chore(deps): upgrade project dependencies

Upgrade all project dependencies and add support for Python 3.13.

.github/workflows/ci.yml

@@ -15,6 +15,7 @@ jobs:
         python-version:
           - "3.11"
           - "3.12"
+          - "3.13"
     steps:
       - uses: actions/checkout@v4
       - name: Set up project using python ${{ matrix.python-version }}
@@ -50,7 +51,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           cache: pip
-          python-version: "3.12"
+          python-version: "3.13"
       - name: Install requirements
         run: |
           python -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -3,24 +3,29 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
+      - id: check-ast
       - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-symlinks
       - id: check-toml
       - id: check-vcs-permalinks
       - id: check-yaml
+      - id: debug-statements
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         args:
         - --py311-plus
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.3.6
+    rev: v0.7.4
     hooks:
       - id: ruff
         args:

docs/conf.py

@@ -92,6 +92,7 @@
     ("py:exc", "ResourceDisposedError"),  # docs aren't published yet
     ("py:exc", "sghi.disposable.ResourceDisposedError"),  # docs aren't published yet
     ("py:func", "sghi.disposable.not_disposed"),  # docs aren't published yet
+    ("py:meth", "sghi.etl.core.Processor.apply"),  # docs aren't published yet
     ("py:meth", "sghi.etl.core.Source.draw"),  # docs aren't published yet
     ("py:obj", "sghi.etl.commons.processors._PDT"),  # private type annotations
     ("py:obj", "sghi.etl.commons.processors._RDT"),  # private type annotations

pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 build-backend = "setuptools.build_meta"
 requires = [
-    "setuptools>=69.2.0",
-    "setuptools_scm>=8.0.4",
+    "setuptools>=75.5.0",
+    "setuptools_scm>=8.1.0",
 ]
 
 [project]
@@ -23,9 +23,9 @@ classifiers = [
     "Typing :: Typed"
 ]
 dependencies = [
-    "typing-extensions>=4.10.0",
-    "sghi-commons @ git+https://github.com/savannahghi/sghi-commons.git@v1.4.0",
-    "sghi-etl-core @ git+https://github.com/savannahghi/sghi-etl-core.git@v1.1.1",
+    "typing-extensions>=4.12.2",
+    "sghi-commons @ git+https://github.com/savannahghi/sghi-commons.git@v1.5.1",
+    "sghi-etl-core @ git+https://github.com/savannahghi/sghi-etl-core.git@v1.2.0",
 ]
 description = "Collection of utilities for working with SGHI ETL Workflows."
 dynamic = ["version"]
@@ -40,34 +40,35 @@ readme = "README.md"
 requires-python = ">=3.11" # Support Python 3.10+.
 
 [project.optional-dependencies]
+coveralls = ["coveralls~=4.0.1"]
+
 dev = [
-    "pre-commit~=3.7.0",
+    "pre-commit~=4.0.1",
 ]
 
 docs = [
-    "furo==2024.1.29",
-    "jaraco.packaging~=9.5.0",
-    "rst.linker~=2.4.0",
-    "Sphinx~=7.2.6",
+    "furo==2024.8.6",
+    "jaraco.packaging~=10.2.3",
+    "rst.linker~=2.6.0",
+    "Sphinx~=8.1.3",
     "sphinx-favicon~=1.0.1",
-    "sphinx-hoverxref~=1.3.0",
+    "sphinx-hoverxref~=1.4.2",
     "sphinx-inline-tabs~=2023.4.21",
-    "sphinx-lint~=0.9.1",
+    "sphinx-lint~=1.0.0",
     "sphinx-notfound-page~=1.0.0",
 ]
 
 test = [
-    "coverage~=6.5.0",
-    "coveralls~=3.3.1",
+    "coverage~=7.6.7",
     "packaging",
-    "pyright>=1.1.358",
-    "pytest~=8.1.1",
-    "pytest-cov~=5.0.0",
+    "pyright>=1.1.389",
+    "pytest~=8.3.3",
+    "pytest-cov~=6.0.0",
     "pytest-forked~=1.6.0",
     "pytest-sugar~=1.0.0",
-    "pytest-xdist~=3.5.0",
-    "ruff~=0.3.6",
-    "tox~=4.14.2",
+    "pytest-xdist~=3.6.1",
+    "ruff~=0.7.4",
+    "tox~=4.23.2",
     "tox-gh-actions~=3.2.0",
 ]
 
