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jupyterhub / nbgitpuller

Jupyter server extension to sync a git repository one-way to a local path
https://nbgitpuller.readthedocs.io
BSD 3-Clause "New" or "Revised" License
208 stars 85 forks source link

Issue when file is added and then removed from repo #196

Open ischmidt20 opened 3 years ago

ischmidt20 commented 3 years ago

Bug description

Scenario: We have an assignment released in our public repo. Students pull, work on assignment A. A week later, this assignment gets removed from our repo due to a forced push. Students click link to load in other assignments. Students then see merge issues with their version of the assignment A. Inspection reveals that their copy of assignment A is staged for commit. Students continue to see these issues even after assignment A is restored to the repo.

Expected behaviour

Once Assignment A was restored to the repo, students would no longer see merge issues.

Actual behaviour

Students are unable to sync any other assignments due to a merge conflict with assignment A.

How to reproduce

  1. Push a file to the repo.
  2. Use nbgitpuller to pull a copy of the repo.
  3. Edit the file.
  4. Remove the file from the repo through a force push.
  5. Add another file to the repo.
  6. Try to use nbgitpuller to pull a copy of the repo again.

Your personal set up

I am a course staff member of Data 100 @ UC Berkeley, we are using data100.datahub.berkeley.edu. I do not know the particular configuration.

