SciCatProject · jl-wynen · Aug 17, 2023 · Aug 17, 2023 · Aug 17, 2023 · Aug 17, 2023
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
 - repo: https://github.com/psf/black
-  rev: 23.1.0
+  rev: 23.7.0
   hooks:
     - id: black
 - repo: https://github.com/kynan/nbstripout
@@ -22,12 +22,12 @@ repos:
       args: ["--drop-empty-cells",
              "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'"]
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: 'v0.0.252'
+  rev: 'v0.0.284'
   hooks:
     - id: ruff
       args: ["--fix"]
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.5
   hooks:
     - id: codespell
       additional_dependencies:

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -13,39 +13,43 @@ cffi==1.15.1
     # via
     #   cryptography
     #   pynacl
-charset-normalizer==3.1.0
+charset-normalizer==3.2.0
     # via requests
 cryptography==41.0.3
     # via paramiko
 decorator==5.1.1
     # via fabric
-dnspython==2.3.0
+deprecated==1.2.14
+    # via fabric
+dnspython==2.4.2
     # via email-validator
 email-validator==2.0.0.post2
-    # via -r base.in
-fabric==3.1.0
-    # via -r base.in
+    # via -r requirements/base.in
+fabric==3.2.1
+    # via -r requirements/base.in
 idna==3.4
     # via
     #   email-validator
     #   requests
-invoke==2.1.3
+invoke==2.2.0
     # via fabric
-paramiko==3.2.0
+paramiko==3.3.1
     # via fabric
 pycparser==2.21
     # via cffi
-pydantic==1.10.11
-    # via -r base.in
+pydantic==1.10.12
+    # via -r requirements/base.in
 pynacl==1.5.0
     # via paramiko
 python-dateutil==2.8.2
-    # via -r base.in
+    # via -r requirements/base.in
 requests==2.31.0
-    # via -r base.in
+    # via -r requirements/base.in
 six==1.16.0
     # via python-dateutil
 typing-extensions==4.7.1
     # via pydantic
-urllib3==2.0.3
+urllib3==2.0.4
     # via requests
+wrapt==1.15.0
+    # via deprecated
diff --git a/requirements/ci.txt b/requirements/ci.txt
@@ -7,11 +7,11 @@
 #
 cachetools==5.3.1
     # via tox
-chardet==5.1.0
+chardet==5.2.0
     # via tox
 colorama==0.4.6
     # via tox
-distlib==0.3.6
+distlib==0.3.7
     # via virtualenv
 filelock==3.12.2
     # via
@@ -21,15 +21,15 @@ packaging==23.1
     # via
     #   pyproject-api
     #   tox
-platformdirs==3.8.0
+platformdirs==3.10.0
     # via
     #   tox
     #   virtualenv
 pluggy==1.2.0
     # via tox
-pyproject-api==1.5.2
+pyproject-api==1.5.3
     # via tox
-tox==4.6.3
+tox==4.9.0
     # via -r requirements/ci.in
-virtualenv==20.23.1
+virtualenv==20.24.3
     # via tox
diff --git a/requirements/dev.in b/requirements/dev.in
@@ -6,7 +6,8 @@
 -r wheels.in
 black
 jinja2
-jupyterlab == 3.5.3  # newer has broken dependency on y-py
+jupyterlab
+mypy
 pip-compile-multi
 pre-commit
 pyyaml

diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -1,4 +1,4 @@
-# SHA1:31304de61247705152d0b8ea537e673329d56cc6
+# SHA1:b62c9a475aba9d9670699cc82bd70677b04f2c52
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -13,76 +13,68 @@
 -r wheels.txt
 anyio==3.7.1
     # via jupyter-server
-argon2-cffi==21.3.0
-    # via
-    #   jupyter-server
-    #   nbclassic
-    #   notebook
+argon2-cffi==23.1.0
+    # via jupyter-server
 argon2-cffi-bindings==21.2.0
     # via argon2-cffi
 arrow==1.2.3
     # via isoduration
-black==23.3.0
+async-lru==2.0.4
+    # via jupyterlab
+black==23.7.0
     # via -r requirements/dev.in
-click==8.1.3
+click==8.1.6
     # via
     #   black
     #   pip-compile-multi
     #   pip-tools
 fqdn==1.5.1
     # via jsonschema
-ipython-genutils==0.2.0
-    # via
-    #   nbclassic
-    #   notebook
 isoduration==20.11.0
     # via jsonschema
 json5==0.9.14
     # via jupyterlab-server
 jsonpointer==2.4
     # via jsonschema
-jsonschema[format-nongpl]==4.18.0
+jsonschema[format-nongpl]==4.19.0
     # via
     #   jupyter-events
     #   jupyterlab-server
     #   nbformat
-jupyter-events==0.6.3
+jupyter-events==0.7.0
     # via jupyter-server
-jupyter-server==2.7.0
+jupyter-lsp==2.2.0
+    # via jupyterlab
+jupyter-server==2.7.1
     # via
+    #   jupyter-lsp
     #   jupyterlab
     #   jupyterlab-server
-    #   nbclassic
     #   notebook-shim
 jupyter-server-terminals==0.4.4
     # via jupyter-server
-jupyterlab==3.5.3
+jupyterlab==4.0.5
     # via -r requirements/dev.in
-jupyterlab-server==2.23.0
+jupyterlab-server==2.24.0
     # via jupyterlab
+mypy==1.5.1
+    # via -r requirements/dev.in
 mypy-extensions==1.0.0
-    # via black
-nbclassic==1.0.0
     # via
-    #   jupyterlab
-    #   notebook
-notebook==6.5.4
-    # via jupyterlab
+    #   black
+    #   mypy
 notebook-shim==0.2.3
-    # via nbclassic
-overrides==7.3.1
+    # via jupyterlab
+overrides==7.4.0
     # via jupyter-server
-pathspec==0.11.1
+pathspec==0.11.2
     # via black
 pip-compile-multi==2.6.3
     # via -r requirements/dev.in
-pip-tools==6.14.0
+pip-tools==7.3.0
     # via pip-compile-multi
-prometheus-client==0.17.0
-    # via
-    #   jupyter-server
-    #   nbclassic
-    #   notebook
+prometheus-client==0.17.1
+    # via jupyter-server
 python-json-logger==2.0.7
     # via jupyter-events
 rfc3339-validator==0.1.4
@@ -94,44 +86,35 @@ rfc3986-validator==0.1.1
     #   jsonschema
     #   jupyter-events
 send2trash==1.8.2
-    # via
-    #   jupyter-server
-    #   nbclassic
-    #   notebook
+    # via jupyter-server
 sniffio==1.3.0
     # via anyio
 terminado==0.17.1
     # via
     #   jupyter-server
     #   jupyter-server-terminals
-    #   nbclassic
-    #   notebook
-tomli==2.0.1
-    # via jupyterlab
 toposort==1.10
     # via pip-compile-multi
-types-docutils==0.20.0.1
+types-docutils==0.20.0.3
     # via -r requirements/dev.in
-types-paramiko==3.2.0.0
+types-paramiko==3.3.0.0
     # via -r requirements/dev.in
-types-python-dateutil==2.8.19.13
+types-python-dateutil==2.8.19.14
     # via -r requirements/dev.in
-types-pyyaml==6.0.12.10
+types-pyyaml==6.0.12.11
     # via -r requirements/dev.in
-types-requests==2.31.0.1
+types-requests==2.31.0.2
     # via -r requirements/dev.in
-types-urllib3==1.26.25.13
+types-urllib3==1.26.25.14
     # via types-requests
 uri-template==1.3.0
     # via jsonschema
 webcolors==1.13
     # via jsonschema
 websocket-client==1.6.1
     # via jupyter-server
-wheel==0.40.0
-    # via
-    #   pip-tools
-    #   sphinx-copybutton
+wheel==0.41.1
+    # via pip-tools
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip

diff --git a/requirements/docs.in b/requirements/docs.in
@@ -6,7 +6,7 @@ ipython!=8.7.0  # Breaks syntax highlighting in Jupyter code cells.
 myst-parser
 nbsphinx
 pydata-sphinx-theme>=0.13
-sphinx
+sphinx==7.1  # 7.2 is not compatible with theme
 sphinx-autodoc-typehints
 sphinx-copybutton
 sphinx-design