realiti4
commented
1 month ago Hi,
Thank you for pointing this out. Is it possible for you to share something like requirements.txt from your environment, so that I can recreate the issue on my end?
Open peutch opened 1 month ago
realiti4
commented
1 month ago Hi,
Thank you for pointing this out. Is it possible for you to share something like requirements.txt from your environment, so that I can recreate the issue on my end?
peutch
commented
1 month ago Hi, Sorry, it is a production system and so it is very large. That's also why pip-upgrade is very convenient! ;-)
$ pip freeze
about-time==4.2.1
absl-py==2.1.0
adlfs==2024.4.1
aiobotocore==2.13.1
aiodns==3.2.0
aiofiles==24.1.0
aiohttp==3.9.5
aioitertools==0.11.0
aiosignal==1.3.1
aiosqlite==0.20.0
airr==1.5.1
alabaster==0.7.16
alembic==1.13.2
alive-progress==3.1.5
altair==5.3.0
ampligraph==2.1.0
annotated-types==0.7.0
ansi2html==1.9.2
antlr4-python3-runtime==4.13.1
anyio==4.4.0
appdirs==1.4.4
argcomplete==3.4.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
argparse-dataclass==2.0.0
arrow==1.3.0
aspose-words==24.7.0
astor==0.8.1
astroid==3.2.3
asttokens==2.4.1
astunparse==1.6.3
async-generator==1.10
async-lru==2.0.4
async-timeout==4.0.3
atoti==0.8.14
atoti-core==0.8.14
atoti-jupyterlab==0.8.14
atoti-query==0.8.14
atoti-sql==0.8.14
attrs==23.2.0
autograd==1.6.2
autopep8==2.3.1
azure-core==1.30.2
azure-datalake-store==0.0.53
azure-identity==1.17.1
azure-storage-blob==12.20.0
Babel==2.15.0
backcall==0.2.0
backoff==2.2.1
backports.tarfile==1.2.0
beautifulsoup4==4.12.3
beautifultable==1.1.0
binaryornot==0.4.4
biopython==1.84
bioregistry==0.11.10
bleach==6.1.0
blinker==1.8.2
blis==0.7.9
bokeh==3.4.2
botocore==1.34.106
bottle==0.12.25
bqplot==0.12.43
bs4==0.0.2
cache_decorator==2.2.0
cachetools==5.4.0
catalogue==2.0.10
cattrs==23.2.3
cccs-ipyaggrid==0.5.4
Cerberus==1.3.5
certifi==2024.7.4
certipy==0.1.3
cffi==1.16.0
changeo==1.3.0
chardet==5.2.0
charset-normalizer==3.3.2
class_resolver==0.4.3
cli_helpers==2.3.1
click==8.1.7
click-default-group==1.2.4
cloudpathlib==0.18.1
cloudpickle==3.0.0
cma==3.2.2
cmake==3.30.0
colorama==0.4.6
colorcet==3.1.0
colorclass==2.2.2
coloredlogs==15.0.1
colorlog==6.8.2
comm==0.2.2
compress-json==1.0.10
compress-pickle==2.1.0
compressed-rtf==1.0.6
conda-inject==1.3.2
confection==0.1.5
ConfigArgParse==1.7
configobj==5.0.8
conllu==5.0.1
connection_pool==0.0.3
contextlib2==21.6.0
contourpy==1.2.1
cookiecutter==2.6.0
croniter==2.0.7
cryptography==42.0.8
curies==0.7.10
cycler==0.12.1
cymem==2.0.8
dash==2.17.1
dash-core-components==2.0.0
dash-html-components==2.0.0
dash-table==5.0.0
dask==2024.7.0
dataclasses-json==0.6.7
datasets==2.20.0
dateutils==0.6.12
datrie==0.8.2
ddd-subplots==1.0.27
debugpy==1.8.2
decorator==5.1.1
deepmerge==1.1.1
deflate_dict==1.2.0
defusedxml==0.7.1
Deprecated==1.2.14
deprecation==2.1.0
dgl==2.1.0
dict_hash==1.2.0
dill==0.3.8
diskcache==5.6.3