absl-py==0.13.0
access==1.1.3
aesara-theano-fallback==0.0.4
affine==2.3.0
agate==1.6.1
aiohttp==3.7.4.post0
aiohttp-cors==0.7.0
aioredis==1.3.1
alabaster==0.7.12
alembic==1.6.5
allensdk==2.4.1
altair==4.1.0
anyio==3.2.1
appdirs==1.4.4
appmode==0.8.0
argon2-cffi==20.1.0
argschema==1.17.5
arviz==0.11.2
asn1crypto==1.4.0
ast-scope==0.3.1
astropy==4.2
astroquery==0.4.1
astunparse==1.6.3
async-generator==1.10
async-timeout==3.0.1
attrs==19.3.0
azure-common==1.1.27
azure-core==1.16.0
azure-storage-blob==12.8.1
Babel==2.9.1
backcall==0.2.0
basemap @ https://github.com/matplotlib/basemap/archive/v1.2.2rel.tar.gz
beautifulsoup4==4.9.3
bitarray==1.6.1
bleach==3.3.0
blessings==1.7
blis==0.7.4
bokeh==2.2.3
boto3==1.15.18
botocore==1.18.18
branca==0.4.2
brewer2mpl==1.4.1
brotlipy==0.7.0
cachetools==4.2.2
Cartopy==0.18.0
catalogue==1.0.0
certifi==2019.11.28
certipy==0.1.3
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1613413861439/work
cftime==1.5.0
chardet @ file:///home/conda/feedstock_root/build_artifacts/chardet_1602255302199/work
chart-studio==1.1.0
click==8.0.1
click-plugins==1.1.1
cligj==0.7.2
cloudpickle==1.6.0
codecov==2.1.11
colorama==0.4.3
colorful==0.5.4
colorlover==0.3.0
conda==4.10.3
conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1618231394280/work
contextily==1.1.0
corner==2.1.0
coverage==5.5
coveralls==3.1.0
cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1616851476134/work
cryptorandom==0.2
csaps==1.0.3
cufflinks==0.17.3
cvxpy==1.1.13
cycler==0.10.0
cymem==2.0.5
Cython==0.29.21
cytoolz==0.11.0
daft==0.1.0
dask==2020.12.0
datascience==0.17.0
dbt==0.19.1
dbt-bigquery==0.19.1
dbt-core==0.19.1
dbt-postgres==0.19.1
dbt-redshift==0.19.1
dbt-snowflake==0.19.1
debugpy==1.3.0
decorator==4.4.2
defusedxml==0.7.1
Deprecated==1.2.12
deprecation==2.1.0
descartes==1.1.0
dill==0.3.4
display-timedelta==1.1
distributed==2020.12.0
distro==1.5.0
dm-tree==0.1.6
docker==5.0.0
docopt==0.6.2
docutils==0.17.1
dsassign==0.0.8
dustmaps==1.0.6
ecos==2.0.7.post1
emcee==3.0.2
entrypoints==0.3
esda==2.3.6
et-xmlfile==1.1.0
exoplanet==0.4.3
fancyimpute==0.5.5
fastprogress==1.0.0
ffmpeg-python==0.2.0
filelock==3.0.12
Fiona==1.8.20
flatbuffers==1.12
folium==0.11.0
future==0.18.2
gast==0.3.3
geographiclib==1.52
geojson==2.5.0
geopandas==0.9.0
geopy==2.1.0
george==0.3.1
GetDist==1.1.2
ggplot==0.11.5
giddy==2.3.3
git-credential-helpers==0.2
github3.py==2.0.0
Glymur==0.8.19
gmaps==0.9.0
google==3.0.0
google-api-core==1.31.0
google-api-python-client==1.12.8
google-auth==1.32.1
google-auth-httplib2==0.0.4
google-auth-oauthlib==0.4.1
google-cloud-bigquery==2.3.1
google-cloud-core==1.4.4
google-crc32c==1.1.2
google-pasta==0.2.0
google-resumable-media==1.3.1
googleapis-common-protos==1.53.0
gpustat==0.6.0
graphviz==0.16
greenlet==1.1.0
grpcio==1.32.0
gspread==3.6.0
gspread-pandas==2.2.3
h5py==3.1.0
habanero==0.7.4
hdbscan==0.8.26
hdmf==2.5.8
healpy==1.15.0
HeapDict==1.0.1
hiredis==2.0.0
hologram==0.0.13
html5lib==1.1
httplib2==0.19.1
idna==2.8
imageio==2.9.0
imagesize==1.2.0
importlib-metadata==4.6.1
inequality==1.0.0
iniconfig==1.1.1
ipycanvas==0.8.1
ipykernel==6.0.1
ipympl==0.6.2
ipython==7.25.0
ipython-genutils==0.2.0
ipython-sql==0.4.0
ipywidgets==7.6.3
isodate==0.6.0
jassign==0.0.7
jdcal==1.4.1
jedi==0.18.0
jeepney==0.7.0
Jinja2==3.0.1
jmespath==0.10.0
joblib==1.0.0
json-rpc==1.13.0
json5==0.9.6
jsonschema==3.2.0
jupyter-client==6.1.12
jupyter-contrib-core==0.3.3
jupyter-contrib-nbextensions==0.5.1
jupyter-core==4.7.1
jupyter-highlight-selected-word==0.2.0
jupyter-latex-envs==1.4.6
jupyter-nbextensions-configurator==0.4.1
jupyter-resource-usage==0.5.1
jupyter-rsession-proxy==1.2
jupyter-server==1.9.0
jupyter-server-proxy==3.0.2
jupyter-shiny-proxy==1.1
jupyter-telemetry==0.1.0
jupyter-tree-download==1.0.1
jupyterhub @ git+https://github.com/jupyterhub/jupyterhub@11f00dbbe794191d328c6c2a44a9e85f7eb6ede5
jupyterlab==3.0.16
jupyterlab-geojson==3.1.2
jupyterlab-pygments==0.1.2
jupyterlab-server==2.6.1
jupyterlab-widgets==1.0.0
jwcrypto==0.9.1
Keras==2.4.3
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
keras-vis==0.4.1
keyring==23.0.1
kiwisolver==1.3.1
knnimpute==0.1.0
lcapy==0.77
leather==0.3.3
libpysal==4.5.1
lime==0.2.0.1
llvmlite==0.36.0
Logbook==1.5.3
lxml==4.6.2
Mako==1.1.4
mapclassify==2.4.2
Markdown==3.3.4
MarkupSafe==2.0.1
marshmallow==3.0.0rc6
mashumaro==2.0
matminer==0.6.5
matplotlib==3.3.3
matplotlib-inline==0.1.2
mercantile==1.2.1
mgwr==2.1.2
mimeparse==0.1.3
minimal-snowplow-tracker==0.0.2
