Zotcite Throwing Python Errors Upon Opening Markdown File

aerithnetzer commented 10 months ago

Action: Create test.md, enter @T to a markdown file with vim, put cursor over @T and input C-x, C-o.

Expected Behavior: Show citations matching characters next to the @

Actual Behavior: Upon creating test.md from CLI with vim test.md, the following is shown Screenshot 2023-11-06 at 9 23 57 AM

Further, when I create a citation with @T, cursor over and input C-x, C-o vim outputs -- Omni completion (^O^N^P) Pattern not found

I am at a loss for what is happening, I tried with a minimal config after seeing This issue, and issues kept appearing. Any thoughts on what is causing this issue? Thanks in advance for your help. See below for my configs and pip lists.

Pyyaml and neovim are installed, results of pip list:

aiobotocore                   2.5.0
aiofiles                      22.1.0
aiohttp                       3.8.5
aioitertools                  0.7.1
aiosignal                     1.2.0
aiosqlite                     0.18.0
alabaster                     0.7.12
anaconda-anon-usage           0.4.2
anaconda-catalogs             0.2.0
anaconda-client               1.12.1
anaconda-cloud-auth           0.1.3
anaconda-navigator            2.5.0
anaconda-project              0.11.1
anyio                         3.5.0
appdirs                       1.4.4
applaunchservices             0.3.0
appnope                       0.1.2
appscript                     1.1.2
argon2-cffi                   21.3.0
argon2-cffi-bindings          21.2.0
arrow                         1.2.3
asgiref                       3.7.2
astroid                       2.14.2
astropy                       5.1
asttokens                     2.0.5
async-timeout                 4.0.2
atomicwrites                  1.4.0
attrs                         22.1.0
Automat                       20.2.0
autopep8                      1.6.0
Babel                         2.11.0
backcall                      0.2.0
backports.functools-lru-cache 1.6.4
backports.tempfile            1.0
backports.weakref             1.0.post1
bcrypt                        3.2.0
beautifulsoup4                4.12.2
binaryornot                   0.4.4
black                         0.0
bleach                        4.1.0
bokeh                         3.2.1
boltons                       23.0.0
botocore                      1.29.76
Bottleneck                    1.3.5
brotlipy                      0.7.0
certifi                       2023.7.22
cffi                          1.15.1
chardet                       4.0.0
charset-normalizer            2.0.4
click                         8.0.4
cloudpickle                   2.2.1
clyent                        1.2.2
colorama                      0.4.6
colorcet                      3.0.1
comm                          0.1.2
conda                         23.7.4
conda-build                   3.26.1
conda-content-trust           0.2.0
conda_index                   0.3.0
conda-libmamba-solver         23.7.0
conda-pack                    0.6.0
conda-package-handling        2.2.0
conda_package_streaming       0.9.0
conda-repo-cli                1.0.75
conda-token                   0.4.0
conda-verify                  3.4.2
constantly                    15.1.0
contourpy                     1.0.5
cookiecutter                  1.7.3
cryptography                  41.0.3
cssselect                     1.1.0
cycler                        0.11.0
cytoolz                       0.12.0
dask                          2023.6.0
datasets                      2.12.0
datashader                    0.15.2
datashape                     0.5.4
debugpy                       1.6.7
decorator                     5.1.1
defusedxml                    0.7.1
diff-match-patch              20200713
dill                          0.3.6
distributed                   2023.6.0
Django                        4.2.6
docstring-to-markdown         0.11
docutils                      0.18.1
entrypoints                   0.4
et-xmlfile                    1.1.0
executing                     0.8.3
fastjsonschema                2.16.2
filelock                      3.9.0
flake8                        6.0.0
Flask                         2.2.2
fonttools                     4.25.0
frozenlist                    1.3.3
fsspec                        2023.4.0
future                        0.18.3
gensim                        4.3.0
glob2                         0.7
gmpy2                         2.1.2
greenlet                      2.0.1
h5py                          3.9.0
HeapDict                      1.0.1
holoviews                     1.17.1
huggingface-hub               0.15.1
hvplot                        0.8.4
hyperlink                     21.0.0
idna                          3.4
imagecodecs                   2023.1.23
