From b9280ee540134dfcc264a22579ca26fb77af4f98 Mon Sep 17 00:00:00 2001 From: Ben Jeffery Date: Wed, 2 Aug 2023 15:16:40 +0100 Subject: [PATCH] Update docs deps --- .github/workflows/docs.yml | 2 +- docs/_config.yml | 3 + requirements/CI-docs/requirements.txt | 171 ++------------------------ 3 files changed, 13 insertions(+), 163 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6aaa25a0..1f28e6e2 100644 --- a/.github/workflows/docs.yml +++ b/.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 diff --git a/docs/_config.yml b/docs/_config.yml index 7927d0e1..637914be 100644 --- a/docs/_config.yml +++ b/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 diff --git a/requirements/CI-docs/requirements.txt b/requirements/CI-docs/requirements.txt index 2c1b416d..ab18ba26 100644 --- a/requirements/CI-docs/requirements.txt +++ b/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.