Running around in dependency hell.

[selfcriticalmass]

Hi guys! I need your help.

Issue: Having difficulty with installations.

Context

System: MacOS Sonoma (M3 pro)

I am having issues with installation altogether.

I guess my main question/query boils down to couple of things:

• Has the pip install corems command been tested recently?
• Could be wrong but seems some dependencies are End-of-Life

For notes on how I reached those points please read below.

What I have tried so far

First failure

I tried pip install corems which gave me

Using CPython 3.13.9 interpreter at: /Users/zr4/.nix-profile/bin/python3.13
Creating virtual environment at: .venv
Resolved 65 packages in 521ms
  × Failed to build `netcdf4==1.6.5`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta.build_wheel` failed (exit status: 1)

      [stdout]
      reading from setup.cfg...

          HDF5_DIR environment variable not set, checking some standard locations ..
      checking /Users/zr4/include ...
      hdf5 headers not found in /Users/zr4/include
      checking /usr/local/include ...
      hdf5 headers not found in /usr/local/include
      checking /sw/include ...
      hdf5 headers not found in /sw/include
      checking /opt/include ...
      hdf5 headers not found in /opt/include
      checking /opt/local/include ...
      hdf5 headers not found in /opt/local/include
      checking /opt/homebrew/include ...
      hdf5 headers not found in /opt/homebrew/include
      checking /usr/include ...
      hdf5 headers not found in /usr/include

      [stderr]
      Package hdf5 was not found in the pkg-config search path.
      Perhaps you should add the directory containing `hdf5.pc'
      to the PKG_CONFIG_PATH environment variable
      Package 'hdf5' not found
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
          requires = get_requires_for_build({})
        File "/Users/zr4/.cache/uv/builds-v0/.tmpIrBCHF/lib/python3.13/site-packages/setuptools/build_meta.py", line 333, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/zr4/.cache/uv/builds-v0/.tmpIrBCHF/lib/python3.13/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/Users/zr4/.cache/uv/builds-v0/.tmpIrBCHF/lib/python3.13/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 457, in <module>
        File "<string>", line 398, in _populate_hdf5_info
      ValueError: did not find HDF5 headers

      hint: This usually indicates a problem with the package or the build environment.
  help: If you want to add the package regardless of the failed resolution, provide the `--frozen` flag to skip locking and syncing.
zr4@macwf05420:~/Desktop/Scratch/uv_corems/ > uv add hdf5
  × No solution found when resolving dependencies:
  ╰─▶ Because hdf5 was not found in the package registry and your project depends on hdf5, we can conclude that your project's requirements are unsatisfiable.
  help: If you want to add the package regardless of the failed resolution, provide the `--frozen` flag to skip locking and syncing.

• That seemed to suggest some kind of issue with hdf5
• so I did pip install hdf5 . Which failed.
• so I did pip install HDF5 (distinction being the all-caps). Which failed as well.
• Turns out the name for the HDF5 library on PyPI is h5py
• So, I did pip install h5py , that worked.
• Then I did pip install corems. Which gave me a new error message.

Second failure

After I resolved the HDF5 library manually, I am getting a new error message. It reads

× Failed to build `theano-pymc==1.1.2`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta:__legacy__.build_wheel` failed (exit status: 1)

      [stderr]
      /Users/zr4/.cache/uv/sdists-v9/pypi/theano-pymc/1.1.2/KqOVQIGNSflaZi2JLy15M/src/versioneer.py:564: SyntaxWarning: invalid escape sequence '\s'
        mo = re.search(r'=\s*"(.*)"', line)
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
          requires = get_requires_for_build({})
        File "/Users/zr4/.cache/uv/builds-v0/.tmp1KRDfT/lib/python3.13/site-packages/setuptools/build_meta.py", line 333, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/zr4/.cache/uv/builds-v0/.tmp1KRDfT/lib/python3.13/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/Users/zr4/.cache/uv/builds-v0/.tmp1KRDfT/lib/python3.13/site-packages/setuptools/build_meta.py", line 520, in run_setup
          super().run_setup(setup_script=setup_script)
          ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/zr4/.cache/uv/builds-v0/.tmp1KRDfT/lib/python3.13/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 49, in <module>
        File "/Users/zr4/.cache/uv/sdists-v9/pypi/theano-pymc/1.1.2/KqOVQIGNSflaZi2JLy15M/src/versioneer.py", line 1479, in get_version
          return get_versions()["version"]
                 ~~~~~~~~~~~~^^
        File "/Users/zr4/.cache/uv/sdists-v9/pypi/theano-pymc/1.1.2/KqOVQIGNSflaZi2JLy15M/src/versioneer.py", line 1411, in get_versions
          cfg = get_config_from_root(root)
        File "/Users/zr4/.cache/uv/sdists-v9/pypi/theano-pymc/1.1.2/KqOVQIGNSflaZi2JLy15M/src/versioneer.py", line 342, in get_config_from_root
          parser = configparser.SafeConfigParser()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

      hint: This usually indicates a problem with the package or the build environment.
  help: If you want to add the package regardless of the failed resolution, provide the `--frozen` flag to skip locking and syncing.

• I tried to install Theano-PyMC manually. Which failed.
• I looked the package up on PyPI and the project is archived and no longer maintained.

Not sure how to proceed from here.

Please advice on a solution.

Best regards,
Rijan