From cba85766967ecc84c4a14d44ea9a69c38d82620a Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Sat, 11 Jan 2025 20:07:07 +0530
Subject: [PATCH 01/10] build: switch to hatchling backend with hatch-vcs

- Replace setuptools with hatchling as build backend
- Add hatch-vcs for Git tag-based versioning
- Unify package versioning under a single source
---
 pyproject.toml | 33 ++++++++++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a416544551..c4db497ce1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,11 @@
 [build-system]
 requires = [
-    "setuptools",
+    "hatchling>=1.13.0",
+    "hatch-vcs>=0.3.0",
+    "casadi>=3.6.7; platform_system!='Windows'",
+    "cmake; platform_system!='Windows'",
 ]
-build-backend = "setuptools.build_meta"
+build-backend = "hatchling.build"
 
 [project]
 name = "pybamm"
@@ -86,7 +89,7 @@ cite = [
 ]
 # Battery Parameter eXchange format
 bpx = [
-    "bpx>=0.5.0,<0.6.0",
+    "bpx>=0.4.0",
 ]
 # Low-overhead progress bars
 tqdm = [
@@ -120,6 +123,10 @@ jax = [
     "jax==0.4.27",
     "jaxlib==0.4.27",
 ]
+# For MLIR expression evaluation (IDAKLU Solver)
+iree = [
+    "iree-compiler==20240507.886",
+]
 # Contains all optional dependencies, except for jax, iree, and dev dependencies
 all = [
     "scikit-fem>=8.1.0",
@@ -146,6 +153,21 @@ ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
 Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
+[tool.hatch.version]
+source = "vcs"
+raw-options = { local_scheme = "no-local-version", version_scheme = "python-simplified-semver" }
+
+[tool.hatch.build]
+packages = ["src/pybamm"]
+include = [
+    "src/pybamm/**/*.txt",
+    "src/pybamm/**/*.md",
+    "src/pybamm/**/*.csv",
+    "src/pybamm/**/*.py",
+    "src/pybamm/CITATIONS.bib",
+    "src/pybamm/plotting/mplstyle",
+]
+
 [tool.setuptools]
 include-package-data = true
 
@@ -259,6 +281,11 @@ log_date_format = "%Y-%m-%d %H:%M:%S"
 source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
+[tool.repo-review]
+ignore = [
+    "PP003"
+]
+
 [tool.mypy]
 ignore_missing_imports = true
 allow_redefinition = true

From a92c4c7580470382add6fe0791f004e0f1a121fc Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Tue, 14 Jan 2025 01:59:52 +0530
Subject: [PATCH 02/10] switch to hatchling without VCS integration

- Replace setuptools with hatchling as build backend
- Remove setuptools configurations
- Revert to version 24.11.2
---
 pyproject.toml | 32 ++------------------------------
 1 file changed, 2 insertions(+), 30 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c4db497ce1..642357420c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,9 +1,6 @@
 [build-system]
 requires = [
     "hatchling>=1.13.0",
-    "hatch-vcs>=0.3.0",
-    "casadi>=3.6.7; platform_system!='Windows'",
-    "cmake; platform_system!='Windows'",
 ]
 build-backend = "hatchling.build"
 
@@ -84,12 +81,11 @@ plot = [
     "matplotlib>=3.6.0",
 ]
 cite = [
-    "setuptools", # Fix for a pybtex issue
     "pybtex>=0.24.0",
 ]
 # Battery Parameter eXchange format
 bpx = [
-    "bpx>=0.4.0",
+    "bpx>=0.5.0,<0.6.0",
 ]
 # Low-overhead progress bars
 tqdm = [
@@ -123,10 +119,7 @@ jax = [
     "jax==0.4.27",
     "jaxlib==0.4.27",
 ]
-# For MLIR expression evaluation (IDAKLU Solver)
-iree = [
-    "iree-compiler==20240507.886",
-]
+
 # Contains all optional dependencies, except for jax, iree, and dev dependencies
 all = [
     "scikit-fem>=8.1.0",
@@ -153,10 +146,6 @@ ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
 Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
-[tool.hatch.version]
-source = "vcs"
-raw-options = { local_scheme = "no-local-version", version_scheme = "python-simplified-semver" }
-
 [tool.hatch.build]
 packages = ["src/pybamm"]
 include = [
@@ -168,25 +157,11 @@ include = [
     "src/pybamm/plotting/mplstyle",
 ]
 
