.py → ...mm/expression_tree/printing/print_name.py b/...mm/expression_tree/printing/print_name.py → ...mm/expression_tree/printing/print_name.py
diff --git a/...pression_tree/printing/sympy_overrides.py → ...pression_tree/printing/sympy_overrides.py b/...pression_tree/printing/sympy_overrides.py → ...pression_tree/printing/sympy_overrides.py
diff --git a/pybamm/expression_tree/scalar.py → src/pybamm/expression_tree/scalar.py b/pybamm/expression_tree/scalar.py → src/pybamm/expression_tree/scalar.py
diff --git a/pybamm/expression_tree/state_vector.py → src/pybamm/expression_tree/state_vector.py b/pybamm/expression_tree/state_vector.py → src/pybamm/expression_tree/state_vector.py
diff --git a/pybamm/expression_tree/symbol.py → src/pybamm/expression_tree/symbol.py b/pybamm/expression_tree/symbol.py → src/pybamm/expression_tree/symbol.py
diff --git a/pybamm/expression_tree/unary_operators.py → ...pybamm/expression_tree/unary_operators.py b/pybamm/expression_tree/unary_operators.py → ...pybamm/expression_tree/unary_operators.py
diff --git a/pybamm/expression_tree/variable.py → src/pybamm/expression_tree/variable.py b/pybamm/expression_tree/variable.py → src/pybamm/expression_tree/variable.py
diff --git a/pybamm/expression_tree/vector.py → src/pybamm/expression_tree/vector.py b/pybamm/expression_tree/vector.py → src/pybamm/expression_tree/vector.py
diff --git a/pybamm/geometry/__init__.py → src/pybamm/geometry/__init__.py b/pybamm/geometry/__init__.py → src/pybamm/geometry/__init__.py
diff --git a/pybamm/geometry/battery_geometry.py → src/pybamm/geometry/battery_geometry.py b/pybamm/geometry/battery_geometry.py → src/pybamm/geometry/battery_geometry.py
diff --git a/pybamm/geometry/geometry.py → src/pybamm/geometry/geometry.py b/pybamm/geometry/geometry.py → src/pybamm/geometry/geometry.py
diff --git a/pybamm/geometry/standard_spatial_vars.py → src/pybamm/geometry/standard_spatial_vars.py b/pybamm/geometry/standard_spatial_vars.py → src/pybamm/geometry/standard_spatial_vars.py
diff --git a/pybamm/input/__init__.py → src/pybamm/input/__init__.py b/pybamm/input/__init__.py → src/pybamm/input/__init__.py
diff --git a/pybamm/input/parameters/__init__.py → src/pybamm/input/parameters/__init__.py b/pybamm/input/parameters/__init__.py → src/pybamm/input/parameters/__init__.py
diff --git a/pybamm/input/parameters/ecm/__init__.py → src/pybamm/input/parameters/ecm/__init__.py b/pybamm/input/parameters/ecm/__init__.py → src/pybamm/input/parameters/ecm/__init__.py
diff --git a/...ut/parameters/ecm/data/ecm_example_c1.csv → ...ut/parameters/ecm/data/ecm_example_c1.csv b/...ut/parameters/ecm/data/ecm_example_c1.csv → ...ut/parameters/ecm/data/ecm_example_c1.csv
diff --git a/.../parameters/ecm/data/ecm_example_dudt.csv → .../parameters/ecm/data/ecm_example_dudt.csv b/.../parameters/ecm/data/ecm_example_dudt.csv → .../parameters/ecm/data/ecm_example_dudt.csv
diff --git a/...t/parameters/ecm/data/ecm_example_ocv.csv → ...t/parameters/ecm/data/ecm_example_ocv.csv b/...t/parameters/ecm/data/ecm_example_ocv.csv → ...t/parameters/ecm/data/ecm_example_ocv.csv
diff --git a/...ut/parameters/ecm/data/ecm_example_r0.csv → ...ut/parameters/ecm/data/ecm_example_r0.csv b/...ut/parameters/ecm/data/ecm_example_r0.csv → ...ut/parameters/ecm/data/ecm_example_r0.csv
diff --git a/...ut/parameters/ecm/data/ecm_example_r1.csv → ...ut/parameters/ecm/data/ecm_example_r1.csv b/...ut/parameters/ecm/data/ecm_example_r1.csv → ...ut/parameters/ecm/data/ecm_example_r1.csv
diff --git a/pybamm/input/parameters/ecm/example_set.py → ...ybamm/input/parameters/ecm/example_set.py b/pybamm/input/parameters/ecm/example_set.py → ...ybamm/input/parameters/ecm/example_set.py
diff --git a/.../input/parameters/lead_acid/Sulzer2019.py → .../input/parameters/lead_acid/Sulzer2019.py b/.../input/parameters/lead_acid/Sulzer2019.py → .../input/parameters/lead_acid/Sulzer2019.py
diff --git a/...mm/input/parameters/lead_acid/__init__.py → ...mm/input/parameters/lead_acid/__init__.py b/...mm/input/parameters/lead_acid/__init__.py → ...mm/input/parameters/lead_acid/__init__.py
diff --git a/...mm/input/parameters/lithium_ion/Ai2020.py → ...mm/input/parameters/lithium_ion/Ai2020.py b/...mm/input/parameters/lithium_ion/Ai2020.py → ...mm/input/parameters/lithium_ion/Ai2020.py
diff --git a/.../input/parameters/lithium_ion/Chen2020.py → .../input/parameters/lithium_ion/Chen2020.py b/.../input/parameters/lithium_ion/Chen2020.py → .../input/parameters/lithium_ion/Chen2020.py
diff --git a/...ameters/lithium_ion/Chen2020_composite.py → ...ameters/lithium_ion/Chen2020_composite.py b/...ameters/lithium_ion/Chen2020_composite.py → ...ameters/lithium_ion/Chen2020_composite.py
diff --git a/...input/parameters/lithium_ion/Ecker2015.py → ...input/parameters/lithium_ion/Ecker2015.py b/...input/parameters/lithium_ion/Ecker2015.py → ...input/parameters/lithium_ion/Ecker2015.py
diff --git a/...ithium_ion/Ecker2015_graphite_halfcell.py → ...ithium_ion/Ecker2015_graphite_halfcell.py b/...ithium_ion/Ecker2015_graphite_halfcell.py → ...ithium_ion/Ecker2015_graphite_halfcell.py
diff --git a/...arameters/lithium_ion/MSMR_example_set.py → ...arameters/lithium_ion/MSMR_example_set.py b/...arameters/lithium_ion/MSMR_example_set.py → ...arameters/lithium_ion/MSMR_example_set.py
diff --git a/...put/parameters/lithium_ion/Marquis2019.py → ...put/parameters/lithium_ion/Marquis2019.py b/...put/parameters/lithium_ion/Marquis2019.py → ...put/parameters/lithium_ion/Marquis2019.py
diff --git a/...nput/parameters/lithium_ion/Mohtat2020.py → ...nput/parameters/lithium_ion/Mohtat2020.py b/...nput/parameters/lithium_ion/Mohtat2020.py → ...nput/parameters/lithium_ion/Mohtat2020.py
diff --git a/...put/parameters/lithium_ion/NCA_Kim2011.py → ...put/parameters/lithium_ion/NCA_Kim2011.py b/...put/parameters/lithium_ion/NCA_Kim2011.py → ...put/parameters/lithium_ion/NCA_Kim2011.py
diff --git a/...input/parameters/lithium_ion/OKane2022.py → ...input/parameters/lithium_ion/OKane2022.py b/...input/parameters/lithium_ion/OKane2022.py → ...input/parameters/lithium_ion/OKane2022.py
