From c4c9c87b5dd39e65d5bd1510098c6206ecd37d77 Mon Sep 17 00:00:00 2001
From: Derk Weijers <derk@weijers.xyz>
Date: Tue, 20 May 2025 10:29:52 -0400
Subject: [PATCH 1/3] ci: move to uv and pin versions

---
 pyproject.toml |   49 +-
 uv.lock        | 2455 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 2481 insertions(+), 23 deletions(-)
 create mode 100644 uv.lock

diff --git a/pyproject.toml b/pyproject.toml
index 3c0274a9903..55eb0072354 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,10 +35,10 @@ classifiers = [
 ]
 readme = "README.md"
 dependencies = [
-  "numpy",
-  "pandas",
-  "tqdm",
-  "scipy"
+  "numpy>=2.2.6,<3",
+  "pandas>=2.2.3,<3",
+  "scipy>=1.15.3,<2",
+  "tqdm>=4.67.1,<5",
 ]
 dynamic = ["version"]
 
@@ -48,36 +48,36 @@ rec = ["mesa[network,viz]"]
 all = ["mesa[network,viz,dev,examples,docs]"]
 # Core dependencies
 network = [
-  "networkx",
+  "networkx>=3.4.2,<4",
 ]
 viz = [
-  "matplotlib",
-  "solara",
-  "altair",
+  "matplotlib[viz]>=3.10.3,<4",
+  "altair[viz]>=5.5.0,<6",
+  "solara>=1.47.0,<2",
 ]
 # Dev and CI stuff
 dev = [
   "mesa[rec]",
-  "ruff",
-  "pytest",
-  "pytest-cov",
-  "sphinx",
-  "pytest-mock",
+  "ruff>=0.11.10,<1",
+  "pytest-mock>=3.14.0,<4",
+  "sphinx>=8.2.3,<9",
+  "pytest-cov>=6.1.1,<7",
+  "pytest>=8.3.5,<9",
 ]
 examples = [
   "mesa[rec]",
-  "pytest",
-  "scipy",
+  "pytest>=8.3.5,<9",
+  "scipy>=1.15.3,<2",
 ]
 docs = [
+  "ipython>=9.2.0,<10",
   "mesa[rec]",
-  "sphinx",
-  "ipython",
-  "pydata_sphinx_theme",
-  "seaborn",
-  "myst-nb",
-  "myst-parser",  # Markdown in Sphinx
-  "sphinx-copybutton", # Add a copy option in docs
+  "myst-nb>=1.2.0,<2",
+  "myst-parser>=4.0.1,<5",
+  "pydata-sphinx-theme>=0.16.1,<1",
+  "seaborn>=0.13.2,<1",
+  "sphinx>=8.2.3,<9",
+  "sphinx-copybutton>=0.5.2,<1",
 ]
 
 [project.urls]
@@ -149,4 +149,7 @@ extend-ignore = [
 per-file-ignores = {"mesa/examples/*"= ["D"], "docs/tutorials/*" = ["D", "E", "F", "N"], "docs/conf.py"=["C", "D", "DTZ011", "E"]}
 
 [tool.ruff.lint.pydocstyle]
-convention = "google"
\ No newline at end of file
+convention = "google"
+
+[tool.uv.sources]
+mesa = { workspace = true }
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 00000000000..4269512e7b6
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,2455 @@
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+revision = 2
+requires-python = ">=3.11"
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+]
+
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+]

From 1789a8453b0be8a47af5ee0ce0d3848387ae9083 Mon Sep 17 00:00:00 2001
From: Derk Weijers <derk@weijers.xyz>
Date: Tue, 20 May 2025 11:42:53 -0400
Subject: [PATCH 2/3] chore: cleanup

---
 pyproject.toml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 55eb0072354..dd245929ffc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -149,7 +149,4 @@ extend-ignore = [
 per-file-ignores = {"mesa/examples/*"= ["D"], "docs/tutorials/*" = ["D", "E", "F", "N"], "docs/conf.py"=["C", "D", "DTZ011", "E"]}
 
 [tool.ruff.lint.pydocstyle]
-convention = "google"
-
-[tool.uv.sources]
-mesa = { workspace = true }
+convention = "google"
\ No newline at end of file

From f6012e4be0e02879564208511691c1d810918160 Mon Sep 17 00:00:00 2001
From: Derk Weijers <derk@weijers.xyz>
Date: Wed, 21 May 2025 07:19:33 -0400
Subject: [PATCH 3/3] ci: fix merge conflicts

---
 pyproject.toml |  4 +++-
 uv.lock        | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dd245929ffc..fdbe9bfa287 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,6 +39,7 @@ dependencies = [
   "pandas>=2.2.3,<3",
   "scipy>=1.15.3,<2",
   "tqdm>=4.67.1,<5",
+  "pythran>=0.17.0,<1 ; sys_platform == 'darwin'", # required for darwin scipy overrides in nix
 ]
 dynamic = ["version"]
 
@@ -63,6 +64,7 @@ dev = [
   "sphinx>=8.2.3,<9",
   "pytest-cov>=6.1.1,<7",
   "pytest>=8.3.5,<9",
+  "ipython>=9.2.0,<10",
 ]
 examples = [
   "mesa[rec]",
@@ -149,4 +151,4 @@ extend-ignore = [
 per-file-ignores = {"mesa/examples/*"= ["D"], "docs/tutorials/*" = ["D", "E", "F", "N"], "docs/conf.py"=["C", "D", "DTZ011", "E"]}
 
