formatting

BALSAMIC/commands/run/analysis.py

@@ -10,7 +10,8 @@
 
 # CLI commands and decorators
 from BALSAMIC.utils.cli import (createDir, get_schedulerpy, get_snakefile,
-                                SnakeMake, get_config, get_fastq_bind_path, job_id_dump_to_yaml)
+                                SnakeMake, get_config, get_fastq_bind_path,
+                                job_id_dump_to_yaml)
 from BALSAMIC.utils.constants import ANALYSIS_TYPES, VCF_DICT, BALSAMIC_SCRIPTS
 
 LOG = logging.getLogger(__name__)

BALSAMIC/utils/cli.py

@@ -587,9 +587,11 @@ def generate_h5(job_name: str, job_id: str, file_path: str) -> str:
     h5_file_name = Path(file_path, job_name + ".h5")
     sh5util_output = subprocess.check_output(
         ["sh5util", "-o",
-         h5_file_name.as_posix(), "-S", "-j", job_id], stderr=subprocess.STDOUT)
-
-    if "sh5util: No node-step files found for jobid" in sh5util_output.decode("utf-8"):
+         h5_file_name.as_posix(), "-S", "-j", job_id],
+        stderr=subprocess.STDOUT)
+
+    if "sh5util: No node-step files found for jobid" in sh5util_output.decode(
+            "utf-8"):
         h5_file_name = None
 
     return h5_file_name
@@ -598,8 +600,6 @@ def generate_h5(job_name: str, job_id: str, file_path: str) -> str:
 def job_id_dump_to_yaml(job_id_dump: Path, job_id_yaml: Path, case_name: str):
     """Write an input job_id_sacct_file to yaml output"""
     with open(job_id_dump, "r") as jobid_in, open(job_id_yaml,
-                                                 "w") as jobid_out:
+                                                  "w") as jobid_out:
         jobid_list = jobid_in.read().splitlines()
-        yaml.dump({case_name: jobid_list},
-                  jobid_out)
-
+        yaml.dump({case_name: jobid_list}, jobid_out)

BALSAMIC/utils/workflowscripts.py

@@ -120,7 +120,11 @@ def plot_analysis(log_file: Path, h5_file: Path,
     max_cpu_line.set_label("Max available")
 
     mem_ax_color = 'g'
-    df.plot(y="VMSize", x="ElapsedTime", ax=mem_ax, color=mem_ax_color, style="--")
+    df.plot(y="VMSize",
+            x="ElapsedTime",
+            ax=mem_ax,
+            color=mem_ax_color,
+            style="--")
     mem_ax.set_title("Memory statistics")
     mem_ax.set_xlabel("Wall seconds")
     mem_ax.set_ylabel("Memory usage GB (max {}GB)".format(
@@ -156,7 +160,8 @@ def plot_analysis(log_file: Path, h5_file: Path,
                           x="ElapsedTime",
                           ax=write_io_ax,
                           color=write_io_ax_color,
-                          style="--", legend=False)
+                          style="--",
+                          legend=False)
     write_io_ax.set_title("Disk I/O statistics")
     write_io_ax.set_xlabel("Wall seconds")
     write_io_ax.set_ylabel("Disk write (MB)")

tests/commands/report/test_status.py

@@ -51,7 +51,7 @@ def test_status_tumor_normal_panel(invoke_cli, tumor_normal_config, helpers,
 
 
 def test_status_analysis_finish(invoke_cli, tumor_normal_config, helpers,
-                                    sentieon_install_dir, sentieon_license):
+                                sentieon_install_dir, sentieon_license):
     # GIVEN a tumor-normal config file
     helpers.read_config(tumor_normal_config)
 

tests/commands/run/test_run_analysis.py

@@ -73,8 +73,8 @@ def test_run_analysis_create_dir(invoke_cli, tumor_only_config):
     with mock.patch.object(subprocess, 'run') as mocked:
         mocked.return_value.stdout = 1
         invoke_cli([
-            'run', 'analysis', '-s', tumor_only_config, '-r', '--benchmark', '--account',
-            'development'
+            'run', 'analysis', '-s', tumor_only_config, '-r', '--benchmark',
+            '--account', 'development'
         ])
         # THEN it should abort with error
         assert Path(re.sub('/$', '.1/', log_dir)).exists()

tests/commands/run/test_scheduler.py

@@ -33,7 +33,8 @@ def test_scheduler_slurm_py(snakemake_job_script, tumor_normal_config, capsys):
         "--sample-config", tumor_normal_config, "--profile",
         scheduler_profile_slurm, "--qos", "low", "--account", "development",
         "--log-dir", log_dir, "--script-dir", script_dir, "--result-dir",
-        sample_config['analysis']['result'], "--slurm-profiler", "task", "--slurm-profiler-interval", "10"
+        sample_config['analysis']['result'], "--slurm-profiler", "task",
+        "--slurm-profiler-interval", "10"
     ]
     scheduler_cmd.extend(scheduler_args)
 

tests/utils/test_utils.py

@@ -23,7 +23,8 @@
     get_file_status_string, get_from_two_key, find_file_index, merge_json,
     validate_fastq_pattern, get_panel_chrom, create_fastq_symlink,
     get_fastq_bind_path, singularity, get_file_extension,
-    get_bioinfo_tools_version, convert_deliverables_tags, check_executable, job_id_dump_to_yaml, generate_h5)
+    get_bioinfo_tools_version, convert_deliverables_tags, check_executable,
+    job_id_dump_to_yaml, generate_h5)
 
 from BALSAMIC.utils.rule import (get_chrom, get_vcf, get_sample_type,
                                  get_picard_mrkdup, get_variant_callers,
@@ -791,7 +792,7 @@ def test_check_executable_not_existing():
 
 
 def test_job_id_dump_to_yaml(tmp_path):
-    
+
     # GIVEN a file with one job id per line, a key (case name), and an output file name
     dummy_dir = tmp_path / "job_id_dump_dir"
     dummy_dir.mkdir()
@@ -801,43 +802,43 @@ def test_job_id_dump_to_yaml(tmp_path):
     dummy_name = "angrybird"
 
     dummy_yaml_out = dummy_dir / "jod_id.yaml"
-    
+
     # WHEN creating yaml from job id dump
     job_id_dump_to_yaml(dummy_job_id_dump, dummy_yaml_out, dummy_name)
 
     # THEN file should exist
-    assert dummy_yaml_out.exists() 
+    assert dummy_yaml_out.exists()
 
 
 def test_generate_h5(tmp_path):
-    
+
     # GIVEN a job name, a path, and a job id
-    dummy_path= tmp_path / "h5dir"
+    dummy_path = tmp_path / "h5dir"
     dummy_path.mkdir()
     dummy_job_name = "awesome_name"
     dummy_job_id = "31415.123123"
     correct_output = Path(dummy_path, dummy_job_name + ".h5")
 
     # WHEN generating a h5 output
-    with mock.patch.object(subprocess, 'check_output') as mocked: 
+    with mock.patch.object(subprocess, 'check_output') as mocked:
         actual_output = generate_h5(dummy_job_name, dummy_job_id, dummy_path)
-      
+
     assert actual_output == correct_output
 
 
 def test_generate_h5_capture_no_output(tmp_path):
-    
+
     # GIVEN a job name, a path, and a job id
-    dummy_path= tmp_path / "h5dir"
+    dummy_path = tmp_path / "h5dir"
     dummy_path.mkdir()
     dummy_job_name = "awesome_name"
     dummy_job_id = "31415.123123"
     mocked_output = "sh5util: No node-step files found for jobid"
     correct_output = Path(dummy_path, dummy_job_name + ".h5")
 
     # WHEN generating a h5 output
-    with mock.patch.object(subprocess, 'check_output') as mocked: 
+    with mock.patch.object(subprocess, 'check_output') as mocked:
         mocked.return_value = mocked_output.encode("utf-8")
         actual_output = generate_h5(dummy_job_name, dummy_job_id, dummy_path)
-      
+
     assert actual_output == None

tests/utils/test_workflowscripts.py

@@ -80,4 +80,4 @@ def test_plot_analysis_bad_h5(tmp_path_factory):
     # WHEN calling plot_analysis
     actual_pdf_file = plot_analysis(dummy_log_file, dummy_h5, dummy_pdf_name)
 
-    assert actual_pdf_file is None 
+    assert actual_pdf_file is None