diff --git a/...m_ion/OKane2022_graphite_SiOx_halfcell.py → ...m_ion/OKane2022_graphite_SiOx_halfcell.py b/...m_ion/OKane2022_graphite_SiOx_halfcell.py → ...m_ion/OKane2022_graphite_SiOx_halfcell.py
diff --git a/...nput/parameters/lithium_ion/ORegan2022.py → ...nput/parameters/lithium_ion/ORegan2022.py b/...nput/parameters/lithium_ion/ORegan2022.py → ...nput/parameters/lithium_ion/ORegan2022.py
diff --git a/...input/parameters/lithium_ion/Prada2013.py → ...input/parameters/lithium_ion/Prada2013.py b/...input/parameters/lithium_ion/Prada2013.py → ...input/parameters/lithium_ion/Prada2013.py
diff --git a/...ut/parameters/lithium_ion/Ramadass2004.py → ...ut/parameters/lithium_ion/Ramadass2004.py b/...ut/parameters/lithium_ion/Ramadass2004.py → ...ut/parameters/lithium_ion/Ramadass2004.py
diff --git a/...mm/input/parameters/lithium_ion/Xu2019.py → ...mm/input/parameters/lithium_ion/Xu2019.py b/...mm/input/parameters/lithium_ion/Xu2019.py → ...mm/input/parameters/lithium_ion/Xu2019.py
diff --git a/.../input/parameters/lithium_ion/__init__.py → .../input/parameters/lithium_ion/__init__.py b/.../input/parameters/lithium_ion/__init__.py → .../input/parameters/lithium_ion/__init__.py
diff --git a/..._ion/data/graphite_LGM50_ocp_Chen2020.csv → ..._ion/data/graphite_LGM50_ocp_Chen2020.csv b/..._ion/data/graphite_LGM50_ocp_Chen2020.csv → ..._ion/data/graphite_LGM50_ocp_Chen2020.csv
diff --git a/...thium_ion/data/graphite_ocp_Ecker2015.csv → ...thium_ion/data/graphite_ocp_Ecker2015.csv b/...thium_ion/data/graphite_ocp_Ecker2015.csv → ...thium_ion/data/graphite_ocp_Ecker2015.csv
diff --git a/...ion/data/graphite_ocp_Enertech_Ai2020.csv → ...ion/data/graphite_ocp_Enertech_Ai2020.csv b/...ion/data/graphite_ocp_Enertech_Ai2020.csv → ...ion/data/graphite_ocp_Enertech_Ai2020.csv
diff --git a/...ers/lithium_ion/data/lico2_ocp_Ai2020.csv → ...ers/lithium_ion/data/lico2_ocp_Ai2020.csv b/...ers/lithium_ion/data/lico2_ocp_Ai2020.csv → ...ers/lithium_ion/data/lico2_ocp_Ai2020.csv
diff --git a/...asured_graphite_diffusivity_Ecker2015.csv → ...asured_graphite_diffusivity_Ecker2015.csv b/...asured_graphite_diffusivity_Ecker2015.csv → ...asured_graphite_diffusivity_Ecker2015.csv
diff --git a/...ta/measured_nco_diffusivity_Ecker2015.csv → ...ta/measured_nco_diffusivity_Ecker2015.csv b/...ta/measured_nco_diffusivity_Ecker2015.csv → ...ta/measured_nco_diffusivity_Ecker2015.csv
diff --git a/...lithium_ion/data/nca_ocp_Kim2011_data.csv → ...lithium_ion/data/nca_ocp_Kim2011_data.csv b/...lithium_ion/data/nca_ocp_Kim2011_data.csv → ...lithium_ion/data/nca_ocp_Kim2011_data.csv
diff --git a/...rs/lithium_ion/data/nco_ocp_Ecker2015.csv → ...rs/lithium_ion/data/nco_ocp_Ecker2015.csv b/...rs/lithium_ion/data/nco_ocp_Ecker2015.csv → ...rs/lithium_ion/data/nco_ocp_Ecker2015.csv
diff --git a/...thium_ion/data/nmc_LGM50_ocp_Chen2020.csv → ...thium_ion/data/nmc_LGM50_ocp_Chen2020.csv b/...thium_ion/data/nmc_LGM50_ocp_Chen2020.csv → ...thium_ion/data/nmc_LGM50_ocp_Chen2020.csv
diff --git a/pybamm/logger.py → src/pybamm/logger.py b/pybamm/logger.py → src/pybamm/logger.py
diff --git a/pybamm/meshes/__init__.py → src/pybamm/meshes/__init__.py b/pybamm/meshes/__init__.py → src/pybamm/meshes/__init__.py
diff --git a/pybamm/meshes/meshes.py → src/pybamm/meshes/meshes.py b/pybamm/meshes/meshes.py → src/pybamm/meshes/meshes.py
diff --git a/pybamm/meshes/one_dimensional_submeshes.py → ...ybamm/meshes/one_dimensional_submeshes.py b/pybamm/meshes/one_dimensional_submeshes.py → ...ybamm/meshes/one_dimensional_submeshes.py
diff --git a/pybamm/meshes/scikit_fem_submeshes.py → src/pybamm/meshes/scikit_fem_submeshes.py b/pybamm/meshes/scikit_fem_submeshes.py → src/pybamm/meshes/scikit_fem_submeshes.py
diff --git a/pybamm/meshes/zero_dimensional_submesh.py → ...pybamm/meshes/zero_dimensional_submesh.py b/pybamm/meshes/zero_dimensional_submesh.py → ...pybamm/meshes/zero_dimensional_submesh.py
diff --git a/pybamm/models/__init__.py → src/pybamm/models/__init__.py b/pybamm/models/__init__.py → src/pybamm/models/__init__.py
diff --git a/pybamm/models/base_model.py → src/pybamm/models/base_model.py b/pybamm/models/base_model.py → src/pybamm/models/base_model.py
diff --git a/pybamm/models/event.py → src/pybamm/models/event.py b/pybamm/models/event.py → src/pybamm/models/event.py
diff --git a/...mm/models/full_battery_models/__init__.py → ...mm/models/full_battery_models/__init__.py b/...mm/models/full_battery_models/__init__.py → ...mm/models/full_battery_models/__init__.py
diff --git a/...full_battery_models/base_battery_model.py → ...full_battery_models/base_battery_model.py b/...full_battery_models/base_battery_model.py → ...full_battery_models/base_battery_model.py
diff --git a/...ery_models/equivalent_circuit/__init__.py → ...ery_models/equivalent_circuit/__init__.py b/...ery_models/equivalent_circuit/__init__.py → ...ery_models/equivalent_circuit/__init__.py
diff --git a/...s/equivalent_circuit/ecm_model_options.py → ...s/equivalent_circuit/ecm_model_options.py b/...s/equivalent_circuit/ecm_model_options.py → ...s/equivalent_circuit/ecm_model_options.py
diff --git a/...ery_models/equivalent_circuit/thevenin.py → ...ery_models/equivalent_circuit/thevenin.py b/...ery_models/equivalent_circuit/thevenin.py → ...ery_models/equivalent_circuit/thevenin.py
diff --git a/...full_battery_models/lead_acid/__init__.py → ...full_battery_models/lead_acid/__init__.py b/...full_battery_models/lead_acid/__init__.py → ...full_battery_models/lead_acid/__init__.py
diff --git a/..._models/lead_acid/base_lead_acid_model.py → ..._models/lead_acid/base_lead_acid_model.py b/..._models/lead_acid/base_lead_acid_model.py → ..._models/lead_acid/base_lead_acid_model.py
diff --git a/...ll_battery_models/lead_acid/basic_full.py → ...ll_battery_models/lead_acid/basic_full.py b/...ll_battery_models/lead_acid/basic_full.py → ...ll_battery_models/lead_acid/basic_full.py
diff --git a/...els/full_battery_models/lead_acid/full.py → ...els/full_battery_models/lead_acid/full.py b/...els/full_battery_models/lead_acid/full.py → ...els/full_battery_models/lead_acid/full.py
