Version mismatch

[HelloWorldLTY]

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Hi, I also found that the pertpy from pip and pertpy from github are in different version. For example, milo plot function is not included in the pip install version. Would you please condsider revising it? Thanks.

Version information

absl-py 1.4.0 adjustText 0.7.3 aiohttp 3.8.5 aiosignal 1.3.1 anndata 0.9.2 annotated-types 0.5.0 anyio 4.0.0 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 arrow 1.2.3 arviz 0.15.1 asciitree 0.3.3 asttokens 2.2.1 async-lru 2.0.4 async-timeout 4.0.3 attrs 23.1.0 Babel 2.12.1 backcall 0.2.0 backports.zoneinfo 0.2.1 beautifulsoup4 4.12.2 bleach 6.0.0 cached-property 1.5.2 cachetools 5.3.1 certifi 2023.7.22 cffi 1.15.1 chardet 5.2.0 charset-normalizer 3.2.0 chex 0.1.7 click 8.1.7 cloudpickle 2.2.1 cmake 3.27.2 comm 0.1.4 contextlib2 21.6.0 contourpy 1.1.0 custom-inherit 2.4.1 cycler 0.11.0 dask 2023.5.0 dask-image 2023.3.0 debugpy 1.6.7.post1 decorator 5.1.1 decoupler 1.6.0 defusedxml 0.7.1 dm-tree 0.1.8 docrep 0.3.2 entrypoints 0.4 et-xmlfile 1.1.0 etils 1.3.0 exceptiongroup 1.1.3 executing 1.2.0 fasteners 0.18 fastjsonschema 2.18.0 filelock 3.12.3 flax 0.7.2 fonttools 4.42.1 fqdn 1.5.1 frozenlist 1.4.0 fsspec 2023.6.0 future 0.18.3 google-auth 2.22.0 google-auth-oauthlib 1.0.0 grpcio 1.57.0 h5netcdf 1.1.0 h5py 3.9.0 idna 3.4 igraph 0.10.6 imageio 2.31.2 importlib-metadata 6.8.0 importlib-resources 6.0.1 inflect 7.0.0 ipykernel 6.25.1 ipython 8.12.2 ipython-genutils 0.2.0 ipywidgets 8.1.0 isoduration 20.11.0 jax 0.4.13 jaxlib 0.4.13 jaxopt 0.8.3 jedi 0.19.0 Jinja2 3.1.2 joblib 1.3.2 json5 0.9.14 jsonpointer 2.4 jsonschema 4.19.0 jsonschema-specifications 2023.7.1 jupyter 1.0.0 jupyter_client 8.3.1 jupyter-console 6.6.3 jupyter_core 5.3.1 jupyter-events 0.7.0 jupyter-lsp 2.2.0 jupyter_server 2.7.3 jupyter_server_terminals 0.4.4 jupyterlab 4.0.5 jupyterlab-pygments 0.2.2 jupyterlab_server 2.24.0 jupyterlab-widgets 3.0.8 kiwisolver 1.4.5 lazy_loader 0.3 leidenalg 0.9.1 lightning-utilities 0.9.0 lit 16.0.6 llvmlite 0.39.1 locket 1.0.0 Markdown 3.4.4 markdown-it-py 3.0.0 MarkupSafe 2.1.3 matplotlib 3.7.2 matplotlib-inline 0.1.6 matplotlib-scalebar 0.8.1 mdurl 0.1.2 mistune 3.0.1 mizani 0.9.3 ml-collections 0.1.1 ml-dtypes 0.2.0 mpmath 1.3.0 msgpack 1.0.5 mudata 0.2.3 multidict 6.0.4 multipledispatch 1.0.0 muon 0.1.6 natsort 8.4.0 nbclient 0.8.0 nbconvert 7.8.0 nbformat 5.9.2 nest-asyncio 1.5.7 networkx 3.1 notebook 7.0.3 notebook_shim 0.2.3 numba 0.56.4 numcodecs 0.11.0 numpy 1.22.4 numpyro 0.11.0 nvidia-cublas-cu11 11.10.3.66 nvidia-cuda-cupti-cu11 11.7.101 nvidia-cuda-nvrtc-cu11 11.7.99 nvidia-cuda-runtime-cu11 11.7.99 nvidia-cudnn-cu11 8.5.0.96 nvidia-cufft-cu11 10.9.0.58 