Modifications to notebook are remembered even when notebook is deleted

[phys119]

I'm distributing template notebooks to students with nbgitpuller.
Some of my students have managed to delete instruction cells from the template. I've told them to delete the notebook and click the link again, as that should download a fresh copy of the notebook, but it turns out that the deletion has been committed locally in the student's account, and is merged when the new copy is downloaded, so they don't get the deleted cells back!

This behaviour seems to be in contradiction to the documentation on automatic merge which suggests that if the notebook is deleted they should get a pristine template when they click the link again.

I'm using a jupyter hub operated by my University (at open.jupyter.ubc.ca).

pip freeze:
aiodns==3.0.0
aiohttp==3.8.1
aiosignal==1.2.0
alembic @ file:///home/conda/feedstock_root/build_artifacts/alembic_1657813896088/work
altair @ file:///home/conda/feedstock_root/build_artifacts/altair_1640799865332/work
analytics-python==1.4.0
ansi2html @ file:///home/conda/feedstock_root/build_artifacts/ansi2html_1657236128758/work
anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1652463865103/work/dist
argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1640817743617/work
argon2-cffi-bindings @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi-bindings_1649500328244/work
astroid @ file:///home/conda/feedstock_root/build_artifacts/astroid_1655142257854/work
asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1618968359944/work
async-generator==1.10
async-timeout==4.0.2
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work
autopep8 @ file:///home/conda/feedstock_root/build_artifacts/autopep8_1619771482781/work
Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1655419414885/work
backcall @ file:///home/conda/feedstock_root/build_artifacts/backcall_1592338393461/work
backoff==1.10.0
backports.functools-lru-cache @ file:///home/conda/feedstock_root/build_artifacts/backports.functools_lru_cache_1618230623929/work
beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1649463573192/work
black==22.6.0
bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1656355450470/work
blinker==1.4
bokeh @ file:///home/conda/feedstock_root/build_artifacts/bokeh_1652969564789/work
Bottleneck @ file:///home/conda/feedstock_root/build_artifacts/bottleneck_1656803756069/work
Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1648883617327/work
brotlipy @ file:///home/conda/feedstock_root/build_artifacts/brotlipy_1648854167867/work
cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
ccxt==1.91.20
certifi==2022.6.15
certipy==0.1.3
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1656782834004/work
chardet==5.0.0
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1655906222726/work
click @ file:///home/conda/feedstock_root/build_artifacts/click_1651215151197/work
cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1653061851209/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1655412516417/work
conda==4.13.0
conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1649385045972/work
cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1657173997940/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work
Cython @ file:///home/conda/feedstock_root/build_artifacts/cython_1652809237949/work
cytoolz @ file:///home/conda/feedstock_root/build_artifacts/cytoolz_1657553432917/work
dash @ file:///home/conda/feedstock_root/build_artifacts/dash_1657882603280/work
dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1657315353846/work
debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1649586344343/work
decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work
defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work
dill @ file:///home/conda/feedstock_root/build_artifacts/dill_1653058582944/work
distributed @ file:///home/conda/feedstock_root/build_artifacts/distributed_1657319800717/work
entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1643888246732/work
et-xmlfile==1.1.0
executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1646044401614/work
fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/python-fastjsonschema_1658064924516/work/dist
flake8 @ file:///home/conda/feedstock_root/build_artifacts/flake8_1620668104928/work
Flask @ file:///home/conda/feedstock_root/build_artifacts/flask_1657844361786/work
Flask-Compress @ file:///home/conda/feedstock_root/build_artifacts/flask-compress_1651163502372/work
flit_core @ file:///home/conda/feedstock_root/build_artifacts/flit-core_1645629044586/work/source/flit_core
fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1657249373943/work
frozenlist==1.3.0
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1653010523205/work
gitdb==4.0.9
