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h5py and paramiko packages not installed with 'python -m pip install suite2p[gui]' #987

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Atika-Syeda opened this issue Jun 22, 2023 · 1 comment
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h5py and paramiko packages not installed with 'python -m pip install suite2p[gui]' #987

Atika-Syeda opened this issue Jun 22, 2023 · 1 comment

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@Atika-Syeda
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Describe the issue:

Followed installation instructions for GUI version on a linux machine but the commands suite2p --version and python -m suite2p resulted in following errors:
ModuleNotFoundError: No module named 'h5py'
and
ModuleNotFoundError: No module named 'paramiko'
Errors were resolved after installing the packages in the conda env.

Provide environment info:

 active environment : suite2p
active env location : /home/stringlab/anaconda3/envs/suite2p
        shell level : 1
   user config file : /home/stringlab/.condarc

populated config files : /home/stringlab/.condarc
conda version : 4.11.0
conda-build version : 3.21.5
python version : 3.9.7.final.0
virtual packages : __cuda=11.6=0
__linux=5.15.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/stringlab/anaconda3 (writable)
conda av data dir : /home/stringlab/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/stringlab/anaconda3/pkgs
/home/stringlab/.conda/pkgs
envs directories : /home/stringlab/anaconda3/envs
/home/stringlab/.conda/envs
platform : linux-64
user-agent : conda/4.11.0 requests/2.26.0 CPython/3.9.7 Linux/5.15.0-75-generic ubuntu/20.04.6 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
carsen-stringer added a commit that referenced this issue Jun 22, 2023
@carsen-stringer
fixing import error with h5py and paramiko #987
82b75f7
@carsen-stringer
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carsen-stringer commented Jun 22, 2023 •
edited
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thanks this is now fixed + with more documentation

tbabola added a commit to tbabola/suite2p that referenced this issue Jun 19, 2024
@tbabola @tdincer
@chriski777 @dependabot @carsen-stringer @kabilar @itsb @sidhulyalkar @amorsi1 @marius10p @hmacomber @rly @arielleleon @landoskape @yael-prilutski @nguyemi5 @liadJB
Merge with devleoper branch (#2)
8adfc64 
* add get_nd2_list method

* remove comment

* support pipelining nd2 files

* support pipelining nd2 files

* fix docstring and whitespaces

* bug fix

* final touch

* Modified README to contain updated suite2p installation instructions for mac Ventura OS. Addresses issue MouseLand#897.

* Fixed issue MouseLand#908 regarding badframes for register.py. Detection module was fixed to properly bin movies AFTEr taking into account bad frames.

* Fix blocks issue for nonrigid registration in MouseLand#907

* Update test_and_deploy.yml

* Removed whitespace from display xauthority line in tox.ini.

* Update test_and_deploy.yml

Add apt-get update for linux runner and remove dvc requirement.

* Update test_and_deploy.yml

Added py import to workflow file and added debugging only during job failures

* Update test_and_deploy.yml

* Update tox.ini

* Update test_and_deploy.yml

Remove the up-term step.

* Updated TwophotonSeries initialization for save_nwb in io

* Bump torch from 1.11.0 to 1.13.1

Bumps [torch](https://github.com/pytorch/pytorch) from 1.11.0 to 1.13.1.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/master/RELEASE.md)
- [Commits](pytorch/pytorch@v1.11.0...v1.13.1)

---
updated-dependencies:
- dependency-name: torch
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update issue templates

* Update installation-issues.yml for issues

* Rename installation-issues.yml to installation-issue.yml

* Update installation issue.yml

* Update bug_report.yml

* Added bug_report.yml issue template

* Update all issue templates

* Update feature_request issue

* Update feature_request.yml

* Fixes issue MouseLand#914 for saving news ops parameters

* Update documentation_issue.yml

* Update documentation_issue.yml

* Fixes multiplane issue MouseLand#905 with save_nwb

* Fixes issue MouseLand#904 for 2 channel manual labeling

* Update .readthedocs.yml

* remove spaces

* conform to function signature and usage pattern a few lines above

* add nd2 in requirements

* minor revision

* new logic

* refactor dim sorting

* revert to previous code

* Fixes the from_stat_dict bug mentioned in MouseLand#935.

* Update run suite2p jupyter notebook to fix issue MouseLand#935

* Addresses MouseLand#930 in which bin_data has trouble dealing with cases in which the current batch has fewer frames than the bin_size

* removed ops assignment

* removed deprecated np.bool

* Update the version of the dependencies for suite2p

* Update np.bool to 'bool' to account for numpy deprecation with latest version

* Add Sparse detection to gui as a setting for running suite2p

* Addresses MouseLand#951 and adds nd2 as an input to gui

* Fix issue with np.asanyarray being changed in numpy 1.24.4

* addressed IndexError

* Update README.md

* Update README.md

* fixing skip torch if version 2.0

* adding pep8 style to repo

* fixing dictionary splitting

* modifying imports

* converting to "" from ''

* converting binaryfile to memmap

* rewriting binarycombined

* removing scanimage-tiff-reader for now

* fixing dragging in gui and linewidth=88

* removing old testing yml

* adding py39, updating readme

* adding option for MouseLand#955

* fixing bug in docstring  (MouseLand#902)

* adding iplane to saved manual ROIs (MouseLand#789)

