search

nel-lab / mesmerize-core

High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
Other
61 stars 15 forks source link

Installation discrepancies with Caiman #237

Closed kfouke1 closed 1 year ago

kfouke1 commented 1 year ago

Hi,

I am trying to install mesmerize-core into a new envs just as the installation docs explain using mambaforge. I have a successful caiman environment already in mambaforge working, but it is an older caiman package that I do not want to update, so I am trying to install a completely new environment. However, even when creating the envs from my base mamba envs, this issue arises:

Encountered problems while solving:

  • package mesmerize-core-0.1.0.b1-pyhd8ed1ab_0 requires caiman >=1.9.10, but none of the providers can be installed

I have tried to install caiman of an updated version first (1.9.10), but still will not work as there are issues with tensorflow and pandas that pop up. Any advice?

Thanks! Kaitlyn Screenshot 2023-10-26 171317

kushalkolar commented 1 year ago

What mambaforge version and pyhton version?

kfouke1 commented 1 year ago

mamba 1.1.0 conda 22.11.1 I was setting it up with python 3.9?

kushalkolar commented 1 year ago

For some reason it seems to be trying to install mescore v0.10.b1 which is an old beta, can you try:

mamba create -n mescore -c conda-forge mesmerize-core=0.2.2
kfouke1 commented 1 year ago

Same issue unfortunately image

kushalkolar commented 1 year ago

Can you try:

mamba create -n test-caiman -c conda-forge caiman=1.9.16
kfouke1 commented 1 year ago

I got this issue before when I tried to only install caiman as well: image

kushalkolar commented 1 year ago

@pgunn suggests this is because tensorflow is only on the defaults channels 

mamba create -n mescore -c defaults -c conda-forge mesmerize-core
kfouke1 commented 1 year ago

It worked a little bit! It could download all the packages, but then did not verify the transaction: image

kushalkolar commented 1 year ago

This is an issue where Windows does not work with long file paths, you have to enable it: https://lifehacker.com/windows-10-allows-file-names-longer-than-260-characters-1785201032

After that you should be able to do:

mamba create -n mescore -c defaults -c conda-forge mesmerize-core
kushalkolar commented 1 year ago

did that work?

kfouke1 commented 1 year ago

Yes it did! Thank you so much for your help, I appreciate it.

Best, Kaitlyn

kushalkolar commented 1 year ago

Let us know if you have other issues or questions!

kfouke1 commented 1 year ago

Hi! I am now trying to update my mesmerize environment in preparation for the workshop, however I am unable to update caiman higher than 1.9.12. I have the current versions: caiman 1.9.12 mesmerize-core: 0.2.2 fastplotlib: 0.1.0a15 mesmerize-viz 0.1.0b1 Will these versions be sufficient for the workshop? Thanks! Kaitlyn

pgunn commented 1 year ago

@kfouke1 Can you send the output of conda info and conda list from inside the environment? Maybe we can figure out and fix this before the workshop.

kfouke1 commented 1 year ago

This is conda info: active environment : C:\Users\NaumannLab_KEF\mambaforge\envs\mescore active env location : C:\Users\NaumannLab_KEF\mambaforge\envs\mescore shell level : 2 user config file : C:\Users\NaumannLab_KEF\.condarc populated config files : C:\Users\NaumannLab_KEF\.condarc conda version : 22.11.1 conda-build version : 3.21.8 python version : 3.9.12.final.0 virtual packages : __archspec=1=x86_64 __cuda=11.6=0 __win=0=0 base environment : C:\Users\NaumannLab_KEF\anaconda3 (writable) conda av data dir : C:\Users\NaumannLab_KEF\anaconda3\etc\conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/win-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\Users\NaumannLab_KEF\anaconda3\pkgs C:\Users\NaumannLab_KEF\.conda\pkgs C:\Users\NaumannLab_KEF\AppData\Local\conda\conda\pkgs envs directories : C:\Users\NaumannLab_KEF\anaconda3\envs C:\Users\NaumannLab_KEF\.conda\envs C:\Users\NaumannLab_KEF\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/22.11.1 requests/2.27.1 CPython/3.9.12 Windows/10 Windows/10.0.22000 administrator : False netrc file : None offline mode : False

