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scverse / scirpy

A scanpy extension to analyse single-cell TCR and BCR data.
https://scirpy.scverse.org/en/latest/
BSD 3-Clause "New" or "Revised" License
219 stars 34 forks source link

Issues with installing SCIRPY #182

Closed taopeng1100 closed 3 years ago

taopeng1100 commented 4 years ago

I am trying to install Scirpy using anaconda/Jupyter on my desktop window.

**when I try this: conda install -c conda-forge -c bioconda scirpy

I go the error message:**

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

Note: you may need to restart the kernel to use updated packages.

Building graph of deps:   0%|          | 0/2 [00:00<?, ?it/s]
Examining python=3.8:   0%|          | 0/2 [00:00<?, ?it/s]  
Examining scirpy:  50%|#####     | 1/2 [00:00<00:00,  2.94it/s]
Examining scirpy: 100%|##########| 2/2 [00:00<00:00,  5.88it/s]

Determining conflicts:   0%|          | 0/2 [00:00<?, ?it/s]
Examining conflict for python scirpy:   0%|          | 0/2 [00:00<?, ?it/s]

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

THEN I tried this: pip install scirpy, I got another error message:

ERROR: Command errored out with exit status 1:
   command: 'C:\Users\tpeng\Anaconda3\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\tpeng\\AppData\\Local\\Temp\\pip-install-jpyjqkeg\\python-levenshtein\\setup.py'"'"'; __file__='"'"'C:\\Users\\tpeng\\AppData\\Local\\Temp\\pip-install-jpyjqkeg\\python-levenshtein\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\tpeng\AppData\Local\Temp\pip-wheel-3n51vnw0'
       cwd: C:\Users\tpeng\AppData\Local\Temp\pip-install-jpyjqkeg\python-levenshtein\
  Complete output (27 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.8
  creating build\lib.win-amd64-3.8\Levenshtein
  copying Levenshtein\StringMatcher.py -> build\lib.win-amd64-3.8\Levenshtein
  copying Levenshtein\__init__.py -> build\lib.win-amd64-3.8\Levenshtein
  running egg_info
  writing python_Levenshtein.egg-info\PKG-INFO
  writing dependency_links to python_Levenshtein.egg-info\dependency_links.txt
  writing entry points to python_Levenshtein.egg-info\entry_points.txt
  writing namespace_packages to python_Levenshtein.egg-info\namespace_packages.txt
  writing requirements to python_Levenshtein.egg-info\requires.txt
  writing top-level names to python_Levenshtein.egg-info\top_level.txt
  reading manifest file 'python_Levenshtein.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files matching '*pyc' found anywhere in distribution
  warning: no previously-included files matching '*so' found anywhere in distribution
  warning: no previously-included files matching '.project' found anywhere in distribution
  warning: no previously-included files matching '.pydevproject' found anywhere in distribution
  writing manifest file 'python_Levenshtein.egg-info\SOURCES.txt'
  copying Levenshtein\_levenshtein.c -> build\lib.win-amd64-3.8\Levenshtein
  copying Levenshtein\_levenshtein.h -> build\lib.win-amd64-3.8\Levenshtein
  running build_ext
  building 'Levenshtein._levenshtein' extension
  error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
  ----------------------------------------
  ERROR: Failed building wheel for python-levenshtein
    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\tpeng\Anaconda3\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\tpeng\\AppData\\Local\\Temp\\pip-install-jpyjqkeg\\python-levenshtein\\setup.py'"'"'; __file__='"'"'C:\\Users\\tpeng\\AppData\\Local\\Temp\\pip-install-jpyjqkeg\\python-levenshtein\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\tpeng\AppData\Local\Temp\pip-record-spj3ycwj\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\tpeng\Anaconda3\Include\python-levenshtein'
         cwd: C:\Users\tpeng\AppData\Local\Temp\pip-install-jpyjqkeg\python-levenshtein\
    Complete output (27 lines):
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.8
    creating build\lib.win-amd64-3.8\Levenshtein
    copying Levenshtein\StringMatcher.py -> build\lib.win-amd64-3.8\Levenshtein
    copying Levenshtein\__init__.py -> build\lib.win-amd64-3.8\Levenshtein
    running egg_info
    writing python_Levenshtein.egg-info\PKG-INFO
    writing dependency_links to python_Levenshtein.egg-info\dependency_links.txt
    writing entry points to python_Levenshtein.egg-info\entry_points.txt
    writing namespace_packages to python_Levenshtein.egg-info\namespace_packages.txt
    writing requirements to python_Levenshtein.egg-info\requires.txt
    writing top-level names to python_Levenshtein.egg-info\top_level.txt
    reading manifest file 'python_Levenshtein.egg-info\SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '*pyc' found anywhere in distribution
    warning: no previously-included files matching '*so' found anywhere in distribution
    warning: no previously-included files matching '.project' found anywhere in distribution
    warning: no previously-included files matching '.pydevproject' found anywhere in distribution
    writing manifest file 'python_Levenshtein.egg-info\SOURCES.txt'
    copying Levenshtein\_levenshtein.c -> build\lib.win-amd64-3.8\Levenshtein
    copying Levenshtein\_levenshtein.h -> build\lib.win-amd64-3.8\Levenshtein
    running build_ext
    building 'Levenshtein._levenshtein' extension
    error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
    ----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\tpeng\Anaconda3\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\tpeng\\AppData\\Local\\Temp\\pip-install-jpyjqkeg\\python-levenshtein\\setup.py'"'"'; __file__='"'"'C:\\Users\\tpeng\\AppData\\Local\\Temp\\pip-install-jpyjqkeg\\python-levenshtein\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\tpeng\AppData\Local\Temp\pip-record-spj3ycwj\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\tpeng\Anaconda3\Include\python-levenshtein' Check the logs for full command output.

  Stored in directory: c:\users\tpeng\appdata\local\pip\cache\wheels\8c\51\cb\423184c62cc06c302d2f54f9853e5acee6c15a3b04d49a5eb3
  Building wheel for python-levenshtein (setup.py): started
  Building wheel for python-levenshtein (setup.py): finished with status 'error'
  Running setup.py clean for python-levenshtein
  Building wheel for yamlordereddictloader (setup.py): started
  Building wheel for yamlordereddictloader (setup.py): finished with status 'done'
  Created wheel for yamlordereddictloader: filename=yamlordereddictloader-0.4.0-py3-none-any.whl size=4058 sha256=05980b7e37960621917874dd26c59adf1eb9d304ca1f21d7c81d38adc8bc2674
  Stored in directory: c:\users\tpeng\appdata\local\pip\cache\wheels\50\9a\6f\9cb3312fd9cd01ea93c3fdc1dbee95f5fa0133125d4c7cb09a
Successfully built airr yamlordereddictloader
Failed to build python-levenshtein
Installing collected packages: yamlordereddictloader, airr, python-levenshtein, squarify, parasail, pytoml, scirpy
    Running setup.py install for python-levenshtein: started
    Running setup.py install for python-levenshtein: finished with status 'error'
grst commented 4 years ago

Regarding the conda installation, I suspect that you are installing scirpy into an environment that already contains some packages which cause a version conflict.

