Merge pull request #252 from benjeffery/fixCI

Test CI

Author: benjeffery

.github/workflows/build.yml

@@ -21,15 +21,15 @@ jobs:
       uses: actions/checkout@v2
 
     # Install dependencies
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
         python-version: "3.10"
 
     - name: Install python dependencies
       run: |
         pip install --upgrade pip wheel
-        cat requirements-CI.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 pip install --no-dependencies
+        pip install -r requirements-CI.txt
 
     - name: Install R support
       run: |

requirements-CI.txt

@@ -1,176 +1,14 @@
-alabaster==0.7.13
-anyio==3.6.2
-appdirs==1.4.4
-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
-comm==0.1.2
-contourpy==1.0.7
-cvxpy==1.3.0
-cycler==0.11.0
-dask==2023.1.0
-debugpy==1.6.5
-decorator==5.1.1
-defusedxml==0.7.1
-demes==0.2.2
-demesdraw==0.3.1
-DendroPy==4.5.2
-docutils==0.17.1
-ecos==2.0.12
-entrypoints==0.4
-executing==1.2.0
-fasteners==0.18
-fastjsonschema==2.16.2
-fonttools==4.38.0
-fqdn==1.5.1
-fsspec==2023.1.0
-gitdb==4.0.10
-GitPython==3.1.30
-greenlet==2.0.1
-humanize==4.4.0
-idna==3.4
-imagesize==1.4.1
-importlib-metadata==6.0.0
-ipykernel==6.20.2
-ipython==8.10.0
-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
-kiwisolver==1.4.4
-latexcodec==2.0.1
-linkify-it-py==1.0.3
-locket==1.0.0
-lxml==4.9.2
-markdown-it-py==1.1.0
-MarkupSafe==2.1.2
-matplotlib==3.6.3
-matplotlib-inline==0.1.6
-mdit-py-plugins==0.2.8
-mistune==0.8.4
+git+https://github.com/tskit-dev/tsconvert@e99c837e4e26ccbf4f480a4c48626338eeff7dc3
+demes==0.2.3
+demesdraw==0.4.0
+jupyter-book==0.15.1
+jupyter-cache==0.6.1
 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
-networkx==3.0
-newick==1.6.0
-notebook==6.5.2
-notebook_shim==0.2.2
-numcodecs==0.11.0
-numpy==1.24.1
-osqp==0.6.2.post8
-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
-Pillow==9.4.0
-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
-pyparsing==3.0.9
-pyrsistent==0.19.3
-pyslim==1.0.1
-python-dateutil==2.8.2
-python-json-logger==2.0.4
-pytz==2022.7.1
-PyYAML==6.0
-pyzmq==25.0.0
-qdldl==0.1.5.post3
-requests==2.31.0
-rfc3339-validator==0.1.4
-rfc3986-validator==0.1.1
-ruamel.yaml==0.17.21
-ruamel.yaml.clib==0.2.7
-scikit-allel==1.3.5
-scipy==1.10.0
-scs==3.2.2
-Send2Trash==1.8.0
-six==1.16.0
-smmap==5.0.0
-sniffio==1.3.0
-snowballstemmer==2.2.0
-soupsieve==2.3.2.post1
-Sphinx==4.5.0
-sphinx-book-theme==0.3.3
-sphinx-comments==0.0.3
-sphinx-copybutton==0.5.1
-sphinx-external-toc==0.2.4
-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-applehelp==1.0.4
-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
-SQLAlchemy==1.4.46
-stack-data==0.6.2
+networkx==3.1
+pandas==2.0.3
+scikit-allel==1.3.6
 stdpopsim==0.2.0
-svgwrite==1.4.3
-terminado==0.17.1
-tinycss2==1.2.1
-toolz==0.12.0
-tornado==6.3.2
-tqdm==4.64.1
-traitlets==5.8.1
-git+https://github.com/tskit-dev/tsconvert@e99c837e4e26ccbf4f480a4c48626338eeff7dc3
-tskit==0.5.4
-tskit-book-theme==0.3.2
+tqdm==4.65.0
+tskit==0.5.5
+tskit-book-theme #Unpinned for easy updating
 tszip==0.2.2
-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==3.11.0

requirements.txt

@@ -1,19 +1,14 @@
-sphinx
-jupyter-book>=0.12.0
+git+https://github.com/tskit-dev/tsconvert@e99c837e4e26ccbf4f480a4c48626338eeff7dc3
 demes
 demesdraw
-matplotlib>=3.4.0
+jupyter-book>=0.12.0
+jupyter-cache
+msprime>=1.0
+networkx
+pandas
 scikit-allel
+stdpopsim
 tqdm
-numpy
-networkx
 tskit>=0.5.4
-msprime>=1.0
-stdpopsim
-tskit-book-theme==0.3.2
+tskit-book-theme
 tszip
-pandas
-git+https://github.com/tskit-dev/tsconvert  # for newick parsing in phylogen.md
-# Specified here due to failing build with jupyter-book specified version #214
-jsonschema[format-nongpl]==4.17.3
-nbclient==0.5.13