I am trying to set up a clean environment for contributing to PyMC3 development. In particular, I am trying to build the documentation locally.
I followed the instructions in CONTRIBUTING.md and created a dedicated conda environment from conda_envs\environment-dev-py39.yaml, which installs all necessary packages. The process completed without errors.
However, when running the make.bat file in pymc3\docs\source, the follow error appears:
(pymc3-dev-py39) PS C:\Users\qwer\Documents\Work\code\PyMC3\docs\source> ./make.bat html
Running Sphinx v3.5.4
You are running the v4 development version of PyMC3 which currently still lacks key features. You probably want to use the stable v3 instead which you can either install via conda or find on the v3 GitHub branch: https://github.com/pymc-devs/pymc3/tree/v3
WARNING (aesara.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
making output directory... done
WARNING: html_static_path entry '_static' does not exist
WARNING: html_static_path entry 'nb_tutorials/_images' does not exist
WARNING: html_static_path entry 'nb_examples/_images' does not exist
loading intersphinx inventory from https://arviz-devs.github.io/arviz/objects.inv...
Extension error (gallery_generator):
Handler <function main at 0x000001730458F790> for event 'builder-inited' threw an exception (exception: 'charmap' codec can't decode byte 0x9d in position 38243: character maps to <undefined>)
The non-existing directories are not an issue, it’s the error thrown by a Spinx extension. Any suggestions on how to get around this?
For completeness, here is the output from conda list for the pymc3-dev-py39 environment:
output
aesara 2.1.3 py39h7fcc1c2_1 conda-forge
alabaster 0.7.12 py_0 conda-forge
anyio 3.3.0 py39hcbf5309_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 20.1.0 py39hb82d6ee_2 conda-forge
arviz 0.11.2 pyhd8ed1ab_1 conda-forge
async_generator 1.10 py_0 conda-forge
atomicwrites 1.4.0 pyh9f0ad1d_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.9.3 pyhb0f4dca_0 conda-forge
bleach 4.0.0 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py39hb82d6ee_1001 conda-forge
bzip2 1.0.8 h8ffe710_4 conda-forge
ca-certificates 2021.5.30 h5b45459_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 4.2.2 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 hb19e0ff_1008 conda-forge
certifi 2021.5.30 py39hcbf5309_0 conda-forge
cffi 1.14.6 py39h0878f49_0 conda-forge
cfgv 3.3.0 pyhd8ed1ab_0 conda-forge
cftime 1.5.0 py39h5d4886f_0 conda-forge
chardet 4.0.0 py39hcbf5309_1 conda-forge
charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge
click 8.0.1 py39hcbf5309_0 conda-forge
click-completion 0.5.2 py39hcbf5309_2 conda-forge
click-log 0.3.2 pyh9f0ad1d_0 conda-forge
cloudpickle 1.6.0 py_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
commonmark 0.9.1 py_0 conda-forge
coverage 5.5 py39hb82d6ee_0 conda-forge
cryptography 3.4.7 py39hd8d06c1_0 conda-forge
curl 7.78.0 h789b8ee_0 conda-forge
cycler 0.10.0 py_2 conda-forge