diff --git a/...els/full_battery_models/lead_acid/loqs.py → ...els/full_battery_models/lead_acid/loqs.py b/...els/full_battery_models/lead_acid/loqs.py → ...els/full_battery_models/lead_acid/loqs.py
diff --git a/...ll_battery_models/lithium_ion/Yang2017.py → ...ll_battery_models/lithium_ion/Yang2017.py b/...ll_battery_models/lithium_ion/Yang2017.py → ...ll_battery_models/lithium_ion/Yang2017.py
diff --git a/...ll_battery_models/lithium_ion/__init__.py → ...ll_battery_models/lithium_ion/__init__.py b/...ll_battery_models/lithium_ion/__init__.py → ...ll_battery_models/lithium_ion/__init__.py
diff --git a/...els/lithium_ion/base_lithium_ion_model.py → ...els/lithium_ion/base_lithium_ion_model.py b/...els/lithium_ion/base_lithium_ion_model.py → ...els/lithium_ion/base_lithium_ion_model.py
diff --git a/...l_battery_models/lithium_ion/basic_dfn.py → ...l_battery_models/lithium_ion/basic_dfn.py b/...l_battery_models/lithium_ion/basic_dfn.py → ...l_battery_models/lithium_ion/basic_dfn.py
diff --git a/...models/lithium_ion/basic_dfn_composite.py → ...models/lithium_ion/basic_dfn_composite.py b/...models/lithium_ion/basic_dfn_composite.py → ...models/lithium_ion/basic_dfn_composite.py
diff --git a/...models/lithium_ion/basic_dfn_half_cell.py → ...models/lithium_ion/basic_dfn_half_cell.py b/...models/lithium_ion/basic_dfn_half_cell.py → ...models/lithium_ion/basic_dfn_half_cell.py
diff --git a/...l_battery_models/lithium_ion/basic_spm.py → ...l_battery_models/lithium_ion/basic_spm.py b/...l_battery_models/lithium_ion/basic_spm.py → ...l_battery_models/lithium_ion/basic_spm.py
diff --git a/...ls/full_battery_models/lithium_ion/dfn.py → ...ls/full_battery_models/lithium_ion/dfn.py b/...ls/full_battery_models/lithium_ion/dfn.py → ...ls/full_battery_models/lithium_ion/dfn.py
diff --git a/...ttery_models/lithium_ion/electrode_soh.py → ...ttery_models/lithium_ion/electrode_soh.py b/...ttery_models/lithium_ion/electrode_soh.py → ...ttery_models/lithium_ion/electrode_soh.py
diff --git a/...ls/lithium_ion/electrode_soh_half_cell.py → ...ls/lithium_ion/electrode_soh_half_cell.py b/...ls/lithium_ion/electrode_soh_half_cell.py → ...ls/lithium_ion/electrode_soh_half_cell.py
diff --git a/...ls/full_battery_models/lithium_ion/mpm.py → ...ls/full_battery_models/lithium_ion/mpm.py b/...ls/full_battery_models/lithium_ion/mpm.py → ...ls/full_battery_models/lithium_ion/mpm.py
diff --git a/...s/full_battery_models/lithium_ion/msmr.py → ...s/full_battery_models/lithium_ion/msmr.py b/...s/full_battery_models/lithium_ion/msmr.py → ...s/full_battery_models/lithium_ion/msmr.py
diff --git a/...ttery_models/lithium_ion/newman_tobias.py → ...ttery_models/lithium_ion/newman_tobias.py b/...ttery_models/lithium_ion/newman_tobias.py → ...ttery_models/lithium_ion/newman_tobias.py
diff --git a/...ls/full_battery_models/lithium_ion/spm.py → ...ls/full_battery_models/lithium_ion/spm.py b/...ls/full_battery_models/lithium_ion/spm.py → ...ls/full_battery_models/lithium_ion/spm.py
diff --git a/...s/full_battery_models/lithium_ion/spme.py → ...s/full_battery_models/lithium_ion/spme.py b/...s/full_battery_models/lithium_ion/spme.py → ...s/full_battery_models/lithium_ion/spme.py
diff --git a/.../full_battery_models/lithium_metal/dfn.py → .../full_battery_models/lithium_metal/dfn.py b/.../full_battery_models/lithium_metal/dfn.py → .../full_battery_models/lithium_metal/dfn.py
diff --git a/pybamm/models/submodels/__init__.py → src/pybamm/models/submodels/__init__.py b/pybamm/models/submodels/__init__.py → src/pybamm/models/submodels/__init__.py
diff --git a/...els/submodels/active_material/__init__.py → ...els/submodels/active_material/__init__.py b/...els/submodels/active_material/__init__.py → ...els/submodels/active_material/__init__.py
diff --git a/...s/active_material/base_active_material.py → ...s/active_material/base_active_material.py b/...s/active_material/base_active_material.py → ...s/active_material/base_active_material.py
diff --git a/...tive_material/constant_active_material.py → ...tive_material/constant_active_material.py b/...tive_material/constant_active_material.py → ...tive_material/constant_active_material.py
diff --git a/...s/active_material/loss_active_material.py → ...s/active_material/loss_active_material.py b/...s/active_material/loss_active_material.py → ...s/active_material/loss_active_material.py
diff --git a/.../active_material/total_active_material.py → .../active_material/total_active_material.py b/.../active_material/total_active_material.py → .../active_material/total_active_material.py
diff --git a/pybamm/models/submodels/base_submodel.py → src/pybamm/models/submodels/base_submodel.py b/pybamm/models/submodels/base_submodel.py → src/pybamm/models/submodels/base_submodel.py
diff --git a/...m/models/submodels/convection/__init__.py → ...m/models/submodels/convection/__init__.py b/...m/models/submodels/convection/__init__.py → ...m/models/submodels/convection/__init__.py
diff --git a/...s/submodels/convection/base_convection.py → ...s/submodels/convection/base_convection.py b/...s/submodels/convection/base_convection.py → ...s/submodels/convection/base_convection.py
diff --git a/...odels/convection/through_cell/__init__.py → ...odels/convection/through_cell/__init__.py b/...odels/convection/through_cell/__init__.py → ...odels/convection/through_cell/__init__.py
diff --git a/...ough_cell/base_through_cell_convection.py → ...ough_cell/base_through_cell_convection.py b/...ough_cell/base_through_cell_convection.py → ...ough_cell/base_through_cell_convection.py
diff --git a/...ction/through_cell/explicit_convection.py → ...ction/through_cell/explicit_convection.py b/...ction/through_cell/explicit_convection.py → ...ction/through_cell/explicit_convection.py
diff --git a/...onvection/through_cell/full_convection.py → ...onvection/through_cell/full_convection.py b/...onvection/through_cell/full_convection.py → ...onvection/through_cell/full_convection.py