Try to install scirpy into a new conda environment: 

conda create -n scirpy python=3.8
conda activate scirpy
conda install -c conda-forge -c bioconda scirpy ipykernel

You can use different conda envs from jupyter. Check out this answer on stackoverflow.

Regarding the pip installation, it's already in the error message: 

Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/

Apparently, on Windows, one of the dependency packages needs to be compiled from scratch, which requires the Build Tool dependency.

Hope that helps!

grst commented 4 years ago

Feel free to reopen if the problem persists.

taopeng1100 commented 4 years ago

H Gregor, as you have suggested, I tried the code like this: conda install -c conda-forge -c bioconda scirpy ipykernel

I go this error message:

Building graph of deps: 0%| | 0/3 [00:00<?, ?it/s] Examining scirpy: 0%| | 0/3 [00:00<?, ?it/s] Examining python=3.7: 33%|###3 | 1/3 [00:00<00:01, 1.74it/s] Examining python=3.7: 67%|######6 | 2/3 [00:00<00:00, 3.49it/s] Examining ipykernel: 67%|######6 | 2/3 [00:00<00:00, 3.49it/s] Examining ipykernel: 100%|##########| 3/3 [00:00<00:00, 3.26it/s]

Determining conflicts: 0%| | 0/3 [00:00<?, ?it/s] Examining conflict for scirpy ipykernel: 0%| | 0/3 [00:00<?, ?it/s] Examining conflict for scirpy python ipykernel: 33%|###3 | 1/3 [00:00<00:01, 1.41it/s] Examining conflict for scirpy python ipykernel: 67%|######6 | 2/3 [00:00<00:00, 2.81it/s] Examining conflict for scirpy python: 67%|######6 | 2/3 [00:00<00:00, 2.81it/s] Examining conflict for python ipykernel: 100%|##########| 3/3 [00:00<00:00, 2.81it/s] Examining conflict for python ipykernel: : 4it [00:00, 3.51it/s]

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python_abi conflicts for: ipykernel -> python_abi[version='3.6.|3.7.|3.9.|3.8.',build='_cp36m|_cp39|_cp37m|_cp38'] ipykernel -> traitlets[version='>=4.1'] -> python_abi=2.7[build=_cp27m] scirpy -> anndata[version='>=0.7.3'] -> python_abi[version='3.6.|3.7.|3.8.|3.9.',build='_cp39|_cp36m|_cp37m|*_cp38']

Package packaging conflicts for: python=3.7 -> pip -> packaging scirpy -> anndata[version='>=0.7.3'] -> packaging

Package ca-certificates conflicts for: python=3.7 -> openssl[version='>=1.1.1g,<1.1.2a'] -> ca-certificates ipykernel -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates

From: Gregor Sturm notifications@github.com Sent: Friday, October 2, 2020 5:00 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

Feel free to reopen if the problem persists.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D702694096&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=Hnq9LlnIRA68H5yeQAyRU7dQgYVT0ct1XfiA79BqwL8&s=8SsUN_DGaIl6wxB30HMyThwDwTbGFo9Rw1dEsnLYSvg&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3COJLTWV4BRAE5RR2CDSIW6DFANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=Hnq9LlnIRA68H5yeQAyRU7dQgYVT0ct1XfiA79BqwL8&s=m-SYGVY6xDYQTGaF56M_ID6_QC3vkh5fBpajvzXU_hc&e=.

grst commented 4 years ago

are you sure you are in an empty environment with no other packages (except Python) installed?

You can check with conda env export.

taopeng1100 commented 4 years ago

I did : conda env export and got a long list below?

name: base channels:

From: Gregor Sturm notifications@github.com Sent: Saturday, October 17, 2020 1:06 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

are you sure you are in an empty environment with no other packages (except Python) installed?

You can check with conda env export.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D710770205&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=2OW4smKxCkEqsdFZNMZBY6D_eStJeIX3RH7a1lkUAFI&s=rPAi1jirRX5Ssi6gdL-fAbtgQjiWFXWNorQBf9nWPyM&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CIHC22AAP4GRDIZJNTSLFF5DANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=2OW4smKxCkEqsdFZNMZBY6D_eStJeIX3RH7a1lkUAFI&s=qEQkZf_Om8yZtHSRFRjho8taY90bg-tAihLuS_FTx60&e=.

grst commented 4 years ago

that means you are not in an empty conda env and there's some package that's conflicting. Make a new one with conda create and install scirpy there.

taopeng1100 commented 4 years ago

Ok that is what I thought!

I try to execute the three lines of codes below together and it don’t’ run so I am executing one line at a time and it seems to take a long time?

conda create -n scirpy python=3.8

conda activate scirpy

conda install -c conda-forge -c bioconda scirpy ipykernel

From: Gregor Sturm notifications@github.com Sent: Saturday, October 17, 2020 9:23 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

that means you are not in an empty conda env and there's some package that's conflicting. Make a new one with conda create and install scirpy there.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D711039021&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=uvMyl2aTPZwVmD1cVpfXVJ4OcAA19CiWb0wwz0HxB8M&s=Y0YUy674aAsJU-XW5zb0BOtk-kP19-fXJ5Bx-AX8A8w&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CMZVPO3XARFP7SXX5LSLHAG7ANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=uvMyl2aTPZwVmD1cVpfXVJ4OcAA19CiWb0wwz0HxB8M&s=ZVtgeewxN-jwQqHGU0ZGPSOLmJlI90cQPAmiDnJo9bQ&e=.

grst commented 4 years ago

It can take minutes, but shouldn't take longer.

Another common source of conda problems is a wrong channel configuration. Setting up conda channels is described here: https://bioconda.github.io/user/install.html#set-up-channels

To reset existing conda configuration, you can use conda config --remove-key channels.

taopeng1100 commented 4 years ago

I run each line in individual cell. It has been 40 mins and still running?

conda create -n scirpy python=3.7 ## my labtop PC has anaconda with python 3.7.3

conda activate scirpy

conda install -c conda-forge -c bioconda scirpy ipykernel

From: Gregor Sturm notifications@github.com Sent: Saturday, October 17, 2020 9:44 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

It can take minutes, but shouldn't take longer.