debugpy 1.4.1 py39h415ef7b_0 conda-forge
decorator 5.0.9 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
distlib 0.3.2 pyhd8ed1ab_0 conda-forge
docutils 0.16 py39hcbf5309_3 conda-forge
editdistance-s 1.0.0 py39h2e07f2f_1 conda-forge
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.4.1 h39d44d4_0 conda-forge
fastprogress 1.0.0 py_0 conda-forge
filelock 3.0.12 pyh9f0ad1d_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.1 h1989441_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h546665d_1 conda-forge
fribidi 1.0.10 h8d14728_0 conda-forge
future 0.18.2 py39hcbf5309_3 conda-forge
getopt-win32 0.1 h8ffe710_0 conda-forge
gettext 0.19.8.1 h1a89ca6_1005 conda-forge
gitdb 4.0.7 pyhd8ed1ab_0 conda-forge
gitpython 3.1.18 pyhd8ed1ab_0 conda-forge
graphite2 1.3.13 1000 conda-forge
graphviz 2.48.0 hefbd956_0 conda-forge
greenlet 1.1.1 py39h415ef7b_0 conda-forge
gts 0.7.6 h7c369d9_2 conda-forge
h5py 3.3.0 nompi_py39hf27771d_100 conda-forge
harfbuzz 2.9.0 hc601d6f_0 conda-forge
hdf4 4.2.15 h0e5069d_3 conda-forge
hdf5 1.10.6 nompi_h5268f04_1114 conda-forge
icu 68.1 h0e60522_0 conda-forge
identify 2.2.13 pyhd8ed1ab_0 conda-forge
idna 3.1 pyhd3deb0d_0 conda-forge
imagesize 1.2.0 py_0 conda-forge
importlib-metadata 4.6.4 py39hcbf5309_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
intel-openmp 2021.3.0 h57928b3_3372 conda-forge
ipykernel 6.2.0 py39h832f523_0 conda-forge
ipython 7.26.0 py39h832f523_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge
jbig 2.1 h8d14728_2003 conda-forge
jedi 0.18.0 py39hcbf5309_2 conda-forge
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9d h8ffe710_0 conda-forge
jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge
jupyter-cache 0.4.3 pyhd8ed1ab_0 conda-forge
jupyter-server-mathjax 0.2.3 pyhd8ed1ab_0 conda-forge
jupyter-sphinx 0.3.2 py_0 conda-forge
jupyter_client 6.1.12 pyhd8ed1ab_0 conda-forge
jupyter_core 4.7.1 py39hcbf5309_0 conda-forge
jupyter_server 1.10.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge
kiwisolver 1.3.1 py39h2e07f2f_1 conda-forge
krb5 1.19.2 hbae68bd_0 conda-forge
lcms2 2.12 h2a16943_0 conda-forge
lerc 2.2.1 h0e60522_0 conda-forge
libblas 3.9.0 11_win64_mkl conda-forge
libcblas 3.9.0 11_win64_mkl conda-forge
libcurl 7.78.0 h789b8ee_0 conda-forge
libdeflate 1.7 h8ffe710_5 conda-forge
libffi 3.3 h0e60522_2 conda-forge
libgd 2.3.2 h138e682_0 conda-forge
libglib 2.68.3 h1e62bf3_0 conda-forge
libgpuarray 0.7.6 h8ffe710_1003 conda-forge
libiconv 1.16 he774522_0 conda-forge
liblapack 3.9.0 11_win64_mkl conda-forge
libnetcdf 4.8.0 nompi_hf689e7d_103 conda-forge
libpng 1.6.37 h1d00b33_2 conda-forge
libsodium 1.0.18 h8d14728_1 conda-forge
libssh2 1.9.0 h680486a_6 conda-forge
libtiff 4.3.0 h0c97f57_1 conda-forge
libwebp 1.2.1 h57928b3_0 conda-forge
libwebp-base 1.2.1 h8ffe710_0 conda-forge
libxcb 1.13 hcd874cb_1003 conda-forge
libxml2 2.9.12 hf5bbc77_0 conda-forge
libzip 1.8.0 hfed4ece_0 conda-forge
livereload 2.6.3 pyh9f0ad1d_0 conda-forge
lz4-c 1.9.3 h8ffe710_1 conda-forge
