Closed dengzeyu closed 8 months ago
Just for tracking - this issue is related to the joss submission: https://github.com/openjournals/joss-reviews/issues/5984#issuecomment-1793653579
Ah this is because there is a separate set of dependencies in the pyproject.toml
for the docs. I have add the following commits that explain this in the documentation (https://github.com/bjmorgan/kinisi/commit/28be82680216bdc6bcf24ca77a4f9d618393ae41 and https://github.com/bjmorgan/kinisi/commit/0ee39d47d616db3c73626ea6fe26e41ba5d8f9f7)
@arm61 I just tried to build the documentation, but I got following error. Could you please help me fix it?
pip install -e '.[docs]'
make html
Notebook error:
PandocMissing in arrhenius_t.ipynb:
Pandoc wasn't found.
Please check that pandoc is installed:
https://pandoc.org/installing.html
make: *** [Makefile:19: html] Error 2
I confirm I've installed the pandoc
Package Version Editable project location
----------------------------- ------------ -----------------------------
accessible-pygments 0.0.4
alabaster 0.7.13
ase 3.22.1
asttokens 2.4.1
attrs 23.1.0
Babel 2.13.1
beautifulsoup4 4.12.2
biopython 1.81
bleach 6.1.0
certifi 2022.12.7
charset-normalizer 3.3.2
codeclimate-test-reporter 0.2.3
comm 0.1.4
contourpy 1.2.0
corner 2.2.2
coverage 7.3.2
cycler 0.12.1
debugpy 1.8.0
decorator 5.1.1
defusedxml 0.7.1
docutils 0.20.1
dynesty 2.1.3
emcee 3.1.4
exceptiongroup 1.1.3
executing 2.0.1
fasteners 0.19
fastjsonschema 2.18.1
fonttools 4.44.0
future 0.18.3
GridDataFormats 1.0.2
h5py 3.10.0
idna 3.4
imagesize 1.4.1
importlib-metadata 6.8.0
importlib-resources 6.1.0
iniconfig 2.0.0
ipykernel 6.26.0
ipython 8.17.2
jedi 0.19.1
Jinja2 3.1.2
joblib 1.3.2
jsonschema 4.19.2
jsonschema-specifications 2023.7.1
jupyter_client 8.5.0
jupyter_core 5.5.0
jupyterlab-pygments 0.2.2
kinisi 0.7.2 /home/jerry/app/source/kinisi
kiwisolver 1.4.5
latexcodec 2.0.1
markdown-it-py 3.0.0
MarkupSafe 2.1.3
matplotlib 3.8.1
matplotlib-inline 0.1.6
MDAnalysis 2.6.1
mdit-py-plugins 0.4.0
mdurl 0.1.2
mistune 3.0.2
mmtf-python 1.1.3
monty 2023.11.3
mpmath 1.3.0
mrcfile 1.4.3
msgpack 1.0.7
myst-parser 2.0.0
nbclient 0.8.0
nbconvert 7.10.0
nbformat 5.9.2
nbsphinx 0.9.3
nest-asyncio 1.5.8
networkx 3.2.1
numpy 1.26.1
packaging 23.2
palettable 3.3.3
pandas 2.1.2
pandoc 2.3
pandocfilters 1.5.0
parso 0.8.3
pexpect 4.8.0
Pillow 10.1.0
pip 23.0.1
platformdirs 3.11.0
plotly 5.18.0
pluggy 1.3.0
plumbum 1.8.2
ply 3.11
prompt-toolkit 3.0.39
psutil 5.9.6
ptyprocess 0.7.0
pure-eval 0.2.2
pybtex 0.24.0
pydata-sphinx-theme 0.14.3
Pygments 2.16.1
pymatgen 2023.10.11
pymatgen-analysis-diffusion 2023.8.15
pyparsing 3.1.1
pytest 7.4.3
pytest-cov 4.1.0
python-dateutil 2.8.2
pytz 2023.3.post1
PyYAML 6.0.1
pyzmq 25.1.1
referencing 0.30.2
requests 2.31.0
rpds-py 0.12.0
ruamel.yaml 0.18.5
ruamel.yaml.clib 0.2.8
scikit-learn 1.3.2
scipy 1.11.3
setuptools 65.6.3
six 1.16.0
snowballstemmer 2.2.0
soupsieve 2.5
spglib 2.1.0
Sphinx 7.2.6
sphinx-autodoc-typehints 1.24.1
sphinxcontrib-applehelp 1.0.7
sphinxcontrib-devhelp 1.0.5
sphinxcontrib-htmlhelp 2.0.4
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.6
sphinxcontrib-serializinghtml 1.1.9
stack-data 0.6.3
sympy 1.12
tabulate 0.9.0
tenacity 8.2.3
threadpoolctl 3.2.0
tinycss2 1.2.1
tomli 2.0.1
tornado 6.3.3
tqdm 4.66.1
traitlets 5.13.0
typing_extensions 4.8.0
tzdata 2023.3
uncertainties 3.1.7
uravu 1.3.0
urllib3 2.0.7
wcwidth 0.2.9
webencodings 0.5.1
wheel 0.38.4
yapf 0.40.2
zipp 3.17.0
I am able to build successfully with pandoc 3.1.3
perhaps updating will help?
