From 1442b4851c304575ef4b923bcfa2afc6631ed0a5 Mon Sep 17 00:00:00 2001
From: Julien St-Laurent <julien.stl@valencelabs.com>
Date: Tue, 8 Apr 2025 16:13:32 -0400
Subject: [PATCH 1/2] fix: Make FastPDB a full conda dependency

---
 env.yml |   12 +-
 uv.lock | 1843 ++++++++++++++++++++++++++++---------------------------
 2 files changed, 944 insertions(+), 911 deletions(-)

diff --git a/env.yml b/env.yml
index 43105582..5aeeb03b 100644
--- a/env.yml
+++ b/env.yml
@@ -2,7 +2,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - python >=3.10
+  - python >=3.10,<3.13
   - pip
   - typer
   - pyyaml
@@ -12,7 +12,7 @@ dependencies:
   - typing-extensions >=4.12.0
   - boto3 <1.36.0
   - pyroaring
-  - rich
+  - rich >=13.9.4
 
   # Hub client
   - authlib
@@ -27,11 +27,12 @@ dependencies:
 
   # Chemistry
   - datamol >=0.12.1
+  - fastpdb
 
   # Storage
   - zarr >=2,<3
-  - pyarrow
-  - numcodecs
+  - pyarrow <18
+  - numcodecs >=0.13.1
 
   # Dev
   - pytest
@@ -52,6 +53,3 @@ dependencies:
   - mdx_truly_sane_lists
   - nbconvert
   - mike >=1.0.0
-
-  - pip:
-      - fastpdb
diff --git a/uv.lock b/uv.lock
index 448c249a..175c1919 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,4 +1,5 @@
 version = 1
+revision = 1
 requires-python = ">=3.10, <3.13"
 resolution-markers = [
     "python_full_version >= '3.12'",
@@ -8,16 +9,16 @@ resolution-markers = [
 
 [[package]]
 name = "aiohappyeyeballs"
-version = "2.4.6"
+version = "2.6.1"
 source = { registry = "https://pypi.org/simple" }
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+sdist = { url = "https://files.pythonhosted.org/packages/26/30/f84a107a9c4331c14b2b586036f40965c128aa4fee4dda5d3d51cb14ad54/aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558", size = 22760 }
 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/0f/15/5bf3b99495fb160b63f95972b81750f18f7f4e02ad051373b669d17d44f2/aiohappyeyeballs-2.6.1-py3-none-any.whl", hash = "sha256:f349ba8f4b75cb25c99c5c2d84e997e485204d2902a9597802b0371f09331fb8", size = 15265 },
 ]
 
 [[package]]
 name = "aiohttp"
-version = "3.11.12"
+version = "3.11.16"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -29,56 +30,56 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
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 [[package]]
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+    { name = "zarr", version = "2.18.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+]
+
+[package.optional-dependencies]
+codecs = [
+    { name = "imagecodecs" },
+]
+dev = [
+    { name = "ipywidgets" },
+    { name = "jupyterlab" },
+    { name = "moto", extra = ["s3"] },
+    { name = "pytest" },
+    { name = "pytest-cov" },
+    { name = "pytest-xdist" },
+    { name = "ruff" },
+]
+doc = [
+    { name = "markdown-include" },
+    { name = "mdx-truly-sane-lists" },
+    { name = "mike" },
+    { name = "mkdocs" },
+    { name = "mkdocs-jupyter" },
+    { name = "mkdocs-material" },
+    { name = "mkdocstrings" },
+    { name = "mkdocstrings-python" },
+    { name = "nbconvert" },
 ]
 
 [package.dev-dependencies]
@@ -2305,6 +2377,19 @@ requires-dist = [
     { name = "fastpdb" },
     { name = "fsspec", extras = ["http"] },
     { name = "httpx" },
+    { name = "imagecodecs", marker = "extra == 'codecs'" },
+    { name = "ipywidgets", marker = "extra == 'dev'" },
+    { name = "jupyterlab", marker = "extra == 'dev'" },
+    { name = "markdown-include", marker = "extra == 'doc'" },
+    { name = "mdx-truly-sane-lists", marker = "extra == 'doc'" },
+    { name = "mike", marker = "extra == 'doc'", specifier = ">=1.0.0" },
+    { name = "mkdocs", marker = "extra == 'doc'" },
+    { name = "mkdocs-jupyter", marker = "extra == 'doc'" },
+    { name = "mkdocs-material", marker = "extra == 'doc'", specifier = ">=9.4.7" },
+    { name = "mkdocstrings", marker = "extra == 'doc'" },
+    { name = "mkdocstrings-python", marker = "extra == 'doc'" },
+    { name = "moto", extras = ["s3"], marker = "extra == 'dev'", specifier = ">=5.0.14" },
+    { name = "nbconvert", marker = "extra == 'doc'" },
     { name = "numcodecs", extras = ["msgpack"], specifier = ">=0.13.1" },
     { name = "numpy", specifier = "<3" },
     { name = "pandas" },
@@ -2312,8 +2397,12 @@ requires-dist = [
     { name = "pydantic", specifier = ">=2" },
     { name = "pydantic-settings", specifier = ">=2" },
     { name = "pyroaring" },
+    { name = "pytest", marker = "extra == 'dev'", specifier = ">=7" },
+    { name = "pytest-cov", marker = "extra == 'dev'" },
+    { name = "pytest-xdist", marker = "extra == 'dev'" },
     { name = "pyyaml" },
     { name = "rich", specifier = ">=13.9.4" },
+    { name = "ruff", marker = "extra == 'dev'" },
     { name = "scikit-learn" },
     { name = "scipy" },
     { name = "seaborn" },
@@ -2321,6 +2410,7 @@ requires-dist = [
     { name = "typing-extensions", specifier = ">=4.12.0" },
     { name = "zarr", specifier = ">=2,<3" },
 ]
+provides-extras = ["dev", "doc", "codecs"]
 
