Crash during install (pyanddoc not installed)

[joaoe]

Hello !

I'm trying to install pyensembl latest and it fails.

  Using cached pyensembl-1.2.1.tar.gz
    Complete output from command python setup.py egg_info:
    No module named 'pypandoc'
    Failed to convert %s to reStructuredText README.md
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-szmm6fj4/pyensembl/setup.py", line 86, in <module>
        long_description=readme_restructured,
    NameError: name 'readme_restructured' is not defined

Issues:

1. Should be print("%s" % readme_filename) https://github.com/openvax/pyensembl/blob/master/setup.py#L40
2. Then readme_restructured might not be defined. https://github.com/openvax/pyensembl/blob/master/setup.py#L86 (would setting it to None work?).
3. You need to specify the pypandoc dependency somewhere, preferably before it is used.

Thanks.

[joaoe]

Btw, the exact same crash happens with varcode.

[iskandr]

Thanks for letting me know @joaoe -- I introduced this bug while mass updating the configs of all the repos we're moving from hammerlab -> openvax. This is fixed in Varcode & others and will be fixed in pyensembl momentarily once I merge https://github.com/openvax/pyensembl/pull/198

[iskandr]

Just merged, should be fixed.