distlib==0.3.8
distributed==2024.7.0
distro==1.9.0
dm-tree==0.1.8
docdata==0.0.3
docker==7.1.0
docopt==0.6.2
docstring-to-markdown==0.15
docstring_parser==0.16
docutils==0.17.1
docx2txt==0.8
downloaders==1.0.20
dpath==2.2.0
duckdb==1.0.0
duckdb_engine==0.13.0
easygui==0.98.3
ebbe==1.13.2
ebcdic==1.1.1
einops==0.8.0
embiggen==0.11.95
ensmallen==0.8.94
entrypoints==0.4
environments-utils==1.0.13
et-xmlfile==1.1.0
executing==2.0.1
expecttest==0.2.1
faiss-cpu==1.8.0
fastcore==1.5.54
fasteners==0.19
fastjsonschema==2.20.0
filelock==3.15.4
flake8==7.1.0
Flask==3.0.3
flatbuffers==24.3.25
flyteidl==1.13.0
fonttools==4.53.1
fqdn==1.5.1
frozenlist==1.4.1
fsspec==2024.5.0
future==1.0.0
gast==0.4.0
ghp-import==2.1.0
gitdb==4.0.11
GitPython==3.1.43
gliner==0.2.7
google-api-core==2.19.1
google-auth==2.32.0
google-auth-oauthlib==1.2.1
google-cloud-core==2.4.1
google-cloud-storage==2.17.0
google-crc32c==1.5.0
google-pasta==0.2.0
google-resumable-media==2.7.1
googleapis-common-protos==1.63.2
gpt4all==2.7.0
GPUtil==1.4.0
grape==0.2.4
graph4nlp==0.5.5
grapheme==0.6.0
greenlet==3.0.3
grpcio==1.64.1
gw_dsl_parser==0.1.49
h11==0.14.0
h5py==3.11.0
holoviews==1.19.1
httpcore==1.0.5
httpx==0.27.0
huggingface-hub==0.23.5
humanfriendly==10.0
humanize==4.10.0
hypothesis==6.108.2
idna==3.7
imageio==2.34.2
imagesize==1.4.1
IMAPClient==3.0.1
immutables==0.20
importlib_metadata==8.0.0
importlib_resources==6.4.0
iniconfig==2.0.0
intel-cmplr-lib-ur==2024.2.0
intel-openmp==2024.2.0
IPy==1.1
ipyaggrid==0.5.4
ipycytoscape==1.3.3
ipydatagrid==1.3.2
ipykernel==6.29.5
ipylab==1.0.0
ipysigma==0.24.2
ipytablewidgets==0.3.1
ipython==8.26.0
ipython-genutils==0.2.0
ipytree==0.2.2
ipywidgets==8.1.3
isodate==0.6.1
isoduration==20.11.0
isort==5.13.2
itsdangerous==2.2.0
jaraco.classes==3.4.0
jaraco.context==5.3.0
jaraco.functools==4.0.1
jaro-winkler==2.0.3
jdk4py==17.0.9.2
jedi==0.19.1
jedi-language-server==0.41.4
jeepney==0.8.0
Jinja2==3.1.4
jlab-enhanced-cell-toolbar==3.5.1
jmespath==1.0.1
joblib==1.4.2
json2html==1.3.0
json5==0.9.25
jsonpatch==1.33
jsonpath-ng==1.6.1
jsonpickle==3.2.2
jsonpointer==3.0.0
jsonschema==4.23.0
jsonschema-specifications==2023.12.1
jstyleson==0.0.2
jupysql==0.10.12
jupysql-plugin==0.4.4
jupyter==1.0.0
jupyter-console==6.6.3
jupyter-events==0.10.0
jupyter-git==1.0.22
jupyter-lsp==2.2.5
jupyter-plz==0.1.6
jupyter-resource-usage==1.0.2
jupyter-server-mathjax==0.2.6
jupyter-telemetry==0.1.0
jupyter-ydoc==2.1.1
jupyter_ai==2.19.0
jupyter_ai_magics==2.19.0
jupyter_bokeh==4.0.5
jupyter_client==8.6.2
jupyter_core==5.7.2
jupyter_packaging==0.12.3
jupyter_server==2.14.2
jupyter_server_fileid==0.9.2
jupyter_server_proxy==4.3.0
jupyter_server_terminals==0.5.3
jupyterhub==5.0.0
jupyterlab==4.2.3
jupyterlab-dash==0.1.0a3
jupyterlab-language-pack-el-GR==4.2.post1
jupyterlab-language-pack-fr-FR==4.2.post1
jupyterlab-lsp==5.1.0
jupyterlab-quarto==0.3.5
jupyterlab_nvdashboard==0.11.0