I have mentioned installing pandoc
in this commit (https://github.com/bjmorgan/kinisi/commit/f123cc46a1c01198a17a557a095b121502f8516b)
Can we not specify pandoc (with a suitable minimum version) in the usual way as a requirement?
Pandoc isn't a Python package (there is a python interface but you still need to conda/mamba/brew install pandoc to get it to work).
Is that why it shows up in pip
? Also, this means the pip list
output
doesn’t actually tell us if pandoc
is correctly installed.
Yeah, that makes sense.
Also why my version is so much higher than @dengzeyu's (it is actually a different thing)...
@dengzeyu: what do you get from pandoc -v
from the command line?
@arm61 suggestion that you link to the "installing pandoc" page (https://pandoc.org/installing.html) from installation.md
.
@dengzeyu: what do you get from
pandoc -v
from the command line?
I got following
pandoc -v
pandoc 2.12
Compiled with pandoc-types 1.22, texmath 0.12.1.1, skylighting 0.10.4,
citeproc 0.3.0.8, ipynb 0.1.0.1
User data directory: /home/jerry/.local/share/pandoc
Copyright (C) 2006-2021 John MacFarlane. Web: https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
Actually, I tried to install using conda but I can only find the version 2.12, maybe some channels should be added?
conda search pandoc
Loading channels: done
# Name Version Build Channel
pandoc 1.19.2.1 hea2e7c5_1 pkgs/main
pandoc 2.2.1 h629c226_0 pkgs/main
pandoc 2.2.3.2 0 pkgs/main
pandoc 2.9.2.1 0 pkgs/main
pandoc 2.10 0 pkgs/main
pandoc 2.10.1 0 pkgs/main
pandoc 2.11 hb0f4dca_0 pkgs/main
pandoc 2.12 h06a4308_0 pkgs/main
pandoc 2.12 h06a4308_1 pkgs/main
pandoc 2.12 h06a4308_3 pkgs/main
I think the pandoc in conda/pip is too old... Yeah adding a sentence in the installation page and asking for install the new version should be fine.
kinisi/lib/python3.9/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.12).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Actually, I tried to install using conda but I can only find the version 2.12, maybe some channels should be added?
It is unclear whether that refers to the pandoc Python interface, or pandoc itself. I usually install pandoc using the recommended package manager as per the installation instructions (conda is not mentioned on that page).
Actually, I tried to install using conda but I can only find the version 2.12, maybe some channels should be added?
It is unclear whether that refers to the pandoc Python interface, or pandoc itself. I usually install pandoc using the recommended package manager as per the installation instructions (conda is not mentioned on that page).
Yes. I just installed the pandoc using the system package manager and now it's working.
Running mamba install pandoc
got me the 3.1.3 version. I have added the link to the installation instructions.
Please add instructions showing how to build the documentation. It looks like the Makefile under the doc is not working properly.