-[tool.setuptools]
-include-package-data = true
-
 # List of files to include as package data. These are mainly the parameter CSV files in
 # the input/parameters/ subdirectories. Other files such as the CITATIONS file, relevant
 # README.md files, and specific .txt files inside the pybamm/ directory are also included.
 # These are specified to be included in the SDist through MANIFEST.in.
-[tool.setuptools.package-data]
-pybamm = [
-    "*.txt",
-    "*.md",
-    "*.csv",
-    "*.py",
-    "src/pybamm/CITATIONS.bib",
-    "src/pybamm/plotting/mplstyle",
-]
 
-[tool.setuptools.packages.find]
-where = ["src"]
 [tool.ruff]
 extend-include = ["*.ipynb"]
 extend-exclude = ["__init__.py"]
@@ -282,9 +257,6 @@ source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
 [tool.repo-review]
-ignore = [
-    "PP003"
-]
 
 [tool.mypy]
 ignore_missing_imports = true

From 98a8e8686ad4671230d9a8e3af91937da163987b Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Tue, 14 Jan 2025 13:24:58 +0530
Subject: [PATCH 03/10] switch to hatch with automatic file handling

- Replace setuptools with hatch as build backend
- Remove setuptools configurations
- Add automatic file handling in hatch config
---
 noxfile.py     |  5 -----
 pyproject.toml | 21 +++++----------------
 2 files changed, 5 insertions(+), 21 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 5c1b263f97..8af1e2f346 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -37,7 +37,6 @@ def set_environment_variables(env_dict, session):
 def run_coverage(session):
     """Run the coverage tests and generate an XML report."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("setuptools", silent=False)
     session.install("coverage", silent=False)
     # Using plugin here since coverage runs unit tests on linux with latest python version.
     if "CI" in os.environ:
@@ -50,7 +49,6 @@ def run_coverage(session):
 def run_integration(session):
     """Run the integration tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("setuptools", silent=False)
     if (
         "CI" in os.environ
         and sys.version_info[:2] == (3, 12)
@@ -80,7 +78,6 @@ def run_doctests(session):
 def run_unit(session):
     """Run the unit tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,jax]", silent=False)
     session.run("python", "-m", "pytest", "-m", "unit")
 
@@ -89,7 +86,6 @@ def run_unit(session):
 def run_examples(session):
     """Run the examples tests for Jupyter notebooks."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,jax]", silent=False)
     notebooks_to_test = session.posargs if session.posargs else []
     session.run(
@@ -134,7 +130,6 @@ def set_dev(session):
 def run_tests(session):
     """Run the unit tests and integration tests sequentially."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,jax]", silent=False)
     session.run(
         "python",
diff --git a/pyproject.toml b/pyproject.toml
index 642357420c..b4fbf11022 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,6 +81,7 @@ plot = [
     "matplotlib>=3.6.0",
 ]
 cite = [
+    "setuptools", # Fix for a pybtex issue
     "pybtex>=0.24.0",
 ]
 # Battery Parameter eXchange format
@@ -146,22 +147,12 @@ ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
 Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
-[tool.hatch.build]
-packages = ["src/pybamm"]
-include = [
-    "src/pybamm/**/*.txt",
-    "src/pybamm/**/*.md",
-    "src/pybamm/**/*.csv",
-    "src/pybamm/**/*.py",
-    "src/pybamm/CITATIONS.bib",
-    "src/pybamm/plotting/mplstyle",
+[tool.hatch]
+build.targets.sdist.include = [
+    "src/pybamm",
+    "CITATION.cff",
 ]
 
-# List of files to include as package data. These are mainly the parameter CSV files in
-# the input/parameters/ subdirectories. Other files such as the CITATIONS file, relevant
-# README.md files, and specific .txt files inside the pybamm/ directory are also included.
-# These are specified to be included in the SDist through MANIFEST.in.
-
 [tool.ruff]
 extend-include = ["*.ipynb"]
 extend-exclude = ["__init__.py"]
@@ -256,8 +247,6 @@ log_date_format = "%Y-%m-%d %H:%M:%S"
 source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
-[tool.repo-review]
-
 [tool.mypy]
 ignore_missing_imports = true
 allow_redefinition = true

From f3e80305b684dbade025560b14c523692a148670 Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Sat, 11 Jan 2025 20:07:07 +0530
Subject: [PATCH 04/10] build: switch to hatchling backend with hatch-vcs

