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theislab / cellrank

CellRank: dynamics from multi-view single-cell data
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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Simple cellrank 2 installation and loading error; scvelo compatibility #1186

Closed darrentyson closed 5 months ago

darrentyson commented 5 months ago

... I'm trying to simply install cellrank into a conda environment and load it within a jupyter notebook. Seems like package version incompatibilities are present.

conda create -c conda-forge -n cellrank cellrank jupyterlab scipy=1.12.0
conda activate cellrank

NOTE: had to downgrade scipy to 1.12.0 to prevent error about tril being missing from linalg. 

import scanpy as sc
import os.path as op
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import sys
import os
import seaborn as sns
from pathlib import Path

All load fine 

import cellrank
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[2], line 1
----> 1 import cellrank

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/__init__.py:3](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/__init__.py#line=2)
      1 from importlib import metadata
----> 3 from cellrank import datasets, estimators, kernels, logging, models, pl
      4 from cellrank._utils._lineage import Lineage
      5 from cellrank.settings import settings

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/estimators/__init__.py:1](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/estimators/__init__.py#line=0)
----> 1 from cellrank.estimators import mixins
      2 from cellrank.estimators._base_estimator import BaseEstimator
      3 from cellrank.estimators.terminal_states import CFLARE, GPCCA, TermStatesEstimator

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/estimators/mixins/__init__.py:3](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/estimators/mixins/__init__.py#line=2)
      1 from cellrank.estimators.mixins._fate_probabilities import FateProbsMixin
      2 from cellrank.estimators.mixins._kernel import KernelMixin
----> 3 from cellrank.estimators.mixins._lineage_drivers import LinDriversMixin
      4 from cellrank.estimators.mixins.decomposition import EigenMixin, SchurMixin
      6 __all__ = ["FateProbsMixin", "KernelMixin", "LinDriversMixin", "EigenMixin", "SchurMixin"]

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/estimators/mixins/_lineage_drivers.py:6](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/cellrank/estimators/mixins/_lineage_drivers.py#line=5)
      3 import types
      4 from typing import Any, Dict, Literal, Mapping, Optional, Sequence, Tuple, Union
----> 6 import scvelo as scv
      8 import numpy as np
      9 import pandas as pd

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/__init__.py:6](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/__init__.py#line=5)
      3 from scanpy import read, read_loom
      5 from scvelo import datasets, logging
----> 6 from scvelo import plotting as pl
      7 from scvelo import preprocessing as pp
      8 from scvelo import settings

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/__init__.py:3](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/__init__.py#line=2)
      1 from scanpy.plotting import paga_compare, rank_genes_groups
----> 3 from .gridspec import gridspec
      4 from .heatmap import heatmap
      5 from .paga import paga

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/gridspec.py:6](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/gridspec.py#line=5)
      3 import matplotlib.pyplot as pl
      5 # todo: auto-complete and docs wrapper
----> 6 from .scatter import scatter
      7 from .utils import get_figure_params, hist
      8 from .velocity_embedding import velocity_embedding

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/scatter.py:16](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/scatter.py#line=15)
     14 from scvelo.preprocessing.neighbors import get_connectivities
     15 from .docs import doc_params, doc_scatter
---> 16 from .utils import (
     17     default_basis,
     18     default_color,
     19     default_color_map,
     20     default_legend_loc,
     21     default_size,
     22     default_xkey,
     23     default_ykey,
     24     get_ax,
     25     get_components,
     26     get_figure_params,
     27     get_kwargs,
     28     get_obs_vector,
     29     get_value_counts,
     30     gets_vals_from_color_gradients,
     31     groups_to_bool,
     32     interpret_colorkey,
     33     is_categorical,
     34     is_int,
     35     is_list,
     36     is_list_of_int,
     37     is_list_of_list,
     38     is_list_of_str,
     39     make_dense,
     40     plot_density,
     41     plot_linfit,
     42     plot_outline,
     43     plot_polyfit,
     44     plot_rug,
     45     plot_velocity_fits,
     46     rgb_custom_colormap,
     47     savefig_or_show,
     48     set_colorbar,
     49     set_colors_for_categorical_obs,
     50     set_label,
     51     set_legend,
     52     set_margin,
     53     set_title,
     54     to_list,
     55     to_val,
     56     to_valid_bases_list,
     57     update_axes,
     58 )
     61 @doc_params(scatter=doc_scatter)
     62 def scatter(
     63     adata=None,
   (...)
    123     **kwargs,
    124 ):
    125     """Scatter plot along observations or variables axes.
    126 
    127     Arguments:
   (...)
    139     If `show==False` a `matplotlib.Axis`
    140     """

