Conda environment: requirements installation failure

[SuhasSrinivasan]

Thank you for developing this pipeline.

After installing the packages in the conda YAML file, the following issue occurs.

conda activate pepatac
unset PYTHONPATH
python -m pip install --ignore-installed --upgrade -r requirements.txt

python -m pip install --ignore-installed --upgrade -r requirements.txt
Collecting attmap>=0.13.2
  Downloading attmap-0.13.2-py3-none-any.whl (12 kB)
Collecting bio>=0.2.4
  Downloading bio-1.6.2-py3-none-any.whl (278 kB)
     |████████████████████████████████| 278 kB 20.9 MB/s
Collecting blosc2>=2.0.0
  Downloading blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
     |████████████████████████████████| 4.4 MB 320.8 MB/s
Collecting clyent==1.2.1
  Downloading clyent-1.2.1.tar.gz (20 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/svasan/miniconda3/envs/pepatac/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-oj7b4ccr/clyent_7f94d3f79e9446e9ad034bb8409e417e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-oj7b4ccr/clyent_7f94d3f79e9446e9ad034bb8409e417e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-vnsjvpqh
       cwd: /tmp/pip-install-oj7b4ccr/clyent_7f94d3f79e9446e9ad034bb8409e417e/
  Complete output (51 lines):
  running egg_info
  creating /tmp/pip-pip-egg-info-vnsjvpqh/clyent.egg-info
  writing /tmp/pip-pip-egg-info-vnsjvpqh/clyent.egg-info/PKG-INFO
  writing dependency_links to /tmp/pip-pip-egg-info-vnsjvpqh/clyent.egg-info/dependency_links.txt
  writing top-level names to /tmp/pip-pip-egg-info-vnsjvpqh/clyent.egg-info/top_level.txt
  writing manifest file '/tmp/pip-pip-egg-info-vnsjvpqh/clyent.egg-info/SOURCES.txt'
  /home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/command/sdist.py:122: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`.
  !!

          ********************************************************************************
          Custom 'build_py' does not implement 'get_data_files_without_manifest'.
          Please extend command classes from setuptools instead of distutils.

          See https://peps.python.org/pep-0632/ for details.
          ********************************************************************************

  !!
    self._add_data_files(self._safe_data_files(build_py))
  reading manifest file '/tmp/pip-pip-egg-info-vnsjvpqh/clyent.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-oj7b4ccr/clyent_7f94d3f79e9446e9ad034bb8409e417e/setup.py", line 4, in <module>
      setup(
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/__init__.py", line 117, in setup
      return distutils.core.setup(**attrs)
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 186, in setup
      return run_commands(dist)
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
      dist.run_commands()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
      self.run_command(cmd)
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
      cmd_obj.run()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 312, in run
      self.find_sources()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 320, in find_sources
      mm.run()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 548, in run
      self.prune_file_list()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/command/sdist.py", line 162, in prune_file_list
      super().prune_file_list()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_distutils/command/sdist.py", line 380, in prune_file_list
      base_dir = self.distribution.get_fullname()
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_core_metadata.py", line 272, in get_fullname
      return _distribution_fullname(self.get_name(), self.get_version())
    File "/home/svasan/miniconda3/envs/pepatac/lib/python3.9/site-packages/setuptools/_core_metadata.py", line 290, in _distribution_fullname
      canonicalize_version(version, strip_trailing_zero=False),
  TypeError: canonicalize_version() got an unexpected keyword argument 'strip_trailing_zero'
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/e9/1b/f73dd0efcacfcadb4beaa075d1f2cfe675fd8baf7658f21a3a7fd5c84aae/clyent-1.2.1.tar.gz#sha256=72b977e7c115224f474f9c70c549c0977b8daf5ac00452301cff065ff14129e5 (from https://pypi.org/simple/clyent/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement clyent==1.2.1 (from versions: 0.1.0, 0.2.0, 0.2.1, 0.3.0, 0.3.2, 0.3.3, 0.3.4, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1)
ERROR: No matching distribution found for clyent==1.2.1

[donaldcampbelljr]

Interesting, you could attempt to take that requirement out of the requirements.txt file and instead try to install it via conda:
conda install conda-forge::clyent