 [tool.ruff.lint.pydocstyle]
-convention = "google"
\ No newline at end of file
+convention = "google"
diff --git a/uv.lock b/uv.lock
index 4269512e7b6..1cf91aabf55 100644
--- a/uv.lock
+++ b/uv.lock
@@ -106,6 +106,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/50/cd/30110dc0ffcf3b131156077b90e9f60ed75711223f306da4db08eff8403b/beautifulsoup4-4.13.4-py3-none-any.whl", hash = "sha256:9bbbb14bfde9d79f38b8cd5f8c7c85f4b8f2523190ebed90e950a8dea4cb1c4b", size = 187285, upload-time = "2025-04-15T17:05:12.221Z" },
 ]
 
+[[package]]
+name = "beniget"
+version = "0.4.2.post1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "gast" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/2e/27/5bb01af8f2860d431b98d0721b96ff2cea979106cae3f2d093ec74f6400c/beniget-0.4.2.post1.tar.gz", hash = "sha256:a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae", size = 32274, upload-time = "2024-06-28T10:20:05.708Z" }
+wheels = [
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+]
+
 [[package]]
 name = "cachetools"
 version = "5.5.2"
@@ -467,6 +479,15 @@ wheels = [
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 ]
 
+[[package]]
+name = "gast"
+version = "0.6.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/3c/14/c566f5ca00c115db7725263408ff952b8ae6d6a4e792ef9c84e77d9af7a1/gast-0.6.0.tar.gz", hash = "sha256:88fc5300d32c7ac6ca7b515310862f71e6fdf2c029bbec7c66c0f5dd47b6b1fb", size = 27708, upload-time = "2024-06-27T20:31:49.527Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/a3/61/8001b38461d751cd1a0c3a6ae84346796a5758123f3ed97a1b121dfbf4f3/gast-0.6.0-py3-none-any.whl", hash = "sha256:52b182313f7330389f72b069ba00f174cfe2a06411099547288839c6cbafbd54", size = 21173, upload-time = "2024-07-09T13:15:15.615Z" },
+]
+
 [[package]]
 name = "greenlet"
 version = "3.2.2"
@@ -991,6 +1012,7 @@ source = { editable = "." }
 dependencies = [
     { name = "numpy" },
     { name = "pandas" },
+    { name = "pythran", marker = "sys_platform == 'darwin'" },
     { name = "scipy" },
     { name = "tqdm" },
 ]
@@ -1016,6 +1038,7 @@ all = [
 ]
 dev = [
     { name = "altair" },
+    { name = "ipython" },
     { name = "matplotlib" },
     { name = "networkx" },
     { name = "pytest" },
@@ -1070,6 +1093,7 @@ requires-dist = [
     { name = "altair", extras = ["viz"], marker = "extra == 'rec'", specifier = ">=5.5.0,<6" },
     { name = "altair", extras = ["viz"], marker = "extra == 'viz'", specifier = ">=5.5.0,<6" },
     { name = "ipython", marker = "extra == 'all'", specifier = ">=9.2.0,<10" },
+    { name = "ipython", marker = "extra == 'dev'", specifier = ">=9.2.0,<10" },
     { name = "ipython", marker = "extra == 'docs'", specifier = ">=9.2.0,<10" },
     { name = "matplotlib", extras = ["viz"], marker = "extra == 'all'", specifier = ">=3.10.3,<4" },
     { name = "matplotlib", extras = ["viz"], marker = "extra == 'dev'", specifier = ">=3.10.3,<4" },
@@ -1098,6 +1122,7 @@ requires-dist = [
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     { name = "pytest-mock", marker = "extra == 'all'", specifier = ">=3.14.0,<4" },
     { name = "pytest-mock", marker = "extra == 'dev'", specifier = ">=3.14.0,<4" },
+    { name = "pythran", marker = "sys_platform == 'darwin'", specifier = ">=0.17.0,<1" },
     { name = "ruff", marker = "extra == 'all'", specifier = ">=0.11.10,<1" },
     { name = "ruff", marker = "extra == 'dev'", specifier = ">=0.11.10,<1" },
     { name = "scipy", specifier = ">=1.15.3,<2" },
@@ -1411,6 +1436,15 @@ wheels = [
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 ]
 
+[[package]]
+name = "ply"
+version = "3.11"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/e5/69/882ee5c9d017149285cab114ebeab373308ef0f874fcdac9beb90e0ac4da/ply-3.11.tar.gz", hash = "sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3", size = 159130, upload-time = "2018-02-15T19:01:31.097Z" }
+wheels = [
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+
 [[package]]
 name = "prompt-toolkit"
 version = "3.0.51"
@@ -1566,6 +1600,22 @@ wheels = [
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 ]
 
+[[package]]
+name = "pythran"
+version = "0.17.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "beniget" },
+    { name = "gast" },
+    { name = "numpy" },
+    { name = "ply" },
+    { name = "setuptools" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/34/2d/4ac363a2eecd68c372b058d1b95a5f262c70776e107619cdcb5a4b68e1a3/pythran-0.17.0.tar.gz", hash = "sha256:3b77d6d970a6cf5b448facc7d4f6229c3e73909ac27ea2480c843afdadbad0fb", size = 2394494, upload-time = "2024-10-31T09:34:20.043Z" }
+wheels = [
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 [[package]]
 name = "pytz"
 version = "2025.2"
@@ -1918,6 +1968,15 @@ wheels = [
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 ]
 
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+version = "80.8.0"
+source = { registry = "https://pypi.org/simple" }
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 [[package]]
 name = "six"
 version = "1.17.0"