This is conda list: Name Version Build Channel _tflow_select 2.3.0 mkl abseil-cpp 20211102.0 hd77b12b_0 absl-py 1.4.0 py39haa95532_0 aiofiles 22.1.0 py39haa95532_0 aiohttp 3.8.5 py39h2bbff1b_0 aiosignal 1.2.0 pyhd3eb1b0_0 aiosqlite 0.18.0 py39haa95532_0 anyio 3.5.0 py39haa95532_0 argon2-cffi 21.3.0 pyhd3eb1b0_0 argon2-cffi-bindings 21.2.0 py39h2bbff1b_0 arrow 1.3.0 pypi_0 pypi asttokens 2.0.5 pyhd3eb1b0_0 astunparse 1.6.3 py_0 async-timeout 4.0.2 py39haa95532_0 attrs 23.1.0 py39haa95532_0 babel 2.11.0 py39haa95532_0 backcall 0.2.0 pyhd3eb1b0_0 beautifulsoup4 4.12.2 py39haa95532_0 blas 1.0 mkl bleach 4.1.0 pyhd3eb1b0_0 blinker 1.6.2 py39haa95532_0 blosc 1.21.3 h6c2663c_0 bokeh 3.2.1 py39h9909e9c_0 bottleneck 1.3.5 py39h080aedc_0 bqplot 0.12.42 pypi_0 pypi brotli 1.0.9 h2bbff1b_7 brotli-bin 1.0.9 h2bbff1b_7 brotli-python 1.0.9 py39hd77b12b_7 bzip2 1.0.8 he774522_0 ca-certificates 2023.08.22 haa95532_0 cachetools 4.2.2 pyhd3eb1b0_0 caiman 1.9.12 py39h2ba5b7c_0 conda-forge certifi 2023.7.22 py39haa95532_0 cffi 1.15.1 py39h2bbff1b_3 cfitsio 3.470 h2bbff1b_7 charls 2.2.0 h6c2663c_0 charset-normalizer 2.0.4 pyhd3eb1b0_0 click 8.1.7 py39haa95532_0 cloudpickle 2.2.1 py39haa95532_0 colorama 0.4.6 py39haa95532_0 colorcet 3.0.1 py39haa95532_0 comm 0.1.2 py39haa95532_0 contourpy 1.0.5 py39h59b6b97_0 cryptography 41.0.3 py39h3438e0d_0 cycler 0.11.0 pyhd3eb1b0_0 cytoolz 0.12.0 py39h2bbff1b_0 dask-core 2023.6.0 py39haa95532_0 debugpy 1.6.7 py39hd77b12b_0 decorator 5.1.1 pyhd3eb1b0_0 defusedxml 0.7.1 pyhd3eb1b0_0 eigen 3.3.7 h59b6b97_1 entrypoints 0.4 py39haa95532_0 exceptiongroup 1.0.4 py39haa95532_0 executing 0.8.3 pyhd3eb1b0_0 fastplotlib 0.1.0a15 pypi_0 pypi flatbuffers 2.0.0 h6c2663c_0 fonttools 4.25.0 pyhd3eb1b0_0 fqdn 1.5.1 pypi_0 pypi freetype 2.10.4 hd328e21_0 freetype-py 2.4.0 pypi_0 pypi frozenlist 1.3.3 py39h2bbff1b_0 fsspec 2023.9.2 py39haa95532_0 future 0.18.3 py39haa95532_0 gast 0.4.0 pypi_0 pypi giflib 5.2.1 h8cc25b3_3 glib 2.69.1 h5dc1a3c_1 google-auth 2.22.0 py39haa95532_0 google-auth-oauthlib 0.4.4 pyhd3eb1b0_0 google-pasta 0.2.0 pyhd3eb1b0_0 grpcio 1.42.0 py39hc60d5dd_0 gst-plugins-base 1.18.5 h9e645db_0 gstreamer 1.18.5 hd78058f_0 h5py 3.9.0 py39hfc34f40_0 hdf5 1.12.1 h1756f20_2 hdmf 3.10.0 pyh1ea47a8_0 conda-forge holoviews 1.17.1 py39haa95532_0 icc_rt 2022.1.0 h6049295_2 icu 58.2 ha925a31_3 idna 3.4 py39haa95532_0 imagecodecs 2021.8.26 py39hc0a7faf_1 imageio 2.31.4 py39haa95532_0 importlib-metadata 6.0.0 py39haa95532_0 importlib_metadata 6.0.0 hd3eb1b0_0 importlib_resources 6.1.0 py39haa95532_0 iniconfig 1.1.1 pyhd3eb1b0_0 intel-openmp 2023.1.0 h59b6b97_46319 ipydatagrid 1.2.0 pypi_0 pypi ipykernel 6.25.0 py39h9909e9c_0 ipyparallel 8.4.1 py39haa95532_0 ipython 8.15.0 py39haa95532_0 ipython_genutils 0.2.0 pyhd3eb1b0_1 ipywidgets 8.0.4 py39haa95532_0 isoduration 20.11.0 pypi_0 pypi jedi 0.18.1 py39haa95532_1 jinja2 3.1.2 py39haa95532_0 joblib 1.2.0 py39haa95532_0 jpeg 9e h2bbff1b_1 json5 0.9.6 pyhd3eb1b0_0 jsonpointer 2.4 pypi_0 pypi jsonschema 4.17.3 py39haa95532_0 jupyter 1.0.0 py39haa95532_8 jupyter-rfb 0.4.1 pypi_0 pypi jupyter_client 7.4.9 py39haa95532_0 jupyter_console 6.6.3 py39haa95532_0 jupyter_core 5.3.0 py39haa95532_0 jupyter_events 0.6.3 py39haa95532_0 jupyter_server 1.23.4 py39haa95532_0 jupyter_server_fileid 