Merge pull request #237 from SciCatProject/support-py3-13

Support python 3.13

.github/workflows/ci.yml

@@ -41,14 +41,15 @@ jobs:
     strategy:
       matrix:
         include:
+          - {python: '3.13', os: ubuntu-22.04, tox: py313-full}
           - {python: '3.12', os: ubuntu-22.04, tox: py312-full}
           - {python: '3.11', os: ubuntu-22.04, tox: py311-full}
           - {python: '3.10', os: ubuntu-22.04, tox: py310-full}
           - {python: '3.10', os: macos-14, tox: py310}
           - {python: '3.10', os: windows-2022, tox: py310}
     steps:
       - run: sudo apt install --yes docker-compose
-        if: ${{ contains(matrix.variant.os, 'ubuntu') }}
+        if: ${{ contains(matrix.os, 'ubuntu') }}
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:

.gitignore

@@ -25,3 +25,7 @@ __pycache__/
 # Environments
 Pipfile
 venv
+.venv
+
+# We don't use uv for project management
+uv.lock

.pre-commit-config.yaml

@@ -1,8 +1,10 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
     - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-illegal-windows-names
     - id: check-json
     - id: check-merge-conflict
     - id: check-toml
@@ -19,7 +21,7 @@ repos:
       args: ["--drop-empty-cells",
              "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'"]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.3
+  rev: v0.6.9
   hooks:
     - id: ruff-format
       types_or: [ python, pyi ]
@@ -40,3 +42,7 @@ repos:
     - id: rst-directive-colons
     - id: rst-inline-touching-normal
     - id: text-unicode-replacement-char
+- repo: https://github.com/rhysd/actionlint
+  rev: v1.7.3
+  hooks:
+    - id: actionlint

pyproject.toml

@@ -23,6 +23,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
     "Typing :: Typed",
 ]

requirements/base.txt

@@ -7,42 +7,44 @@
 #
 annotated-types==0.7.0
     # via pydantic
-anyio==4.4.0
+anyio==4.6.0
     # via httpx
 bcrypt==4.2.0
     # via paramiko
 certifi==2024.8.30
     # via
     #   httpcore
     #   httpx
-cffi==1.17.0
+cffi==1.17.1
     # via
     #   cryptography
     #   pynacl
 cryptography==43.0.1
     # via paramiko
-dnspython==2.6.1
+dnspython==2.7.0
     # via email-validator
 email-validator==2.2.0
     # via -r base.in
+exceptiongroup==1.2.2
+    # via anyio
 h11==0.14.0
     # via httpcore
-httpcore==1.0.5
+httpcore==1.0.6
     # via httpx
 httpx==0.27.2
     # via -r base.in
-idna==3.8
+idna==3.10
     # via
     #   anyio
     #   email-validator
     #   httpx
-paramiko==3.4.1
+paramiko==3.5.0
     # via -r base.in
 pycparser==2.22
     # via cffi
-pydantic==2.8.2
+pydantic==2.9.2
     # via -r base.in
-pydantic-core==2.20.1
+pydantic-core==2.23.4
     # via pydantic
 pynacl==1.5.0
     # via paramiko
@@ -56,5 +58,6 @@ sniffio==1.3.1
     #   httpx
 typing-extensions==4.12.2
     # via
+    #   anyio
     #   pydantic
     #   pydantic-core

requirements/ci.txt

@@ -11,25 +11,31 @@ chardet==5.2.0
     # via tox
 colorama==0.4.6
     # via tox
-distlib==0.3.8
+distlib==0.3.9
     # via virtualenv
-filelock==3.15.4
+filelock==3.16.1
     # via
     #   tox
     #   virtualenv
 packaging==24.1
     # via
     #   pyproject-api
     #   tox
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via
     #   tox
     #   virtualenv
 pluggy==1.5.0
     # via tox
-pyproject-api==1.7.1
+pyproject-api==1.8.0
     # via tox
-tox==4.18.0
+tomli==2.0.2
+    # via
+    #   pyproject-api
+    #   tox
+tox==4.21.2
     # via -r ci.in
-virtualenv==20.26.3
+typing-extensions==4.12.2
+    # via tox
+virtualenv==20.26.6
     # via tox

requirements/dev.txt

@@ -61,7 +61,7 @@ pip-compile-multi==2.6.4
     # via -r dev.in
 pip-tools==7.4.1
     # via pip-compile-multi
-prometheus-client==0.20.0
+prometheus-client==0.21.0
     # via jupyter-server
 python-json-logger==2.0.7
     # via jupyter-events
@@ -73,7 +73,7 @@ rfc3986-validator==0.1.1
     # via
     #   jsonschema
     #   jupyter-events
-ruff==0.6.3
+ruff==0.6.9
     # via -r dev.in
 send2trash==1.8.3
     # via jupyter-server