diff --git a/.../convection/through_cell/no_convection.py → .../convection/through_cell/no_convection.py b/.../convection/through_cell/no_convection.py → .../convection/through_cell/no_convection.py
diff --git a/...bmodels/convection/transverse/__init__.py → ...bmodels/convection/transverse/__init__.py b/...bmodels/convection/transverse/__init__.py → ...bmodels/convection/transverse/__init__.py
diff --git a/.../transverse/base_transverse_convection.py → .../transverse/base_transverse_convection.py b/.../transverse/base_transverse_convection.py → .../transverse/base_transverse_convection.py
diff --git a/.../convection/transverse/full_convection.py → .../convection/transverse/full_convection.py b/.../convection/transverse/full_convection.py → .../convection/transverse/full_convection.py
diff --git a/...ls/convection/transverse/no_convection.py → ...ls/convection/transverse/no_convection.py b/...ls/convection/transverse/no_convection.py → ...ls/convection/transverse/no_convection.py
diff --git a/...nvection/transverse/uniform_convection.py → ...nvection/transverse/uniform_convection.py b/...nvection/transverse/uniform_convection.py → ...nvection/transverse/uniform_convection.py
diff --git a/...s/submodels/current_collector/__init__.py → ...s/submodels/current_collector/__init__.py b/...s/submodels/current_collector/__init__.py → ...s/submodels/current_collector/__init__.py
diff --git a/...rrent_collector/base_current_collector.py → ...rrent_collector/base_current_collector.py b/...rrent_collector/base_current_collector.py → ...rrent_collector/base_current_collector.py
diff --git a/...effective_resistance_current_collector.py → ...effective_resistance_current_collector.py b/...effective_resistance_current_collector.py → ...effective_resistance_current_collector.py
diff --git a/...ollector/homogeneous_current_collector.py → ...ollector/homogeneous_current_collector.py b/...ollector/homogeneous_current_collector.py → ...ollector/homogeneous_current_collector.py
diff --git a/...odels/current_collector/potential_pair.py → ...odels/current_collector/potential_pair.py b/...odels/current_collector/potential_pair.py → ...odels/current_collector/potential_pair.py
diff --git a/...mm/models/submodels/electrode/__init__.py → ...mm/models/submodels/electrode/__init__.py b/...mm/models/submodels/electrode/__init__.py → ...mm/models/submodels/electrode/__init__.py
diff --git a/...els/submodels/electrode/base_electrode.py → ...els/submodels/electrode/base_electrode.py b/...els/submodels/electrode/base_electrode.py → ...els/submodels/electrode/base_electrode.py
diff --git a/...odels/submodels/electrode/ohm/__init__.py → ...odels/submodels/electrode/ohm/__init__.py b/...odels/submodels/electrode/ohm/__init__.py → ...odels/submodels/electrode/ohm/__init__.py
diff --git a/...odels/submodels/electrode/ohm/base_ohm.py → ...odels/submodels/electrode/ohm/base_ohm.py b/...odels/submodels/electrode/ohm/base_ohm.py → ...odels/submodels/electrode/ohm/base_ohm.py
diff --git a/.../submodels/electrode/ohm/composite_ohm.py → .../submodels/electrode/ohm/composite_ohm.py b/.../submodels/electrode/ohm/composite_ohm.py → .../submodels/electrode/ohm/composite_ohm.py
diff --git a/...odels/submodels/electrode/ohm/full_ohm.py → ...odels/submodels/electrode/ohm/full_ohm.py b/...odels/submodels/electrode/ohm/full_ohm.py → ...odels/submodels/electrode/ohm/full_ohm.py
diff --git a/...ls/submodels/electrode/ohm/leading_ohm.py → ...ls/submodels/electrode/ohm/leading_ohm.py b/...ls/submodels/electrode/ohm/leading_ohm.py → ...ls/submodels/electrode/ohm/leading_ohm.py
diff --git a/...odels/submodels/electrode/ohm/li_metal.py → ...odels/submodels/electrode/ohm/li_metal.py b/...odels/submodels/electrode/ohm/li_metal.py → ...odels/submodels/electrode/ohm/li_metal.py
diff --git a/...bmodels/electrode/ohm/surface_form_ohm.py → ...bmodels/electrode/ohm/surface_form_ohm.py b/...bmodels/electrode/ohm/surface_form_ohm.py → ...bmodels/electrode/ohm/surface_form_ohm.py
diff --git a/...dels/electrolyte_conductivity/__init__.py → ...dels/electrolyte_conductivity/__init__.py b/...dels/electrolyte_conductivity/__init__.py → ...dels/electrolyte_conductivity/__init__.py
diff --git a/...uctivity/base_electrolyte_conductivity.py → ...uctivity/base_electrolyte_conductivity.py b/...uctivity/base_electrolyte_conductivity.py → ...uctivity/base_electrolyte_conductivity.py
diff --git a/...te_conductivity/composite_conductivity.py → ...te_conductivity/composite_conductivity.py b/...te_conductivity/composite_conductivity.py → ...te_conductivity/composite_conductivity.py
diff --git a/...trolyte_conductivity/full_conductivity.py → ...trolyte_conductivity/full_conductivity.py b/...trolyte_conductivity/full_conductivity.py → ...trolyte_conductivity/full_conductivity.py
diff --git a/...e_conductivity/integrated_conductivity.py → ...e_conductivity/integrated_conductivity.py b/...e_conductivity/integrated_conductivity.py → ...e_conductivity/integrated_conductivity.py
diff --git a/...onductivity/leading_order_conductivity.py → ...onductivity/leading_order_conductivity.py b/...onductivity/leading_order_conductivity.py → ...onductivity/leading_order_conductivity.py
diff --git a/...tivity/surface_potential_form/__init__.py → ...tivity/surface_potential_form/__init__.py b/...tivity/surface_potential_form/__init__.py → ...tivity/surface_potential_form/__init__.py
diff --git a/...rm/composite_surface_form_conductivity.py → ...rm/composite_surface_form_conductivity.py b/...rm/composite_surface_form_conductivity.py → ...rm/composite_surface_form_conductivity.py
diff --git a/...orm/explicit_surface_form_conductivity.py → ...orm/explicit_surface_form_conductivity.py b/...orm/explicit_surface_form_conductivity.py → ...orm/explicit_surface_form_conductivity.py
diff --git a/...al_form/full_surface_form_conductivity.py → ...al_form/full_surface_form_conductivity.py b/...al_form/full_surface_form_conductivity.py → ...al_form/full_surface_form_conductivity.py