Another common source of conda problems is a wrong channel configuration. Setting up conda channels is described here: https://bioconda.github.io/user/install.html#set-up-channelshttps://urldefense.proofpoint.com/v2/url?u=https-3A__bioconda.github.io_user_install.html-23set-2Dup-2Dchannels&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=zJUizOYrzWCoHtQrMGxKEI95fYqYSDnyzrI7xfRqHuU&s=rjpce6gcvN_PXhoD_7Wd7XeWRv4MDg_q6MfPOqgy8lE&e=

To reset existing conda configuration, you can use conda config --remove-key channels.

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grst commented 4 years ago

Then sth is wrong. Did you check the channels as described above?

taopeng1100 commented 4 years ago

When I run: conda env export

I see: ame: base Note: you may need to restart the kernel to use updated packages. channels:

From: Gregor Sturm notifications@github.com Sent: Saturday, October 17, 2020 11:26 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

Then sth is wrong. Did you check the channels as described above?

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grst commented 3 years ago

Try this to add the channels in the right order. Also you're not need the vtraag channels any more, the leiden/louvain packages are now on conda-forge. 

conda config --remove-key channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
taopeng1100 commented 3 years ago

Herr is what I did:

conda config --remove-key channels Note: you may need to restart the kernel to use updated packages. In [2]: conda config --add channels defaults Note: you may need to restart the kernel to use updated packages. Warning: 'defaults' already in 'channels' list, moving to the top In [3]: conda config --add channels bioconda Note: you may need to restart the kernel to use updated packages. In [4]: conda config --add channels conda-forge Note: you may need to restart the kernel to use updated packages. In [5]: import sys In [6]: sys.version Out[6]: '3.8.3 (default, Jul 2 2020, 17:30:36) [MSC v.1916 64 bit (AMD64)]' In [ ]: conda create -n scirpy python=3.8 In [ ]: conda activate scirpy In [ ]: conda install -c conda-forge -c bioconda scirpy ipykernel In [ ]: It has been running for 20 mins?

Tao

From: Gregor Sturm notifications@github.com Sent: Monday, October 19, 2020 3:40 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

Try this to add the channels in the right order. Also you're not need the vtraag channels any more, the leiden/louvain packages are now on conda-forge.

conda config --remove-key channels

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

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grst commented 3 years ago

ah, you are trying to do all this within jupyter... The conda activate has no effect there. You'll need to run that in the terminal.

You can then choose the notebook to run in the scirpy environment. This should help: https://stackoverflow.com/questions/39604271/conda-environments-not-showing-up-in-jupyter-notebook

If you feel that's too compilcated, you can go for the nuclear option and delete and reinstall Miniconda. However, I would recommend to familiarize yourself with environments - it saves a lot of pain in the long run.

taopeng1100 commented 3 years ago

Should I run the following three lines of codes in terminal?

conda create -n scirpy python=3.8 conda activate scirpy conda install -c conda-forge -c bioconda scirpy ipykernel

Tao From: Gregor Sturm notifications@github.com Sent: Monday, October 19, 2020 10:56 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

ah, you are trying to do all this within jupyter... The conda activate has no effect there. You'll need to run that in the terminal.

You can then choose the notebook to run in the scirpy environment. This should help: https://stackoverflow.com/questions/39604271/conda-environments-not-showing-up-in-jupyter-notebookhttps://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=SjPZ5kbaTWEn4iq_XtB19bEVGJgHMc0lNwJ6p5R9pT0&e=

If you feel that's too compilcated, you can go for the nuclear option and delete and reinstall Miniconda. However, I would recommend to familiarize yourself with environments - it saves a lot of pain in the long run.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D712338611&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=_Hi8KVyOKZV73LwAclYW4sWV3l6F9iuYpGOPPOz7IFU&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CL5UWFXJ2AWOEETUM3SLR4R3ANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=TF21Ep_qXmGWuHAdCKJzvGMTEo9uzHmo_ZjVYN6zhfc&e=.

grst commented 3 years ago

yes.

But then you need to make sure to use the scirpy env in jupyter (see the stackoverflow link for that)

On Mon, 19 Oct 2020 at 20:10, taopeng1100 notifications@github.com wrote:

Should I run the following three lines of codes in terminal?

conda create -n scirpy python=3.8 conda activate scirpy conda install -c conda-forge -c bioconda scirpy ipykernel

Tao From: Gregor Sturm notifications@github.com Sent: Monday, October 19, 2020 10:56 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

ah, you are trying to do all this within jupyter... The conda activate has no effect there. You'll need to run that in the terminal.

You can then choose the notebook to run in the scirpy environment. This should help:

https://stackoverflow.com/questions/39604271/conda-environments-not-showing-up-in-jupyter-notebook < https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=SjPZ5kbaTWEn4iq_XtB19bEVGJgHMc0lNwJ6p5R9pT0&e=>

If you feel that's too compilcated, you can go for the nuclear option and delete and reinstall Miniconda. However, I would recommend to familiarize yourself with environments - it saves a lot of pain in the long run.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D712338611&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=_Hi8KVyOKZV73LwAclYW4sWV3l6F9iuYpGOPPOz7IFU&e=>, or unsubscribe< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CL5UWFXJ2AWOEETUM3SLR4R3ANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=TF21Ep_qXmGWuHAdCKJzvGMTEo9uzHmo_ZjVYN6zhfc&e=>.

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taopeng1100 commented 3 years ago

OK I will try to figure this out. One question:

After I install Scirpy, will I be able to use it in jupyter with Scanpy together?

Tao

From: Gregor Sturm notifications@github.com Sent: Monday, October 19, 2020 11:13 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

yes.

But then you need to make sure to use the scirpy env in jupyter (see the stackoverflow link for that)

On Mon, 19 Oct 2020 at 20:10, taopeng1100 notifications@github.com<mailto:notifications@github.com> wrote:

Should I run the following three lines of codes in terminal?

conda create -n scirpy python=3.8 conda activate scirpy conda install -c conda-forge -c bioconda scirpy ipykernel

Tao From: Gregor Sturm notifications@github.com<mailto:notifications@github.com> Sent: Monday, October 19, 2020 10:56 AM To: icbi-lab/scirpy scirpy@noreply.github.com<mailto:scirpy@noreply.github.com> Cc: Peng, Tao tpeng@fredhutch.org<mailto:tpeng@fredhutch.org>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

ah, you are trying to do all this within jupyter... The conda activate has no effect there. You'll need to run that in the terminal.