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+version = "2.18.6"
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 resolution-markers = [
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@@ -3686,12 +3721,12 @@ resolution-markers = [
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-    { name = "numcodecs", version = "0.15.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "numcodecs", version = "0.16.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
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 [[package]]

From ed9be220291233b9974eac5cd36fb75d2f984dee Mon Sep 17 00:00:00 2001
From: Julien St-Laurent <julien.stl@valencelabs.com>
Date: Tue, 8 Apr 2025 16:29:02 -0400
Subject: [PATCH 2/2] fix: Pin numcodecs, whose latest release breaks Zarr 2

---
 env.yml        |  2 +-
 pyproject.toml |  2 +-
 uv.lock        | 47 ++++++-----------------------------------------
 3 files changed, 8 insertions(+), 43 deletions(-)

diff --git a/env.yml b/env.yml
index 5aeeb03b..d466ab92 100644
--- a/env.yml
+++ b/env.yml
@@ -32,7 +32,7 @@ dependencies:
   # Storage
   - zarr >=2,<3
   - pyarrow <18
-  - numcodecs >=0.13.1
+  - numcodecs >=0.13.1,<0.16.0
 
   # Dev
   - pytest
diff --git a/pyproject.toml b/pyproject.toml
index 8975b918..9094961f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ dependencies = [
     "fastpdb",
     "fsspec[http]",
     "httpx",
-    "numcodecs[msgpack]>=0.13.1",
+    "numcodecs[msgpack] >=0.13.1, <0.16.0",
     "numpy <3",
     "pandas",
     "pyarrow < 18",
diff --git a/uv.lock b/uv.lock
index 175c1919..c312f696 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2023,11 +2023,8 @@ wheels = [
 name = "numcodecs"
 version = "0.13.1"
 source = { registry = "https://pypi.org/simple" }
-resolution-markers = [
-    "python_full_version < '3.11'",
-]
 dependencies = [
-    { name = "numpy", marker = "python_full_version < '3.11'" },
+    { name = "numpy" },
 ]
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 wheels = [
@@ -2047,38 +2044,7 @@ wheels = [
 
 [package.optional-dependencies]
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-]
-
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-]
-
-[package.optional-dependencies]
-msgpack = [
-    { name = "msgpack", marker = "python_full_version >= '3.11'" },
+    { name = "msgpack" },
 ]
 
 [[package]]
@@ -2300,8 +2266,7 @@ dependencies = [
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     { name = "fsspec", extra = ["http"] },
     { name = "httpx" },
-    { name = "numcodecs", version = "0.13.1", source = { registry = "https://pypi.org/simple" }, extra = ["msgpack"], marker = "python_full_version < '3.11'" },
-    { name = "numcodecs", version = "0.16.0", source = { registry = "https://pypi.org/simple" }, extra = ["msgpack"], marker = "python_full_version >= '3.11'" },
+    { name = "numcodecs", extra = ["msgpack"] },
     { name = "numpy" },
     { name = "pandas" },
     { name = "pyarrow" },
@@ -2390,7 +2355,7 @@ requires-dist = [
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     { name = "moto", extras = ["s3"], marker = "extra == 'dev'", specifier = ">=5.0.14" },
     { name = "nbconvert", marker = "extra == 'doc'" },
-    { name = "numcodecs", extras = ["msgpack"], specifier = ">=0.13.1" },
+    { name = "numcodecs", extras = ["msgpack"], specifier = ">=0.13.1,<0.16.0" },
     { name = "numpy", specifier = "<3" },
     { name = "pandas" },
     { name = "pyarrow", specifier = "<18" },
@@ -3702,7 +3667,7 @@ resolution-markers = [
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-    { name = "numcodecs", version = "0.13.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numcodecs", marker = "python_full_version < '3.11'" },
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