diff --git a/...form/leading_surface_form_conductivity.py → ...form/leading_surface_form_conductivity.py b/...form/leading_surface_form_conductivity.py → ...form/leading_surface_form_conductivity.py
diff --git a/...bmodels/electrolyte_diffusion/__init__.py → ...bmodels/electrolyte_diffusion/__init__.py b/...bmodels/electrolyte_diffusion/__init__.py → ...bmodels/electrolyte_diffusion/__init__.py
diff --git a/...e_diffusion/base_electrolyte_diffusion.py → ...e_diffusion/base_electrolyte_diffusion.py b/...e_diffusion/base_electrolyte_diffusion.py → ...e_diffusion/base_electrolyte_diffusion.py
diff --git a/...olyte_diffusion/constant_concentration.py → ...olyte_diffusion/constant_concentration.py b/...olyte_diffusion/constant_concentration.py → ...olyte_diffusion/constant_concentration.py
diff --git a/...s/electrolyte_diffusion/full_diffusion.py → ...s/electrolyte_diffusion/full_diffusion.py b/...s/electrolyte_diffusion/full_diffusion.py → ...s/electrolyte_diffusion/full_diffusion.py
diff --git a/...lyte_diffusion/leading_order_diffusion.py → ...lyte_diffusion/leading_order_diffusion.py b/...lyte_diffusion/leading_order_diffusion.py → ...lyte_diffusion/leading_order_diffusion.py
diff --git a/...s/equivalent_circuit_elements/__init__.py → ...s/equivalent_circuit_elements/__init__.py b/...s/equivalent_circuit_elements/__init__.py → ...s/equivalent_circuit_elements/__init__.py
diff --git a/...ent_circuit_elements/diffusion_element.py → ...ent_circuit_elements/diffusion_element.py b/...ent_circuit_elements/diffusion_element.py → ...ent_circuit_elements/diffusion_element.py
diff --git a/...quivalent_circuit_elements/ocv_element.py → ...quivalent_circuit_elements/ocv_element.py b/...quivalent_circuit_elements/ocv_element.py → ...quivalent_circuit_elements/ocv_element.py
diff --git a/...equivalent_circuit_elements/rc_element.py → ...equivalent_circuit_elements/rc_element.py b/...equivalent_circuit_elements/rc_element.py → ...equivalent_circuit_elements/rc_element.py
diff --git a/...lent_circuit_elements/resistor_element.py → ...lent_circuit_elements/resistor_element.py b/...lent_circuit_elements/resistor_element.py → ...lent_circuit_elements/resistor_element.py
diff --git a/...ls/equivalent_circuit_elements/thermal.py → ...ls/equivalent_circuit_elements/thermal.py b/...ls/equivalent_circuit_elements/thermal.py → ...ls/equivalent_circuit_elements/thermal.py
diff --git a/...ivalent_circuit_elements/voltage_model.py → ...ivalent_circuit_elements/voltage_model.py b/...ivalent_circuit_elements/voltage_model.py → ...ivalent_circuit_elements/voltage_model.py
diff --git a/...ls/submodels/external_circuit/__init__.py → ...ls/submodels/external_circuit/__init__.py b/...ls/submodels/external_circuit/__init__.py → ...ls/submodels/external_circuit/__init__.py
diff --git a/...external_circuit/base_external_circuit.py → ...external_circuit/base_external_circuit.py b/...external_circuit/base_external_circuit.py → ...external_circuit/base_external_circuit.py
diff --git a/.../external_circuit/discharge_throughput.py → .../external_circuit/discharge_throughput.py b/.../external_circuit/discharge_throughput.py → .../external_circuit/discharge_throughput.py
diff --git a/...cuit/explicit_control_external_circuit.py → ...cuit/explicit_control_external_circuit.py b/...cuit/explicit_control_external_circuit.py → ...cuit/explicit_control_external_circuit.py
diff --git a/...cuit/function_control_external_circuit.py → ...cuit/function_control_external_circuit.py b/...cuit/function_control_external_circuit.py → ...cuit/function_control_external_circuit.py
diff --git a/...mm/models/submodels/interface/__init__.py → ...mm/models/submodels/interface/__init__.py b/...mm/models/submodels/interface/__init__.py → ...mm/models/submodels/interface/__init__.py
diff --git a/...els/submodels/interface/base_interface.py → ...els/submodels/interface/base_interface.py b/...els/submodels/interface/base_interface.py → ...els/submodels/interface/base_interface.py
diff --git a/...terface/interface_utilisation/__init__.py → ...terface/interface_utilisation/__init__.py b/...terface/interface_utilisation/__init__.py → ...terface/interface_utilisation/__init__.py
diff --git a/...interface_utilisation/base_utilisation.py → ...interface_utilisation/base_utilisation.py b/...interface_utilisation/base_utilisation.py → ...interface_utilisation/base_utilisation.py
diff --git a/...rface_utilisation/constant_utilisation.py → ...rface_utilisation/constant_utilisation.py b/...rface_utilisation/constant_utilisation.py → ...rface_utilisation/constant_utilisation.py
diff --git a/...utilisation/current_driven_utilisation.py → ...utilisation/current_driven_utilisation.py b/...utilisation/current_driven_utilisation.py → ...utilisation/current_driven_utilisation.py
diff --git a/...interface_utilisation/full_utilisation.py → ...interface_utilisation/full_utilisation.py b/...interface_utilisation/full_utilisation.py → ...interface_utilisation/full_utilisation.py
diff --git a/.../submodels/interface/kinetics/__init__.py → .../submodels/interface/kinetics/__init__.py b/.../submodels/interface/kinetics/__init__.py → .../submodels/interface/kinetics/__init__.py
diff --git a/...odels/interface/kinetics/base_kinetics.py → ...odels/interface/kinetics/base_kinetics.py b/...odels/interface/kinetics/base_kinetics.py → ...odels/interface/kinetics/base_kinetics.py
diff --git a/...odels/interface/kinetics/butler_volmer.py → ...odels/interface/kinetics/butler_volmer.py b/...odels/interface/kinetics/butler_volmer.py → ...odels/interface/kinetics/butler_volmer.py
diff --git a/...s/interface/kinetics/diffusion_limited.py → ...s/interface/kinetics/diffusion_limited.py b/...s/interface/kinetics/diffusion_limited.py → ...s/interface/kinetics/diffusion_limited.py
diff --git a/...ace/kinetics/inverse_kinetics/__init__.py → ...ace/kinetics/inverse_kinetics/__init__.py b/...ace/kinetics/inverse_kinetics/__init__.py → ...ace/kinetics/inverse_kinetics/__init__.py
diff --git a/...inverse_kinetics/inverse_butler_volmer.py → ...inverse_kinetics/inverse_butler_volmer.py b/...inverse_kinetics/inverse_butler_volmer.py → ...inverse_kinetics/inverse_butler_volmer.py
