RGT package on PyPi does not install due to deprecation of numpy.distutils #291
Description
Even with our almost one year old versions (python 3.12.3 , numpy 1.26.4) it is not possible to install RGT obviously due to the use of the deprecated numpy.distutils in hmmlearn as a subpackage/dependency of RGT 1.0.2.
Setting up a VM with older versions of python/numpy just for RGT does not make much sense for me. Current versions in most distributions are the 3.13.x series of python and numpy >2.0.0 .
error msg:
`
python -m pip install RGT
Defaulting to user installation because normal site-packages is not writeable
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Collecting RGT
Downloading RGT-1.0.2.tar.gz (36.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.8/36.8 MB 147.8 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Requirement already satisfied: cython in /p/software/default/stages/2025/software/Cython/3.0.10-GCCcore-13.3.0/lib/python3.12/site-packages (from RGT) (3.0.10)
Requirement already satisfied: numpy>=1.4.0 in /p/software/default/stages/2025/software/SciPy-bundle/2024.05-gcccoreflexiblas-13.3.0-3.4.4/lib/python3.12/site-packages (from RGT) (1.26.4)
Requirement already satisfied: scipy>=1.0.0 in /p/software/default/stages/2025/software/SciPy-bundle/2024.05-gcccoreflexiblas-13.3.0-3.4.4/lib/python3.12/site-packages (from RGT) (1.13.1)
Collecting pysam>=0.12.0 (from RGT)
Downloading pysam-0.23.3-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (1.7 kB)
Collecting pyBigWig (from RGT)
Downloading pyBigWig-0.3.24-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Requirement already satisfied: Biopython>=1.64 in ./.local/lib/python3.12/site-packages (from RGT) (1.85)
Collecting fisher>=0.1.5 (from RGT)
Downloading fisher-0.1.14.tar.gz (22 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting moods-python>=1.9.4.1 (from RGT)
Downloading MOODS-python-1.9.4.1.tar.gz (250 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.9/250.9 kB 210.8 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Collecting scikit-learn>=0.19.0 (from RGT)
Downloading scikit_learn-1.7.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (17 kB)
Collecting hmmlearn==0.2.2 (from RGT)
Downloading hmmlearn-0.2.2.tar.gz (146 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 146.4/146.4 kB 102.8 MB/s eta 0:00:00
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [83 lines of output]
/tmp/pip-install-0zmwfiho/hmmlearn_49750eaaaef14ba39def4a52906892ce/setup.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(setuptools.version) < "36.2":
/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/init.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
[07/07/25 16:58:04] WARNING toml section missing pyproject_reading.py:42
'pyproject.toml does not
contain a
tool.setuptools_scm
section'
Traceback (most recent call
last):
File
"/p/software/jurecadc/stage
s/2025/software/Python/3.12
.3-GCCcore-13.3.0/lib/pytho
n3.12/site-packages/setupto
ols_scm/_integration/pyproj
ect_reading.py", line 36,
in read_pyproject
section =
defn.get("tool",
{})[tool_name]
~~~~~~~~~~~~~
~~~~~~~^^^^^^^^^^^
KeyError: 'setuptools_scm'
running egg_info
creating /tmp/pip-pip-egg-info-032c6a9o/hmmlearn.egg-info
writing /tmp/pip-pip-egg-info-032c6a9o/hmmlearn.egg-info/PKG-INFO
writing dependency_links to /tmp/pip-pip-egg-info-032c6a9o/hmmlearn.egg-info/dependency_links.txt
writing requirements to /tmp/pip-pip-egg-info-032c6a9o/hmmlearn.egg-info/requires.txt
writing top-level names to /tmp/pip-pip-egg-info-032c6a9o/hmmlearn.egg-info/top_level.txt
writing manifest file '/tmp/pip-pip-egg-info-032c6a9o/hmmlearn.egg-info/SOURCES.txt'
INFO: Disabling color, you really want to install colorlog.
Disabling color, you really want to install colorlog.
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-0zmwfiho/hmmlearn_49750eaaaef14ba39def4a52906892ce/setup.py", line 47, in <module>
setup(
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/dist.py", line 968, in run_command
super().run_command(command)
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/command/egg_info.py", line 321, in run
self.find_sources()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/command/egg_info.py", line 329, in find_sources
mm.run()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/command/egg_info.py", line 550, in run
self.add_defaults()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/command/egg_info.py", line 588, in add_defaults
sdist.add_defaults(self)
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/command/sdist.py", line 102, in add_defaults
super().add_defaults()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/command/sdist.py", line 250, in add_defaults
self._add_defaults_ext()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/command/sdist.py", line 334, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 303, in get_finalized_command
cmd_obj.ensure_finalized()
File "/p/software/jurecadc/stages/2025/software/Python/3.12.3-GCCcore-13.3.0/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 111, in ensure_finalized
self.finalize_options()
File "/tmp/pip-install-0zmwfiho/hmmlearn_49750eaaaef14ba39def4a52906892ce/setup.py", line 28, in finalize_options
import numpy.distutils
ModuleNotFoundError: No module named 'numpy.distutils'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
`