Merge pull request #852 from benjeffery/update-docs

Update docs deps

.github/workflows/docs.yml

@@ -43,7 +43,7 @@ jobs:
           python -m venv venv
           . venv/bin/activate
           pip install --upgrade pip wheel
-          cat requirements/CI-docs/requirements.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 pip install --no-dependencies          
+          pip install -r requirements/CI-docs/requirements.txt          
           
 
       - name: Build C module

docs/_config.yml

@@ -40,6 +40,9 @@ sphinx:
 
     config:
       html_theme: tskit_book_theme
+      html_theme_options:
+        pygment_light_style: monokai
+        pygment_dark_style: monokai
       pygments_style: monokai
       myst_enable_extensions:
       - colon_fence

requirements/CI-docs/requirements.txt

@@ -1,164 +1,11 @@
-alabaster==0.7.13
-anyio==3.6.2
-argon2-cffi==21.3.0
-argon2-cffi-bindings==21.2.0
-arrow==1.2.3
-asciitree==0.3.3
-asttokens==2.2.1
-attrs==21.4.0
-Babel==2.11.0
-backcall==0.2.0
-beautifulsoup4==4.11.1
-bleach==5.0.1
-certifi==2022.12.7
-cffi==1.15.1
-charset-normalizer==3.0.1
-click==8.1.3
-cloudpickle==2.2.1
-colorama==0.4.6
-coloredlogs==15.0.1
-comm==0.1.2
-cyvcf2==0.30.18
+jupyter-book==0.15.1
+sphinx-issues==3.0.1
+sphinx-argparse==0.4.0
+humanize==4.7.0
+lmdb==1.4.1
+tqdm==4.65.0
 daiquiri==3.2.1
-dask==2022.1.0
-debugpy==1.6.5
-decorator==5.1.1
-defusedxml==0.7.1
-demes==0.2.2
-docutils==0.17.1
-entrypoints==0.4
-executing==1.2.0
-fasteners==0.18
-fastjsonschema==2.16.2
-fqdn==1.5.1
-fsspec==2023.1.0
-gitdb==4.0.10
-GitPython==3.1.30
-greenlet==2.0.1
-humanfriendly==10.0
-humanize==4.4.0
-idna==3.4
-imagesize==1.4.1
-importlib-metadata==6.0.0
-ipykernel==6.20.2
-ipython==8.8.0
-ipython-genutils==0.2.0
-ipywidgets==7.7.2
-isoduration==20.11.0
-jedi==0.18.2
-Jinja2==3.1.2
-jsonpointer==2.3
-jsonschema==4.17.3
-jupyter-book==0.13.1
-jupyter-cache==0.4.3
-jupyter-events==0.6.3
-jupyter-server-mathjax==0.2.6
-jupyter-sphinx==0.3.2
-jupyter_client==7.4.9
-jupyter_core==5.1.3
-jupyter_server==2.1.0
-jupyter_server_terminals==0.4.4
-jupyterlab-pygments==0.2.2
-jupyterlab-widgets==1.1.1
-latexcodec==2.0.1
-linkify-it-py==1.0.3
-llvmlite==0.40.1rc1
-lmdb==1.4.0
-locket==1.0.0
-lxml==4.9.2
-markdown-it-py==1.1.0
-MarkupSafe==2.1.2
-matplotlib-inline==0.1.6
-mdit-py-plugins==0.2.8
-mistune==0.8.4
 msprime==1.2.0
-myst-nb==0.13.2
-myst-parser==0.15.2
-nbclassic==0.4.8
-nbclient==0.5.13
-nbconvert==6.5.4
-nbdime==3.1.1
-nbformat==5.7.3
-nest-asyncio==1.5.6
-newick==1.6.0
-notebook==6.5.2
-notebook_shim==0.2.2
-numba==0.57.0
-numcodecs==0.11.0
-numpy==1.24.3
-packaging==23.0
-pandas==1.5.3
-pandocfilters==1.5.0
-parso==0.8.3
-partd==1.3.0
-pexpect==4.8.0
-pickleshare==0.7.5
-platformdirs==2.6.2
-prometheus-client==0.15.0
-prompt-toolkit==3.0.36
-psutil==5.9.4
-ptyprocess==0.7.0
-pure-eval==0.2.2
-pybtex==0.24.0
-pybtex-docutils==1.0.2
-pycparser==2.21
-pydata-sphinx-theme==0.8.1
-Pygments==2.14.0
-pyrsistent==0.19.3
-python-dateutil==2.8.2
-python-json-logger==2.0.4
-pytz==2022.7.1
-PyYAML==6.0
-pyzmq==25.0.0
-requests==2.28.2
-rfc3339-validator==0.1.4
-rfc3986-validator==0.1.1
-ruamel.yaml==0.17.21
-ruamel.yaml.clib==0.2.7
-Send2Trash==1.8.0
-six==1.16.0
-smmap==5.0.0
-sniffio==1.3.0
-snowballstemmer==2.2.0
-sortedcontainers==2.4.0
-soupsieve==2.3.2.post1
-Sphinx==4.5.0
-sphinx-argparse==0.4.0
-sphinx-book-theme==0.3.3
-sphinx-comments==0.0.3
-sphinx-copybutton==0.5.1
-sphinx-external-toc==0.2.4
-sphinx-issues==3.0.1
-sphinx-jupyterbook-latex==0.4.7
-sphinx-multitoc-numbering==0.1.3
-sphinx-thebe==0.1.2
-sphinx-togglebutton==0.3.2
-sphinx_design==0.1.0
-sphinxcontrib-bibtex==2.5.0
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.0
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
-sphinxcontrib.applehelp==1.0.3
-SQLAlchemy==1.4.46
-stack-data==0.6.2
-svgwrite==1.4.3
-terminado==0.17.1
-tinycss2==1.2.1
-toolz==0.12.0
-tornado==6.2
-tqdm==4.64.1
-traitlets==5.8.1
-tskit==0.5.4
-tskit-book-theme==0.3.2
-uc-micro-py==1.0.1
-uri-template==1.2.0
-urllib3==1.26.14
-wcwidth==0.2.6
-webcolors==1.12
-webencodings==0.5.1
-websocket-client==1.4.2
-widgetsnbextension==3.6.1
-zarr==2.13.6
-zipp==3.15.0
+sgkit[vcf]==0.7.0
+ipywidgets==8.1.0
+tskit-book-theme #Unpinned to allow easy updating.