0.9.0 py39haa95532_0 jupyter_server_ydoc 0.8.0 py39haa95532_1 jupyter_ydoc 0.2.4 py39haa95532_0 jupyterlab 3.6.3 py39haa95532_0 jupyterlab_pygments 0.1.2 py_0 jupyterlab_server 2.22.0 py39haa95532_0 jupyterlab_widgets 3.0.5 py39haa95532_0 keras 2.8.0 py39haa95532_0 keras-preprocessing 1.1.2 pyhd3eb1b0_0 kiwisolver 1.4.4 py39hd77b12b_0 lcms2 2.12 h83e58a3_0 lerc 3.0 hd77b12b_0 libaec 1.0.4 h33f27b4_1 libbrotlicommon 1.0.9 h2bbff1b_7 libbrotlidec 1.0.9 h2bbff1b_7 libbrotlienc 1.0.9 h2bbff1b_7 libclang 12.0.0 default_h627e005_2 libcurl 7.84.0 h86230a5_0 libdeflate 1.8 h2bbff1b_5 libffi 3.4.4 hd77b12b_0 libiconv 1.16 h2bbff1b_2 libogg 1.3.5 h2bbff1b_1 libpng 1.6.37 h2a8f88b_0 libprotobuf 3.20.1 h23ce68f_0 libsodium 1.0.18 h62dcd97_0 libssh2 1.10.0 hcd4344a_2 libtiff 4.5.0 h8a3f274_0 libvorbis 1.3.7 he774522_0 libwebp 1.2.4 hbc33d0d_1 libwebp-base 1.2.4 h2bbff1b_1 libxml2 2.9.14 h0ad7f3c_0 libxslt 1.1.35 h2bbff1b_0 libzlib 1.2.12 h8ffe710_2 conda-forge libzopfli 1.0.3 ha925a31_0 linkify-it-py 2.0.0 py39haa95532_0 llvmlite 0.41.1 pypi_0 pypi locket 1.0.0 py39haa95532_0 lxml 4.9.1 py39h1985fb9_0 lz4-c 1.9.4 h2bbff1b_0 markdown 3.4.1 py39haa95532_0 markdown-it-py 2.2.0 py39haa95532_1 markupsafe 2.1.1 py39h2bbff1b_0 matplotlib 3.7.2 py39haa95532_0 matplotlib-base 3.7.2 py39h4ed8f06_0 matplotlib-inline 0.1.6 py39haa95532_0 mdit-py-plugins 0.3.0 py39haa95532_0 mdurl 0.1.0 py39haa95532_0 mesmerize-core 0.2.2 pyhd8ed1ab_0 conda-forge mesmerize-viz 0.1.0b1 dev_0 <develop> mistune 0.8.4 py39h2bbff1b_1000 mkl 2023.1.0 h6b88ed4_46357 mkl-service 2.4.0 py39h2bbff1b_1 mkl_fft 1.3.8 py39h2bbff1b_0 mkl_random 1.2.4 py39h59b6b97_0 multidict 6.0.2 py39h2bbff1b_0 munkres 1.1.4 py_0 mypy 1.5.1 py39haa95532_0 mypy_extensions 1.0.0 py39haa95532_0 nbclassic 0.5.5 py39haa95532_0 nbclient 0.5.13 py39haa95532_0 nbconvert 6.5.4 py39haa95532_0 nbformat 5.9.2 py39haa95532_0 nest-asyncio 1.5.6 py39haa95532_0 networkx 3.1 py39haa95532_0 nose 1.3.7 pyhd3eb1b0_1008 notebook 6.5.4 py39haa95532_1 notebook-shim 0.2.2 py39haa95532_0 numba 0.58.1 pypi_0 pypi numexpr 2.8.7 py39h2cd9be0_0 numpy 1.26.0 py39h055cbcc_0 numpy-base 1.26.0 py39h65a83cf_0 oauthlib 3.2.2 py39haa95532_0 opencv 4.6.0 py39h104de81_2 openjpeg 2.4.0 h4fc8c34_0 openssl 1.1.1w h2bbff1b_0 opt_einsum 3.3.0 pyhd3eb1b0_1 packaging 23.1 py39haa95532_0 pandas 2.1.1 py39h4ed8f06_0 pandocfilters 1.5.0 pyhd3eb1b0_0 panel 1.2.3 py39haa95532_0 param 1.13.0 py39haa95532_0 parso 0.8.3 pyhd3eb1b0_0 partd 1.4.0 py39haa95532_0 pcre 8.45 hd77b12b_0 peakutils 1.3.4 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 pyhd3eb1b0_1003 pillow 9.3.0 py39hdc2b20a_1 pims 0.5 pyhd3eb1b0_1 pip 23.3 py39haa95532_0 platformdirs 3.10.0 py39haa95532_0 pluggy 1.0.0 py39haa95532_1 ply 3.11 py39haa95532_0 prometheus_client 0.14.1 py39haa95532_0 prompt-toolkit 3.0.36 py39haa95532_0 prompt_toolkit 3.0.36 hd3eb1b0_0 protobuf 3.20.1 py39hd77b12b_0 psutil 5.9.0 py39h2bbff1b_0 pure_eval 0.2.2 pyhd3eb1b0_0 py2vega 0.6.1 pypi_0 pypi pyasn1 0.4.8 pyhd3eb1b0_0 pyasn1-modules 0.2.8 py_0 pycparser 2.21 pyhd3eb1b0_0 pyct 0.5.0 py39haa95532_0 pygfx 0.1.15 pypi_0 pypi pygments 2.15.1 py39haa95532_1 pyjwt 2.4.0 py39haa95532_0 pylinalg 0.4.1 pypi_0 pypi pynwb 2.5.0 pyh267d04e_0 conda-forge pyopenssl 23.2.0 py39haa95532_0 pyparsing 3.0.9 