Progress bars in Cobra are printed as text

[sandervh14]

Bug Report

Bug: Progress bars in Cobra are printed as text.

Description

When running Cobra methods in a Jupyter Lab notebook, Cobra's progress bars appear as text.

Steps to Reproduce

Run Cobra's main library functions from within a Jupyter Lab notebook.

Expected Result

An HTML progress bar should appear, indicating progress during execution of Cobra's functionality.

Actual Results

Cobra's progress bars appear as follows:

HBox(children=(HTML(value='Computing discretization bins...'), FloatProgress(value=0.0, max=12.0), HTML(value=…

Possible help in solving the issue

tqdm/tqdm#645

[sandervh14]

I'm adding this issue to our current milestone: on our third evaluation use case at our client, Cobra takes minutes on end per substep of fit() and transform() of the preprocessor.
It's annoying to not be able to track progress without adding prints in the for loops of Cobra's development branch code.

[hendrikdewinter8]

Here are the version of packages that work for me!

alabaster @ file:///home/ktietz/src/ci/alabaster_1611921544520/work
anaconda-client==1.7.2
anaconda-navigator==2.0.3
anaconda-project @ file:///tmp/build/80754af9/anaconda-project_1610472525955/work
anyio @ file:///C:/ci/anyio_1620153418380/work/dist
appdirs==1.4.4
argh==0.26.2
argon2-cffi @ file:///C:/ci/argon2-cffi_1613037959010/work
asn1crypto @ file:///tmp/build/80754af9/asn1crypto_1596577642040/work
astroid @ file:///C:/ci/astroid_1613501047216/work
astropy @ file:///C:/ci/astropy_1617745647203/work
async-generator @ file:///home/ktietz/src/ci/async_generator_1611927993394/work
atomicwrites==1.4.0
attrs @ file:///tmp/build/80754af9/attrs_1604765588209/work
autopep8 @ file:///tmp/build/80754af9/autopep8_1615918855173/work
Babel @ file:///tmp/build/80754af9/babel_1607110387436/work
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
backports.functools-lru-cache @ file:///tmp/build/80754af9/backports.functools_lru_cache_1618170165463/work
backports.shutil-get-terminal-size @ file:///tmp/build/80754af9/backports.shutil_get_terminal_size_1608222128777/work
backports.tempfile @ file:///home/linux1/recipes/ci/backports.tempfile_1610991236607/work
backports.weakref==1.0.post1
bcrypt @ file:///C:/ci/bcrypt_1597936263757/work
beautifulsoup4 @ file:///home/linux1/recipes/ci/beautifulsoup4_1610988766420/work
bitarray @ file:///C:/ci/bitarray_1618435038389/work
bkcharts==0.2
black==19.10b0
bleach @ file:///tmp/build/80754af9/bleach_1612211392645/work
bokeh @ file:///C:/ci/bokeh_1620784067744/work
boto==2.49.0
Bottleneck==1.3.2
brotlipy==0.7.0
certifi==2020.12.5
cffi @ file:///C:/ci/cffi_1613247279197/work
chardet @ file:///C:/ci/chardet_1607690654534/work
click @ file:///home/linux1/recipes/ci/click_1610990599742/work
cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1598884132938/work
clyent==1.2.2
colorama @ file:///tmp/build/80754af9/colorama_1607707115595/work
comtypes==1.1.9
conda==4.10.1
conda-build==3.21.4
conda-content-trust @ file:///tmp/build/80754af9/conda-content-trust_1617045594566/work
conda-package-handling @ file:///C:/ci/conda-package-handling_1618262320430/work
conda-repo-cli @ file:///tmp/build/80754af9/conda-repo-cli_1620168426516/work
conda-token @ file:///tmp/build/80754af9/conda-token_1620076980546/work
conda-verify==3.4.2
contextlib2==0.6.0.post1
cryptography @ file:///C:/ci/cryptography_1616769344312/work
cycler==0.10.0
Cython @ file:///C:/ci/cython_1618435363327/work
cytoolz==0.11.0
dask @ file:///tmp/build/80754af9/dask-core_1617390489108/work
