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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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Updated repo to work with Python3. Included support for direct virtua… #34

Closed sammeier closed 7 years ago

sammeier commented 7 years ago

…lenvs.

noblem commented 7 years ago

This looks nice, and the standard "make test" does indeed pass. But if you change into the tests directory and type "make test_all" it fails the dicing test for Python 3 (see below); while the same test_all runs to completion on Python2. BTW, I put a few Makefile commits onto this py3 branch, so you'll want to pull first before any more testing.

Test dice: on subset of cohorts, to show CLI args override config file set -o pipefail && /usr/local/bin/python3 ../gdctools/gdc_dice.py --config tcgaSmoketest.cfg --projects TCGA-ACC TCGA-SKCM -- latest 2>&1 | tee test_dice.log | grep "Dicing TCGA" make: *** [test_dice] Error 1

/tmp/gdctools.py3/tests(wm964-18a-gce-gce) cat test_dice.log 2017-03-31 18:43:13,334[INFO]: GDC Dicer Version: 0.5.1 (GDCtools: 0.1.7) 2017-03-31 18:43:13,334[INFO]: Command: ../gdctools/gdc_dice.py --config tcgaSmoketest.cfg --projects TCGA-ACC TCGA-SKCM -- latest 2017-03-31 18:43:13,334[ERROR]: Dicing FAILED: Traceback (most recent call last): File "../gdctools/gdc_dice.py", line 244, in execute self.dice() File "../gdctools/gdc_dice.py", line 88, in dice cohort_agg_dict = self.cohort_aggregates() File "../gdctools/gdc_dice.py", line 252, in cohort_aggregates for k, v in self.config.aggregates.iteritems(): TypeError: 'NoneType' object is not callable

noblem commented 7 years ago

This is just about ready to pull the trigger for merge to master: Sam, can you do one last test?