imageio                       2.31.1
imagesize                     1.4.1
imbalanced-learn              0.10.1
importlib-metadata            6.0.0
incremental                   21.3.0
inflection                    0.5.1
iniconfig                     1.1.1
intake                        0.6.8
intervaltree                  3.1.0
ipykernel                     6.25.0
ipython                       8.15.0
ipython-genutils              0.2.0
ipywidgets                    8.0.4
isort                         5.9.3
itemadapter                   0.3.0
itemloaders                   1.0.4
itsdangerous                  2.0.1
jaraco.classes                3.2.1
jedi                          0.18.1
jellyfish                     1.0.1
Jinja2                        3.1.2
jinja2-time                   0.2.0
jmespath                      0.10.0
joblib                        1.2.0
json5                         0.9.6
jsonpatch                     1.32
jsonpointer                   2.1
jsonschema                    4.17.3
jupyter                       1.0.0
jupyter_client                7.4.9
jupyter-console               6.6.3
jupyter_core                  5.3.0
jupyter-events                0.6.3
jupyter-server                1.23.4
jupyter_server_fileid         0.9.0
jupyter_server_ydoc           0.8.0
jupyter-ydoc                  0.2.4
jupyterlab                    3.6.3
jupyterlab-pygments           0.1.2
jupyterlab_server             2.22.0
jupyterlab-widgets            3.0.5
kaleido                       0.2.1
keyring                       23.13.1
kiwisolver                    1.4.4
latexcodec                    2.0.1
lazy_loader                   0.2
lazy-object-proxy             1.6.0
libarchive-c                  2.9
libmambapy                    1.5.1
linkify-it-py                 2.0.0
llvmlite                      0.40.0
lmdb                          1.4.1
locket                        1.0.0
lxml                          4.9.3
lz4                           4.3.2
Markdown                      3.4.1
markdown-it-py                2.2.0
MarkupSafe                    2.1.1
matplotlib                    3.7.2
matplotlib-inline             0.1.6
mccabe                        0.7.0
mdit-py-plugins               0.3.0
mdurl                         0.1.0
mistune                       0.8.4
more-itertools                8.12.0
mpmath                        1.3.0
msgpack                       1.0.3
multidict                     6.0.2
multipledispatch              0.6.0
multiprocess                  0.70.14
munkres                       1.1.4
mypy-extensions               1.0.0
navigator-updater             0.4.0
nbclassic                     0.5.5
nbclient                      0.5.13
nbconvert                     6.5.4
nbformat                      5.9.2
neovim                        0.3.1
nest-asyncio                  1.5.6
networkx                      3.1
nltk                          3.8.1
notebook                      6.5.4
notebook_shim                 0.2.2
numba                         0.57.1
numexpr                       2.8.4
numpy                         1.24.3
numpydoc                      1.5.0
openpyxl                      3.0.10
packaging                     23.1
pandas                        2.0.3
pandoc-eqnos                  2.5.0
pandoc-fignos                 2.4.0
pandoc-secnos                 2.2.2
pandoc-tablenos               2.3.0
pandoc-xnos                   2.5.0
pandocfilters                 1.5.0
panel                         1.2.3
param                         1.13.0
parsel                        1.6.0
parso                         0.8.3
partd                         1.4.0
pathlib                       1.0.1
pathspec                      0.10.3
patsy                         0.5.3
pep8                          1.7.1
pexpect                       4.8.0
pickleshare                   0.7.5
Pillow                        9.4.0
pip                           23.2.1
pkce                          1.0.3
pkginfo                       1.9.6
platformdirs                  3.10.0
plotly                        5.9.0
pluggy                        1.0.0
ply                           3.11
poyo                          0.5.0
prometheus-client             0.14.1
prompt-toolkit                3.0.36
Protego                       0.1.16
psutil                        5.9.0
ptyprocess                    0.7.0
pure-eval                     0.2.2
py-cpuinfo                    8.0.0
pyarrow                       11.0.0
pyasn1                        0.4.8
pyasn1-modules                0.2.8
pybtex                        0.24.0
pycodestyle                   2.10.0
pycosat                       0.6.4
pycparser                     2.21
pyct                          0.5.0
pycurl                        7.45.2
pydantic                      1.10.8