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.3
jupyterlab_sos==0.10.3
jupyterlab_sql_editor==1.1.3
jupyterlab_widgets==3.0.11
kanaries_track==0.0.5
keras==3.4.1
Keras-Preprocessing==1.1.2
keras_mixed_sequence==1.0.29
keyring==25.2.1
kiwisolver==1.4.5
langchain==0.2.8
langchain-community==0.2.7
langchain-core==0.2.20
langchain-text-splitters==0.2.2
langcodes==3.4.0
langsmith==0.1.88
language_data==1.2.0
lark-parser==0.12.0
latexcodec==3.0.0
lazy-object-proxy==1.10.0
lazy_loader==0.4
leather==0.4.0
libclang==18.1.1
linkify-it-py==2.0.3
lit==18.1.8
littleutils==0.2.4
llist==0.7.1
locket==1.0.0
Logbook==1.7.0.post0
lsprotocol==2023.0.1
lxml==5.2.2
lz4==4.3.3
Mako==1.3.5
mariadb==1.1.10
marisa-trie==1.2.0
Markdown==3.6
markdown-it-py==2.2.0
MarkupSafe==2.1.5
marshmallow==3.21.3
marshmallow-enum==1.5.1
marshmallow-jsonschema==0.13.0
mashumaro==3.13.1
matplotlib==3.9.1
matplotlib-inline==0.1.7
mccabe==0.7.0
mdit-py-plugins==0.3.5
mdurl==0.1.2
mergedeep==1.3.4
metakernel==0.30.2
minimal-snowplow-tracker==0.0.2
mistune==3.0.2
mkdocs==1.6.0
mkdocs-get-deps==0.2.0
mkl==2024.2.0
ml-dtypes==0.3.2
monotonic==1.6
more-click==0.1.2
more-itertools==10.3.0
mpmath==1.3.0
msal==1.30.0
msal-extensions==1.2.0
msgpack==1.0.8
msoffcrypto-tool==5.4.1
multidict==6.0.5
multiprocess==0.70.16
murmurhash==1.0.10
mypy-extensions==1.0.0
mysqlclient==2.2.4
myst-parser==0.18.0
namex==0.0.8
natsort==8.4.0
nbclassic==1.1.0
nbclient==0.10.0
nbconvert==7.16.4
nbdime==4.0.1
nbformat==5.10.4
nest-asyncio==1.6.0
networkx==3.1
ninja==1.11.1.1
nltk==3.8.1
nncf==2.11.0
notebook==7.2.1
notebook_shim==0.2.4
numexpr==2.10.1
numpy==1.26.4
nvidia-cublas-cu12==12.1.3.1
nvidia-cuda-cupti-cu12==12.1.105
nvidia-cuda-nvcc-cu12==12.5.82
nvidia-cuda-nvrtc-cu12==12.1.105
nvidia-cuda-runtime-cu12==12.1.105
nvidia-cudnn-cu12==8.9.2.26
nvidia-cufft-cu12==11.0.2.54
nvidia-curand-cu12==10.3.2.106
nvidia-cusolver-cu12==11.4.5.107
nvidia-cusparse-cu12==12.1.0.106
nvidia-nccl-cu12==2.20.5
nvidia-nvjitlink-cu12==12.5.82
nvidia-nvtx-cu12==12.1.105
oauthlib==3.2.2
octave_kernel==0.36.0
ogb==1.3.6
olefile==0.47
onnx==1.16.1
onnxruntime==1.18.1
openai==1.35.14
openapi-schema-pydantic==1.2.4
opencv-python==4.10.0.84
openpyxl==3.1.5
openvino==2024.2.0
openvino-dev==2024.2.0
openvino-telemetry==2024.1.0
opt-einsum==3.3.0
optree==0.12.1
optuna==3.6.1
orjson==3.10.6
outdated==0.2.2
overrides==7.7.0
packaging==24.1
pamela==1.1.0
pandas==2.2.2
pandocfilters==1.5.1
panel==1.4.4
param==2.1.1
parsedatetime==2.6
parso==0.8.4
partd==1.4.2
pathlib_abc==0.1.1
pathspec==0.12.1
pathy==0.11.0
pdfminer==20191125
pdfminer.six==20231228
pdfplumber==0.11.2
pep517==0.13.1
peppercorn==0.6
perceiver-pytorch==0.8.8
pexpect==4.9.0
pickleshare==0.7.5
pillow==10.4.0
pip-api==0.0.34
pip-search==0.0.12
pip-upgrade-outdated==1.5
pip-upgrade-tool==0.7.4
plac==1.4.3
platformdirs==4.2.2
plette==2.1.0
ploomber-core==0.2.25