decorator @ file:///tmp/build/80754af9/decorator_1617916966915/work
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
diff-match-patch @ file:///tmp/build/80754af9/diff-match-patch_1594828741838/work
distributed @ file:///C:/ci/distributed_1617384289923/work
docutils @ file:///C:/ci/docutils_1617481617511/work
entrypoints==0.3
et-xmlfile==1.0.1
fastcache==1.1.0
filelock @ file:///home/linux1/recipes/ci/filelock_1610993975404/work
flake8 @ file:///tmp/build/80754af9/flake8_1615834841867/work
Flask @ file:///home/ktietz/src/ci/flask_1611932660458/work
fsspec @ file:///tmp/build/80754af9/fsspec_1617959894824/work
future==0.18.2
gevent @ file:///C:/ci/gevent_1616773090559/work
glob2 @ file:///home/linux1/recipes/ci/glob2_1610991677669/work
greenlet @ file:///C:/ci/greenlet_1611958565931/work
h5py==2.10.0
HeapDict==1.0.1
html5lib @ file:///tmp/build/80754af9/html5lib_1593446221756/work
idna @ file:///home/linux1/recipes/ci/idna_1610986105248/work
imagecodecs @ file:///C:/ci/imagecodecs_1617996768495/work
imageio @ file:///tmp/build/80754af9/imageio_1617700267927/work
imagesize @ file:///home/ktietz/src/ci/imagesize_1611921604382/work
importlib-metadata @ file:///C:/ci/importlib-metadata_1617877484576/work
iniconfig @ file:///home/linux1/recipes/ci/iniconfig_1610983019677/work
intervaltree @ file:///tmp/build/80754af9/intervaltree_1598376443606/work
ipykernel @ file:///C:/ci/ipykernel_1596190155316/work/dist/ipykernel-5.3.4-py3-none-any.whl
ipython @ file:///C:/ci/ipython_1617121002983/work
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
ipywidgets @ file:///tmp/build/80754af9/ipywidgets_1610481889018/work
isort @ file:///tmp/build/80754af9/isort_1616355431277/work
itsdangerous @ file:///home/ktietz/src/ci/itsdangerous_1611932585308/work
jdcal==1.4.1
jedi @ file:///C:/ci/jedi_1606914528444/work
Jinja2 @ file:///tmp/build/80754af9/jinja2_1612213139570/work
joblib @ file:///tmp/build/80754af9/joblib_1613502643832/work
json5==0.9.5
jsonschema @ file:///tmp/build/80754af9/jsonschema_1602607155483/work
jupyter==1.0.0
jupyter-client @ file:///tmp/build/80754af9/jupyter_client_1616770841739/work
jupyter-console @ file:///tmp/build/80754af9/jupyter_console_1616615302928/work
jupyter-core @ file:///C:/ci/jupyter_core_1612213356021/work
jupyter-packaging @ file:///tmp/build/80754af9/jupyter-packaging_1613502826984/work
jupyter-server @ file:///C:/ci/jupyter_server_1616084298403/work
jupyterlab @ file:///tmp/build/80754af9/jupyterlab_1619133235951/work
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
jupyterlab-server @ file:///tmp/build/80754af9/jupyterlab_server_1617134334258/work
jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work
keyring @ file:///C:/ci/keyring_1614616910860/work
kiwisolver @ file:///C:/ci/kiwisolver_1612282606037/work
lazy-object-proxy @ file:///C:/ci/lazy-object-proxy_1616529307648/work
libarchive-c @ file:///tmp/build/80754af9/python-libarchive-c_1617780486945/work
llvmlite==0.36.0
locket==0.2.1
lxml @ file:///C:/ci/lxml_1616443455957/work
MarkupSafe==1.1.1
matplotlib @ file:///C:/ci/matplotlib-suite_1613408055530/work
mccabe==0.6.1
menuinst==1.4.16
mistune==0.8.4
mkl-fft==1.3.0
mkl-random @ file:///C:/ci/mkl_random_1618854156666/work
mkl-service==2.3.0
mock @ file:///tmp/build/80754af9/mock_1607622725907/work
more-itertools @ file:///tmp/build/80754af9/more-itertools_1613676688952/work
mpmath==1.2.1
msgpack @ file:///C:/ci/msgpack-python_1612287368835/work
multipledispatch==0.6.0
mypy-extensions==0.4.3
