error in create environment with cNMF_benchmarking_pipeline/Inference/torch-cNMF/environment.yml

[ShanshanHe-44]

Hi Alexander,

Thanks for the latest update. I tried to re-install the tor-cnmf env but keep getting error;

• Fix: Remove name: so prefix: is used;
• move compiled packages (scipy, matplotlib, numpy, pyyaml) to conda dependencies;
• install pure-Python pip packages separately with PIP_CACHE_DIR/TMPDIR set to the shared filesystem

I record the error below.

1. python version:

• solution: 3.9 -> 3.11

2. nmf-torch and torch-cnmf

• solution: comment out, need to install manually once the environment has settled.

Pip subprocess error:
ERROR: Ignored the following versions that require a different python version: 0.1.7 Requires-Python >=3.10; 0.11.0 Requires-Python >=3.10; 0.11.0rc3 Requires-Python >=3.10; 0.11.1 Requires-Python >=3.10; 
ERROR: Could not find a version that satisfies the requirement nmf-torch==0.1.dev108+g218c29c08.d20260402 (from versions: 0.1.0, 0.1.1)
ERROR: No matching distribution found for nmf-torch==0.1.dev108+g218c29c08.d20260402

3. scipy install failed, same as matplotlib, etc.

The pip: section in the YAML is installing scipy from PyPI, but it can't find OpenBLAS. This happens because pip builds scipy from source and doesn't see the conda-installed openblas.
The fix: scipy should be a conda dependency (not pip), since conda handles the BLAS linkage correctly. The conda section already has all the BLAS/OpenBLAS libs but scipy itself is missing from it.

• solution: add some pkgs to the conda dependencies

 Configuring scipy_config.h using configuration
      Program f2py found: YES (/tmp/pip-build-env-sm7uyo6w/overlay/bin/f2py)
      Run-time dependency scipy-openblas found: NO  (tried pkg-config)
      Run-time dependency openblas found: NO  (tried pkg-config and cmake)
      Run-time dependency openblas found: NO  (tried pkg-config)

      ../scipy/meson.build:285:9: ERROR: Dependency "OpenBLAS" not found (tried pkg-config)

      A full log can be found at /tmp/pip-install-go9noa2o/scipy_cc2e426d0816434694d7180af4bbc62c/.mesonpy-8abl31m2/meson-logs/meson-log.txt
      [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.
failed
CondaEnvException: Pip failed