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Remove database generation from main function #21
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…s global. DB paths separated into two separate ini files
All unit tests pass as well as output regression tests. Documentation updated and all changed files have been reviewed. |
Attaching zips of output directory used for output regression test. |
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This pull request and branch is an offshoot of Refactor ini files to be arguments, instead focusing on refactoring the use of the config.ini file instead of both config.ini and colnames.ini. The interpreter version number was increased to 0.7.0 for this pull request.
Additions:
databases
andpreclinical
sections ofconfig.ini
were refactored into their own ini files,annotation-databases.ini
andpreclinical-databases.ini
, respectively.config.ini
andannotation-databases.ini
are now required input arguments tomoalmanac.py
andsimplified_input.py
, andpreclinical-databases.ini
is optional.Revisions:
moalmanac/datasources/
was moved to the root directory of the repository,datasources/
.moalmanac/moalmanac.py
was updated to accept the config and datasource dictionaries as arguments. As a result of removingconfig.ini
as a global variable, many functions throughout the codebase now require the config ini to be passed as an argument.moalmanac/README.md
was updated to reflect the changes to the ini files.config.py
toreader.py
.moalmanac/test/datasources_tests.py
,moalmanac/test/evaluator_tests.py
,moalmanac/test/features_tests.py
, andmoalmanac/test/investigator_tests.py
.Secondary changes:
moalmanac/run_deconstructSigs.R
andmoalmanac/wrapper_deconstructSigs.sh
from repository.run_example.py
was revised to add the date in ISO format to the default output directoryPre-pull request check list,