MAINT: update lock files (#27)

* DX: convert Tox config to native TOML * FIX: downgrade `pygments` and `sphinx-codeautolink` * MAINT: address Ruff LOG015 error * MAINT: remove `PYTHONHASHSEED` Co-authored-by: GitHub <noreply@github.com>
ComPWA · Jan 13, 2025 · 3a75185 · 3a75185
1 parent 0fed08b
commit 3a75185
Show file tree

Hide file tree

Showing 7 changed files with 725 additions and 667 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,9 +5,6 @@ concurrency:
   cancel-in-progress: |-
     ${{ github.ref != format('refs/heads/{0}', github.event.repository.default_branch) }}
 
-env:
-  PYTHONHASHSEED: "0"
-
 on:
   push:
     branches:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/ComPWA/policy
-    rev: 0.5.5
+    rev: 0.5.15
     hooks:
       - id: check-dev-files
         args:
@@ -24,7 +24,7 @@ repos:
       - id: remove-empty-tags
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args:
@@ -52,7 +52,7 @@ repos:
             metadata.vscode
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.1
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -76,7 +76,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/ComPWA/prettier-pre-commit
-    rev: v3.3.3
+    rev: v3.4.2
     hooks:
       - id: prettier
 
@@ -86,7 +86,7 @@ repos:
       - id: taplo-format
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.23.1
+    rev: v0.24.2
     hooks:
       - id: toml-sort
         args:
@@ -104,11 +104,11 @@ repos:
           )$
 
   - repo: https://github.com/ComPWA/pyright-pre-commit
-    rev: v1.1.386
+    rev: v1.1.391
     hooks:
       - id: pyright
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.4.27
+    rev: 0.5.18
     hooks:
       - id: uv-lock
diff --git a/.taplo.toml b/.taplo.toml
@@ -10,3 +10,10 @@ compact_inline_tables = true
 indent_string = "    "
 reorder_arrays = true
 reorder_keys = true
+
+[[rule]]
+include = ["**/pyproject.toml"]
+keys = ["tool.tox"]
+
+[rule.formatting]
+reorder_arrays = false
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -10,6 +10,8 @@
     "mhutchie.git-graph",
     "ms-python.python",
     "ms-python.vscode-pylance",
+    "ms-toolsai.jupyter",
+    "ms-toolsai.vscode-jupyter-cell-tags",
     "ms-vscode.live-server",
     "ms-vsliveshare.vsliveshare",
     "oijaz.unicode-latex",
@@ -28,6 +30,7 @@
     "ms-python.isort",
     "ms-python.mypy-type-checker",
     "ms-python.pylint",
+    "ms-toolsai.vscode-jupyter-slideshow",
     "streetsidesoftware.code-spell-checker",
     "travisillig.vscode-json-stable-stringify",
     "tyriar.sort-lines"

diff --git a/pyproject.toml b/pyproject.toml
@@ -177,7 +177,7 @@ split-on-trailing-comma = false
     "PLW0603",
     "S101",
     "T20",
-    "TCH00",
+    "TC00",
 ]
 "docs/*" = [
     "E402",
@@ -201,98 +201,104 @@ sort_first = [
     "build-system",
     "project",
     "tool.setuptools",
-    "tool.setuptools_scm",
+    "tool.tox.env_run_base",
 ]
 spaces_indent_inline_array = 4
 trailing_comma_inline_array = true
 
 [tool.tox]
-legacy_tox_ini = """
-[tox]
-envlist =
-    docnb-force,
-    linkcheck,
-    sty,
-skip_install = True
-skip_missing_interpreters = True
-skipsdist = True
+env_list = [
+    "docnb-force",
+    "linkcheck",
+    "sty",
+]
+no_package = true
+requires = ["tox>=4.21.0"]
+skip_install = true
+skip_missing_interpreters = true
 
-[testenv]
-passenv = *
-setenv =
-    PYTHONHASHSEED = 0
+[tool.tox.env_run_base]
+pass_env = ["*"]
 