You can then choose the notebook to run in the scirpy environment. This should help:

https://stackoverflow.com/questions/39604271/conda-environments-not-showing-up-in-jupyter-notebookhttps://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=yGM_z0D2bSqV16LrKlyMiObAUF6tFsEzwvGLhdXx3Fo&s=5gAIyXIzUlzjNc_vL8cIgH1G4wniEmdcO58CgM7zMBw&e= < https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=SjPZ5kbaTWEn4iq_XtB19bEVGJgHMc0lNwJ6p5R9pT0&e=%3E

If you feel that's too compilcated, you can go for the nuclear option and delete and reinstall Miniconda. However, I would recommend to familiarize yourself with environments - it saves a lot of pain in the long run.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D712338611&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=_Hi8KVyOKZV73LwAclYW4sWV3l6F9iuYpGOPPOz7IFU&e=%3E, or unsubscribe< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CL5UWFXJ2AWOEETUM3SLR4R3ANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=TF21Ep_qXmGWuHAdCKJzvGMTEo9uzHmo_ZjVYN6zhfc&e=%3E.

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taopeng1100 commented 3 years ago

I try to execute the three lines of codes in anaconda Prompt:

conda create -n scirpy python=3.8 ## I have pyton 3.8.3 on my laptop PC. conda activate scirpy conda install -c conda-forge -c bioconda scirpy ipykernel

I got the error message:

(base) PS C:\Users\tpeng> conda activate scirpy (scirpy) PS C:\Users\tpeng> conda install -c conda-forge -c bioconda scirpy ipykernel Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining scirpy: 67%|████████████████████████████████████████████ | 2/3 [00:11<00:05, 5.43s/it]/failed -

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package colorama conflicts for: python=3.8 -> pip -> colorama ipykernel -> ipython[version='>=5.0'] -> colorama

Package packaging conflicts for: scirpy -> anndata[version='>=0.7.3'] -> packaging python=3.8 -> pip -> packaging

Package tzdata conflicts for: ipykernel -> python[version='>=3.9,<3.10.0a0'] -> tzdata scirpy -> python[version='>=3.6'] -> tzdata

Package python_abi conflicts for: ipykernel -> traitlets[version='>=4.1'] -> python_abi=2.7[build=_cp27m] ipykernel -> python_abi[version='3.6.|3.7.|3.9.|3.8.',build='_cp36m|_cp37m|_cp39|*_cp38']

Tao From: Gregor Sturm notifications@github.com Sent: Monday, October 19, 2020 11:13 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

yes.

But then you need to make sure to use the scirpy env in jupyter (see the stackoverflow link for that)

On Mon, 19 Oct 2020 at 20:10, taopeng1100 notifications@github.com<mailto:notifications@github.com> wrote:

Should I run the following three lines of codes in terminal?

conda create -n scirpy python=3.8 conda activate scirpy conda install -c conda-forge -c bioconda scirpy ipykernel

Tao From: Gregor Sturm notifications@github.com<mailto:notifications@github.com> Sent: Monday, October 19, 2020 10:56 AM To: icbi-lab/scirpy scirpy@noreply.github.com<mailto:scirpy@noreply.github.com> Cc: Peng, Tao tpeng@fredhutch.org<mailto:tpeng@fredhutch.org>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

ah, you are trying to do all this within jupyter... The conda activate has no effect there. You'll need to run that in the terminal.

You can then choose the notebook to run in the scirpy environment. This should help:

https://stackoverflow.com/questions/39604271/conda-environments-not-showing-up-in-jupyter-notebookhttps://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=yGM_z0D2bSqV16LrKlyMiObAUF6tFsEzwvGLhdXx3Fo&s=5gAIyXIzUlzjNc_vL8cIgH1G4wniEmdcO58CgM7zMBw&e= < https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=SjPZ5kbaTWEn4iq_XtB19bEVGJgHMc0lNwJ6p5R9pT0&e=%3E

If you feel that's too compilcated, you can go for the nuclear option and delete and reinstall Miniconda. However, I would recommend to familiarize yourself with environments - it saves a lot of pain in the long run.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D712338611&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=_Hi8KVyOKZV73LwAclYW4sWV3l6F9iuYpGOPPOz7IFU&e=%3E, or unsubscribe< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CL5UWFXJ2AWOEETUM3SLR4R3ANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=TF21Ep_qXmGWuHAdCKJzvGMTEo9uzHmo_ZjVYN6zhfc&e=%3E.

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taopeng1100 commented 3 years ago

I am somehow able to download visual studio and pip install Scirpy.

Many thx!

Tao

From: Gregor Sturm notifications@github.com Sent: Monday, October 19, 2020 11:13 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

yes.

But then you need to make sure to use the scirpy env in jupyter (see the stackoverflow link for that)

On Mon, 19 Oct 2020 at 20:10, taopeng1100 notifications@github.com<mailto:notifications@github.com> wrote:

Should I run the following three lines of codes in terminal?

conda create -n scirpy python=3.8 conda activate scirpy conda install -c conda-forge -c bioconda scirpy ipykernel

Tao From: Gregor Sturm notifications@github.com<mailto:notifications@github.com> Sent: Monday, October 19, 2020 10:56 AM To: icbi-lab/scirpy scirpy@noreply.github.com<mailto:scirpy@noreply.github.com> Cc: Peng, Tao tpeng@fredhutch.org<mailto:tpeng@fredhutch.org>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

ah, you are trying to do all this within jupyter... The conda activate has no effect there. You'll need to run that in the terminal.

You can then choose the notebook to run in the scirpy environment. This should help:

https://stackoverflow.com/questions/39604271/conda-environments-not-showing-up-in-jupyter-notebookhttps://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=yGM_z0D2bSqV16LrKlyMiObAUF6tFsEzwvGLhdXx3Fo&s=5gAIyXIzUlzjNc_vL8cIgH1G4wniEmdcO58CgM7zMBw&e= < https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_39604271_conda-2Denvironments-2Dnot-2Dshowing-2Dup-2Din-2Djupyter-2Dnotebook&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=30cFYXasZ4o4dOqRpfIu1VXwS4japAae3m0Cto2uH2E&s=SjPZ5kbaTWEn4iq_XtB19bEVGJgHMc0lNwJ6p5R9pT0&e=%3E

If you feel that's too compilcated, you can go for the nuclear option and delete and reinstall Miniconda. However, I would recommend to familiarize yourself with environments - it saves a lot of pain in the long run.

