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rapidsai / cudf

cuDF - GPU DataFrame Library
https://docs.rapids.ai/api/cudf/stable/
Apache License 2.0
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[BUG] ImportError cudf, cannot import name 'pa_version_under14p1' from 'pandas.compat' #16142

Closed RijndertAriese closed 2 months ago

RijndertAriese commented 2 months ago

Hi all,

I'm having trouble importing cudf (cudf-cu12==24.6.0) on our Linux server. 

ImportError                               Traceback (most recent call last)
Cell In[102], line 1
----> 1 import cudf

File /.../lib/python3.10/site-packages/cudf/__init__.py:9
      6 from cudf.utils._numba import _setup_numba
      7 from cudf.utils.gpu_utils import validate_setup
----> 9 _setup_numba()
     10 validate_setup()
     12 import cupy

File /.../lib/python3.10/site-packages/cudf/utils/_numba.py:124, in _setup_numba()
    121 if versions != NO_DRIVER:
    122     driver_version, runtime_version = versions
    123     ptx_toolkit_version = _get_cuda_version_from_ptx_file(
--> 124         _get_cc_60_ptx_file()
    125     )
    127     # MVC is required whenever any PTX is newer than the driver
    128     # This could be the shipped PTX file or the PTX emitted by
    129     # the version of NVVM on the user system, the latter aligning
    130     # with the runtime version
    131     if (driver_version < ptx_toolkit_version) or (
    132         driver_version < runtime_version
    133     ):

File /.../lib/python3.10/site-packages/cudf/utils/_numba.py:16, in _get_cc_60_ptx_file()
     14 @lru_cache
     15 def _get_cc_60_ptx_file():
---> 16     from cudf._lib import strings_udf
     18     return os.path.join(
     19         os.path.dirname(strings_udf.__file__),
     20         "..",
   (...)
     23         "shim_60.ptx",
     24     )

File /.../lib/python3.10/site-packages/cudf/_lib/__init__.py:4
      1 # Copyright (c) 2020-2023, NVIDIA CORPORATION.
      2 import numpy as np
----> 4 from . import (
      5     avro,
      6     binaryop,
      7     concat,
      8     copying,
      9     csv,
     10     datetime,
     11     expressions,
     12     filling,
     13     groupby,
     14     hash,
     15     interop,
     16     join,
     17     json,
     18     labeling,
     19     merge,
     20     null_mask,
     21     nvtext,
     22     orc,
     23     parquet,
     24     partitioning,
     25     pylibcudf,
     26     quantiles,
     27     reduce,
     28     replace,
     29     reshape,
     30     rolling,
     31     round,
     32     search,
     33     sort,
     34     stream_compaction,
     35     string_casting,
     36     strings,
     37     strings_udf,
     38     text,
     39     timezone,
     40     transpose,
     41     unary,
     42 )
     44 MAX_COLUMN_SIZE = np.iinfo(np.int32).max
     45 MAX_COLUMN_SIZE_STR = "INT32_MAX"

File avro.pyx:1, in init cudf._lib.avro()

File column.pyx:1, in init cudf._lib.column()

File scalar.pyx:17, in init cudf._lib.scalar()

File /.../lib/python3.10/site-packages/cudf/core/dtypes.py:16
     14 from pandas.api import types as pd_types
     15 from pandas.api.extensions import ExtensionDtype
---> 16 from pandas.core.arrays.arrow.extension_types import ArrowIntervalType
     18 import cudf
     19 from cudf._typing import Dtype

File /.../lib/python3.10/site-packages/pandas/core/arrays/arrow/extension_types.py:8
      4 from typing import TYPE_CHECKING
      6 import pyarrow
----> 8 from pandas.compat import pa_version_under14p1
     10 from pandas.core.dtypes.dtypes import (
     11     IntervalDtype,
     12     PeriodDtype,
     13 )
     15 from pandas.core.arrays.interval import VALID_CLOSED

ImportError: cannot import name 'pa_version_under14p1' from 'pandas.compat' (/.../lib/python3.10/site-packages/pandas/compat/__init__.py)

I've tried downgrading pandas to 2.2.1 and lower and pyarrow to 16.0.0 and lower but this did not resolve the issue

cuDF was installed using 

pip install \
    --extra-index-url=https://pypi.nvidia.com \
    cudf-cu12==24.6.* dask-cudf-cu12==24.6.* cuml-cu12==24.6.* \
    cugraph-cu12==24.6.* cuspatial-cu12==24.6.* cuproj-cu12==24.6.* \
    cuxfilter-cu12==24.6.* cucim-cu12==24.6.* pylibraft-cu12==24.6.* \
    raft-dask-cu12==24.6.* cuvs-cu12==24.6.*

Environment details

**git***
     Not inside a git repository

     ***OS Information***
     Rocky Linux release 8.10 (Green Obsidian)
     NAME="Rocky Linux"
     VERSION="8.10 (Green Obsidian)"
     ID="rocky"
     ID_LIKE="rhel centos fedora"
     VERSION_ID="8.10"
     PLATFORM_ID="platform:el8"
     PRETTY_NAME="Rocky Linux 8.10 (Green Obsidian)"
     ANSI_COLOR="0;32"
     LOGO="fedora-logo-icon"
     CPE_NAME="cpe:/o:rocky:rocky:8:GA"
     HOME_URL="https://rockylinux.org/"
     BUG_REPORT_URL="https://bugs.rockylinux.org/"
     SUPPORT_END="2029-05-31"
     ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8"
     ROCKY_SUPPORT_PRODUCT_VERSION="8.10"
     REDHAT_SUPPORT_PRODUCT="Rocky Linux"
     REDHAT_SUPPORT_PRODUCT_VERSION="8.10"
     Rocky Linux release 8.10 (Green Obsidian)
     Rocky Linux release 8.10 (Green Obsidian)
     Rocky Linux release 8.10 (Green Obsidian)
     Linux n0130.manage.hpc 4.18.0-553.el8_10.x86_64 #1 SMP Fri May 24 13:05:10 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

     ***GPU Information***
     Mon Jul  1 12:49:31 2024
     +-----------------------------------------------------------------------------------------+
     | NVIDIA-SMI 555.42.02              Driver Version: 555.42.02      CUDA Version: 12.5     |
     |-----------------------------------------+------------------------+----------------------+
     | GPU  Name                 Persistence-M | Bus-Id          Disp.A | Volatile Uncorr. ECC |
     | Fan  Temp   Perf          Pwr:Usage/Cap |           Memory-Usage | GPU-Util  Compute M. |
     |                                         |                        |               MIG M. |
     |=========================================+========================+======================|
     |   0  NVIDIA A100 80GB PCIe          On  |   00000000:17:00.0 Off |                   On |
     | N/A   37C    P0             43W /  300W |       1MiB /  81920MiB |     N/A      Default |
     |                                         |                        |              Enabled |
     +-----------------------------------------+------------------------+----------------------+

     +-----------------------------------------------------------------------------------------+
     | MIG devices:                                                                            |
     +------------------+----------------------------------+-----------+-----------------------+
     | GPU  GI  CI  MIG |                     Memory-Usage |        Vol|      Shared           |
     |      ID  ID  Dev |                       BAR1-Usage | SM     Unc| CE ENC DEC OFA JPG    |
     |                  |                                  |        ECC|                       |
     |==================+==================================+===========+=======================|
     |  0    0   0   0  |               1MiB / 81158MiB    | 98      0 |  7   0    5    1    1 |
     |                  |                 1MiB / 131072MiB |           |                       |
     +------------------+----------------------------------+-----------+-----------------------+

     +-----------------------------------------------------------------------------------------+
     | Processes:                                                                              |
     |  GPU   GI   CI        PID   Type   Process name                              GPU Memory |
     |        ID   ID                                                               Usage      |
     |=========================================================================================|
     |  No running processes found                                                             |
     +-----------------------------------------------------------------------------------------+

     ***CPU***
     Architecture:        x86_64
     CPU op-mode(s):      32-bit, 64-bit
     Byte Order:          Little Endian
     CPU(s):              96
     On-line CPU(s) list: 0-95
     Thread(s) per core:  2
     Core(s) per socket:  24
     Socket(s):           2
     NUMA node(s):        2
     Vendor ID:           GenuineIntel
     CPU family:          6
     Model:               106
     Model name:          Intel(R) Xeon(R) Gold 6342 CPU @ 2.80GHz
     Stepping:            6
     CPU MHz:             2800.000
     BogoMIPS:            5600.00
     Virtualization:      VT-x
     L1d cache:           48K
     L1i cache:           32K
     L2 cache:            1280K
     L3 cache:            36864K
     NUMA node0 CPU(s):   0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94
     NUMA node1 CPU(s):   1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95
     Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 invpcid_single intel_ppin ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb intel_pt avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local split_lock_detect wbnoinvd dtherm ida arat pln pts avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg tme avx512_vpopcntdq la57 rdpid fsrm md_clear pconfig flush_l1d arch_capabilities

     ***CMake***
     /hpc/pmc_rios/2.personal/rariese/miniconda/envs/scanpy/bin/cmake
     cmake version 3.29.0

     CMake suite maintained and supported by Kitware (kitware.com/cmake).

     ***g++***
     /usr/bin/g++
     g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-22)
     Copyright (C) 2018 Free Software Foundation, Inc.
     This is free software; see the source for copying conditions.  There is NO
     warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

     ***nvcc***
     /hpc/pmc_rios/2.personal/rariese/miniconda/envs/scanpy/bin/nvcc
     nvcc: NVIDIA (R) Cuda compiler driver
     Copyright (c) 2005-2024 NVIDIA Corporation
     Built on Tue_Feb_27_16:19:38_PST_2024
     Cuda compilation tools, release 12.4, V12.4.99
     Build cuda_12.4.r12.4/compiler.33961263_0

     ***Python***
     /hpc/pmc_rios/2.personal/rariese/miniconda/envs/scanpy/bin/python
     Python 3.10.13

     ***Environment Variables***
     PATH                            : /hpc/pmc_rios/2.personal/rariese/miniconda/envs/scanpy/bin:/hpc/local/Rocky8/pmc_rios/bedtools/bin:/hpc/local/Rocky8/pmc_rios/R-4.3.2/bin:/hpc/local/Rocky8/pmc_rios/samtools/bin:/hpc/local/Rocky8/pmc_rios/parallel/bin:/hpc/local/Rocky8/pmc_rios/miniconda3/bin/python3.11:/home/pmc_research/rariese/.cargo/bin:/hpc/local/Rocky8/pmc_rios/miniconda3/condabin:/hpc/local/Rocky8/pmc_research/bin:/hpc/local/Rocky8/pmc_research/sbin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/gnu/profiles/base/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin:/home/pmc_research/rariese/bin:/gnu/profiles/base/bin
     LD_LIBRARY_PATH                 : /hpc/local/Rocky8/pmc_research/lib
     NUMBAPRO_NVVM                   :
     NUMBAPRO_LIBDEVICE              :
     CONDA_PREFIX                    : /hpc/pmc_rios/2.personal/rariese/miniconda/envs/scanpy
     PYTHON_PATH                     :

     ***conda packages***
     /hpc/local/Rocky8/pmc_rios/miniconda3/condabin/conda
wence- commented 2 months ago

Can you import that pandas that was installed using the command? That looks like a problem with the version of pandas that was installed? Perhaps you have multiple versions kicking around? To that end, could you please show the output of conda list and pip freeze? Thanks!

RijndertAriese commented 2 months ago

Hi, thanks for your reply!

These are the packages in my env. There are quite some, so a dependency issue is likely at some point. But afaik I have the pandas and pyarrow (where 'pa_version_under14p1' points towards) packages that was installed with the cuml installation in there.

Conda list ``` conda list # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.0 anacondar_1 _sysroot_linux-64_curr_repodata_hack 3 haa98f57_10 absl-py 2.1.0 pyhd8ed1ab_0 conda-forge adjusttext 1.1.1 pypi_0 pypi aiobotocore 2.5.4 pypi_0 pypi aiohttp 3.9.3 pypi_0 pypi aioitertools 0.11.0 pypi_0 pypi aiosignal 1.3.1 pypi_0 pypi airr 1.5.1 pypi_0 pypi alabaster 0.7.16 pypi_0 pypi alembic 1.13.1 pypi_0 pypi anndata 0.10.8 pypi_0 pypi anndata2ri 1.3.1 pyhdfd78af_1 bioconda annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge annoy 1.17.3 pypi_0 pypi anyio 3.7.1 pyhd8ed1ab_0 conda-forge aom 3.8.2 h59595ed_0 conda-forge app-model 0.2.7 pypi_0 pypi appdirs 1.4.4 pypi_0 pypi argon2-cffi 21.3.0 pyhd3eb1b0_0 argon2-cffi-bindings 21.2.0 py310h7f8727e_0 array-api-compat 1.5.1 pyhd8ed1ab_0 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asciitree 0.3.3 pypi_0 pypi asttokens 2.4.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pypi_0 pypi async-lru 2.0.4 py310h06a4308_0 async-timeout 4.0.3 pypi_0 pypi asyncio-atexit 1.0.1 pypi_0 pypi attrs 23.1.0 py310h06a4308_0 awkward 2.6.5 pypi_0 pypi awkward-cpp 34 pypi_0 pypi babel 2.11.0 py310h06a4308_0 backoff 2.2.1 pyhd8ed1ab_0 conda-forge bbknn 1.6.0 pypi_0 pypi beautifulsoup4 4.12.3 pyha770c72_0 conda-forge binaryornot 0.4.4 pypi_0 pypi binutils_impl_linux-64 2.38 h2a08ee3_1 bleach 4.1.0 pyhd3eb1b0_0 blessed 1.19.1 pyhe4f9e05_2 conda-forge blosc 1.21.5 h0f2a231_0 conda-forge blosc2 2.6.0 pypi_0 pypi bokeh 3.4.2 pypi_0 pypi boltons 24.0.0 pypi_0 pypi boto3 1.34.71 pyhd8ed1ab_0 conda-forge botocore 1.34.131 pypi_0 pypi brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bwidget 1.9.16 h9eba36c_0 bzip2 1.0.8 h5eee18b_5 c-ares 1.27.0 hd590300_0 conda-forge ca-certificates 2024.6.2 hbcca054_0 conda-forge cachecontrol 0.14.0 pyhd8ed1ab_0 conda-forge cachecontrol-with-filecache 0.14.0 pyhd8ed1ab_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.3 pypi_0 pypi cachey 0.2.1 pypi_0 pypi cairo 1.18.0 h3faef2a_0 conda-forge captum 0.7.0 pypi_0 pypi cellrank 2.0.3 pypi_0 pypi celltypist 1.6.2 pypi_0 pypi certifi 2024.6.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge chardet 5.2.0 pypi_0 pypi charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge chex 0.1.86 pyhd8ed1ab_0 conda-forge clarabel 0.7.1 pypi_0 pypi cleo 2.1.0 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge click-plugins 1.1.1 pypi_0 pypi cligj 0.7.2 pypi_0 pypi cloudpickle 3.0.0 pypi_0 pypi cmake 3.29.0.1 pypi_0 pypi colorama 0.4.6 pyhd8ed1ab_0 conda-forge colorcet 3.1.0 pypi_0 pypi colorlog 6.8.2 pypi_0 pypi comet-ml 3.35.5 pypi_0 pypi comm 0.2.2 pyhd8ed1ab_0 conda-forge configobj 5.0.8 pypi_0 pypi contextlib2 21.6.0 pyhd8ed1ab_0 conda-forge contourpy 1.2.0 py310hd41b1e2_0 conda-forge cookiecutter 2.6.0 pypi_0 pypi crashtest 0.4.1 pyhd8ed1ab_0 conda-forge croniter 1.4.1 pyhd8ed1ab_0 conda-forge crossref-commons 0.0.7 pypi_0 pypi cryptography 42.0.5 py310h75e40e8_0 conda-forge cucim-cu12 24.6.0 pypi_0 pypi cuda-nvcc 12.4.99 0 nvidia cuda-python 12.5.0 pypi_0 pypi cuda-version 11.8 h70ddcb2_3 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cudf-cu12 24.6.0 pypi_0 pypi cudnn 8.9.7.29 hbc23b4c_3 conda-forge cugraph-cu12 24.6.1 pypi_0 pypi cuproj-cu12 24.6.0 pypi_0 pypi cupy-cuda12x 13.2.0 pypi_0 pypi curl 8.7.1 hca28451_0 conda-forge cuspatial-cu12 24.6.0 pypi_0 pypi cuvs-cu12 24.6.0 pypi_0 pypi cuxfilter-cu12 24.6.0 pypi_0 pypi cvxpy 1.4.2 pypi_0 pypi cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.9 pypi_0 pypi dask 2024.5.1 pypi_0 pypi dask-cuda 24.6.0 pypi_0 pypi dask-cudf-cu12 24.6.0 pypi_0 pypi dask-expr 1.1.1 pypi_0 pypi dask-image 2023.8.1 pypi_0 pypi datashader 0.16.1 pypi_0 pypi dateutils 0.6.12 py_0 conda-forge dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge debugpy 1.8.1 py310hc6cd4ac_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge decoupler 1.6.0 pypi_0 pypi deepdiff 6.7.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd3eb1b0_0 deprecated 1.2.14 pypi_0 pypi distlib 0.3.8 pyhd8ed1ab_0 conda-forge distributed 2024.5.1 pypi_0 pypi distributed-ucxx-cu12 0.38.0 pypi_0 pypi docrep 0.3.2 pyh44b312d_0 conda-forge docstring-parser 0.16 pypi_0 pypi docutils 0.21.2 pypi_0 pypi dulwich 0.21.7 py310h2372a71_0 conda-forge dunamai 1.19.2 pyhd8ed1ab_0 conda-forge ecos 2.0.13 pypi_0 pypi et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge etils 1.7.0 pyhd8ed1ab_0 conda-forge everett 3.1.0 pypi_0 pypi exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fa2 0.3.5 py310h5764c6d_2 conda-forge fastapi 0.110.0 pyhd8ed1ab_0 conda-forge fastcluster 1.2.6 pypi_0 pypi fasteners 0.19 pypi_0 pypi fastrlock 0.8.2 pypi_0 pypi fcsparser 0.2.8 pypi_0 pypi filelock 3.13.3 pyhd8ed1ab_0 conda-forge fiona 1.9.6 pypi_0 pypi 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r-lava 1.7.2.1 r43h6115d3f_0 r-lifecycle 1.0.3 r43h142f84f_0 r-listenv 0.9.0 r43h142f84f_0 r-lubridate 1.9.3 r43h76d94ec_0 r-magrittr 2.0.3 r43h76d94ec_0 r-mass 7.3_60 r43h76d94ec_0 r-matrix 1.6_1.1 r43h76d94ec_0 r-memoise 2.0.1 r43h6115d3f_0 r-mgcv 1.9_0 r43h76d94ec_0 r-mime 0.12 r43h76d94ec_0 r-modelmetrics 1.2.2.2 r43h884c59f_0 r-modelr 0.1.11 r43h6115d3f_0 r-munsell 0.5.0 r43h6115d3f_0 r-nlme 3.1_163 r43h640688f_0 r-nnet 7.3_19 r43h76d94ec_0 r-numderiv 2016.8_1.1 r43h6115d3f_0 r-openssl 2.1.1 r43h76d94ec_0 r-parallelly 1.36.0 r43h6115d3f_0 r-pbdzmq 0.3_10 r43h884c59f_0 r-pillar 1.9.0 r43h6115d3f_0 r-pkgconfig 2.0.3 r43h6115d3f_0 r-plyr 1.8.9 r43h884c59f_0 r-prettyunits 1.2.0 r43h142f84f_0 r-proc 1.18.4 r43h884c59f_0 r-processx 3.8.2 r43h76d94ec_0 r-prodlim 2023.08.28 r43h884c59f_0 r-progress 1.2.2 r43h142f84f_0 r-progressr 0.14.0 r43h6115d3f_0 