Reorganize and clean up tests

[dhimmel]

Places tests closer to the code they're testing in the project's directory tree.

This PR does not create new tests, just moves existing tests to the new directory structure. Tests should functionally be the same.

[dhimmel]

Builds are failing due to an intermittent 504 bad-gateway error on the translation-server:
https://ci.appveyor.com/project/greenelab/manubot/builds/21018471/job/yd35t230v6ni6ty8#L186

CC @dongbohu

[agitter]

The restructuring looks good to me except for the error you noted above.

[dongbohu]

I tried this command:

curl -d https://bigthink.com/neurobonkers/a-pirate-bay-for-science -H 'Content-Type: text/plain' http://translate.manubot.org/web

and got the output:

[
  {
    "key": "8V3UIHBX",
    "version": 0,
    "itemType": "webpage",
    "creators": [],
    "tags": [],
    "title": "Meet the Robin Hood of Science",
    "websiteTitle": "Big Think",
    "date": "2016-02-09T20:12:00",
    "url": "https://bigthink.com/neurobonkers/a-pirate-bay-for-science",
    "abstractNote": "How one researcher created a pirate bay for science more powerful than even libraries at top universities.",
    "language": "en",
    "accessDate": "2018-12-14T18:43:33Z"
  }
]

[dhimmel]

pytest manubot/cite/tests/test_cite_command.py::test_cite_command_render_stdout

is failing because DataCite is down again. AppVeyor did not fail because these tests are skipped, which is bizzare. Pandoc is now version 2.5 on AppVeyor, but don't see why that would skip the test.

[dhimmel]

de2ef52 added the -rs flag to pytest to show why tests are skipped. Result

SKIP [5] manubot\cite\tests\test_cite_command.py:52: pandoc-citeproc installation not found on system

@jgm in the past, the following commands installed pandoc and pandoc-citeproc on windows:

https://github.com/greenelab/manubot/blob/26a6fbd91ce70a1f8a424df1d3b8c7354afdfa77/.appveyor.yml#L20-L21

Has something changed? Any advice?

[agitter]

@dhimmel I believe you want this line for the pandoc install from chocolatey command

https://github.com/greenelab/manubot/blob/26a6fbd91ce70a1f8a424df1d3b8c7354afdfa77/.appveyor.yml#L25

The chocolatey pandoc package maintainer has a GitHub profile if we can't debug this.

I reviewed the AppVeyor build log, and it looks like pandoc is installed to a different path now.

Originally:

The install of pandoc was successful.
  Software installed to 'C:\Program Files (x86)\Pandoc\'
Chocolatey installed 2/2 packages. 
 See the log for details (C:\ProgramData\chocolatey\logs\chocolatey.log).
$env:Path += ";C:\Program Files (x86)\Pandoc\"

Currently:

The install of pandoc was successful.
  Software installed to 'C:\Program Files\Pandoc\'
Chocolatey installed 2/2 packages. 
 See the log for details (C:\ProgramData\chocolatey\logs\chocolatey.log).
$env:Path += ";C:\Program Files (x86)\Pandoc\"

Can you try updating
https://github.com/greenelab/manubot/blob/26a6fbd91ce70a1f8a424df1d3b8c7354afdfa77/.appveyor.yml#L26
to use C:\Program Files\Pandoc\?

[dhimmel]

I reviewed the AppVeyor build log, and it looks like pandoc is installed to a different path now.

Thanks @agitter... that fixed the AppVeyor issue. I also switched to specifying which version of pandoc in choco install for AppVeyor. Also removed the DataCite DOI from the cite command tests because the uptime of DataCite DOI Content Negotiation has been so poor. Hopefully, these changes will make test_cite_command_render_stdout less subject to whimsical failures.

[agitter]

With your latest changes, this looks good to me.