- Replace setuptools with hatchling as build backend
- Add hatch-vcs for Git tag-based versioning
- Unify package versioning under a single source
---
 pyproject.toml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b4fbf11022..08491fbb17 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -86,7 +86,7 @@ cite = [
 ]
 # Battery Parameter eXchange format
 bpx = [
-    "bpx>=0.5.0,<0.6.0",
+    "bpx>=0.4.0",
 ]
 # Low-overhead progress bars
 tqdm = [
@@ -120,7 +120,6 @@ jax = [
     "jax==0.4.27",
     "jaxlib==0.4.27",
 ]
-
 # Contains all optional dependencies, except for jax, iree, and dev dependencies
 all = [
     "scikit-fem>=8.1.0",
@@ -247,6 +246,11 @@ log_date_format = "%Y-%m-%d %H:%M:%S"
 source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
+[tool.repo-review]
+ignore = [
+    "PP003"
+]
+
 [tool.mypy]
 ignore_missing_imports = true
 allow_redefinition = true

From 385674f67eaad64eabcffcb4e0aef5a4253df1eb Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Tue, 14 Jan 2025 01:59:52 +0530
Subject: [PATCH 05/10] switch to hatchling without VCS integration

- Replace setuptools with hatchling as build backend
- Remove setuptools configurations
- Revert to version 24.11.2
---
 pyproject.toml | 46 +++++++++++++++++++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 08491fbb17..9fad0de7a7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,12 +81,11 @@ plot = [
     "matplotlib>=3.6.0",
 ]
 cite = [
-    "setuptools", # Fix for a pybtex issue
     "pybtex>=0.24.0",
 ]
 # Battery Parameter eXchange format
 bpx = [
-    "bpx>=0.4.0",
+    "bpx>=0.5.0,<0.6.0",
 ]
 # Low-overhead progress bars
 tqdm = [
@@ -120,6 +119,10 @@ jax = [
     "jax==0.4.27",
     "jaxlib==0.4.27",
 ]
+# For MLIR expression evaluation (IDAKLU Solver)
+iree = [
+    "iree-compiler==20240507.886",
+]
 # Contains all optional dependencies, except for jax, iree, and dev dependencies
 all = [
     "scikit-fem>=8.1.0",
@@ -146,12 +149,40 @@ ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
 Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
-[tool.hatch]
-build.targets.sdist.include = [
-    "src/pybamm",
-    "CITATION.cff",
+[tool.hatch.version]
+source = "vcs"
+raw-options = { local_scheme = "no-local-version", version_scheme = "python-simplified-semver" }
+
+[tool.hatch.build]
+packages = ["src/pybamm"]
+include = [
+    "src/pybamm/**/*.txt",
+    "src/pybamm/**/*.md",
+    "src/pybamm/**/*.csv",
+    "src/pybamm/**/*.py",
+    "src/pybamm/CITATIONS.bib",
+    "src/pybamm/plotting/mplstyle",
 ]
 
+[tool.setuptools]
+include-package-data = true
+
+# List of files to include as package data. These are mainly the parameter CSV files in
+# the input/parameters/ subdirectories. Other files such as the CITATIONS file, relevant
+# README.md files, and specific .txt files inside the pybamm/ directory are also included.
+# These are specified to be included in the SDist through MANIFEST.in.
+[tool.setuptools.package-data]
+pybamm = [
+    "*.txt",
+    "*.md",
+    "*.csv",
+    "*.py",
+    "src/pybamm/CITATIONS.bib",
+    "src/pybamm/plotting/mplstyle",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
 [tool.ruff]
 extend-include = ["*.ipynb"]
 extend-exclude = ["__init__.py"]
@@ -247,9 +278,6 @@ source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
 [tool.repo-review]
-ignore = [
-    "PP003"
-]
 
 [tool.mypy]
 ignore_missing_imports = true

From b3a5de50790fc117e3490eebbb40b280ffc4f3ff Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Tue, 14 Jan 2025 13:24:58 +0530
Subject: [PATCH 06/10] switch to hatch with automatic file handling

- Replace setuptools with hatch as build backend
- Remove setuptools configurations
- Add automatic file handling in hatch config
---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9fad0de7a7..fb47d14cec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,6 +81,7 @@ plot = [
     "matplotlib>=3.6.0",
 ]
 cite = [
+    "setuptools", # Fix for a pybtex issue
     "pybtex>=0.24.0",
 ]
 # Battery Parameter eXchange format
@@ -277,8 +278,6 @@ log_date_format = "%Y-%m-%d %H:%M:%S"
 source = ["src/pybamm"]
 concurrency = ["multiprocessing"]
 