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/utils.py:24](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/plotting/utils.py#line=23)
     22 from scvelo import logging as logg
     23 from scvelo import settings
---> 24 from scvelo.tools.utils import strings_to_categoricals
     25 from . import palettes
     27 """helper functions"""

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/tools/__init__.py:28](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/tools/__init__.py#line=27)
     25 from .velocity_pseudotime import velocity_map, velocity_pseudotime
     27 with contextlib.suppress(ImportError):
---> 28     from ._vi_model import VELOVI
     31 __all__ = [
     32     "align_dynamics",
     33     "differential_kinetic_test",
   (...)
     61     "ExpectationMaximizationModel",
     62 ]
     63 if "VELOVI" in locals():

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/tools/_vi_model.py:14](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvelo/tools/_vi_model.py#line=13)
     11 from scipy.stats import ttest_ind
     13 from anndata import AnnData
---> 14 from scvi.data import AnnDataManager
     15 from scvi.data.fields import LayerField
     16 from scvi.dataloaders import DataSplitter

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/__init__.py:11](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/__init__.py#line=10)
      8 from ._settings import settings
     10 # this import needs to come after prior imports to prevent circular import
---> 11 from . import data, model, external, utils
     13 from importlib.metadata import version
     15 package_name = "scvi-tools"

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/data/__init__.py:25](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/data/__init__.py#line=24)
      4 from ._datasets import (
      5     annotation_simulation,
      6     brainlarge_dataset,
   (...)
     22     synthetic_iid,
     23 )
     24 from ._manager import AnnDataManager, AnnDataManagerValidationCheck
---> 25 from ._preprocessing import (
     26     add_dna_sequence,
     27     organize_cite_seq_10x,
     28     organize_multiome_anndatas,
     29     poisson_gene_selection,
     30     reads_to_fragments,
     31 )
     32 from ._read import read_10x_atac, read_10x_multiome
     34 __all__ = [
     35     "AnnTorchDataset",
     36     "AnnDataManagerValidationCheck",
   (...)
     66     "cellxgene",
     67 ]

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/data/_preprocessing.py:12](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/data/_preprocessing.py#line=11)
      9 import torch
     10 from scipy.sparse import issparse
---> 12 from scvi.model._utils import parse_device_args
     13 from scvi.utils import dependencies, track
     14 from scvi.utils._docstrings import devices_dsp

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/model/__init__.py:2](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/model/__init__.py#line=1)
      1 from . import utils
----> 2 from ._amortizedlda import AmortizedLDA
      3 from ._autozi import AUTOZI
      4 from ._condscvi import CondSCVI

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/model/_amortizedlda.py:15](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/model/_amortizedlda.py#line=14)
     13 from scvi.data import AnnDataManager
     14 from scvi.data.fields import LayerField
---> 15 from scvi.module import AmortizedLDAPyroModule
     16 from scvi.utils import setup_anndata_dsp
     18 from .base import BaseModelClass, PyroSviTrainMixin

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/__init__.py:1](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/__init__.py#line=0)
----> 1 from ._amortizedlda import AmortizedLDAPyroModule
      2 from ._autozivae import AutoZIVAE
      3 from ._classifier import Classifier

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/_amortizedlda.py:15](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/_amortizedlda.py#line=14)
     13 from scvi._constants import REGISTRY_KEYS
     14 from scvi._types import Tunable
---> 15 from scvi.module.base import PyroBaseModuleClass, auto_move_data
     16 from scvi.nn import Encoder
     18 _AMORTIZED_LDA_PYRO_MODULE_NAME = "amortized_lda"

