Documentation does not build

[schtandard]

I followed the instructions in CONTRIBUTING.md to set up an environment for development (using conda). This seemed to work fine, the test suite ran successfully (with a couple of warnings and three skipped tests). However, I can't seem to build the documentation.

Since no target is specified in the instructions, I guessed that make html is the way to go. However, this fails with the following error.

Warning, treated as error:
D:\Projekte\miscellaneous_git_repos\lmfit-py\examples\documentation\model_loadmodel.py failed to execute correctly: Traceback (most recent call last):
  File "D:\Projekte\miscellaneous_git_repos\lmfit-py\examples\documentation\model_loadmodel.py", line 33, in <module>
    result = model.fit(y, params, x=x)
             ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Projekte\miscellaneous_git_repos\lmfit-py\lmfit\model.py", line 1103, in fit
    output.fit(data=data, weights=weights)
  File "D:\Projekte\miscellaneous_git_repos\lmfit-py\lmfit\model.py", line 1466, in fit
    self.init_fit = self.model.eval(params=self.params, **self.userkws)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Projekte\miscellaneous_git_repos\lmfit-py\lmfit\model.py", line 930, in eval
    return coerce_arraylike(self.func(**self.make_funcargs(params, kwargs)))
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "d:\Projekte\miscellaneous_git_repos\lmfit-py\examples\documentation\model_savemodel.py", line 14, in mysine
    return amp * np.sin(x*freq + shift)
                 ^^
NameError: name 'np' is not defined

Copying model_savemodel.py, model_loadmodel.py and sinedata.dat to another directory and executing them there works fine though, so I'm not sure what the problem is.

Commenting out the offending part of doc_model_loadmodel.py and trying again, I get a different error.

Warning, treated as error:
Cell printed to stderr:
WARNING:root:Pandas support in corner is deprecated; use ArviZ directly

Building the documentation without using Sphinx' -W flag confirmed that those were the only two warnings occuring.

Is there something wrong with my setup or is there some other problem?

Here's a list of the package versions I have installed in the environment, in case that's relevant.

