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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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AttributeError: module 'pycisTopic' has no attribute '__version__' #54

Closed ramadatta closed 1 year ago

ramadatta commented 1 year ago

Hi, thank you for creating this very nice tool!

I am getting the errors even after successful pycisTopic installation.

%cd /data01/SingleCell/Python_notebooks/pycisTopic
!git clone https://github.com/aertslab/pycisTopic.git
%cd pycisTopic
!pip3 install -e .

....
Installing collected packages: pycisTopic
Running setup.py develop for pycisTopic
Successfully installed pycisTopic-1.0.2.dev12+g1e354e6

check pycisTopic using below:

!pip list | grep pycisTopic

pycisTopic                    1.0.2.dev12+g1e354e6 /data01/SingleCell/Python_notebooks/pycisTopic

Error 1: But when I import, it does not seem to load the modules.

import pycisTopic
pycisTopic.__version__

module 'pycisTopic' has no attribute '__version__'

Error2: For the code chunk below, I cannot find the module

from pycisTopic.pseudobulk_peak_calling import export_pseudobulk
bw_paths, bed_paths = export_pseudobulk(input_data = cell_data,
                 variable = 'celltype',                                                                     # variable by which to generate pseubulk profiles, in this case we want pseudobulks per celltype
                 sample_id_col = 'sample_id',
                 chromsizes = chromsizes,
                 bed_path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/pseudobulk_bed_files/'),  # specify where pseudobulk_bed_files should be stored
                 bigwig_path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/pseudobulk_bw_files/'),# specify where pseudobulk_bw_files should be stored
                 path_to_fragments = fragments_dict,                                                        # location of fragment fiels
                 n_cpu = 8,                                                                                 # specify the number of cores to use, we use ray for multi processing
                 normalize_bigwig = True,
                 remove_duplicates = True,
                 _temp_dir = os.path.join(tmp_dir, 'ray_spill'),
                 split_pattern = '-')

ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-155-0d21b884e816> in <module>
----> 1 from pycisTopic.pseudobulk_peak_calling import export_pseudobulk
      2 bw_paths, bed_paths = export_pseudobulk(input_data = cell_data,
      3                  variable = 'celltype',                                                                     # variable by which to generate pseubulk profiles, in this case we want pseudobulks per celltype
      4                  sample_id_col = 'sample_id',
      5                  chromsizes = chromsizes,

ModuleNotFoundError: No module named 'pycisTopic.pseudobulk_peak_calling'

my python version seems to be correct

import sys
print(sys.version)
!python --version

3.6.4 (default, Sep 25 2020, 13:18:17) 
[GCC 7.5.0]
Python 3.8.0

Please help me how I can resolve this issue. Many thanks in advance.

cbravo93 commented 1 year ago

Hi @ramadatta !

Unfortunately I am not able to reproduce your error.

cd pycisTopic
git pull
pip install -e .

gives the right output:

✔ [Jan/17 11:24] vsc31305@tier2-p-login-4 /staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/pycisTopic $ python
Python 3.7.4 (default, Aug 28 2019, 10:48:28) 
[GCC 6.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pycisTopic
>>> pycisTopic.__version__
'1.0.2.dev12+g1e354e6'

Can you provide the whole output of the installation?

Cheers!

C

ramadatta commented 1 year ago

Thank you @cbravo93. My apologies for delay! Will revert back soon with details.

ramadatta commented 1 year ago

Hi @cbravo93 ,

Please find below commands in my jupyter notebook:

%cd /data01/SingleCell/Python_notebooks
!git clone https://github.com/aertslab/pycisTopic.git
%cd pycisTopic
!pip3 install -e .
/data01/SingleCell/Python_notebooks
Cloning into 'pycisTopic'...
remote: Enumerating objects: 1850, done.
remote: Counting objects: 100% (433/433), done.
remote: Compressing objects: 100% (183/183), done.
remote: Total 1850 (delta 262), reused 417 (delta 247), pack-reused 1417
Receiving objects: 100% (1850/1850), 33.05 MiB | 5.21 MiB/s, done.
Resolving deltas: 100% (1272/1272), done.
/data01/SingleCell/Python_notebooks/pycisTopic
Obtaining file:///data01/SingleCell/Python_notebooks/pycisTopic
  Preparing metadata (setup.py) ... done
Collecting pyscenic@ git+https://github.com/aertslab/pySCENIC@master
  Cloning https://github.com/aertslab/pySCENIC (to revision master) to /tmp/pip-install-golf06tv/pyscenic_e3283c431b6a4245bb940e55eb1a3d80
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pySCENIC /tmp/pip-install-golf06tv/pyscenic_e3283c431b6a4245bb940e55eb1a3d80
  Resolved https://github.com/aertslab/pySCENIC to commit 0a90cb5ca615c633b2e012a992669f784e98bc8b
  Preparing metadata (setup.py) ... done
Collecting loomxpy@ git+https://github.com/aertslab/LoomXpy@main
  Cloning https://github.com/aertslab/LoomXpy (to revision main) to /tmp/pip-install-golf06tv/loomxpy_6d552544a71d4049aeb094868d84b8c7
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/LoomXpy /tmp/pip-install-golf06tv/loomxpy_6d552544a71d4049aeb094868d84b8c7
  Resolved https://github.com/aertslab/LoomXpy to commit 61995ff10940968eac2cee8fe48300ab477a15d0
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: adjusttext in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.7.3)
Requirement already satisfied: annoy in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.17.1)
Requirement already satisfied: bbknn in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.5.1)
Requirement already satisfied: ctxcore in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.2.0)
Requirement already satisfied: Cython in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.29.32)
Requirement already satisfied: ipython in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (8.7.0)
Requirement already satisfied: ipykernel in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (6.19.4)
Requirement already satisfied: gensim in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (4.3.0)
Requirement already satisfied: harmonypy in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.0.9)
Requirement already satisfied: ipympl in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.9.2)
Requirement already satisfied: leidenalg in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.9.1)
Requirement already satisfied: lda in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (2.0.0)
Requirement already satisfied: loompy in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (3.0.7)
Requirement already satisfied: matplotlib in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (3.6.2)
Requirement already satisfied: macs2 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (2.2.7.1)
Requirement already satisfied: networkx in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (2.8.8)
Requirement already satisfied: numba in /home/prakki/.local/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.56.4)
Requirement already satisfied: numpy in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.23.5)
Requirement already satisfied: pyopenssl in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (22.1.0)
Requirement already satisfied: pandas!=1.3.0,>=1.2.0 in /home/prakki/.local/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.5.2)
Requirement already satisfied: polars in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.15.8)
Requirement already satisfied: pybedtools in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.9.0)
Requirement already satisfied: pyfasta in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.5.2)
Requirement already satisfied: pyranges in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.0.120)
Requirement already satisfied: pybiomart in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.2.0)
Requirement already satisfied: pyBigWig in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.3.18)
Requirement already satisfied: python-Levenshtein in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.20.9)
Requirement already satisfied: python-igraph in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.10.2)
Requirement already satisfied: ray[default] in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (2.2.0)
Requirement already satisfied: scipy in /home/prakki/.local/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.10.0)
Requirement already satisfied: scikit-learn in /home/prakki/.local/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.2.0)
Requirement already satisfied: scanpy in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.8.2)
Requirement already satisfied: scanorama in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.7.3)
Requirement already satisfied: scrublet in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.2.3)
Requirement already satisfied: seaborn in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.12.1)
Requirement already satisfied: statsmodels in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.13.5)
Requirement already satisfied: tables in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (3.8.0)
Requirement already satisfied: tmtoolkit in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.11.2)
Requirement already satisfied: typing in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (3.7.4.3)
Requirement already satisfied: umap-learn in /home/prakki/.local/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.5.3)
Requirement already satisfied: xlrd in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (2.0.1)
Requirement already satisfied: papermill in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (2.4.0)
Requirement already satisfied: bs4 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.0.1)
Requirement already satisfied: lxml in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (4.9.2)
Requirement already satisfied: tspex in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.6.2)
Requirement already satisfied: sphinx_rtd_theme in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.1.1)
Requirement already satisfied: nbsphinx in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (0.8.11)
Requirement already satisfied: nbsphinx_link in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.3.0)
