From 71e5dc4dd96b187579761063bece54d07d9c6411 Mon Sep 17 00:00:00 2001
From: Zexin Yuan <git@yzx9.xyz>
Date: Thu, 17 Apr 2025 16:08:51 +0800
Subject: [PATCH 1/3] python3Packages.sdflit: init at 0.2.6

---
 .../python-modules/sdflit/default.nix         | 47 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 49 insertions(+)
 create mode 100644 pkgs/development/python-modules/sdflit/default.nix

diff --git a/pkgs/development/python-modules/sdflit/default.nix b/pkgs/development/python-modules/sdflit/default.nix
new file mode 100644
index 000000000000..fbb48e9bb131
--- /dev/null
+++ b/pkgs/development/python-modules/sdflit/default.nix
@@ -0,0 +1,47 @@
+{
+  lib,
+  fetchFromGitHub,
+  buildPythonPackage,
+  cargo,
+  rustPlatform,
+  rustc,
+}:
+
+let
+  version = "0.2.6";
+
+  src = fetchFromGitHub {
+    owner = "yzx9";
+    repo = "sdflit";
+    tag = "v${version}";
+    hash = "sha256-Ze3J5Dp+TskhIiGP6kMK3AIHLnhVBuEaKJokccIr+SM=";
+  };
+in
+buildPythonPackage {
+  pname = "sdflit";
+  inherit version src;
+  pyproject = true;
+
+  cargoDeps = rustPlatform.fetchCargoVendor {
+    inherit src;
+    hash = "sha256-CrMe5DuO9sQZZ50Hy+av4nF4gbOe296zSWJfJ8th7zs=";
+  };
+
+  build-system = [
+    cargo
+    rustPlatform.cargoSetupHook
+    rustPlatform.maturinBuildHook
+    rustc
+  ];
+
+  pythonImportsCheck = [
+    "sdflit"
+  ];
+
+  meta = {
+    description = "Fast and Robust Signed Distance Function Library";
+    homepage = "https://github.com/yzx9/sdflit";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ yzx9 ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 488efa43c9bf..da56c50d4fac 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -15469,6 +15469,8 @@ self: super: with self; {
 
   sdds = callPackage ../development/python-modules/sdds { };
 
+  sdflit = callPackage ../development/python-modules/sdflit { };
+
   sdjson = callPackage ../development/python-modules/sdjson { };
 
   sdkmanager = callPackage ../development/python-modules/sdkmanager { };

From c1d3a123a4440b2e365eea94aa01c6acfdd88953 Mon Sep 17 00:00:00 2001
From: Zexin Yuan <git@yzx9.xyz>
Date: Thu, 17 Apr 2025 16:09:34 +0800
Subject: [PATCH 2/3] python3Packages.imagecodecs: init at 2025.3.30

---
 .../python-modules/imagecodecs/default.nix    | 90 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 92 insertions(+)
 create mode 100644 pkgs/development/python-modules/imagecodecs/default.nix

diff --git a/pkgs/development/python-modules/imagecodecs/default.nix b/pkgs/development/python-modules/imagecodecs/default.nix
new file mode 100644
index 000000000000..30dfe4dc7de7
--- /dev/null
+++ b/pkgs/development/python-modules/imagecodecs/default.nix
@@ -0,0 +1,90 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  cython,
+  numpy,
+  setuptools,
+  pkgs,
+  jxrlib,
+  lcms2,
+  lerc,
+  libdeflate,
+  libpng,
+  libtiff,
+  libwebp,
+  openjpeg,
+  xz,
+  zlib,
+  zstd,
+  pytest,
+}:
+
+let
+  version = "2025.3.30";
+in
+buildPythonPackage {
+  pname = "imagecodecs";
+  inherit version;
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "cgohlke";
+    repo = "imagecodecs";
+    tag = "v${version}";
+    hash = "sha256-KtrQNABQOr3mNiWOfaZBcFceSCixPGV8Hte2uPKn1+k=";
+  };
+
+  build-system = [
+    cython
+    numpy
+    setuptools
+  ];
+
+  nativeBuildInputs = [
+    pkgs.lz4.dev # lz4 was hidden by python3Packages.lz4
+    lcms2.dev
+    openjpeg.dev
+  ];
+
+  buildInputs = [
+    pkgs.lz4
+    jxrlib
+    lcms2
+    lerc
+    libdeflate
+    libpng
+    libtiff
+    libwebp
+    openjpeg
+    xz # liblzma
+    zlib
+    zstd
+  ];
+
+  dependencies = [
+    numpy
+  ];
+
+  prePatch = ''
+    substituteInPlace setup.py \
+      --replace-fail "/usr/include/openjpeg" "${openjpeg.dev}/include/openjpeg" \
+      --replace-fail "/usr/include/jxrlib" "${jxrlib}/include/jxrlib"
+  '';
+
+  nativeCheckInputs = [
+    pytest
+  ];
+
+  pythonImportsCheck = [
+    "imagecodecs"
+  ];
+
+  meta = {
+    description = "Image transformation, compression, and decompression codecs";
+    homepage = "https://github.com/cgohlke/imagecodecs";
+    changelog = "https://github.com/cgohlke/imagecodecs/blob/v${version}/CHANGES.rst";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ yzx9 ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index da56c50d4fac..f2d7e44aa04f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -6572,6 +6572,8 @@ self: super: with self; {
 