# Name                    Version                   Build  Channel
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
algopy                    0.5.7                      py_0    conda-forge
annotated-types           0.6.0              pyhd8ed1ab_0    conda-forge
arviz                     0.16.1             pyhd8ed1ab_1    conda-forge
asteval                   0.9.31             pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.13.1             pyhd8ed1ab_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hcfcfb64_1    conda-forge
brotli-bin                1.1.0                hcfcfb64_1    conda-forge
brotli-python             1.1.0           py311h12c1d0e_1    conda-forge
build                     0.7.0              pyhd8ed1ab_0    conda-forge
bzip2                     1.0.8                hcfcfb64_5    conda-forge
ca-certificates           2023.7.22            h56e8100_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.18.0               h1fef639_0    conda-forge
cairocffi                 1.6.1              pyhd8ed1ab_0    conda-forge
cairosvg                  2.7.1              pyhd8ed1ab_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311ha68e1ae_0    conda-forge
cfgv                      3.3.1              pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
check-wheel-contents      0.6.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           win_pyh7428d3b_0    conda-forge
cmarkgfm                  0.8.0           py311ha68e1ae_3    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.0           py311h005e61a_0    conda-forge
corner                    2.2.2              pyhd8ed1ab_0    conda-forge
coverage                  7.3.2           py311ha68e1ae_0    conda-forge
cssselect2                0.2.1              pyh9f0ad1d_1    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
debugpy                   1.8.0           py311h12c1d0e_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.7              pyhd8ed1ab_0    conda-forge
distlib                   0.3.7              pyhd8ed1ab_0    conda-forge
docutils                  0.20.1          py311h1ea47a8_2    conda-forge
emcee                     3.1.4              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h63175ca_1    conda-forge
filelock                  3.13.1             pyhd8ed1ab_0    conda-forge
flaky                     3.7.0              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                2.14.2               hbde0cde_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.44.3          py311ha68e1ae_0    conda-forge
freetype                  2.12.1               hdaf720e_2    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h5728263_0    conda-forge
glib                      2.78.1               h12be248_1    conda-forge
glib-tools                2.78.1               h12be248_1    conda-forge
gst-plugins-base          1.22.7               h001b923_0    conda-forge
gstreamer                 1.22.7               hb4038d2_0    conda-forge
h5netcdf                  1.3.0              pyhd8ed1ab_0    conda-forge
h5py                      3.10.0          nompi_py311h0d04526_100    conda-forge
hdf5                      1.14.2          nompi_h73e8ff5_100    conda-forge
icu                       73.2                 h63175ca_0    conda-forge
identify                  2.5.31             pyhd8ed1ab_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.1.1              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
intel-openmp              2023.2.0         h57928b3_50497    conda-forge
ipykernel                 6.26.0             pyha63f2e9_0    conda-forge
ipython                   8.17.2             pyh5737063_0    conda-forge
ipywidgets                8.1.1              pyhd8ed1ab_0    conda-forge
jaraco.classes            3.3.0              pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.20.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.11.1          pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.5.0           py311h1ea47a8_0    conda-forge
jupyter_sphinx            0.4.0           py311h1ea47a8_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.9              pyhd8ed1ab_0    conda-forge
keyring                   24.3.0          py311h1ea47a8_0    conda-forge
kiwisolver                1.4.5           py311h005e61a_1    conda-forge
krb5                      1.21.2               heb0366b_0    conda-forge
lcms2                     2.15                 h67d730c_3    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libaec                    1.1.2                h63175ca_1    conda-forge
libblas                   3.9.0              19_win64_mkl    conda-forge
libbrotlicommon           1.1.0                hcfcfb64_1    conda-forge
libbrotlidec              1.1.0                hcfcfb64_1    conda-forge
libbrotlienc              1.1.0                hcfcfb64_1    conda-forge
libcblas                  3.9.0              19_win64_mkl    conda-forge
libclang                  15.0.7          default_h77d9078_3    conda-forge
libclang13                15.0.7          default_h77d9078_3    conda-forge
libcurl                   8.4.0                hd5e4a3a_0    conda-forge
libdeflate                1.19                 hcfcfb64_0    conda-forge
libexpat                  2.5.0                h63175ca_1    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libglib                   2.78.1               h16e383f_1    conda-forge
libhwloc                  2.9.3           default_haede6df_1009    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
libjpeg-turbo             3.0.0                hcfcfb64_1    conda-forge
liblapack                 3.9.0              19_win64_mkl    conda-forge
libogg                    1.3.4                h8ffe710_1    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.44.0               hcfcfb64_0    conda-forge
libssh2                   1.11.0               h7dfc565_0    conda-forge
libtiff                   4.6.0                h6e2ebb7_2    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp-base              1.3.2                hcfcfb64_0    conda-forge
libxcb                    1.15                 hcd874cb_0    conda-forge
libxml2                   2.11.6               hc3477c8_0    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
lmfit                     0.0.post2796+g4e2470a.d20231118          pypi_0    pypi
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-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.3           py311ha68e1ae_1    conda-forge
matplotlib                3.8.1           py311h1ea47a8_0    conda-forge
matplotlib-base           3.8.1           py311h6e989c2_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mkl                       2023.2.0         h6a75c08_50496    conda-forge
more-itertools            10.1.0             pyhd8ed1ab_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.11.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.11.0             pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.11.0             pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