ploomber-extension==0.1.1
plotly==5.22.0
pluggy==1.5.0
ply==3.11
portalocker==2.10.1
posthog==3.5.0
preshed==3.0.9
presto==0.7.2
prettytable==3.10.2
prometheus_client==0.20.0
prompt_toolkit==3.0.47
proto-plus==1.24.0
protobuf==4.25.3
protoc-gen-openapiv2==0.0.1
proxy-tools==0.1.0
psutil==5.9.8
ptyprocess==0.7.0
PuLP==2.8.0
pure-eval==0.2.2
py-cpuinfo==9.0.0
py2vega==0.6.1
py3Dmol==2.2.0
py4j==0.10.9.7
pyaes==1.6.1
pyarrow==17.0.0
pyarrow-hotfix==0.6
pyasn1==0.6.0
pyasn1_modules==0.4.0
pybind11==2.13.1
pybtex==0.24.0
pybtex-docutils==1.0.3
pycairo==1.26.1
pycares==4.4.0
pycodestyle==2.12.0
pycparser==2.22
pycrdt==0.9.2
pycryptodome==3.20.0
pyct==0.5.0
pydantic==2.8.2
pydantic_core==2.20.1
pydeck==0.9.1
pydgn==1.5.7
pydocstyle==6.3.0
pydot==3.0.1
pydotplus==2.0.2
pyflakes==3.2.0
pyfuseki==1.6
pyg-lib==0.4.0+pt22cu121
pygifsicle==1.1.0
pygls==1.3.1
Pygments==2.18.0
pygwalker==0.4.9.1
PyJWT==2.8.0
pykeen==1.10.2
pylint==3.2.5
pymoo==0.6.1.1
Pympler==1.1
PyMySQL==1.1.1
pynvml==11.5.3
pyOpenSSL==24.1.0
pyparsing==3.1.2
pypdf==4.3.0
PyPDF2==3.0.1
pypdfium2==4.30.0
pyperclip==1.9.0
pyrsistent==0.20.0
pysbd==0.3.4
pyspark==3.5.1
pystow==0.5.4
pytest==8.2.2
python-dateutil==2.9.0.post0
python-json-logger==2.0.7
python-lsp-jsonrpc==1.1.2
python-lsp-server==1.11.0
python-pptx==0.6.23
python-slugify==8.0.4
pythonds==1.2.1
pytimeparse==1.1.8
pytoolconfig==1.3.1
PyTrie==0.4.0
pytz==2024.1
pytz-deprecation-shim==0.1.0.post0
pyviz_comms==3.0.2
pywebview==5.1
PyYAML==6.0.1
pyyaml_env_tag==0.1
pyzmq==26.0.3
qtconsole==5.5.2
QtPy==2.4.1
ray==2.32.0
rdflib==7.0.0
red-black-tree-mod==1.22
referencing==0.35.1
regex==2023.12.25
requests==2.32.3
requests-oauthlib==2.0.0
requirementslib==3.0.0
reretry==0.11.8
retrying==1.3.4
rexmex==0.1.3
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
ric==0.0.4
rich==13.7.1
rich-click==1.8.3
rope==1.13.0
rpds-py==0.19.0
rsa==4.9
ruamel.yaml==0.18.6
ruamel.yaml.clib==0.2.8
safetensors==0.4.3
sanitize-ml-labels==1.0.51
schema==0.7.5
scikit-image==0.24.0
scikit-learn==1.5.1
scipy==1.10.0
scispacy==0.5.4
SecretStorage==3.3.3
segment-analytics-python==2.2.3
Send2Trash==1.8.3
sentencepiece==0.2.0
seqeval==1.2.2
setuptools-scm==8.1.0
shellingham==1.5.4
simpervisor==1.0.0
simplejson==3.19.2
six==1.16.0
smart-open==6.4.0
smmap==5.0.1
snakemake==8.16.0
snakemake-interface-common==1.17.2
snakemake-interface-executor-plugins==9.2.0
snakemake-interface-report-plugins==1.0.0
snakemake-interface-storage-plugins==3.2.3
sniffio==1.3.1
snowballstemmer==2.2.0
sortedcontainers==2.4.0
sos==0.25.1
sos-julia==0.20.0
sos-notebook==0.24.4
sos-pbs==0.20.9
soupsieve==2.5
spacy==3.7.5
spacy-legacy==3.0.12
spacy-loggers==1.0.5
SPARQLWrapper==2.0.0
spectate==1.0.1
SpeechRecognition==3.10.4
Sphinx==5.0.2
sphinx-rtd-theme==1.0.0
sphinxcontrib-applehelp==1.0.8
sphinxcontrib-bibtex==2.4.2
sphinxcontrib-devhelp==1.0.6
sphinxcontrib-htmlhelp==2.0.5
