-
Notifications
You must be signed in to change notification settings - Fork 96
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Neuronunit reduced cells #348
Open
russelljjarvis
wants to merge
132
commits into
BlueBrain:master
Choose a base branch
from
russelljjarvis:neuronunit_reduced_cells
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Changes from all commits
Commits
Show all changes
132 commits
Select commit
Hold shift + click to select a range
e2af7e2
adding in appropriate notebooks, removed call to pebble pool in neuro…
russelljjarvis 1a6d38c
third example
russelljjarvis a54de02
adding in single file
russelljjarvis cc57e0b
reverted algorithms file to the original
russelljjarvis acd1fb7
reintroduce constructor BPO_deap_opt() argument/ neuronunit=boolean f…
russelljjarvis c46e5b2
Update README.md
russelljjarvis 3a5e6e2
Update README.md
russelljjarvis e9253f8
update build instructions pertaining to git to see if using different…
russelljjarvis 5b06b00
Merge branch 'neuronunit_reduced_cells' of https://github.com/russell…
russelljjarvis 938c5c2
Updated config.yml
russelljjarvis c1de908
converted spaces to tabs
russelljjarvis d2a75f3
converted spaces to tabs
russelljjarvis ab4de1f
converted spaces to tabs
russelljjarvis 109a1c4
shorter build+tests
russelljjarvis 7b66fdc
more ci fixing
russelljjarvis 6fad627
perhaps ci will work with different test dependency
russelljjarvis 0f60ea2
added in necessary test
russelljjarvis d765305
changed setup.py to try to coax tox to run
russelljjarvis a5e028b
abolished DataTC useful methods persist because of inheritance
russelljjarvis 947666e
change dependencies to run on tox
russelljjarvis 5517669
change dependencies to run on tox
russelljjarvis 7a3f98f
process dependency links
russelljjarvis 27546ab
install requires
russelljjarvis 5f32589
install requires
russelljjarvis f17f674
install requires
russelljjarvis 2bf11d0
install requires
russelljjarvis 3b89f1b
ci dependency change
russelljjarvis 68bafb6
ci setup dependency change
russelljjarvis ada84c9
merge
russelljjarvis c46a5b0
factored out dtc and replaced with models
russelljjarvis 58bd45f
update requirements
russelljjarvis f979f8d
update CI
russelljjarvis af4e848
update
russelljjarvis dbd56ce
update ci
russelljjarvis ee32666
update CI
russelljjarvis f9050f7
update
russelljjarvis 4eb3fd3
try to get tox CI working
russelljjarvis 7bac473
update for pull request
russelljjarvis 94e7f90
Fix py2 testing error due to PR #998 in nrn.
5c0be1a
Merge pull request #349 from AurelienJaquier/master
wvangeit c2661a0
Add feature computation functions to CellEvaluator, ObjectivesCalcula…
ceda365
Merge branch 'master' into feature_values
wvangeit cc732a1
Updated documentation to add the README on RTD.
alex4200 42dd6bb
Add tests
4b05e8f
Merge branch 'feature_values' of https://github.com/BlueBrain/BluePyO…
0b17fda
Merge pull request #350 from BlueBrain/feature_values
wvangeit 3ac2257
Fixed the bagde table.
alex4200 eb62c27
Merge branch 'master' into alexdoc
wvangeit 4f25199
Merge pull request #351 from alex4200/alexdoc
wvangeit a076a2f
Added config files for RTD
alex4200 f0ea22a
Merge branch 'alexdoc' of github.com:alex4200/BluePyOpt into alexdoc
alex4200 57206ce
Merge branch 'master' into alexdoc
wvangeit 5c8267d
Merge pull request #352 from alex4200/alexdoc
wvangeit fd29f6c
Commenting out the license text.