nest-asyncio              1.5.8              pyhd8ed1ab_0    conda-forge
nh3                       0.2.14          py311h633b200_1    conda-forge
nodeenv                   1.8.0              pyhd8ed1ab_0    conda-forge
numdifftools              0.9.41             pyhd8ed1ab_0    conda-forge
numpy                     1.26.0          py311h0b4df5a_0    conda-forge
openjpeg                  2.5.0                h3d672ee_3    conda-forge
openssl                   3.1.4                hcfcfb64_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.1.3           py311hf63dbb6_0    conda-forge
pandoc                    3.1.3                h57928b3_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.42                h17e33f8_0    conda-forge
pep517                    0.13.0             pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.1.0          py311h4dd8a23_0    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h63175ca_0    conda-forge
pkginfo                   1.9.6              pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
pre-commit                3.5.0              pyha770c72_0    conda-forge
prompt-toolkit            3.0.41             pyha770c72_0    conda-forge
prompt_toolkit            3.0.41               hd8ed1ab_0    conda-forge
psutil                    5.9.5           py311ha68e1ae_1    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.25.1          py311h99894aa_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  2.5.1              pyhd8ed1ab_0    conda-forge
pydantic-core             2.14.3          py311hc37eb10_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.9          py311h125bc19_5    conda-forge
pyqt5-sip                 12.12.2         py311h12c1d0e_5    conda-forge
pysocks                   1.7.1              pyh0701188_6    conda-forge
pytest                    7.4.3              pyhd8ed1ab_0    conda-forge
pytest-cov                4.1.0              pyhd8ed1ab_0    conda-forge
python                    3.11.6          h2628c8c_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.19.0             pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pywin32                   306             py311h12c1d0e_2    conda-forge
pywin32-ctypes            0.2.2           py311h1ea47a8_1    conda-forge
pyyaml                    6.0.1           py311ha68e1ae_1    conda-forge
pyzmq                     25.1.1          py311h9250fbb_2    conda-forge
qt-main                   5.15.8              h9e85ed6_17    conda-forge
readme_renderer           42.0               pyhd8ed1ab_0    conda-forge
referencing               0.31.0             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
requests-toolbelt         1.0.0              pyhd8ed1ab_0    conda-forge
rfc3986                   2.0.0              pyhd8ed1ab_0    conda-forge
rich                      13.7.0             pyhd8ed1ab_0    conda-forge
rpds-py                   0.13.0          py311hc37eb10_0    conda-forge
scipy                     1.11.3          py311h0b4df5a_1    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.0.4              pyhd8ed1ab_0    conda-forge
setuptools_scm            8.0.4                hd8ed1ab_0    conda-forge
sip                       6.7.12          py311h12c1d0e_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    7.2.6              pyhd8ed1ab_0    conda-forge
sphinx-gallery            0.14.0             pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.7              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.5              pyhd8ed1ab_0    conda-forge
sphinxcontrib-htmlhelp    2.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-qthelp      1.0.6              pyhd8ed1ab_0    conda-forge
sphinxcontrib-serializinghtml 1.1.9              pyhd8ed1ab_0    conda-forge
sphinxcontrib-svg2pdfconverter 1.2.2                    pypi_0    pypi
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.0          py311h59ca53f_2    conda-forge
sympy                     1.12               pyh04b8f61_3    conda-forge
tbb                       2021.10.0            h91493d7_2    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5226925_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3           py311ha68e1ae_1    conda-forge
traitlets                 5.13.0             pyhd8ed1ab_0    conda-forge
twine                     4.0.2              pyhd8ed1ab_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
ukkonen                   1.0.1           py311h005e61a_4    conda-forge
uncertainties             3.1.7              pyhd8ed1ab_0    conda-forge
urllib3                   2.1.0              pyhd8ed1ab_0    conda-forge
vc                        14.3                h64f974e_17    conda-forge
vc14_runtime              14.36.32532         hdcecf7f_17    conda-forge
virtualenv                20.24.6            pyhd8ed1ab_0    conda-forge
vs2015_runtime            14.36.32532         h05e6639_17    conda-forge
wcwidth                   0.2.10             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
wheel-filename            1.4.1              pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.9              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyhd8ed1ab_6    conda-forge
xarray                    2023.10.1          pyhd8ed1ab_0    conda-forge
xarray-einstats           0.6.0              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zeromq                    4.3.5                h63175ca_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hcfcfb64_5    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge

[newville]

@schtandard Weird, I cannot reproduce this problem.
For sure, examples\documentation\model_savemodel.py does an import numpy as np.

I guess I have not tried building the docs on Windows in a while. FWIW, typically one would just use make, but make html will be the same.

[schtandard]

For sure, examples\documentation\model_savemodel.py does an import numpy as np.

Indeed.

FWIW, typically one would just use make, but make html will be the same.

Interesting, maybe this is also a Windows thing. When I try just make I get

Sphinx v7.2.6
Please use `make target' where target is one of

and then a list of possible targets.

[newville]

@schtandard The docs do build for me on Windows. I did pip install lmfit[all]. I don't know how much effort we want to devote to trying to address problems people have building the docs.

Is it important to get the docs built locally?

[schtandard]

Hmm, ok, weird. I tried some more setups (installing packages with pip instead of conde, oder python versions -- but versions pins always in place) and got different results but never a run without a warning (preventing the build with the -W option). So maybe it is something about python and package versions..

But no, as long as this is just me, it is not important to fix this. (And I can still build without the -W, the warnings do no affect the parts of the documentation that I'm editing.)