Update project template

tare · Oct 25, 2024 · e2bac5a · e2bac5a
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diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -17,29 +17,33 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
+          uv venv
+          uv pip install nox
       - name: Run tests
         run: |
-          python -m tox
+          uv run --no-project nox --python ${{ matrix.python-version }}
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox
+          uv venv
+          uv pip install nox
       - name: Lint the code
-        run: python -m tox -e lint
+        run: uv run --no-project nox -e lint
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,17 +3,19 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
         exclude_types: [json, binary]
       - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.7.0
     hooks:
       - id: ruff
-        types_or: [python, pyi, jupyter]
         args: [--fix]
       - id: ruff-format
-        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.11.2"
+    hooks:
+      - id: mypy
diff --git a/noxfile.py b/noxfile.py
@@ -0,0 +1,29 @@
+"""noxfile.py."""
+
+import nox
+
+nox.options.default_venv_backend = "uv"
+
+
+@nox.session(python=["3.10", "3.11", "3.12"])
+def tests(session: nox.Session) -> None:
+    """Test session."""
+    session.install("pytest~=8.3", "pytest-cov~=5.0")
+    session.install(".")
+    session.run("python", "-m", "pytest", *session.posargs)
+
+
+@nox.session(default=False)
+def coverage(session: nox.Session) -> None:
+    """Coverage session."""
+    tests(session)
+    session.install("pytest-cov~=5.0")
+    session.run("coverage", "html")
+    session.run("coverage", "report")
+
+
+@nox.session
+def lint(session: nox.Session) -> None:
+    """Lint session."""
+    session.install("pre-commit~=3.8")
+    session.run("pre-commit", "run", "--all-files", *session.posargs)
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -28,35 +28,43 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.10"
-numpyro = "^0.13.2"
+numpyro = "^0.15"
+jax = "<=0.4.30"
+jaxlib = "<=0.4.30"
 matplotlib = "^3.8.1"
 jupyterlab = {version = "^4.0.8", optional = true}
-scipy = "^1.11.3"
+scipy = "^1.14"
 ipywidgets = {version = "^8.1.1", optional = true}
-pandas = "^2.1.3"
-funsor = "^0.4.5"
-pillow = "^10.1.0"
-networkx = "^3.2.1"
+pandas = "^2"
+funsor = "^0.4"
+pillow = "^10.1"
+networkx = "^3.2"
 
 [tool.poetry.extras]
 examples = ["jupyterlab", "ipywidgets"]
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4"
-tox = "^4.11"
-ruff = "^0.1"
-mypy = "^1.6"
-pre-commit = "^3.5"
-pytest-cov = "^4.1"
+nox = {extras = ["uv"], version = "^2024.10.9"}
+pre-commit = "^3.8"
+pytest = "^8.3"
+ruff = "^0.7"
+pytest-cov = "^5.0"
+mypy = "^1.11"
+ipykernel = "^6.29.5"
 
