jupyterlab / jupyterlab

JupyterLab computational environment.
https://jupyterlab.readthedocs.io/
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Markdown table with empty row not rendered in JupyterLab #16593

Closed stefansimik closed 4 months ago

stefansimik commented 4 months ago

Description

Simple Markdown table with empty row cannot be rendered in JupyterLab

Reproduce

Create Markdown cell in JupyterLab and paste this code:

| Number | Variable | Description |
|--------|----------|-------------|
| 1      | CRIM     | per capita crime rate by town |
| 2      | ZN       | proportion of residential land zoned for lots over 25,000 sq.ft. |
| 3      | INDUS    | proportion of non-retail business acres per town |
| 4      | CHAS     | Charles River dummy variable (1 if tract bounds river; 0 otherwise) |
| 5      | NOX      | nitric oxides concentration (parts per 10 million) |
| 6      | RM       | average number of rooms per dwelling |
| 7      | AGE      | proportion of owner-occupied units built prior to 1940 |
| 8      | DIS      | weighted distances to five Boston employment centres |
| 9      | RAD      | index of accessibility to radial highways |
| 10     | TAX      | full-value property-tax rate per $10,000 |
| 11     | PTRATIO  | pupil-teacher ratio by town |
| 12     | B        | The result of the equation B=1000(Bk - 0.63)^2 where Bk is the proportion of blacks by town |
| 13     | LSTAT    | % lower status of the population |
|        |          |             |
| Target | MEDV     | Median value of owner-occupied homes in $1000's |

This is cell in Edit mode (not rendered):

CleanShot 2024-07-16 at 13 28 58@2x

This is cell in Rendered mode:

CleanShot 2024-07-16 at 13 29 44@2x

Expected behavior

Table should be rendered correctly with empty row.

Context

Troubleshoot Output
Last login: Tue Jul 16 11:22:51 on ttys000
(base) stesim@Stefans-MacBook-Pro ~ % jupyter troubleshoot
$PATH:
    /opt/anaconda3/bin
    /opt/anaconda3/condabin
    /usr/local/bin
    /System/Cryptexes/App/usr/bin
    /usr/bin
    /bin
    /usr/sbin
    /sbin
    /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin
    /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin
    /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
    /Users/stesim/Applications/quarto/bin
    /Users/stesim/Library/Application Support/JetBrains/Toolbox/scripts

sys.path:
    /opt/anaconda3/bin
    /opt/anaconda3/lib/python311.zip
    /opt/anaconda3/lib/python3.11
    /opt/anaconda3/lib/python3.11/lib-dynload
    /opt/anaconda3/lib/python3.11/site-packages
    /opt/anaconda3/lib/python3.11/site-packages/aeosa

sys.executable:
    /opt/anaconda3/bin/python

sys.version:
    3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:49:36) [Clang 16.0.6 ]