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taopeng1100 commented 3 years ago

Hi I am trying to go through the tutorial using ir.datasets.wu2020_3k()

At the step: ir.tl.clonotype_network(adata, min_size=2) ir.pl.clonotype_network(adata, color="clonotype", legend_loc="none")

I go this error message:

ValueError Traceback (most recent call last)

in ----> 1 ir.tl.clonotype_network(adata, min_size=2) 2 ir.pl.clonotype_network(adata, color="clonotype", legend_loc="none") ~\AppData\Local\Continuum\anaconda3\lib\site-packages\scirpy\_tools\_clonotypes.py in clonotype_network(adata, sequence, metric, min_size, layout, layout_kwargs, neighbors_key, key_clonotype_size, key_added, inplace, random_state) 307 layout_kwargs = default_layout_kwargs if layout_kwargs is None else layout_kwargs 308 if layout == "components": --> 309 coords = layout_components(graph, **layout_kwargs) 310 else: 311 coords = graph.layout(layout, **layout_kwargs).coords ~\AppData\Local\Continuum\anaconda3\lib\site-packages\scirpy\util\graph.py in layout_components(graph, component_layout, arrange_boxes, pad_x, pad_y) 95 ] 96 # get vertexes back into their original order ---> 97 coords = np.vstack(component_layouts)[vertex_sorter, :] 98 return coords 99 <__array_function__ internals> in vstack(*args, **kwargs) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\numpy\core\shape_base.py in vstack(tup) 281 if not isinstance(arrs, list): 282 arrs = [arrs] --> 283 return _nx.concatenate(arrs, 0) 284 285 <__array_function__ internals> in concatenate(*args, **kwargs) ValueError: need at least one array to concatenate I appreciate your help! Tao
taopeng1100 commented 3 years ago

This is the version of packages:

scanpy==1.6.0 anndata==0.7.4 umap==0.4.6 numpy==1.18.5 scipy==1.5.0 pandas==1.0.5 scikit-learn==0.23.1 statsmodels==0.11.1 python-igraph==0.7.1+5.3b99dbf6 leidenalg==0.7.0

From: Peng, Tao Sent: Thursday, October 22, 2020 10:18 AM To: icbi-lab/scirpy reply@reply.github.com Subject: Error at "ir.tl.clonotype_network(adata, min_size=2)"

Hi I am trying to go through the tutorial using ir.datasets.wu2020_3k()

At the step: ir.tl.clonotype_network(adata, min_size=2) ir.pl.clonotype_network(adata, color="clonotype", legend_loc="none")

I go this error message:

ValueError Traceback (most recent call last)

in ----> 1 ir.tl.clonotype_network(adata, min_size=2) 2 ir.pl.clonotype_network(adata, color="clonotype", legend_loc="none") ~\AppData\Local\Continuum\anaconda3\lib\site-packages\scirpy\_tools\_clonotypes.py in clonotype_network(adata, sequence, metric, min_size, layout, layout_kwargs, neighbors_key, key_clonotype_size, key_added, inplace, random_state) 307 layout_kwargs = default_layout_kwargs if layout_kwargs is None else layout_kwargs 308 if layout == "components": --> 309 coords = layout_components(graph, **layout_kwargs) 310 else: 311 coords = graph.layout(layout, **layout_kwargs).coords ~\AppData\Local\Continuum\anaconda3\lib\site-packages\scirpy\util\graph.py in layout_components(graph, component_layout, arrange_boxes, pad_x, pad_y) 95 ] 96 # get vertexes back into their original order ---> 97 coords = np.vstack(component_layouts)[vertex_sorter, :] 98 return coords 99 <__array_function__ internals> in vstack(*args, **kwargs) ~\AppData\Local\Continuum\anaconda3\lib\site-packages\numpy\core\shape_base.py in vstack(tup) 281 if not isinstance(arrs, list): 282 arrs = [arrs] --> 283 return _nx.concatenate(arrs, 0) 284 285 <__array_function__ internals> in concatenate(*args, **kwargs) ValueError: need at least one array to concatenate I appreciate your help! Tao
grst commented 3 years ago

I think I've seen this error before in this issue: https://github.com/icbi-lab/scirpy/issues/137 In that case it was sth with the environment.

To rule out that you have an old version of the wu2020 dataset, can you try to delete the wu2020_3k.h5ad file from the data directory and download it again?

taopeng1100 commented 3 years ago

Can you guide on how to remove the old wu dataset and download the new one?

From: Gregor Sturm notifications@github.com Sent: Thursday, October 22, 2020 10:33 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

I think I've seen this error before in this issue: #137https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_137&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=3xq1Y22FyfL1JH7avyldVmK9SFrruln0s8Vocyf7PT4&s=fyy7rwd17LrtcxHNFnRYkDYzYqjLSQEHDnlprgXQ-G0&e= In that case it was sth with the environment.

To rule out that you have an old version of the wu2020 dataset, can you try to delete the wu2020_3k.h5ad file from the data directory and download it again?

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grst commented 3 years ago

there should be a data directory in the same folder as your notebook. just delete that.

The dataset is downloaded again automatically when you run ir.datasets.wu2020_3k().

taopeng1100 commented 3 years ago

I did as you suggested here and the same error !

From: Gregor Sturm notifications@github.com Sent: Thursday, October 22, 2020 10:39 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

there should be a data directory in the same folder as your notebook. just delete that.

The dataset is downloaded again automatically when you run ir.datasets.wu2020_3k().

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grst commented 3 years ago

Hmm, tricky.

Do you exactely run the commands from the tutorial, in the same order, or do you do something (even slightly) different? If so, could you please provide the exact commands you run from the point you start python until the error occurs?

And can you provide the result of pip freeze?

taopeng1100 commented 3 years ago

Attached is HTML file for the steps I have taken to follow the tutorial.

I will look into pip freeze?

From: Gregor Sturm notifications@github.com Sent: Thursday, October 22, 2020 11:25 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

Hmm, tricky.

Do you exactely run the commands from the tutorial, in the same order, or do you do something (even slightly) different? If so, could you please provide the exact commands you run from the point you start python until the error occurs?

And can you provide the result of pip freeze?