@@ -87,7 +88,7 @@ extend-exclude = """
 """
 include = ["src", "test"]
 line-length = 79
-target-version = ["py311", "py312"]
+target-version = ["py311", "py312", "py313"]
 
 [tool.coverage.html]
 directory = "coverage"
@@ -264,71 +265,62 @@ where = ["src"]
 root = "."
 
 [tool.tox]
-legacy_tox_ini = """
-    [tox]
-    env_list = {py311, py312}, coveralls, docs, package
-    isolated_build = true
-    no_package = false
-    requires =
-        tox>4
-    skip_missing_interpreters = true
-
-
-    [gh-actions]
-    python =
-        3.11: py311
-        3.12: py312, coveralls, docs, package
-
-
-    [testenv]
-    commands =
-        ruff check .
-        ruff format --check .
-        pyright .
-        coverage erase
-        pytest {posargs:.}
-        coverage html
-    deps =
-        .
-    description = test and lint the project
-    download = true
-    extras =
-        test
-    set_env =
-        PYTHONPATH = {toxinidir}/src
-        PYRIGHT_PYTHON_FORCE_VERSION = latest
-
-
-    ;If running outside Github, ensure that the the `COVERALLS_REPO_TOKEN`
-    ;environment variable is set.
-    [testenv:coveralls]
-    commands =
-        coveralls --service=github
-    description = submit coverage results to coverall.io
-    extras =
-        test
-    pass_env =
-        COVERALLS_REPO_TOKEN
-        GITHUB_*
-
-
-    [testenv:docs]
-    changedir = docs
-    commands =
-        sphinx-build -EW --keep-going -b html . {toxinidir}/docs/build/html
-        sphinx-lint -i api
-    description = build sphinx documentation
-    extras =
-        docs
-
-
-    [testenv:package]
-    commands =
-        python -c "import shutil; shutil.rmtree('dist', ignore_errors=True)"
-        python -m build
-    depends = testenv
-    deps =
-        build
-    description = build the library
-    skip_install = true
+env_list = ["py311", "py312", "py313", "coveralls", "docs", "package"]
+isolated_build = true
+requires = ["tox>=4.23.2", "tox-uv>=1.16.0"]
+no_package = false
+skip_missing_interpreters = true
+
+[tool.tox.env_run_base]
+# allowlist_externals = ["uv"]
+commands = [
+    ["ruff", "check", "."],
+    ["ruff", "format", "--check", "."],
+    ["pyright", "."],
+    ["coverage", "erase"],
+    ["pytest", { replace = "posargs", default = ["."], extend = true}],
+    ["coverage", "html"],
+]
+deps = ["."]
+description = "test and lint the project"
+download = true
+extras = ["test"]
+set_env = { PYTHONPATH = "{toxinidir}/src", PYRIGHT_PYTHON_FORCE_VERSION = "latest" }
+
+[tool.tox.env.coveralls]
+# If running outside Github, ensure that the the `COVERALLS_REPO_TOKEN`
+# environment variable is set.
+# Also, this only works for Python = ">=3.8,<3.13".
+# See https://github.com/TheKevJames/coveralls-python/issues/523
+base_python = ["py312"]
+commands = [["coveralls", "--service=github"]]
+description = "submit coverage results to coverall.io"
+depends = ["env_run_base"]
+extras = ["coveralls"]
+pass_env = ["COVERALLS_REPO_TOKEN", "GITHUB_*"]
+
+[tool.tox.env.docs]
+changedir = "docs"
+commands = [
+    ["sphinx-build", "-EW", "--keep-going", "-b", "html", ".", "{toxinidir}/docs/build/html"],
+    ["sphinx-lint", "-i", "api"]
+]
+description = "build sphinx documentation"
+extras = ["docs"]
+
+[tool.tox.env.package]
+commands = [
+    ["python", "-c", "import shutil; shutil.rmtree('dist', ignore_errors=True)"],
+    ["python", "-m", "build"]
+]
+depends = ["env_run_base"]
+deps = ["build"]
+description = "build the library"
+skip_install = true
+
+[tool.tox.gh-actions]
+python = """
+   3.11: py311
+   3.12: py312, coveralls
+   3.13: py313, docs, package
 """