py39haa95532_0 pyqt 5.15.7 py39hd77b12b_0 pyqt5-sip 12.11.0 py39hd77b12b_0 pyqt6 6.6.0 pypi_0 pypi pyqt6-qt6 6.6.0 pypi_0 pypi pyqt6-sip 13.6.0 pypi_0 pypi pyqtgraph 0.13.1 py39haa95532_0 pyrsistent 0.18.0 py39h196d8e1_0 pysocks 1.7.1 py39haa95532_0 pytest 7.4.0 py39haa95532_0 python 3.9.18 h6244533_0 python-dateutil 2.8.2 pyhd3eb1b0_0 python-fastjsonschema 2.16.2 py39haa95532_0 python-flatbuffers 2.0 pyhd3eb1b0_0 python-json-logger 2.0.7 py39haa95532_0 python-tzdata 2023.3 pyhd3eb1b0_0 python_abi 3.9 2_cp39 conda-forge pytz 2023.3.post1 py39haa95532_0 pyviz_comms 2.3.0 py39haa95532_0 pywavelets 1.4.1 py39h2bbff1b_0 pywin32 305 py39h2bbff1b_0 pywinpty 2.0.10 py39h5da7b33_0 pyyaml 6.0.1 py39h2bbff1b_0 pyzmq 23.2.0 py39hd77b12b_0 qt-main 5.15.2 he8e5bd7_7 qt-webengine 5.15.9 h5bd16bc_7 qtconsole 5.4.2 py39haa95532_0 qtpy 2.2.0 py39haa95532_0 qtwebkit 5.212 h3ad3cdb_4 requests 2.31.0 py39haa95532_0 requests-oauthlib 1.3.0 py_0 rfc3339-validator 0.1.4 py39haa95532_0 rfc3986-validator 0.1.1 py39haa95532_0 rsa 4.7.2 pyhd3eb1b0_1 ruamel.yaml 0.17.21 py39h2bbff1b_0 ruamel.yaml.clib 0.2.6 py39h2bbff1b_1 scikit-image 0.19.3 py39hd77b12b_1 scikit-learn 1.3.0 py39h4ed8f06_0 scipy 1.11.3 py39h309d312_0 send2trash 1.8.0 pyhd3eb1b0_1 setuptools 68.0.0 py39haa95532_0 sidecar 0.7.0 pypi_0 pypi simplejpeg 1.7.2 pypi_0 pypi sip 6.6.2 py39hd77b12b_0 six 1.16.0 pyhd3eb1b0_1 slicerator 1.0.0 pyhd3eb1b0_0 snappy 1.1.9 h6c2663c_0 sniffio 1.2.0 py39haa95532_1 soupsieve 2.5 py39haa95532_0 sqlite 3.41.2 h2bbff1b_0 stack_data 0.2.0 pyhd3eb1b0_0 tbb 2021.8.0 h59b6b97_0 tensorboard 2.8.0 py39haa95532_0 tensorboard-data-server 0.6.1 py39haa95532_0 tensorboard-plugin-wit 1.8.1 py39haa95532_0 tensorflow 2.8.2 mkl_py39hfd350ca_0 tensorflow-base 2.8.2 mkl_py39h6a7f48e_0 tensorflow-estimator 2.8.0 py39hd4e2768_0 termcolor 2.1.0 py39haa95532_0 terminado 0.17.1 py39haa95532_0 threadpoolctl 2.2.0 pyh0d69192_0 tifffile 2021.7.2 pyhd3eb1b0_2 tinycss2 1.2.1 py39haa95532_0 tk 8.6.12 h2bbff1b_0 toml 0.10.2 pyhd3eb1b0_0 tomli 2.0.1 py39haa95532_0 toolz 0.12.0 py39haa95532_0 tornado 6.3.3 py39h2bbff1b_0 tqdm 4.65.0 py39hd4e2768_0 traitlets 5.7.1 py39haa95532_0 traittypes 0.2.1 pypi_0 pypi tslearn 0.6.2 pypi_0 pypi types-python-dateutil 2.8.19.14 pypi_0 pypi typing-extensions 4.7.1 py39haa95532_0 typing_extensions 4.7.1 py39haa95532_0 tzdata 2023c h04d1e81_0 uc-micro-py 1.0.1 py39haa95532_0 ucrt 10.0.22621.0 h57928b3_0 conda-forge uharfbuzz 0.37.3 pypi_0 pypi uri-template 1.3.0 pypi_0 pypi urllib3 1.26.18 py39haa95532_0 vc 14.2 h21ff451_1 vc14_runtime 14.36.32532 hdcecf7f_17 conda-forge vs2015_runtime 14.36.32532 h05e6639_17 conda-forge wcwidth 0.2.5 pyhd3eb1b0_0 webcolors 1.13 pypi_0 pypi webencodings 0.5.1 py39haa95532_1 websocket-client 0.58.0 py39haa95532_4 werkzeug 2.2.3 py39haa95532_0 wgpu 0.11.0 pypi_0 pypi wheel 0.41.2 py39haa95532_0 widgetsnbextension 4.0.5 py39haa95532_0 win_inet_pton 1.1.0 py39haa95532_0 winpty 0.4.3 4 wrapt 1.14.1 py39h2bbff1b_0 xyzservices 2022.9.0 py39haa95532_1 xz 5.4.2 h8cc25b3_0 y-py 0.5.9 py39hb6bf4ef_0 yaml 0.2.5 he774522_0 yarl 1.8.1 py39h2bbff1b_0 ypy-websocket 0.8.2 py39haa95532_0 z5py 2.0.15 py39hcf4c0ac_0 conda-forge zeromq 4.3.4 hd77b12b_0 zfp 0.5.5 hd77b12b_6 zipp 3.11.0 py39haa95532_0 zlib 1.2.12 h8cc25b3_2 zstd 1.5.2 h19a0ad4_0

