Kacper_Domzal#7

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KacDom wants to merge 9879 commits intobarwil:masterfrom

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Commits on Jan 22, 2020

Remove python 2 assertion

Andrey Raspopov
authored and
peterjc
committed

Commits on Jan 23, 2020

Remove python 2 crutch for cmp

Harmitage
authored and
peterjc
committed
black, version 19.10b, Bio/Blast/Applications.py

black
authored and
peterjc
committed
post-black string concatenation
peterjc
committed
Fix triple quotes in Bio/Blast/Applications.py
peterjc
committed

Commits on Jan 24, 2020

Apply black to Test/test_PDB* (#2571)

svalqui
authored and
peterjc
committed
updates Bio.Graphics for pyton3 (#2560)
mdehoon
authored
Add support for passing sets to Entrez.efetch()

austinv11
authored and
peterjc
committed
More generically support iterables in Entrez.efetch

austinv11
authored and
peterjc
committed
Raise TypeError when ids is not an int

austinv11
authored and
peterjc
committed
Thank Austin in NEWS file
peterjc
committed
Quote fix
peterjc
committed
TravisCI: Mark s390x as an allowed fail.
peterjc
committed
black, version 19.10b, does tuple assignment

black
authored and
peterjc
committed
black, version 19.10b, for recent edits

black
authored and
peterjc
committed
Missing space on string concatenation
peterjc
committed
Avoid triple-quote string; suggest f-string
peterjc
committed
More black on top of recent edits

black
authored and
peterjc
committed
black, version 19.10b0, on Bio.Graphics

black
authored and
peterjc
committed
Fix sort order (my mistake in rebasing)
peterjc
committed

Commits on Jan 26, 2020

update Bio.PopGen for python3 (#2578)
mdehoon
authored
change all "r" args

chris-rands
authored and
peterjc
committed
gzip and bgzf stuff

chris-rands
authored and
peterjc
committed
typo

chris-rands
authored and
peterjc
committed
revert changes

chris-rands
authored and
peterjc
committed
Add pygments python file to .gitignore

hwalinga
authored and
peterjc
committed
Kwargs in pairwise aligner constructor (#2569)

hwalinga
authored and
peterjc
committed

Commits on Jan 27, 2020

Commits on Jan 28, 2020

_ -> \_ fixes interruption when running make

bganglia
authored and
peterjc
committed
Remove obsolete comment
peterjc
authored
update Exceptions in Bio.Seq to python3

mdehoon
authored and
peterjc
committed
update Exceptions in Bio.SeqFeature for python3

mdehoon
authored and
peterjc
committed
Bio.GenBank: Remove error-hiding __gettattr__ method (#2528)

kblin
authored and
peterjc
committed
Bio.Genbank: Add molecule_type handler to _RecordConsumer

kblin
authored and
peterjc
committed
Bio.GenBank: Fix a _FeatureConsumer typo masked by blanked __getattr___ pass

kblin
authored and
peterjc
committed
Bio.Genbank: Add topology handler to _RecordConsumer

kblin
authored and
peterjc
committed
Bio.GenBank: Silence a false flake8 warning

kblin
authored and
peterjc
committed
Disable black on Bio/pairwise2.py temporarily
peterjc
committed
Refresh black on recent edits

black
authored and
peterjc
committed
flake8: enforce black on Bio/
peterjc
committed

Commits on Jan 29, 2020

black on long comment line

black
authored and
peterjc
committed
Apply black style to test_SeqIO_Gck.py and test_SeqIO_SnapGene.py, version 19.10b0.

svalqui
authored and
peterjc
committed
REBASE Jan 2020
peterjc
committed
updated and ran ranacompiler.py

mdehoon
authored and
peterjc
committed
Most of Restriction_Dictionary.py follows black style now
peterjc
committed
Remove obsolete comment and reference to deleted file
peterjc
committed
python3 updates Bio.SeqIO.AbiIO (#2591)
mdehoon
authored
updated Bio.SearchIO for python3 + some cleanup

mdehoon
authored and
peterjc
committed
updated Bio.Restriction for python3 (#2581)
mdehoon
authored
updating Bio.Sequencing for python3 (#2594)
mdehoon
authored

Commits on Jan 30, 2020

Commits on Feb 1, 2020

Commits on Feb 2, 2020

Seqio igio python3 (#2606)
mdehoon
authored
Apply black style to test_SeqIO_AbiIO.py, version 19.10b0.

svalqui
authored and
peterjc
committed

Commits on Feb 3, 2020

Commits on Feb 4, 2020

Apply black style, version 19.10b0. test_SeqIO_convert.py and test_SeqIO_FastaIO.py

svalqui
authored and
peterjc
committed
TravisCI also runs doc8 on the RST files
peterjc
authored
SnapGene cleanup (#2621)
mdehoon
authored