mistune==0.8.4
mne==0.22.0
monty==2021.7.8
mplleaflet==0.0.5
mpmath==1.1.0
msgpack==1.0.2
msrest==0.6.21
multidict==5.1.0
munch==2.5.0
murmurhash==1.0.5
nb2pdf==0.6.2
nbclassic==0.3.1
nbclient==0.5.3
nbconvert==6.1.0
nbformat==5.0.8
nbforms==0.5.1
nbgitpuller==0.10.0
nbpdfexport==0.2.1
nbsphinx==0.8.6
nest-asyncio==1.2.0
netCDF4==1.5.5.1
networkx==2.5
nibabel==3.2.1
nilearn==0.7.0
nlmpy==1.0.0
nltk==3.5
nose==1.3.7
notebook==6.4.0
numba==0.53.1
numexpr==2.7.2
numpy==1.19.5
nvidia-ml-py3==7.352.0
oauthlib==3.1.1
obspy==1.2.2
okpy==1.18.1
opencensus==0.7.13
opencensus-context==0.1.2
opencv-contrib-python==4.5.3.56
opencv-python==4.5.1.48
openpyxl==3.0.6
opt-einsum==3.3.0
orjson==3.6.0
oscrypto==1.2.1
osqp==0.6.2.post0
otter-grader==2.2.0
packaging==21.0
palettable==3.3.0
pamela==1.0.0
pandas==1.2.0
pandocfilters==1.4.3
parsedatetime==2.6
parso==0.8.2
patsy==0.5.1
pdfkit==0.6.1
pep257==0.7.0
permute @ git+https://github.com/statlab/permute@bb2e9303f582121c1e25ffb898804cba1fbeea8b
pexpect==4.8.0
pgspecial==1.11.10
pickleshare==0.7.5
Pillow==8.1.0
Pint==0.16.1
plac==1.1.3
plotly==4.14.3
plotly-express==0.4.1
pluggy==0.13.1
pointpats==2.2.0
popularity-contest==0.4.1
preshed==3.0.5
prettytable==0.7.2
prob140==0.4.1.5
progressbar2==3.53.1
prometheus-client==0.11.0
prompt-toolkit==3.0.19
proto-plus==1.19.0
protobuf==3.17.3
psutil==5.8.0
psycopg2==2.8.6
psycopg2-binary==2.9.1
ptyprocess==0.7.0
py==1.10.0
py-spy==0.3.7
pyaes==1.6.1
pyasn1==0.4.8
pyasn1-modules==0.2.8
pybind11==2.6.2
pycodestyle==2.6.0
pycosat @ file:///home/conda/feedstock_root/build_artifacts/pycosat_1610094800877/work
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1593275161868/work
pycryptodomex==3.10.1
pydot==1.4.1
pyee==8.1.0
pyerfa==2.0.0
pygeos==0.10.1
Pygments==2.9.0
PyJWT==1.7.1
pymatgen==2020.10.20
pymc3==3.11.0
pymc3-ext==0.1.0
pymdptoolbox==4.0b3
pymongo==3.11.3
pynndescent==0.5.4
pynrrd==0.4.2
pynwb==1.5.1
pyOpenSSL==19.1.0
pyparsing==2.4.7
PyPDF2==1.26.0
pyppeteer==0.2.5
pyproj==3.1.0
pyreadstat==1.0.8
pyro-api==0.1.2
pyro-ppl==1.5.2
pyrsistent==0.18.0
pysal==2.3.0
pyshp==2.1.3
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1610291447907/work
pytest==6.2.4
pytest-cov==2.12.1
python-dateutil==2.8.1
python-editor==1.0.4
python-json-logger==2.0.1
python-slugify==5.0.2
python-utils==2.5.6
pytimeparse==1.1.8
pytutor==1.0.0
pytz==2020.5
PyVCF==0.6.8
pyvo==1.1
PyWavelets==1.1.1
PyYAML==5.4.1
pyzmq==22.1.0
qdldl==0.1.5.post0
qgrid==1.3.1
quantecon==0.5.1
rasterio==1.2.6
rasterstats==0.15.0
ray==1.1.0
redis==3.5.3
regex==2021.7.6
requests==2.25.1
requests-oauthlib==1.3.0
requests-toolbelt==0.9.1
requests-unixsocket==0.2.0
retrolab==0.2.1
retrying==1.3.3
rsa==4.7.2
Rtree==0.9.7
ruamel-yaml-conda @ file:///home/conda/feedstock_root/build_artifacts/ruamel_yaml_1611943339799/work
ruamel.yaml==0.17.10
ruamel.yaml.clib==0.2.6
s3transfer==0.3.7
scikit-build==0.11.1
scikit-image==0.18.1
scikit-learn==0.24.0
scipy==1.6.0
scs==2.1.4
seaborn==0.11.1
SecretStorage==3.3.1
segregation==2.0.0
Send2Trash==1.7.1
setuptools-scm==6.0.1
shap==0.39.0
Shapely==1.7.1
simpervisor==0.4
SimpleITK==1.2.4
simplejson==3.17.3
six @ file:///home/conda/feedstock_root/build_artifacts/six_1590081179328/work
slicer==0.0.7
sniffio==1.2.0
snowballstemmer==2.1.0
snowflake-connector-python==2.3.6
snuggs==1.4.7
sortedcontainers==2.4.0
soupsieve==2.2.1
spacy==2.3.5
spaghetti==1.6.2
spglib==1.16.1
spglm==1.0.8
Sphinx==4.1.0
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
spint==1.0.7
splot==1.1.3
spreg==1.2.4
spvcm==0.3.0
SQLAlchemy==1.4.20
sqlparse==0.4.1
srsly==1.0.5
statsd==3.3.0
statsmodels==0.11.1
sympy==1.7.1
tables==3.6.1
tabulate==0.8.9
tblib==1.7.0
tensorboard==2.5.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
tensorflow==2.4.0
tensorflow-estimator==2.4.0
tensorflow-hub==0.11.0
tensorflow-probability==0.12.1
termcolor==1.1.0
terminado==0.10.1
testpath==0.5.0
text-unidecode==1.3
Theano==1.0.5
Theano-PyMC==1.1.0
thinc==7.4.5
threadpoolctl==2.2.0
tifffile==2021.7.2
tobler==0.8.2
toml==0.10.2
toolz==0.11.1
torch==1.7.1
torchvision==0.8.2
tornado==6.1
tqdm==4.56.0
traitlets==5.0.5
tweepy==3.10.0
typing-extensions==3.10.0.0
umap-learn==0.5.0
uncertainties==3.1.5
uritemplate==3.0.1
urllib3==1.25.7
wasabi==0.8.2
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.1.0
websockets==8.1
Werkzeug==2.0.1
widgetsnbextension==3.5.1
wordcloud==1.8.1
wrapt==1.12.1
xarray==0.16.2
xlrd==2.0.1
yarl==1.6.3
zict==2.0.0
zipp==3.5.0

# jupyterhub_config.py