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taopeng1100 commented 3 years ago

Here is the output of pip freeze:

airr==1.3.0 alabaster==0.7.12 anaconda-client==1.7.2 anaconda-navigator==1.9.12 anaconda-project==0.8.3 anndata==0.7.4 annoy @ file:///D:/bld/python-annoy_1589264717844/work argh==0.26.2 asn1crypto @ file:///C:/ci/asn1crypto_1594339244757/work astroid @ file:///C:/ci/astroid_1592481955828/work astropy==4.0.1.post1 atomicwrites==1.4.0 attrs==19.3.0 Automat==0.8.0 autopep8 @ file:///tmp/build/80754af9/autopep8_1592412889138/work Babel==2.8.0 backcall==0.2.0 backports.shutil-get-terminal-size==1.0.0 bbknn==1.3.12 bcrypt==3.1.7 beautifulsoup4==4.9.1 biopython==1.78 bitarray @ file:///C:/ci/bitarray_1594753961793/work bkcharts==0.2 bleach==3.1.5 bokeh @ file:///C:/ci/bokeh_1593179283802/work boto==2.49.0 Bottleneck==1.3.2 brotlipy==0.7.0 certifi==2020.6.20 cffi==1.14.0 changeo==1.0.0 chardet==3.0.4 click==7.1.2 cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1594141588948/work clyent==1.2.2 colorama==0.4.3 comtypes==1.1.7 conda==4.8.4 conda-build==3.17.8 conda-package-handling==1.7.0 Note: you may need to restart the kernel to use updated packages.conda-verify==3.1.1 constantly==15.1.0 contextlib2==0.6.0.post1 cryptography==2.9.2

cssselect==1.1.0 cycler==0.10.0 Cython @ file:///C:/ci/cython_1594834055134/work cytoolz==0.10.1 dask @ file:///tmp/build/80754af9/dask-core_1594156306305/work decorator==4.4.2 defusedxml==0.6.0 descartes==1.1.0 diff-match-patch @ file:///tmp/build/80754af9/diff-match-patch_1594828741838/work distributed @ file:///C:/ci/distributed_1594319358820/work docutils==0.16 entrypoints==0.3 et-xmlfile==1.0.1 fastcache==1.1.0 filelock==3.0.12 flake8==3.8.3 Flask==1.1.2 fsspec==0.7.4 future==0.18.2 get-version==2.1 gevent @ file:///C:/ci/gevent_1593010757573/work glob2==0.7 gmpy2==2.0.8 greenlet==0.4.16 h5py==2.10.0 HeapDict==1.0.1 html5lib @ file:///tmp/build/80754af9/html5lib_1593446221756/work hyperlink==19.0.0 idna @ file:///tmp/build/80754af9/idna_1593446292537/work imageio @ file:///tmp/build/80754af9/imageio_1594161405741/work imagesize==1.2.0 importlib-metadata @ file:///C:/ci/importlib-metadata_1593446525189/work incremental==17.5.0 intervaltree @ file:///tmp/build/80754af9/intervaltree_1594361675072/work ipykernel @ file:///C:/ci/ipykernel_1595342053367/work/dist/ipykernel-5.3.3-py3-none-any.whl ipython @ file:///C:/ci/ipython_1593433781269/work ipython-genutils==0.2.0 ipywidgets==7.5.1 isort==4.3.21 itemadapter @ file:///home/conda/feedstock_root/build_artifacts/itemadapter_1593694453559/work itsdangerous==1.1.0 jdcal==1.4.1 jedi @ file:///C:/ci/jedi_1592833832328/work Jinja2==2.11.2 joblib @ file:///tmp/build/80754af9/joblib_1594236160679/work json5==0.9.5 jsonschema @ file:///C:/ci/jsonschema_1594363671836/work jupyter==1.0.0 jupyter-client @ file:///tmp/build/80754af9/jupyter_client_1594826976318/work jupyter-console==6.1.0 jupyter-core==4.6.3 jupyterlab==2.1.5 jupyterlab-server @ file:///tmp/build/80754af9/jupyterlab_server_1594164409481/work keyring @ file:///C:/ci/keyring_1593109817825/work kiwisolver==1.2.0 lazy-object-proxy==1.4.3 legacy-api-wrap==1.2 leidenalg==0.7.0 libarchive-c==2.9 llvmlite==0.33.0+1.g022ab0f locket==0.2.0 lxml @ file:///C:/ci/lxml_1594826938446/work MarkupSafe @ file:///C:/ci/markupsafe_1594405949945/work matplotlib==3.3.0 matplotlib-venn==0.11.5 mccabe==0.6.1 menuinst==1.4.16 mistune @ file:///C:/ci/mistune_1594373272338/work mizani==0.7.1 mkl-fft==1.1.0 mkl-random==1.1.1 mkl-service==2.3.0 mock==4.0.2 more-itertools==8.4.0 mpmath==1.1.0 msgpack==1.0.0 multipledispatch==0.6.0 natsort==6.2.0 navigator-updater==0.2.1 nbconvert @ file:///C:/ci/nbconvert_1594372737468/work nbformat==5.0.7 networkx @ file:///tmp/build/80754af9/networkx_1594377231366/work nltk @ file:///tmp/build/80754af9/nltk_1592496090529/work nose @ file:///C:/ci/nose_1594377973236/work notebook==6.0.3 numba==0.50.1 numexpr==2.7.1 numpy==1.18.5 numpydoc @ file:///tmp/build/80754af9/numpydoc_1594166760263/work olefile==0.46 openpyxl @ file:///tmp/build/80754af9/openpyxl_1594167385094/work packaging==20.4 palettable==3.3.0 pandas @ file:///C:/ci/pandas_1592841747005/work pandocfilters==1.4.2 paramiko==2.7.1 parasail==1.2 parsel==1.5.2 parso==0.7.0 partd==1.1.0 path==14.0.1 path.py==12.0.2 pathlib2 @ file:///C:/ci/pathlib2_1594381094851/work pathtools==0.1.2 patsy==0.5.1 pep8==1.7.1 pexpect @ file:///C:/ci/pexpect_1594383465186/work pickleshare @ file:///C:/ci/pickleshare_1594374056827/work Pillow @ file:///C:/ci/pillow_1594298234712/work pkginfo==1.5.0.1 plotnine==0.5.1 pluggy==0.13.1 ply==3.11 presto==0.6.1 prometheus-client==0.8.0 prompt-toolkit==3.0.5 Protego==0.1.16 psutil==5.7.0 py @ file:///tmp/build/80754af9/py_1593446248552/work pyasn1==0.4.8 pyasn1-modules==0.2.7 pycairo==1.20.0 pycodestyle==2.6.0 pycosat==0.6.3 pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work pycrypto==2.6.1 pycurl==7.43.0.5 PyDispatcher==2.0.5 pydocstyle @ file:///tmp/build/80754af9/pydocstyle_1592848020240/work pyflakes==2.2.0 Pygments==2.6.1 PyHamcrest @ file:///tmp/build/80754af9/pyhamcrest_1594390921726/work pylint @ file:///C:/ci/pylint_1592487534522/work PyNaCl @ file:///C:/ci/pynacl_1595009241355/work pyodbc===4.0.0-unsupported pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1594392929924/work pyparsing==2.4.7 pyreadline==2.1 pyrsistent==0.16.0 PySocks @ file:///C:/ci/pysocks_1594394709107/work pytest==5.4.3 pytest-runner==5.2 python-dateutil==2.8.1 python-igraph==0.7.1.post7 python-jsonrpc-server @ file:///tmp/build/80754af9/python-jsonrpc-server_1594397536060/work python-language-server @ file:///C:/ci/python-language-server_1594152769556/work python-Levenshtein==0.12.0 python-louvain==0.13 pytoml==0.1.21 pytz==2020.1 pyvdj @ git+https://github.com/veghp/pyVDJ.git@31cec7d6123853fb9307458a205677101983d845 PyWavelets==1.1.1 pywin32==227 pywin32-ctypes @ file:///C:/ci/pywin32-ctypes_1594392691209/work pywinpty==0.5.7 PyYAML==5.3.1 pyzmq==19.0.1 QDarkStyle==2.8.1 QtAwesome==0.7.2 qtconsole @ file:///tmp/build/80754af9/qtconsole_1592848611704/work QtPy==1.9.0 queuelib==1.5.0 regex @ file:///C:/ci/regex_1593435644645/work requests @ file:///tmp/build/80754af9/requests_1592841827918/work rope==0.17.0 Rtree==0.9.4 ruamel-yaml==0.15.87 scanpy==1.6.0 scikit-image==0.16.2 scikit-learn==0.23.1 scipy @ file:///C:/ci/scipy_1592916958183/work scirpy==0.5.0 Scrapy @ file:///D:/bld/scrapy_1593704860927/work seaborn==0.10.1 Send2Trash==1.5.0 service-identity==18.1.0 setuptools-scm==4.1.2 simplegeneric==0.8.1 sinfo==0.3.1 singledispatch==3.4.0.3 six==1.15.0 snowballstemmer==2.0.0 sortedcollections==1.2.1 sortedcontainers==2.2.2 soupsieve==2.0.1 Sphinx @ file:///tmp/build/80754af9/sphinx_1594223420021/work sphinxcontrib-applehelp==1.0.2 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==1.0.3 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.4 sphinxcontrib-websupport @ file:///tmp/build/80754af9/sphinxcontrib-websupport_1593446360927/work spyder @ file:///C:/ci/spyder_1594826266791/work spyder-kernels @ file:///C:/ci/spyder-kernels_1594751701920/work SQLAlchemy @ file:///C:/ci/sqlalchemy_1593445585180/work squarify==0.4.3 statsmodels==0.11.1 stdlib-list==0.7.0 sympy @ file:///C:/ci/sympy_1594234541241/work tables==3.5.1 tbb==2019.0 tblib==1.6.0 terminado==0.8.3 testpath==0.4.4 threadpoolctl @ file:///tmp/tmp9twdgx9k/threadpoolctl-2.1.0-py3-none-any.whl toml @ file:///tmp/build/80754af9/toml_1592853716807/work toolz==0.10.0 tornado==6.0.4 tqdm @ file:///tmp/build/80754af9/tqdm_1593446365756/work traitlets==4.3.3 Twisted==20.3.0 typed-ast==1.4.1 typing-extensions @ file:///tmp/build/80754af9/typing_extensions_1592847887441/work ujson==1.35 umap-learn @ file:///D:/bld/umap-learn_1593739921313/work unicodecsv==0.14.1 UpSetPlot==0.3.0.post3 urllib3==1.25.9 w3lib==1.21.0 watchdog @ file:///C:/ci/watchdog_1593446515400/work wcwidth @ file:///tmp/build/80754af9/wcwidth_1593447189090/work webencodings==0.5.1 Werkzeug==1.0.1 widgetsnbextension==3.5.1 win-inet-pton==1.1.0 win-unicode-console==0.5 wincertstore==0.2 wrapt==1.11.2 xlrd==1.2.0 XlsxWriter==1.2.9 xlwings==0.19.5 xlwt==1.3.0 xmltodict==0.12.0 yamlordereddictloader==0.4.0 yapf @ file:///tmp/build/80754af9/yapf_1593528177422/work zict==2.0.0 zipp==3.1.0 zope.event==4.4 zope.interface==4.7.1