src/sghi/etl/commons/processors.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import logging
+import sys
 from collections.abc import Callable, Iterable, Sequence
 from concurrent.futures import Executor, Future, ThreadPoolExecutor
 from contextlib import ExitStack
@@ -803,7 +804,11 @@ def do_apply(raw_data: Sequence[_RDT]) -> _PDT:
 
 @final
 class _ProcessorOfCallable(Processor[_RDT, _PDT], Generic[_RDT, _PDT]):
-    __slots__ = ("_delegate_to", "_is_disposed", "_logger")
+    # See: https://github.com/python/cpython/pull/106771
+    if sys.version_info[:3] >= (3, 13, 0):  # pragma: no cover
+        __slots__ = ("_delegate_to", "_is_disposed", "_logger", "__dict__")
+    else:  # pragma: no cover
+        __slots__ = ("_delegate_to", "_is_disposed", "_logger")
 
     def __init__(self, delegate_to: _ProcessorCallable[_RDT, _PDT]) -> None:
         super().__init__()

src/sghi/etl/commons/sinks.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import logging
+import sys
 from collections.abc import Callable, Iterable, Sequence
 from concurrent.futures import Executor, Future, ThreadPoolExecutor
 from contextlib import ExitStack
@@ -596,7 +597,11 @@ def do_drain(processed_data: Sequence[_PDT]) -> None:
 
 @final
 class _SinkOfCallable(Sink[_PDT], Generic[_PDT]):
-    __slots__ = ("_delegate_to", "_is_disposed", "_logger")
+    # See: https://github.com/python/cpython/pull/106771
+    if sys.version_info[:3] >= (3, 13, 0):  # pragma: no cover
+        __slots__ = ("_delegate_to", "_is_disposed", "_logger", "__dict__")
+    else:  # pragma: no cover
+        __slots__ = ("_delegate_to", "_is_disposed", "_logger")
 
     def __init__(self, delegate_to: _SinkCallable[_PDT]) -> None:
         super().__init__()

src/sghi/etl/commons/sources.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import logging
+import sys
 from collections.abc import Callable, Iterable, Sequence
 from concurrent.futures import Executor, Future, ThreadPoolExecutor
 from contextlib import ExitStack
@@ -299,7 +300,11 @@ def do_draw() -> _RDT:
 
 @final
 class _SourceOfCallable(Source[_RDT], Generic[_RDT]):
-    __slots__ = ("_delegate_to", "_is_disposed", "_logger")
+    # See: https://github.com/python/cpython/pull/106771
+    if sys.version_info[:3] >= (3, 13, 0):  # pragma: no cover
+        __slots__ = ("_delegate_to", "_is_disposed", "_logger", "__dict__")
+    else:  # pragma: no cover
+        __slots__ = ("_delegate_to", "_is_disposed", "_logger")
 
     def __init__(self, delegate_to: _SourceCallable[_RDT]) -> None:
         super().__init__()

src/sghi/etl/commons/utils/result_gatherers.py

@@ -90,7 +90,7 @@ def _do_gather() -> Iterable[_T]:
         for future in futures:
             try:
                 yield future.result()
-            except BaseException as exp:  # noqa: BLE001
+            except BaseException as exp:
                 if exc_wrapper_factory:
                     raise exc_wrapper_factory(exc_wrapper_message) from exp
                 else: