From eed82ce7adf140e17963374b45fcabe908049faf Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 5 Aug 2026 14:39:08 -0400
Subject: [PATCH 1/2] chore: setup dependabot

---
 .github/dependabot.yml | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..d960e62
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,32 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directories:
+      - "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+    cooldown:
+      default-days: 7
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      runtime:
+        dependency-type: "production"
+        exclude-patterns:
+          - "ccbr_tools"
+      build:
+        patterns:
+          - "ccbr_tools"
+          - "setuptools"
+          - "setuptools-scm"
+          - "wheel"
+      dev:
+        dependency-type: "development"
+    cooldown:
+      default-days: 7

From 16d1bdcce6e3164aa6c5f137877c31616b5560b9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 5 Aug 2026 18:43:37 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scripts/extract_value_from_json.py            |  2 +-
 scripts/extract_value_from_yaml.py            |  3 +-
 scripts/filter_bam_by_readids.py              |  3 +-
 scripts/filter_fastq_by_readids_highmem.py    |  3 +-
 scripts/filter_fastq_by_readids_highmem_pe.py |  3 +-
 src/ccbr_tools/GSEA/deg2gs.py                 | 25 +++++++-------
 src/ccbr_tools/GSEA/multitext2excel.py        | 25 ++++++--------
 src/ccbr_tools/GSEA/ncbr_huse.py              | 16 +++------
 src/ccbr_tools/__main__.py                    |  8 ++---
 src/ccbr_tools/gb2gtf.py                      |  3 +-
 src/ccbr_tools/github.py                      |  3 +-
 src/ccbr_tools/homologfinder/hf.py            |  8 ++---
 src/ccbr_tools/hooks/__main__.py              |  4 +--
 src/ccbr_tools/intersect.py                   |  1 -
 src/ccbr_tools/jobby.py                       | 12 +++----
 src/ccbr_tools/jobinfo.py                     | 18 +++++-----
 src/ccbr_tools/paths.py                       |  8 ++---
 src/ccbr_tools/peek.py                        | 12 +++----
 src/ccbr_tools/pipeline/__init__.py           |  2 +-
 src/ccbr_tools/pipeline/cache.py              | 16 ++++-----
 src/ccbr_tools/pipeline/hpc.py                |  2 +-
 src/ccbr_tools/pipeline/nextflow.py           | 12 +++----
 src/ccbr_tools/pipeline/util.py               | 33 +++++++------------
 src/ccbr_tools/pkg_util.py                    | 13 ++++----
 src/ccbr_tools/send_email.py                  |  2 +-
 src/ccbr_tools/software.py                    | 10 +++---
 src/ccbr_tools/spooker.py                     |  7 ++--
 src/ccbr_tools/versions.py                    |  2 +-
 tests/test_cli.py                             |  5 +--
 tests/test_gb2gtf.py                          |  2 +-
 tests/test_github.py                          |  3 +-
 tests/test_gsea.py                            |  6 ++--
 tests/test_gsea_cli.py                        |  2 +-
 tests/test_homologfinder.py                   |  2 +-
 tests/test_hooks.py                           |  2 +-
 tests/test_intersect.py                       |  1 +
 tests/test_jobby.py                           | 15 +++++----
 tests/test_jobinfo.py                         |  3 +-
 tests/test_module_list.py                     |  2 +-
 tests/test_nextflow.py                        |  7 ++--
 tests/test_peek.py                            |  2 +-
 tests/test_pipeline_cache.py                  |  2 +-
 tests/test_pipeline_util.py                   |  6 ++--
 tests/test_pkg_util.py                        |  3 +-
 tests/test_scripts.py                         |  2 +-
 tests/test_shell.py                           |  2 +-
 tests/test_software.py                        | 14 ++++----
 tests/test_spooker.py                         | 10 ++----
 tests/test_templates.py                       |  3 +-
 tests/test_versions.py                        | 10 +++---
 50 files changed, 168 insertions(+), 192 deletions(-)

diff --git a/scripts/extract_value_from_json.py b/scripts/extract_value_from_json.py
index 3acbd62..7f8cb5b 100755
--- a/scripts/extract_value_from_json.py
+++ b/scripts/extract_value_from_json.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
-import json
 import argparse
+import json
 
 parser = argparse.ArgumentParser(description="extract value for key from JSON")
 parser.add_argument("-j", dest="json", required=True, help="input JSON file")
diff --git a/scripts/extract_value_from_yaml.py b/scripts/extract_value_from_yaml.py
index 56f7b92..31012a0 100755
--- a/scripts/extract_value_from_yaml.py
+++ b/scripts/extract_value_from_yaml.py
@@ -1,7 +1,8 @@
 #!/usr/bin/env python
-import yaml
 import argparse
 
+import yaml
+
 parser = argparse.ArgumentParser(description="extract value for key from YAML")
 parser.add_argument("-y", dest="yaml", required=True, help="input YAML file")
 parser.add_argument(
diff --git a/scripts/filter_bam_by_readids.py b/scripts/filter_bam_by_readids.py
index c2df125..19f5242 100755
--- a/scripts/filter_bam_by_readids.py
+++ b/scripts/filter_bam_by_readids.py
@@ -1,7 +1,8 @@
 #!/usr/bin/env python
-import pysam
 import argparse
 