navigator-updater==0.2.1
nbclassic @ file:///tmp/build/80754af9/nbclassic_1616085367084/work
nbclient @ file:///tmp/build/80754af9/nbclient_1614364831625/work
nbconvert @ file:///C:/ci/nbconvert_1601914925608/work
nbformat @ file:///tmp/build/80754af9/nbformat_1617383369282/work
nest-asyncio @ file:///tmp/build/80754af9/nest-asyncio_1613680548246/work
networkx @ file:///tmp/build/80754af9/networkx_1598376031484/work
nltk @ file:///tmp/build/80754af9/nltk_1618327084230/work
nose @ file:///tmp/build/80754af9/nose_1606773131901/work
notebook @ file:///C:/ci/notebook_1616443715883/work
numba @ file:///C:/ci/numba_1616774458845/work
numexpr @ file:///C:/ci/numexpr_1618856738664/work
numpy @ file:///C:/ci/numpy_and_numpy_base_1618497418457/work
numpydoc @ file:///tmp/build/80754af9/numpydoc_1605117425582/work
olefile==0.46
openpyxl @ file:///tmp/build/80754af9/openpyxl_1615411699337/work
packaging @ file:///tmp/build/80754af9/packaging_1611952188834/work
pandas @ file:///C:/ci/pandas_1618365634936/work
pandocfilters @ file:///C:/ci/pandocfilters_1605102497129/work
paramiko @ file:///tmp/build/80754af9/paramiko_1598886428689/work
parso==0.7.0
partd @ file:///tmp/build/80754af9/partd_1618000087440/work
path @ file:///C:/ci/path_1614022440181/work
pathlib2 @ file:///C:/ci/pathlib2_1607025069150/work
pathspec==0.7.0
patsy==0.5.1
pep8==1.7.1
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow @ file:///C:/ci/pillow_1617386341487/work
pkginfo==1.7.0
pluggy @ file:///C:/ci/pluggy_1615976358795/work
ply==3.11
prometheus-client @ file:///tmp/build/80754af9/prometheus_client_1618088486455/work
prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1616415428029/work
psutil @ file:///C:/ci/psutil_1612298324802/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
py @ file:///tmp/build/80754af9/py_1607971587848/work
pycodestyle @ file:///home/ktietz/src/ci_mi/pycodestyle_1612807597675/work
pycosat==0.6.3
pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
pycurl==7.43.0.6
pydocstyle @ file:///tmp/build/80754af9/pydocstyle_1616182067796/work
pyerfa @ file:///C:/ci/pyerfa_1619391071834/work
pyflakes @ file:///home/ktietz/src/ci_ipy2/pyflakes_1612551159640/work
Pygments @ file:///tmp/build/80754af9/pygments_1615143339740/work
pylint @ file:///C:/ci/pylint_1617136058775/work
pyls-black @ file:///tmp/build/80754af9/pyls-black_1607553132291/work
pyls-spyder @ file:///tmp/build/80754af9/pyls-spyder_1613849700860/work
PyNaCl @ file:///C:/ci/pynacl_1595000047588/work
pyodbc===4.0.0-unsupported
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1608057966937/work
pyparsing @ file:///home/linux1/recipes/ci/pyparsing_1610983426697/work
pyreadline==2.1
pyrsistent @ file:///C:/ci/pyrsistent_1600141795814/work
PySocks @ file:///C:/ci/pysocks_1605287845585/work
pytest==6.2.3
python-dateutil @ file:///home/ktietz/src/ci/python-dateutil_1611928101742/work
python-jsonrpc-server @ file:///tmp/build/80754af9/python-jsonrpc-server_1600278539111/work
python-language-server @ file:///tmp/build/80754af9/python-language-server_1607972495879/work
pytz @ file:///tmp/build/80754af9/pytz_1612215392582/work
PyWavelets @ file:///C:/ci/pywavelets_1601658407916/work
pywin32==227
pywin32-ctypes==0.2.0
pywinpty==0.5.7
PyYAML==5.4.1
pyzmq==20.0.0
QDarkStyle==2.8.1
QtAwesome @ file:///tmp/build/80754af9/qtawesome_1615991616277/work
qtconsole @ file:///tmp/build/80754af9/qtconsole_1616775094278/work
QtPy==1.9.0
regex @ file:///C:/ci/regex_1617569893741/work
requests @ file:///tmp/build/80754af9/requests_1608241421344/work