diff --git a/...ls/submodels/interface/kinetics/linear.py → ...ls/submodels/interface/kinetics/linear.py b/...ls/submodels/interface/kinetics/linear.py → ...ls/submodels/interface/kinetics/linear.py
diff --git a/...ls/submodels/interface/kinetics/marcus.py → ...ls/submodels/interface/kinetics/marcus.py b/...ls/submodels/interface/kinetics/marcus.py → ...ls/submodels/interface/kinetics/marcus.py
diff --git a/.../interface/kinetics/msmr_butler_volmer.py → .../interface/kinetics/msmr_butler_volmer.py b/.../interface/kinetics/msmr_butler_volmer.py → .../interface/kinetics/msmr_butler_volmer.py
diff --git a/...bmodels/interface/kinetics/no_reaction.py → ...bmodels/interface/kinetics/no_reaction.py b/...bmodels/interface/kinetics/no_reaction.py → ...bmodels/interface/kinetics/no_reaction.py
diff --git a/...els/submodels/interface/kinetics/tafel.py → ...els/submodels/interface/kinetics/tafel.py b/...els/submodels/interface/kinetics/tafel.py → ...els/submodels/interface/kinetics/tafel.py
diff --git a/...interface/kinetics/total_main_kinetics.py → ...interface/kinetics/total_main_kinetics.py b/...interface/kinetics/total_main_kinetics.py → ...interface/kinetics/total_main_kinetics.py
diff --git a/...els/interface/lithium_plating/__init__.py → ...els/interface/lithium_plating/__init__.py b/...els/interface/lithium_plating/__init__.py → ...els/interface/lithium_plating/__init__.py
diff --git a/...interface/lithium_plating/base_plating.py → ...interface/lithium_plating/base_plating.py b/...interface/lithium_plating/base_plating.py → ...interface/lithium_plating/base_plating.py
diff --git a/...s/interface/lithium_plating/no_plating.py → ...s/interface/lithium_plating/no_plating.py b/...s/interface/lithium_plating/no_plating.py → ...s/interface/lithium_plating/no_plating.py
diff --git a/...dels/interface/lithium_plating/plating.py → ...dels/interface/lithium_plating/plating.py b/...dels/interface/lithium_plating/plating.py → ...dels/interface/lithium_plating/plating.py
diff --git a/.../lithium_plating/total_lithium_plating.py → .../lithium_plating/total_lithium_plating.py b/.../lithium_plating/total_lithium_plating.py → .../lithium_plating/total_lithium_plating.py
diff --git a/...erface/open_circuit_potential/__init__.py → ...erface/open_circuit_potential/__init__.py b/...erface/open_circuit_potential/__init__.py → ...erface/open_circuit_potential/__init__.py
diff --git a/...erface/open_circuit_potential/base_ocp.py → ...erface/open_circuit_potential/base_ocp.py b/...erface/open_circuit_potential/base_ocp.py → ...erface/open_circuit_potential/base_ocp.py
diff --git a/..._circuit_potential/current_sigmoid_ocp.py → ..._circuit_potential/current_sigmoid_ocp.py b/..._circuit_potential/current_sigmoid_ocp.py → ..._circuit_potential/current_sigmoid_ocp.py
diff --git a/...erface/open_circuit_potential/msmr_ocp.py → ...erface/open_circuit_potential/msmr_ocp.py b/...erface/open_circuit_potential/msmr_ocp.py → ...erface/open_circuit_potential/msmr_ocp.py
diff --git a/...face/open_circuit_potential/single_ocp.py → ...face/open_circuit_potential/single_ocp.py b/...face/open_circuit_potential/single_ocp.py → ...face/open_circuit_potential/single_ocp.py
diff --git a/...face/open_circuit_potential/wycisk_ocp.py → ...face/open_circuit_potential/wycisk_ocp.py b/...face/open_circuit_potential/wycisk_ocp.py → ...face/open_circuit_potential/wycisk_ocp.py
diff --git a/...odels/submodels/interface/sei/__init__.py → ...odels/submodels/interface/sei/__init__.py b/...odels/submodels/interface/sei/__init__.py → ...odels/submodels/interface/sei/__init__.py
diff --git a/...odels/submodels/interface/sei/base_sei.py → ...odels/submodels/interface/sei/base_sei.py b/...odels/submodels/interface/sei/base_sei.py → ...odels/submodels/interface/sei/base_sei.py
diff --git a/...s/submodels/interface/sei/constant_sei.py → ...s/submodels/interface/sei/constant_sei.py b/...s/submodels/interface/sei/constant_sei.py → ...s/submodels/interface/sei/constant_sei.py
diff --git a/.../models/submodels/interface/sei/no_sei.py → .../models/submodels/interface/sei/no_sei.py b/.../models/submodels/interface/sei/no_sei.py → .../models/submodels/interface/sei/no_sei.py
diff --git a/...els/submodels/interface/sei/sei_growth.py → ...els/submodels/interface/sei/sei_growth.py b/...els/submodels/interface/sei/sei_growth.py → ...els/submodels/interface/sei/sei_growth.py
diff --git a/...dels/submodels/interface/sei/total_sei.py → ...dels/submodels/interface/sei/total_sei.py b/...dels/submodels/interface/sei/total_sei.py → ...dels/submodels/interface/sei/total_sei.py
diff --git a/...ls/interface/total_interfacial_current.py → ...ls/interface/total_interfacial_current.py b/...ls/interface/total_interfacial_current.py → ...ls/interface/total_interfacial_current.py
diff --git a/...ls/submodels/oxygen_diffusion/__init__.py → ...ls/submodels/oxygen_diffusion/__init__.py b/...ls/submodels/oxygen_diffusion/__init__.py → ...ls/submodels/oxygen_diffusion/__init__.py
diff --git a/...oxygen_diffusion/base_oxygen_diffusion.py → ...oxygen_diffusion/base_oxygen_diffusion.py b/...oxygen_diffusion/base_oxygen_diffusion.py → ...oxygen_diffusion/base_oxygen_diffusion.py
diff --git a/...oxygen_diffusion/full_oxygen_diffusion.py → ...oxygen_diffusion/full_oxygen_diffusion.py b/...oxygen_diffusion/full_oxygen_diffusion.py → ...oxygen_diffusion/full_oxygen_diffusion.py
diff --git a/...gen_diffusion/leading_oxygen_diffusion.py → ...gen_diffusion/leading_oxygen_diffusion.py b/...gen_diffusion/leading_oxygen_diffusion.py → ...gen_diffusion/leading_oxygen_diffusion.py
diff --git a/...s/submodels/oxygen_diffusion/no_oxygen.py → ...s/submodels/oxygen_diffusion/no_oxygen.py b/...s/submodels/oxygen_diffusion/no_oxygen.py → ...s/submodels/oxygen_diffusion/no_oxygen.py
diff --git a/pybamm/models/submodels/particle/__init__.py → ...amm/models/submodels/particle/__init__.py b/pybamm/models/submodels/particle/__init__.py → ...amm/models/submodels/particle/__init__.py
