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v1.2.0 #76

Merged
merged 71 commits into from
Jun 5, 2020
Merged

v1.2.0 #76

merged 71 commits into from
Jun 5, 2020

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apriha
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@apriha apriha commented Jun 5, 2020

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apriha and others added 30 commits February 24, 2020 21:11
@apriha
Merge branch 'master' into develop
0f2f5df
@willgdjones
gVCF parser fix
a14496c
@apriha
Move SNPs tests to test_snps.py
547c32b
@apriha
Remove redundant tests
ce444ed
@apriha
Consolidate parsing tests
631eed0
@apriha
Consolidate I/O tests
02dd14c
add generic support
844987f
add support for multi rsids
33d99e0
add clarifying comment
67201c4
add non standard columns test case
0651ed6
add back pos
7872e91
@apriha
Try parsing with C engine
47ebf77
@apriha
Find multiple rsids as part of dict comp
d475762
@apriha
Merge pull request #69 from apriha/feature/add-generic-support
c3f7263 
Feature/add generic support
@apriha
Copy io.py as new files in io subpackage
30b6818 
https://stackoverflow.com/a/33992444
@apriha
Refactor Reader and Writer into separate files
221fd5c 
https://stackoverflow.com/a/33992444
@apriha
Move Reader and Writer tests to io subpackage
d00752a
@apriha
Rename Reader tests
320b9c2
@apriha
Add compression functions to utils.py
d4eb982
@apriha
Merge branch 'develop' into refactor-tests
0cfda15 
# Conflicts:
#	tests/test_snps_collection.py
@apriha
Move tests to test_reader.py
2426475
@apriha
Refactor VCF tests
e5ff1a3
@apriha
Remove redundant tests
3e55ffc
@apriha
Rearrange tests
72f95f5
@apriha
Test phased property when running parsing tests
5008953
@apriha
Use temp directories for dynamically generated files
cd879e5
@apriha
Test reading compressed input files
fe6aa26
@apriha
Refactor Writer tests
dc854b3
@apriha
Move test to test_resources.py
277f039
@apriha
Rearrange tests
8cdc7f9
apriha added 28 commits May 16, 2020 23:07
@apriha
Rearrange imports
b167362
@apriha
Read Ancestry files with multiple separator tabs
b1af52e 
https://stackoverflow.com/a/41320761
https://stackoverflow.com/a/30368735
https://stackoverflow.com/a/52463661
https://docs.python.org/3/library/warnings.html#warning-filter
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.errors.DtypeWarning.html
@apriha
Read FTDNA files with a second header
0e2c176 
https://www.python.org/dev/peps/pep-3132/
@apriha
Parse VCF bytes
3e9a387
@apriha
Parse compressed files without file extension
2a8e365
@apriha
Read FTDNA concatenated gzip files with extra data
57a0bdc
@apriha
Add SNPs to detect_build
511c040
@apriha
Read Ancestry files with multiple separators
d6d1c45
@apriha
Add scripts to parse openSNP files
39a6a91
@apriha
Handle socket timeout when downloading file
6fa9090 
https://docs.python.org/3/library/unittest.mock-examples.html
@apriha
Add test for URL error
1fa41e8 
https://docs.python.org/3/library/unittest.mock-examples.html
@apriha
Add downloads_enabled property
69c292d
@apriha
Mock responses for test_build_detected_PAR_snps
b5344e9
@apriha
Update references
8d4ef63
@apriha
Mock data for test_remap_snps_37_to_38_with_PAR_SNP
fc99001
@apriha
Mock data for remapping SNPs
7c03623
@apriha
Update dataframe assertions to check exact equality
6200419
@apriha
Consolidate expected dataframes
91e5db4
@apriha
Mock resource downloads
a7d0a21
@apriha
Consolidate PAR data
58c3ab7
@apriha
Limit downloads to selected job
63a415f
@apriha
Create environment variable
4a5d318
@apriha
Merge pull request #75 from apriha/perform-minimal-downloads-during-t…
71a8881 
…ests

Perform minimal downloads during tests
@apriha
Merge branch 'develop' into enhance-file-parsing
22bbdad 
# Conflicts:
#	tests/__init__.py
@apriha
Specify sep as raw string
5ea82b7 
pallets/jinja#646 (comment)
@apriha
Merge branch 'develop' into handle-download-exceptions
a5abca7 
# Conflicts:
#	tests/test_resources.py
@apriha
Merge pull request #74 from apriha/handle-download-exceptions
621ad0e 
Handle download exceptions
@apriha
Merge pull request #72 from apriha/enhance-file-parsing
5a1a6bf 
Enhance file parsing and build detection
@codecov-commenter
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Codecov Report

Merging #76 into master will increase coverage by 0.64%.
The diff coverage is 92.77%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #76      +/-   ##
==========================================
+ Coverage   92.47%   93.12%   +0.64%     
==========================================
  Files           5        9       +4     
  Lines        1236     1352     +116     
  Branches      222      244      +22     
==========================================
+ Hits         1143     1259     +116     
  Misses         48       48              
  Partials       45       45
Impacted Files Coverage Δ
src/snps/io/writer.py 85.84% <85.84%> (ø)
src/snps/snps_collection.py 92.50% <92.50%> (ø)
src/snps/snps.py 93.03% <93.03%> (ø)
src/snps/io/reader.py 97.05% <97.24%> (ø)
src/snps/__init__.py 100.00% <100.00%> (+7.24%) ⬆️
src/snps/io/__init__.py 100.00% <100.00%> (ø)
src/snps/resources.py 95.07% <100.00%> (+0.48%) ⬆️
src/snps/utils.py 90.12% <100.00%> (+2.06%) ⬆️
... and 3 more

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@apriha apriha merged commit 3ef1699 into master Jun 5, 2020
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3 participants
@apriha @codecov-commenter @willgdjones