neptune-ai / neptune-client

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BUG: Upload fails with Pandas DF #1192

Closed lmrios closed 1 year ago

lmrios commented 1 year ago

After running the train process for may model, I want to save a Pandas DataFrame with some metrics inside a method of the training class. It seems .upload() is not looking in the right path I am running GoogleColab, after the training cell crashed. I wrote the following code. Please see Option1 it is the closest to my code

run['MyProcess/training/demo_number']= 1
run['MyProcess/training/demo_dict']= {'Name': "Tom", 'Age': 20}
demo_data = {'Name': ['Tom', 'nick', 'krish', 'jack'], 'Age': [20, 21, 19, 18]}
demo_data_df = pd.DataFrame(demo_data)

#-# Option1 - does not work
#-# FileNotFoundError: [Errno 2] No such file or directory: '.neptune/async/run__98597299-1a56-477a-8b1e-6b7f740c4549/exec-1675099421.646683-2023-01-30_17.23.41.646683/upload_path/MyProcess_training_demo_df-1675099739.015558-2023-01-30_17.28.59.015558.html'
#-# !ls .neptune/async/
#-# shows only one directory run__9711c145-a969-49d5-b860-1f0631942d14
#run['MyProcess/training/demo_df'].upload(File.as_html(demo_data_df))

#-# Option2 - does not work
#demo_data_html = File.as_html(demo_data_df)
#run['MyProcess/training/demo_df'].upload(demo_data_html)

#-# Option3-  works :)  but I dont want to save it to disk
demo_data_df.to_csv("tmp.csv", sep=",", index=False)
run['MyProcess/training/demo_df'].upload("tmp.csv")

I managed to solve it but I dont want to save my DF to disk

Environment

The output of pip list:

Package                       Version
----------------------------- ----------------------
absl-py                       1.3.0
aeppl                         0.0.33
aesara                        2.7.9
aiohttp                       3.8.3
aiosignal                     1.3.1
alabaster                     0.7.12
albumentations                1.2.1
altair                        4.2.0
appdirs                       1.4.4
arrow                         1.2.3
arviz                         0.12.1
astor                         0.8.1
astropy                       4.3.1
astunparse                    1.6.3
async-timeout                 4.0.2
atari-py                      0.2.9
atomicwrites                  1.4.1
attrs                         22.2.0
audioread                     3.0.0
autograd                      1.5
Babel                         2.11.0
backcall                      0.2.0
beautifulsoup4                4.6.3
bleach                        5.0.1
blis                          0.7.9
bokeh                         2.3.3
boto3                         1.26.59
botocore                      1.29.59
branca                        0.6.0
bravado                       11.0.3
bravado-core                  5.17.1
bs4                           0.0.1
CacheControl                  0.12.11
cachetools                    5.2.1
catalogue                     2.0.8
certifi                       2022.12.7
cffi                          1.15.1
cftime                        1.6.2
chardet                       4.0.0
charset-normalizer            2.1.1
click                         7.1.2
clikit                        0.6.2
cloudpickle                   2.2.0
cmake                         3.22.6
cmdstanpy                     1.0.8
colorcet                      3.0.1
colorlover                    0.3.0
community                     1.0.0b1
confection                    0.0.3
cons                          0.4.5
contextlib2                   0.5.5
convertdate                   2.4.0
crashtest                     0.3.1
crcmod                        1.7
cufflinks                     0.17.3
cupy-cuda11x                  11.0.0
cvxopt                        1.3.0
cvxpy                         1.2.3
cycler                        0.11.0
cymem                         2.0.7
Cython                        0.29.33
daft                          0.0.4
dask                          2022.2.1
datascience                   0.17.5
db-dtypes                     1.0.5
dbus-python                   1.2.16
debugpy                       1.0.0
decorator                     4.4.2
defusedxml                    0.7.1
descartes                     1.1.0
dill                          0.3.6
distributed                   2022.2.1
dlib                          19.24.0
dm-tree                       0.1.8
dnspython                     2.2.1
docutils                      0.16
dopamine-rl                   1.0.5
earthengine-api               0.1.335
easydict                      1.10
ecos                          2.0.12
editdistance                  0.5.3
en-core-web-sm                3.4.1
entrypoints                   0.4
ephem                         4.1.4
et-xmlfile                    1.1.0
etils                         1.0.0
etuples                       0.3.8
fa2                           0.3.5
fastai                        2.7.10
fastcore                      1.5.27
fastdownload                  0.0.7
fastdtw                       0.3.4
fastjsonschema                2.16.2
fastprogress                  1.0.3
fastrlock                     0.8.1
feather-format                0.4.1
filelock                      3.9.0
firebase-admin                5.3.0
fix-yahoo-finance             0.0.22
Flask                         1.1.4
flatbuffers                   1.12
folium                        0.12.1.post1
fqdn                          1.5.1
frozenlist                    1.3.3
fsspec                        2022.11.0
future                        0.18.3
gast                          0.4.0
GDAL                          3.0.4
gdown                         4.4.0
gensim                        3.6.Warning: string series 'monitoring/stdout' value was longer than 1000 characters and was truncated. This warning is printed only once per series.
0
geographiclib                 1.52
geopy                         1.17.0
gin-config                    0.5.0
gitdb                         4.0.10
GitPython                     3.1.30
glob2                         0.7
google                        2.0.3
google-api-core               2.11.0
google-api-python-client      2.70.0
google-auth                   2.16.0
google-auth-httplib2          0.1.0
google-auth-oauthlib          0.4.6
google-cloud-bigquery         3.4.1
google-cloud-bigquery-storage 2.17.0
google-cloud-core             2.3.2
google-cloud-datastore        2.11.1
google-cloud-firestore        2.7.3
google-cloud-language         2.6.1
google-cloud-storage          2.7.0
google-cloud-translate        3.8.4
google-colab                  1.0.0
google-crc32c                 1.5.0
google-pasta                  0.2.0
google-resumable-media        2.4.0
googleapis-common-protos      1.58.0
googledrivedownloader         0.4
graphviz                      0.10.1
greenlet                      2.0.1
grpcio                        1.51.1
grpcio-status                 1.48.2
gspread                       3.4.2
gspread-dataframe             3.0.8
gym                           0.25.2
gym-notices                   0.0.8
h5py                          3.1.0
HeapDict                      1.0.1
hijri-converter               2.2.4
holidays                      0.18
holoviews                     1.14.9