Commits on Feb 5, 2020

Commits on Feb 6, 2020

Commits on Feb 8, 2020

Commits on Feb 9, 2020

trivial update in Bio.Sequencing.Phd and Bio.SwissProt for python3 (#2652)
mdehoon
authored
Sequtils checksum python3 (#2651)
mdehoon
authored
test updates for python3 (#2655)
mdehoon
authored
updates to tools tests for python3 (#2657)
mdehoon
authored
update test_Cluster.py for python3 (#2658)
mdehoon
authored
updates to test_Compass.py for python3 (#2660)
mdehoon
authored
remove Jython stuff from Entrez tests (#2662)
mdehoon
authored
use with in test_Enzyme (#2663)
mdehoon
authored
use with statement (#2664)
mdehoon
authored
use with (#2666)
mdehoon
authored
use with to open files in test_KEGG_online.py (#2667)
mdehoon
authored
BioSQL updates for python3 (#2654)
mdehoon
authored
trivial update in Bio.TogoWS for python3 (#2653)
mdehoon
authored
update test_NCBI_qblast.py for python3

mdehoon
authored and
peterjc
committed
update learning tests for python3

mdehoon
authored and
peterjc
committed
Apply black style to test_seq* files, version 19.10b0.

svalqui
authored and
peterjc
committed
Rewrite assertEqual to match style of the other assertEqual.

svalqui
authored and
peterjc
committed
Style cosmetics, adjust line length for better look.

svalqui
authored and
peterjc
committed
Style cosmetics, removed comments as they do not align with black style.

svalqui
authored and
peterjc
committed

Commits on Feb 10, 2020

fix Emboss tests for python3, and one more mutli test in FastaIO (#2661)
mdehoon
authored
updates to Bio.Graphics tests for python3 (#2659)
mdehoon
authored
python3 updates to PDB tests

mdehoon
authored and
peterjc
committed
python3 updates to test_AlignIO_MauveIO

mdehoon
authored and
peterjc
committed
updating phylo tests for python3

mdehoon
authored and
peterjc
committed
python3 updates for SeqIO tests

mdehoon
authored and
peterjc
committed
update test_TogoWS.py for python3

mdehoon
authored and
peterjc
committed
update test_Tutorial.py for python3

mdehoon
authored and
peterjc
committed
update test_codonalign for python3

mdehoon
authored and
peterjc
committed
update test_align_substitution_matrices.py for python3

mdehoon
authored and
peterjc
committed
update Bio.phenotype tests for python3

mdehoon
authored and
peterjc
committed
update Bio.SeqRecord for python3 (#2680)
mdehoon
authored

Commits on Feb 11, 2020

update test_Uniprot for python3 (#2676)
mdehoon
authored
use with statement in test_NCBITextParser.py (#2683)
mdehoon
authored
use with statement in test_motifs (#2684)
mdehoon
authored
use with statement in test_NCBIXML (#2685)
mdehoon
authored
use with statement in test_KeyWList.py (#2687)
mdehoon
authored
use with statement (#2688)
mdehoon
authored
use with to open files (#2689)
mdehoon
authored
use with statement in test_GenBank (#2682)
mdehoon
authored
Initial commit for parsing

Andrey Raspopov
authored and
peterjc
committed
I'm the news

Andrey Raspopov
authored and
peterjc
committed
Fix newline

Andrey Raspopov
authored and
peterjc
committed
Use alphabetical order

Andrey Raspopov
authored and
peterjc
committed
First take on explicit tls/tsa check

Andrey Raspopov
authored and
peterjc
committed
Apply black style to test_pro* files, version 19.10b0.

svalqui
authored and
peterjc
committed
Style cosmetic, join strings implicit concatenation, making one line literal; looks better.

svalqui
authored and
peterjc
committed
Apply black style to test_SearchIO_blast*, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_SearchIO_* last files, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_SearchIO_fasta*, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_SearchIO_h*, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_SearchIO_blat*, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to more test_SeqIO* files , version 19.10b0.

svalqui
authored and
peterjc
committed
Style cosmetics, split line looks better.

svalqui
authored and
peterjc
committed
Apply black style to test_SearchIO_exonerate*, version 19.10b0.

svalqui
authored and
peterjc
committed
use with in test_GenomeDiagram.py (#2686)
mdehoon
authored

Commits on Feb 12, 2020

Black on pairwise2

MarkusPiotrowski
authored and
peterjc
committed
Black on pairwise2 tests

MarkusPiotrowski
authored and
peterjc
committed
Update flake8 settings (#2696)
MarkusPiotrowski
authored
Apply black style to test_SeqIO_QualityIO.py and index files , version 19.10b0.

svalqui
authored and
peterjc
committed
Style cosmetics, align first line with the rest of paragraph.

svalqui
authored and
peterjc
committed
Fix E731, relocated # noqa E731, misplaced after black style.

