Added support for .clustering output and central config through ClusteringParameters

jgriss commented 3 years ago

Key changes:

.clustering as additional output format
CusteringParameters is used throughout all classes as the only source for configuration parameters
Minor bugfixes

Still missing:

GitHub Actions still fail in building the project - any help would be highly appreciated

ypriverol commented 3 years ago

@jgriss the test is failing, should i merge without it ?

jgriss commented 3 years ago

Hi @ypriverol

Do you mean the tests run on your local machine or the ones in the GitHub Action?

GitHub action tests currently fail since it can't find all dependencies. But the tests (if they run) should all work.

Here's the exact error message

It can't find cpdetector 1.0.7

Apparently it's not available on sonatepy.org but it is in the EBI repo. Not sure why it doesn't try to get it form there.

(https://oss.sonatype.org/service/local/staging/deploy/maven2): Authentication failed for https://oss.sonatype.org/service/local/staging/deploy/maven2/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.jar 401 Unauthorized -> [Help 1]

spectra-cluster / spectra-cluster-2

Added support for .clustering output and central config through ClusteringParameters #109