kfouke1 commented 1 year ago

sorry for the weird formatting! here is each command again: conda info:

 active environment : C:\Users\NaumannLab_KEF\mambaforge\envs\mescore
active env location : C:\Users\NaumannLab_KEF\mambaforge\envs\mescore
        shell level : 2
   user config file : C:\Users\NaumannLab_KEF\.condarc

populated config files : C:\Users\NaumannLab_KEF.condarc conda version : 22.11.1 conda-build version : 3.21.8 python version : 3.9.12.final.0 virtual packages : __archspec=1=x86_64 cuda=11.6=0 win=0=0 base environment : C:\Users\NaumannLab_KEF\anaconda3 (writable) conda av data dir : C:\Users\NaumannLab_KEF\anaconda3\etc\conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/win-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\Users\NaumannLab_KEF\anaconda3\pkgs C:\Users\NaumannLab_KEF.conda\pkgs C:\Users\NaumannLab_KEF\AppData\Local\conda\conda\pkgs envs directories : C:\Users\NaumannLab_KEF\anaconda3\envs C:\Users\NaumannLab_KEF.conda\envs C:\Users\NaumannLab_KEF\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/22.11.1 requests/2.27.1 CPython/3.9.12 Windows/10 Windows/10.0.22000 administrator : False netrc file : None offline mode : False

conda list:

Name Version Build Channel _tflow_select 2.3.0 mkl abseil-cpp 20211102.0 hd77b12b_0 absl-py 1.4.0 py39haa95532_0 aiofiles 22.1.0 py39haa95532_0 aiohttp 3.8.5 py39h2bbff1b_0 aiosignal 1.2.0 pyhd3eb1b0_0 aiosqlite 0.18.0 py39haa95532_0 anyio 3.5.0 py39haa95532_0 argon2-cffi 21.3.0 pyhd3eb1b0_0 argon2-cffi-bindings 21.2.0 py39h2bbff1b_0 arrow 1.3.0 pypi_0 pypi asttokens 2.0.5 pyhd3eb1b0_0 astunparse 1.6.3 py_0 async-timeout 4.0.2 py39haa95532_0 attrs 23.1.0 py39haa95532_0 babel 2.11.0 py39haa95532_0 backcall 0.2.0 pyhd3eb1b0_0 beautifulsoup4 4.12.2 py39haa95532_0 blas 1.0 mkl bleach 4.1.0 pyhd3eb1b0_0 blinker 1.6.2 py39haa95532_0 blosc 1.21.3 h6c2663c_0 bokeh 3.2.1 py39h9909e9c_0 bottleneck 1.3.5 py39h080aedc_0 bqplot 0.12.42 pypi_0 pypi brotli 1.0.9 h2bbff1b_7 brotli-bin 1.0.9 h2bbff1b_7 brotli-python 1.0.9 py39hd77b12b_7 bzip2 1.0.8 he774522_0 ca-certificates 2023.08.22 haa95532_0 cachetools 4.2.2 pyhd3eb1b0_0 caiman 1.9.12 py39h2ba5b7c_0 conda-forge certifi 2023.7.22 py39haa95532_0 cffi 1.15.1 py39h2bbff1b_3 cfitsio 3.470 h2bbff1b_7 charls 2.2.0 h6c2663c_0 charset-normalizer 2.0.4 pyhd3eb1b0_0 click 8.1.7 py39haa95532_0 cloudpickle 2.2.1 py39haa95532_0 colorama 0.4.6 py39haa95532_0 colorcet 3.0.1 py39haa95532_0 comm 0.1.2 py39haa95532_0 contourpy 1.0.5 py39h59b6b97_0 cryptography 41.0.3 py39h3438e0d_0 cycler 0.11.0 pyhd3eb1b0_0 cytoolz 0.12.0 py39h2bbff1b_0 dask-core 2023.6.0 py39haa95532_0 debugpy 1.6.7 py39hd77b12b_0 decorator 5.1.1 pyhd3eb1b0_0 defusedxml 0.7.1 pyhd3eb1b0_0 eigen 3.3.7 h59b6b97_1 entrypoints 0.4 py39haa95532_0 exceptiongroup 1.0.4 py39haa95532_0 executing 0.8.3 pyhd3eb1b0_0 fastplotlib 0.1.0a15 pypi_0 pypi flatbuffers 2.0.0 h6c2663c_0 fonttools 4.25.0 pyhd3eb1b0_0 fqdn 1.5.1 pypi_0 pypi freetype 2.10.4 hd328e21_0 freetype-py 2.4.0 pypi_0 pypi frozenlist 1.3.3 py39h2bbff1b_0 fsspec 2023.9.2 py39haa95532_0 future 0.18.3 py39haa95532_0 gast 0.4.0 pypi_0 pypi giflib 5.2.1 h8cc25b3_3 glib 2.69.1 h5dc1a3c_1 google-auth 2.22.0 py39haa95532_0 google-auth-oauthlib 0.4.4 pyhd3eb1b0_0 google-pasta 0.2.0 pyhd3eb1b0_0 grpcio 1.42.0 py39hc60d5dd_0 gst-plugins-base 1.18.5 h9e645db_0 gstreamer 1.18.5 hd78058f_0 h5py 3.9.0 py39hfc34f40_0 hdf5 1.12.1 h1756f20_2 hdmf 3.10.0 pyh1ea47a8_0 conda-forge holoviews 1.17.1 py39haa95532_0 icc_rt 2022.1.0 h6049295_2 icu 58.2 ha925a31_3 idna 3.4 py39haa95532_0 imagecodecs 2021.8.26 py39hc0a7faf_1 imageio 2.31.4 py39haa95532_0 importlib-metadata 6.0.0 py39haa95532_0 importlib_metadata 6.0.0 hd3eb1b0_0 importlib_resources 6.1.0 py39haa95532_0 iniconfig 1.1.1 pyhd3eb1b0_0 intel-openmp 2023.1.0 h59b6b97_46319 ipydatagrid 1.2.0 pypi_0 pypi ipykernel 6.25.0 py39h9909e9c_0 ipyparallel 8.4.1 py39haa95532_0 ipython 8.15.0 py39haa95532_0 ipython_genutils 0.2.0 pyhd3eb1b0_1 ipywidgets 8.0.4 py39haa95532_0 isoduration 20.11.0 pypi_0 pypi jedi 0.18.1 py39haa95532_1 jinja2 3.1.2 py39haa95532_0 joblib 1.2.0 py39haa95532_0 jpeg 9e h2bbff1b_1 json5 0.9.6 pyhd3eb1b0_0 jsonpointer 2.4 pypi_0 pypi jsonschema 4.17.3 py39haa95532_0 jupyter 1.0.0 py39haa95532_8 jupyter-rfb 0.4.1 pypi_0 pypi jupyter_client 7.4.9 py39haa95532_0 jupyter_console 6.6.3 py39haa95532_0 jupyter_core 5.3.0 py39haa95532_0 jupyter_events 0.6.3 py39haa95532_0 jupyter_server 1.23.4 py39haa95532_0 jupyter_server_fileid 0.9.0 py39haa95532_0 jupyter_server_ydoc 0.8.0 py39haa95532_1 jupyter_ydoc 0.2.4 py39haa95532_0 jupyterlab 3.6.3 py39haa95532_0 jupyterlab_pygments 0.1.2 py_0 jupyterlab_server 2.22.0 py39haa95532_0 jupyterlab_widgets 3.0.5 py39haa95532_0 keras 2.8.0 py39haa95532_0 keras-preprocessing 1.1.2 pyhd3eb1b0_0 kiwisolver 1.4.4 py39hd77b12b_0 lcms2 2.12 h83e58a3_0 lerc 3.0 hd77b12b_0 libaec 1.0.4 h33f27b4_1 libbrotlicommon 1.0.9 h2bbff1b_7 libbrotlidec 1.0.9 h2bbff1b_7 libbrotlienc 1.0.9 h2bbff1b_7 libclang 12.0.0 default_h627e005_2 libcurl 7.84.0 h86230a5_0 libdeflate 1.8 h2bbff1b_5 libffi 3.4.4 hd77b12b_0 libiconv 1.16 h2bbff1b_2 libogg 1.3.5 h2bbff1b_1 libpng 1.6.37 h2a8f88b_0 libprotobuf 3.20.1 h23ce68f_0 libsodium 1.0.18 h62dcd97_0 libssh2 1.10.0 hcd4344a_2 libtiff 4.5.0 h8a3f274_0 libvorbis 1.3.7 he774522_0 libwebp 1.2.4 hbc33d0d_1 libwebp-base 1.2.4 h2bbff1b_1 libxml2 2.9.14 h0ad7f3c_0 libxslt 1.1.35 h2bbff1b_0 libzlib 1.2.12 h8ffe710_2 conda-forge libzopfli 1.0.3 ha925a31_0 linkify-it-py 2.0.0 py39haa95532_0 llvmlite 0.41.1 pypi_0 pypi locket 1.0.0 py39haa95532_0 lxml 4.9.1 py39h1985fb9_0 lz4-c 1.9.4 h2bbff1b_0 markdown 3.4.1 py39haa95532_0 markdown-it-py 2.2.0 py39haa95532_1 markupsafe 2.1.1 py39h2bbff1b_0 matplotlib 3.7.2 py39haa95532_0 matplotlib-base 3.7.2 py39h4ed8f06_0 matplotlib-inline 0.1.6 py39haa95532_0 mdit-py-plugins 0.3.0 py39haa95532_0 mdurl 0.1.0 py39haa95532_0 mesmerize-core 0.2.2 pyhd8ed1ab_0 conda-forge mesmerize-viz 0.1.0b1 dev_0 mistune 0.8.4 py39h2bbff1b_1000 mkl 2023.1.0 h6b88ed4_46357 mkl-service 2.4.0 py39h2bbff1b_1 mkl_fft 1.3.8 py39h2bbff1b_0 mkl_random 1.2.4 py39h59b6b97_0 multidict 6.0.2 