-[testenv:doc]
-allowlist_externals =
-    sphinx-build
-commands =
-    sphinx-build \
-        --builder=html \
-        --fail-on-warning \
-        --keep-going \
-        --show-traceback \
-        docs/ docs/_build/html
-description = Build documentation and API through Sphinx
+[tool.tox.env.doc]
+allowlist_externals = ["sphinx-build"]
+commands = [
+    [
+        "sphinx-build",
+        "--builder=html",
+        "--fail-on-warning",
+        "--keep-going",
+        "--show-traceback",
+        "docs/",
+        "docs/_build/html",
+    ],
+]
+description = "Build documentation and API through Sphinx"
+set_env.PYTHONWARNINGS = ""
 
-[testenv:docnb]
-base = doc
-description = {[testenv:doc]description} with cached notebook execution
-setenv =
-    {[testenv:doc]setenv}
-    EXECUTE_NB = yes
+[tool.tox.env.doclive]
+allowlist_externals = ["sphinx-autobuild"]
+commands = [
+    [
+        "sphinx-autobuild",
+        "--open-browser",
+        "--port=0",
+        "--re-ignore='.*/__pycache__/.*'",
+        "--re-ignore='.*/.ipynb_checkpoints/.*'",
+        "--re-ignore='.*/.virtual_documents/.*'",
+        "--re-ignore='.*\\.tmp'",
+        "--watch",
+        "docs",
+        "docs/",
+        "docs/_build/html",
+    ],
+]
+description = "Set up a server to directly preview changes to the HTML pages"
 
-[testenv:docnb-force]
-base = doc
-description = {[testenv:doc]description} with notebook execution (no cache)
-setenv =
-    {[testenv:doc]setenv}
-    FORCE_EXECUTE_NB = yes
+[tool.tox.env.docnb]
+base = ["tool.tox.env.doc", "tool.tox.env_run_base"]
+description = "{[tool.tox.env.doc]description} with cached notebook execution"
+set_env = [
+    {replace = "ref", of = ["tool.tox.env.doc.set_env"]},
+    {EXECUTE_NB = "yes"},
+]
 
-[testenv:doclive]
-allowlist_externals =
-    sphinx-autobuild
-commands =
-    sphinx-autobuild \
-        --open-browser \
-        --port=0 \
-        --re-ignore='.*/__pycache__/.*' \
-        --re-ignore='.*/.ipynb_checkpoints/.*' \
-        --re-ignore='.*/.virtual_documents/.*' \
-        --re-ignore='.*\\.tmp' \
-        --watch docs \
-        docs/ docs/_build/html
-description = Set up a server to directly preview changes to the HTML pages
+[tool.tox.env.docnb-force]
+base = ["tool.tox.env.doc", "tool.tox.env_run_base"]
+description = "{[tool.tox.env.doc]description} with notebook execution (no cache)"
+set_env = [
+    {replace = "ref", of = ["tool.tox.env.doc.set_env"]},
+    {FORCE_EXECUTE_NB = "yes"},
+]
 
-[testenv:docnblive]
-base = doclive
-description = {[testenv:doclive]description} with cached notebook execution
-setenv =
-    {[testenv:doclive]setenv}
-    EXECUTE_NB = yes
+[tool.tox.env.docnblive]
+base = ["tool.tox.env.doclive", "tool.tox.env_run_base"]
+description = "{[tool.tox.env.doclive]description} with cached notebook execution"
+set_env = [
+    {replace = "ref", of = ["tool.tox.env.doclive.set_env"]},
+    {EXECUTE_NB = "yes"},
+]
 
-[testenv:linkcheck]
-allowlist_externals =
-    sphinx-build
-commands =
-    sphinx-build \
-        --builder=linkcheck \
-        --show-traceback \
-        docs/ docs/_build/linkcheck
-description = Check external links in the documentation (requires internet connection)
-setenv =
-    PYTHONWARNINGS =
+[tool.tox.env.linkcheck]
+allowlist_externals = ["sphinx-build"]
+commands = [
+    [
+        "sphinx-build",
+        "--builder=linkcheck",
+        "--show-traceback",
+        "docs/",
+        "docs/_build/linkcheck",
+    ],
+]
+description = "Check external links in the documentation (requires internet connection)"
+set_env.PYTHONWARNINGS = ""
 