 [tool.poetry.scripts]
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/tare/Splotch/issues"
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py310"
 fix = true
+exclude = ["LuxRep/"]
+force-exclude = true
+
+[tool.ruff.lint]
+preview = true
 fixable = [
     "I001",  # https://docs.astral.sh/ruff/rules/unsorted-imports/
 ]
@@ -71,68 +79,114 @@ select = [
     "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
     "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
     "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "YTT",  # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
     "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
-    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "BLE",  # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
+    "FBT",  # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
     "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "COM",  # https://docs.astral.sh/ruff/rules/#flake8-commas-com
+    # "CPY",  # https://docs.astral.sh/ruff/rules/#flake8-copyright-cpy
     "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "EM101",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-debugger-t10
+    "DJ",  # https://docs.astral.sh/ruff/rules/#flake8-django-dj
+    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
     "EXE",  # https://docs.astral.sh/ruff/rules/#flake8-executable-exe
+    "FA",  # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
     "ISC",  # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
+    "ICN",  # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
+    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
     "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
     "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+    "PYI",  # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi
     "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
     "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
     "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+    "SLOT",  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
     "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
     "TID",  # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
+    "TCH",  # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tch
+    "INT",  # https://docs.astral.sh/ruff/rules/#flake8-gettext-int
     "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-    "TD",  # https://docs.astral.sh/ruff/rules/#flake8-todos-td
+    # "TD",  # https://docs.astral.sh/ruff/rules/#flake8-todos-td
+    # "FIX",  # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix
     "ERA",  # https://docs.astral.sh/ruff/rules/#eradicate-era
+    "PD",  # https://docs.astral.sh/ruff/rules/#pandas-vet-pd
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
     "PL",  # https://docs.astral.sh/ruff/rules/#pylint-pl
     "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
+    "FLY",  # https://docs.astral.sh/ruff/rules/#flynt-fly
     "NPY",  # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
+    "FAST",  # https://docs.astral.sh/ruff/rules/#fastapi-fast
+    "AIR",  # https://docs.astral.sh/ruff/rules/#airflow-air
     "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
     "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
-    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+    "DOC",  # https://docs.astral.sh/ruff/rules/#pydoclint-doc
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
 ignore = [
-    "ANN101",  # https://docs.astral.sh/ruff/rules/missing-type-self/
-    "ISC001",  # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
+    "ANN101",  # https://docs.astral.sh/ruff/rules/missing-type-function-argument/
+    "S101",  # https://docs.astral.sh/ruff/rules/assert/
     "UP034",  # https://docs.astral.sh/ruff/rules/extraneous-parentheses/
+    "PD002",  # https://docs.astral.sh/ruff/rules/pandas-use-of-inplace-argument/
+    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+    "W191",  # https://docs.astral.sh/ruff/rules/tab-indentation/
+    "E111",  # https://docs.astral.sh/ruff/rules/indentation-with-invalid-multiple/
+    "E114",  # https://docs.astral.sh/ruff/rules/indentation-with-invalid-multiple-comment/
+    "E117",  # https://docs.astral.sh/ruff/rules/over-indented/
+    "D206",  # https://docs.astral.sh/ruff/rules/indent-with-spaces/
+    "D300",  # https://docs.astral.sh/ruff/rules/triple-single-quotes/
+    "Q000",  # https://docs.astral.sh/ruff/rules/bad-quotes-inline-string/
+    "Q001",  # https://docs.astral.sh/ruff/rules/bad-quotes-multiline-string/
+    "Q002",  # https://docs.astral.sh/ruff/rules/bad-quotes-docstring/
+    "Q003",  # https://docs.astral.sh/ruff/rules/avoidable-escaped-quote/
+    "COM812",  # https://docs.astral.sh/ruff/rules/missing-trailing-comma/
+    "COM819",  # https://docs.astral.sh/ruff/rules/prohibited-trailing-comma/
+    "ISC001",  # https://docs.astral.sh/ruff/rules/single-line-implicit-string-concatenation/
+    "ISC002",  # https://docs.astral.sh/ruff/rules/multi-line-implicit-string-concatenation/
 ]
 
-[tool.ruff.lint]
-preview = true
-
-[tool.ruff.lint.pylint]
-max-args = 10
-
 [tool.ruff.lint.mccabe]
 max-complexity = 10
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
+[tool.ruff.lint.pylint]
+max-args = 10
+
+[tool.ruff.lint.flake8-builtins]
+builtins-allowed-modules = ["dataclasses"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.uv]
+reinstall-package = ["splotch-st"]
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = """\
     -v \
+    --cov-config=pyproject.toml \
     --cov=splotch \
     --cov=tests \
-    --cov-append \
     --cov-report=term-missing \
     --no-cov-on-fail \
 """
 testpaths = [
     "tests",
 ]
 filterwarnings = [
-    "ignore:There are not enough devices to run parallel chains:UserWarning:luxglm.inference:",
-    "ignore:There are not enough devices to run parallel chains:UserWarning:test_luxglm:",
+    "ignore:There are not enough devices to run parallel chains",
 ]
 
 [tool.coverage.run]

diff --git a/src/splotch/__init__.py b/src/splotch/__init__.py
@@ -4,4 +4,4 @@
 from splotch.registration import register
 from splotch.utils import get_input_data, savagedickey
 
-__all__ = ["get_input_data", "run_nuts", "run_svi", "register", "savagedickey"]
+__all__ = ["get_input_data", "register", "run_nuts", "run_svi", "savagedickey"]