Zed styling

.github/workflows/qiita-plugin-ci.yml

@@ -156,7 +156,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - name: flake8
+      - name: ruff
         uses: actions/setup-python@v2
         with:
           python-version: 3.9
@@ -166,5 +166,5 @@ jobs:
         uses: actions/checkout@v2
       - name: lint
         run: |
-          pip install -q flake8
-          flake8 .
+          pip install -q ruff
+          ruff check .

README.md

@@ -14,7 +14,7 @@ git clone https://github.com/biocore/mg-scripts.git
 Create a Python3 Conda environment in which to run the notebook:
 
 ```bash
-conda create --yes -n spp python='python=3.9' scikit-learn pandas numpy nose pep8 flake8 matplotlib jupyter notebook 'seaborn>=0.7.1' pip openpyxl 'seqtk>=1.4' click scipy fastq-pair
+conda create --yes -n spp python='python=3.9' scikit-learn pandas numpy nose ruff matplotlib jupyter notebook 'seaborn>=0.7.1' pip openpyxl 'seqtk>=1.4' click scipy fastq-pair
 ```
 
 Activate the Conda environment:

pyproject.toml

@@ -43,7 +43,7 @@ dependencies = [
     "pandas",
     "lxml",
     'requests',
-    'flake8',
+    'ruff',
     'nose',
     'coverage',
     'pgzip',

src/sequence_processing_pipeline/Commands.py

@@ -1,34 +1,35 @@
 import glob
 import gzip
 import os
+
 import click
-from sequence_processing_pipeline.util import (iter_paired_files,
-                                               determine_orientation)
+
+from sequence_processing_pipeline.util import determine_orientation, iter_paired_files
 
 
-def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
-                            batch_prefix, allow_fwd_only=False):
-    '''Partitions input fastqs to coarse bins
+def split_similar_size_bins(
+    data_location_path, max_file_list_size_in_gb, batch_prefix, allow_fwd_only=False
+):
+    """Partitions input fastqs to coarse bins
 
     :param data_location_path: Path to the ConvertJob directory.
     :param max_file_list_size_in_gb: Upper threshold for file-size.
     :param batch_prefix: Path + file-name prefix for output-files.
     :param allow_fwd_only: ignore rev match, helpful for long reads.
     :return: The number of output-files created, size of largest bin.
-    '''
+    """
     # to prevent issues w/filenames like the ones below from being mistaken
     # for R1 or R2 files, use determine_orientation().
     # LS_8_22_2014_R2_SRE_S2_L007_I1_001.fastq.gz
     # LS_8_22_2014_R1_SRE_S3_L007_I1_001.fastq.gz
 
     # since the names of all fastq files are being scanned for orientation,
     # collect all of them instead of mistakenly pre-filtering some files.
-    fastq_paths = glob.glob(data_location_path + '/*/*.fastq.gz')
-    fastq_paths = [x for x in fastq_paths
-                   if determine_orientation(x) in ['R1', 'R2']]
+    fastq_paths = glob.glob(data_location_path + "/*/*.fastq.gz")
+    fastq_paths = [x for x in fastq_paths if determine_orientation(x) in ["R1", "R2"]]
 
     # convert from GB and halve as we sum R1
-    max_size = (int(max_file_list_size_in_gb) * (2 ** 30) / 2)
+    max_size = int(max_file_list_size_in_gb) * (2**30) / 2
 
     split_offset = 0
 
@@ -42,7 +43,7 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
     if allow_fwd_only:
         for a in fastq_paths:
             r1_size = os.stat(a).st_size
-            output_base = os.path.dirname(a).split('/')[-1]
+            output_base = os.path.dirname(a).split("/")[-1]
             if current_size + r1_size > max_size:
                 # bucket is full.
                 if bucket_size > max_bucket_size:
@@ -56,7 +57,7 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
 
                 split_offset += 1
                 current_size = r1_size
-                fp = open(batch_prefix + '-%d' % split_offset, 'w')
+                fp = open(batch_prefix + "-%d" % split_offset, "w")
             else:
                 # add to bucket_size
                 bucket_size += r1_size
@@ -68,7 +69,7 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
             r1_size = os.stat(a).st_size
             r2_size = os.stat(b).st_size
 
-            output_base = os.path.dirname(a).split('/')[-1]
+            output_base = os.path.dirname(a).split("/")[-1]
             if current_size + r1_size > max_size:
                 # bucket is full.
                 if bucket_size > max_bucket_size:
@@ -82,7 +83,7 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
 
                 split_offset += 1
                 current_size = r1_size
-                fp = open(batch_prefix + '-%d' % split_offset, 'w')
+                fp = open(batch_prefix + "-%d" % split_offset, "w")
             else:
                 # add to bucket_size
                 bucket_size += r1_size + r2_size
@@ -93,9 +94,10 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
     if fp is not None:
         fp.close()
 