From: Gregor Sturm notifications@github.com Sent: Thursday, October 22, 2020 11:25 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

Hmm, tricky.

Do you exactely run the commands from the tutorial, in the same order, or do you do something (even slightly) different? If so, could you please provide the exact commands you run from the point you start python until the error occurs?

And can you provide the result of pip freeze?

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grst commented 3 years ago

I think github doesn't forward attachments.. But you can drag&drop it in when you answer on the github website directly.

taopeng1100 commented 3 years ago

Scirpy_learn.pdf

taopeng1100 commented 3 years ago

Jus loaded a PDF file for all the steps in repeating tutorial.

From: Gregor Sturm notifications@github.com Sent: Thursday, October 22, 2020 11:33 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

I think github doesn't forward attachments.. But you can drag&drop it in when you answer on the github website directly.

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grst commented 3 years ago

I cannot reproduce the issue. In fact, I cannot even reproduce the environment. There are a lot of packages that are not available on PyPI (any more?).

Also your environment is cluttered with such a vast number of packages. The best advice I have is to start fresh and use a clean conda env (conda create) or just delete your entire Anaconda installation and install a fresh copy of Miniconda.

taopeng1100 commented 3 years ago

Thx for sticking with me. I removed my old anaconda and reinstalled it and pip installed scanpy ands scirpy.

The demo data (wu) is working now.

How can I save the output figures in a high resolution?

Thx again!

Tao

From: Gregor Sturm notifications@github.com Sent: Friday, October 23, 2020 2:45 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

I cannot reproduce the issue. In fact, I cannot even reproduce the environment. There are a lot of packages that are not available on PyPI (any more?).

Also your environment is cluttered with such a vast number of packages. The best advice I have is to start fresh and use a clean conda env (conda create) or just delete your entire Anaconda installation and install a fresh copy of Minicondahttps://urldefense.proofpoint.com/v2/url?u=https-3A__docs.conda.io_en_latest_miniconda.html&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=-LPMjszTHNFmbfA4xEWD0ENWLYxmi4H4fQ9g3dyFzoM&s=HQSuUANS-pUai9Iv8B429E0hU_8v_kkqlHxWT2MwthU&e=.