* fixing MouseLand#747 saving to mat

* making nd2 and scanimage-tiff-reader optional (MouseLand#950)

* removing bruker dependency on scanimage-tiff-reader

* Create codecov.yml

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update BinaryRWFile name usage to BinaryFile

* Add instructions on how to use test_data generation script

* Added instructions on generating new test data

* Add method for writing tiff for binaryFile class

* Update write_tiff for binary.py to crop frames, x, and y too

* fix frame range issue with write_Tiff for binary

* added debugging logs

* removed debugging logs

* removed print statement

* removed unnecessary space

* Fixes MouseLand#943 to address documentation issue with high_pass

* adding copyright to every py file

* Delete .dvc directory

* fixing import error with h5py and paramiko MouseLand#987

* Update README.md

* Add pynwb package to setup.py as tests needs pynwb for one of the io_tests

* Update readme.md to be for python version 3.9

* Addresses MouseLand#944  leading zero issue with tiff filename.

* Addresses MouseLand#944  leading zero issue with tiff filename.

* Update save_path0 to close MouseLand#991.

* Update save_path0 to close MouseLand#991.

* update visualize.py to import rastermap properly

* Re-add connected to GUI options

* Update README.md

Remove note about scanimage-tiff-reader mac incompatibility

* Update README.md

Simplify mac os instructions

* Update setup.py

Update rastermap requirement based on issue ticket suggestions

* Update setup.py

* Updated jupyter notebook to work with new binaryFile class in suite2p.io

* Updated jupyter notebook name

* Update colab 2023 to fully fix MouseLand#1011 and update some comments on notebook

* Updated jupyter notebook to work with new binaryFile class in suite2p.io

* Updated jupyter notebook name

* Update colab 2023 to fully fix MouseLand#1011 and update some comments on notebook

* adding pyqt6 and switching to qtpy

* updating readme and fixing spelling error in copyright

* adding license notice

* adding check in setup.py for installation of a pyqt version

* adding tutorial

* Update tutorial.md with additional comments

* Update suite2p gui to work with QFileDialog.Options() not working with pyqt6

* Update binary.py write_tiff to add all frames to a single series

* Updated tiff.py to use contiguous parameter

* Update README.md

* checking h5py key to open binaries before data_path

* fixing bug in code

* adding new data type

* adding support for binary and mp4/avi files

* enabling ops.json loading in reggui and binary-only processing

* increase tolerance on classification regression test

* add more tolerance

* increasing tolerance again

* increasing tolerance again

* Update README.md

* Add explanation for how to apply classifiers

* CheckState Fix

* Fix conda environment creation for developers

* Update utils.py

* Update README.md to fix MouseLand#1060.

Updates badge links for tests and docs

* Update merge.py of gui subpackage to not use deprecated np.bool

* Update merge.py of gui subpackage to not use deprecated np.bool

* Add import to gui/io.py

* Update gui.rst to have clearer instructions for MouseLand#1002.

* bug in h5py key option

* adding support for multipage bruker ome tiffs

* Update inputs.rst to include multipage bruker instructions

* Update inputs.rst

* Added support for Thorlabs RAW files (io.raw)

* Added xmltodict

* Update raw.py- todo verified

* safe import for xmltodict

* fixing bug with multiplane registration

* allowing reg_file input to compute_zpos

* fixing bug with multi-plane nonrigid ops

* add support for Hamamatsu DCIMG format

* add support for Hamamatsu DCIMG format

* add dcimg_deps to all_deps and restrict cellpose to <3.0

* Addresses MouseLand#1093 with cellpose method having too many arguments

* Addresses MouseLand#1093 with cellpose method having too many arguments

* remove cellpose<3.0 restriction

* Fixes issue MouseLand#1101 with older version of cellpose

* Update zalign.py

Made sure that if a reg_file is given to the zalign function it uses it, rather than the ops reg_file

* Update setup.py

* adding dcimg

* removing dcimg extra

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: tdincer <tolgadincer@gmail.com>
Co-authored-by: Chris Ki <chriski777@berkeley.edu>
Co-authored-by: Chris Ki <cski@andrew.cmu.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: carsen-stringer <carsen.stringer@gmail.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: itsb <itsb@users.noreply.github.com>
Co-authored-by: Sidharth Hulyalkar <sid.soccer.21@gmail.com>
Co-authored-by: Ahmed Morsi <amorsi@berkeley.edu>
Co-authored-by: Marius Pachitariu <marius10p@gmail.com>
Co-authored-by: Heather Ratigan <hmacomber@uchicago.edu>
Co-authored-by: Ryan Ly <rly@lbl.gov>
Co-authored-by: Arielle Leon <ariellel@alleninstitute.org>
Co-authored-by: Andrew Landau <andrewtylerlandau@gmail.com>
Co-authored-by: arielleleon <54869022+arielleleon@users.noreply.github.com>
Co-authored-by: yaelpri <yael.prilutski@gmail.com>
Co-authored-by: yaelpri <61921608+yaelpri@users.noreply.github.com>
Co-authored-by: Yael Prilutski <61921608+yael-prilutski@users.noreply.github.com>
Co-authored-by: nguyemi5 <nguyemi5@github.com>
Co-authored-by: nguyemi5 <38402644+nguyemi5@users.noreply.github.com>
Co-authored-by: liadJB <48135253+liadJB@users.noreply.github.com>
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@carsen-stringer @Atika-Syeda