-    code_dir = 'qp-knight-lab-processing/tests/test_output/'
+    code_dir = "qp-knight-lab-processing/tests/test_output/"
     is_test = data_location_path.endswith(
-        (f'{code_dir}ConvertJob', f'{code_dir}TRIntegrateJob/integrated'))
+        (f"{code_dir}ConvertJob", f"{code_dir}TRIntegrateJob/integrated")
+    )
 
     if split_offset == 0 and not is_test:
         raise ValueError("No splits made")
@@ -104,23 +106,23 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
 
 
 def demux_cmd(id_map_fp, fp_fp, out_d, task, maxtask):
-    with open(id_map_fp, 'r') as f:
+    with open(id_map_fp, "r") as f:
         id_map = f.readlines()
-        id_map = [line.strip().split('\t') for line in id_map]
+        id_map = [line.strip().split("\t") for line in id_map]
 
     # fp needs to be an open file handle.
     # ensure task and maxtask are proper ints when coming from cmd-line.
-    with open(fp_fp, 'r') as fp:
+    with open(fp_fp, "r") as fp:
         demux(id_map, fp, out_d, int(task), int(maxtask))
 
 
 def demux(id_map, fp, out_d, task, maxtask):
     """Split infile data based in provided map"""
-    delimiter = '::MUX::'
-    mode = 'wt'
-    ext = '.fastq.gz'
-    sep = '/'
-    rec = '@'
+    delimiter = "::MUX::"
+    mode = "wt"
+    ext = ".fastq.gz"
+    sep = "/"
+    rec = "@"
 
     openfps = {}
 
@@ -142,7 +144,7 @@ def demux(id_map, fp, out_d, task, maxtask):
                 pass
             current_fp_r1 = gzip.open(fullname_r1, mode)
             current_fp_r2 = gzip.open(fullname_r2, mode)
-            current_fp = {'1': current_fp_r1, '2': current_fp_r2}
+            current_fp = {"1": current_fp_r1, "2": current_fp_r2}
             openfps[idx] = current_fp
 
     # setup a parser
@@ -181,7 +183,7 @@ def demux(id_map, fp, out_d, task, maxtask):
             # no '\n'
             orientation = sid[-1]
             # hexdump confirms separator is ' ', not '\t'
-            sid = rec + sid + ' ' + metadata + '\n'
+            sid = rec + sid + " " + metadata + "\n"
         else:
             raise ValueError(f"'{sid}' is not a recognized form")
 
@@ -201,29 +203,29 @@ def cli():
 
 
 @cli.command()
-@click.option('--id-map', type=click.Path(exists=True), required=True)
-@click.option('--infile', type=click.Path(exists=True), required=True)
-@click.option('--output', type=click.Path(exists=True), required=True)
-@click.option('--task', type=int, required=True)
-@click.option('--maxtask', type=int, required=True)
+@click.option("--id-map", type=click.Path(exists=True), required=True)
+@click.option("--infile", type=click.Path(exists=True), required=True)
+@click.option("--output", type=click.Path(exists=True), required=True)
+@click.option("--task", type=int, required=True)
+@click.option("--maxtask", type=int, required=True)
 def demux_just_fwd(id_map, infile, output, task, maxtask):
-    with open(id_map, 'r') as f:
+    with open(id_map, "r") as f:
         id_map = f.readlines()
-        id_map = [line.strip().split('\t') for line in id_map]
+        id_map = [line.strip().split("\t") for line in id_map]
 
     # fp needs to be an open file handle.
     # ensure task and maxtask are proper ints when coming from cmd-line.
-    with open(infile, 'r') as fp:
+    with open(infile, "r") as fp:
         demux_just_fwd_processing(id_map, fp, output, int(task), int(maxtask))
 
 
 def demux_just_fwd_processing(id_map, fp, out_d, task, maxtask):
     """Split infile data based in provided map"""
-    delimiter = '::MUX::'
-    mode = 'wt'
-    ext = '.fastq.gz'
-    sep = '/'
-    rec = '@'
+    delimiter = "::MUX::"
+    mode = "wt"
+    ext = ".fastq.gz"
+    sep = "/"
+    rec = "@"
 
     openfps = {}
 
@@ -243,7 +245,7 @@ def demux_just_fwd_processing(id_map, fp, out_d, task, maxtask):
             except FileExistsError:
                 pass
             current_fp_r1 = gzip.open(fullname_r1, mode)
-            current_fp = {'1': current_fp_r1}
+            current_fp = {"1": current_fp_r1}
             openfps[idx] = current_fp
 
     # setup a parser
@@ -253,7 +255,7 @@ def demux_just_fwd_processing(id_map, fp, out_d, task, maxtask):
     qual = iter(fp)
 
     # there is only fwd so the orientation is always '1'
-    orientation = '1'
+    orientation = "1"
 
     for i, s, d, q in zip(seq_id, seq, dumb, qual):
         # '@1', 'LH00444:84:227CNHLT4:7:1101:41955:2443/1'
@@ -270,7 +272,7 @@ def demux_just_fwd_processing(id_map, fp, out_d, task, maxtask):
 
         current_fp = openfps[fname_encoded]
 
-        current_fp[orientation].write(f'{rec}{sid}')
+        current_fp[orientation].write(f"{rec}{sid}")
         current_fp[orientation].write(s)
         current_fp[orientation].write(d)
         current_fp[orientation].write(q)