feat: uv and deps update

.envrc

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

.github/workflows/python-app.yml

@@ -14,49 +14,32 @@ jobs:
     strategy:
       matrix:
         operating-system: ["ubuntu-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
 
     runs-on: ${{ matrix.operating-system }}
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: cachix/install-nix-action@v30
+      - uses: cachix/cachix-action@v15
         with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: latest
-          virtualenvs-create: true
-          virtualenvs-in-project: false
-          virtualenvs-path: ~/.virtualenvs
-          installer-parallel: true
-
-      - name: Cache Poetry virtualenv
-        uses: actions/cache@v1
-        id: cache
-        with:
-          path: ~/.virtualenvs
-          key: poetry-${{ secrets.CACHE_VERSION }}-${{ matrix.python-version }}-${{ matrix.operating-system }}-${{ hashFiles('**/poetry.lock') }}
-          restore-keys: |
-            poetry-${{ secrets.CACHE_VERSION }}-${{ matrix.python-version }}-${{ matrix.operating-system }}-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Install Dependencies
-        run: poetry install --all-extras
-        if: steps.cache.outputs.cache-hit != 'true'
-
-      - name: Test & Coverage
-        run: poetry run coverage run --source=hsf -m pytest
+          name: devenv
+      - name: Install devenv.sh
+        run: nix profile install nixpkgs#devenv
+
+      - name: Run tests
+        shell: devenv shell bash -e {0}
+        run: |
+          uv sync
+          uv pip install onnxruntime>=1.8.0 deepsparse>=1.4.0
+          uv run coverage run --source=hsf -m pytest
+          uv run coverage xml
 
       - name: Publish Coverage on CodeClimate
         uses: paambaati/codeclimate-action@v3.0.0
         env:
           CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
         with:
-          coverageCommand: poetry run coverage xml
           coverageLocations: |
             ${{ github.workspace }}/coverage.xml:coverage.py
           debug: true

.gitignore

@@ -161,3 +161,12 @@ cython_debug/
 .ionide
 
 todolist.md
+# Devenv
+.devenv*
+devenv.local.nix
+
+# direnv
+.direnv
+
+# pre-commit
+.pre-commit-config.yaml

.python-version

@@ -0,0 +1 @@
+3.11

LAST_CHANGELOG.md

@@ -2,8 +2,10 @@
 
 ## Software
 
-* Option to override already segmented mris.
-* Minor fixes and optimizations.
+* Updated ROILoc to v0.4.1 (latest ANTs version),
+* Updated dependencies,
+* Added a proper dev env using Nix,
+* Switched from poetry to uv.
 
 ## Models
 

README.rst

@@ -81,6 +81,35 @@ Table of Contents...
 
 .. contents:: ...To guide you in the challenging world of hippocampal subfields segmentation :)
 
+Development Environment
+=======================
+
+ROILoc relies on Nix_ and Devenv_.
+
+.. _Nix: https://nixos.org/download/
+.. _Devenv: https://devenv.sh
+
+**Step 1**: Install Nix_:
+::
+
+    sh <(curl -L https://nixos.org/nix/install) --daemon
+
+**Step 2**: Install Devenv_:
+::
+
+    nix-env -iA devenv -f https://github.com/NixOS/nixpkgs/tarball/nixpkgs-unstable
+
+**Step 3**: 
+::
+
+    devenv shell
+
+That's it :)
+
+If you want something even easier, install direnv_ and
+allow it to automatically activate the current env (``direnv allow``).
+
+.. _direnv: https://direnv.net/
 
 Installation
 ============
@@ -220,6 +249,13 @@ Changelogs
 HSF
 ---
 
+**Version 1.2.2**
+
+* Updated ROILoc to v0.4.1 (latest ANTs version),
+* Updated dependencies,
+* Added a proper dev env using Nix,
+* Switched from poetry to uv.
+
 **Version 1.2.1**
 
 * Option to override already segmented mris.

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 +1,31 @@
+{ 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; };
+    };
+  };
+
+  enterShell = ''
+    uv sync
+    . ./.devenv/state/venv/bin/activate
+  '';
+
+  enterTest = ''
+    uv run pytest
+  '';
+}

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

docs/about/release-notes.md

@@ -16,6 +16,14 @@ Current maintainers:
 
 ## HSF
 
+
+### Version 1.2.1 (2024-10-29)
+
+* Updated ROILoc to v0.4.1 (latest ANTs version),
+* Updated dependencies,
+* Added a proper dev env using Nix,
+* Switched from poetry to uv.
+
 ### Version 1.2.1 (2024-03-29)
 
 * Added an option to override already segmented mris.

docs/index.md

@@ -5,7 +5,7 @@
     <br>
     <font size="+2"><b>Hippocampal</b> <i>Segmentation</i> Factory</font>
     <br>
-    <b>Current HSF version:</b> 1.2.0<br>
+    <b>Current HSF version:</b> 1.2.2<br>
     <b>Built-in Models version:</b> 4.0.0<br>
     <b>Models in the Hub:</b> 4
 </p>

hsf/fetch_models.py

@@ -1,16 +1,15 @@
 import logging
 from pathlib import Path
 
-import wget
+import requests
 import xxhash
 from omegaconf import DictConfig
 from rich.logging import RichHandler
 
 FORMAT = "%(message)s"
-logging.basicConfig(level=logging.INFO,
-                    format=FORMAT,
-                    datefmt="[%X]",
-                    handlers=[RichHandler()])
+logging.basicConfig(
+    level=logging.INFO, format=FORMAT, datefmt="[%X]", handlers=[RichHandler()]
+)
 
 log = logging.getLogger(__name__)
 
@@ -54,7 +53,11 @@ def fetch(directory: str, filename: str, url: str, xxh3_64: str) -> None:
         outfile.unlink()
 
     log.info(f"Fetching {url}")
-    wget.download(url, out=str(outfile))
+    response = requests.get(url, stream=True)
+    response.raise_for_status()
+    with open(outfile, "wb") as f:
+        for chunk in response.iter_content(chunk_size=8192):
+            f.write(chunk)
     print("\n")
 
     if not xxh3_64 == get_hash(str(outfile)):