py39h2bbff1b_0 munkres 1.1.4 py_0 mypy 1.5.1 py39haa95532_0 mypy_extensions 1.0.0 py39haa95532_0 nbclassic 0.5.5 py39haa95532_0 nbclient 0.5.13 py39haa95532_0 nbconvert 6.5.4 py39haa95532_0 nbformat 5.9.2 py39haa95532_0 nest-asyncio 1.5.6 py39haa95532_0 networkx 3.1 py39haa95532_0 nose 1.3.7 pyhd3eb1b0_1008 notebook 6.5.4 py39haa95532_1 notebook-shim 0.2.2 py39haa95532_0 numba 0.58.1 pypi_0 pypi numexpr 2.8.7 py39h2cd9be0_0 numpy 1.26.0 py39h055cbcc_0 numpy-base 1.26.0 py39h65a83cf_0 oauthlib 3.2.2 py39haa95532_0 opencv 4.6.0 py39h104de81_2 openjpeg 2.4.0 h4fc8c34_0 openssl 1.1.1w h2bbff1b_0 opt_einsum 3.3.0 pyhd3eb1b0_1 packaging 23.1 py39haa95532_0 pandas 2.1.1 py39h4ed8f06_0 pandocfilters 1.5.0 pyhd3eb1b0_0 panel 1.2.3 py39haa95532_0 param 1.13.0 py39haa95532_0 parso 0.8.3 pyhd3eb1b0_0 partd 1.4.0 py39haa95532_0 pcre 8.45 hd77b12b_0 peakutils 1.3.4 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 pyhd3eb1b0_1003 pillow 9.3.0 py39hdc2b20a_1 pims 0.5 pyhd3eb1b0_1 pip 23.3 py39haa95532_0 platformdirs 3.10.0 py39haa95532_0 pluggy 1.0.0 py39haa95532_1 ply 3.11 py39haa95532_0 prometheus_client 0.14.1 py39haa95532_0 prompt-toolkit 3.0.36 py39haa95532_0 prompt_toolkit 3.0.36 hd3eb1b0_0 protobuf 3.20.1 py39hd77b12b_0 psutil 5.9.0 py39h2bbff1b_0 pure_eval 0.2.2 pyhd3eb1b0_0 py2vega 0.6.1 pypi_0 pypi pyasn1 0.4.8 pyhd3eb1b0_0 pyasn1-modules 0.2.8 py_0 pycparser 2.21 pyhd3eb1b0_0 pyct 0.5.0 py39haa95532_0 pygfx 0.1.15 pypi_0 pypi pygments 2.15.1 py39haa95532_1 pyjwt 2.4.0 py39haa95532_0 pylinalg 0.4.1 pypi_0 pypi pynwb 2.5.0 pyh267d04e_0 conda-forge pyopenssl 23.2.0 py39haa95532_0 pyparsing 3.0.9 py39haa95532_0 pyqt 5.15.7 py39hd77b12b_0 pyqt5-sip 12.11.0 py39hd77b12b_0 pyqt6 6.6.0 pypi_0 pypi pyqt6-qt6 6.6.0 pypi_0 pypi pyqt6-sip 13.6.0 pypi_0 pypi pyqtgraph 0.13.1 py39haa95532_0 pyrsistent 0.18.0 py39h196d8e1_0 pysocks 1.7.1 py39haa95532_0 pytest 7.4.0 py39haa95532_0 python 3.9.18 h6244533_0 python-dateutil 2.8.2 pyhd3eb1b0_0 python-fastjsonschema 2.16.2 py39haa95532_0 python-flatbuffers 2.0 pyhd3eb1b0_0 python-json-logger 2.0.7 py39haa95532_0 python-tzdata 2023.3 pyhd3eb1b0_0 python_abi 3.9 2_cp39 conda-forge pytz 2023.3.post1 py39haa95532_0 pyviz_comms 2.3.0 py39haa95532_0 pywavelets 1.4.1 py39h2bbff1b_0 pywin32 305 py39h2bbff1b_0 pywinpty 2.0.10 py39h5da7b33_0 pyyaml 6.0.1 py39h2bbff1b_0 pyzmq 23.2.0 py39hd77b12b_0 qt-main 5.15.2 he8e5bd7_7 qt-webengine 5.15.9 h5bd16bc_7 qtconsole 5.4.2 py39haa95532_0 qtpy 2.2.0 py39haa95532_0 qtwebkit 5.212 h3ad3cdb_4 requests 2.31.0 py39haa95532_0 requests-oauthlib 1.3.0 py_0 rfc3339-validator 0.1.4 py39haa95532_0 rfc3986-validator 0.1.1 py39haa95532_0 rsa 4.7.2 pyhd3eb1b0_1 ruamel.yaml 0.17.21 py39h2bbff1b_0 ruamel.yaml.clib 0.2.6 py39h2bbff1b_1 scikit-image 0.19.3 py39hd77b12b_1 scikit-learn 1.3.0 py39h4ed8f06_0 scipy 1.11.3 py39h309d312_0 send2trash 1.8.0 pyhd3eb1b0_1 setuptools 68.0.0 py39haa95532_0 sidecar 0.7.0 pypi_0 pypi simplejpeg 1.7.2 pypi_0 pypi sip 6.6.2 py39hd77b12b_0 six 1.16.0 pyhd3eb1b0_1 slicerator 1.0.0 pyhd3eb1b0_0 snappy 1.1.9 h6c2663c_0 sniffio 1.2.0 py39haa95532_1 soupsieve 2.5 py39haa95532_0 sqlite 3.41.2 h2bbff1b_0 stack_data 0.2.0 pyhd3eb1b0_0 tbb 2021.8.0 h59b6b97_0 tensorboard 2.8.0 py39haa95532_0 tensorboard-data-server 0.6.1 py39haa95532_0 tensorboard-plugin-wit 1.8.1 py39haa95532_0 tensorflow 2.8.2 mkl_py39hfd350ca_0 tensorflow-base 2.8.2 mkl_py39h6a7f48e_0 tensorflow-estimator 2.8.0 py39hd4e2768_0 termcolor 2.1.0 py39haa95532_0 terminado 0.17.1 py39haa95532_0 threadpoolctl 2.2.0 pyh0d69192_0 tifffile 2021.7.2 pyhd3eb1b0_2 tinycss2 1.2.1 py39haa95532_0 tk 8.6.12 h2bbff1b_0 toml 0.10.2 pyhd3eb1b0_0 tomli 2.0.1 py39haa95532_0 toolz 0.12.0 py39haa95532_0 tornado 6.3.3 py39h2bbff1b_0 tqdm 4.65.0 py39hd4e2768_0 traitlets 5.7.1 py39haa95532_0 traittypes 0.2.1 pypi_0 pypi tslearn 0.6.2 pypi_0 pypi types-python-dateutil 2.8.19.14 pypi_0 pypi typing-extensions 4.7.1 py39haa95532_0 typing_extensions 4.7.1 py39haa95532_0 tzdata 2023c h04d1e81_0 uc-micro-py 1.0.1 py39haa95532_0 ucrt 10.0.22621.0 h57928b3_0 conda-forge uharfbuzz 0.37.3 pypi_0 pypi uri-template 1.3.0 pypi_0 pypi urllib3 1.26.18 py39haa95532_0 vc 14.2 h21ff451_1 vc14_runtime 14.36.32532 hdcecf7f_17 conda-forge vs2015_runtime 14.36.32532 h05e6639_17 conda-forge wcwidth 0.2.5 pyhd3eb1b0_0 webcolors 1.13 pypi_0 pypi webencodings 0.5.1 py39haa95532_1 websocket-client 0.58.0 py39haa95532_4 werkzeug 2.2.3 py39haa95532_0 wgpu 0.11.0 pypi_0 pypi wheel 0.41.2 py39haa95532_0 widgetsnbextension 4.0.5 py39haa95532_0 win_inet_pton 1.1.0 py39haa95532_0 winpty 0.4.3 4 wrapt 1.14.1 py39h2bbff1b_0 xyzservices 2022.9.0 py39haa95532_1 xz 5.4.2 h8cc25b3_0 y-py 0.5.9 py39hb6bf4ef_0 yaml 0.2.5 he774522_0 yarl 1.8.1 py39h2bbff1b_0 ypy-websocket 0.8.2 py39haa95532_0 z5py 2.0.15 py39hcf4c0ac_0 conda-forge zeromq 4.3.4 hd77b12b_0 zfp 0.5.5 hd77b12b_6 zipp 3.11.0 py39haa95532_0 zlib 1.2.12 h8cc25b3_2 zstd 1.5.2 h19a0ad4_0