   image-go-nord = callPackage ../development/python-modules/image-go-nord { };
 
+  imagecodecs = callPackage ../development/python-modules/imagecodecs { };
+
   imagecodecs-lite = callPackage ../development/python-modules/imagecodecs-lite { };
 
   imagecorruptions = callPackage ../development/python-modules/imagecorruptions { };

From dab4055530793b8753e3990a109138839c5c4b09 Mon Sep 17 00:00:00 2001
From: Zexin Yuan <git@yzx9.xyz>
Date: Thu, 17 Apr 2025 16:09:57 +0800
Subject: [PATCH 3/3] python3Packages.swcgeom: init at 0.19.3

---
 .../python-modules/swcgeom/default.nix        | 90 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 92 insertions(+)
 create mode 100644 pkgs/development/python-modules/swcgeom/default.nix

diff --git a/pkgs/development/python-modules/swcgeom/default.nix b/pkgs/development/python-modules/swcgeom/default.nix
new file mode 100644
index 000000000000..7de34846241a
--- /dev/null
+++ b/pkgs/development/python-modules/swcgeom/default.nix
@@ -0,0 +1,90 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  cython,
+  numpy,
+  setuptools,
+  wheel,
+  imagecodecs,
+  matplotlib,
+  pandas,
+  pynrrd,
+  scipy,
+  sdflit,
+  seaborn,
+  tifffile,
+  tqdm,
+  typing-extensions,
+  beautifulsoup4,
+  certifi,
+  chardet,
+  lmdb,
+  requests,
+  urllib3,
+  pytest,
+}:
+
+let
+  version = "0.19.3";
+in
+buildPythonPackage {
+  pname = "swcgeom";
+  inherit version;
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "yzx9";
+    repo = "swcgeom";
+    tag = "v${version}";
+    hash = "sha256-mpp8Dw0XcU59fYt7vjswAnXCmrRP3mhbgTDG+J4UwzI=";
+  };
+
+  build-system = [
+    cython
+    numpy
+    setuptools
+    wheel
+  ];
+
+  dependencies = [
+    imagecodecs
+    matplotlib
+    numpy
+    pandas
+    pynrrd
+    scipy
+    sdflit
+    seaborn
+    tifffile
+    tqdm
+    typing-extensions
+  ];
+
+  optional-dependencies = {
+    all = [
+      beautifulsoup4
+      certifi
+      chardet
+      lmdb
+      requests
+      urllib3
+    ];
+  };
+
+  nativeCheckInputs = [
+    pytest
+  ];
+
+  pythonImportsCheck = [
+    "swcgeom"
+  ];
+
+  meta = {
+    description = "Neuron geometry library for swc format";
+    homepage = "https://github.com/yzx9/swcgeom";
+    changelog = "https://github.com/yzx9/swcgeom/blob/v${version}/CHANGELOG.md";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ yzx9 ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index f2d7e44aa04f..873534a5a8bc 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -16765,6 +16765,8 @@ self: super: with self; {
 
   swagger-ui-bundle = callPackage ../development/python-modules/swagger-ui-bundle { };
 
+  swcgeom = callPackage ../development/python-modules/swcgeom { };
+
   swh-auth = callPackage ../development/python-modules/swh-auth { };
 
   swh-core = callPackage ../development/python-modules/swh-core { };