v0.2.0 (Sourcery refactored) #218

sourcery-ai · 2022-06-04T15:23:55Z

Pull Request #142 refactored by Sourcery.

If you're happy with these changes, merge this Pull Request using the Squash and merge strategy.

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will be closed automatically.

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sourcery-ai · 2022-06-04T15:24:01Z

Sourcery Code Quality Report

❌ Merging this PR will decrease code quality in the affected files by 0.26%.

Quality metrics	Before	After	Change
Complexity	2.08 ⭐	2.04 ⭐	-0.04 👍
Method Length	37.92 ⭐	37.76 ⭐	-0.16 👍
Working memory	5.66 ⭐	5.78 ⭐	0.12 👎
Quality	84.43% ⭐	84.17% ⭐	-0.26% 👎

Other metrics	Before	After	Change
Lines	697	687	-10

Changed files	Quality Before	Quality After	Quality Change
fastx_barber/flag.py	84.29% ⭐	84.21% ⭐	-0.08% 👎
fastx_barber/seqio.py	84.35% ⭐	84.17% ⭐	-0.18% 👎
fastx_barber/trim.py	85.08% ⭐	84.04% ⭐	-1.04% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation

Legend and Explanation

The emojis denote the absolute quality of the code:

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⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

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sourcery-ai · 2023-01-05T08:35:03Z

fastx_barber/flag.py

-            flag_data.update([flag])
+            flag_data |= [flag]


Function FastaFlagExtractor.extract_all refactored with the following changes:

Merge dictionary updates via the union operator (dict-assign-update-to-union)

sourcery-ai · 2023-01-05T08:35:03Z

fastx_barber/flag.py

-            flag_data.update([flag])
+            flag_data |= [flag]


Function FastqFlagExtractor.__add_qual_flags refactored with the following changes:

Merge dictionary updates via the union operator (dict-assign-update-to-union)

sourcery-ai · 2023-01-05T08:35:03Z

fastx_barber/flag.py

-    if FastxFormats.FASTQ == fmt:
-        return FastqFlagExtractor
-    return ABCFlagExtractor
+    return FastqFlagExtractor if FastxFormats.FASTQ == fmt else ABCFlagExtractor


Function get_fastx_flag_extractor refactored with the following changes:

Lift code into else after jump in control flow (reintroduce-else)

Replace if statement with if expression (assign-if-exp)

sourcery-ai · 2023-01-05T08:35:03Z

fastx_barber/flag.py

-            flag_data.update([(name, (value, -1, -1))])
+            flag_data |= [(name, (value, -1, -1))]


Function FastxFlagReader.read refactored with the following changes:

Merge dictionary updates via the union operator (dict-assign-update-to-union)

sourcery-ai · 2023-01-05T08:35:03Z

fastx_barber/seqio.py

-    if FastxFormats.FASTQ == fmt:
-        return SimpleFastqWriter
-    return SimpleFastxWriter
+    return SimpleFastqWriter if FastxFormats.FASTQ == fmt else SimpleFastxWriter


Function get_fastx_writer refactored with the following changes:

Lift code into else after jump in control flow (reintroduce-else)

Replace if statement with if expression (assign-if-exp)

sourcery-ai · 2023-01-05T08:35:04Z

fastx_barber/trim.py

-        while bases_qscores:
-            if bases_qscores[0] >= qscore_thr:
-                break
+        while bases_qscores and bases_qscores[0] < qscore_thr:


Function FastqTrimmer.__trim_qual_5 refactored with the following changes:

Move a guard clause in a while statement's body into its test (while-guard-to-condition)

Simplify logical expression using De Morgan identities (de-morgan)

sourcery-ai · 2023-01-05T08:35:04Z

fastx_barber/trim.py

-        while bases_qscores:
-            if bases_qscores[-1] >= qscore_thr:
-                break
+        while bases_qscores and bases_qscores[-1] < qscore_thr:


Function FastqTrimmer.__trim_qual_3 refactored with the following changes:

Move a guard clause in a while statement's body into its test (while-guard-to-condition)

Simplify logical expression using De Morgan identities (de-morgan)

sourcery-ai · 2023-01-05T08:35:04Z

fastx_barber/trim.py

-    if FastxFormats.FASTQ == fmt:
-        return FastqTrimmer
-    return ABCTrimmer
+    return FastqTrimmer if FastxFormats.FASTQ == fmt else ABCTrimmer


Function get_fastx_trimmer refactored with the following changes:

Lift code into else after jump in control flow (reintroduce-else)

Replace if statement with if expression (assign-if-exp)

sourcery-ai bot requested a review from ggirelli June 4, 2022 15:23

sourcery-ai bot force-pushed the sourcery/dev branch from 2d91a54 to 24a6ee1 Compare June 7, 2022 12:03

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'Refactored by Sourcery'

dd73a96

sourcery-ai bot force-pushed the sourcery/dev branch from 3cddecf to dd73a96 Compare January 5, 2023 08:34

sourcery-ai bot commented Jan 5, 2023

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v0.2.0 (Sourcery refactored) #218

v0.2.0 (Sourcery refactored) #218

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		flag_data.update([(name, (value, -1, -1))])
		flag_data \|= [(name, (value, -1, -1))]

v0.2.0 (Sourcery refactored) #218

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v0.2.0 (Sourcery refactored) #218

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sourcery-ai bot commented Jun 4, 2022 •

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