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v1.0.0 #51

Merged
merged 90 commits into from
Oct 26, 2021
Merged

v1.0.0 #51

merged 90 commits into from
Oct 26, 2021

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ggirelli
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ggirelli and others added 30 commits March 23, 2021 21:35
@ggirelli
Updated requirements.
5de0d3d
@dependabot
Bump numpy from 1.20.1 to 1.20.2 (#6)
f493a0f
@dependabot
Bump rich from 9.13.0 to 10.0.0 (#7)
baa368a
@dependabot
Bump rich from 10.0.0 to 10.0.1 (#8)
915e71f
@dependabot
Bump tqdm from 4.59.0 to 4.60.0 (#11)
b8d7779
@dependabot
Bump pytest from 6.2.2 to 6.2.3 (#10)
aea0200
@dependabot
Bump rich from 10.0.1 to 10.1.0 (#9)
d5a44b4
@dependabot
Bump black from 20.8b1 to 21.4b0 (#12)
17789d3
@dependabot
Bump black from 21.4b0 to 21.4b1 (#13)
fd7b78d
@dependabot
Bump black from 21.4b1 to 21.4b2 (#14)
8ef2272
@dependabot
Bump pytest from 6.2.3 to 6.2.4 (#15)
1d176f8
@dependabot
Bump black from 21.4b2 to 21.5b0 (#16)
7e1e1ab
@dependabot
Bump rich from 10.1.0 to 10.2.0 (#19)
f9f05a7
@dependabot
Bump black from 21.5b0 to 21.5b1 (#17)
01e224e
@dependabot
Bump numpy from 1.20.2 to 1.20.3 (#18)
a61ec84
@dependabot
Bump rich from 10.2.0 to 10.2.2 (#21)
8da594b
@dependabot
Bump black from 21.5b1 to 21.5b2 (#23)
ef3c462
@dependabot
Bump tqdm from 4.60.0 to 4.61.0 (#22)
e18b5a3
@dependabot
Bump biopython from 1.78 to 1.79 (#24)
75b4cec
@dependabot
Bump rich from 10.2.2 to 10.3.0 (#25)
3f20224
@dependabot
Bump black from 21.5b2 to 21.6b0 (#26)
617859e
@dependabot
Bump tqdm from 4.61.0 to 4.61.1 (#27)
708cea0
@dependabot
Bump rich from 10.3.0 to 10.4.0 (#28)
048d12e
@dependabot
Bump h5py from 3.2.1 to 3.3.0 (#30)
41bae6d
@dependabot
Bump numpy from 1.20.3 to 1.21.0 (#29)
a64dc27
@dependabot
Bump rich from 10.4.0 to 10.5.0 (#31)
cf481f5
@dependabot
Bump tqdm from 4.61.1 to 4.61.2 (#32)
91acb7c
@dependabot
Bump rich from 10.5.0 to 10.6.0 (#33)
244ba2d
@dependabot
Bump black from 21.6b0 to 21.7b0 (#34)
412e992
@dependabot
Bump numpy from 1.21.0 to 1.21.1 (#35)
59622fc
@deepsource-autofix
Refactor unnecessary else / elif when if block has a break st…
a26ca30 
…atement (#68)

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@deepsource-autofix
Use is to compare type of objects (#69)
8cc1063 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@sourcery-ai sourcery-ai bot mentioned this pull request Oct 25, 2021
Merged
deepsource-autofix bot and others added 12 commits October 25, 2021 23:56
@deepsource-autofix
raise NotImplementedError in empty functions (#71)
83d7ebf 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@deepsource-autofix
Remove implicit object from the base class (#72)
748539a 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@deepsource-autofix
Merge collapsible with statements (#73)
6a3c53d 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@sourcery-ai
'Refactored by Sourcery' (#70)
9db14bd 
Co-authored-by: Sourcery AI <>
@ggirelli
fix: reversed wrong automatic fix
12928b2
@deepsource-autofix
Remove assert statement from non-test files (#74)
5d2d266 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@ggirelli
fix: unassigned string
cfa2fe3
@ggirelli
ci: removed empty line
40d9215
@ggirelli
Merge branch 'dev' of github.com:ggirelli/kmermaid into dev
f5e138a
@ggirelli
fix: removed empty line before docstring
9d74f74
@ggirelli
fix: addedd missing raises docstrings
c7c582d
@ggirelli
fix: added missing class docstring
949d5a4
@ggirelli ggirelli linked an issue Oct 26, 2021 that may be closed by this pull request
(PY-D0002) Missing class docstring #80
Closed
ggirelli and others added 3 commits October 26, 2021 16:25
@ggirelli @sourcery-ai
fix: add missing docstrings, see issue #79 (#81)
d9d1395 
* fix: added missing docstrings

* fix: added missing docstrings

* fix: accidental recursion

* fix: pytested and added missing docstring

* docs: added missing method docstrings

* docs: added missing docstrings to parsers module

* docs: added missing docstrings to join module

* docs: added docstrings to io module

* docs: added missing docstrings to batcher module

* fix: added missing docstrings to batch module

* docs: added missing docstrings to abundance module

* 'Refactored by Sourcery' (#82)

Co-authored-by: Sourcery AI <>

* ci: blacked after sourcery

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>
@ggirelli
fix: function contains unused argument (PYL-W0613), closes #75 (#83)
918fe61 
* fix: removed unused method arguments from join module

* fix: fixed unused method arguments in abundance module
@ggirelli
fix: incorrect method overriding
75f9f3e
@ggirelli ggirelli linked an issue Oct 26, 2021 that may be closed by this pull request
(PYL-W0221) Mismatched parameters in overridden method #76
Closed
@ggirelli ggirelli linked an issue Oct 26, 2021 that may be closed by this pull request
(PTC-W0063) Unguarded next inside generator #77
Closed
@ggirelli ggirelli linked an issue Oct 26, 2021 that may be closed by this pull request
(PYL-E1126) Invalid sequence index found #78
Closed
@ggirelli ggirelli merged commit 67e8a3c into main Oct 26, 2021
@ggirelli ggirelli deleted the dev branch October 26, 2021 21:32
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