From e8bfd7f392fd82880fee2ec2c226ea7bfcd500c2 Mon Sep 17 00:00:00 2001
From: Christoph Harmel <christoph.harmel@unibas.ch>
Date: Mon, 12 Dec 2022 16:27:01 +0100
Subject: [PATCH] fix: updated linters in CI
---
.gitlab-ci.yml | 2 +-
readsequencer/read_sequencer.py | 12 ++++++++----
2 files changed, 9 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1c9d381..2880e20 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,7 +30,7 @@ lint-test-job: # This job also runs in the test stage.
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
- pip install -e .
- #- flake8 --docstring-convention google readsequencer/ tests/
+ - flake8 --docstring-convention google --max-line-length 120 readsequencer/ --ignore=D212,D103,D104,D107,D100,D017,D415
#- pylint readsequencer/ tests/
deploy-job: # This job runs in the deploy stage.
diff --git a/readsequencer/read_sequencer.py b/readsequencer/read_sequencer.py
index 1868adf..6cd7565 100644
--- a/readsequencer/read_sequencer.py
+++ b/readsequencer/read_sequencer.py
@@ -7,6 +7,7 @@ from Bio.SeqRecord import SeqRecord
class ReadSequencer:
"""ReadSequencer class
+
Args:
fasta: path fasta file
output: path output fasta file(s)
@@ -72,7 +73,8 @@ class ReadSequencer:
return seq
def resize_sequence(self, record: SeqRecord) -> SeqRecord:
- """
+ """Resizes sequence
+
Resizes sequence according to set read length. If sequence is
shorter than read length, fills up with random nucleotides.
@@ -83,7 +85,7 @@ class ReadSequencer:
resized SeqRecord
"""
if (len(record)) >= self.read_length:
- record.seq = record.seq[0:self.read_length-1]
+ record.seq = record.seq[0:self.read_length - 1]
else:
n_add = self.read_length - len(record)
add_seq = self.generate_random_sequence(n_add)
@@ -91,7 +93,8 @@ class ReadSequencer:
return record.seq
def batch_iterator(self, iterator: Iterator, batch_size: int) -> Generator:
- """
+ """Generates batch iterator.
+
This is a generator function, and it returns lists of the
entries from the supplied iterator. Each list will have
batch_size entries, although the final list may be shorter.
@@ -111,7 +114,8 @@ class ReadSequencer:
batch = []
def run_sequencing(self) -> None:
- """
+ """Runs sequencing.
+
Runs read sequencing of specified sequences from input fasta file or
generates random sequences for a given read length. If number of
sequences exceeds chunk-size, it will switch to batch processing mode.
--
GitLab