PyDispatcher                  2.0.5
pydocstyle                    6.3.0
pyerfa                        2.0.0
pyflakes                      3.0.1
Pygments                      2.15.1
PyJWT                         2.4.0
pylint                        2.16.2
pylint-venv                   2.3.0
pyls-spyder                   0.4.0
pynvim                        0.4.3
pyobjc-core                   9.0
pyobjc-framework-Cocoa        9.0
pyobjc-framework-CoreServices 9.0
pyobjc-framework-FSEvents     9.0
pyodbc                        4.0.34
pyOpenSSL                     23.2.0
pyparsing                     3.0.9
PyQt5                         5.15.10
PyQt5-Qt5                     5.15.11
PyQt5-sip                     12.13.0
pyrsistent                    0.18.0
PySocks                       1.7.1
pytest                        7.4.0
python-dateutil               2.8.2
python-dotenv                 0.21.0
python-json-logger            2.0.7
python-lsp-black              1.2.1
python-lsp-jsonrpc            1.0.0
python-lsp-server             1.7.2
python-slugify                5.0.2
python-snappy                 0.6.1
pytoolconfig                  1.2.5
pytz                          2023.3.post1
pyviz-comms                   2.3.0
PyWavelets                    1.4.1
PyYAML                        6.0
pyzmq                         23.2.0
QDarkStyle                    3.0.2
qstylizer                     0.2.2
QtAwesome                     1.2.2
qtconsole                     5.4.2
QtPy                          2.2.0
queuelib                      1.5.0
regex                         2022.7.9
requests                      2.31.0
requests-file                 1.5.1
requests-toolbelt             1.0.0
responses                     0.13.3
rfc3339-validator             0.1.4
rfc3986-validator             0.1.1
rope                          1.7.0
Rtree                         1.0.1
ruamel.yaml                   0.17.21
ruamel-yaml-conda             0.17.21
s3fs                          2023.4.0
safetensors                   0.3.2
scikit-image                  0.20.0
scikit-learn                  1.3.0
scipy                         1.11.1
Scrapy                        2.8.0
seaborn                       0.12.2
Send2Trash                    1.8.0
service-identity              18.1.0
setuptools                    68.0.0
sip                           6.6.2
six                           1.16.0
smart-open                    5.2.1
sniffio                       1.2.0
snowballstemmer               2.2.0
sortedcontainers              2.4.0
soupsieve                     2.4
Sphinx                        5.0.2
sphinxcontrib-applehelp       1.0.2
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
spyder                        5.4.3
spyder-kernels                2.4.4
SQLAlchemy                    1.4.39
sqlparse                      0.4.4
stack-data                    0.2.0
statsmodels                   0.14.0
sympy                         1.11.1
tables                        3.8.0
tabulate                      0.8.10
tblib                         1.7.0
tenacity                      8.2.2
terminado                     0.17.1
text-unidecode                1.3
textdistance                  4.2.1
threadpoolctl                 2.2.0
three-merge                   0.1.1
tifffile                      2023.4.12
tinycss2                      1.2.1
tldextract                    3.2.0
tokenizers                    0.13.2
toml                          0.10.2
tomlkit                       0.11.1
toolz                         0.12.0
tornado                       6.3.2
tqdm                          4.65.0
traitlets                     5.7.1
transformers                  4.32.1
Twisted                       22.10.0
typing_extensions             4.7.1
tzdata                        2023.3
uc-micro-py                   1.0.1
ujson                         5.4.0
Unidecode                     1.2.0
urllib3                       1.26.16
w3lib                         1.21.0
watchdog                      2.1.6
wcwidth                       0.2.5
webencodings                  0.5.1
websocket-client              0.58.0
Werkzeug                      2.2.3
whatthepatch                  1.0.2
wheel                         0.38.4
widgetsnbextension            4.0.5
wrapt                         1.14.1
wurlitzer                     3.0.2
xarray                        2023.6.0
xlwings                       0.29.1
xxhash                        2.0.2
xyzservices                   2022.9.0
y-py                          0.5.9
yapf                          0.31.0
yarl                          1.8.1
ypy-websocket                 0.8.2
zict                          2.2.0
zipp                          3.11.0
zope.interface                5.4.0
zstandard                     0.19.0