GitPython==3.1.27
gmpy2 @ file:///home/conda/feedstock_root/build_artifacts/gmpy2_1641732907644/work
greenlet @ file:///home/conda/feedstock_root/build_artifacts/greenlet_1648882383677/work
h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1656336064499/work
HeapDict==1.0.1
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1642433548627/work
imagecodecs @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs_1655137597069/work
imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1654071881944/work
importlib-metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1653252803161/work
importlib-resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1655356668708/work
ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1657295047882/work
ipympl @ file:///home/conda/feedstock_root/build_artifacts/ipympl_1650889123350/work
ipysheet==0.5.0
ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1653754916420/work
ipython-genutils==0.2.0
ipython-sql @ file:///home/conda/feedstock_root/build_artifacts/ipython-sql_1636816912182/work
ipywidgets @ file:///home/conda/feedstock_root/build_artifacts/ipywidgets_1655973868664/work
isort @ file:///home/conda/feedstock_root/build_artifacts/isort_1636447814597/work
itsdangerous @ file:///home/conda/feedstock_root/build_artifacts/itsdangerous_1648147185463/work
jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1649067100958/work
Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1654302431367/work
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1633637554808/work
json5 @ file:///home/conda/feedstock_root/build_artifacts/json5_1600692310011/work
jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema-meta_1657629641118/work
jupyter-archive==3.3.1
jupyter-bokeh @ file:///home/conda/feedstock_root/build_artifacts/jupyter_bokeh_1638244308716/work
jupyter-client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1654730843242/work
jupyter-core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1652365243968/work
jupyter-dash @ file:///home/conda/feedstock_root/build_artifacts/jupyter-dash_1648919001274/work
jupyter-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1639326415622/work/jupyter-lsp
jupyter-resource-usage==0.6.1
jupyter-server @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_1657107521771/work
jupyter-server-mathjax==0.2.6
jupyter-telemetry @ file:///home/conda/feedstock_root/build_artifacts/jupyter_telemetry_1605173804246/work
jupyterhub @ file:///home/conda/feedstock_root/build_artifacts/jupyterhub-feedstock_1654538669080/work
jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1654621376725/work
jupyterlab-code-formatter==1.5.1
jupyterlab-drawio @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab-drawio_1620212636855/work
jupyterlab-git==0.37.1
jupyterlab-github==3.0.1
jupyterlab-latex==3.1.0
jupyterlab-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1647904782549/work/jupyterlab-lsp
jupyterlab-pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1649936611996/work
jupyterlab-server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server_1657063151834/work
jupyterlab-spellchecker @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab-spellchecker_1633697061174/work
jupyterlab-system-monitor==0.8.0
jupyterlab-templates==0.3.1
jupyterlab-topbar==0.6.1
jupyterlab-widgets==1.0.2
jupytext==1.14.0
kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1657953096987/work
lazy-object-proxy @ file:///home/conda/feedstock_root/build_artifacts/lazy-object-proxy_1649033164427/work
lckr-jupyterlab-variableinspector==3.0.9
libmambapy @ file:///home/conda/feedstock_root/build_artifacts/mamba-split_1654091934149/work/libmambapy
llvmlite==0.38.1
locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work
lz4 @ file:///home/conda/feedstock_root/build_artifacts/lz4_1652795530538/work
Mako @ file:///home/conda/feedstock_root/build_artifacts/mako_1656619049246/work
mamba @ file:///home/conda/feedstock_root/build_artifacts/mamba-split_1654091934149/work/mamba
markdown-it-py==2.1.0
MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1648737547956/work
matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1651609453931/work
matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1631080358261/work
mccabe==0.6.1
mdit-py-plugins==0.3.0
mdurl==0.1.1
mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1635844663025/work
mitosheet3==0.3.223
monotonic==1.6
mpmath @ file:///home/conda/feedstock_root/build_artifacts/mpmath_1612895720168/work
msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1654260638735/work
multidict==6.0.2
munkres==1.1.4
mypy-extensions==0.4.3
nbclassic @ file:///home/conda/feedstock_root/build_artifacts/nbclassic_1657631862903/work
nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1656688109017/work
nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert-meta_1649676641343/work
nbdime==3.1.1
nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1651607001005/work
nbgitpuller==1.1.0
nest-asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1648959695634/work
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1655215393654/work
notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1654636967533/work
notebook-shim @ file:///home/conda/feedstock_root/build_artifacts/notebook-shim_1646330736330/work
numba @ file:///home/conda/feedstock_root/build_artifacts/numba_1655473324812/work
numexpr @ file:///home/conda/feedstock_root/build_artifacts/numexpr_1658076419034/work
numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1653325310407/work
oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1643507977997/work
openpyxl==3.0.10
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1637239678211/work
pamela==1.0.0
pandas==1.4.3
pandas-ta==0.3.14b0
pandocfilters @ file:///home/conda/feedstock_root/build_artifacts/pandocfilters_1631603243851/work
parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1638334955874/work
partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1617910651905/work
pathspec==0.9.0
patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1632667180946/work
pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1602535608087/work
pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1657007160045/work
platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1657729053205/work
plotly @ file:///home/conda/feedstock_root/build_artifacts/plotly_1656046979833/work
pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1648772594861/work
prettytable @ file:///home/conda/feedstock_root/build_artifacts/prettytable_1651787307815/work
prometheus-client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1649447152425/work
prompt-toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1656332401605/work
protobuf==3.20.1
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1653089181607/work
ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work
pycares==4.2.1
pycodestyle @ file:///home/conda/feedstock_root/build_artifacts/pycodestyle_1615833610040/work
pycosat @ file:///home/conda/feedstock_root/build_artifacts/pycosat_1649384799612/work
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work
pycurl==7.45.1
pydocstyle @ file:///home/conda/feedstock_root/build_artifacts/pydocstyle_1621377123289/work
pyflakes @ file:///home/conda/feedstock_root/build_artifacts/pyflakes_1616623675904/work
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1650904496387/work
PyJWT @ file:///home/conda/feedstock_root/build_artifacts/pyjwt_1652398519695/work
pylint @ file:///home/conda/feedstock_root/build_artifacts/pylint_1658157521144/work
pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1643496850550/work
pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1652235407899/work
pyrsistent @ file:///home/conda/feedstock_root/build_artifacts/pyrsistent_1649013351988/work
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1648857264958/work
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
python-json-logger @ file:///home/conda/feedstock_root/build_artifacts/python-json-logger_1602545356084/work
python-lsp-jsonrpc @ file:///home/conda/feedstock_root/build_artifacts/python-lsp-jsonrpc_1618530352985/work
python-lsp-server @ file:///home/conda/feedstock_root/build_artifacts/python-lsp-server_1628113199343/work
pytoolconfig @ file:///home/conda/feedstock_root/build_artifacts/pytoolconfig_1656898078212/work
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1647961439546/work
pytz-deprecation-shim @ file:///home/conda/feedstock_root/build_artifacts/pytz-deprecation-shim_1656249448407/work
PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1649616405488/work
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1648757090803/work
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1656183556820/work
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1656534056640/work
retrying==1.3.3
rope @ file:///home/conda/feedstock_root/build_artifacts/rope_1656025934395/work
rpy2 @ file:///home/conda/feedstock_root/build_artifacts/rpy2_1649599347730/work
ruamel-yaml-conda @ file:///home/conda/feedstock_root/build_artifacts/ruamel_yaml_1653464396679/work
ruamel.yaml @ file:///home/conda/feedstock_root/build_artifacts/ruamel.yaml_1649033201098/work
ruamel.yaml.clib @ file:///home/conda/feedstock_root/build_artifacts/ruamel.yaml.clib_1649013063403/work
scikit-image @ file:///home/conda/feedstock_root/build_artifacts/scikit-image_1655254001151/work
scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1652976692230/work
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1653073872310/work
seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1629095986539/work