r-promises 1.2.1 r43h884c59f_0 r-proxy 0.4_27 r43h76d94ec_0 r-ps 1.7.5 r43h76d94ec_0 r-purrr 1.0.2 r43h76d94ec_0 r-quantmod 0.4.25 r43h6115d3f_0 r-r6 2.5.1 r43h6115d3f_0 r-ragg 1.2.6 r43h884c59f_0 r-randomforest 4.7_1.1 r43h640688f_0 r-rappdirs 0.3.3 r43h76d94ec_0 r-rcolorbrewer 1.1_3 r43h6115d3f_1 r-rcpp 1.0.11 r43h884c59f_0 r-rcppeigen 0.3.3.9.3 r43h884c59f_0 r-readr 2.1.4 r43h884c59f_0 r-readxl 1.4.3 r43h884c59f_0 r-recipes 1.0.8 r43h6115d3f_0 r-recommended 4.3.1 r43_0 r-rematch 2.0.0 r43h6115d3f_0 r-rematch2 2.1.2 r43h142f84f_0 r-repr 1.1.6 r43h6115d3f_0 r-reprex 2.0.2 r43h6115d3f_0 r-reshape2 1.4.4 r43h884c59f_0 r-rlang 1.1.1 r43h884c59f_0 r-rmarkdown 2.25 r43h6115d3f_0 r-rpart 4.1.21 r43h76d94ec_0 r-rstudioapi 0.15.0 r43h6115d3f_0 r-rvest 1.0.3 r43h6115d3f_0 r-sass 0.4.7 r43h884c59f_0 r-scales 1.2.1 r43h6115d3f_0 r-selectr 0.4_2 r43h6115d3f_0 r-shape 1.4.6 r43h142f84f_0 r-shiny 1.7.5.1 r43h6115d3f_0 r-sourcetools 0.1.7_1 r43h884c59f_0 r-spatial 7.3_17 r43h76d94ec_0 r-squarem 2021.1 r43h142f84f_0 r-stringi 1.7.12 r43h884c59f_0 r-stringr 1.5.0 r43h6115d3f_0 r-survival 3.5_7 r43h76d94ec_0 r-sys 3.4.2 r43h76d94ec_0 r-systemfonts 1.0.5 r43h884c59f_0 r-textshaping 0.3.7 r43h884c59f_0 r-tibble 3.2.1 r43h76d94ec_0 r-tidyr 1.3.0 r43h884c59f_0 r-tidyselect 1.2.0 r43h6115d3f_0 r-tidyverse 2.0.0 r43h6115d3f_0 r-timechange 0.2.0 r43h884c59f_0 r-timedate 4022.108 r43h6115d3f_0 r-tinytex 0.48 r43h142f84f_0 r-ttr 0.24.3 r43h76d94ec_0 r-tzdb 0.4.0 r43h884c59f_0 r-utf8 1.2.4 r43h76d94ec_0 r-uuid 1.1_1 r43h76d94ec_0 r-vctrs 0.6.4 r43h884c59f_0 r-viridislite 0.4.2 r43h6115d3f_0 r-vroom 1.6.4 r43h884c59f_0 r-withr 2.5.1 r43h6115d3f_0 r-xfun 0.40 r43h76d94ec_0 r-xml2 1.3.5 r43h884c59f_0 r-xtable 1.8_4 r43h6115d3f_0 r-xts 0.13.1 r43h76d94ec_0 r-yaml 2.3.7 r43h76d94ec_0 r-zoo 1.8_12 r43h76d94ec_0 raft-dask-cu12 24.6.0 pypi_0 pypi rapidfuzz 3.9.3 pypi_0 pypi rapids-dask-dependency 24.6.0 pypi_0 pypi ratelimit 2.2.1 pypi_0 pypi rav1e 0.6.6 he8a937b_2 conda-forge re2 2023.09.01 h7f4b329_1 conda-forge readchar 4.0.5 pyhd8ed1ab_0 conda-forge readfcs 1.1.8 pypi_0 pypi readline 8.2 h5eee18b_0 referencing 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setuptools 68.2.2 py310h06a4308_0 sfaira 0.3.12 pypi_0 pypi shapely 2.0.4 pypi_0 pypi shellingham 1.5.4 pyhd8ed1ab_0 conda-forge simpervisor 1.0.0 pypi_0 pypi simplegeneric 0.8.1 py310h06a4308_2 simplejson 3.19.2 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge sleef 3.5.1 h9b69904_2 conda-forge slicerator 1.1.0 pypi_0 pypi snappy 1.1.10 h9fff704_0 conda-forge sniffio 1.3.1 pyhd8ed1ab_0 conda-forge snowballstemmer 2.2.0 pypi_0 pypi sorted-nearest 0.0.39 pypi_0 pypi sortedcontainers 2.4.0 pypi_0 pypi soupsieve 2.5 pyhd8ed1ab_1 conda-forge sparse 0.15.1 pyhd8ed1ab_1 conda-forge spatial-image 0.3.0 pypi_0 pypi spatialdata 0.1.2 pypi_0 pypi spatialdata-io 0.1.2 pypi_0 pypi spatialdata-plot 0.2.2 pypi_0 pypi sphinx 7.3.7 pypi_0 pypi sphinxcontrib-applehelp 1.0.8 pypi_0 pypi sphinxcontrib-devhelp 1.0.6 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.5 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 1.0.7 pypi_0 pypi sphinxcontrib-serializinghtml 1.1.10 pypi_0 pypi sqlalchemy 2.0.31 pypi_0 pypi sqlite 3.41.2 h5eee18b_0 squarify 0.4.3 pypi_0 pypi squidpy 1.4.1 pypi_0 pypi stack_data 0.6.2 pyhd8ed1ab_0 conda-forge starlette 0.36.3 pyhd8ed1ab_0 conda-forge starsessions 1.3.0 pyhd8ed1ab_0 conda-forge statsmodels 0.14.2 pypi_0 pypi stdlib-list 0.10.0 pypi_0 pypi superqt 0.6.6 pypi_0 pypi svt-av1 2.0.0 h59595ed_0 conda-forge switchlang 0.1.0 pypi_0 pypi sympy 1.12 pyh04b8f61_3 conda-forge synapseclient 4.2.0 pypi_0 pypi sysroot_linux-64 2.17 h57e8cba_10 tables 3.9.2 pypi_0 pypi tabulate 0.9.0 pypi_0 pypi tbb 2021.13.0 pypi_0 pypi tblib 3.0.0 pypi_0 pypi tenacity 8.3.0 pypi_0 pypi tensorboard 2.16.2 pypi_0 pypi tensorboard-data-server 0.7.2 pypi_0 pypi tensorflow 2.16.1 pypi_0 pypi tensorflow-io-gcs-filesystem 0.37.0 pypi_0 pypi tensorstore 0.1.51 py310h122cdbb_1 conda-forge termcolor 2.4.0 pypi_0 pypi terminado 0.17.1 py310h06a4308_0 text-unidecode 1.3 pypi_0 pypi texttable 1.7.0 pypi_0 pypi tf-keras 2.16.0 pypi_0 pypi threadpoolctl 3.4.0 pyhc1e730c_0 conda-forge tifffile 2024.5.3 pypi_0 pypi tinycss2 1.2.1 py310h06a4308_0 tk 8.6.13 noxft_h4845f30_101 conda-forge tktable 2.10 h3d55465_1 tomli 2.0.1 pyhd8ed1ab_0 conda-forge tomli-w 1.0.0 pypi_0 pypi tomlkit 0.12.4 pyha770c72_0 conda-forge toolz 0.12.1 pyhd8ed1ab_0 conda-forge torch 2.3.1+cu121 pypi_0 pypi torch-geometric 2.5.3 pypi_0 pypi torchaudio 2.3.1+cu121 pypi_0 pypi torchmetrics 1.3.2 pyhd8ed1ab_0 conda-forge torchvision 0.18.1+cu121 pypi_0 pypi tornado 6.4 py310h2372a71_0 conda-forge tqdm 4.66.1 pypi_0 pypi traitlets 5.14.2 pyhd8ed1ab_0 conda-forge treelite 4.1.2 pypi_0 pypi triton 2.3.1 pypi_0 pypi trove-classifiers 2024.3.25 pyhd8ed1ab_0 conda-forge typeguard 4.2.1 pypi_0 pypi typer 0.12.3 pypi_0 pypi types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge typing-extensions 4.10.0 hd8ed1ab_0 conda-forge typing_extensions 4.10.0 pyha770c72_0 conda-forge tzdata 2024a h04d1e81_0 tzlocal 2.1 py310h06a4308_1 uc-micro-py 1.0.3 pypi_0 pypi ucx-py-cu12 0.38.0 pypi_0 pypi ucxx-cu12 0.38.0 pypi_0 pypi umap-learn 0.5.4 pypi_0 pypi unicodedata2 15.1.0 py310h2372a71_0 conda-forge unitvelo 0.2.5.2 pypi_0 pypi uri-template 1.3.0 pypi_0 pypi urllib3 1.26.18 pypi_0 pypi uvicorn 0.29.0 py310hff52083_0 conda-forge validators 0.28.1 pypi_0 pypi velocyto 0.17.17 pypi_0 pypi versioneer 0.29 pypi_0 pypi virtualenv 20.25.1 pyhd8ed1ab_0 conda-forge vispy 0.14.2 pypi_0 pypi wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 1.13 pypi_0 pypi webencodings 0.5.1 py310h06a4308_1 websocket-client 1.3.3 pypi_0 pypi websockets 12.0 py310h2372a71_0 conda-forge werkzeug 3.0.3 pypi_0 pypi wheel 0.41.2 py310h06a4308_0 widgetsnbextension 4.0.10 pypi_0 pypi wrapt 1.16.0 pypi_0 pypi wurlitzer 3.1.1 pypi_0 pypi xarray 2023.12.0 pypi_0 pypi xarray-dataclasses 1.7.0 pypi_0 pypi xarray-datatree 0.0.14 pypi_0 pypi xarray-schema 0.0.3 pypi_0 pypi xarray-spatial 0.4.0 pypi_0 pypi xlrd 1.2.0 pyh9f0ad1d_1 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h27cfd23_1007 xyzservices 2024.6.0 pypi_0 pypi xz 5.4.6 h5eee18b_0 yaml 0.2.5 h7f98852_2 conda-forge yamlordereddictloader 0.4.2 pypi_0 pypi yarl 1.9.4 pypi_0 pypi zarr 2.17.2 pypi_0 pypi zeromq 4.3.5 h59595ed_1 conda-forge zict 3.0.0 pypi_0 pypi zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge ```