-[tool.repo-review]
-
 [tool.mypy]
 ignore_missing_imports = true
 allow_redefinition = true

From 8adc0ead434f08a166f417e1baf6f007b08654c9 Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Wed, 22 Jan 2025 18:50:19 +0530
Subject: [PATCH 07/10] revert changes to the original state

---
 pyproject.toml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7627d2c114..12ddc45f5f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -120,10 +120,7 @@ jax = [
     "jax==0.4.27",
     "jaxlib==0.4.27",
 ]
-# For MLIR expression evaluation (IDAKLU Solver)
-iree = [
-    "iree-compiler==20240507.886",
-]
+
 # Contains all optional dependencies, except for jax, iree, and dev dependencies
 all = [
     "scikit-fem>=8.1.0",
@@ -150,10 +147,6 @@ ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
 Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
-[tool.hatch.version]
-source = "vcs"
-raw-options = { local_scheme = "no-local-version", version_scheme = "python-simplified-semver" }
-
 [tool.hatch.build]
 packages = ["src/pybamm"]
 include = [

From 3e1ca8146538e82a68c81da2012da33fbd2992e8 Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Thu, 23 Jan 2025 00:49:14 +0530
Subject: [PATCH 08/10] revert to original state before conflicts

---
 pyproject.toml | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 12ddc45f5f..82a0884e4f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -147,20 +147,12 @@ ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
 Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
-[tool.hatch.build]
-packages = ["src/pybamm"]
-include = [
-    "src/pybamm/**/*.txt",
-    "src/pybamm/**/*.md",
-    "src/pybamm/**/*.csv",
-    "src/pybamm/**/*.py",
-    "src/pybamm/CITATIONS.bib",
-    "src/pybamm/plotting/mplstyle",
+[tool.hatch]
+build.targets.sdist.include = [
+  "src/pybamm",
+  "CITATION.cff",
 ]
 
-[tool.setuptools]
-include-package-data = true
-
 # List of files to include as package data. These are mainly the parameter CSV files in
 # the input/parameters/ subdirectories. Other files such as the CITATIONS file, relevant
 # README.md files, and specific .txt files inside the pybamm/ directory are also included.

From adc7e0c3670ad2bf9571ff4f02d8472dda874ed3 Mon Sep 17 00:00:00 2001
From: "Eric G. Kratz" <kratman@users.noreply.github.com>
Date: Wed, 22 Jan 2025 15:22:51 -0500
Subject: [PATCH 09/10] Update pyproject.toml

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 82a0884e4f..358e0cb6b9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -120,7 +120,6 @@ jax = [
     "jax==0.4.27",
     "jaxlib==0.4.27",
 ]
-
 # Contains all optional dependencies, except for jax, iree, and dev dependencies
 all = [
     "scikit-fem>=8.1.0",

From 0b8db17b8442db54fc8e6207d70b519535b77872 Mon Sep 17 00:00:00 2001
From: Vidip Singh <112854574+vidipsingh@users.noreply.github.com>
Date: Thu, 23 Jan 2025 20:52:44 +0530
Subject: [PATCH 10/10] remove setuptools references and MANIFEST.in

---
 MANIFEST.in    |  7 -------
 pyproject.toml | 16 ----------------
 2 files changed, 23 deletions(-)
 delete mode 100644 MANIFEST.in

diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index c1a77ac2f4..0000000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,7 +0,0 @@
-graft src
-include CITATION.cff
-prune tests
-
-exclude CHANGELOG.md CODE-OF-CONDUCT.md CONTRIBUTING.md all_contributors.md
-
-global-exclude __pycache__ *.py[cod] .venv
diff --git a/pyproject.toml b/pyproject.toml
index 358e0cb6b9..b34fcf9aeb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -152,22 +152,6 @@ build.targets.sdist.include = [
   "CITATION.cff",
 ]
 
-# List of files to include as package data. These are mainly the parameter CSV files in
-# the input/parameters/ subdirectories. Other files such as the CITATIONS file, relevant
-# README.md files, and specific .txt files inside the pybamm/ directory are also included.
-# These are specified to be included in the SDist through MANIFEST.in.
-[tool.setuptools.package-data]
-pybamm = [
-    "*.txt",
-    "*.md",
-    "*.csv",
-    "*.py",
-    "src/pybamm/CITATIONS.bib",
-    "src/pybamm/plotting/mplstyle",
-]
-
-[tool.setuptools.packages.find]
-where = ["src"]
 [tool.ruff]
 extend-include = ["*.ipynb"]
 extend-exclude = ["__init__.py"]