elephant dir packages are back

[dizcza]

Fixes #237: dir(elephant) should contain its internal packages.
Current travis release parses "- python -c '<python command>'" lines in .travis.yml correctly, however it still does not download fim.so module during the pip install .

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Old comment. Not actual anymore (see updates 1 & 2).

That's why I created tools folder for setup package maintenance and moved fim_manager.py there. tools dir is not included in elephant wheel tarball.

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Update 1.
I removed tools folder, because we should not ship it with elephant, and moved downloading fim.so in setup.py under the if sys.argv[1] != 'sdist' condition. It means Travis builds won't have fim installed. I also skipped time-consuming test_spade_cpp when we don't have fim.so since this test takes >10 min and causes Travis to hang.

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Update 2.
python setup.py install now downloads fim.so in Travis.
Keep in mind, nosetests --cover-package=elephant is run in the project root folder and actually, travis never uses elephant from its lib/site-packages/elephant/, because it finds elephant module in the current project dir. So I included python setup.py install only to download fim.so.

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Outdated. See Updates 1 & 2.
I want to explain what is happening behind the travis code:

  - python -c "from tools.fim_manager import download_spade_fim; download_spade_fim()"
  - pip install .
  - python -c "from elephant.spade import HAVE_FIM; assert HAVE_FIM"

1. download fim.so to elephant/spade_src/fim.so
2. pip install . copies downloaded fim.so file into the site-packages folder, because there is a line in MANIFEST.in recursive-include elephant/spade_src *.so *.pyd
3. assert that fim is available (the build will fail if assert is triggered)

[coveralls]

Coverage decreased (-0.02%) to 70.954% when pulling 11ca2e8 on INM-6:elephant_dir_packages into 3c30574 on NeuralEnsemble:master.

[dizcza]

Ready to merge.

[mdenker]

pip install . still failed for me regarding fim.so, and with several files missing from the installed packaged. I think this should be fixed by the two inline comments. My complete MANIFEST.in read

include requirements*.txt
include README.rst
include LICENSE.txt
include AUTHORS.txt
recursive-include elephant *.py
include elephant/VERSION
include elephant/current_source_density_src/README.md
include elephant/current_source_density_src/test_data.mat
include elephant/spade_src/LICENSE
recursive-include elephant/spade_src *.so *.pyd
recursive-include tools *.py
include elephant/test/spike_extraction_test_data.txt
recursive-include doc *
prune doc/_build

[dizcza]

pip install . still failed for me regarding fim.so

How did you check it? Are you sure you've updated elephant_dir_packages branch locally? Did you leave your project source dir once you installed elephant package with pip install .? Because when you run pip install . and then python -c "from elephant.spade import HAVE_FIM; print(HAVE_FIM)" inside the same folder it tries to find fim.so in your source project dir rather than in .../lib/python3.7/site-packages/elephant/.
Just to be sure, cd ~ each time after you run pip install ..

and with several files missing from the installed packaged

Please double check. If you use conda, navigate to ~/anaconda3/envs/<env-name>/lib/python3.7/site-packages/elephant and check the files there. There should be all .py files and fim.so in spade_src folder.

P.S. I just rerun pip install . and it works as expected: all .py are preserved (even though I removed recursive-include elephant *.py line) and fim.so in downloaded.

[mdenker]

True, I think I made some mistake regarding fim.so (maybe I forgot to cd, that could be), however, regarding the second point, the .py files in spade_src and current_source_density_src are definitely missing in the site-packages folder.

My local branch is updated to 8c41e65.

ls ~/miniconda3/envs/tttt/lib/python3.7/site-packages/elephant/current_source_density_src/
README.md  test_data.mat

(Also, due to this, import elephant fails, since it is missing the KCSD modules.)

[dizcza]

the .py files in spade_src and current_source_density_src are definitely missing in the site-packages folder

This is strange because I do see these files in my conda env when I do a fresh pip install .. Maybe, once again, it's the issue of pip caching policy about which I'm not aware of.
Anyway, I put recursive-include elephant *.py line back in the manifest. Could you confirm it works now for you? Both

• pip install .
• python setup.py sdist ; pip install dist/elephant-0.6.2.tar.gz

[mdenker]

Yes, with this latest line, it works. Strange, indeed. My pip version is 19.1.1, not sure if this has something to do with it. Anyhow, I think we tested all possibilities by now.
Checking on the setup.py commands, I think sdist is the only one we need to consider. When using bdist for a binary distribution, I guess we "do" want to have the binaries included as well. For me, this is good to go now.