Pip freeze ``` pip freeze absl-py @ file:///home/conda/feedstock_root/build_artifacts/absl-py_1705494584803/work adjustText==1.1.1 aiobotocore==2.5.4 aiohttp==3.9.3 aioitertools==0.11.0 aiosignal==1.3.1 airr==1.5.1 alabaster==0.7.16 alembic==1.13.1 anndata==0.10.8 anndata2ri @ file:///opt/conda/conda-bld/anndata2ri_1709223422752/work annotated-types @ file:///home/conda/feedstock_root/build_artifacts/annotated-types_1696634205638/work annoy==1.17.3 anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1688651106312/work/dist app-model==0.2.7 appdirs==1.4.4 argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644553347904/work array_api_compat @ file:///home/conda/feedstock_root/build_artifacts/array-api-compat_1710986294074/work arrow @ file:///home/conda/feedstock_root/build_artifacts/arrow_1696128962909/work asciitree==0.3.3 asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1698341106958/work astunparse==1.6.3 async-lru @ file:///croot/async-lru_1699554519285/work async-timeout==4.0.3 asyncio-atexit==1.0.1 attrs @ file:///croot/attrs_1695717823297/work awkward==2.6.5 awkward-cpp==34 Babel @ file:///croot/babel_1671781930836/work backoff @ file:///home/conda/feedstock_root/build_artifacts/backoff_1665004764738/work bbknn==1.6.0 beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1705564648255/work binaryornot==0.4.4 bleach @ file:///opt/conda/conda-bld/bleach_1641577558959/work blessed @ file:///home/conda/feedstock_root/build_artifacts/blessed_1666523113356/work blosc2==2.6.0 bokeh==3.4.2 boltons==24.0.0 boto3 @ file:///home/conda/feedstock_root/build_artifacts/boto3_1711493884805/work botocore==1.34.131 Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1695989787169/work build @ file:///home/conda/feedstock_root/build_artifacts/python-build_1709251527949/work CacheControl @ file:///home/conda/feedstock_root/build_artifacts/cachecontrol-split_1706895135817/work cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work cachetools==5.3.3 cachey==0.2.1 captum==0.7.0 cellrank==2.0.3 celltypist==1.6.2 certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1718025014955/work/certifi cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1696001684923/work chardet==5.2.0 charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1698833585322/work chex @ file:///home/conda/feedstock_root/build_artifacts/chex_1710850908421/work clarabel==0.7.1 cleo @ file:///home/conda/feedstock_root/build_artifacts/cleo_1698693584261/work click @ file:///home/conda/feedstock_root/build_artifacts/click_1692311806742/work click-plugins==1.1.1 cligj==0.7.2 cloudpickle==3.0.0 cmake==3.29.0.1 colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work colorcet==3.1.0 colorlog==6.8.2 comet-ml==3.35.5 comm @ file:///home/conda/feedstock_root/build_artifacts/comm_1710320294760/work configobj==5.0.8 contextlib2 @ file:///home/conda/feedstock_root/build_artifacts/contextlib2_1624848568296/work contourpy @ file:///home/conda/feedstock_root/build_artifacts/contourpy_1699041363598/work cookiecutter==2.6.0 crashtest @ file:///home/conda/feedstock_root/build_artifacts/crashtest_1667467006729/work croniter @ file:///home/conda/feedstock_root/build_artifacts/croniter_1686929181238/work crossref-commons==0.0.7 cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography-split_1708780263085/work cucim-cu12==24.6.0 cuda-python==12.5.0 cudf-cu12==24.6.0 cugraph-cu12==24.6.1 cuproj-cu12==24.6.0 cupy-cuda12x==13.2.0 cuspatial-cu12==24.6.0 cuvs-cu12==24.6.0 cuxfilter-cu12==24.6.0 cvxpy==1.4.2 cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work Cython==3.0.9 dask==2024.5.1 dask-cuda==24.6.0 dask-cudf-cu12==24.6.0 dask-expr==1.1.1 dask-image==2023.8.1 datashader==0.16.1 dateutils @ file:///home/conda/feedstock_root/build_artifacts/dateutils_1603450192521/work debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1707444420542/work decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work decoupler==1.6.0 deepdiff @ file:///home/conda/feedstock_root/build_artifacts/deepdiff_1699970200924/work defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work Deprecated==1.2.14 distlib @ file:///home/conda/feedstock_root/build_artifacts/distlib_1702383208639/work distributed==2024.5.1 distributed-ucxx-cu12==0.38.0 docrep @ file:///home/conda/feedstock_root/build_artifacts/docrep_1613487293529/work docstring_parser==0.16 docutils==0.21.2 dulwich @ file:///home/conda/feedstock_root/build_artifacts/dulwich_1701831374201/work dunamai @ file:///home/conda/feedstock_root/build_artifacts/dunamai_1708295115897/work ecos==2.0.13 et-xmlfile @ file:///home/conda/feedstock_root/build_artifacts/et_xmlfile_1674664118162/work etils @ file:///home/conda/feedstock_root/build_artifacts/etils_1708071068010/work everett==3.1.0 exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1704921103267/work executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1698579936712/work