alex4200 ae14666
Merge branch 'alexdoc' of github.com:alex4200/BluePyOpt into alexdoc
alex4200 3821813
Fixing image in README: Provide proper path depending where the READM…
alex4200 c9428ad
Merge pull request #353 from alex4200/alexdoc
wvangeit 3aa210c
Fix path in readthedocs yaml
wvangeit ce4af5c
Fixing image location in README
wvangeit 45b922a
update testing
russelljjarvis c490139
update
russelljjarvis 22a7d49
update
russelljjarvis 30ae737
update
russelljjarvis d5755fb
merge
russelljjarvis fd48264
merged with origin master @bbp.bpo, checked nose test compatibility, …
russelljjarvis 15e28e0
moved dependencies into extras_require
russelljjarvis e7c3526
update for CI unittesting passing
russelljjarvis af20008
local CI verification
russelljjarvis fe7f1e3
update
russelljjarvis 0dc016b
might work
russelljjarvis 98a2ac7
changed test file names
russelljjarvis 087ff46
update file names
russelljjarvis 799e39a
before merge master/origin
russelljjarvis a35930b
update tox
russelljjarvis 0230b38
update for PR
russelljjarvis 97f3ddb
add missing s into https of extra requirement
russelljjarvis 4515427
update
russelljjarvis d7ba56e
update
russelljjarvis 1c6941f
neuronunit opt is pip installable, make numba models pip installable
russelljjarvis d80aa5f
edited CI
russelljjarvis f88dc6b
update
russelljjarvis 9d8a8e8
update
russelljjarvis 074d948
ci test
russelljjarvis 2d2f964
update
russelljjarvis 7f95c04
update CI
russelljjarvis bd88a63
update CI
russelljjarvis 50cd426
CI update
russelljjarvis 5b221a6
CI update
russelljjarvis b6528ed
CI update
russelljjarvis 1acec2f
CI update
russelljjarvis 358f7c2
update
russelljjarvis 140efa2
turn off allensdk logging
russelljjarvis a406b2c
update CI
russelljjarvis 4736968
update
russelljjarvis 9f8f253
update CI
russelljjarvis 1643059
update CI
russelljjarvis 1141b08
update CI
russelljjarvis 161a5f4
update CI
russelljjarvis 6154405
update
russelljjarvis 35e0325
update
russelljjarvis 7f5d164
update
russelljjarvis f9fa9ef
update
russelljjarvis 9d782a4
update
russelljjarvis 05f8df9
update
russelljjarvis ead29d2
update
russelljjarvis 8e787c4
update
russelljjarvis 581e8ed
update ci
russelljjarvis 7413e02
update
russelljjarvis aa88f5e
blah
russelljjarvis 8552245
blah
russelljjarvis db3dd29
update
russelljjarvis 1e620dc
tox might work now
russelljjarvis 6bdae3a
update
russelljjarvis afaca14
update
russelljjarvis 8318b23
update
russelljjarvis ba5fc85
update CI
russelljjarvis 79dcba0
update CI
russelljjarvis a300854
try remote machine
russelljjarvis 80a0c8a
update CI
russelljjarvis ca03190
update CI
russelljjarvis b9f5658
update
russelljjarvis 1a73bfc
update
russelljjarvis 28c9165
update
russelljjarvis 3613105
update
russelljjarvis 6cac975
Update main.yml
russelljjarvis 915ba1b
wqMerge branch 'neuronunit_reduced_cells' of https://github.com/russe…
russelljjarvis e1dbace
modified some files with black so that they would pass tox style check
russelljjarvis 8c3a805
update for remote
russelljjarvis 4f0ea68
update
russelljjarvis 7345ee3
update
russelljjarvis 73d85c1
update
russelljjarvis b2cc789
fixed tab/space error in bpo
russelljjarvis File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| defaults: &defaults | ||
| working_directory: ~/markovmodel/PyEMMA | ||
| docker: | ||
| - image: continuumio/miniconda3 | ||
|
|
||
| inst_conda_bld: &inst_conda_bld | ||
| - run: conda config --add channels conda-forge | ||
| - run: conda config --set always_yes true | ||
| - run: conda config --set quiet true | ||
| - run: conda install conda-build | ||
|
|
||
| version: 2 | ||
|
|
||
| jobs: | ||
| build: | ||
| <<: *defaults | ||
| parallelism: 1 | ||
| steps: | ||
| - checkout | ||
| - run: git fetch --unshallow || true | ||
| - run: apt-get update | ||
| - run: sh reduced_cell_install.sh | ||
| #- run: apt-get install -y gcc | ||
| #- run: apt-get install -y libx11-6 python-dev git build-essential | ||
| #- run: apt-get install -y autoconf automake gcc g++ make gfortran | ||
| #- run: apt-get install -y python-tables | ||
| #- run: apt-get install -y libhdf5-serial-dev | ||
|
|
||
| #- run: conda config --add channels conda-forge | ||
| #- run: conda config --set always_yes true | ||
| #- run: conda config --set quiet true | ||
| #- run: conda install conda-build | ||
| #- run: conda install scipy; | ||
| #- run: conda install numpy; | ||
| #- run: conda install numba; | ||
| #- run: conda install dask; | ||
| - run: pip install tables | ||
| - run: pip install pip --upgrade; pip install -r requirements.txt; | ||
| - run: pip install -e .[extra] | ||
| - run: pip install jithub==0.1.0 | ||
| - run: pip install git+https://github.com/russelljjarvis/jit_hub.git@neuronunit | ||
| - run: git clone -b neuronunit https://github.com/russelljjarvis/jit_hub.git | ||
| - run: cd jit_hub; pip install -e .; cd ..; | ||
| - run: git clone -b optimization https://github.com/russelljjarvis/neuronunit | ||
| - run: cd neuronunit; pip install -e .; cd ..; | ||
| - run: pip install neuronunitopt==0.19 | ||
| - run: git clone https://github.com/russelljjarvis/eFEL | ||