Send2Trash @ file:///home/conda/feedstock_root/build_artifacts/send2trash_1628511208346/work
simplegeneric==0.8.1
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
smmap==5.0.0
sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1648819179288/work
snowballstemmer @ file:///home/conda/feedstock_root/build_artifacts/snowballstemmer_1637143057757/work
sortedcontainers @ file:///home/conda/feedstock_root/build_artifacts/sortedcontainers_1621217038088/work
soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1638550740809/work
SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/sqlalchemy_1656115934245/work
sqlparse @ file:///home/conda/feedstock_root/build_artifacts/sqlparse_1631317292236/work
stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1655315839047/work
statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1654787107327/work
sympy @ file:///home/conda/feedstock_root/build_artifacts/sympy_1647802543069/work
tables @ file:///home/conda/feedstock_root/build_artifacts/pytables_1643135944604/work
tblib @ file:///home/conda/feedstock_root/build_artifacts/tblib_1616261298899/work
tenacity @ file:///home/conda/feedstock_root/build_artifacts/tenacity_1626090218611/work
terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1652790610172/work
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1643647933166/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1651666912743/work
tinycss2 @ file:///home/conda/feedstock_root/build_artifacts/tinycss2_1637612658783/work
toml @ file:///home/conda/feedstock_root/build_artifacts/toml_1604308577558/work
tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work
tomlkit @ file:///home/conda/feedstock_root/build_artifacts/tomlkit_1657178191936/work
toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work
tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1648827254365/work
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1649051611147/work
traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1655411388954/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1656706066251/work
tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1647621564023/work
tzlocal @ file:///home/conda/feedstock_root/build_artifacts/tzlocal_1656259936310/work
ujson @ file:///home/conda/feedstock_root/build_artifacts/ujson_1653057323486/work
unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1649111910890/work
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1657224465922/work
wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1600965781394/work
webencodings==0.5.1
websocket-client @ file:///home/conda/feedstock_root/build_artifacts/websocket-client_1655796432389/work
Werkzeug @ file:///home/conda/feedstock_root/build_artifacts/werkzeug_1651670883478/work
widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1655939017940/work
wrapt @ file:///home/conda/feedstock_root/build_artifacts/wrapt_1651495243689/work
xlrd @ file:///home/conda/feedstock_root/build_artifacts/xlrd_1610224409810/work
XlsxWriter==3.0.2
yapf @ file:///home/conda/feedstock_root/build_artifacts/yapf_1641487982943/work
yarl==1.7.2
zict @ file:///home/conda/feedstock_root/build_artifacts/zict_1651156074437/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1649012893348/work

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[farcila]

We are experiencing the same Issue @phys119, did you find a workaround?

[phys119]

Nothing very pretty. I made a copy of the template and pushed that to the repository as well. Then gave those students a link to the copy. Very ugly. Thinking about it again, you could probably have the student open a terminal, cd into the local repository and git checkout template.ipynb to restore the pristine template. I hesitate to do that for my current class - git is out of scope...

[farcila]

hm, ours is an introductory course so I think we can also rule out students running git commands. The odder part is that this behavior persists even after deleting the ipynb_checkpoints folder

[phys119]

It looks to me that when you click on an nbgitpuller link, changes are committed to the local repository first, before updates are pulled - so the student's deletions are stored in the repository as a commit which gets merged into the pulled file.

Another poor and somewhat dangerous idea for a workaround is to create a notebook that does the cd and git checkout commands as shell commands - so the student wouldn't have to open a terminal, they'd just have to execute a cell in a notebook. This is probably a terrible idea though, since it seems like a great pathway for people to lose work inadvertently. I suppose your cell could back up the notebook before it wipes it out, or even check that the template is smaller than its supposed to be, or something...