feat: updated deps and switched from poetry to uv

.envrc

@@ -0,0 +1,3 @@
+source_url "https://raw.githubusercontent.com/cachix/devenv/82c0147677e510b247d8b9165c54f73d32dfd899/direnvrc" "sha256-7u4iDd1nZpxL4tCzmPG0dQgC5V+/44Ba+tHkPob1v2k="
+
+use devenv

.gitignore

@@ -156,3 +156,12 @@ poetry.lock
 # Ignore all local history of files
 .history
 .ionide
+# Devenv
+.devenv*
+devenv.local.nix
+
+# direnv
+.direnv
+
+# pre-commit
+.pre-commit-config.yaml

.python-version

@@ -0,0 +1 @@
+[email protected]

README.rst

@@ -16,8 +16,6 @@ It requires the following packages:
 
 - ANTs (Can be a system installation or anaconda installation),
 - ANTsPyX,
-- importlib_resources,
-- Pandas,
 - Rich.
 
 

devenv.lock

@@ -0,0 +1,116 @@
+{
+  "nodes": {
+    "devenv": {
+      "locked": {
+        "dir": "src/modules",
+        "lastModified": 1730028891,
+        "owner": "cachix",
+        "repo": "devenv",
+        "rev": "a337f8862efa9bde348c48a48b5b943f710604dd",
+        "type": "github"
+      },
+      "original": {
+        "dir": "src/modules",
+        "owner": "cachix",
+        "repo": "devenv",
+        "type": "github"
+      }
+    },
+    "flake-compat": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1696426674,
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33",
+        "type": "github"
+      },
+      "original": {
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "gitignore": {
+      "inputs": {
+        "nixpkgs": [
+          "pre-commit-hooks",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1709087332,
+        "owner": "hercules-ci",
+        "repo": "gitignore.nix",
+        "rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
+        "type": "github"
+      },
+      "original": {
+        "owner": "hercules-ci",
+        "repo": "gitignore.nix",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1729980323,
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "86e78d3d2084ff87688da662cf78c2af085d8e73",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-stable": {
+      "locked": {
+        "lastModified": 1729973466,
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "cd3e8833d70618c4eea8df06f95b364b016d4950",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-24.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pre-commit-hooks": {
+      "inputs": {
+        "flake-compat": "flake-compat",
+        "gitignore": "gitignore",
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "nixpkgs-stable": "nixpkgs-stable"
+      },
+      "locked": {
+        "lastModified": 1729104314,
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "rev": "3c3e88f0f544d6bb54329832616af7eb971b6be6",
+        "type": "github"
+      },
+      "original": {
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "devenv": "devenv",
+        "nixpkgs": "nixpkgs",
+        "pre-commit-hooks": "pre-commit-hooks"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

devenv.nix

@@ -0,0 +1,22 @@
+{ pkgs, lib, config, inputs, ... }:
+let
+  buildInputs = with pkgs; [
+    pythonManylinuxPackages.manylinux2014Package
+    stdenv.cc.cc
+    libuv
+    zlib
+  ];
+in {
+  # https://devenv.sh/packages/
+  #packages = [ pkgs.git ];
+  env = { LD_LIBRARY_PATH = "${with pkgs; lib.makeLibraryPath buildInputs}"; };
+
+  # https://devenv.sh/languages/
+  languages.python = {
+    enable = true;
+    uv = {
+      enable = true;
+      sync = { enable = true; };
+    };
+  };
+}

devenv.yaml

@@ -0,0 +1,15 @@
+# yaml-language-server: $schema=https://devenv.sh/devenv.schema.json
+inputs:
+  nixpkgs:
+    url: github:NixOS/nixpkgs/nixpkgs-unstable
+
+# If you're using non-OSS software, you can set allowUnfree to true.
+# allowUnfree: true
+
+# If you're willing to use a package that's vulnerable
+# permittedInsecurePackages:
+#  - "openssl-1.1.1w"
+
+# If you have more than one devenv you can merge them
+#imports:
+# - ./backend

pyproject.toml

@@ -1,33 +1,37 @@
-[tool.poetry]
-name = "ROILoc"
-version = "0.2.9"
+[project]
+name = "roiloc"
+version = "0.3.0"
 description = "A simple package to center and crop T1w & T2w MRIs around a given region of interest by its name."
-license = "MIT"
-readme = "README.rst"
-authors = ["Clément POIRET <[email protected]>"]
+license = {text = "MIT License"}
+readme = {file = "README.rst", content-type = "text/x-rst"}
+authors = [
+    {name = "Clément POIRET", email = "[email protected]"}
+]
 keywords = ["mri", "brain", "t1w", "t2w", "registration"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "License :: OSI Approved :: MIT License",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Image Processing"
 ]
-homepage = "https://hippomnesis.dev"
-repository = "https://github.com/clementpoiret/ROILoc"
-
-[tool.poetry.dependencies]
-python = "^3.7"
-antspyx = ">=0.2.7"
-pandas = "^1.3.0"
-rich = "^11.0.0"
-importlib-resources = "^5.2.0"
+urls = {homepage = "https://hippomnesis.dev", repository = "https://github.com/clementpoiret/ROILoc"}
+requires-python = ">=3.9"
+dependencies = [
+    "antspyx>=0.5.0",
+    "pandas>=2.0.0",
+    "rich>=11.0.0",
+]
 
-[tool.poetry.scripts]
-roiloc = 'roiloc.roiloc:start'
+[dependency-groups]
+dev = [
+  "pytest"
+]
+lint = [
+  "ruff"
+]
 
-[tool.poetry.dev-dependencies]
-pytest = "^5.2"
+[project.scripts]
+roiloc = "roiloc.roiloc:start"
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+[tool.uv]
+package = true

roiloc/__init__.py

@@ -1 +1 @@
-__version__ = "0.2.9"
+__version__ = "0.3.0"

roiloc/template.py

@@ -1,5 +1,5 @@
+import importlib
 import ants
-import importlib_resources
 import pandas as pd
 from ants.core.ants_image import ANTsImage
 
@@ -22,7 +22,7 @@ def get_mni(contrast: str, bet: bool) -> ANTsImage:
     betstr = "bet" if bet else ""
 
     template = f"mni_icbm152_{contrast}{betstr}_tal_nlin_sym_09c.nii"
-    res = importlib_resources.files("roiloc")
+    res = importlib.resources.files("roiloc")
     data = str(res / "MNI" / "icbm152" / template)
     return ants.image_read(str(data), pixeltype="float", reorient="LPI")
 
@@ -38,7 +38,7 @@ def get_roi_indices(roi: str) -> list:
     """
     roi = roi.title()
 
-    res = importlib_resources.files("roiloc")
+    res = importlib.resources.files("roiloc")
     data = str(res / "MNI" / "cerebra" / "CerebrA_LabelDetails.csv")
     cerebra = pd.read_csv(data, index_col="Label Name")
 
@@ -51,7 +51,7 @@ def get_atlas() -> ANTsImage:
     Returns:
         ANTsImage: CerebrA atlas
     """
-    res = importlib_resources.files("roiloc")
+    res = importlib.resources.files("roiloc")
     data = str(res / "MNI" / "cerebra" /
                "mni_icbm152_CerebrA_tal_nlin_sym_09c.nii")
     return ants.image_read(data, pixeltype="unsigned int", reorient="LPI")

tests/test_roiloc.py

@@ -2,4 +2,4 @@
 
 
 def test_version():
-    assert __version__ == '0.2.9'
+    assert __version__ == "0.3.0"