fa2 @ file:///home/conda/feedstock_root/build_artifacts/fa2_1667383684020/work fastapi @ file:///home/conda/feedstock_root/build_artifacts/fastapi_1708823750898/work fastcluster==1.2.6 fasteners==0.19 fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/python-fastjsonschema_1703780968325/work/dist fastrlock==0.8.2 fcsparser==0.2.8 filelock @ file:///home/conda/feedstock_root/build_artifacts/filelock_1711394622191/work fiona==1.9.6 flatbuffers==24.3.25 flatten-dict==0.4.2 flax @ file:///home/conda/feedstock_root/build_artifacts/flax_1710420339098/work fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1710865510907/work fqdn==1.5.1 freetype-py==2.4.0 frozenlist==1.4.1 fsspec==2023.6.0 fuzzywuzzy==0.18.0 gast==0.5.4 gdown==5.1.0 geopandas==0.14.4 get_version @ file:///home/conda/feedstock_root/build_artifacts/get_version_1701081996587/work/get_version-3.5.5 google-pasta==0.2.0 googleapis-common-protos==1.63.0 greenlet==3.0.3 grpcio==1.63.0 gseapy==1.1.2 h11 @ file:///home/conda/feedstock_root/build_artifacts/h11_1664132893548/work h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1702471429234/work harmonypy==0.0.9 HeapDict==1.0.1 hnoca==0.1.0 holoviews==1.19.0 hsluv==5.0.4 httpcore==1.0.5 httpx==0.27.0 huggingface-hub==0.23.4 idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1701026962277/work igraph==0.10.8 imagecodecs==2024.1.1 imageio==2.34.1 imagesize==1.4.1 importlib-metadata==6.11.0 importlib_resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1711040877059/work in-n-out==0.2.1 inflect==7.2.1 iniconfig==2.0.0 inquirer @ file:///home/conda/feedstock_root/build_artifacts/inquirer_1700596410127/work installer @ file:///home/conda/feedstock_root/build_artifacts/python-installer_1679300325491/work IProgress==0.4 ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1708996548741/work ipython==8.18.0 ipython-genutils==0.2.0 ipywidgets==8.1.2 isoduration==20.11.0 itsdangerous @ file:///home/conda/feedstock_root/build_artifacts/itsdangerous_1648147185463/work jaraco.classes @ file:///home/conda/feedstock_root/build_artifacts/jaraco.classes_1707378080076/work jax @ file:///home/conda/feedstock_root/build_artifacts/jax_1709239676092/work jaxlib==0.4.23.dev20240224 jaxopt==0.8.3 jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1696326070614/work jeepney @ file:///home/conda/feedstock_root/build_artifacts/jeepney_1649085214306/work Jinja2==3.1.4 jmespath @ file:///home/conda/feedstock_root/build_artifacts/jmespath_1655568249366/work joblib==1.4.2 json5 @ file:///tmp/build/80754af9/json5_1624432770122/work jsonpointer==2.4 jsonschema @ file:///croot/jsonschema_1699041609003/work jsonschema-specifications @ file:///croot/jsonschema-specifications_1699032386549/work jupyter==1.0.0 jupyter-console==6.6.3 jupyter-contrib-core==0.4.2 jupyter-contrib-nbextensions==0.7.0 jupyter-events @ file:///croot/jupyter_events_1699282461638/work jupyter-highlight-selected-word==0.2.0 jupyter-lsp @ file:///croot/jupyter-lsp-meta_1699978238815/work jupyter-nbextensions-configurator==0.6.3 jupyter_client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1710255804825/work jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1710257277185/work jupyter_server @ file:///croot/jupyter_server_1699466442171/work jupyter_server_proxy==4.2.0 jupyter_server_terminals @ file:///croot/jupyter_server_terminals_1686870725608/work jupyterlab @ file:///croot/jupyterlab_1706802623017/work jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work jupyterlab_server @ file:///croot/jupyterlab_server_1699555425460/work jupyterlab_widgets==3.0.10 keras==3.3.3 keyring @ file:///home/conda/feedstock_root/build_artifacts/keyring_1709129623794/work kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1695379902431/work lamin_utils==0.13.2 lazy_loader==0.4 legacy-api-wrap==1.4 leidenalg==0.10.1 Levenshtein==0.25.1 libclang==18.1.1 libucx-cu12==1.15.0.post1 lightning @ file:///home/conda/feedstock_root/build_artifacts/lightning_1695971291138/work lightning-utilities @ file:///home/conda/feedstock_root/build_artifacts/lightning-utilities_1711382239122/work lightning_cloud @ file:///home/conda/feedstock_root/build_artifacts/lightning-cloud_1710635834081/work linkify-it-py==2.0.3 llvmlite==0.42.0 locket==1.0.0 loguru==0.7.2 loky==3.0.0 loompy==3.0.7 lxml==5.2.2 magicgui==0.8.2 Mako==1.3.5 Markdown==3.6 markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1686175045316/work MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1706899921127/work matplotlib==3.8.3 matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1660814786464/work matplotlib-scalebar==0.8.1 mdit-py-plugins==0.4.1 mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1704317613764/work mellon==1.4.2 metacells==0.9.4 mistune @ file:///opt/conda/conda-bld/mistune_1661496219659/work ml-collections @ file:///home/conda/feedstock_root/build_artifacts/ml-collections_1664451628929/work ml-dtypes @ file:///home/conda/feedstock_root/build_artifacts/ml_dtypes_1704727647076/work mnnpy==0.1.9.5 more-itertools @ file:///home/conda/feedstock_root/build_artifacts/more-itertools_1704738417589/work mpmath @ file:///home/conda/feedstock_root/build_artifacts/mpmath_1678228039184/work msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1700926504817/work mudata @ file:///home/conda/feedstock_root/build_artifacts/mudata_1686129262768/work multidict==6.0.5 multigrate==0.0.2 multipledispatch==0.6.0 multiscale_spatial_image==0.11.2 munkres==1.1.4 muon==0.1.5 mvtcr==0.2.0 namex==0.0.8 napari==0.4.19.post1 napari-console==0.0.9 napari-matplotlib==2.0.1 napari-plugin-engine==0.2.0 napari-spatialdata==0.4.1 