MAINT: update lock files (#315)

* DX: convert Tox config to native TOML
* FIX: downgrade `pygments` and `sphinx-codeautolink`
* FIX: remove Codacy badge
* FIX: set `CODECOV_TOKEN`
* FIX: set `sphinx.configuration`
* FIX: update link to `uv.lock` file explanation
* MAINT: clean up Codecov config

Co-authored-by: GitHub <[email protected]>

Author: pre-commit-ci[bot]

.cspell.json

@@ -30,6 +30,7 @@
     ".pre-commit-config.yaml",
     ".prettierignore",
     ".readthedocs.yml",
+    ".taplo.toml",
     ".vscode/*",
     "CITATION.cff",
     "codecov.yml",
@@ -50,7 +51,6 @@
     "bgcolor",
     "cano",
     "celltoolbar",
-    "codacy",
     "codecov",
     "codemirror",
     "colab",

.github/workflows/ci.yml

@@ -39,6 +39,8 @@ jobs:
       macos-python-version: "3.9"
       specific-pip-packages: ${{ inputs.specific-pip-packages }}
       test-output-path: tests/output/
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   style:
     if: inputs.specific-pip-packages == ''
     secrets:

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/ComPWA/policy
-    rev: 0.5.8
+    rev: 0.5.15
     hooks:
       - id: check-dev-files
         args:
@@ -60,7 +60,7 @@ repos:
             metadata.vscode
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -109,7 +109,7 @@ repos:
           - --in-place
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.30.0
+    rev: 0.31.0
     hooks:
       - id: check-jsonschema
         name: Check CITATION.cff
@@ -153,6 +153,6 @@ repos:
       - id: pyright
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.5.11
+    rev: 0.5.18
     hooks:
       - id: uv-lock

.readthedocs.yml

@@ -13,9 +13,11 @@ build:
       export UV_LINK_MODE=copy
       uv run \
         --group doc \
-        --locked \
         --no-dev \
         --with tox \
         tox -e doc
       mkdir -p $READTHEDOCS_OUTPUT
       mv docs/_build/html $READTHEDOCS_OUTPUT
+
+sphinx:
+  configuration: docs/conf.py

.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

CONTRIBUTING.md

@@ -12,7 +12,7 @@ git clone https://github.com/ComPWA/qrules
 cd qrules
 ```
 
-Now it's simply a matter of creating and activating the [virtual environment](https://docs.astral.sh/uv/pip/environments) with [`uv sync`](https://docs.astral.sh/uv/reference/cli/#uv-sync). The dependencies for the project are 'pinned' in each commit through the [`uv.lock` file](https://docs.astral.sh/uv/concepts/projects/#project-lockfile).
+Now it's simply a matter of creating and activating the [virtual environment](https://docs.astral.sh/uv/pip/environments) with [`uv sync`](https://docs.astral.sh/uv/reference/cli/#uv-sync). The dependencies for the project are 'pinned' in each commit through the [`uv.lock` file](https://docs.astral.sh/uv/concepts/projects/layout/#the-lockfile).
 
 ```shell
 uv sync --all-extras

README.md

@@ -16,7 +16,6 @@
 [![pytest](https://github.com/ComPWA/qrules/workflows/pytest/badge.svg)](https://github.com/ComPWA/qrules/actions?query=branch%3Amain+workflow%3Apytest)
 [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy.readthedocs.io)
 [![Test coverage](https://codecov.io/gh/ComPWA/qrules/branch/main/graph/badge.svg)](https://codecov.io/gh/ComPWA/qrules)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/deeee5b9e2bb4b3daa655942c71e17da)](https://www.codacy.com/gh/ComPWA/qrules)
 [![Spelling checked](https://img.shields.io/badge/cspell-checked-brightgreen.svg)](https://github.com/streetsidesoftware/cspell/tree/master/packages/cspell)
 [![code style: prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=flat-square)](https://github.com/prettier/prettier)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)

codecov.yml

@@ -1,5 +1,5 @@
 codecov:
-  require_ci_to_pass: yes
+  require_ci_to_pass: true
 
 coverage:
   precision: 2
@@ -9,33 +9,23 @@ coverage:
   status:
     project:
       default:
-        # basic
-        target: 85% # can't go below this percentage
-        threshold: 1% # allow drops by this percentage
+        target: 85%
+        threshold: 1%
         base: auto
-        # advanced
-        branches: null
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: error
         only_pulls: false
-        flags: null
-        paths: null
     patch:
       default:
-        # basic
         target: 0
         threshold: 5%
         base: auto
-        # advanced
-        branches: null
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: error
         only_pulls: false
-        flags: null
-        paths: null
-    changes: no
+    changes: false
 
 parsers:
   gcov: