feat(add): Linters

crunchy/__main__.py

@@ -24,6 +24,7 @@
 Invoke as ``crunchy`` (if installed)
 or ``python -m crunchy`` (no install required).
 """
+
 import sys
 
 from crunchy.cli.base import base_command

crunchy/cli/auto_cmd.py

@@ -1,4 +1,5 @@
 """Code for CLI auto command"""
+
 import logging
 import pathlib
 
@@ -19,8 +20,7 @@ def abort_if_false(ctx, param, value):
 
 @click.group()
 def auto():
-    """Run whole pipeline by compressing, comparing and deleting original files.
-    """
+    """Run whole pipeline by compressing, comparing and deleting original files."""
     LOG.info("Running crunchy auto")
 
 
@@ -57,7 +57,8 @@ def fastq(ctx, indir, spring_path, first, second, dry_run):
 
     if indir:
         LOG.info(
-            "This will recursively compress and delete fastqs in %s", indir,
+            "This will recursively compress and delete fastqs in %s",
+            indir,
         )
         indir = pathlib.Path(indir)
         if not indir.is_dir():
@@ -67,9 +68,7 @@ def fastq(ctx, indir, spring_path, first, second, dry_run):
 
     else:
         if not (first and second and spring_path):
-            LOG.warning(
-                "Please specify either a directory or two fastqs and a spring path"
-            )
+            LOG.warning("Please specify either a directory or two fastqs and a spring path")
             return
         LOG.info(
             "Running auto, this will compress and delete fastqs %s, %s into %s",

crunchy/cli/base.py

@@ -1,4 +1,5 @@
 """CLI functionality for crunchy"""
+
 import logging
 
 import click
@@ -18,9 +19,7 @@
 
 
 @click.group()
-@click.option(
-    "--spring-binary", default="spring", show_default=True, help="Path to spring binary"
-)
+@click.option("--spring-binary", default="spring", show_default=True, help="Path to spring binary")
 @click.option(
     "--samtools-binary",
     default="samtools",
@@ -36,7 +35,9 @@
 )
 @click.version_option(__version__)
 @click.option(
-    "--reference", "-r", help="Path to reference genome",
+    "--reference",
+    "-r",
+    help="Path to reference genome",
 )
 @click.option(
     "--log-level",
@@ -45,12 +46,11 @@
     help="Choose what log messages to show",
 )
 @click.option(
-    "--tmp-dir", help="If specific temp dir should be used",
+    "--tmp-dir",
+    help="If specific temp dir should be used",
 )
 @click.pass_context
-def base_command(
-    ctx, spring_binary, samtools_binary, threads, reference, log_level, tmp_dir
-):
+def base_command(ctx, spring_binary, samtools_binary, threads, reference, log_level, tmp_dir):
     """Base command for crunchy
 
     \b

crunchy/cli/checksum_cmd.py

@@ -12,11 +12,8 @@
 
 @click.command()
 @click.argument("infile", type=click.Path(exists=True))
-@click.option(
-    "--algorithm", "-a", type=click.Choice(["md5", "sha1", "sha256"]), default="sha256"
-)
+@click.option("--algorithm", "-a", type=click.Choice(["md5", "sha1", "sha256"]), default="sha256")
 def checksum(infile, algorithm):
-    """Generate the checksum for a file
-    """
+    """Generate the checksum for a file"""
     LOG.info("Running checksum")
     click.echo(get_checksum(pathlib.Path(infile), algorithm))

crunchy/cli/compare_cmd.py

@@ -1,4 +1,5 @@
 """Code for checksum module."""
+
 import logging
 import pathlib
 
@@ -13,11 +14,11 @@
 @click.option("--first", "-f", type=click.Path(exists=True), required=True)
 @click.option("--second", "-s", type=click.Path(exists=True))
 @click.option(
-    "--checksum", "-c", help="If the file should be compared to a checksum directly",
-)
-@click.option(
-    "--algorithm", "-a", type=click.Choice(["md5", "sha1", "sha256"]), default="sha256"
+    "--checksum",
+    "-c",
+    help="If the file should be compared to a checksum directly",
 )
+@click.option("--algorithm", "-a", type=click.Choice(["md5", "sha1", "sha256"]), default="sha256")
 @click.option("--dry-run", is_flag=True)
 def compare(first, second, algorithm, checksum, dry_run):
     """Compare two files by generating checksums. Fails if two files differ.

crunchy/cli/compress_cmd.py

@@ -1,4 +1,5 @@
 """CLI functions to compress."""
+
 import logging
 from pathlib import Path
 from typing import Optional
@@ -36,7 +37,9 @@ def compress():
     help="Second read in pair",
 )
 @click.option(
-    "--spring-path", "-o", help="Path to spring file",
+    "--spring-path",
+    "-o",
+    help="Path to spring file",
 )
 @click.option(
     "--check-integrity",
@@ -50,9 +53,7 @@ def compress():
     help="If a json file with metada should be produced",
 )
 @click.pass_context
-def fastq(
-    ctx, first_read, second_read, spring_path, dry_run, check_integrity, metadata_file
-):
+def fastq(ctx, first_read, second_read, spring_path, dry_run, check_integrity, metadata_file):
     """Compress a pair of FASTQ files with Spring."""
     LOG.info("Running compress fastq")
     if dry_run:
@@ -77,7 +78,7 @@ def fastq(
         first_read=first_read, second_read=second_read, spring=spring_path
     )
 
-    metadata_path: Optional[Path]= dump_spring_metadata(metadata) if metadata_file else None
+    metadata_path: Optional[Path] = dump_spring_metadata(metadata) if metadata_file else None
     if not check_integrity:
         return
 
@@ -101,12 +102,8 @@ def fastq(
 
     success = True
     try:
-        ctx.invoke(
-            compare, first=str(first_spring), checksum=checksums[0], dry_run=dry_run
-        )
-        ctx.invoke(
-            compare, first=str(second_spring), checksum=checksums[1], dry_run=dry_run
-        )
+        ctx.invoke(compare, first=str(first_spring), checksum=checksums[0], dry_run=dry_run)
+        ctx.invoke(compare, first=str(second_spring), checksum=checksums[1], dry_run=dry_run)
     except click.Abort:
         LOG.error("Uncompressed Spring differ from original FASTQs")
         success = False
@@ -137,7 +134,9 @@ def fastq(
     help="Path to bam file",
 )
 @click.option(
-    "--cram-path", "-c", help="Path to cram file",
+    "--cram-path",
+    "-c",
+    help="Path to cram file",
 )
 @click.option("--dry-run", is_flag=True)
 @click.pass_context
@@ -155,12 +154,14 @@ def bam(ctx, bam_path: click.Path, cram_path: str, dry_run: bool):
     cram_path: Path = Path(cram_path) if cram_path else cram_outpath(bam_path)
     file_exists(cram_path, exists=False)
     compress_cram(
-        bam_path=bam_path, cram_path=cram_path, cram_api=cram_api, dry_run=dry_run,
+        bam_path=bam_path,
+        cram_path=cram_path,
+        cram_api=cram_api,
+        dry_run=dry_run,
     )
 
     LOG.info("Compression successful")
 
 
 for sub_cmd in [fastq, bam]:
     compress.add_command(sub_cmd)
-

crunchy/cli/decompress_cmd.py

@@ -1,4 +1,5 @@
 """Code for decompress CLI fuctions"""
+
 import logging
 import pathlib
 
@@ -32,18 +33,20 @@ def decompress():
     help="Fastq file that spring archive will be decompressed to. Second read in pair",
 )
 @click.option(
-    "--first-checksum", help="Checksum from the original fastq file, first in pair",
+    "--first-checksum",
+    help="Checksum from the original fastq file, first in pair",
 )
 @click.option(
-    "--second-checksum", help="Checksum from the original fastq file, second in pair",
+    "--second-checksum",
+    help="Checksum from the original fastq file, second in pair",
 )
 @click.option(
-    "--dry-run", is_flag=True, help="Skip deleting original files",
+    "--dry-run",
+    is_flag=True,
+    help="Skip deleting original files",
 )
 @click.pass_context
-def spring(
-    ctx, spring_path, first_read, second_read, first_checksum, second_checksum, dry_run
-):
+def spring(ctx, spring_path, first_read, second_read, first_checksum, second_checksum, dry_run):
     """Decompress a spring file to fastq files"""
     LOG.info("Running decompress spring")
     spring_api = ctx.obj.get("spring_api")
@@ -74,12 +77,8 @@ def spring(
         return
 
     try:
-        ctx.invoke(
-            compare, first=str(first_read), checksum=first_checksum, dry_run=dry_run
-        )
-        ctx.invoke(
-            compare, first=str(second_read), checksum=second_checksum, dry_run=dry_run
-        )
+        ctx.invoke(compare, first=str(first_read), checksum=first_checksum, dry_run=dry_run)
+        ctx.invoke(compare, first=str(second_read), checksum=second_checksum, dry_run=dry_run)
     except click.Abort:
         LOG.error("Uncompressed spring differ from given checksum")
         LOG.info("Deleting decompressed fastq files")
@@ -100,7 +99,9 @@ def spring(
     help="Path to bam file",
 )
 @click.option(
-    "--dry-run", is_flag=True, help="Skip deleting original files",
+    "--dry-run",
+    is_flag=True,
+    help="Skip deleting original files",
 )
 @click.pass_context
 def cram(ctx, cram_path, bam_path, dry_run):
@@ -111,7 +112,10 @@ def cram(ctx, cram_path, bam_path, dry_run):
     bam_path = pathlib.Path(bam_path)
 
     decompress_cram(
-        cram_path=cram_path, bam_path=bam_path, cram_api=cram_api, dry_run=dry_run,
+        cram_path=cram_path,
+        bam_path=bam_path,
+        cram_api=cram_api,
+        dry_run=dry_run,
     )
 
 

crunchy/cli/utils.py

@@ -1,4 +1,5 @@
 """Utilities for crunchy cli functions"""
+
 import logging
 import pathlib
 

crunchy/command.py

@@ -7,7 +7,7 @@
 import subprocess
 from pathlib import Path
 from subprocess import CalledProcessError
-from typing import Optional, List, Generator
+from typing import Generator, List, Optional
 
 LOG = logging.getLogger(__name__)
 
@@ -19,7 +19,9 @@ class Process:
     called, that will be handled in this module.Output form stdout and stdin will be handeld here.
     """
 
-    def __init__(self, binary: str, config: Optional[str] = None, config_parameter: str = "--config"):
+    def __init__(
+        self, binary: str, config: Optional[str] = None, config_parameter: str = "--config"
+    ):
         """
         Args:
             binary(str): Path to binary for the process to use
@@ -46,14 +48,14 @@ def run_command(self, parameters=None):
             command.extend(parameters)
 
         LOG.info("Running command %s", " ".join(command))
-        res = subprocess.run(
-            command, check=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE
-        )
+        res = subprocess.run(command, check=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         self.stdout = res.stdout.decode("utf-8").rstrip()
         self.stderr = res.stderr.decode("utf-8").rstrip()
         if res.returncode != 0:
-            LOG.critical(f"Call {command} exit with a non zero exit code", )
+            LOG.critical(
+                f"Call {command} exit with a non zero exit code",
+            )
             LOG.critical(self.stderr)
             raise CalledProcessError(command, res.returncode)
 
@@ -106,9 +108,7 @@ def __init__(self, binary: str, threads: int = 8, tmp_dir: Optional[str] = None)
         self.threads: int = threads
         self.tmp: Optional[str] = tmp_dir
 
-    def decompress(
-        self, spring_path: Path, first: Path, second: Path
-    ) -> bool:
+    def decompress(self, spring_path: Path, first: Path, second: Path) -> bool:
         """Run the spring decompress command."""
         parameters = ["-d", "-i", str(spring_path), "-o", str(first), str(second)]
         if first.suffix == ".gz":
@@ -138,9 +138,7 @@ def decompress(
         LOG.error(self.stderr)
         return False
 
-    def compress(
-        self, first: Path, second: Path, outfile: Path
-    ) -> bool:
+    def compress(self, first: Path, second: Path, outfile: Path) -> bool:
         """Run the spring compression command."""
         parameters = [
             "-c",

crunchy/utils.py

@@ -36,9 +36,7 @@ def find_fastq_pairs(directory: pathlib.Path) -> Iterator[tuple]:
             LOG.debug("Read already found: %s", pth)
             continue
         if len(splitted) < 3:
-            LOG.info(
-                "Fastq filename %s does not follow illumina conventions", file_name
-            )
+            LOG.info("Fastq filename %s does not follow illumina conventions", file_name)
             continue
         # Check if we have a part of a read pair
         spring_name = pathlib.Path("_".join(splitted[:-2]))

crunchy/version.py

@@ -1,2 +1,3 @@
 """Holds the current version"""
+
 __version__ = "1.0.3"

setup.py

@@ -1,6 +1,5 @@
 """Based on https://github.com/kennethreitz/setup.py"""
 
-
 import contextlib
 import io
 import os
@@ -26,9 +25,7 @@ def parse_reqs(req_path="./requirements.txt"):
     install_requires = []
     with io.open(os.path.join(HERE, req_path), encoding="utf-8") as handle:
         # remove comments and empty lines
-        lines = (
-            line.strip() for line in handle if line.strip() and not line.startswith("#")
-        )
+        lines = (line.strip() for line in handle if line.strip() and not line.startswith("#"))
 
         for line in lines:
             if line.startswith("-i") or line.startswith("-e"):