platform.platform():
    macOS-14.5-arm64-arm-64bit

which -a jupyter:
    /opt/anaconda3/bin/jupyter

pip list:
    Package                           Version
    --------------------------------- ------------
    aiobotocore                       2.7.0
    aiohttp                           3.9.3
    aioitertools                      0.7.1
    aiosignal                         1.2.0
    alabaster                         0.7.12
    altair                            5.0.1
    anaconda-anon-usage               0.4.3
    anaconda-catalogs                 0.2.0
    anaconda-client                   1.12.3
    anaconda-cloud-auth               0.1.4
    anaconda-navigator                2.5.3
    anaconda-project                  0.11.1
    anyio                             4.2.0
    appdirs                           1.4.4
    applaunchservices                 0.3.0
    appnope                           0.1.2
    appscript                         1.1.2
    archspec                          0.2.1
    argon2-cffi                       21.3.0
    argon2-cffi-bindings              21.2.0
    arrow                             1.2.3
    astroid                           2.14.2
    astropy                           5.3.4
    asttokens                         2.0.5
    async-lru                         2.0.4
    atomicwrites                      1.4.0
    attrs                             23.1.0
    Automat                           20.2.0
    autopep8                          1.6.0
    Babel                             2.11.0
    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                             23.11.0
    bleach                            4.1.0
    blinker                           1.6.2
    bokeh                             3.3.4
    boltons                           23.0.0
    botocore                          1.31.64
    Bottleneck                        1.3.7
    Brotli                            1.0.9
    cachetools                        4.2.2
    certifi                           2024.2.2
    cffi                              1.16.0
    chardet                           4.0.0
    charset-normalizer                2.0.4
    click                             8.1.7
    cloudpickle                       2.2.1
    clyent                            1.2.2
    colorama                          0.4.6
    colorcet                          3.0.1
    comm                              0.1.2
    conda                             24.1.2
    conda-build                       24.1.2
    conda-content-trust               0.2.0
    conda_index                       0.4.0
    conda-libmamba-solver             24.1.0
    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                        23.10.4
    contourpy                         1.2.0
    cookiecutter                      2.5.0
    cryptography                      42.0.2
    cssselect                         1.2.0
    cycler                            0.11.0
    cytoolz                           0.12.2
    dask                              2023.11.0
    datashader                        0.16.0
    debugpy                           1.6.7
    decorator                         5.1.1
    defusedxml                        0.7.1
    diff-match-patch                  20200713
    dill                              0.3.7
    distributed                       2023.11.0
    distro                            1.8.0
    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                          3.13.1
    flake8                            6.0.0
    Flask                             2.2.5
    fonttools                         4.25.0
    frozenlist                        1.4.0
    fsspec                            2023.10.0
    future                            0.18.3
    gensim                            4.3.0
    gitdb                             4.0.7
    GitPython                         3.1.37
    gmpy2                             2.1.2
    greenlet                          3.0.1
    h11                               0.14.0
    h2                                4.1.0
    h5py                              3.9.0
    HeapDict                          1.0.1
    holoviews                         1.18.3
    hpack                             4.0.0
    httpcore                          1.0.5
    httpx                             0.27.0
    hvplot                            0.9.2
    hyperframe                        6.0.1
    hyperlink                         21.0.0
    idna                              3.4
    imagecodecs                       2023.1.23
    imageio                           2.33.1
    imagesize                         1.4.1
    imbalanced-learn                  0.11.0
    importlib-metadata                7.0.1
    importlib_resources               6.4.0
    incremental                       22.10.0
    inflection                        0.5.1
    iniconfig                         1.1.1
    intake                            0.6.8
    intervaltree                      3.1.0
    ipykernel                         6.28.0
    ipython                           8.20.0
    ipython-genutils                  0.2.0
    ipywidgets                        7.6.5
    isort                             5.9.3
    itemadapter                       0.3.0
    itemloaders                       1.1.0
    itsdangerous                      2.0.1
    jaraco.classes                    3.2.1
    jedi                              0.18.1
    jellyfish                         1.0.1
    Jinja2                            3.1.3
    jmespath                          1.0.1
    joblib                            1.2.0
    json5                             0.9.6
    jsonpatch                         1.32
    jsonpointer                       2.1
    jsonschema                        4.19.2
    jsonschema-specifications         2023.7.1
    jupyter                           1.0.0
    jupyter_client                    8.6.0
    jupyter-console                   6.6.3
    jupyter_core                      5.5.0
    jupyter-events                    0.8.0
    jupyter-lsp                       2.2.0
    jupyter_server                    2.10.0
    jupyter_server_terminals          0.4.4
    jupyterlab                        4.2.0
    jupyterlab-pygments               0.1.2
    jupyterlab-quarto                 0.3.3
    jupyterlab_server                 2.27.1
    jupyterlab-widgets                3.0.9
    kaleido                           0.2.1
    keyring                           23.13.1
    kiwisolver                        1.4.4
    lazy_loader                       0.3
    lazy-object-proxy                 1.6.0
    lckr_jupyterlab_variableinspector 3.1.0
    libarchive-c                      2.9
    libmambapy                        1.5.6
    linkify-it-py                     2.0.0
    llvmlite                          0.42.0
    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                        2.1.3
    matplotlib                        3.8.0
    matplotlib-inline                 0.1.6
    mccabe                            0.7.0
    mdit-py-plugins                   0.3.0
    mdurl                             0.1.0
    menuinst                          2.0.2
