[BUG] Error when installing anvio-dev at the "pip install" step

[uguyet]

Short description of the problem

I got an error at the “pip install” step when re-installing anvio-dev.

anvi'o version

anvio-dev

System info

CentOS Linux release 7.9.2009

Detailed description of the issue

Here the following error message I got:

 Traceback (most recent call last):
          scripts/mupdfwrap.py:6:<module>(): wrap.__main__.main()
          scripts/wrap/__main__.py:3056:main(): jlib.exception_info()
          ^except raise:
          scripts/wrap/__main__.py:3054:main(): main2()
          scripts/wrap/__main__.py:2437:main2(): build( build_dirs, swig_command, args, vs_upgrade, make_command)
          scripts/wrap/__main__.py:1562:build(): jlib.system( command, prefix=jlib.log_text(), out='log', verbose=1)
          scripts/jlib.py:1710:system(): raise Exception( message)
      Exception: Command failed: cd /tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/mupdf-1.26.7-source && XLIB_LDFLAGS=-Wl,-Bsymbolic make -j 8 HAVE_GLUT=no HAVE_PTHREAD=yes verbose=yes barcode=yes shared=yes HAVE_LEPTONICA=yes HAVE_TESSERACT=yes build=release OUT=build/x86_64-shared-tesseract-bsymbolic-Py_LIMITED_API_0x030a0000-release libs libmupdf-threads
      Traceback (most recent call last):
        File "/env/export/cns_n02_scratch/uguyet/0_tools/conda_env/anvio-dev/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
        File "/env/export/cns_n02_scratch/uguyet/0_tools/conda_env/anvio-dev/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
        File "/env/export/cns_n02_scratch/uguyet/0_tools/conda_env/anvio-dev/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 178, in prepare_metadata_for_build_wheel
          whl_basename = backend.build_wheel(metadata_directory, config_settings)
        File "/tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/pipcl.py", line 665, in build_wheel
          items = self._call_fn_build(config_settings)
        File "/tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/pipcl.py", line 954, in _call_fn_build
          ret = self.fn_build()
        File "/tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/setup.py", line 631, in build
          mupdf_build_dir = build_mupdf_unix(
        File "/tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/setup.py", line 1050, in build_mupdf_unix
          subprocess.run( command, shell=True, check=True)
        File "/env/export/cns_n02_scratch/uguyet/0_tools/conda_env/anvio-dev/lib/python3.10/subprocess.py", line 526, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command 'cd /tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/mupdf-1.26.7-source && XCFLAGS=-DTOFU_CJK_EXT XCXXFLAGS=-DTOFU_CJK_EXT /env/export/cns_n02_scratch/uguyet/0_tools/conda_env/anvio-dev/bin/python3.10 ./scripts/mupdfwrap.py -d build/x86_64-shared-tesseract-bsymbolic-Py_LIMITED_API_0x030a0000-release -b all && echo /tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/mupdf-1.26.7-source/build/x86_64-shared-tesseract-bsymbolic-Py_LIMITED_API_0x030a0000-release: && ls -l /tmp/pip-install-kzidz6v1/pymupdf_b2aba09fae6d45fd92325fd698c7808a/mupdf-1.26.7-source/build/x86_64-shared-tesseract-bsymbolic-Py_LIMITED_API_0x030a0000-release' returned non-zero exit status 1.
      [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. 

[ivagljiva]

Looks like its specifically an issue with installing the pymupdf package, which is a dependency of `anvi-draw-kegg-pathways.

I'm not really sure what is making it fail, though. If you try running pip install -v pymupdf while in your anvi'o-dev environment, the output might yield more helpful information.