nvidia-curand-cu11 10.2.10.91 nvidia-cusolver-cu11 11.4.0.1 nvidia-cusparse-cu11 11.7.4.91 nvidia-nccl-cu11 2.14.3 nvidia-nvtx-cu11 11.7.91 oauthlib 3.2.2 omnipath 1.0.7 openpyxl 3.1.2 opt-einsum 3.3.0 optax 0.1.7 orbax-checkpoint 0.2.3 ott-jax 0.4.6 overrides 7.4.0 packaging 23.1 pandas 1.5.3 pandocfilters 1.5.0 parso 0.8.3 partd 1.4.0 patsy 0.5.3 pertpy 0.4.0 pertvi 0.0.1 pexpect 4.8.0 pickleshare 0.7.5 Pillow 10.0.0 PIMS 0.6.1 pip 23.2.1 pkgutil_resolve_name 1.3.10 platformdirs 3.10.0 plotnine 0.10.1 ply 3.11 prometheus-client 0.17.1 prompt-toolkit 3.0.36 protobuf 3.20.1 psutil 5.9.5 ptyprocess 0.7.0 pure-eval 0.2.2 py-pcha 0.1.3 pyasn1 0.5.0 pyasn1-modules 0.3.0 pycparser 2.21 pydantic 2.3.0 pydantic_core 2.6.3 pyDeprecate 0.3.1 Pygments 2.16.1 pynndescent 0.5.10 Pyomo 6.8.0 pyparsing 3.0.9 pypi-latest 0.1.2 pypng 0.20220715.0 PyQt5 5.15.11 PyQt5-Qt5 5.15.15 PyQt5_sip 12.15.0 pyro-api 0.1.2 pyro-ppl 1.8.6 python-dateutil 2.8.2 python-json-logger 2.0.7 pytorch-lightning 1.7.7 pytz 2023.3 PyWavelets 1.4.1 PyYAML 6.0.1 pyzmq 25.1.1 qtconsole 5.4.3 QtPy 2.4.0 questionary 2.0.1 referencing 0.30.2 reportlab 4.2.5 requests 2.31.0 requests-oauthlib 1.3.1 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rich 13.5.2 rpds-py 0.10.0 rpy2 3.5.16 rsa 4.9 scanpy 1.9.4 scikit-image 0.21.0 scikit-learn 1.3.0 scikit-misc 0.1.4 scipy 1.10.1 scvi-tools 0.19.0 seaborn 0.11.2 Send2Trash 1.8.2 session-info 1.0.0 setuptools 75.2.0 simvi 0.1.0 six 1.16.0 sklearn 0.0.post7 slicerator 1.1.0 sniffio 1.3.0 soupsieve 2.4.1 sparsecca 0.3.1 squidpy 1.2.3 stack-data 0.6.2 statannotations 0.5.0 statsmodels 0.14.0 stdlib-list 0.9.0 switchlang 0.1.0 sympy 1.12 tensorboard 2.14.0 tensorboard-data-server 0.7.1 tensorstore 0.1.41 terminado 0.17.1 texttable 1.6.7 threadpoolctl 3.2.0 tifffile 2023.7.10 tinycss2 1.2.1 tomli 2.0.1 toolz 0.12.0 torch 2.0.1 torch-geometric 2.3.1 torchmetrics 0.11.4 tornado 6.3.3 toyplot 2.0.0 toytree 2.0.5 tqdm 4.66.1 traitlets 5.9.0 triton 2.0.0 typing_extensions 4.7.1 tzdata 2023.3 tzlocal 5.2 umap-learn 0.5.3 uri-template 1.3.0 urllib3 1.26.16 validators 0.21.2 wcwidth 0.2.6 webcolors 1.13 webencodings 0.5.1 websocket-client 1.6.2 Werkzeug 2.3.7 wheel 0.41.2 widgetsnbextension 4.0.8 wrapt 1.15.0 xarray 2023.1.0 xarray-einstats 0.5.1 yarl 1.9.2 zarr 2.16.1 zipp 3.16.2

[Zethson]

They should be very similar and the plotting functions should be available. Please fill out the issue template! Which versions are you using?

[HelloWorldLTY]

Hi I have updated, running pip install pertpy -U gives me 0.4.0.

[Zethson]

Yeah this is ancient. The latest version on pypi is https://pypi.org/project/pertpy/ 0.9.4 . You must be using an old Python version. Please use 3.10 or 3.11 in a virtual environment.