requirements/docs.txt

@@ -25,11 +25,11 @@ beautifulsoup4==4.12.3
     #   pydata-sphinx-theme
 bleach==6.1.0
     # via nbconvert
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 comm==0.2.2
     # via ipykernel
-debugpy==1.8.5
+debugpy==1.8.7
     # via ipykernel
 decorator==5.1.1
     # via ipython
@@ -41,15 +41,15 @@ docutils==0.21.2
     #   nbsphinx
     #   pydata-sphinx-theme
     #   sphinx
-executing==2.0.1
+executing==2.1.0
     # via stack-data
 fastjsonschema==2.20.0
     # via nbformat
 imagesize==1.4.1
     # via sphinx
 ipykernel==6.29.5
     # via -r docs.in
-ipython==8.27.0
+ipython==8.28.0
     # via
     #   -r docs.in
     #   ipykernel
@@ -63,9 +63,9 @@ jinja2==3.1.4
     #   sphinx
 jsonschema==4.23.0
     # via nbformat
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
-jupyter-client==8.6.2
+jupyter-client==8.6.3
     # via
     #   ipykernel
     #   nbclient
@@ -82,15 +82,15 @@ markdown-it-py==3.0.0
     # via
     #   mdit-py-plugins
     #   myst-parser
-markupsafe==2.1.5
+markupsafe==3.0.1
     # via
     #   jinja2
     #   nbconvert
 matplotlib-inline==0.1.7
     # via
     #   ipykernel
     #   ipython
-mdit-py-plugins==0.4.1
+mdit-py-plugins==0.4.2
     # via myst-parser
 mdurl==0.1.2
     # via markdown-it-py
@@ -117,17 +117,17 @@ parso==0.8.4
     # via jedi
 pexpect==4.9.0
     # via ipython
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via jupyter-core
-prompt-toolkit==3.0.47
+prompt-toolkit==3.0.48
     # via ipython
 psutil==6.0.0
     # via ipykernel
 ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
-pydantic-settings==2.4.0
+pydantic-settings==2.5.2
     # via autodoc-pydantic
 pydata-sphinx-theme==0.15.4
     # via -r docs.in
@@ -158,7 +158,7 @@ snowballstemmer==2.2.0
     # via sphinx
 soupsieve==2.6
     # via beautifulsoup4
-sphinx==8.0.2
+sphinx==8.1.0
     # via
     #   -r docs.in
     #   autodoc-pydantic
@@ -168,7 +168,7 @@ sphinx==8.0.2
     #   sphinx-autodoc-typehints
     #   sphinx-copybutton
     #   sphinx-design
-sphinx-autodoc-typehints==2.3.0
+sphinx-autodoc-typehints==2.5.0
     # via -r docs.in
 sphinx-copybutton==0.5.2
     # via -r docs.in
@@ -206,7 +206,7 @@ traitlets==5.14.3
     #   nbconvert
     #   nbformat
     #   nbsphinx
-urllib3==2.2.2
+urllib3==2.2.3
     # via requests
 wcwidth==0.2.13
     # via prompt-toolkit

requirements/mypy.txt

@@ -10,15 +10,15 @@ mypy==1.11.2
     # via -r mypy.in
 mypy-extensions==1.0.0
     # via mypy
-types-docutils==0.21.0.20240724
+types-docutils==0.21.0.20241005
     # via -r mypy.in
-types-paramiko==3.4.0.20240423
+types-paramiko==3.5.0.20240928
     # via -r mypy.in
-types-python-dateutil==2.9.0.20240821
+types-python-dateutil==2.9.0.20241003
     # via -r mypy.in
-types-pyyaml==6.0.12.20240808
+types-pyyaml==6.0.12.20240917
     # via -r mypy.in
-types-requests==2.32.0.20240712
+types-requests==2.32.0.20240914
     # via -r mypy.in
-urllib3==2.2.2
+urllib3==2.2.3
     # via types-requests

requirements/static.txt

@@ -7,19 +7,19 @@
 #
 cfgv==3.4.0
     # via pre-commit
-distlib==0.3.8
+distlib==0.3.9
     # via virtualenv
-filelock==3.15.4
+filelock==3.16.1
     # via virtualenv
-identify==2.6.0
+identify==2.6.1
     # via pre-commit
 nodeenv==1.9.1
     # via pre-commit
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via virtualenv
-pre-commit==3.8.0
+pre-commit==4.0.1
     # via -r static.in
 pyyaml==6.0.2
     # via pre-commit
-virtualenv==20.26.3
+virtualenv==20.26.6
     # via pre-commit

requirements/test.txt

@@ -10,19 +10,19 @@ attrs==24.2.0
     # via hypothesis
 execnet==2.1.1
     # via pytest-xdist
-filelock[typing]==3.15.4
+filelock[typing]==3.16.1
     # via -r test.in
-hypothesis==6.111.2
+hypothesis==6.114.1
     # via -r test.in
 iniconfig==2.0.0
     # via pytest
 packaging==24.1
     # via pytest
 pluggy==1.5.0
     # via pytest
-pyfakefs==5.6.0
+pyfakefs==5.7.0
     # via -r test.in
-pytest==8.3.2
+pytest==8.3.3
     # via
     #   -r test.in
     #   pytest-randomly
@@ -38,3 +38,5 @@ pyyaml==6.0.2
     # via -r test.in
 sortedcontainers==2.4.0
     # via hypothesis
+tomli==2.0.2
+    # via pytest

requirements/wheels.txt

@@ -5,9 +5,11 @@
 #
 #    pip-compile-multi
 #
-build==1.2.1
+build==1.2.2.post1
     # via -r wheels.in
 packaging==24.1
     # via build
-pyproject-hooks==1.1.0
+pyproject-hooks==1.2.0
+    # via build
+tomli==2.0.2
     # via build