angelolab / ark-analysis / 4876
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Update pixel clustering pipeline (#530)

* Fix random seed

* Change 99.9% normalization and train in batches

* Update notebooks for new 99.9% and batching

* Standardize the tests and ensure PYCODESTYLE checks out

* Fix 99.9% normalization for Docker deployment

* Try forcing R 4.1 installation

* Force yes for all installations

* Change distribution of R to Xenial

* Run update command after setting the R repo

* Add another update command

* Cat sources file to see if there are offending R deb lines

* Try running upgrade on top of update

* Need to force 'Y' for all upgrade prompts

* Add a few more download dependencies

* Change installations

* Update installations again

* Add dependency

* Swap lsb_release line

* Change lsb_release line

* Need to use bullseye Linux distro install

* Comment Dockerfile

* Remove an offending list command

* Change path to Debian (bullseye) and keyserver

* Try specifying Ubuntu 16.04

* Add add-apt-repository requirement

* Force yes to install

* Add dependencies

* Allow unauthenticated install param for gcc and r-base

* Add Python installation

* Try swapping the Python install

* Revert back to previous Dockerfile and update pixel notebook

* Redirect stdout to /dev/null, but keep stderr printed

* Force docker build command to wait 60 minutes

* Remove initial travis_wait command

* Try increasing time to 60 minutes

* Remove batching for now

* Fix tab issues

* Fix quantile computation, and remove batch arg from testing

* Fix quantiles (again)

* Try removing 1.75 BH download and convert to 1.78

* Need to install cmake

* Add more time for deployment

* Don't automatically deploy on PR anymore

* Remove print commands from Dockerfile

Co-authored-by: alex-l-kong <alkong@ucdavis.edu>
Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>

2382 of 2600 relevant lines covered (91.62%)

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Jobs
ID Job ID Ran Files Coverage
1 4876.1 (MPLBACKEND=Agg) 0
91.62
 Travis Job 4876.1
Source Files on build 4876
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