No module named 'gseapy.gse'

ShriHarshaAdapalaThirumala commented 1 year ago

Setup

I am reporting a problem with GSEApy version, Python version, and operating system as follows:

import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())

3.11.4 | packaged by conda-forge | (main, Jun 10 2023, 18:08:41) [Clang 15.0.7 ]
CPython
macOS-13.4.1-arm64-arm-64bit

(Please copy and run the above in your Python, and copy-and-paste the output)

Expected behaviour

import gseapy as gp

Should get import without any issue

Actual behaviour

ModuleNotFoundError Traceback (most recent call last) Cell In[57], line 1 ----> 1 import gseapy as gp

File ~/Documents/programming_environments/bio_env/lib/python3.11/site-packages/gseapy/init.py:9 7 from .biomart import Biomart 8 from .enrichr import Enrichr ----> 9 from .gsea import GSEA, Prerank, Replot, SingleSampleGSEA 10 from .parser import get_library_name 11 from .plot import barplot, dotplot, gseaplot, heatmap

File ~/Documents/programming_environments/bio_env/lib/python3.11/site-packages/gseapy/gsea.py:15 12 import pandas as pd 14 from gseapy.base import GSEAbase ---> 15 from gseapy.gse import Metric, gsea_rs, prerank_rs, ssgsea_rs # import gseapy rust lib 16 from gseapy.parser import gsea_cls_parser 17 from gseapy.plot import gseaplot

ModuleNotFoundError: No module named 'gseapy.gse'

Steps to reproduce

Just imported.

zqfang commented 1 year ago

please use pip install. Bioconda don't have py311 build yet.

# install rust compiler
curl https://sh.rustup.rs -sSf | sh -s -- -y
# export rust compiler
export PATH="$PATH:$HOME/.cargo/bin"
# install gseapy
pip install gseapy

ShriHarshaAdapalaThirumala commented 1 year ago

On trying to install via pip I am getting following error:

@.***

From: Zhuoqing Fang @.> Date: Wednesday, July 12, 2023 at 2:26 PM To: zqfang/GSEApy @.> Cc: Shri Harsha Adapala Thirumala @.>, Author @.> Subject: Re: [zqfang/GSEApy] No module named 'gseapy.gse' (Issue #214)

please use pip install. Bioconda don't have py311 build yet.

pip install gseapy

— Reply to this email directly, view it on GitHubhttps://github.com/zqfang/GSEApy/issues/214#issuecomment-1633013638, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ASRMZGZWWT4MID3AMDOM3XP3T3FANCNFSM6AAAAAA2HTKIVU. You are receiving this because you authored the thread.Message ID: @.***>

ShriHarshaAdapalaThirumala commented 1 year ago

please use pip install. Bioconda don't have py311 build yet.
pip install gseapy

Getting following error on trying to install via pip

zqfang commented 1 year ago

I'm sorry, I just notice you're using "ARM-Macos". I don't have a M1-chip Mac to build the binary.

In this case, you have to install rust additionally, see here: https://www.rust-lang.org/tools/install

mari-ga commented 1 year ago

Hi, sorry I'm having exactly the same issue. I installed Rust and then gseapy using conda but I still get the same error: ModuleNotFoundError: No module named 'gseapy.gse' did you manage to find a solution for this? I'm also working from ARM-MacOS - M2-Chip

zqfang commented 1 year ago

@mari-ga, uninstall the gseapy and run

pip install gseapy

since v1.0.6, MacOS-ARM64 pre-compiled binaries are shipped.

if it still failed, then follow the code below

# install rust compiler
curl https://sh.rustup.rs -sSf | sh -s -- -y
# export rust compiler
export PATH="$PATH:$HOME/.cargo/bin"
# install gseapy
pip install gseapy

zqfang commented 3 months ago

You shoud use

pip install gseapy

Not gseasy

Zhuoqing From: 77 @.> Date: Thursday, July 18, 2024 at 08:14 To: zqfang/GSEApy @.> Cc: Zhuoqing Fang @.>, Comment @.> Subject: Re: [zqfang/GSEApy] No module named 'gseapy.gse' (Issue #214)

Excuse me. I have tried the methods you mentioned above,

curl https://sh.rustup.rs -sSf | sh -s -- -y

. "$HOME/.cargo/env"

export PATH="$PATH:$HOME/.cargo/bin"

pip install gseasy

and got an error

ERROR: Could not find a version that satisfies the requirement gseasy (from versions: none)

ERROR: No matching distribution found for gseasy

My system info

3.9.18 (main, Sep 11 2023, 13:41:44)

[GCC 11.2.0]

CPython

Linux-5.4.0-165-generic-x86_64-with-glibc2.31

Could you please help with this installation issue? Thank you.

— Reply to this email directly, view it on GitHubhttps://github.com/zqfang/GSEApy/issues/214#issuecomment-2236831056, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABM52OEPKBUNRO5QORZQP2LZM7LUPAVCNFSM6AAAAABLC4RKL2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWHAZTCMBVGY. You are receiving this because you commented.Message ID: @.***>

Yecats77 commented 3 months ago

Yes. I realized that it was my mistake, and the issue was not actually valid. As soon as I recognized this, I proceeded to delete the issue from the repository.

Sorry for any confusion or inconvenience. And thank you for developing the nice tool!

From: Zhuoqing Fang @.> Sent: Thursday, July 18, 2024 11:55 PM To: zqfang/GSEApy @.> Cc: 77 @.>; Comment @.> Subject: Re: [zqfang/GSEApy] No module named 'gseapy.gse' (Issue #214)

You shoud use

pip install gseapy

Not gseasy

Zhuoqing From: 77 @.> Date: Thursday, July 18, 2024 at 08:14 To: zqfang/GSEApy @.> Cc: Zhuoqing Fang @.>, Comment @.> Subject: Re: [zqfang/GSEApy] No module named 'gseapy.gse' (Issue #214)

Excuse me. I have tried the methods you mentioned above,

curl https://sh.rustup.rs -sSf | sh -s -- -y

. "$HOME/.cargo/env"

export PATH="$PATH:$HOME/.cargo/bin"

pip install gseasy

and got an error

ERROR: Could not find a version that satisfies the requirement gseasy (from versions: none)

ERROR: No matching distribution found for gseasy

My system info

3.9.18 (main, Sep 11 2023, 13:41:44)

[GCC 11.2.0]

CPython

Linux-5.4.0-165-generic-x86_64-with-glibc2.31

Could you please help with this installation issue? Thank you.

— Reply to this email directly, view it on GitHubhttps://github.com/zqfang/GSEApy/issues/214#issuecomment-2236831056, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABM52OEPKBUNRO5QORZQP2LZM7LUPAVCNFSM6AAAAABLC4RKL2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWHAZTCMBVGY. You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/zqfang/GSEApy/issues/214#issuecomment-2236918091, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARAYIEPB5BALPIZRT5P24ALZM7QNRAVCNFSM6AAAAABLC4RKL2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWHEYTQMBZGE. You are receiving this because you commented.Message ID: @.***>

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