rope @ file:///tmp/build/80754af9/rope_1602264064449/work
Rtree @ file:///C:/ci/rtree_1618421009405/work
ruamel-yaml-conda @ file:///C:/ci/ruamel_yaml_1616016967756/work
scikit-image==0.18.1
scikit-learn @ file:///C:/ci/scikit-learn_1614446896245/work
scipy @ file:///C:/ci/scipy_1618856128765/work
seaborn @ file:///tmp/build/80754af9/seaborn_1608578541026/work
Send2Trash @ file:///tmp/build/80754af9/send2trash_1607525499227/work
simplegeneric==0.8.1
singledispatch @ file:///tmp/build/80754af9/singledispatch_1614366001199/work
sip==4.19.13
six @ file:///C:/ci/six_1605187374963/work
sniffio @ file:///C:/ci/sniffio_1614030707456/work
snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1611258885636/work
sortedcollections @ file:///tmp/build/80754af9/sortedcollections_1611172717284/work
sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1606865132123/work
soupsieve @ file:///tmp/build/80754af9/soupsieve_1616183228191/work
Sphinx @ file:///tmp/build/80754af9/sphinx_1620777493457/work
sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work
sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work
sphinxcontrib-htmlhelp @ file:///home/ktietz/src/ci/sphinxcontrib-htmlhelp_1611920974801/work
sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work
sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work
sphinxcontrib-serializinghtml @ file:///home/ktietz/src/ci/sphinxcontrib-serializinghtml_1611920755253/work
sphinxcontrib-websupport @ file:///tmp/build/80754af9/sphinxcontrib-websupport_1597081412696/work
spyder @ file:///C:/ci/spyder_1616776239898/work
spyder-kernels @ file:///C:/ci/spyder-kernels_1614030842607/work
SQLAlchemy @ file:///C:/ci/sqlalchemy_1618090063261/work
statsmodels==0.12.2
sympy @ file:///C:/ci/sympy_1618255511605/work
tables==3.6.1
tblib @ file:///tmp/build/80754af9/tblib_1597928476713/work
terminado==0.9.4
testpath @ file:///home/ktietz/src/ci/testpath_1611930608132/work
textdistance @ file:///tmp/build/80754af9/textdistance_1612461398012/work
threadpoolctl @ file:///tmp/tmp9twdgx9k/threadpoolctl-2.1.0-py3-none-any.whl
three-merge @ file:///tmp/build/80754af9/three-merge_1607553261110/work
tifffile @ file:///tmp/build/80754af9/tifffile_1619636090847/work
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
toolz @ file:///home/linux1/recipes/ci/toolz_1610987900194/work
tornado @ file:///C:/ci/tornado_1606942392901/work
tqdm @ file:///tmp/build/80754af9/tqdm_1615925068909/work
traitlets @ file:///home/ktietz/src/ci/traitlets_1611929699868/work
typed-ast @ file:///C:/ci/typed-ast_1610466535590/work
typing-extensions @ file:///home/ktietz/src/ci_mi/typing_extensions_1612808209620/work
ujson @ file:///C:/ci/ujson_1611241570789/work
unicodecsv==0.14.1
urllib3 @ file:///tmp/build/80754af9/urllib3_1615837158687/work
watchdog @ file:///C:/ci/watchdog_1612471251191/work
wcwidth @ file:///tmp/build/80754af9/wcwidth_1593447189090/work
webencodings==0.5.1
Werkzeug @ file:///home/ktietz/src/ci/werkzeug_1611932622770/work
widgetsnbextension==3.5.1
win-inet-pton @ file:///C:/ci/win_inet_pton_1605306167264/work
win-unicode-console==0.5
wincertstore==0.2
wrapt==1.12.1
xlrd @ file:///tmp/build/80754af9/xlrd_1608072521494/work
XlsxWriter @ file:///tmp/build/80754af9/xlsxwriter_1617224712951/work
xlwings==0.23.0
xlwt==1.3.0
xmltodict==0.12.0
yapf @ file:///tmp/build/80754af9/yapf_1615749224965/work
zict==2.0.0
zipp @ file:///tmp/build/80754af9/zipp_1615904174917/work
zope.event==4.5.0
zope.interface @ file:///C:/ci/zope.interface_1616357322857/work

