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elephant dir packages are back #239
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…at setup while macking a tarball with 'sdist' command travis not fixed downloading fim
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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
How did you check it? Are you sure you've updated
Please double check. If you use conda, navigate to P.S. I just rerun |
True, I think I made some mistake regarding My local branch is updated to 8c41e65.
(Also, due to this, |
This is strange because I do see these files in my conda env when I do a fresh
|
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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.
commit 19d3c7b Author: Danylo Ulianych <dizcza@gmail.com> Date: Thu Aug 1 15:09:34 2019 +0200 fixed min requirements (NeuralEnsemble#235) * fixed min requirements * travis install libopenmpi-dev * added .coveragerc omit=elephant/test* rule not to count test files as source code commit 36e6096 Author: Danylo Ulianych <dizcza@gmail.com> Date: Wed Jul 31 16:55:47 2019 +0200 Integrated GPFA (NeuralEnsemble#233) * Rename neural_trajectory to gpfa and refactor the codes accordingly * Remove codes related to the (not fully implemented) cross-validation feature * added tqdm as an extra requirement * push coverage only for requirements-extras test * gpfa verbose flag; added licence in the docs * Fixed and extended documentation, removed misleading function outputs. commit d6822d6 Author: Danylo Ulianych <dizcza@gmail.com> Date: Tue Jul 23 16:35:45 2019 +0300 Acknowledgments (NeuralEnsemble#241) * acknowledgments * removed reference file AUTHORS.txt * recursive-exclude . *~ commit 6fd3a5b Author: Danylo Ulianych <dizcza@gmail.com> Date: Mon Jul 22 23:14:36 2019 +0300 Release v0.6.3 (NeuralEnsemble#240) * Release v0.6.3 * Update doc/reference/waveform_features.rst Co-Authored-By: Michael Denker <m.denker@fz-juelich.de> commit c013e39 Author: Danylo Ulianych <dizcza@gmail.com> Date: Sun Jul 21 09:18:03 2019 +0300 elephant dir packages are back (NeuralEnsemble#239) * reverted removed imports of elephant's internal packages; download fim during the setup * download fim from tools/fim_manager.py * dummy tools/__init__.py to support py2 * include requirements in MANIFEST back * fixed spade licence typo * included waveform_features module; removed tools; don't donwload fim at setup while macking a tarball with 'sdist' command travis not fixed downloading fim * skip time consuming test_spade_cpp if not HAVE_FIM * travis pip install generated tarball * recursive-include elephant *.py commit 3c30574 Author: Danylo Ulianych <dizcza@gmail.com> Date: Wed Jul 10 18:21:37 2019 +0200 Butterworth supports sosfiltfilt filter_function (NeuralEnsemble#234) * Butterworth supports sosfiltfilt filter_function * higher order filters comment
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 thepip install .
Old comment. Not actual anymore (see updates 1 & 2).
That's why I created
tools
folder for setup package maintenance and movedfim_manager.py
there.tools
dir is not included in elephant wheel tarball.Update 1.
I removed
tools
folder, because we should not ship it with elephant, and moved downloading fim.so in setup.py under theif sys.argv[1] != 'sdist'
condition. It means Travis builds won't have fim installed. I also skipped time-consumingtest_spade_cpp
when we don't have fim.so since this test takes >10 min and causes Travis to hang.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 itslib/site-packages/elephant/
, because it findselephant
module in the current project dir. So I includedpython setup.py install
only to download fim.so.Outdated. See Updates 1 & 2.
I want to explain what is happening behind the travis code:
fim.so
toelephant/spade_src/fim.so
pip install .
copies downloadedfim.so
file into the site-packages folder, because there is a line in MANIFEST.inrecursive-include elephant/spade_src *.so *.pyd