| - run: cd eFEL; pip install -e .; cd ..; | ||
| - run: pip install cython | ||
| - run: pip install streamlit; | ||
| - run: pip install seaborn; | ||
| - run: pip install sklearn | ||
| - run: pip install allensdk==0.16.3 | ||
| - run: pip install frozendict | ||
| - run: pip install nose | ||
| - run: pip install pynwb | ||
| #- run: rm -rf /opt/conda/lib/python3.8/site-packages/sciunit | ||
| - run: git clone -b dev https://github.com/russelljjarvis/sciunit.git | ||
| - run: cd sciunit; pip install -e .; cd ..; | ||
| - run: cd bluepyopt/tests; nosetests test_numba_models.py | ||
| - run: cd bluepyopt/tests; nosetests test_evaluators.py | ||
| - run: cd bluepyopt/tests; nosetests test_rheobase_model.py | ||
| - run: pip install --no-binary=h5py h5py | ||
| - run: pip install allensdk==0.16.3 | ||
| - run: pip install tox && tox | ||
| - run: cd bluepyopt/tests; nosetests test_adexp_opt.py | ||
| - run: cd bluepyopt/tests; nosetests test_scores_unit.py | ||
| #- run: cd bluepyopt/tests; nosetests test_izhi_opt.py | ||
|
|
||
| # causes time out | ||
| #- run: cd bluepyopt/tests; python izhi_opt.py | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| defaults: &defaults | ||
| working_directory: ~/markovmodel/PyEMMA | ||
| docker: | ||
| - image: continuumio/miniconda3 | ||
|
|
||
| inst_conda_bld: &inst_conda_bld | ||
| - run: conda config --add channels conda-forge | ||
| - run: conda config --set always_yes true | ||
| - run: conda config --set quiet true | ||
| - run: conda install conda-build | ||
|
|
||
| version: 2 | ||
|
|
||
| jobs: | ||
| build: | ||
| <<: *defaults | ||
| parallelism: 1 | ||
| steps: | ||
| - checkout | ||
| - run: git fetch --unshallow || true | ||
| - run: apt-get install -y cpp gcc | ||
| - run: apt-get install -y libx11-6 python-dev git build-essential | ||
| - run: apt-get install -y autoconf automake gcc g++ make gfortran | ||
| - run: apt-get install -y python-tables | ||
| - run: apt-get install -y libhdf5-serial-dev | ||
|
|
||
| - run: conda config --add channels conda-forge | ||
| - run: conda config --set always_yes true | ||
| - run: conda config --set quiet true | ||
| - run: conda install conda-build | ||
| - run: conda install scipy; | ||
| - run: conda install numpy; | ||
| - run: conda install numba; | ||
| - run: conda install dask; | ||
| - run: pip install tables | ||
| - run: pip install pip --upgrade; pip install -r requirements.txt; | ||
| - run: pip install -e . | ||
| - run: git clone -b neuronunit https://github.com/russelljjarvis/jit_hub.git | ||
|
|
||
| - run: cd jit_hub; pip install -e .; cd ..; | ||
| - run: git clone -b optimization https://github.com/russelljjarvis/neuronunit | ||
| <<<<<<< HEAD | ||
| - run: cd neuronunit; pip install -e .; cd ..; | ||
|
|
||
| #- run: pip install ipfx | ||
| - run: pip install efel | ||
| #- run: git clone https://github.com/russelljjarvis/eFEL | ||
| #- run: cd eFEL; python | ||
|
|
||
| ======= | ||
| - run: cd jit_hub; pip install -e .; cd ..; | ||
| - run: pip install efel | ||
| >>>>>>> 938c5c225d1efef3357ef78b0071a29ea77a0f3c | ||
| - run: pip install cython | ||
| - run: pip install streamlit; | ||
| - run: pip install seaborn; | ||
| - run: pip install sklearn | ||
| - run: pip install allensdk==0.16.3 | ||
| - run: pip install frozendict | ||
| - run: pip install nose | ||
| - run: rm -rf /opt/conda/lib/python3.8/site-packages/sciunit | ||
| - run: git clone -b dev https://github.com/russelljjarvis/sciunit.git | ||
| - run: cd sciunit; pip install -e .; cd ..; | ||
| - run: cd bluepyopt/tests; python rheobase_dtc_test.py | ||
| - run: cd bluepyopt/tests; python adexp_opt.py | ||
| - run: cd bluepyopt/tests; python test_evaluators.py | ||
|
|
||
| # causes time out | ||
| #- run: cd bluepyopt/tests; python izhi_opt.py |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| # .readthedocs.yml | ||
| # Read the Docs configuration file | ||
| # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details | ||
|
|
||
| # Required | ||
| version: 2 | ||
|
|
||
| sphinx: | ||
| configuration: docs/source/conf.py | ||
| fail_on_warning: true | ||
|
|
||
| python: | ||
| install: | ||
| - method: pip | ||
| path: . | ||
| - requirements: requirements_docs.txt |
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
We can leave this file here for now while you're testing your PR. But in the end everything will need to run on Github Actions (using tox).
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yes, that would be awesome. I will write a clear message somewhere here on the PR, when all the items are finished, but I wont leave it hanging. I still might need 2-3 weeks.
There is a big parallel effort to PR into neuronunit proper. I am also trying to make a streamlit application with a heroku/AWS deployment, that you should be able to log into and actively validate this approach without a big install on your end. Not sure if I will ever get there. But the PRs at least will work.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Ok, thanks.