[hendrikdewinter8]

AND installed with conda

packages in environment at C:\Users\hendrik.dewinter\Anaconda3:

Name Version Build Channel

_ipyw_jlab_nb_ext_conf 0.1.0 py38_0
alabaster 0.7.12 pyhd3eb1b0_0
anaconda 2021.05 py38_0
anaconda-client 1.7.2 py38_0
anaconda-navigator 2.0.3 py38_0
anaconda-project 0.9.1 pyhd3eb1b0_1
anyio 2.2.0 py38haa95532_2
appdirs 1.4.4 py_0
argh 0.26.2 py38_0
argon2-cffi 20.1.0 py38h2bbff1b_1
asn1crypto 1.4.0 py_0
astroid 2.5 py38haa95532_1
astropy 4.2.1 py38h2bbff1b_1
async_generator 1.10 pyhd3eb1b0_0
atomicwrites 1.4.0 py_0
attrs 20.3.0 pyhd3eb1b0_0
autopep8 1.5.6 pyhd3eb1b0_0
babel 2.9.0 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
backports 1.0 pyhd3eb1b0_2
backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0
backports.shutil_get_terminal_size 1.0.0 pyhd3eb1b0_3
backports.tempfile 1.0 pyhd3eb1b0_1
backports.weakref 1.0.post1 py_1
bcrypt 3.2.0 py38he774522_0
beautifulsoup4 4.9.3 pyha847dfd_0
bitarray 1.9.2 py38h2bbff1b_1
bkcharts 0.2 py38_0
black 19.10b0 py_0
blas 1.0 mkl
bleach 3.3.0 pyhd3eb1b0_0
blosc 1.21.0 h19a0ad4_0
bokeh 2.3.2 py38haa95532_0
boto 2.49.0 py38_0
bottleneck 1.3.2 py38h2a96729_1
brotli 1.0.9 ha925a31_2
brotlipy 0.7.0 py38h2bbff1b_1003
bzip2 1.0.8 he774522_0
ca-certificates 2021.4.13 haa95532_1
certifi 2020.12.5 py38haa95532_0
cffi 1.14.5 py38hcd4344a_0
chardet 4.0.0 py38haa95532_1003
charls 2.2.0 h6c2663c_0
click 7.1.2 pyhd3eb1b0_0
cloudpickle 1.6.0 py_0
clyent 1.2.2 py38_1
colorama 0.4.4 pyhd3eb1b0_0
comtypes 1.1.9 py38haa95532_1002
conda 4.10.1 py38haa95532_1
conda-build 3.21.4 py38haa95532_0
conda-content-trust 0.1.1 pyhd3eb1b0_0
conda-env 2.6.0 1
conda-package-handling 1.7.3 py38h8cc25b3_1
conda-repo-cli 1.0.4 pyhd3eb1b0_0
conda-token 0.3.0 pyhd3eb1b0_0
conda-verify 3.4.2 py_1
console_shortcut 0.1.1 4
contextlib2 0.6.0.post1 py_0
cryptography 3.4.7 py38h71e12ea_0
curl 7.71.1 h2a8f88b_1
cycler 0.10.0 py38_0
cython 0.29.23 py38hd77b12b_0
cytoolz 0.11.0 py38he774522_0
dask 2021.4.0 pyhd3eb1b0_0
dask-core 2021.4.0 pyhd3eb1b0_0
decorator 5.0.6 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
diff-match-patch 20200713 py_0
distributed 2021.4.0 py38haa95532_0
docutils 0.17 py38haa95532_1
entrypoints 0.3 py38_0
et_xmlfile 1.0.1 py_1001
fastcache 1.1.0 py38he774522_0
filelock 3.0.12 pyhd3eb1b0_1
flake8 3.9.0 pyhd3eb1b0_0
