Merge pull request #81 from grosenberger/master

[FIX] Minor patches & Release 2.1.5

Author: grosenberger

.travis.yml

@@ -5,6 +5,7 @@ python:
   - "3.5"
   - "3.6"
   - "3.7"
+  - "3.8"
 before_install:
  - sudo apt-get update
 install:
@@ -25,4 +26,5 @@ script:
   - if [[ $TRAVIS_PYTHON_VERSION == 3.5* ]]; then py.test tests/; fi
   - if [[ $TRAVIS_PYTHON_VERSION == 3.6* ]]; then py.test tests/; fi
   - if [[ $TRAVIS_PYTHON_VERSION == 3.7* ]]; then py.test tests/; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.8* ]]; then py.test tests/; fi
 cache: pip

setup.py

@@ -12,7 +12,7 @@
     long_description = f.read()
 
 setup(name='pyprophet',
-      version="2.1.4",
+      version="2.1.5",
       author="The PyProphet Developers",
       author_email="[email protected]",
       description="PyProphet: Semi-supervised learning and scoring of OpenSWATH results.",

tests/_regtest_outputs/test_pyprophet_export.test_compound_1.out

@@ -10,5 +10,5 @@
 97    M+H+       1   8140.1400  145.778               6678.0           18505.5670   146.160  146.1603       Acephate   2.8313      0    -0.382   -0.3823  /Users/alka/Documents/work/projects/OpenSWATH_...   726467501366503692    143.249   0.0045  184.0192                1     149.010  2408145804652532658  C4H10NO3PS                   27
 98    M+H+       1   1688.6600  144.121               1632.0            4300.0667   146.160  146.1601       Acephate   2.5718      0    -2.039   -2.0391  /Users/alka/Documents/work/projects/OpenSWATH_...   829341238503978341    141.603   0.0072  184.0192                1     147.363  1007350642398073598  C4H10NO3PS                   27
 99    M+H+       1    907.0830  145.815                738.0            1741.9189   146.160  146.1597       Acephate   1.8453      0    -0.345   -0.3447  /Users/alka/Documents/work/projects/OpenSWATH_...  4292801597472146447    143.249   0.0263  184.0192                1     149.009   214379053049545951  C4H10NO3PS                   27
-   
+
 [100 rows x 23 columns]

tests/_regtest_outputs/test_pyprophet_score.test_osw_5.out

@@ -1,14 +1,14 @@
              feature_id  ms1_precursor_pep  ms2_peakgroup_pep  ms2_precursor_pep
-0  -4409520928686189639             0.0036             0.0037             0.0042
-1  -7771919224870429764             0.0036             0.0037             0.0042
-2   -797725006165535344             0.0036             0.0037             0.0042
-3  -1732939685941081620             0.0036             0.0037             0.0042
-4  -6747816958328369759             0.0036             0.0037             0.0042
+0  -4409520928686189639             0.0066             0.0043             0.0033
+1  -7771919224870429764             0.0066             0.0043             0.0033
+2   -797725006165535344             0.0066             0.0043             0.0033
+3  -1732939685941081620             0.0066             0.0043             0.0033
+4  -6747816958328369759             0.0066             0.0043             0.0033
 ..                  ...                ...                ...                ...
-95  1161581412877623390             0.0036             0.0037             1.0000
-96 -5977524328878179832             0.0036             0.0037             0.0042
-97 -6034887541083502974             0.0036             0.0037             0.0042
-98   483971408708572459             0.0036             0.0037             0.9977
-99  5086440667566053402             0.0036             0.0037             0.0042
+95 -6764315401363298084             0.0066             0.0043             0.0033
+96  1161581412877623390             0.0066             0.0043             0.6030
+97 -5977524328878179832             0.0066             0.0043             0.0033
+98 -6034887541083502974             0.0066             0.0043             0.0033
+99   483971408708572459             0.0066             0.0043             0.9915
 
 [100 rows x 4 columns]

tests/test_ipf.py

@@ -6,7 +6,7 @@
 import pandas as pd
 import numpy as np
 
-from pandas.util.testing import assert_frame_equal
+from pandas.testing import assert_frame_equal
 from numpy.testing import assert_almost_equal
 
 pd.options.display.expand_frame_repr = False