sphinxcontrib-jquery==4.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.7
sphinxcontrib-serializinghtml==1.1.10
SQLAlchemy==2.0.31
sqlglot==25.6.0
sqlparse==0.5.1
srsly==2.4.8
st_link_analysis==0.1.0
stack-data==0.6.3
stanfordcorenlp==3.9.1.1
statsd==4.0.1
stopit==1.1.2
stqdm==0.0.5
streamlit==1.36.0
streamlit-agraph==0.0.45
support-developer==1.0.5
sympy==1.13.0
tabulate==0.9.0
tbb==2021.13.0
tblib==3.0.0
tenacity==8.5.0
tensorboard==2.16.2
tensorboard-data-server==0.7.2
tensorboard-plugin-wit==1.8.1
tensorflow==2.16.2
tensorflow-estimator==2.15.0
tensorflow-io-gcs-filesystem==0.37.1
termcolor==2.4.0
terminado==0.18.1
terminaltables==3.1.10
text-unidecode==1.3
textract-py3==2.0.1
texttable==1.7.0
thinc==8.2.3
threadpoolctl==3.5.0
throttler==1.2.2
tifffile==2024.7.2
tinycss2==1.3.0
tokenizers==0.19.1
toml==0.10.2
tomli==2.0.1
tomlkit==0.13.0
toolz==0.12.1
toposort==1.10
torch==2.3.1
torch-ppr==0.0.8
torch_cluster @ file:///srv/scratch/patrice/src/python/pytorch_cluster
torch_geometric==2.5.3
torch_max_mem @ file:///srv/scratch/patrice/src/python/torch-max-mem
torch_scatter @ file:///srv/scratch/patrice/src/python/torch_scatter
torch_sparse @ file:///srv/scratch/patrice/src/python/pytorch_sparse
torchaudio==2.3.1
torchdata==0.7.1
torchvision==0.18.1
tornado==6.4.1
tqdm==4.66.4
traitlets==5.14.2
traittypes==0.2.1
transformers==4.42.4
transient_display_data==0.4.4
trino==0.329.0
triton==2.3.1
typeguard==4.3.0
typer==0.12.3
types-dataclasses==0.6.6
types-python-dateutil==2.9.0.20240316
typing==3.7.4.3
typing-inspect==0.9.0
typing_extensions==4.12.2
tzdata==2024.1
tzlocal==5.2
uc-micro-py==1.0.3
ujson==5.10.0
uri-template==1.3.0
urllib3==2.2.2
userinput==1.0.22
validate-email==1.3
validate-version-code==1.0.4
validators==0.33.0
vega-datasets==0.9.0
Wand==0.6.13
wasabi==1.1.3
wasmtime==22.0.0
watchdog==4.0.1
wcwidth==0.2.13
weasel==0.4.1
webcolors==24.6.0
webencodings==0.5.1
websocket-client==1.8.0
websockets==12.0
Werkzeug==3.0.3
whatthepatch==1.0.6
widgetsnbextension==4.0.11
wrapt==1.16.0
xlrd==2.0.1
XlsxWriter==3.2.0
xxhash==3.4.1
xyzservices==2024.6.0
y-py==0.6.2
yamlordereddictloader==0.4.2
yapf==0.40.2
yarg==0.1.9
yarl==1.9.4
yfiles_jupyter_graphs==1.7.3
ypy-websocket==0.12.4
yte==1.5.4
zict==3.0.0
zipp==3.19.2
zstandard==0.23.0Subsidiary question: is there a way to list "obsolete"/ "abandoned" packages? Or to have their corresponding release date for instance to help cleaning up such an environment. Or get the list of "leaf" ones so that they could be removed at least without breaking others (may be users but that is another problem). Thanks!
realiti4
commented
1 month ago Currently not possible with this tool, but it is a really good idea. I'm adding this to the TODOs, I will try to implement this with the next release, it would be a nice feature.
Hi, pip-upgrade command shows bokeh as possible upgrade candidate but doing this breaks the panel package. Thanks!