Update requirements.txt for #844

[mugitty]

Bringing in changes from biolink/ontobio#632

Will test on Jenkins test branch

[kltm]

@mugitty This is a trivial change, so merge at will.

[kltm]

@mugitty @dustine32 It looks like your pipeline has failed. Odd error in the reports. Are you up-to-date with master/snapshot?

[mugitty]

Jenkins file got to be large, so I temporarily removed part of the publishing step. This may have caused the problem. I need to look in detail

[kltm]

@mugitty Importantly, "Publishing" and "Archiving" should be either kept intact or removed entirely--having a partial publish step could cause problems, such as overwriting live data with bad data.
That said, it was in reports where it failed, so I'd doubt the error was there.

[mugitty]

It failed while comparing stats from previous to current release. Specifically, it cannot find 'process' aspect items in the json file.

[dustine32]

65b1bdf is for fixing pip install ../graphstore/rule-runner errors:

20:00:22  Collecting SPARQLWrapper==1.8.0
20:00:22    Downloading SPARQLWrapper-1.8.0.zip (36 kB)
20:00:22    Preparing metadata (setup.py): started
20:00:22    Preparing metadata (setup.py): finished with status 'error'
20:00:22    error: subprocess-exited-with-error
20:00:22    
20:00:22    × python setup.py egg_info did not run successfully.
20:00:22    │ exit code: 1
20:00:22    ╰─> [1 lines of output]
20:00:22        error in SPARQLWrapper setup command: use_2to3 is invalid.
20:00:22        [end of output]

Also another error installing pyYaml==5.4.1:

        (a long, long stack trace and then...)
        File "/private/var/folders/mn/4r4wdgk16z7cvnq3t2zrhkf40000gp/T/pip-build-env-dvoojr4k/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/sdist.py", line 251, in add_defaults
          self._add_defaults_ext()
        File "/private/var/folders/mn/4r4wdgk16z7cvnq3t2zrhkf40000gp/T/pip-build-env-dvoojr4k/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/sdist.py", line 336, in _add_defaults_ext
          self.filelist.extend(build_ext.get_source_files())
        File "<string>", line 201, in get_source_files
        File "/private/var/folders/mn/4r4wdgk16z7cvnq3t2zrhkf40000gp/T/pip-build-env-dvoojr4k/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 107, in __getattr__
          raise AttributeError(attr)
      AttributeError: cython_sources

We'll see in testing how this affects the GO pipeline build and whether we need to pin to any specific versions.

[dustine32]

@mugitty and I sorted out the python3.10 upgrade bugs on this branch as we saw them pop up on the Jenkins build pipeline. A lot of unpinning dependencies.

Hopefully this is everything we need to do. But if there are more, newly discovered bugs we can just continue to fight through them.