    mistune                           2.0.4
    more-itertools                    10.1.0
    mpmath                            1.3.0
    msgpack                           1.0.3
    multidict                         6.0.4
    multipledispatch                  0.6.0
    munkres                           1.1.4
    mypy                              1.8.0
    mypy-extensions                   1.0.0
    navigator-updater                 0.4.0
    nbclient                          0.8.0
    nbconvert                         7.10.0
    nbformat                          5.9.2
    nest-asyncio                      1.6.0
    networkx                          3.1
    nltk                              3.8.1
    notebook                          7.2.0
    notebook_shim                     0.2.3
    numba                             0.59.0
    numexpr                           2.8.7
    numpy                             1.26.4
    numpydoc                          1.5.0
    openpyxl                          3.0.10
    overrides                         7.4.0
    packaging                         23.1
    pandas                            2.1.4
    pandocfilters                     1.5.0
    panel                             1.3.8
    param                             2.0.2
    parsel                            1.8.1
    parso                             0.8.3
    partd                             1.4.1
    pathlib                           1.0.1
    pathspec                          0.10.3
    patsy                             0.5.3
    pexpect                           4.8.0
    pickleshare                       0.7.5
    pillow                            10.2.0
    pip                               23.3.1
    pkce                              1.0.3
    pkginfo                           1.9.6
    platformdirs                      3.10.0
    plotly                            5.9.0
    pluggy                            1.0.0
    ply                               3.11
    prometheus-client                 0.14.1
    prompt-toolkit                    3.0.43
    Protego                           0.1.16
    protobuf                          3.20.3
    psutil                            5.9.0
    ptyprocess                        0.7.0
    pure-eval                         0.2.2
    py-cpuinfo                        9.0.0
    pyarrow                           14.0.2
    pyasn1                            0.4.8
    pyasn1-modules                    0.2.8
    pycodestyle                       2.10.0
    pycosat                           0.6.6
    pycparser                         2.21
    pyct                              0.5.0
    pycurl                            7.45.2
    pydantic                          1.10.12
    pydeck                            0.8.0
    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
    pyobjc-core                       9.0
    pyobjc-framework-Cocoa            9.0
    pyobjc-framework-CoreServices     9.0
    pyobjc-framework-FSEvents         9.0
    pyodbc                            5.0.1
    pyOpenSSL                         24.0.0
    pyparsing                         3.0.9
    PyQt5                             5.15.10
    PyQt5-sip                         12.13.0
    PyQtWebEngine                     5.15.6
    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-pptx                       0.6.23
    python-slugify                    5.0.2
    python-snappy                     0.6.1
    pytoolconfig                      1.2.6
    pytz                              2023.3.post1
    pyviz_comms                       3.0.0
    pywavelets                        1.5.0
    PyYAML                            6.0.1
    pyzmq                             25.1.2
    QDarkStyle                        3.0.2
    qstylizer                         0.2.2
    QtAwesome                         1.2.2
    qtconsole                         5.4.2
    QtPy                              2.4.1
    queuelib                          1.6.2
    referencing                       0.30.2
    regex                             2023.10.3
    requests                          2.31.0
    requests-file                     1.5.1
    requests-toolbelt                 1.0.0
    rfc3339-validator                 0.1.4
    rfc3986-validator                 0.1.1
    rich                              13.3.5
    rope                              1.7.0
    rpds-py                           0.10.6
    Rtree                             1.0.1
    ruamel.yaml                       0.17.21
    ruamel-yaml-conda                 0.17.21
    s3fs                              2023.10.0
    scikit-image                      0.22.0
    scikit-learn                      1.2.2
    scipy                             1.11.4
    Scrapy                            2.8.0
    seaborn                           0.12.2
    semver                            2.13.0
    Send2Trash                        1.8.2
    service-identity                  18.1.0
    setuptools                        68.2.2
    sip                               6.7.12
    six                               1.16.0
    smart-open                        5.2.1
    smmap                             4.0.0
    sniffio                           1.3.0
    snowballstemmer                   2.2.0
    sortedcontainers                  2.4.0
    soupsieve                         2.5
    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                        2.0.25
    stack-data                        0.2.0
    statsmodels                       0.14.0
    streamlit                         1.30.0
    sympy                             1.12
    tables                            3.9.2
    tabulate                          0.9.0
    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
    toml                              0.10.2
    tomli                             2.0.1
    tomlkit                           0.11.1
    toolz                             0.12.0
    tornado                           6.3.3
    tqdm                              4.65.0
    traitlets                         5.7.1
    truststore                        0.8.0
    Twisted                           23.10.0
    typing_extensions                 4.9.0
    tzdata                            2023.3
    tzlocal                           2.1
    uc-micro-py                       1.0.1
    ujson                             5.4.0
    Unidecode                         1.2.0
    urllib3                           2.0.7
    validators                        0.18.2
    w3lib                             2.1.2
    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                             0.41.2
    widgetsnbextension                3.5.2
    wrapt                             1.14.1
    wurlitzer                         3.0.2
    xarray                            2023.6.0
    XlsxWriter                        3.2.0
    xlwings                           0.29.1
    xyzservices                       2022.9.0
    yapf                              0.31.0
    yarl                              1.9.3
    zict                              3.0.0
    zipp                              3.17.0
    zope.interface                    5.4.0
    zstandard                         0.19.0