pgunn commented 1 year ago

What command did you use to make this environment? We can do a variant of it to see what went wrong, but I need to know which to start with.

kfouke1 commented 1 year ago

I used this one! mamba create -n mescore -c defaults -c conda-forge mesmerize-core

pgunn commented 1 year ago

Remove the mescore environment, then try this: mamba create -n mescore -c defaults -c conda-forge mesmerize-core caiman=1.9.16

You will probably get an error. Please paste it all here.

kfouke1 commented 1 year ago

here is the error:

Looking for: ['mesmerize-core', 'caiman=1.9.16']

pkgs/r/win-64 No change pkgs/msys2/win-64 No change pkgs/main/win-64 No change pkgs/main/noarch No change pkgs/r/noarch No change pkgs/msys2/noarch No change conda-forge/noarch 14.5MB @ 6.7MB/s 2.5s conda-forge/win-64 23.0MB @ 6.1MB/s 4.6s Could not solve for environment specs Encountered problems while solving:

The environment can't be solved, aborting the operation

pgunn commented 1 year ago

What if you do this? mamba create -n mescore -c defaults -c conda-forge mesmerize-core caiman=1.9.16 ucrt=10.0.22621.0

kfouke1 commented 1 year ago

here is the error:

Looking for: ['mesmerize-core', 'caiman=1.9.16', 'ucrt=10.0.22621.0']

conda-forge/win-64 Using cache conda-forge/noarch Using cache pkgs/msys2/win-64 No change pkgs/r/noarch No change pkgs/main/noarch No change pkgs/r/win-64 No change pkgs/main/win-64 No change pkgs/msys2/noarch No change Could not solve for environment specs Encountered problems while solving:

The environment can't be solved, aborting the operation

pgunn commented 1 year ago

mamba create --no-channel-priority -n mescore -c defaults -c conda-forge mesmerize-core caiman=1.9.16

kfouke1 commented 1 year ago

It worked! I have now caiman 1.9.16, fastplotlib Version: 0.1.0a15, and mesmerize-core 0.3.0. Thank you so much!!

pgunn commented 1 year ago

Glad it worked; we'll have to look into why this is necessary and maybe adjust the instructions.

Best wishes.