m2w64-binutils 2.25.1 5 conda-forge
m2w64-bzip2 1.0.6 6 conda-forge
m2w64-crt-git 5.0.0.4636.2595836 2 conda-forge
m2w64-gcc 5.3.0 6 conda-forge
m2w64-gcc-ada 5.3.0 6 conda-forge
m2w64-gcc-fortran 5.3.0 6 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gcc-objc 5.3.0 6 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-headers-git 5.0.0.4636.c0ad18a 2 conda-forge
m2w64-isl 0.16.1 2 conda-forge
m2w64-libiconv 1.14 6 conda-forge
m2w64-libmangle-git 5.0.0.4509.2e5a9a2 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
m2w64-make 4.1.2351.a80a8b8 2 conda-forge
m2w64-mpc 1.0.3 3 conda-forge
m2w64-mpfr 3.1.4 4 conda-forge
m2w64-pkg-config 0.29.1 2 conda-forge
m2w64-toolchain 5.3.0 7 conda-forge
m2w64-toolchain_win-64 2.4.0 0 conda-forge
m2w64-tools-git 5.0.0.4592.90b8472 2 conda-forge
m2w64-windows-default-manifest 6.4 3 conda-forge
m2w64-winpthreads-git 5.0.0.4634.697f757 2 conda-forge
m2w64-zlib 1.2.8 10 conda-forge
mako 1.1.4 pyh44b312d_0 conda-forge
markdown-it-py 0.6.2 pyhd8ed1ab_0 conda-forge
markupsafe 2.0.1 py39hb82d6ee_0 conda-forge
matplotlib-base 3.4.3 py39h581301d_0 conda-forge
matplotlib-inline 0.1.2 pyhd8ed1ab_2 conda-forge
mdit-py-plugins 0.2.6 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py39hb82d6ee_1004 conda-forge
mkl 2021.3.0 hb70f87d_564 conda-forge
mkl-service 2.4.0 py39hb82d6ee_0 conda-forge
more-itertools 8.8.0 pyhd8ed1ab_0 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
myst-nb 0.12.3 pyhd8ed1ab_0 conda-forge
myst-parser 0.13.7 pyhd8ed1ab_0 conda-forge
nbclient 0.5.4 pyhd8ed1ab_0 conda-forge
nbconvert 5.6.0 py_0 conda-forge
nbdime 3.1.0 pyhd8ed1ab_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
nbsphinx 0.8.7 pyhd8ed1ab_0 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
netcdf4 1.5.7 nompi_py39hc20e565_100 conda-forge
nodeenv 1.6.0 pyhd8ed1ab_0 conda-forge
notebook 6.4.3 pyha770c72_0 conda-forge
numpy 1.21.2 py39h6635163_0 conda-forge
numpydoc 1.1.0 py_1 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.4.0 hb211442_1 conda-forge
openssl 1.1.1k h8ffe710_1 conda-forge
packaging 21.0 pyhd8ed1ab_0 conda-forge
pandas 1.3.2 py39h2e25243_0 conda-forge
pandoc 2.14.1 h8ffe710_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.48.9 hd84fcdd_0 conda-forge
parso 0.8.2 pyhd8ed1ab_0 conda-forge
patsy 0.5.1 pypi_0 pypi
pcre 8.45 h0e60522_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 8.3.1 py39h916092e_0 conda-forge
pip 21.2.4 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h8ffe710_0 conda-forge
pluggy 0.13.1 py39hcbf5309_4 conda-forge
pre-commit 2.14.0 py39hcbf5309_0 conda-forge
prometheus_client 0.11.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.19 pyha770c72_0 conda-forge
pthread-stubs 0.4 hcd874cb_1001 conda-forge
py 1.10.0 pyhd3deb0d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pydata-sphinx-theme 0.6.3 pyhd8ed1ab_0 conda-forge
pygments 2.10.0 pyhd8ed1ab_0 conda-forge
pygpu 0.7.6 py39h5d4886f_1002 conda-forge
pymc3 4.0 dev_0 <develop>
pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyreadline 2.1 py39hcbf5309_1003 conda-forge
pyrsistent 0.17.3 py39hb82d6ee_2 conda-forge
pysocks 1.7.1 py39hcbf5309_3 conda-forge
pytest 6.2.4 py39hcbf5309_0 conda-forge
pytest-cov 2.12.1 pyhd8ed1ab_0 conda-forge
python 3.9.6 h7840368_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-graphviz 0.17 pyhaef67bd_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2021.1 pyhd8ed1ab_0 conda-forge
pywin32 301 py39hb82d6ee_0 conda-forge
pywinpty 1.1.3 py39h99910a6_0 conda-forge
pyyaml 5.4.1 py39hb82d6ee_1 conda-forge
pyzmq 22.2.1 py39he46f08e_0 conda-forge
recommonmark 0.7.1 pyhd8ed1ab_0 conda-forge
requests 2.26.0 pyhd8ed1ab_0 conda-forge
requests-unixsocket 0.2.0 py_0 conda-forge
scipy 1.7.1 py39hc0c34ad_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 57.4.0 py39hcbf5309_0 conda-forge
shellingham 1.4.0 pyh44b312d_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
sniffio 1.2.0 py39hcbf5309_1 conda-forge
snowballstemmer 2.1.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.0.1 py_1 conda-forge
sphinx 3.5.4 pyh44b312d_0 conda-forge
sphinx-autobuild 2021.3.14 pyhd8ed1ab_0 conda-forge
sphinx-panels 0.6.0 pyhd8ed1ab_0 conda-forge
sphinx-togglebutton 0.2.3 pyhd3deb0d_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_0 conda-forge
sqlalchemy 1.4.23 py39hb82d6ee_0 conda-forge
sqlite 3.36.0 h8ffe710_0 conda-forge
tbb 2021.3.0 h2d74725_0 conda-forge
terminado 0.11.1 py39hcbf5309_0 conda-forge
testpath 0.5.0 pyhd8ed1ab_0 conda-forge
tk 8.6.10 h8ffe710_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39hb82d6ee_1 conda-forge
traitlets 5.0.5 py_0 conda-forge
typing-extensions 3.10.0.0 hd8ed1ab_0 conda-forge
typing_extensions 3.10.0.0 pyha770c72_0 conda-forge
tzdata 2021a he74cb21_1 conda-forge
ucrt 10.0.20348.0 h57928b3_0 conda-forge
urllib3 1.26.6 pyhd8ed1ab_0 conda-forge
vc 14.2 hb210afc_5 conda-forge
virtualenv 20.4.7 py39hcbf5309_0 conda-forge
vs2015_runtime 14.29.30037 h902a5da_5 conda-forge
watermark 2.2.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 0.57.0 py39hcbf5309_4 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 3.5.1 py39hcbf5309_4 conda-forge
win_inet_pton 1.1.0 py39hcbf5309_2 conda-forge
winpty 0.4.3 4 conda-forge
xarray 0.19.0 pyhd8ed1ab_1 conda-forge
xorg-kbproto 1.0.7 hcd874cb_1002 conda-forge
xorg-libice 1.0.10 hcd874cb_0 conda-forge
xorg-libsm 1.2.3 hcd874cb_1000 conda-forge
xorg-libx11 1.7.2 hcd874cb_0 conda-forge
xorg-libxau 1.0.9 hcd874cb_0 conda-forge
xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge
xorg-libxext 1.3.4 hcd874cb_1 conda-forge
xorg-libxpm 3.5.13 hcd874cb_0 conda-forge
xorg-libxt 1.2.1 hcd874cb_2 conda-forge
xorg-xextproto 7.3.0 hcd874cb_1002 conda-forge
xorg-xproto 7.0.31 hcd874cb_1007 conda-forge
xz 5.2.5 h62dcd97_1 conda-forge
yaml 0.2.5 he774522_0 conda-forge
zeromq 4.3.4 h0e60522_0 conda-forge
zipp 3.5.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h62dcd97_1010 conda-forge
zstd 1.5.0 h6255e5f_0 conda-forge