html5lib                      1.0.1
httpimport                    0.5.18
httplib2                      0.17.4
httpstan                      4.6.1
humanize                      0.5.1
hyperopt                      0.1.2
idna                          2.10
imageio                       2.9.0
imagesize                     1.4.1
imbalanced-learn              0.8.1
imblearn                      0.0
imgaug                        0.4.0
importlib-metadata            6.0.0
importlib-resources           5.10.2
imutils                       0.5.4
inflect                       2.1.0
intel-openmp                  2023.0.0
intervaltree                  2.1.0
ipykernel                     5.3.4
ipython                       7.9.0
ipython-genutils              0.2.0
ipython-sql                   0.3.9
ipywidgets                    7.7.1
isoduration                   20.11.0
itsdangerous                  1.1.0
jax                           0.3.25
jaxlib                        0.3.25+cuda11.cudnn805
jieba                         0.42.1
Jinja2                        2.11.3
jmespath                      1.0.1
joblib                        1.2.0
jpeg4py                       0.1.4
jsonpointer                   2.3
jsonref                       1.1.0
jsonschema                    4.3.3
jupyter-client                6.1.12
jupyter-console               6.1.0
jupyter_core                  5.1.3
jupyterlab-widgets            3.0.5
kaggle                        1.5.12
kapre                         0.3.7
keras                         2.9.0
Keras-Preprocessing           1.1.2
keras-vis                     0.4.1
kiwisolver                    1.4.4
korean-lunar-calendar         0.3.1
langcodes                     3.3.0
libclang                      15.0.6.1
librosa                       0.8.1
lightgbm                      2.2.3
llvmlite                      0.39.1
lmdb                          0.99
locket                        1.0.0
logical-unification           0.4.5
LunarCalendar                 0.0.9
lxml                          4.9.2
Markdown                      3.4.1
MarkupSafe                    2.0.1
marshmallow                   3.19.0
matplotlib                    3.2.2
matplotlib-venn               0.11.7
miniKanren                    1.0.3
missingno                     0.5.1
mistune                       0.8.4
mizani                        0.7.3
mkl                           2019.0
mlxtend                       0.14.0
monotonic                     1.6
more-itertools                9.0.0
moviepy                       0.2.3.5
mpmath                        1.2.1
msgpack                       1.0.4
multidict                     6.0.4
multipledispatch              0.6.0
multitasking                  0.0.11
murmurhash                    1.0.9
music21                       5.5.0
natsort                       5.5.0
nbconvert                     5.6.1
nbformat                      5.7.1
neptune-client                0.16.16
netCDF4                       1.6.2
networkx                      3.0
nibabel                       3.0.2
nltk                          3.7
notebook                      5.7.16
numba                         0.56.4
numexpr                       2.8.4
numpy                         1.21.6
oauth2client                  4.1.3
oauthlib                      3.2.2
okgrade                       0.4.3
opencv-contrib-python         4.6.0.66
opencv-python                 4.6.0.66
opencv-python-headless        4.7.0.68
openpyxl                      3.0.10
opt-einsum                    3.3.0
osqp                          0.6.2.post0
packaging                     21.3
palettable                    3.3.0
pandas                        1.3.5
pandas-datareader             0.9.0
pandas-gbq                    0.17.9
pandas-profiling              1.4.1
pandocfilters                 1.5.0
panel                         0.12.1
param                         1.12.3
parso                         0.8.3
partd                         1.3.0
pastel                        0.2.1
pathlib                       1.0.1
pathy                         0.10.1
patsy                         0.5.3
pep517                        0.13.0
pexpect                       4.8.0
pickleshare                   0.7.5
Pillow                        7.1.2
pip                           22.0.4
pip-tools                     6.6.2
platformdirs                  2.6.2
plotly                        5.5.0
plotnine                      0.8.0
pluggy                        0.7.1
pooch                         1.6.0
portpicker                    1.3.9
prefetch-generator            1.0.3
preshed                       3.0.8
prettytable                   3.6.0
progressbar2                  3.38.0
prometheus-client             0.15.0
promise                       2.3
prompt-toolkit                2.0.10
prophet                       1.1.1
proto-plus                    1.22.2
protobuf                      3.19.6
psutil                        5.4.8
psycopg2                      2.9.5
ptyprocess                    0.7.0
py                            1.11.0
pyarrow                       9.0.0
pyasn1                        0.4.8
pyasn1-modules                0.2.8
pycocotools                   2.0.6
pycparser                     2.21
pyct                          0.4.8
pydantic                      1.10.4
pydata-google-auth            1.5.0
pydot                         1.3.0
pydot-ng                      2.0.0
pydotplus                     2.0.2
PyDrive                       1.3.1
pyemd                         0.5.1
pyerfa                        2.0.0.1
Pygments                      2.6.1
PyGObject                     3.36.0
PyJWT                         2.6.0