Requirement already satisfied: numpydoc in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from pycisTopic==1.0.2.dev12+g1e354e6) (1.5.0)
Requirement already satisfied: python-dateutil>=2.8.1 in /home/prakki/.local/lib/python3.8/site-packages (from pandas!=1.3.0,>=1.2.0->pycisTopic==1.0.2.dev12+g1e354e6) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/prakki/.local/lib/python3.8/site-packages (from pandas!=1.3.0,>=1.2.0->pycisTopic==1.0.2.dev12+g1e354e6) (2022.7)
Requirement already satisfied: packaging in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from bbknn->pycisTopic==1.0.2.dev12+g1e354e6) (22.0)
Requirement already satisfied: pynndescent in /home/prakki/.local/lib/python3.8/site-packages (from bbknn->pycisTopic==1.0.2.dev12+g1e354e6) (0.5.8)
Requirement already satisfied: beautifulsoup4 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from bs4->pycisTopic==1.0.2.dev12+g1e354e6) (4.11.1)
Requirement already satisfied: cytoolz in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ctxcore->pycisTopic==1.0.2.dev12+g1e354e6) (0.12.1)
Requirement already satisfied: frozendict in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ctxcore->pycisTopic==1.0.2.dev12+g1e354e6) (2.3.4)
Requirement already satisfied: pyarrow>=8.0.0 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ctxcore->pycisTopic==1.0.2.dev12+g1e354e6) (10.0.1)
Requirement already satisfied: pyyaml in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ctxcore->pycisTopic==1.0.2.dev12+g1e354e6) (6.0)
Requirement already satisfied: tqdm in /home/prakki/.local/lib/python3.8/site-packages (from ctxcore->pycisTopic==1.0.2.dev12+g1e354e6) (4.64.1)
Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in /home/prakki/.local/lib/python3.8/site-packages (from numba->pycisTopic==1.0.2.dev12+g1e354e6) (0.39.1)
Requirement already satisfied: setuptools in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from numba->pycisTopic==1.0.2.dev12+g1e354e6) (65.5.1)
Requirement already satisfied: importlib-metadata in /home/prakki/.local/lib/python3.8/site-packages (from numba->pycisTopic==1.0.2.dev12+g1e354e6) (6.0.0)
Requirement already satisfied: smart-open>=1.8.1 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from gensim->pycisTopic==1.0.2.dev12+g1e354e6) (6.3.0)
Requirement already satisfied: FuzzyTM>=0.4.0 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from gensim->pycisTopic==1.0.2.dev12+g1e354e6) (2.0.5)
Requirement already satisfied: pyzmq>=17 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (24.0.1)
Requirement already satisfied: tornado>=6.1 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (6.2)
Requirement already satisfied: nest-asyncio in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (1.5.6)
Requirement already satisfied: debugpy>=1.0 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (1.6.4)
Requirement already satisfied: traitlets>=5.4.0 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (5.8.0)
Requirement already satisfied: jupyter-client>=6.1.12 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (7.4.8)
Requirement already satisfied: psutil in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (5.9.4)
Requirement already satisfied: comm>=0.1.1 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (0.1.2)
Requirement already satisfied: matplotlib-inline>=0.1 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipykernel->pycisTopic==1.0.2.dev12+g1e354e6) (0.1.6)
Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.11 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (3.0.36)
Requirement already satisfied: jedi>=0.16 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (0.18.2)
Requirement already satisfied: stack-data in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (0.6.2)
Requirement already satisfied: pygments>=2.4.0 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (2.13.0)
Requirement already satisfied: pickleshare in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (0.7.5)
Requirement already satisfied: pexpect>4.3 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (4.8.0)
Requirement already satisfied: backcall in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (0.2.0)
Requirement already satisfied: decorator in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipython->pycisTopic==1.0.2.dev12+g1e354e6) (5.1.1)
Requirement already satisfied: pillow in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipympl->pycisTopic==1.0.2.dev12+g1e354e6) (9.3.0)
Requirement already satisfied: ipython-genutils in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipympl->pycisTopic==1.0.2.dev12+g1e354e6) (0.2.0)
Requirement already satisfied: ipywidgets<9,>=7.6.0 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ipympl->pycisTopic==1.0.2.dev12+g1e354e6) (8.0.4)
Requirement already satisfied: cycler>=0.10 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from matplotlib->pycisTopic==1.0.2.dev12+g1e354e6) (0.11.0)
Requirement already satisfied: pyparsing>=2.2.1 in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from matplotlib->pycisTopic==1.0.2.dev12+g1e354e6) (3.0.9)
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Requirement already satisfied: jsonschema in /home/prakki/anaconda3/envs/scenicplus/lib/python3.8/site-packages (from ray[default]->pycisTopic==1.0.2.dev12+g1e354e6) (4.17.3)
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Installing collected packages: pycisTopic
  Running setup.py develop for pycisTopic
Successfully installed pycisTopic-1.0.2.dev12+g1e354e6

When I try importing pycisTopic in my scenicplus conda environment, seems to be working but the jupyter notebook does not. Please let me know if I am missing something.

(scenicplus) prakki@ramadatta:/data01/SingleCell/Python_notebooks$ python
Python 3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:38) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pycisTopic
>>> pycisTopic.__version__
'1.0.2.dev12+g1e354e6'
ramadatta commented 1 year ago

Hi @cbravo93 ,

thanks. I think I resolved the issue for now.

Based on this SO post, I linked my kernel to my conda environment which then can be used by jupyter notebook.

For this, I ran the following commands in Bash:

conda install ipykernel
python -m ipykernel install --user --name scenicplus
/home/user/anaconda3/envs/scenicplus/bin/jupyter notebook --allow-root &

now, in jupyter notebook, I chose the kernel "scenicplus" and run the following to load pycisTopic successfully.

import pycisTopic
pycisTopic.__version__

'1.0.2.dev15+g242c2a4'
cbravo93 commented 1 year ago

cool :)