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/base/__init__.py:1](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/base/__init__.py#line=0)
----> 1 from ._base_module import (
      2     BaseMinifiedModeModuleClass,
      3     BaseModuleClass,
      4     JaxBaseModuleClass,
      5     LossOutput,
      6     PyroBaseModuleClass,
      7     TrainStateWithState,
      8 )
      9 from ._decorators import auto_move_data, flax_configure
     11 __all__ = [
     12     "BaseModuleClass",
     13     "LossOutput",
   (...)
     19     "BaseMinifiedModeModuleClass",
     20 ]

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/base/_base_module.py:14](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/scvi/module/base/_base_module.py#line=13)
     12 import pyro
     13 import torch
---> 14 from flax.training import train_state
     15 from jax import random
     16 from jaxlib.xla_extension import Device

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/flax/training/train_state.py:19](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/flax/training/train_state.py#line=18)
     17 from flax import core
     18 from flax import struct
---> 19 import optax
     22 class TrainState(struct.PyTreeNode):
     23   """Simple train state for the common case with a single Optax optimizer.
     24 
     25   Synopsis::
   (...)
     50     opt_state: The state for `tx`.
     51   """

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/optax/__init__.py:18](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/optax/__init__.py#line=17)
     15 """Optax: composable gradient processing and optimization, in JAX."""
     17 from optax import contrib
---> 18 from optax import losses
     19 from optax import monte_carlo
     20 from optax import projections

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/optax/losses/__init__.py:17](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/optax/losses/__init__.py#line=16)
      1 # Copyright 2019 DeepMind Technologies Limited. All Rights Reserved.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     13 # limitations under the License.
     14 # ==============================================================================
     15 """The losses sub-package."""
---> 17 from optax.losses._classification import convex_kl_divergence
     18 from optax.losses._classification import ctc_loss
     19 from optax.losses._classification import ctc_loss_with_forward_probs

File [~/mambaforge/envs/cellrank/lib/python3.11/site-packages/optax/losses/_classification.py:64](http://localhost:8888/~/mambaforge/envs/cellrank/lib/python3.11/site-packages/optax/losses/_classification.py#line=63)
     59   log_not_p = jax.nn.log_sigmoid(-logits)
     60   return -labels * log_p - (1. - labels) * log_not_p
     63 @functools.partial(
---> 64     chex.warn_deprecated_function,
     65     replacement='sigmoid_binary_cross_entropy')
     66 def binary_logistic_loss(logits, labels):
     67   return sigmoid_binary_cross_entropy(logits, labels)
     70 def hinge_loss(
     71     predictor_outputs: chex.Array,
     72     targets: chex.Array
     73 ) -> chex.Array:

AttributeError: module 'chex' has no attribute 'warn_deprecated_function'

Versions:

# can't run due to cellrank not loading

# packages in environment at ~/mambaforge/envs/cellrank:
#
# Name                    Version                   Build  Channel
absl-py                   2.1.0              pyhd8ed1ab_0    conda-forge
anndata                   0.10.6             pyhd8ed1ab_0    conda-forge
annotated-types           0.6.0              pyhd8ed1ab_0    conda-forge
anyio                     4.3.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311heffc1b2_4    conda-forge
array-api-compat          1.6                pyhd8ed1ab_0    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
backoff                   2.2.1              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blessed                   1.19.1             pyhe4f9e05_2    conda-forge
boto3                     1.34.79            pyhd8ed1ab_0    conda-forge
botocore                  1.34.80         pyge310_1234567_0    conda-forge
brotli                    1.1.0                hb547adb_1    conda-forge
brotli-bin                1.1.0                hb547adb_1    conda-forge
brotli-python             1.1.0           py311ha891d26_1    conda-forge
bzip2                     1.0.8                h93a5062_5    conda-forge
c-ares                    1.28.1               h93a5062_0    conda-forge
ca-certificates           2024.2.2             hf0a4a13_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
cellrank                  2.0.4              pyhd8ed1ab_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311h4a08483_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
chex                      0.1.83             pyhd8ed1ab_0    conda-forge
cleo                      2.1.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contextlib2               21.6.0             pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1           py311hcc98501_0    conda-forge
crashtest                 0.4.1              pyhd8ed1ab_0    conda-forge
croniter                  1.4.1              pyhd8ed1ab_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dateutils                 0.6.12                     py_0    conda-forge
debugpy                   1.8.1           py311h92babd0_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
deepdiff                  6.7.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distlib                   0.3.8              pyhd8ed1ab_0    conda-forge
dm-tree                   0.1.8           py311h4acf6a1_0    conda-forge
docrep                    0.3.2              pyh44b312d_0    conda-forge
dulwich                   0.21.7          py311h05b510d_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et_xmlfile                1.1.0              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fastapi                   0.110.1            pyhd8ed1ab_1    conda-forge
fftw                      3.3.10          mpi_openmpi_haef8dc3_8    conda-forge
filelock                  3.13.3             pyhd8ed1ab_0    conda-forge
flax                      0.6.1              pyhd8ed1ab_1    conda-forge
fonttools                 4.51.0          py311h05b510d_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
fsspec                    2024.3.1           pyhca7485f_0    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
get-annotations           0.1.2              pyhd8ed1ab_0    conda-forge
gmp                       6.3.0                hebf3989_1    conda-forge
gmpy2                     2.1.2           py311h2ba9262_1    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
h5py                      3.10.0          nompi_py311hd00467f_101    conda-forge
hdf5                      1.14.3          mpi_openmpi_h20f603a_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
hypre                     2.28.0          mpi_openmpi_haba3941_0    conda-forge
icu                       73.2                 hc8870d7_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
importlib-metadata        7.1.0              pyha770c72_0    conda-forge
importlib_metadata        7.1.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
inquirer                  3.1.4              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.3             pyh3cd1d5f_0    conda-forge
ipython                   8.22.2             pyh707e725_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
itsdangerous              2.1.2              pyhd8ed1ab_0    conda-forge
jaraco.classes            3.4.0              pyhd8ed1ab_0    conda-forge
jax                       0.4.13             pyhd8ed1ab_0    conda-forge
jaxlib                    0.4.12          cpu_py311h2dd720e_1    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.3              pyhd8ed1ab_0    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.4.0              pyhd8ed1ab_0    conda-forge
json5                     0.9.24             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py311h267d04e_3    conda-forge
jsonschema                4.21.1             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.21.1             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.4              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py311h267d04e_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.13.0             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.1.6              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.26.0             pyhd8ed1ab_0    conda-forge
keyring                   24.3.1          py311h267d04e_0    conda-forge
kiwisolver                1.4.5           py311he4fd1f5_1    conda-forge
krb5                      1.21.2               h92f50d5_0    conda-forge
lcms2                     2.16                 ha0e7c42_0    conda-forge
legacy-api-wrap           1.4                pyhd8ed1ab_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libabseil                 20230125.3      cxx17_h13dd4ca_0    conda-forge
libaec                    1.1.3                hebf3989_0    conda-forge
libblas                   3.9.0           22_osxarm64_openblas    conda-forge
libbrotlicommon           1.1.0                hb547adb_1    conda-forge
libbrotlidec              1.1.0                hb547adb_1    conda-forge
libbrotlienc              1.1.0                hb547adb_1    conda-forge
libcblas                  3.9.0           22_osxarm64_openblas    conda-forge
libcurl                   8.7.1                h2d989ff_0    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libdeflate                1.20                 h93a5062_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libexpat                  2.6.2                hebf3989_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
libgrpc                   1.56.2               h9075ed4_1    conda-forge
libhwloc                  2.9.3           default_h4394839_1009    conda-forge
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
liblapack                 3.9.0           22_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hd1a9a77_4    conda-forge
libnghttp2                1.58.0               ha4dd798_1    conda-forge
libopenblas               0.3.27          openmp_h6c19121_0    conda-forge
libpng                    1.6.43               h091b4b1_0    conda-forge
libprotobuf               4.23.3               hf32f9b9_1    conda-forge
libptscotch               7.0.4                h820b06d_1    conda-forge
libscotch                 7.0.4                hf7fe8bf_1    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.45.2               h091b4b1_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libtiff                   4.6.0                h07db509_3    conda-forge
libuv                     1.48.0               h93a5062_0    conda-forge
libwebp-base              1.3.2                h93a5062_1    conda-forge
libxcb                    1.15                 hf346824_0    conda-forge
libxml2                   2.12.6               h0d0cfa8_1    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
lightning                 2.0.9.post0        pyhd8ed1ab_0    conda-forge
lightning-cloud           0.5.65             pyhd8ed1ab_0    conda-forge
lightning-utilities       0.11.2             pyhd8ed1ab_0    conda-forge
llvm-openmp               18.1.3               hcd81f8e_0    conda-forge
llvmlite                  0.42.0          py311hf5d242d_1    conda-forge
loompy                    3.0.6                      py_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5           py311h05b510d_0    conda-forge
matplotlib-base           3.8.4           py311hb58f1d1_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
metis                     5.1.0             h13dd4ca_1007    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
ml-collections            0.1.1              pyhd8ed1ab_0    conda-forge
ml_dtypes                 0.4.0           py311hfbe21a1_0    conda-forge
more-itertools            10.2.0             pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                h91ba8db_0    conda-forge
mpfr                      4.2.1                h41d338b_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpi4py                    3.1.5           py311h321fb25_1    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.7           py311hd03642b_0    conda-forge
mudata                    0.2.3              pyhd8ed1ab_0    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
mumps-include             5.6.2                hce30654_4    conda-forge
mumps-mpi                 5.6.2                hc6b315c_4    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.4.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.3             pyhd8ed1ab_0    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.4.20240210         h078ce10_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
networkx                  3.3                pyhd8ed1ab_1    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
numba                     0.59.1          py311h00351ea_0    conda-forge
numpy                     1.26.4          py311h7125741_0    conda-forge
numpy_groupies            0.10.2             pyhd8ed1ab_0    conda-forge
numpyro                   0.13.2             pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.2                h9f1df11_0    conda-forge
openmpi                   4.1.6              h526c993_101    conda-forge
openpyxl                  3.1.2           py311heffc1b2_0    conda-forge
openssl                   3.2.1                h0d3ecfb_1    conda-forge
opt_einsum                3.3.0              pyhc1e730c_2    conda-forge
optax                     0.2.2              pyhd8ed1ab_0    conda-forge
ordered-set               4.1.0              pyhd8ed1ab_0    conda-forge
orjson                    3.9.15          py311h94f323b_0    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandas                    2.2.1           py311hfbe21a1_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmetis                  4.0.3             h6eb5794_1005    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
petsc                     3.21.0          real_hdd9ae42_100    conda-forge
petsc4py                  3.21.0          real_h2cf9c7c_101    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.3.0          py311h0b5d0a1_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pkginfo                   1.10.0             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
poetry                    1.8.2           osx_pyh534df25_0    conda-forge
poetry-core               1.9.0              pyhd8ed1ab_0    conda-forge
poetry-plugin-export      1.7.1              pyhd8ed1ab_0    conda-forge
progressbar2              4.4.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
psutil                    5.9.8           py311h05b510d_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptscotch                  7.0.4                hc1c4572_1    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pydantic                  2.1.1              pyhd8ed1ab_0    conda-forge
pydantic-core             2.4.0           py311h0563b04_0    conda-forge
pygam                     0.9.1              pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pygpcca                   1.0.4              pyhd8ed1ab_2    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_1    conda-forge
pynndescent               0.5.12             pyhca7485f_0    conda-forge
pyobjc-core               10.2            py311h665608e_0    conda-forge
pyobjc-framework-cocoa    10.2            py311h665608e_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pyproject_hooks           1.0.0              pyhd8ed1ab_0    conda-forge
pyro-api                  0.1.2              pyhd8ed1ab_0    conda-forge
pyro-ppl                  1.9.0              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.11.8          hdf0ec26_0_cpython    conda-forge
python-build              1.2.1              pyhd8ed1ab_0    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-fastjsonschema     2.19.1             pyhd8ed1ab_0    conda-forge
python-installer          0.7.0              pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-multipart          0.0.9              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python-utils              3.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pytorch                   2.0.0           cpu_generic_py311h35eba3d_1    conda-forge
pytorch-lightning         2.2.1              pyhd8ed1ab_0    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py311heffc1b2_1    conda-forge
pyzmq                     25.1.2          py311h6727e71_0    conda-forge
rapidfuzz                 3.8.1           py311h92babd0_0    conda-forge
re2                       2023.03.02           hc5e2d97_0    conda-forge
readchar                  4.0.5              pyhd8ed1ab_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
referencing               0.34.0             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
requests-toolbelt         1.0.0              pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.7.1             pyhd8ed1ab_0    conda-forge
rpds-py                   0.18.0          py311ha958965_0    conda-forge
s3transfer                0.10.1             pyhd8ed1ab_0    conda-forge
scalapack                 2.2.0                h515df86_1    conda-forge
scanpy                    1.10.0             pyhd8ed1ab_0    conda-forge
scikit-learn              1.1.3           py311hba7d9bc_1    conda-forge
scipy                     1.12.0          py311h4f9446f_2    conda-forge
scotch                    7.0.4                hc1c4572_1    conda-forge
scvelo                    0.3.2              pyhd8ed1ab_1    conda-forge
scvi-tools                1.1.2              pyhd8ed1ab_0    conda-forge
seaborn                   0.13.2               hd8ed1ab_0    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.3              pyh31c8845_0    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4              pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleef                     3.5.1                h156473d_2    conda-forge
slepc                     3.21.0          real_h9d303e5_101    conda-forge
slepc4py                  3.21.0          real_heb818f2_100    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sparse                    0.15.1             pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.37.2             pyhd8ed1ab_0    conda-forge
starsessions              1.3.0              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.1          py311h9ea6feb_0    conda-forge
stdlib-list               0.10.0             pyhd8ed1ab_0    conda-forge
suitesparse               5.10.1               h79486c6_3    conda-forge
superlu                   5.2.2                hc615359_0    conda-forge
superlu_dist              8.2.1                h3dacc9e_1    conda-forge
sympy                     1.12            pypyh9d50eac_103    conda-forge
tbb                       2021.11.0            h2ffa867_1    conda-forge
terminado                 0.18.1             pyh31c8845_0    conda-forge
threadpoolctl             3.4.0              pyhc1e730c_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tomlkit                   0.12.4             pyha770c72_0    conda-forge
toolz                     0.12.1             pyhd8ed1ab_0    conda-forge
torchmetrics              1.3.2              pyhd8ed1ab_0    conda-forge
tornado                   6.4             py311h05b510d_0    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.2             pyhd8ed1ab_0    conda-forge
trove-classifiers         2024.3.25          pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.11.0               hd8ed1ab_0    conda-forge
typing_extensions         4.11.0             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
umap-learn                0.5.5           py311h267d04e_1    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
uvicorn                   0.29.0          py311h267d04e_0    conda-forge
virtualenv                20.25.1            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.7.0              pyhd8ed1ab_0    conda-forge
websockets                12.0            py311h05b510d_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
wrapt                     1.16.0          py311h05b510d_0    conda-forge
xarray                    2024.3.0           pyhd8ed1ab_0    conda-forge
xattr                     1.1.0           py311h05b510d_0    conda-forge
xlrd                      1.2.0              pyh9f0ad1d_1    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.5                hebf3989_1    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h53f4e23_5    conda-forge
zstd                      1.5.5                h4f39d0f_0    conda-forge
darrentyson commented 5 months ago

adding optax=0.2.0 fixed the issue.