Migrate to uv package manager (#198)

This commit configures the project to use the `uv` package manager,
a modern, solid, and faster alterative to `pip`. Note that
this change only affects the development toolchain: the plugin can
still be installed with `pip`. However, now the `bandit`, `lint`
and `test` optional dependencies became dependency groups, meaning
that the `pip install streamflow-postgresql[lint]` command does not
work anymore, and should be substituted with `pip install --group lint`
with `pip>=25.1`.

Co-authored-by: colonne <colonne@di.unito.it>

Author: GlassOfWhiskey

.github/dependabot.yml

@@ -4,7 +4,7 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
-  - package-ecosystem: "pip"
+  - package-ecosystem: "uv"
     directory: "/"
     schedule:
       interval: "daily"

.github/workflows/ci-tests.yaml

@@ -32,18 +32,14 @@ jobs:
       TOXENV: ${{ matrix.step }}
     steps:
       - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.16"
       - uses: actions/setup-python@v6
         with:
           python-version: "3.13"
-          cache: pip
-          cache-dependency-path: |
-            requirements.txt
-            test-requirements.txt
-            tox.ini
-      - name: "Install Python Dependencies and plugin"
-        run: |
-          python -m pip install tox --user
-          python -m pip install . --user
+      - name: "Install Tox"
+        run: uv tool install tox --with tox-uv
       - name: "Run static analysis via Tox"
         run: tox
   unit-tests:
@@ -64,13 +60,12 @@ jobs:
       TOXENV: ${{ format('py{0}-unit', matrix.python) }}
     steps:
       - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.16"
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
-          cache: pip
-          cache-dependency-path: |
-            requirements.txt
-            tox.ini
       - uses: actions/setup-node@v6
         with:
           node-version: "20"
@@ -93,12 +88,10 @@ jobs:
       - name: "Install Postgresql client"
         run: brew install libpq@17
         if: ${{ startsWith(matrix.on, 'macos-') }}
-      - name: "Install Python Dependencies and plugin"
-        run: |
-          python -m pip install tox --user
-          python -m pip install . --user
+      - name: "Install Tox"
+        run: uv tool install tox --with tox-uv
       - name: "Run tests via Tox"
-        run: python -m tox
+        run: tox
       - name: "Upload coverage report for unit tests"
         uses: actions/upload-artifact@v6
         with:

MANIFEST.in

@@ -1,6 +1,2 @@
 include LICENSE
 include README.md
-include requirements.txt
-include bandit-requirements.txt
-include lint-requirements.txt
-include test-requirements.txt

bandit-requirements.txt

@@ -27,7 +27,12 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Topic :: System :: Distributed Computing",
 ]
-dynamic = ["dependencies", "optional-dependencies", "version"]
+dependencies = [
+    "asyncpg==0.31.0",
+    "streamflow==0.2.0.dev13"
+]
+dynamic = ["version"]
+
 
 [project.urls]
 Package = "https://pypi.org/project/streamflow-postgresql"
@@ -36,6 +41,29 @@ Repository = "https://github.com/alpha-unito/streamflow-postgresql"
 [project.entry-points]
 "unito.streamflow.plugin" = {"unito.postgresql" = "streamflow.plugins.unito.postgresql.plugin:PostgreSQLStreamFlowPlugin"}
 
+[dependency-groups]
+dev = [
+    {include-group = "bandit"},
+    {include-group = "lint"},
+    {include-group = "test"}
+]
+bandit = [
+    "bandit==1.9.2"
+]
+lint = [
+    "black==25.11.0",
+    "codespell==2.4.1",
+    "flake8-bugbear==25.11.29",
+    "isort==6.1.0",
+    "pyupgrade==3.21.0"
+]
+test = [
+    "pytest==9.0.2",
+    "pytest-asyncio==1.3.0",
+    "pytest-cov==7.0.0",
+    "pytest-xdist==3.8.0"
+]
+
 [tool.setuptools]
 packages = [
     "streamflow.plugins.unito.postgresql"
@@ -46,13 +74,7 @@ zip-safe = true
 "streamflow.plugins.unito.postgresql" = ["schemas/*.json", "schemas/*.sql"]
 
 [tool.setuptools.dynamic]
-dependencies = {file = "requirements.txt"}
 version = {attr = "streamflow.plugins.unito.postgresql.version.VERSION"}
 
-[tool.setuptools.dynamic.optional-dependencies]
-bandit = {file = "bandit-requirements.txt"}
-lint = {file = "lint-requirements.txt"}
-test = {file = "test-requirements.txt"}
-
 [tool.isort]
 profile = "black"

lint-requirements.txt

@@ -13,13 +13,10 @@ testpaths = tests
 
 [testenv]
 allowlist_externals = make
-commands_pre =
-  py3.{10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
 commands =
   py3.{10,11,12,13}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
-deps =
-  py3.{10,11,12,13}-unit: -rrequirements.txt
-  py3.{10,11,12,13}-unit: -rtest-requirements.txt
+dependency_groups =
+  py3.{10,11,12,13}-unit: test
 description =
   py3.{10,11,12,13}-unit: Run the unit tests
 passenv =
@@ -30,9 +27,7 @@ setenv =
 
 [testenv:bandit]
 commands = bandit -r streamflow
-deps =
-  -rrequirements.txt
-  -rbandit-requirements.txt
+dependency_groups = bandit
 description = Search for common security issues
 passenv =
   CI
@@ -41,7 +36,5 @@ passenv =
 [testenv:lint]
 allowlist_externals = make
 commands = make flake8 format-check codespell-check pyupgrade
-deps =
-  -rrequirements.txt
-  -rlint-requirements.txt
+dependency_groups = lint
 description = Lint the Python code