flask 1.1.2 pyhd3eb1b0_0
freetype 2.10.4 hd328e21_0
fsspec 0.9.0 pyhd3eb1b0_0
future 0.18.2 py38_1
get_terminal_size 1.0.0 h38e98db_0
gevent 21.1.2 py38h2bbff1b_1
giflib 5.2.1 h62dcd97_0
glob2 0.7 pyhd3eb1b0_0
greenlet 1.0.0 py38hd77b12b_2
h5py 2.10.0 py38h5e291fa_0
hdf5 1.10.4 h7ebc959_0
heapdict 1.0.1 py_0
html5lib 1.1 py_0
icc_rt 2019.0.0 h0cc432a_1
icu 58.2 ha925a31_3
idna 2.10 pyhd3eb1b0_0
imagecodecs 2021.3.31 py38h5da4933_0
imageio 2.9.0 pyhd3eb1b0_0
imagesize 1.2.0 pyhd3eb1b0_0
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[sborms]

When testing in a Jupyter Notebook, it works for me as well. I have tqdm version 4.62.2. Maybe upgrading works.

I checked the issue you referenced, and some seem to refer to JupyterLab as the culprit. The fact that it works for Hendrik and me means that the implementation in our library is correct, so I suggest to close this issue.

[sandervh14]

For anyone later also having the issue of progress bars being printed as text: for me, the main solution was to update the jupyter lab environment I was using.

Details:
Before, when I ran jupyter lab from my command line, after having my conda environment activated (conda activate my-env), it must be that my notebook was actually using the jupyterlab package from elsewhere (my conda base environment or default python?), since when I ran conda update jupyterlab (still from the command line when my-env was activated), the result warned that the package jupyterlab was not installed on my-env.
So, after conda install jupyterlab and restarting Jupyter Lab, I've got the nice green progress bars now.

Sidenote
It may also be necessary to upgrade tqdm from 4.50.2 to at least version 4.62.2. I had tried this first before updating jupyterlab.
Before that, I had this type of progress bars:
HBox(children=(HTML(value='Discretizing columns...'), FloatProgress(value=0.0, max=12.0), HTML(value='')))
After that, I had this type of progress bars:
0%| | 0/100 [00:00<?, ?it/s]
(though still 0% after all 100 items, so no progress bar update)

[sandervh14]

By the way, from tests conducted on Databricks: tqdm works there as well. I was afraid tqdm would have been tied to jupyter only, but it works on Databricks.

[hendrikdewinter8]

@sandervh14, aha, okay!! Nice that you were able to find the cause.