pip3 install HAPPE failed...

[hughesdj]

... with this error message:

Collecting sklearn (from HAPPE)
Downloading sklearn-0.0.post12.tar.gz (2.6 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [15 lines of output]
The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
rather than 'sklearn' for pip commands.

  Here is how to fix this error in the main use cases:
  - use 'pip install scikit-learn' rather than 'pip install sklearn'
  - replace 'sklearn' by 'scikit-learn' in your pip requirements files
    (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
  - if the 'sklearn' package is used by one of your dependencies,
    it would be great if you take some time to track which package uses
    'sklearn' instead of 'scikit-learn' and report it to their issue tracker
  - as a last resort, set the environment variable
    SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error

[fengcong3]

Thank you for trying HAPPE. As the error message says: set the environment variable SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error, You can install and use it first. I will update the HAPPE version on github and pypi when I have time.

[hughesdj]

Thank you. We got HAPPE running in the way you suggest.
However, it fails on test data, because the script provided wants to read a hard coded file
/public/agis/chengshifeng_group/fengcong/WGRS/software/Fc-code/partlen.txt
which is not provided.

[fengcong3]

Can you provide detailed installation and execution commands and complete error output?

[hughesdj]

Please see below for installation, execution commands and output.
The example script provided wants to read a hard coded file
/public/agis/chengshifeng_group/fengcong/WGRS/software/Fc-code/partlen.txt
which is not provided.

cd HAPPE/
module load Python/3.12.3-GCCcore-13.3.0
python3 -m venv happe
source happe/bin/activate
export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
env |grep SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL
pip3 install HAPPE
HAPPE -h
which bcftools	##not found, must load
module load BCFtools
which bcftools	##to find path
which bgzip	##to find path
which tabix	##to find path
#	[edit config.ini]
cd example/
./example.sh 
#		#ModuleNotFoundError: No module named 'sklearn'
python -m pip list
pip install scikit-learn
python -m pip list
./example.sh >out.log 2>&1
##

[2025-01-22 10:42:20,846] - HAPPE - INFO - deal args.
[2025-01-22 10:42:20,852] - HAPPE - INFO - Filter samples and variants.
[2025-01-22 10:42:20,952] - HAPPE - INFO - convert file format.
[2025-01-22 10:42:21,141] - HAPPE - INFO - hierarchy clustering.
cluster min and max: 1 5
[2025-01-22 10:42:36,463] - HAPPE - INFO - read snp information file.
[2025-01-22 10:42:36,463] - HAPPE - INFO - calc out the snp_info_row_num = 7.
[2025-01-22 10:42:36,463] - HAPPE - INFO - plot tree to excel file.
[2025-01-22 10:42:39,844] - HAPPE - INFO - get sample information start col and get sample order.
[2025-01-22 10:42:39,877] - HAPPE - INFO - write sample information to excel file.
[2025-01-22 10:42:43,020] - HAPPE - INFO - plot genotype matrix to excel file.
[2025-01-22 10:42:50,495] - HAPPE - INFO - plot RDV to excel file.
Traceback (most recent call last):
  File "/home/data/bioinf_resources/Wheat_resources/HAPPE/happe/lib/python3.12/site-packages/HAPPE/normalization_depth_from_mosdepth_output.py", line 47, in <module>
    infp = open(part_len,"r")
           ^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/public/agis/chengshifeng_group/fengcong/WGRS/software/Fc-code/partlen.txt'

########################[lines omitted]

/home/data/bioinf_resources/Wheat_resources/HAPPE/happe/lib/python3.12/site-packages/numpy/_core/fromnumeric.py:3860: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/data/bioinf_resources/Wheat_resources/HAPPE/happe/lib/python3.12/site-packages/numpy/_core/_methods.py:145: RuntimeWarning: invalid value encountered in scalar divide
  ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/home/data/bioinf_resources/Wheat_resources/HAPPE/happe/lib/python3.12/site-packages/HAPPE/depth2excel.py", line 185, in <module>
    ws.cell(row=start_row+index1*cell_row+i,column=col+1).value = round(np.mean(sample_depth[sample]),2)
                                          ^
NameError: name 'i' is not defined. Did you mean: 'id'?
[2025-01-22 10:43:01,844] - HAPPE - ERROR - add RDV matrix -- retrun code:256