svalqui
authored and
peterjc
committed
Apply black to Tests/test_run_tests.py

martonlanga
authored and
peterjc
committed
Remove TODO comments about empty __init__.py
peterjc
committed
updated Bio.Phylo for python3 (#2577)
mdehoon
authored
use with in test_Medline.py

mdehoon
authored and
peterjc
committed
trim_str is no longer used (#2702)
mdehoon
authored
use with (#2703)
mdehoon
authored

Commits on Feb 13, 2020

Commits on Feb 14, 2020

Commits on Feb 16, 2020

Commits on Feb 17, 2020

Apply black style to test_SCOP* files, version 19.10b0.

svalqui
authored and
peterjc
committed
Fixed "MMCIF2Dict ValueError: Opening quote in middle of word #2261" (#2716)
andrei-istrate
authored

Commits on Feb 18, 2020

Apply black style to T* files, version 19.10b0.

svalqui
authored and
peterjc
committed
Style cosmetics, joining strings for more standard look.

svalqui
authored and
peterjc
committed
Apply black style to test_PopGen* files, version 19.10b0.

svalqui
authored and
peterjc
committed

Commits on Feb 19, 2020

Remove unused imports (flake8 F401)
peterjc
committed
Update .flake8 comments
peterjc
committed
No need for 'except XXX as local_var' here (flake8 F841)
peterjc
committed
Apply black style to test_phenotype* files, version 19.10b0.

svalqui
authored and
peterjc
committed
Style cosmetics, split the strings, looks better.

svalqui
authored and
peterjc
committed
Apply black style to test_PAML* files, version 19.10b0.

svalqui
authored and
peterjc
committed

Commits on Feb 20, 2020

Use the base class in Bio.SeqIO.Interface to check the number of sequences while writing (#2717)
mdehoon
authored

Commits on Feb 21, 2020

Commits on Feb 22, 2020

Commits on Feb 23, 2020

use defaultdict (#2745)
mdehoon
authored
update crc32 in Bio.SeqUtils

mdehoon
authored and
peterjc
committed
remove ancient comment

mdehoon
authored and
peterjc
committed

Commits on Feb 24, 2020

Commits on Feb 25, 2020

Remove unused imports and 'EmbossWriter' Class (#2759)
chris-rands
authored
update Bio.PDB for python3

mdehoon
authored and
peterjc
committed

Commits on Feb 27, 2020

free view buffer (#2760)
mdehoon
authored
deprecate class

chris-rands
authored and
peterjc
committed
Apply black style to test_GenBank.py, version 19.10b0; after v19.3b0 had been applied.

svalqui
authored and
peterjc
committed

Commits on Feb 29, 2020

Commits on Mar 3, 2020

Commits on Mar 4, 2020

Apply black style to test_Entrez* files, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black to Tests/test_raxml_tool.py (#2780)
peterjc
authored

Commits on Mar 5, 2020

Commits on Mar 6, 2020

Make mocked version of NCBI_qblast tests (#2779)
MarkusPiotrowski
authored

Commits on Mar 8, 2020

Use StreamModeError consistently, and avoid the _BinaryFormats local variable (#2786)
mdehoon
authored

Commits on Mar 9, 2020

Commits on Mar 10, 2020

Adding remaining changes from #2649, and using StreamModeError consistently

mdehoon
authored and
peterjc
committed
Apply black style to test_AlignIO* files, version 19.10b0.

svalqui
authored and
peterjc
committed

Commits on Mar 11, 2020

Apply black style to test_Wise.py, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_XXmotif_tool.py, version 19.10b0.

svalqui
authored and
peterjc
committed

Commits on Mar 12, 2020

Apply black style to test_Tutorial.py, version 19.10b0.

svalqui
authored and
peterjc
committed
Cosmetic change, change string with f-string, looks better.

svalqui
authored and
peterjc
committed

Commits on Mar 13, 2020

Apply black style to test_SffIO.py, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_samtools_tool.py, version 19.10b0.

svalqui
authored and
peterjc
committed
Apply black style to test_SubsMat.py, version 19.10b0.

svalqui
authored and
peterjc
committed

Commits on Mar 14, 2020

use assertIn

mdehoon
authored and
peterjc
committed
assertListEqual will check for length

mdehoon
authored and
peterjc
committed
don't add tests at runtime in test_AlignIO_convert.py

mdehoon
authored and
peterjc
committed
travis worries about having too many blank lines

mdehoon
authored and
peterjc
committed

Commits on Mar 15, 2020

Use unittest in test_PopGen_GenePop.py (#2805)
mdehoon
authored

Commits on Mar 18, 2020

Don't add tests at run time, and use unittest asserts

mdehoon
authored and
peterjc
committed

Commits on Mar 19, 2020

don't add tests at run time

mdehoon
authored and
peterjc
committed
use unittest API (#2812)
mdehoon
authored