Moving to src layout (#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>

.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
 

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}

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")

MANIFEST.in

@@ -1,4 +1,4 @@
-graft pybamm
+graft src
 include CITATION.cff
 prune tests
 

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

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"

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\")"
    ]
   },
   {

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")
 

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")
 

noxfile.py

@@ -180,7 +180,7 @@ def run_doctests(session):
         "-m",
         "pytest",
         "--doctest-plus",
-        "pybamm",
+        "src",
     )
 
 

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]

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

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 []

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)