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grst commented 3 years ago

You can use savefig to save as pdf or other high res graphic. 

ax = ir.pl.plot_something()
ax.get_figure().savefig("figure.pdf")
taopeng1100 commented 3 years ago

I have enjoyed learning Scirpy so far. Many thx!

From: Gregor Sturm notifications@github.com Sent: Saturday, October 24, 2020 2:50 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

You can use savefighttps://urldefense.proofpoint.com/v2/url?u=https-3A__matplotlib.org_3.1.1_api_-5Fas-5Fgen_matplotlib.pyplot.savefig.html&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=w0RsfuqS4Kl680osE5j7WbE2Z_zT2gYcl8lgchHv-LY&s=ltQAomkz2KXc6-WxpCOgoo8TpxlZ4bDNwED7BryTFXI&e= to save as pdf or other high res graphic.

ax = ir.pl.plot_something()

ax.get_figure().savefig("figure.pdf")

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_182-23issuecomment-2D715889985&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=w0RsfuqS4Kl680osE5j7WbE2Z_zT2gYcl8lgchHv-LY&s=OhTdzhOJkhRNhZsJdICjHI6ut3dUgbdmp266QdbjfNo&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3COJG77ULVRJT6VZHN3SMKPK5ANCNFSM4RPKR27Q&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=w0RsfuqS4Kl680osE5j7WbE2Z_zT2gYcl8lgchHv-LY&s=3qGqmmwOmVTF795Feq7aj_Lgbf9ylVNwHk-Efg2yyFE&e=.

taopeng1100 commented 3 years ago

I got the nice graph with this code:

ir.pl.repertoire_overlap( adata, "leiden", pair_to_plot=["2", "4"], fig_kws={"dpi": 200} )

I wonder how I can see the individual clonotypes in leiden cluster “2” and “4”? How can I get the VDJ genes and CDR AA seq for the clonotypes in these two clusters?

I appreciate you made such a grant tool for scRNA+TCR!

Tao

From: Gregor Sturm notifications@github.com Sent: Saturday, October 24, 2020 2:50 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

You can use savefighttps://urldefense.proofpoint.com/v2/url?u=https-3A__matplotlib.org_3.1.1_api_-5Fas-5Fgen_matplotlib.pyplot.savefig.html&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=w0RsfuqS4Kl680osE5j7WbE2Z_zT2gYcl8lgchHv-LY&s=ltQAomkz2KXc6-WxpCOgoo8TpxlZ4bDNwED7BryTFXI&e= to save as pdf or other high res graphic.

ax = ir.pl.plot_something()

ax.get_figure().savefig("figure.pdf")

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taopeng1100 commented 3 years ago

I am trying to change the scale on both X- & Y-axis of plots using the code below:

ir.pl.repertoire_overlap( adata, "leiden", pair_to_plot=["3", "4"], fig_kws={"dpi": 200}, ax.yaxis.set_major_locator(FixedLocator(np.arange(0, 20, 5))) )

It did not work! I know I need to learn matplotlib better. Is it an easy way to set the scale for axis in scirpy plots?

Thx,

Tao From: Peng, Tao Sent: Tuesday, October 27, 2020 12:14 PM To: icbi-lab/scirpy reply@reply.github.com Subject: RE: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

I got the nice graph with this code:

ir.pl.repertoire_overlap( adata, "leiden", pair_to_plot=["2", "4"], fig_kws={"dpi": 200} )

I wonder how I can see the individual clonotypes in leiden cluster “2” and “4”? How can I get the VDJ genes and CDR AA seq for the clonotypes in these two clusters?

I appreciate you made such a grant tool for scRNA+TCR!

Tao

From: Gregor Sturm notifications@github.com<mailto:notifications@github.com> Sent: Saturday, October 24, 2020 2:50 AM To: icbi-lab/scirpy scirpy@noreply.github.com<mailto:scirpy@noreply.github.com> Cc: Peng, Tao tpeng@fredhutch.org<mailto:tpeng@fredhutch.org>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

You can use savefighttps://urldefense.proofpoint.com/v2/url?u=https-3A__matplotlib.org_3.1.1_api_-5Fas-5Fgen_matplotlib.pyplot.savefig.html&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=w0RsfuqS4Kl680osE5j7WbE2Z_zT2gYcl8lgchHv-LY&s=ltQAomkz2KXc6-WxpCOgoo8TpxlZ4bDNwED7BryTFXI&e= to save as pdf or other high res graphic.

ax = ir.pl.plot_something()

ax.get_figure().savefig("figure.pdf")

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grst commented 3 years ago

I wonder how I can see the individual clonotypes in leiden cluster “2” and “4”? How can I get the VDJ genes and CDR AA seq for the clonotypes in these two clusters?

You can filter adata.obs (it's just a pandas data frame):

adata.obs.loc[adata.obs["leiden"].isin(["2", "4"]), :]

I am trying to change the scale on both X- & Y-axis of plots using the code below: ir.pl.repertoire_overlap( adata, "leiden", pair_to_plot=["3", "4"], fig_kws={"dpi": 200}, ax.yaxis.set_major_locator(FixedLocator(np.arange(0, 20, 5))) )

close ;) 

ax = ir.pl.repertoire_overlap(...)
ax.yaxis.set_major_locator(FixedLocator(np.arange(0, 20, 5)))
taopeng1100 commented 3 years ago

I really appreciate your help!

From: Gregor Sturm notifications@github.com Sent: Wednesday, October 28, 2020 12:03 AM To: icbi-lab/scirpy scirpy@noreply.github.com Cc: Peng, Tao tpeng@fredhutch.org; Author author@noreply.github.com Subject: Re: [icbi-lab/scirpy] Issues with installing SCIRPY (#182)

I wonder how I can see the individual clonotypes in leiden cluster “2” and “4”? How can I get the VDJ genes and CDR AA seq for the clonotypes in these two clusters?

You can filter adata.obs (it's just a pandas data frame):

adata.obs.loc[adata.obs["leiden"].isin(["2", "4"]), :]

I am trying to change the scale on both X- & Y-axis of plots using the code below: ir.pl.repertoire_overlap( adata, "leiden", pair_to_plot=["3", "4"], fig_kws={"dpi": 200}, ax.yaxis.set_major_locator(FixedLocator(np.arange(0, 20, 5))) )

close ;)

ax = ir.pl.repertoire_overlap(...)

ax.yaxis.set_major_locator(FixedLocator(np.arange(0, 20, 5)))

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grst commented 3 years ago

Hi @taopeng1100,

I'm closing this issue now. Feel free to reopen or create a new one if you encounter any other problems.