Deploy to PyPI on release

.travis.yml

@@ -1,39 +1,31 @@
-notifications: # set notification options
-  email:
-    recipients:
-      - mgopez95@gmail.com
-      - peter.kruczkiewicz@gmail.com
-
-    # change is when the repo status goes from pass to fail or vice versa
-    on_success: change
-    on_failure: change
-
 language: python
 python:
-  - '3.6'
+- '3.6'
 os:
-  - linux
-#  - osx
-
-# Whitelist of branches to run CI Testing on.
+- linux
 branches:
   only:
-    - master
-    - development
-
-# Blacklist of branches to not run CI testing on.
-# branches:
-#  except:
-#   - dontrunme 
-#   - test 
-
-before_install:
-  - sudo apt-get -qq update;
-
-install:
-  - python setup.py install
-  #Install pytest for testing.
-  - pip install pytest
-
-script:
-  - pytest
+  - master
+  - development
+install: pip install -U tox-travis
+script: tox
+deploy:
+  provider: pypi
+  distributions: sdist bdist_wheel
+  user: peterk87
+  deployment: bio-hansel
+  password:
+    secure: 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
+  on:
+    tags: true
+    repo: phac-nml/bio_hansel
+    python: 3.6
+notifications:
+  email:
+    recipients:
+    - mgopez95@gmail.com
+    - peter.kruczkiewicz@gmail.com
+    - darian.hole@canada.ca
+    - philip.mabon@canada.ca
+    on_success: change
+    on_failure: change

bio_hansel/__init__.py

@@ -1,9 +1,9 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '2.2.0'
+__version__ = '2.3.0'
 program_name = 'bio_hansel'
 program_summary = 'Subtype microbial genomes using SNV targeting k-mer subtyping schemes.'
 program_desc = program_summary + '''
-Includes schemes for Salmonella enterica spp. enterica serovar Heidelberg, Enteritidis, and Typhi subtyping. Also includes a Mycobacterium Tuberculosis scheme. 
+Includes schemes for Salmonella enterica spp. enterica serovar Heidelberg, Enteritidis, Typhi, and Typhimurium subtyping. Also includes a Mycobacterium Tuberculosis scheme. 
 Developed by Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, David Son, Darian Hole, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.
 '''

bio_hansel/const.py

@@ -13,13 +13,13 @@
                                  'version': '1.0.7',
                                  'subtyping_params': SubtypingParams(low_coverage_depth_freq=50)},
                  'typhi': {'file': resource_filename(program_name, 'data/typhi/kmers.fasta'),
-                                 'version': '1.1.0',
+                                 'version': '1.2.0',
                                  'subtyping_params': SubtypingParams(low_coverage_depth_freq=20)},
-                 'tb_speciation': {'file': resource_filename(program_name, 'data/m.tuberculosis/kmers.fasta'),
-                                 'version': '1.0.1;',
+                 'tb_speciation': {'file': resource_filename(program_name, 'data/tb_speciation/kmers.fasta'),
+                                 'version': '1.0.5',
                                  'subtyping_params': SubtypingParams(low_coverage_depth_freq=20)},
                  'typhimurium': {'file': resource_filename(program_name, 'data/typhimurium/kmers.fasta'),
-                                 'version': '0.5.5;',
+                                 'version': '0.5.5',
                                  'subtyping_params': SubtypingParams(low_coverage_depth_freq=20)}}
 
 

bio_hansel/data/m.tuberculosis/kmers.fasta → bio_hansel/data/tb_speciation/kmers.fasta

@@ -22,13 +22,13 @@ CGACATCCTCGATACGGGCCCCCTCGCGGATTG
 ACGCGTCCTTCGGGAAATGCGCTGGGACCCAAT
 >negative1491275-1.1.3
 ACGCGTCCTTCGGGAAGTGCGCTGGGACCCAAT
->3479545-1.2.1
+>3479545-1.2
 ACCGCAGTTTCAGTCGCAGCCTTGACTATCTAC
->negative3479545-1.2.1
-CCGCAGTTTCAGTCGCCGCCTTGACTATCTACG
->3470377-1.2.2
+>negative3479545-1.2
+ACCGCAGTTTCAGTCGCCGCCTTGACTATCTAC
+>3470377-1.3
 TGGCATCGTCATAGGCTTGCTGGCGGTTAAGGA
->negative3470377-1.2.2
+>negative3470377-1.3
 TGGCATCGTCATAGGCCTGCTGGCGGTTAAGGA
 >497491-2
 AGGGCTGGTCGGCCATATCGGGCCCGACGATAT
@@ -62,26 +62,26 @@ ACCGGGAACAGTATTCGGATCCGGAAAAGCCGA
 CGAGGATCGAGCTAGCAGATATTGCGCTGCGCC
 >negative3273107-3
 CGAGGATCGAGCTAGCCGATATTGCGCTGCGCC
->1084911-3.1.1
+>1084911-3.1
 TGTTCATCTCCAGGAAATAGAACTCACCTTCCC
->negative1084911-3.1.1
+>negative1084911-3.1
 TGTTCATCTCCAGGAAGTAGAACTCACCTTCCC
->3722702-3.1.2
+>3722702-3.2
 GCTGCGCCCCGGCGGCCAGCACGGCCTCCAGCT
->negative3722702-3.1.2
+>negative3722702-3.2
 GCTGCGCCCCGGCGGCGAGCACGGCCTCCAGCT
->1237818-3.1.2.1
+>1237818-3.2.1
 CGCCGGCAGCCGTGCCGAGCATCAGCGGGAAAC
->negative1237818-3.1.2.1
+>negative1237818-3.2.1
 CGCCGGCAGCCGTGCCCAGCATCAGCGGGAAAC
->2874344-3.1.2.2
+>2874344-3.2.2
 CGTAGGCCTCCACCCGACGCACCCCGGAGCCGA
->negative2874344-3.1.2.2
+>negative2874344-3.2.2
 CGTAGGCCTCCACCCGGCGCACCCCGGAGCCGA
 >931123-4
 GGCGCATCGCCAACTATGAGGAGCTCGCCGCAC
 >negative931123-4
-GGCGCATCGCCAACTAGGAGGAGCTCGCCGCAC
+GGCGCATCGCCAACTACGAGGAGCTCGCCGCAC
 >62657-4.1
 TGTGGAAGCATTCCCCAAGCCGGTCAAGGCCGC
 >negative62657-4.1
@@ -245,5 +245,4 @@ CCCGCACGTAGCCCTTACCGAGGTCTCGGACGG
 >1882180-8
 CCGGTGTTATCCATGCTGGCTATGGGGGCCAGC
 >negative1882180-8
-CCGGTGTTATCCATGCCGGCTATGGGGGCCAGC
-
+CCGGTGTTATCCATGCCGGCTATGGGGGCCAGC

bio_hansel/data/tb_speciation/metadata.tsv

@@ -0,0 +1,61 @@
+subtype	Coll_et_al_genotype
+1	1
+1.1	1.1
+2.1	2.1
+3	3
+4	4
+4.1	4.1
+4.2	4.2
+4.3	4.3
+4.4	4.4
+4.5	4.5
+4.6	4.6
+4.7	4.7
+4.8	4.8
+4.9	4.9
+5	5
+7	7
+8	bov_afr
+8.1	bov
+8.2	6 
+1.1.1	1.1.1
+1.1.1.1	1.1.1.1
+1.1.2	1.1.2
+1.1.3	1.1.3
+1.2	1.2.1
+1.3	1.2.2
+2.2.1	2.2.1
+2.2.1.1	2.2.1.1
+2.2.1.2	2.2.1.2
+2.2.2	2.2.2
+3.1	3.1.1
+3.2	3.1.2
+3.2.1	3.1.2.1
+3.2.2	3.1.2.2
+4.1.1	4.1.1
+4.1.1.1	4.1.1.1
+4.1.1.2	4.1.1.2
+4.1.1.3	4.1.1.3
+4.1.2	4.1.2
+4.1.2.1	4.1.2.1
+4.2.1	4.2.1
+4.2.2	4.2.2
+4.2.2.1	4.2.2.1
+4.3.1	4.3.1
+4.3.2	4.3.2
+4.3.2.1	4.3.2.1
+4.3.3	4.3.3
+4.3.4	4.3.4
+4.3.4.1	4.3.4.1
+4.3.4.2	4.3.4.2
+4.3.4.2.1	4.3.4.2.1
+4.4.1	4.4.1
+4.4.1.1	4.4.1.1
+4.4.1.2	4.4.1.2
+4.4.2	4.4.2
+4.6.1	4.6.1
+4.6.1.1	4.6.1.1
+4.6.1.2	4.6.1.2
+4.6.2	4.6.2
+4.6.2.1	4.6.2.1
+4.6.2.2	4.6.2.2

bio_hansel/data/typhi/kmers.fasta

@@ -1,10 +1,10 @@
 >655112-0.1
 GGCTCCATCCTTAGACTTGGTCGGTAAAATCTA
->773487-0.0.1
+>773487-0.4
 TCTATGGATTTGTTGTAGTGTGGGGTGTGTAAT
->1804415-0.0.2
+>1804415-0.2
 TTATTACCTATAAAGGCGAACAAGGCGCGAAAG
->1840727-0.0.3
+>1840727-0.3
 GGTTACGCGGTACGCAAAGTAACGCCTGGCGCG
 >3640678-0.1.1
 ACACGCCGGTGGAAGTACTGCATTCCGGGCTAA
@@ -14,25 +14,25 @@ ATGGCAGGTAGCCCAATTGGCGCGCCATCCGCA
 ACACGGGAATGTCGATAGTAAAGGCGTCGCCAT
 >316489-0
 GCAGCCTGCCGCTGACCCCCTTTTTCTGGGGAT
->4105384-1.1
+>4105384-1
 GATTTTTTTGCAACTGTTGCGATACGGCGCGAT
->555826-1.1.1
+>555826-1.1
 AATTTAAGTTAATTACAGGTCCTTCTGGCTGCG
->2360997-1.1.2
+>2360997-1.2
 CACTGAAGGCTTTACCTAGCGCTCTGGCATCTT
->4664137-1.1.3
+>4664137-1.3
 AAGTCACCTGCGCGCCTTGGTCGAACGCGGCGA
->2166082-1.1.4
+>2166082-1.4
 GCAATTCGCGGTAAAGAGTACTGGCAATAAGAC
->30192-1.2
+>30192-3
 CGGGCGACGGTTCCGCTTGGCAACCTTTTGCTA
->4288272-1.2.1
+>4288272-3.1
 CGGAACAGTATCTGGGTGCGAATTACTTTCCGG
 >2737027-2
 ACGAATATGGGTTGCAAGACGTCCTGGATTGTA
->1215983-2.0.1
+>1215983-2.6
 CGTTGTGGGAGCAGGGGGATGAGCAGGCGCACG
->4132985-2.0.2
+>4132985-2.7
 CCAACCAGGTCTTTGCAGAAGTGTTACGCGGCA
 >146673-2.1
 TACGTATGCAGGTACCAGCGCGGGTGGTGGCGT
@@ -74,7 +74,7 @@ AGGCTGCGGCACAGAGTAAATGCAGAGCATGGT
 TTGCCACCCTTGTCACTGCCAGCGCTTTCGCTG
 >3092900-2.2.3.4
 GCTGACCTTGCAGATATGCTTCGTTTTCTTTGT
->2723724-2.2.3.3.1
+>2723724-2.2.3.5
 TTAATACACCGAACGGGCATCTGGTCGCCAGCG
 >3437570-2.4
 AGACATCTGGCGGCGTCAGCAGCATCCCCACAA
@@ -86,9 +86,9 @@ TATTCACCAGCACCGGTGCCAGACTGGCGTCAT
 CGCCAAACAGCACAAATGGCAGGTCATTTGCCA
 >3062270-2.3
 TTTCTTGATCGCTTCATGCATGGTCAGTTTTTC
->1799842-2.3.0.1
+>1799842-2.3.7
 ATATGCTGCAACTGAACCTGGATAACCCAATCG
->432732-2.3.0.2
+>432732-2.3.8
 CCGGCAAGCCGTTGAGTGAAGAGGTTCGGGAAG
 >3069182-2.3.1
 TACGTGCTTTATTGTGGATATCCATGTTCTTCC
@@ -136,11 +136,11 @@ GGCAGGCGCGATTGCAACAACGTAAATTGCGCT
 TTGATGGCTTCATTACTATTACCGGCGGGAAGC
 >negative655112-0.1
 GGCTCCATCCTTAGACCTGGTCGGTAAAATCTA
->negative773487-0.0.1