-[testenv:nb]
-allowlist_externals =
-    pytest
-commands =
-    pytest --nbmake {posargs:docs}
-description = Run all notebooks with pytest
+[tool.tox.env.nb]
+allowlist_externals = ["pytest"]
+commands = [["pytest", "--nbmake", "{posargs:docs}"]]
+description = "Run all notebooks with pytest"
 
-[testenv:sty]
-allowlist_externals =
-    pre-commit
-commands =
-    pre-commit run --all-files {posargs}
-description = Perform all linting, formatting, and spelling checks
-"""
+[tool.tox.env.sty]
+allowlist_externals = ["pre-commit"]
+commands = [["pre-commit", "run", "--all-files", {replace = "posargs", extend = true}]]
+description = "Perform all linting, formatting, and spelling checks"
diff --git a/scripts/execute_jax_benchmark.py b/scripts/execute_jax_benchmark.py
@@ -33,9 +33,8 @@
     format="%(asctime)s.%(msecs)03d %(levelname)-8s %(message)s",
     datefmt="%Y-%m-%d %H:%M:%S",
 )
-LOGGER = logging.getLogger()
+_LOGGER = logging.getLogger()
 mute_jax_warnings()
-
 yaml.add_representer(defaultdict, Representer.represent_dict)
 
 BENCHMARK_CASES = [
@@ -78,7 +77,7 @@ def main() -> int:
         existing_benchmark = t.get(n)
         if existing_benchmark is not None:
             if all(len(v) == NUMBER_OF_RUNS for v in existing_benchmark.values()):
-                logging.warning(f"Benchmark for {n:,} events already exists")
+                _LOGGER.warning(f"Benchmark for {n:,} events already exists")
                 progress_bar.update(NUMBER_OF_RUNS)
                 continue
             t[n] = defaultdict(list)
@@ -118,33 +117,30 @@ def create_amplitude_model() -> AmplitudeModel:
 def prepare_functions(
     model: AmplitudeModel,
 ) -> tuple[ParametrizedBackendFunction, PositionalArgumentFunction]:
-    original_log_level = LOGGER.getEffectiveLevel()
-    LOGGER.setLevel(logging.INFO)
-    logging.info("Unfolding intensity expression")
+    _LOGGER.info("Unfolding intensity expression")
     unfolded_intensity_expr = perform_cached_doit(model.full_expression)
-    logging.info("Substituting parameters")
+    _LOGGER.info("Substituting parameters")
     substituted_expr = unfolded_intensity_expr.xreplace(model.parameter_defaults)
-    logging.info("Lambdifying full intensity expression")
+    _LOGGER.info("Lambdifying full intensity expression")
     parametrized_func = create_parametrized_function(
         unfolded_intensity_expr,
         parameters=model.parameter_defaults,
         backend="jax",
     )
-    logging.info("Lambdifying substituted intensity expression")
+    _LOGGER.info("Lambdifying substituted intensity expression")
     substituted_func = create_function(substituted_expr, backend="jax")
-    logging.info("Finished function lambdification")
-    LOGGER.setLevel(original_log_level)
+    _LOGGER.info("Finished function lambdification")
     return parametrized_func, substituted_func
 
 
 def generate_sample(
     model: AmplitudeModel, n_events: int, seed: int | None = None
 ) -> DataSample:
     transformer = create_data_transformer(model)
-    original_log_level = LOGGER.getEffectiveLevel()
-    LOGGER.setLevel(logging.ERROR)
+    original_log_level = _LOGGER.getEffectiveLevel()
+    _LOGGER.setLevel(logging.ERROR)
     phsp_sample = generate_phasespace_sample(model.decay, n_events, seed)
-    LOGGER.setLevel(original_log_level)
+    _LOGGER.setLevel(original_log_level)
     return transformer(phsp_sample)