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Conda package #294

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Nusob888 opened this issue Jun 20, 2023 · 5 comments
Open

Conda package #294

Nusob888 opened this issue Jun 20, 2023 · 5 comments
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enhancement New feature or request

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@Nusob888
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Description of feature

Dear authors,

Please can you look into submitting pertpy for a conda implementation. I have tried multiple times to install this within a virtual environment and it causes numerous errors. I have never had an issue with any of the theis lab's conda packages in the past and pip is not conducive when you need an environment that has packages of different dependencies.

It would likely save everyone a whole lot of time and probably make this package more widely used.

Thanks for your consideration.
@Nusob888 Nusob888 added the enhancement New feature or request label Jun 20, 2023
@Zethson Zethson changed the title Conda implementation Conda package Jun 20, 2023
@Zethson
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Zethson commented Jun 20, 2023

Hi,

  1. Yes. It's on our TODO list. Don't expect it anytime soon though.
  2. What installation issues are you running into?

Thanks

@Nusob888
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Thanks,

well one example is installing pertpy with python v 3.10.6 in a venv goes fine, but when you load it, it tells you to use sccoda you have to install ete3 and rpy2. Installing those then gives this error (below) when you attempt to import it. If I do not install those I seem to be able to import fine.

SystemError Traceback (most recent call last)
Cell In[1], line 1
----> 1 import pertpy

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/pertpy/init.py:13
10 pertpy_pypi_latest = PypiLatest("pertpy", version)
11 pertpy_pypi_latest.check_latest()
---> 13 from . import data as dt
14 from . import plot as pl
15 from . import preprocessing as pp

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/pertpy/data/init.py:1
----> 1 from pertpy.data._datasets import (
2 adamson_2016_pilot,
3 adamson_2016_upr_epistasis,
4 adamson_2016_upr_perturb_seq,
5 aissa_2021,
6 bhattacherjee,
7 burczynski_crohn,
8 chang_2021,
9 datlinger_2017,
10 datlinger_2021,
11 dialogue_example,
12 distance_example_data,
13 dixit_2016,
14 dixit_2016_raw,
15 dixit_2016_scperturb,
16 frangieh_2021,
17 frangieh_2021_protein,
18 frangieh_2021_raw,
19 frangieh_2021_rna,
20 gasperini_2019_atscale,
21 gasperini_2019_highmoi,
22 gasperini_2019_lowmoi,
23 gehring_2019,
24 haber_2017_regions,
25 kang_2018,
26 mcfarland_2020,
27 norman_2019,
28 norman_2019_raw,
29 papalexi_2021,
30 replogle_2022_k562_essential,
31 replogle_2022_k562_gwps,
32 replogle_2022_rpe1,
33 sc_sim_augur,
34 schiebinger_2019_16day,
35 schiebinger_2019_18day,
36 schraivogel_2020_tap_screen_chr8,
37 schraivogel_2020_tap_screen_chr11,
38 sciplex3_raw,
39 shifrut_2018,
40 smillie,
41 srivatsan_2020_sciplex2,
42 srivatsan_2020_sciplex3,
43 srivatsan_2020_sciplex4,
44 stephenson_2021_subsampled,
45 tian_2019_day7neuron,
46 tian_2019_ipsc,
47 tian_2021_crispra,
48 tian_2021_crispri,
49 weinreb_2020,
50 xie_2017,
51 zhao_2021,
52 )

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/pertpy/data/_datasets.py:3
1 from pathlib import Path
----> 3 import muon as mu
4 import scanpy as sc
5 from anndata import AnnData

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/muon/init.py:6
3 from mudata import MuData
4 from mudata._core.io import *
----> 6 from ._core import preproc as pp
7 from ._core import tools as tl
8 from ._core import plot as pl

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/muon/_core/preproc.py:13
10 from sklearn.utils import check_random_state
12 from anndata import AnnData
---> 13 from scanpy import logging
14 from scanpy.tools._utils import _choose_representation
15 from scanpy.neighbors import _compute_connectivities_umap

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/scanpy/init.py:6
3 from ._metadata import version, within_flit
5 if not within_flit(): # see function docstring on why this is there
----> 6 from ._utils import check_versions
8 check_versions()
9 del check_versions, within_flit

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/scanpy/_utils/init.py:29
26 from .._compat import Literal
27 from .. import logging as logg
---> 29 from .compute.is_constant import is_constant
32 class Empty(Enum):
33 token = 0

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/scanpy/_utils/compute/is_constant.py:5
2 from numbers import Integral
4 import numpy as np
----> 5 from numba import njit
6 from scipy import sparse
9 @singledispatch
10 def is_constant(a, axis=None) -> np.ndarray:

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/numba/init.py:42
38 from numba.core.decorators import (cfunc, generated_jit, jit, njit, stencil,
39 jit_module)
41 # Re-export vectorize decorators and the thread layer querying function
---> 42 from numba.np.ufunc import (vectorize, guvectorize, threading_layer,
43 get_num_threads, set_num_threads,
44 set_parallel_chunksize, get_parallel_chunksize,
45 get_thread_id)
47 # Re-export Numpy helpers
48 from numba.np.numpy_support import carray, farray, from_dtype

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/numba/np/ufunc/init.py:3
1 # -- coding: utf-8 --
----> 3 from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize
4 from numba.np.ufunc._internal import PyUFunc_None, PyUFunc_Zero, PyUFunc_One
5 from numba.np.ufunc import _internal, array_exprs

File /well/immune-rep/users/vbw431/conda/ivybridge/envs/sccoda/lib/python3.10/site-packages/numba/np/ufunc/decorators.py:3
1 import inspect
----> 3 from numba.np.ufunc import _internal
4 from numba.np.ufunc.parallel import ParallelUFuncBuilder, ParallelGUFuncBuilder
6 from numba.core.registry import DelayedRegistry

SystemError: initialization of _internal failed without raising an exception

@Zethson
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Zethson commented Jun 20, 2023 via email

@Nusob888
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Yes, fresh venv and OS is:

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

@Zethson
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Zethson commented Jun 26, 2023

The error that you're getting actually runs when trying to import scanpy and in turn numba. centos7 is really old.

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