chore: converted the project to use UV

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       max-parallel: 1  # Run tests sequentially to avoid conflicts on shared mica-demo.obiba.org server
       matrix:
-        python-version: [3.8.18, 3.10.18, 3.12.11]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
 
@@ -21,11 +21,17 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install Poetry
-        run: pip install poetry
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
 
       - name: Install dependencies
-        run: poetry install -v
+        run: uv sync --all-extras
+
+      # TODO: Re-enable linting once existing code style issues are fixed
+      # - name: Run linting
+      #   run: uv run ruff check .
 
       - name: Run tests
-        run: poetry run pytest
+        run: uv run pytest

.github/workflows/deploy.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.12.11]
+        python-version: ["3.12"]
     steps:
       - uses: actions/checkout@v4
 
@@ -19,17 +19,19 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install Poetry
-        run: pip install poetry
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
 
       - name: Install dependencies
-        run: poetry install -v
+        run: uv sync --all-extras
 
       - name: Run tests
-        run: poetry run pytest
+        run: uv run pytest -m "not integration"
 
-      - name: Configure PyPI credentials
-        run: poetry config http-basic.pypi ${{ secrets.PYPI_USER }} ${{ secrets.PYPI_PASSWORD }}
+      - name: Build package
+        run: uv build
 
       - name: Publish to PyPI
-        run: poetry publish --build --no-interaction
+        run: uv publish
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -27,7 +27,12 @@ coverage
 *.sln
 *.sw?
 
+# VSCode
 .history
 __pycache__
 
-debug.py
+debug.py
+.venv/
+.serena/
+.agent-sandbox
+plans/

.python-version

@@ -0,0 +1 @@
+3.10

.ruff.toml

@@ -0,0 +1,45 @@
+# Ruff configuration file
+
+# Exclude a variety of commonly ignored directories.
+extend-exclude = [
+    "__pycache__",
+    ".git",
+    ".venv",
+    ".eggs",
+    ".nox",
+    ".tox",
+    ".svn",
+    ".hg",
+    "build",
+    "dist",
+    ".mypy_cache",
+    ".pytest_cache",
+]
+
+# Assume Python 3.10.
+target-version = "py310"
+
+# Line length with preview to format
+line-length = 120
+preview = true
+
+[lint]
+# Enable flake8-bugbear rules
+select = [
+    "E",      # pycodestyle errors
+    "W",      # pycodestyle warnings
+    "F",      # pyflakes
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "UP",     # pyupgrade
+    "SIM",    # flake8-simplify
+]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+
+# Ignore E501 - long lines in help text are acceptable
+ignore = ["E501"]
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

Makefile

@@ -1,11 +1,28 @@
 install:
-	poetry install
+	uv sync --all-extras
 
 test:
-	poetry run pytest
+	uv run --all-extras pytest
+
+lint:
+	uv run ruff check .
+
+fix:
+	uv run ruff check . --fix
+
+format:
+	uv run ruff format .
+
+check: format fix
 
 build:
-	poetry build
+	uv build
 
 clean:
 	rm -rf dist
+
+local-install: clean build
+	pip install ./dist/obiba_mica-*.tar.gz
+
+local-install-force: clean build
+	pip install ./dist/obiba_mica-*.tar.gz --break-system-packages

obiba_mica/__init__.py

@@ -1,11 +1,11 @@
-from obiba_mica.core import UriBuilder, MicaClient, MicaRequest, MicaResponse
-from obiba_mica.rest import RestService
-from obiba_mica.file import FileService
-from obiba_mica.access import ProjectAccessService, NetworkAccessService, IndividualStudyAccessService, HarmonizationInitiativeAccessService, CollectedDatasetAccessService, HarmonizationProtocolAccessService, FileAccessService
-from obiba_mica.perm import ProjectPermissionService, NetworkPermissionService, HarmonizationInitiativePermissionService, HarmonizationProtocolPermissionService, IndividualStudyPermissionService, CollectedDatasetPermissionService
-from obiba_mica.import_zip import FileImportService
-from obiba_mica.search import SearchService
-from obiba_mica.annotation import AnnotationService
-from obiba_mica.plugin import PluginService
-from obiba_mica.update_collected_dataset import CollectedDatasetService
-from obiba_mica.update_collected_datasets import CollectedDatasetsService
+from obiba_mica.core import UriBuilder as UriBuilder, MicaClient as MicaClient, MicaRequest as MicaRequest, MicaResponse as MicaResponse
+from obiba_mica.rest import RestService as RestService
+from obiba_mica.file import FileService as FileService
+from obiba_mica.access import ProjectAccessService as ProjectAccessService, NetworkAccessService as NetworkAccessService, IndividualStudyAccessService as IndividualStudyAccessService, HarmonizationInitiativeAccessService as HarmonizationInitiativeAccessService, CollectedDatasetAccessService as CollectedDatasetAccessService, HarmonizationProtocolAccessService as HarmonizationProtocolAccessService, FileAccessService as FileAccessService
+from obiba_mica.perm import ProjectPermissionService as ProjectPermissionService, NetworkPermissionService as NetworkPermissionService, HarmonizationInitiativePermissionService as HarmonizationInitiativePermissionService, HarmonizationProtocolPermissionService as HarmonizationProtocolPermissionService, IndividualStudyPermissionService as IndividualStudyPermissionService, CollectedDatasetPermissionService as CollectedDatasetPermissionService
+from obiba_mica.import_zip import FileImportService as FileImportService
+from obiba_mica.search import SearchService as SearchService
+from obiba_mica.annotation import AnnotationService as AnnotationService
+from obiba_mica.plugin import PluginService as PluginService
+from obiba_mica.update_collected_dataset import CollectedDatasetService as CollectedDatasetService
+from obiba_mica.update_collected_datasets import CollectedDatasetsService as CollectedDatasetsService