pylev                         1.4.0
pymc                          4.1.4
PyMeeus                       0.5.12
pymongo                       4.3.3
pymystem3                     0.2.0
PyOpenGL                      3.1.6
pyparsing                     3.0.9
pyrsistent                    0.19.3
pysimdjson                    3.2.0
PySocks                       1.7.1
pystan                        3.3.0
pytest                        3.6.4
python-apt                    2.0.1
python-dateutil               2.8.2
python-louvain                0.16
python-slugify                7.0.0
python-utils                  3.4.5
pytz                          2022.7
pyviz-comms                   2.2.1
PyWavelets                    1.4.1
PyYAML                        6.0
pyzmq                         23.2.1
qdldl                         0.1.5.post2
qudida                        0.0.4
regex                         2022.6.2
requests                      2.25.1
requests-oauthlib             1.3.1
requests-unixsocket           0.2.0
resampy                       0.4.2
rfc3339-validator             0.1.4
rfc3987                       1.3.8
rpy2                          3.5.5
rsa                           4.9
s3transfer                    0.6.0
scikit-image                  0.18.3
scikit-learn                  1.0.2
scipy                         1.7.3
screen-resolution-extra       0.0.0
scs                           3.2.2
seaborn                       0.11.2
Send2Trash                    1.8.0
setuptools                    57.4.0
setuptools-git                1.2
shapely                       2.0.0
simplejson                    3.18.1
six                           1.15.0
sklearn-pandas                1.8.0
smart-open                    6.3.0
smmap                         5.0.0
snowballstemmer               2.2.0
sortedcontainers              2.4.0
soundfile                     0.11.0
spacy                         3.4.4
spacy-legacy                  3.0.11
spacy-loggers                 1.0.4
Sphinx                        3.5.4
sphinxcontrib.applehelp       1.0.3
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
SQLAlchemy                    1.4.46
sqlparse                      0.4.3
srsly                         2.4.5
statsmodels                   0.12.2
swagger-spec-validator        3.0.3
sympy                         1.7.1
tables                        3.7.0
tabulate                      0.8.10
tblib                         1.7.0
tenacity                      8.1.0
tensorboard                   2.9.1
tensorboard-data-server       0.6.1
tensorboard-plugin-wit        1.8.1
tensorflow                    2.9.2
tensorflow-datasets           4.8.1
tensorflow-estimator          2.9.0
tensorflow-gcs-config         2.9.1
tensorflow-hub                0.12.0
tensorflow-io-gcs-filesystem  0.29.0
tensorflow-metadata           1.12.0
tensorflow-probability        0.17.0
termcolor                     2.2.0
terminado                     0.13.3
testpath                      0.6.0
text-unidecode                1.3
textblob                      0.15.3
thinc                         8.1.6
threadpoolctl                 3.1.0
tifffile                      2022.10.10
toml                          0.10.2
tomli                         2.0.1
toolz                         0.12.0
torch                         1.13.1+cu116
torchaudio                    0.13.1+cu116
torchsummary                  1.5.1
torchtext                     0.14.1
torchvision                   0.14.1+cu116
tornado                       6.0.4
tqdm                          4.64.1
traitlets                     5.7.1
tweepy                        3.10.0
typeguard                     2.7.1
typer                         0.7.0
typing_extensions             4.4.0
tzlocal                       1.5.1
uri-template                  1.2.0
uritemplate                   4.1.1
urllib3                       1.26.14
vega-datasets                 0.9.0
wasabi                        0.10.1
wcwidth                       0.2.5
webargs                       8.2.0
webcolors                     1.12
webencodings                  0.5.1
websocket-client              1.5.0
Werkzeug                      1.0.1
wheel                         0.38.4
widgetsnbextension            3.6.1
wordcloud                     1.8.2.2
wrapt                         1.14.1
xarray                        2022.12.0
xarray-einstats               0.4.0
xgboost                       0.90
xkit                          0.0.0
xlrd                          1.2.0
xlwt                          1.3.0
yarl                          1.8.2
yellowbrick                   1.5
zict                          2.2.0
zipp                          3.11.0

Google Colab Python 3.8.10

Blaizzy commented 1 year ago

Hi @lmrios

Prince here,

Thanks for getting in touch!

I ran your code using Colab, and it worked without issues.

run['MyProcess/training/demo_number']= 1
run['MyProcess/training/demo_dict']= {'Name': "Tom", 'Age': 20}
demo_data = {'Name': ['Tom', 'nick', 'krish', 'jack'], 'Age': [20, 21, 19, 18]}
demo_data_df = pd.DataFrame(demo_data)
run['MyProcess/training/demo_df'].upload(File.as_html(demo_data_df))

Example run: https://app.neptune.ai/o/common/org/showroom/e/SHOW-30049/all?path=MyProcess%2Ftraining%2F&attribute=demo_df

Can you send me a fully reproducible example including your neptune initialization? Note: Please omit your project and api_token arguments.

Blaizzy commented 1 year ago

Hi @lmrios

Just checking in to see if you still need help with this :)

lmrios commented 1 year ago

Hi, I am still cleaning my code. Perhaps something wrong is on my side. Thank you for reaching out. You can close this. Best