diff --git a/...odels/submodels/particle/base_particle.py → ...odels/submodels/particle/base_particle.py b/...odels/submodels/particle/base_particle.py → ...odels/submodels/particle/base_particle.py
diff --git a/...s/submodels/particle/fickian_diffusion.py → ...s/submodels/particle/fickian_diffusion.py b/...s/submodels/particle/fickian_diffusion.py → ...s/submodels/particle/fickian_diffusion.py
diff --git a/...dels/submodels/particle/msmr_diffusion.py → ...dels/submodels/particle/msmr_diffusion.py b/...dels/submodels/particle/msmr_diffusion.py → ...dels/submodels/particle/msmr_diffusion.py
diff --git a/.../submodels/particle/polynomial_profile.py → .../submodels/particle/polynomial_profile.py b/.../submodels/particle/polynomial_profile.py → .../submodels/particle/polynomial_profile.py
diff --git a/.../particle/total_particle_concentration.py → .../particle/total_particle_concentration.py b/.../particle/total_particle_concentration.py → .../particle/total_particle_concentration.py
diff --git a/...particle/x_averaged_polynomial_profile.py → ...particle/x_averaged_polynomial_profile.py b/...particle/x_averaged_polynomial_profile.py → ...particle/x_averaged_polynomial_profile.py
diff --git a/.../submodels/particle_mechanics/__init__.py → .../submodels/particle_mechanics/__init__.py b/.../submodels/particle_mechanics/__init__.py → .../submodels/particle_mechanics/__init__.py
diff --git a/...dels/particle_mechanics/base_mechanics.py → ...dels/particle_mechanics/base_mechanics.py b/...dels/particle_mechanics/base_mechanics.py → ...dels/particle_mechanics/base_mechanics.py
diff --git a/...s/particle_mechanics/crack_propagation.py → ...s/particle_mechanics/crack_propagation.py b/...s/particle_mechanics/crack_propagation.py → ...s/particle_mechanics/crack_propagation.py
diff --git a/...models/particle_mechanics/no_mechanics.py → ...models/particle_mechanics/no_mechanics.py b/...models/particle_mechanics/no_mechanics.py → ...models/particle_mechanics/no_mechanics.py
diff --git a/...odels/particle_mechanics/swelling_only.py → ...odels/particle_mechanics/swelling_only.py b/...odels/particle_mechanics/swelling_only.py → ...odels/particle_mechanics/swelling_only.py
diff --git a/pybamm/models/submodels/porosity/__init__.py → ...amm/models/submodels/porosity/__init__.py b/pybamm/models/submodels/porosity/__init__.py → ...amm/models/submodels/porosity/__init__.py
diff --git a/...odels/submodels/porosity/base_porosity.py → ...odels/submodels/porosity/base_porosity.py b/...odels/submodels/porosity/base_porosity.py → ...odels/submodels/porosity/base_porosity.py
diff --git a/...s/submodels/porosity/constant_porosity.py → ...s/submodels/porosity/constant_porosity.py b/...s/submodels/porosity/constant_porosity.py → ...s/submodels/porosity/constant_porosity.py
diff --git a/...dels/porosity/reaction_driven_porosity.py → ...dels/porosity/reaction_driven_porosity.py b/...dels/porosity/reaction_driven_porosity.py → ...dels/porosity/reaction_driven_porosity.py
diff --git a/.../porosity/reaction_driven_porosity_ode.py → .../porosity/reaction_driven_porosity_ode.py b/.../porosity/reaction_driven_porosity_ode.py → .../porosity/reaction_driven_porosity_ode.py
diff --git a/pybamm/models/submodels/thermal/__init__.py → ...bamm/models/submodels/thermal/__init__.py b/pybamm/models/submodels/thermal/__init__.py → ...bamm/models/submodels/thermal/__init__.py
diff --git a/.../models/submodels/thermal/base_thermal.py → .../models/submodels/thermal/base_thermal.py b/.../models/submodels/thermal/base_thermal.py → .../models/submodels/thermal/base_thermal.py
diff --git a/...mm/models/submodels/thermal/isothermal.py → ...mm/models/submodels/thermal/isothermal.py b/...mm/models/submodels/thermal/isothermal.py → ...mm/models/submodels/thermal/isothermal.py
diff --git a/pybamm/models/submodels/thermal/lumped.py → ...pybamm/models/submodels/thermal/lumped.py b/pybamm/models/submodels/thermal/lumped.py → ...pybamm/models/submodels/thermal/lumped.py
diff --git a/.../submodels/thermal/pouch_cell/__init__.py → .../submodels/thermal/pouch_cell/__init__.py b/.../submodels/thermal/pouch_cell/__init__.py → .../submodels/thermal/pouch_cell/__init__.py
diff --git a/..._cell/pouch_cell_1D_current_collectors.py → ..._cell/pouch_cell_1D_current_collectors.py b/..._cell/pouch_cell_1D_current_collectors.py → ..._cell/pouch_cell_1D_current_collectors.py
diff --git a/..._cell/pouch_cell_2D_current_collectors.py → ..._cell/pouch_cell_2D_current_collectors.py b/..._cell/pouch_cell_2D_current_collectors.py → ..._cell/pouch_cell_2D_current_collectors.py
diff --git a/...ls/submodels/thermal/pouch_cell/x_full.py → ...ls/submodels/thermal/pouch_cell/x_full.py b/...ls/submodels/thermal/pouch_cell/x_full.py → ...ls/submodels/thermal/pouch_cell/x_full.py
diff --git a/...ubmodels/transport_efficiency/__init__.py → ...ubmodels/transport_efficiency/__init__.py b/...ubmodels/transport_efficiency/__init__.py → ...ubmodels/transport_efficiency/__init__.py
diff --git a/...t_efficiency/base_transport_efficiency.py → ...t_efficiency/base_transport_efficiency.py b/...t_efficiency/base_transport_efficiency.py → ...t_efficiency/base_transport_efficiency.py
diff --git a/...bmodels/transport_efficiency/bruggeman.py → ...bmodels/transport_efficiency/bruggeman.py b/...bmodels/transport_efficiency/bruggeman.py → ...bmodels/transport_efficiency/bruggeman.py
diff --git a/...rt_efficiency/cation_exchange_membrane.py → ...rt_efficiency/cation_exchange_membrane.py b/...rt_efficiency/cation_exchange_membrane.py → ...rt_efficiency/cation_exchange_membrane.py
diff --git a/...port_efficiency/heterogeneous_catalyst.py → ...port_efficiency/heterogeneous_catalyst.py b/...port_efficiency/heterogeneous_catalyst.py → ...port_efficiency/heterogeneous_catalyst.py
diff --git a/...ort_efficiency/hyperbola_of_revolution.py → ...ort_efficiency/hyperbola_of_revolution.py b/...ort_efficiency/hyperbola_of_revolution.py → ...ort_efficiency/hyperbola_of_revolution.py
