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Moving to src layout #4311

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merged 18 commits into from
Aug 8, 2024
Merged

Moving to src layout #4311

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2d9edee
Moving to src layout
prady0t Aug 2, 2024
21e7831
Applying require changes according to src path
prady0t Aug 3, 2024
10751fc
Merge branch 'develop' into src-layout-new
arjxn-py Aug 4, 2024
6da8e39
using src/pybamm
prady0t Aug 5, 2024
ee741d8
Merge branch 'src-layout-new' of https://github.com/prady0t/PyBaMM in…
prady0t Aug 5, 2024
b3969ac
changing path of pybamm.root_dir()
prady0t Aug 5, 2024
f81306e
style: pre-commit fixes
pre-commit-ci[bot] Aug 5, 2024
ed5f896
Solved merge conflicts
prady0t Aug 5, 2024
a81e9e8
changing path to src/pybamm in CMakeLists.txt
prady0t Aug 5, 2024
e6883d0
Merge branch 'develop' into src-layout-new
agriyakhetarpal Aug 5, 2024
f6941f9
fixing RTD failure
prady0t Aug 6, 2024
de7372c
Merge branch 'src-layout-new' of https://github.com/prady0t/PyBaMM in…
prady0t Aug 6, 2024
fa8ea7f
Merge branch 'develop' into src-layout-new
prady0t Aug 6, 2024
b9a59d8
using pybamm.__path__[0]
prady0t Aug 8, 2024
414a5ea
style: pre-commit fixes
pre-commit-ci[bot] Aug 8, 2024
cedc5a4
Update noxfile.py
prady0t Aug 8, 2024
a2728e3
Merge branch 'develop' into src-layout-new
agriyakhetarpal Aug 8, 2024
f175d16
Fix notebook paths
agriyakhetarpal Aug 8, 2024
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4 changes: 2 additions & 2 deletions .gitignore
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Expand Up @@ -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

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62 changes: 31 additions & 31 deletions CMakeLists.txt
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Expand Up @@ -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()

Expand All @@ -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}
${IDAKLU_EXPR_IREE_SOURCE_FILES}
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4 changes: 2 additions & 2 deletions CONTRIBUTING.md
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Expand Up @@ -38,7 +38,7 @@ We use [GIT](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedi
2. Create a [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) of this repo (ideally on your own [fork](https://help.github.com/articles/fork-a-repo/)), where all changes will be made
3. Download the source code onto your local system, by [cloning](https://help.github.com/articles/cloning-a-repository/) the repository (or your fork of the repository).
4. [Install](https://docs.pybamm.org/en/latest/source/user_guide/installation/install-from-source.html) PyBaMM with the developer options.
5. [Test](#testing) if your installation worked, using the test script: `$ 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!

Expand Down Expand Up @@ -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")
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2 changes: 1 addition & 1 deletion MANIFEST.in
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@@ -1,4 +1,4 @@
graft pybamm
graft src
include CITATION.cff
prune tests

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docs/conf.py
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Expand Up @@ -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"
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5 changes: 2 additions & 3 deletions docs/source/examples/notebooks/models/SPM.ipynb
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Expand Up @@ -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\")"
]
},
{
Expand Down Expand Up @@ -383,7 +382,7 @@
"metadata": {},
"outputs": [],
"source": [
"model.concatenated_rhs.children[1].visualise(path + \"spm2.png\")"
"model.concatenated_rhs.children[1].visualise(\"spm2.png\")"
]
},
{
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2 changes: 0 additions & 2 deletions examples/scripts/drive_cycle.py
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Expand Up @@ -3,9 +3,7 @@
#
import pybamm
import pandas as pd
import os

os.chdir(pybamm.__path__[0] + "/..")

pybamm.set_logging_level("INFO")

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2 changes: 0 additions & 2 deletions examples/scripts/experiment_drive_cycle.py
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Expand Up @@ -3,9 +3,7 @@
#
import pybamm
import pandas as pd
import os

os.chdir(pybamm.__path__[0] + "/..")

pybamm.set_logging_level("INFO")

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2 changes: 1 addition & 1 deletion noxfile.py
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Expand Up @@ -180,7 +180,7 @@ def run_doctests(session):
"-m",
"pytest",
"--doctest-plus",
"pybamm",
"src",
)


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9 changes: 4 additions & 5 deletions pyproject.toml
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Expand Up @@ -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"]
Expand Down Expand Up @@ -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]
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4 changes: 3 additions & 1 deletion scripts/update_version.py
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Expand Up @@ -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
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68 changes: 34 additions & 34 deletions setup.py
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Expand Up @@ -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 []
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0 pybamm/CITATIONS.bib → src/pybamm/CITATIONS.bib
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0 pybamm/__init__.py → src/pybamm/__init__.py
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2 changes: 1 addition & 1 deletion pybamm/citations.py → src/pybamm/citations.py
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Expand Up @@ -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)
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