conda list:
    # packages in environment at /opt/anaconda3:
    #
    # Name                    Version                   Build  Channel
    _anaconda_depends         2024.02         py311_openblas_1  
    abseil-cpp                20230802.0           h313beb8_2  
    aiobotocore               2.7.0           py311hca03da5_0  
    aiohttp                   3.9.3           py311h80987f9_0  
    aioitertools              0.7.1              pyhd3eb1b0_0  
    aiosignal                 1.2.0              pyhd3eb1b0_0  
    alabaster                 0.7.12             pyhd3eb1b0_0  
    altair                    5.0.1           py311hca03da5_0  
    anaconda-anon-usage       0.4.3           py311hd6b623d_100  
    anaconda-catalogs         0.2.0           py311hca03da5_0  
    anaconda-client           1.12.3          py311hca03da5_0  
    anaconda-cloud-auth       0.1.4           py311hca03da5_0  
    anaconda-navigator        2.5.3           py311hca03da5_0  
    anaconda-project          0.11.1          py311hca03da5_0  
    anyio                     4.2.0           py311hca03da5_0  
    aom                       3.6.0                h313beb8_0  
    appdirs                   1.4.4              pyhd3eb1b0_0  
    applaunchservices         0.3.0           py311hca03da5_0  
    appnope                   0.1.2           py311hca03da5_1001  
    appscript                 1.1.2           py311h80987f9_0  
    archspec                  0.2.1              pyhd3eb1b0_0  
    argon2-cffi               21.3.0             pyhd3eb1b0_0  
    argon2-cffi-bindings      21.2.0          py311h80987f9_0  
    arrow                     1.2.3           py311hca03da5_1  
    arrow-cpp                 14.0.2               hc7aafb3_1  
    astroid                   2.14.2          py311hca03da5_0  
    astropy                   5.3.4           py311hb9f6ed7_0  
    asttokens                 2.0.5              pyhd3eb1b0_0  
    async-lru                 2.0.4           py311hca03da5_0  
    atomicwrites              1.4.0                      py_0  
    attrs                     23.1.0          py311hca03da5_0  
    automat                   20.2.0                     py_0  
    autopep8                  1.6.0              pyhd3eb1b0_1  
    aws-c-auth                0.6.19               h80987f9_0  
    aws-c-cal                 0.5.20               h80987f9_0  
    aws-c-common              0.8.5                h80987f9_0  
    aws-c-compression         0.2.16               h80987f9_0  
    aws-c-event-stream        0.2.15               h313beb8_0  
    aws-c-http                0.6.25               h80987f9_0  
    aws-c-io                  0.13.10              h80987f9_0  
    aws-c-mqtt                0.7.13               h80987f9_0  
    aws-c-s3                  0.1.51               h80987f9_0  
    aws-c-sdkutils            0.1.6                h80987f9_0  
    aws-checksums             0.1.13               h80987f9_0  
    aws-crt-cpp               0.18.16              h313beb8_0  
    aws-sdk-cpp               1.10.55              h313beb8_0  
    babel                     2.11.0          py311hca03da5_0  
    backports                 1.1                pyhd3eb1b0_0  
    backports.functools_lru_cache 1.6.4              pyhd3eb1b0_0  
    backports.tempfile        1.0                pyhd3eb1b0_1  
    backports.weakref         1.0.post1                  py_1  
    bcrypt                    3.2.0           py311h80987f9_1  
    beautifulsoup4            4.12.2          py311hca03da5_0  
    binaryornot               0.4.4              pyhd3eb1b0_1  
    black                     23.11.0         py311hca03da5_0  
    blas                      1.0                    openblas  
    bleach                    4.1.0              pyhd3eb1b0_0  
    blinker                   1.6.2           py311hca03da5_0  
    blosc                     1.21.3               h313beb8_0  
    bokeh                     3.3.4           py311hb6e6a13_0  
    boltons                   23.0.0          py311hca03da5_0  
    boost-cpp                 1.82.0               h48ca7d4_2  
    botocore                  1.31.64         py311hca03da5_0  
    bottleneck                1.3.7           py311hb9f6ed7_0  
    brotli                    1.0.9                h1a28f6b_7  
    brotli-bin                1.0.9                h1a28f6b_7  
    brotli-python             1.0.9           py311h313beb8_7  
    brunsli                   0.1                  hc377ac9_1  
    bzip2                     1.0.8                h620ffc9_4  
    c-ares                    1.19.1               h80987f9_0  
    c-blosc2                  2.12.0               h7df6c2f_0  
    ca-certificates           2024.2.2             hf0a4a13_0    conda-forge
    cachetools                4.2.2              pyhd3eb1b0_0  
    cctools                   949.0.1             hc179dcd_25  
    cctools_osx-arm64         949.0.1             h332cad3_25  
    certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
    cffi                      1.16.0          py311h80987f9_0  
    cfitsio                   3.470                h7f6438f_7  
    chardet                   4.0.0           py311hca03da5_1003  
    charls                    2.2.0                hc377ac9_0  
    charset-normalizer        2.0.4              pyhd3eb1b0_0  
    click                     8.1.7           py311hca03da5_0  
    cloudpickle               2.2.1           py311hca03da5_0  
    clyent                    1.2.2           py311hca03da5_1  
    colorama                  0.4.6           py311hca03da5_0  
    colorcet                  3.0.1           py311hca03da5_0  
    comm                      0.1.2           py311hca03da5_0  
    conda                     24.1.2          py311h267d04e_0    conda-forge
    conda-build               24.1.2          py311hca03da5_0  
    conda-content-trust       0.2.0           py311hca03da5_0  
    conda-index               0.4.0              pyhd3eb1b0_0  
    conda-libmamba-solver     24.1.0             pyhd3eb1b0_0  
    conda-pack                0.6.0              pyhd3eb1b0_0  
    conda-package-handling    2.2.0           py311hca03da5_0  
    conda-package-streaming   0.9.0           py311hca03da5_0  
    conda-repo-cli            1.0.75          py311hca03da5_0  
    conda-token               0.4.0              pyhd3eb1b0_0  
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    jpeg                      9e                   h80987f9_1  
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    tapi                      1100.0.11            h8754e6a_1  
    tbb                       2021.8.0             h48ca7d4_0  
    tblib                     1.7.0              pyhd3eb1b0_0  
    tenacity                  8.2.2           py311hca03da5_0  
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krassowski commented 4 months ago

Do you have jupyterlab-myst or jupyterlab-markup extension installed? Or mathjax2 or katex renderer?

Works for me in 4.2.2:

image

JasonWeill commented 4 months ago

I think the issue that results in @krassowski 's screen shot above is that the $ character is being interpreted as the start of a LaTeX expression. If I escape that to \$, I see the entire markdown table, including the empty row. I'm running JupyterLab 4.3.0 alpha (tip of main) without the jupyterlab-myst or katex extension.

Do you still see the blank cell behavior if you escape all instances of the $ character in your markdown table source?

stefansimik commented 4 months ago

I think the issue that results in @krassowski 's screen shot above is that the $ character is being interpreted as the start of a LaTeX expression. If I escape that to \$, I see the entire markdown table, including the empty row. I'm running JupyterLab 4.3.0 alpha (tip of main) without the jupyterlab-myst or katex extension.

Do you still see the blank cell behavior if you escape all instances of the $ character in your markdown table source?

Hi Jason, the bug is still there - even without $ characters.

I tested on table like this:

| Number | Variable | Description |
|--------|----------|-------------|
| 1      | CRIM     | asdf |
| 2      | ZN       | asdf |
| 3      | INDUS    | asdf |
| 4      | CHAS     | asdf |
|        |          |      |
| Target | MEDV     | adsf |

The rendered table was like the buggy empty one.

stefansimik commented 4 months ago

Do you have jupyterlab-myst or jupyterlab-markup extension installed? Or mathjax2 or katex renderer?

Works for me in 4.2.2:

No of mentioned extensions installed.

This is reality:

CleanShot 2024-07-16 at 20 44 11@2x

I will try to uninstall the jupyterlab-quarto, I see there is potential, this one could cause the problem.

stefansimik commented 4 months ago

Yes, disabling jupyterlab-quarto plugin solved the problem.

CleanShot 2024-07-16 at 20 48 52@2x

Thank you for helping to solve the problem guys.

I will report this bug to the mentioned plugin.

stefansimik commented 4 months ago

Reported to the right place, and closing the issue.

https://github.com/quarto-dev/jupyterlab-quarto/issues/10