diff --git a/...s/transport_efficiency/ordered_packing.py → ...s/transport_efficiency/ordered_packing.py b/...s/transport_efficiency/ordered_packing.py → ...s/transport_efficiency/ordered_packing.py
diff --git a/...ansport_efficiency/overlapping_spheres.py → ...ansport_efficiency/overlapping_spheres.py b/...ansport_efficiency/overlapping_spheres.py → ...ansport_efficiency/overlapping_spheres.py
diff --git a/...fficiency/random_overlapping_cylinders.py → ...fficiency/random_overlapping_cylinders.py b/...fficiency/random_overlapping_cylinders.py → ...fficiency/random_overlapping_cylinders.py
diff --git a/...transport_efficiency/tortuosity_factor.py → ...transport_efficiency/tortuosity_factor.py b/...transport_efficiency/tortuosity_factor.py → ...transport_efficiency/tortuosity_factor.py
diff --git a/pybamm/parameters/__init__.py → src/pybamm/parameters/__init__.py b/pybamm/parameters/__init__.py → src/pybamm/parameters/__init__.py
diff --git a/pybamm/parameters/base_parameters.py → src/pybamm/parameters/base_parameters.py b/pybamm/parameters/base_parameters.py → src/pybamm/parameters/base_parameters.py
diff --git a/pybamm/parameters/bpx.py → src/pybamm/parameters/bpx.py b/pybamm/parameters/bpx.py → src/pybamm/parameters/bpx.py
diff --git a/pybamm/parameters/constants.py → src/pybamm/parameters/constants.py b/pybamm/parameters/constants.py → src/pybamm/parameters/constants.py
diff --git a/pybamm/parameters/ecm_parameters.py → src/pybamm/parameters/ecm_parameters.py b/pybamm/parameters/ecm_parameters.py → src/pybamm/parameters/ecm_parameters.py
diff --git a/pybamm/parameters/electrical_parameters.py → ...ybamm/parameters/electrical_parameters.py b/pybamm/parameters/electrical_parameters.py → ...ybamm/parameters/electrical_parameters.py
diff --git a/pybamm/parameters/geometric_parameters.py → ...pybamm/parameters/geometric_parameters.py b/pybamm/parameters/geometric_parameters.py → ...pybamm/parameters/geometric_parameters.py
diff --git a/pybamm/parameters/lead_acid_parameters.py → ...pybamm/parameters/lead_acid_parameters.py b/pybamm/parameters/lead_acid_parameters.py → ...pybamm/parameters/lead_acid_parameters.py
diff --git a/pybamm/parameters/lithium_ion_parameters.py → ...bamm/parameters/lithium_ion_parameters.py b/pybamm/parameters/lithium_ion_parameters.py → ...bamm/parameters/lithium_ion_parameters.py
diff --git a/pybamm/parameters/parameter_sets.py → src/pybamm/parameters/parameter_sets.py b/pybamm/parameters/parameter_sets.py → src/pybamm/parameters/parameter_sets.py
diff --git a/pybamm/parameters/parameter_values.py → src/pybamm/parameters/parameter_values.py b/pybamm/parameters/parameter_values.py → src/pybamm/parameters/parameter_values.py
diff --git a/pybamm/parameters/process_parameter_data.py → ...bamm/parameters/process_parameter_data.py b/pybamm/parameters/process_parameter_data.py → ...bamm/parameters/process_parameter_data.py
diff --git a/...arameters/size_distribution_parameters.py → ...arameters/size_distribution_parameters.py b/...arameters/size_distribution_parameters.py → ...arameters/size_distribution_parameters.py
diff --git a/pybamm/parameters/thermal_parameters.py → src/pybamm/parameters/thermal_parameters.py b/pybamm/parameters/thermal_parameters.py → src/pybamm/parameters/thermal_parameters.py
diff --git a/pybamm/plotting/__init__.py → src/pybamm/plotting/__init__.py b/pybamm/plotting/__init__.py → src/pybamm/plotting/__init__.py
diff --git a/pybamm/plotting/dynamic_plot.py → src/pybamm/plotting/dynamic_plot.py b/pybamm/plotting/dynamic_plot.py → src/pybamm/plotting/dynamic_plot.py
diff --git a/pybamm/plotting/plot.py → src/pybamm/plotting/plot.py b/pybamm/plotting/plot.py → src/pybamm/plotting/plot.py
diff --git a/pybamm/plotting/plot2D.py → src/pybamm/plotting/plot2D.py b/pybamm/plotting/plot2D.py → src/pybamm/plotting/plot2D.py
diff --git a/pybamm/plotting/plot_summary_variables.py → ...pybamm/plotting/plot_summary_variables.py b/pybamm/plotting/plot_summary_variables.py → ...pybamm/plotting/plot_summary_variables.py
diff --git a/pybamm/plotting/plot_thermal_components.py → ...ybamm/plotting/plot_thermal_components.py b/pybamm/plotting/plot_thermal_components.py → ...ybamm/plotting/plot_thermal_components.py
diff --git a/pybamm/plotting/plot_voltage_components.py → ...ybamm/plotting/plot_voltage_components.py b/pybamm/plotting/plot_voltage_components.py → ...ybamm/plotting/plot_voltage_components.py
diff --git a/pybamm/plotting/quick_plot.py → src/pybamm/plotting/quick_plot.py b/pybamm/plotting/quick_plot.py → src/pybamm/plotting/quick_plot.py
diff --git a/pybamm/pybamm_data.py → src/pybamm/pybamm_data.py b/pybamm/pybamm_data.py → src/pybamm/pybamm_data.py
diff --git a/pybamm/settings.py → src/pybamm/settings.py b/pybamm/settings.py → src/pybamm/settings.py
diff --git a/pybamm/simulation.py → src/pybamm/simulation.py b/pybamm/simulation.py → src/pybamm/simulation.py
diff --git a/pybamm/solvers/__init__.py → src/pybamm/solvers/__init__.py b/pybamm/solvers/__init__.py → src/pybamm/solvers/__init__.py
diff --git a/pybamm/solvers/algebraic_solver.py → src/pybamm/solvers/algebraic_solver.py b/pybamm/solvers/algebraic_solver.py → src/pybamm/solvers/algebraic_solver.py
diff --git a/pybamm/solvers/base_solver.py → src/pybamm/solvers/base_solver.py b/pybamm/solvers/base_solver.py → src/pybamm/solvers/base_solver.py
diff --git a/pybamm/solvers/c_solvers/__init__.py → src/pybamm/solvers/c_solvers/__init__.py b/pybamm/solvers/c_solvers/__init__.py → src/pybamm/solvers/c_solvers/__init__.py
diff --git a/pybamm/solvers/c_solvers/idaklu.cpp → src/pybamm/solvers/c_solvers/idaklu.cpp b/pybamm/solvers/c_solvers/idaklu.cpp → src/pybamm/solvers/c_solvers/idaklu.cpp
diff --git a/...rs/idaklu/Expressions/Base/Expression.hpp → ...rs/idaklu/Expressions/Base/Expression.hpp b/...rs/idaklu/Expressions/Base/Expression.hpp → ...rs/idaklu/Expressions/Base/Expression.hpp
-Original file line number
+Diff line change
@@ Expand Up / @@ -180,7 +180,7 @@ def run_doctests(session): @@
             "-m",
             "pytest",
             "--doctest-plus",
-            "pybamm",
+            "src",
         )
@@ Expand Down @@