+>negative773487-0.4
 TCTATGGATTTGTTGTGGTGTGGGGTGTGTAAT
->negative1804415-0.0.2
+>negative1804415-0.2
 TTATTACCTATAAAGGTGAACAAGGCGCGAAAG
->negative1840727-0.0.3
+>negative1840727-0.3
 GGTTACGCGGTACGCAGAGTAACGCCTGGCGCG
 >negative3640678-0.1.1
 ACACGCCGGTGGAAGTGCTGCATTCCGGGCTAA
@@ -150,25 +150,25 @@ ATGGCAGGTAGCCCAACTGGCGCGCCATCCGCA
 ACACGGGAATGTCGATGGTAAAGGCGTCGCCAT
 >negative316489-0
 GCAGCCTGCCGCTGACTCCCTTTTTCTGGGGAT
->negative4105384-1.1
+>negative4105384-1
 GATTTTTTTGCAACTGCTGCGATACGGCGCGAT
->negative555826-1.1.1
+>negative555826-1.1
 AATTTAAGTTAATTACCGGTCCTTCTGGCTGCG
->negative2360997-1.1.2
+>negative2360997-1.2
 CACTGAAGGCTTTACCCAGCGCTCTGGCATCTT
->negative4664137-1.1.3
+>negative4664137-1.3
 AAGTCACCTGCGCGCCCTGGTCGAACGCGGCGA
->negative2166082-1.1.4
+>negative2166082-1.4
 GCAATTCGCGGTAAAGGGTACTGGCAATAAGAC
->negative30192-1.2
+>negative30192-3
 CGGGCGACGGTTCCGCCTGGCAACCTTTTGCTA
->negative4288272-1.2.1
+>negative4288272-3.1
 CGGAACAGTATCTGGGCGCGAATTACTTTCCGG
 >negative2737027-2
 ACGAATATGGGTTGCAGGACGTCCTGGATTGTA
->negative1215983-2.0.1
+>negative1215983-2.6
 CGTTGTGGGAGCAGGGTGATGAGCAGGCGCACG
->negative4132985-2.0.2
+>negative4132985-2.7
 CCAACCAGGTCTTTGCGGAAGTGTTACGCGGCA
 >negative146673-2.1
 TACGTATGCAGGTACCGGCGCGGGTGGTGGCGT
@@ -210,7 +210,7 @@ AGGCTGCGGCACAGAGCAAATGCAGAGCATGGT
 TTGCCACCCTTGTCACCGCCAGCGCTTTCGCTG
 >negative3092900-2.2.3.4
 GCTGACCTTGCAGATACGCTTCGTTTTCTTTGT
->negative2723724-2.2.3.3.1
+>negative2723724-2.2.3.5
 TTAATACACCGAACGGACATCTGGTCGCCAGCG
 >negative3437570-2.4
 AGACATCTGGCGGCGTAAGCAGCATCCCCACAA
@@ -222,9 +222,9 @@ TATTCACCAGCACCGGCGCCAGACTGGCGTCAT
 CGCCAAACAGCACAAACGGCAGGTCATTTGCCA
 >negative3062270-2.3
 TTTCTTGATCGCTTCACGCATGGTCAGTTTTTC
->negative1799842-2.3.0.1
+>negative1799842-2.3.7
 ATATGCTGCAACTGAATCTGGATAACCCAATCG
->negative432732-2.3.0.2
+>negative432732-2.3.8
 CCGGCAAGCCGTTGAGCGAAGAGGTTCGGGAAG
 >negative3069182-2.3.1
 TACGTGCTTTATTGTGAATATCCATGTTCTTCC