napari-svg==0.1.10 natsort @ file:///home/conda/feedstock_root/build_artifacts/natsort_1687263093793/work nbclient @ file:///croot/nbclient_1698934205032/work nbconvert @ file:///croot/nbconvert_1699022732553/work nbformat @ file:///croot/nbformat_1694616755618/work ncls==0.0.68 ndindex==1.8 nest_asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1705850609492/work networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1698504735452/work newick==1.0.0 notebook @ file:///croot/notebook_1708029864779/work notebook_shim @ file:///croot/notebook-shim_1699455894279/work npe2==0.7.5 numba==0.60.0 numcodecs==0.12.1 numexpr==2.9.0 numpy==1.26.4 numpy-groupies==0.10.2 numpydoc==1.7.0 numpyro @ file:///home/conda/feedstock_root/build_artifacts/numpyro_1709512928552/work nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 nvidia-cuda-nvrtc-cu12==12.1.105 nvidia-cuda-runtime-cu12==12.1.105 nvidia-cudnn-cu12==8.9.2.26 nvidia-cufft-cu12==11.0.2.54 nvidia-curand-cu12==10.3.2.106 nvidia-cusolver-cu12==11.4.5.107 nvidia-cusparse-cu12==12.1.0.106 nvidia-nccl-cu12==2.20.5 nvidia-nvjitlink-cu12==12.1.105 nvidia-nvtx-cu12==12.1.105 nvtx==0.2.10 obonet==1.0.0 ome-zarr==0.8.3 omnipath==1.0.8 openpyxl @ file:///home/conda/feedstock_root/build_artifacts/openpyxl_1695464693876/work opentelemetry-api==1.21.0 opentelemetry-exporter-otlp-proto-common==1.21.0 opentelemetry-exporter-otlp-proto-http==1.21.0 opentelemetry-proto==1.21.0 opentelemetry-sdk==1.21.0 opentelemetry-semantic-conventions==0.42b0 opt-einsum @ file:///home/conda/feedstock_root/build_artifacts/opt_einsum_1696448916724/work optax @ file:///home/conda/feedstock_root/build_artifacts/optax_1709842373685/work optree==0.11.0 optuna==3.4.0 orbax-checkpoint @ file:///home/conda/feedstock_root/build_artifacts/orbax-checkpoint_1701452553681/work ordered-set @ file:///home/conda/feedstock_root/build_artifacts/ordered-set_1643221357603/work orjson @ file:///home/conda/feedstock_root/build_artifacts/orjson_1708717141072/work/target/wheels/orjson-3.9.15-cp310-cp310-linux_x86_64.whl#sha256=0a7c0fa3196da3711ba9a551dda29e568a20de7d33eccb8ff934934cd44bc414 osqp==0.6.5 overrides @ file:///croot/overrides_1699371140756/work owlready2==0.46 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1710075952259/work palantir==1.3.2 pandas==2.2.1 pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work panel==1.4.4 param==2.1.0 parasail==1.3.4 parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1638334955874/work partd==1.4.2 patsy==0.5.6 pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1706113125309/work pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1704252020178/work PIMS==0.6.1 Pint==0.23 pipdeptree==2.23.0 pkginfo @ file:///home/conda/feedstock_root/build_artifacts/pkginfo_1709561090460/work platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1706713388748/work plotly==5.22.0 pluggy==1.5.0 poetry @ file:///home/conda/feedstock_root/build_artifacts/poetry_1709481654924/work poetry-core @ file:///home/conda/feedstock_root/build_artifacts/poetry-core_1706890336114/work poetry-plugin-export @ file:///home/conda/feedstock_root/build_artifacts/poetry-plugin-export_1710940420107/work pooch==1.8.1 progressbar2==4.4.2 prometheus-client @ file:///tmp/abs_d3zeliano1/croots/recipe/prometheus_client_1659455100375/work prompt-toolkit==3.0.36 protobuf==4.25.1 psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1705722392846/work psygnal==0.11.1 ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work py-cpuinfo==9.0.0 py-monocle @ file:///hpc/pmc_rios/2.personal/rariese/py-monocle pyarrow==16.1.0 pybind11==2.12.0 pyconify==0.1.6 pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work pyct==0.5.0 pydantic @ file:///home/conda/feedstock_root/build_artifacts/pydantic_1690351839218/work pydantic-compat==0.1.2 pydantic_core @ file:///home/conda/feedstock_root/build_artifacts/pydantic-core_1690242742031/work pydot==2.0.0 pygam==0.9.1 pygeos==0.14 Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1700607939962/work pygpcca==1.0.4 PyJWT @ file:///home/conda/feedstock_root/build_artifacts/pyjwt_1706895065046/work pylibcugraph-cu12==24.6.1 pylibraft-cu12==24.6.0 pymde==0.1.18 pynndescent==0.5.11 pynvjitlink-cu12==0.2.4 pynvml==11.4.1 PyOpenGL==3.1.7 pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1709721012883/work pyproj==3.6.1 pyproject_hooks @ file:///home/conda/feedstock_root/build_artifacts/pyproject_hooks_1670268672584/work pyr2==2.0.0 pyranges==0.0.129 pyro-api @ file:///home/conda/feedstock_root/build_artifacts/pyro-api_1614940619870/work pyro-ppl @ file:///home/conda/feedstock_root/build_artifacts/pyro-ppl_1708448545301/work pysam==0.22.0 PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work pytest==8.2.2 python-box==6.1.0 python-dateutil==2.9.0.post0 python-editor==1.0.4 python-igraph==0.11.4 python-json-logger @ file:///croot/python-json-logger_1683823803357/work python-Levenshtein==0.25.1 python-multipart @ file:///home/conda/feedstock_root/build_artifacts/python-multipart_1707760088566/work python-slugify==8.0.4 python-utils==3.8.2 pytorch-lightning @ file:///home/conda/feedstock_root/build_artifacts/pytorch-lightning_1709672126724/work pytz==2024.1 pyviz_comms==3.0.2 PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1695373428874/work pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1701783169502/work qdldl==0.1.7.post0 qtconsole==5.5.2 QtPy==2.4.1 questionary==2.0.1 raft-dask-cu12==24.6.0 rapidfuzz==3.9.3 rapids-dask-dependency==24.6.0 ratelimit==2.2.1 readchar @ file:///home/conda/feedstock_root/build_artifacts/readchar_1679045163536/work readfcs==1.1.8 referencing @ file:///croot/referencing_1699012038513/work requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work requests-toolbelt @ file:///home/conda/feedstock_root/build_artifacts/requests-toolbelt_1682953341151/work rfc3339-validator @ file:///croot/rfc3339-validator_1683077044675/work rfc3986-validator @ file:///croot/rfc3986-validator_1683058983515/work rich @ file:///home/conda/feedstock_root/build_artifacts/rich-split_1709150387247/work/dist rmm-cu12==24.6.0 rpds-py @ file:///croot/rpds-py_1698945930462/work rpy2==3.5.15 s3fs==2023.6.0 s3transfer @ file:///home/conda/feedstock_root/build_artifacts/s3transfer_1710497251148/work scanpy==1.10.2 scArches==0.6.1 scHPL==1.0.5 scib==1.1.4 scikit-image==0.23.2 scikit-learn==1.3.2 scikit-misc==0.3.1 scipy==1.14.0 scirpy==0.13.1 scrublet==0.2.3 scs==3.2.4.post1 scvelo==0.3.2 scvi-tools @ file:///home/conda/feedstock_root/build_artifacts/scvi-tools_1709322244966/work seaborn==0.13.2 SEACells==0.3.3 SecretStorage @ file:///home/conda/feedstock_root/build_artifacts/secretstorage_1695551734488/work semantic-version==2.10.0 Send2Trash @ file:///croot/send2trash_1699371139552/work sentry-sdk==2.6.0 session-info==1.0.0 sfaira==0.3.12 shapely==2.0.4 shellingham @ file:///home/conda/feedstock_root/build_artifacts/shellingham_1698144360966/work simpervisor==1.0.0 simplegeneric==0.8.1 simplejson==3.19.2 six==1.16.0 slicerator==1.1.0 sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1708952932303/work snowballstemmer==2.2.0 sorted-nearest==0.0.39 sortedcontainers==2.4.0 soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1693929250441/work sparse @ file:///home/conda/feedstock_root/build_artifacts/sparse_1705921781577/work spatial_image==0.3.0 spatialdata==0.1.2 spatialdata-io==0.1.2 spatialdata-plot==0.2.2 Sphinx==7.3.7 sphinxcontrib-applehelp==1.0.8 sphinxcontrib-devhelp==1.0.6 sphinxcontrib-htmlhelp==2.0.5 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.7 sphinxcontrib-serializinghtml==1.1.10 SQLAlchemy==2.0.31 squarify==0.4.3 squidpy==1.4.1 stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work starlette @ file:///home/conda/feedstock_root/build_artifacts/starlette-recipe_1707149932752/work starsessions @ file:///home/conda/feedstock_root/build_artifacts/starsessions_1659923701614/work statsmodels==0.14.2 stdlib-list==0.10.0 superqt==0.6.6 switchlang==0.1.0 sympy @ file:///home/conda/feedstock_root/build_artifacts/sympy_1684180539862/work synapseclient==4.2.0 tables==3.9.2 tabulate==0.9.0 tbb==2021.13.0 tblib==3.0.0 tenacity==8.3.0 tensorboard==2.16.2 tensorboard-data-server==0.7.2 tensorflow==2.16.1 tensorflow-io-gcs-filesystem==0.37.0 tensorstore @ file:///home/conda/feedstock_root/build_artifacts/tensorstore_1706712823008/work termcolor==2.4.0 terminado @ file:///croot/terminado_1671751832461/work text-unidecode==1.3 texttable==1.7.0 tf_keras==2.16.0 threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1710943558485/work tifffile==2024.5.3 tinycss2 @ file:///croot/tinycss2_1668168815555/work tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work tomli_w==1.0.0 tomlkit @ file:///home/conda/feedstock_root/build_artifacts/tomlkit_1709043728182/work toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1706112571092/work torch==2.3.1+cu121 torch_geometric==2.5.3 torchaudio==2.3.1+cu121 torchmetrics @ file:///home/conda/feedstock_root/build_artifacts/torchmetrics_1710773712978/work torchvision==0.18.1+cu121 tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1708363098266/work tqdm==4.66.1 traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1710254411456/work treelite==4.1.2 triton==2.3.1 trove-classifiers @ file:///home/conda/feedstock_root/build_artifacts/trove-classifiers_1711440080129/work typeguard==4.2.1 typer==0.12.3 types-python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/types-python-dateutil_1710589910274/work typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1708904622550/work tzdata==2024.1 tzlocal @ file:///croot/tzlocal_1668627599277/work uc-micro-py==1.0.3 ucx-py-cu12==0.38.0 ucxx-cu12==0.38.0 umap-learn==0.5.4 unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1695847980273/work unitvelo==0.2.5.2 uri-template==1.3.0 urllib3==1.26.18 uvicorn @ file:///home/conda/feedstock_root/build_artifacts/uvicorn-split_1710932021389/work validators==0.28.1 velocyto==0.17.17 versioneer==0.29 virtualenv @ file:///home/conda/feedstock_root/build_artifacts/virtualenv_1708602083730/work vispy==0.14.2 wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1704731205417/work webcolors==1.13 webencodings==0.5.1 websocket-client==1.3.3 websockets @ file:///home/conda/feedstock_root/build_artifacts/websockets_1697914682990/work Werkzeug==3.0.3 widgetsnbextension==4.0.10 wrapt==1.16.0 wurlitzer==3.1.1 xarray==2023.12.0 xarray-dataclasses==1.7.0 xarray-datatree==0.0.14 xarray-schema==0.0.3 xarray-spatial==0.4.0 xlrd @ file:///home/conda/feedstock_root/build_artifacts/xlrd_1595712200082/work xyzservices==2024.6.0 yamlordereddictloader==0.4.2 yarl==1.9.4 zarr==2.17.2 zict==3.0.0 zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1695255097490/work ```
wence- commented 2 months ago

Thanks, nothing obviously stands out as bad there. Can you confirm that python -c "import pandas" works fine? That is, using pandas without cudf in the loop is not problematic.

RijndertAriese commented 2 months ago

Hi,

In order to proceed with the analysis I opted for falling back to CPU by removing cuml-cu12. So I did a fresh installation (again) and now it can be imported and used in the script. Not sure what changed or why it now works tho.... But I'll take it!

(P.S. thanks for the drop down thing in markup, didn't know how to)