Adopt uv for dependency management

.github/workflows/update_namespaces.yaml

@@ -25,17 +25,16 @@ jobs:
           token: ${{ steps.generate-token.outputs.token }}
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          uv sync
 
       - name: Run script to update namespaces
-        run: python code/create_config_namespace_map.py
+        run: uv run python code/create_config_namespace_map.py
 
       - name: Get Neurobagel Bot App User ID
         id: get-user-id

.github/workflows/update_term_vocab_files.yaml

@@ -47,19 +47,18 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          uv sync
 
       - name: Run script
         env:
           COMMUNITIES_GOOGLE_API_KEY: ${{ secrets.COMMUNITIES_GOOGLE_API_KEY }}
-        run: python code/create_term_vocab_from_gsheet.py "configs/${{ matrix.community_name }}"
+        run: uv run python code/create_term_vocab_from_gsheet.py "configs/${{ matrix.community_name }}"
 
       # NOTE: We upload the entire directory to avoid needing to know/hardcode the name of the specific vocab file
       # (which is technically arbitrary) and to allow for future expansion to files for multiple standardized variables

.gitignore

@@ -208,3 +208,9 @@ __marimo__/
 
 # files generated by hatchling vcs
 _version.py
+
+# jetbrains
+.idea
+
+# uv
+.python-version

.pre-commit-config.yaml

@@ -6,17 +6,12 @@ repos:
     rev: 25.1.0
     hooks:
       - id: black
-        args:
-          - --line-length=79
 
   - repo: https://github.com/PyCQA/flake8
     rev: 7.3.0
     hooks:
       - id: flake8
         language_version: python3
-        args:
-          - --extend-ignore=E501
-          - --extend-select=B950
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
@@ -27,10 +22,6 @@ repos:
     rev: 6.0.1
     hooks:
       - id: isort
-        args:
-          - --profile=black
-          - --line-length=79
-          - --filter-files
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
@@ -42,12 +33,6 @@ repos:
     rev: v1.17.1
     hooks:
       - id: mypy
-        args:
-          - --ignore-missing-imports
-          - --no-warn-no-return
-          - --warn-redundant-casts
-          - --show-error-codes
-          - --pretty
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0

pyproject.toml

@@ -0,0 +1,53 @@
+[project]
+name = "communities"
+description = "Scripts and configuration files for Neurobagel communities Resources."
+readme = "README.md"
+license = { file = "LICENSE" }
+authors = [{ name = "Neurobagel Developers" }]
+maintainers = [
+  { name = "Alyssa Dai", email = "alyssa.dai@mcgill.ca" },
+  { name = "Arman Jahanpour", email = "arman.jahanpour@mcgill.ca" },
+  { name = "Sebastian Urchs", email = "sebastian.urchs@mcgill.ca" }
+]
+version = "0.0.1"
+requires-python = ">=3.10"
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering",
+  "License :: OSI Approved :: MIT License",
+  "Framework :: Pydantic :: 2",
+  "Typing :: Typed",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13"
+]
+
+dependencies = [
+    "gspread",
+    "pandas",
+    "pandera[pandas]"
+]
+
+[dependency-groups]
+dev = [
+    "pytest",
+    "pre-commit"
+]
+
+[tool.black]
+line-length = 79
+
+[tool.isort]
+profile = "black"
+filter_files = true
+line_length = 79
+
+[tool.mypy]
+ignore_missing_imports = true
+warn_no_return = false
+warn_redundant_casts = true
+show_error_codes = true
+pretty = true
+plugins = ["pydantic.mypy"]