Merge pull request #17 from rouskinlab/0.21.0

0.21.0

make_conda_recipe.py

@@ -157,7 +157,7 @@ def calc_github_file_sha256():
     url = find_github_file()
     response = urlopen(url)
     if response.status != 200:
-        raise URLError(f"{url} returned status {response.status}")
+        raise URLError(f"{url} returned status {response.command}")
     return sha256(response.read()).hexdigest()
 
 

meta/license.py

@@ -1,13 +1,8 @@
-"""
-
-Add a summary of the license to the end of each source file.
-
-"""
-
-
 import os
 from logging import DEBUG, basicConfig, getLogger
 
+# This module lies outside the SEISMIC-RNA package, so it needs to use
+# the Logger from Python's standard library, not from SEISMIC-RNA.
 basicConfig(level=DEBUG)
 logger = getLogger(__name__)
 

src/seismicrna/align/fqunit.py

@@ -1,6 +1,5 @@
 from functools import cached_property
 from itertools import chain
-from logging import getLogger
 from pathlib import Path
 from subprocess import CompletedProcess
 
@@ -10,8 +9,7 @@
                            ShellCommand,
                            args_to_cmd,
                            cmds_to_pipe)
-
-logger = getLogger(__name__)
+from ..core.logs import logger
 
 FQ_LINES_PER_READ = 4
 PHRED_ENCS = {33, 64}
@@ -126,9 +124,10 @@ def __init__(self, *,
         self.phred_enc = phred_enc
         self.one_ref = one_ref
         self.sample, self.ref, self.exts = self.get_sample_ref_exts()
-        logger.debug(f"Instantiated a {type(self).__name__} with "
-                     + ", ".join(f"{k} = {v}" for k, v in self.paths.items())
-                     + f", phred_enc = {phred_enc}, one_ref = {one_ref}")
+        logger.detail(
+            f"Instantiated a {type(self).__name__} with paths={self.paths}, "
+            f"phred_enc={phred_enc}, one_ref={one_ref}"
+        )
 
     @cached_property
     def phred_arg(self):
@@ -231,7 +230,7 @@ def _from_files(cls, /, *,
             try:
                 yield cls(phred_enc=phred_enc, one_ref=one_ref, **{key: fq})
             except Exception as error:
-                logger.error(f"Failed to load FASTQ file {fq}: {error}")
+                logger.error(error)
 
     @classmethod
     def _from_mates(cls, /, *,
@@ -276,7 +275,7 @@ def by_tag(fqs_: list[Path], segs: list[path.Segment]):
             try:
                 yield cls(phred_enc=phred_enc, one_ref=one_ref, **fq_args)
             except Exception as error:
-                logger.error(f"Failed to load FASTQ pair {fq_args}: {error}")
+                logger.error(error)
 
     @classmethod
     def from_paths(cls, /, *, phred_enc: int, **fastq_args: list[Path]):

src/seismicrna/align/main.py

@@ -1,4 +1,3 @@
-from logging import getLogger
 from pathlib import Path
 
 from click import command
@@ -66,10 +65,8 @@
                            require_dependency)
 from ..core.run import run_func
 
-logger = getLogger(__name__)
 
-
-@run_func(logger.critical,
+@run_func(CMD_ALIGN,
           with_tmp=True,
           pass_keep_tmp=True,
           extra_defaults=extra_defaults)
@@ -149,51 +146,53 @@ def run(fasta: str, *,
                                          dmfastqx=list(map(Path, dmfastqx)),
                                          phred_enc=phred_enc))
     # Generate and return a BAM file for every FASTQ-reference pair.
-    return align_samples(fq_units=fq_units,
-                         fasta=Path(fasta),
-                         out_dir=Path(out_dir),
-                         tmp_dir=tmp_dir,
-                         keep_tmp=keep_tmp,
-                         force=force,
-                         max_procs=max_procs,
-                         parallel=parallel,
-                         fastp=fastp,
-                         fastp_5=fastp_5,
-                         fastp_3=fastp_3,
-                         fastp_w=fastp_w,
-                         fastp_m=fastp_m,
-                         fastp_poly_g=fastp_poly_g,
-                         fastp_poly_g_min_len=fastp_poly_g_min_len,
-                         fastp_poly_x=fastp_poly_x,
-                         fastp_poly_x_min_len=fastp_poly_x_min_len,
-                         fastp_adapter_trimming=fastp_adapter_trimming,
-                         fastp_adapter_1=fastp_adapter_1,
-                         fastp_adapter_2=fastp_adapter_2,
-                         fastp_adapter_fasta=optional_path(fastp_adapter_fasta),
-                         fastp_detect_adapter_for_pe=fastp_detect_adapter_for_pe,
-                         fastp_min_length=fastp_min_length,
-                         bt2_local=bt2_local,
-                         bt2_discordant=bt2_discordant,
-                         bt2_mixed=bt2_mixed,
-                         bt2_dovetail=bt2_dovetail,
-                         bt2_contain=bt2_contain,
-                         bt2_un=bt2_un,
-                         bt2_score_min_e2e=bt2_score_min_e2e,
-                         bt2_score_min_loc=bt2_score_min_loc,
-                         bt2_i=bt2_i,
-                         bt2_x=bt2_x,
-                         bt2_gbar=bt2_gbar,
-                         bt2_l=bt2_l,
-                         bt2_s=bt2_s,
-                         bt2_d=bt2_d,
-                         bt2_r=bt2_r,
-                         bt2_dpad=bt2_dpad,
-                         bt2_orient=bt2_orient,
-                         min_mapq=min_mapq,
-                         min_reads=min_reads,
-                         sep_strands=sep_strands,
-                         f1r2_fwd=f1r2_fwd,
-                         rev_label=rev_label)
+    return align_samples(
+        fq_units=fq_units,
+        fasta=Path(fasta),
+        out_dir=Path(out_dir),
+        tmp_dir=tmp_dir,
+        keep_tmp=keep_tmp,
+        force=force,
+        max_procs=max_procs,
+        parallel=parallel,
+        fastp=fastp,
+        fastp_5=fastp_5,
+        fastp_3=fastp_3,
+        fastp_w=fastp_w,
+        fastp_m=fastp_m,
+        fastp_poly_g=fastp_poly_g,
+        fastp_poly_g_min_len=fastp_poly_g_min_len,
+        fastp_poly_x=fastp_poly_x,
+        fastp_poly_x_min_len=fastp_poly_x_min_len,
+        fastp_adapter_trimming=fastp_adapter_trimming,
+        fastp_adapter_1=fastp_adapter_1,
+        fastp_adapter_2=fastp_adapter_2,
+        fastp_adapter_fasta=optional_path(fastp_adapter_fasta),
+        fastp_detect_adapter_for_pe=fastp_detect_adapter_for_pe,
+        fastp_min_length=fastp_min_length,
+        bt2_local=bt2_local,
+        bt2_discordant=bt2_discordant,
+        bt2_mixed=bt2_mixed,
+        bt2_dovetail=bt2_dovetail,
+        bt2_contain=bt2_contain,
+        bt2_un=bt2_un,
+        bt2_score_min_e2e=bt2_score_min_e2e,
+        bt2_score_min_loc=bt2_score_min_loc,
+        bt2_i=bt2_i,
+        bt2_x=bt2_x,
+        bt2_gbar=bt2_gbar,
+        bt2_l=bt2_l,
+        bt2_s=bt2_s,
+        bt2_d=bt2_d,
+        bt2_r=bt2_r,
+        bt2_dpad=bt2_dpad,
+        bt2_orient=bt2_orient,
+        min_mapq=min_mapq,
+        min_reads=min_reads,
+        sep_strands=sep_strands,
+        f1r2_fwd=f1r2_fwd,
+        rev_label=rev_label
+    )
 
 
 # Parameters for command line interface

src/seismicrna/align/split.py

@@ -1,4 +1,3 @@
-from logging import getLogger
 from pathlib import Path
 
 from click import command
@@ -50,8 +49,6 @@
 from ..core.tmp import release_to_out
 from ..core.write import need_write
 
-logger = getLogger(__name__)
-
 
 def split_xam_file(xam_file: Path,
                    out_dir: Path,
@@ -98,7 +95,7 @@ def split_xam_file(xam_file: Path,
     return result_dir
 
 
-@run_func(logger.critical, with_tmp=True, pass_keep_tmp=True)
+@run_func(CMD_SPLITBAM, with_tmp=True, pass_keep_tmp=True)
 def run(fasta: str, *,
         # Inputs
         input_path: tuple[str, ...],

src/seismicrna/align/tests/write_test.py

@@ -1,7 +1,7 @@
 import unittest as ut
 
 from seismicrna.align.write import calc_flags_sep_strands
-from seismicrna.core.logs import set_config, restore_config
+from seismicrna.core.logs import Level, set_config, restore_config
 from seismicrna.core.ngs import (FLAG_PAIRED,
                                  FLAG_PROPER,
                                  FLAG_FIRST,
@@ -25,7 +25,7 @@ def test_f1r2_paired_unmixed(self):
 
     @restore_config
     def test_f1r2_paired_mixed(self):
-        set_config(verbose=0, quiet=1)
+        set_config(verbosity=Level.ERROR)
         expect = (([FLAG_FIRST | FLAG_PAIRED | FLAG_PROPER,
                     FLAG_SECOND | FLAG_REVERSE | FLAG_PAIRED | FLAG_PROPER],
                    [FLAG_SECOND | FLAG_REVERSE,
@@ -60,7 +60,7 @@ def test_f2r1_paired_unmixed(self):
 
     @restore_config
     def test_f2r1_paired_mixed(self):
-        set_config(verbose=0, quiet=1)
+        set_config(verbosity=Level.ERROR)
         expect = (([FLAG_FIRST | FLAG_REVERSE | FLAG_PAIRED | FLAG_PROPER,
                     FLAG_SECOND | FLAG_PAIRED | FLAG_PROPER],
                    [FLAG_SECOND,