After entering to clear out error messages:

Input :Zinfo Output There is another omnifunc enabled: htmlcomplete#CompleteTags

omnifunc is set to zotecite#CompletetBib

Vimrc file:

call plug#begin()
" The default plugin directory will be as follows:
"   - Vim (Linux/macOS): '~/.vim/plugged'
"   - Vim (Windows): '~/vimfiles/plugged'
"   - Neovim (Linux/macOS/Windows): stdpath('data') . '/plugged'
" You can specify a custom plugin directory by passing it as the argument
"   - e.g. `call plug#begin('~/.vim/plugged')`
"   - Avoid using standard Vim directory names like 'plugin'

" Make sure you use single quotes

" Shorthand notation; fetches https://github.com/junegunn/vim-easy-align
Plug 'junegunn/vim-easy-align'

" Any valid git URL is allowed
Plug 'https://github.com/junegunn/vim-github-dashboard.git'

" Multiple Plug commands can be written in a single line using | separators
Plug 'SirVer/ultisnips' | Plug 'honza/vim-snippets'

" On-demand loading
Plug 'preservim/nerdtree', { 'on': 'NERDTreeToggle' }
Plug 'tpope/vim-fireplace', { 'for': 'clojure' }

" Using a non-default branch
Plug 'rdnetto/YCM-Generator', { 'branch': 'stable' }

" Using a tagged release; wildcard allowed (requires git 1.9.2 or above)
Plug 'fatih/vim-go', { 'tag': '*' }

" Plugin options
Plug 'nsf/gocode', { 'tag': 'v.20150303', 'rtp': 'vim' }

" Plugin outside ~/.vim/plugged with post-update hook
Plug 'junegunn/fzf', { 'dir': '~/.fzf', 'do': './install --all' }

" Copilot plugin
Plug 'github/copilot.vim'

"VimTex plugin
Plug 'lervag/vimtex'

" Zotcite plugin
Plug 'jalvesaq/zotcite'

call plug#end()

set omnifunc=zotecite#CompleteBib

jalvesaq commented 10 months ago

I'm sorry, but I can't replicate the issue. Anyway, it should not be necessary to set omnifunc at your vimrc because zotcite does this at zotcite#Init(). I don't know why import yaml fails even though 'PyYAML` is installed...

jalvesaq commented 10 months ago

Notes:

There was a bug setting the omnifunc. I fixed it today.
Make sure that pyyaml is installed both system-wide and in the specific virtual environment where pynvim is running.

aerithnetzer commented 10 months ago

No longer getting error, thanks!

dld2517 commented 8 months ago

So there was nothing in the docs indicating that pynvim is required. Also, I must use a virtual environment to install Python modules. Where should the virtual environment be created and how to let Zotcite know which venv to use?

dld2517 commented 8 months ago

There is also nothing in the docs about having to manually load the plugin in .vimrc. Also, no discussion of which plugin to place in the right folder. Should it be ../autoload/zotcite.vim or ../plugin/zotcite.vim

I am just looking for some direction because I am getting these same errors.

jalvesaq commented 8 months ago

I updated the documentation, replaced neovim with pynvim, and suggested the reading of Neovim documentation on provider-python.

It will be easier if you use a plugin manager to install your plugins. I'm using lazy.nvim with the option lazy=false, but there are many other options.

jalvesaq / zotcite

Zotcite Throwing Python Errors Upon Opening Markdown File #64