+import pysam
+
 parser = argparse.ArgumentParser(description="Filter BAM by readids")
 parser.add_argument(
     "--inputBAM", dest="inputBAM", type=str, required=True, help="input BAM file"
diff --git a/scripts/filter_fastq_by_readids_highmem.py b/scripts/filter_fastq_by_readids_highmem.py
index 2767296..43ce62f 100755
--- a/scripts/filter_fastq_by_readids_highmem.py
+++ b/scripts/filter_fastq_by_readids_highmem.py
@@ -1,8 +1,9 @@
 #!/usr/bin/env python3
-import HTSeq
 import argparse
 import os
 
+import HTSeq
+
 
 def get_sname(s):
     """Return the sample name from the input path."""
diff --git a/scripts/filter_fastq_by_readids_highmem_pe.py b/scripts/filter_fastq_by_readids_highmem_pe.py
index dff589c..1802a51 100755
--- a/scripts/filter_fastq_by_readids_highmem_pe.py
+++ b/scripts/filter_fastq_by_readids_highmem_pe.py
@@ -1,8 +1,9 @@
 #!/usr/bin/env python
-import HTSeq
 import argparse
 import os
 
+import HTSeq
+
 
 def get_sname(s):
     """Return the sample name from the input path."""
diff --git a/src/ccbr_tools/GSEA/deg2gs.py b/src/ccbr_tools/GSEA/deg2gs.py
index ac4c91c..23dc26e 100755
--- a/src/ccbr_tools/GSEA/deg2gs.py
+++ b/src/ccbr_tools/GSEA/deg2gs.py
@@ -20,15 +20,16 @@
 __version__ = "1.1"
 __copyright__ = "No copyright protection, can be used freely"
 
-import sys
+import argparse
+import datetime
 import os
 import re
-import datetime
+import sys
+from argparse import RawTextHelpFormatter
+
 import pandas as pd
 
-import argparse
-from argparse import RawTextHelpFormatter
-from .ncbr_huse import send_update, err_out
+from .ncbr_huse import err_out, send_update
 
 
 ####################################
@@ -190,9 +191,7 @@ def main():
         log.write(" ".join(sys.argv) + "\n")
         log.write("deg2gs.py version " + __version__ + "\n")
         log.write(
-            "Exporting genes to {}, n={}, p={}, q={}, ".format(
-                outfile.name, nhits, pvalue, qvalue
-            )
+            f"Exporting genes to {outfile.name}, n={nhits}, p={pvalue}, q={qvalue}, "
         )
         log.flush()
 
@@ -214,9 +213,7 @@ def main():
     #
     if df.shape[1] != len(in_cols):
         errMsg = (
-            '\nYour input file does not match the expected format "{}".\n'.format(
-                fformat
-            )
+            f'\nYour input file does not match the expected format "{fformat}".\n'
             + "Please check the file or the selected format and try again\n."
         )
         if keepLog:
@@ -229,7 +226,7 @@ def main():
 
     # split the ensemblID|Gene if necessary
     if fformat == "topTable":  # and method == 'gsea':
-        df["gene"] = [re.sub("^.*\|", "", i) for i in df.index.values.tolist()]
+        df["gene"] = [re.sub(r"^.*\|", "", i) for i in df.index.values.tolist()]
 
     # Filter the df to the p-values, FDR, and number of hits specified
     df = filter_by_p(df, nhits, pvalue, qvalue)
@@ -253,11 +250,11 @@ def main():
     # Close out the log file
     #
     if keepLog:
-        send_update("deg2gs.py successfully completed.  {} written.".format(fname), log)
+        send_update(f"deg2gs.py successfully completed.  {fname} written.", log)
         send_update(str(datetime.datetime.now()) + "\n", log)
         log.close()
     else:
-        print("deg2gs.py successfully completed.  {} written.".format(fname))
+        print(f"deg2gs.py successfully completed.  {fname} written.")
 
 
 if __name__ == "__main__":
diff --git a/src/ccbr_tools/GSEA/multitext2excel.py b/src/ccbr_tools/GSEA/multitext2excel.py
index 8975923..afba632 100755
--- a/src/ccbr_tools/GSEA/multitext2excel.py
+++ b/src/ccbr_tools/GSEA/multitext2excel.py
@@ -18,23 +18,22 @@
 __copyright__ = "No copyright protection, can be used freely"
 
 # import csv
-import sys
-import os
-import re
-import datetime
-import pandas as pd
-import glob
-
 # import scipy
 # import numpy
-
 import argparse
+import datetime
+import glob
+import os
+import re
+import sys
 from argparse import RawTextHelpFormatter
+
+import pandas as pd
+
 from .ncbr_huse import (
     send_update,
 )
 
-
 ####################################
 #
 # Functions
@@ -150,11 +149,7 @@ def main():
         sheet_name = re.sub(indir + "/", "", filename).split(splitter)[0]
         if firstsplitter != "":
             sheet_name = sheet_name.split(firstsplitter)[1]
-        print(
-            "Writing data from input file: {} to output tab: {}".format(
-                filename, sheet_name
-            )
-        )
+        print(f"Writing data from input file: {filename} to output tab: {sheet_name}")
 
         # Read in the data
         df = pd.read_csv(filename, sep=delimiter, header=0, encoding="unicode_escape")
@@ -169,7 +164,7 @@ def main():
     # Close out the log file
     #
     send_update(
-        "multitext2excel.py successfully completed.  {} written.".format(outfile.name),
+        f"multitext2excel.py successfully completed.  {outfile.name} written.",
         log,
     )
     send_update(str(datetime.datetime.now()) + "\n", log)
diff --git a/src/ccbr_tools/GSEA/ncbr_huse.py b/src/ccbr_tools/GSEA/ncbr_huse.py
index cf793fd..509d2d8 100755
--- a/src/ccbr_tools/GSEA/ncbr_huse.py
+++ b/src/ccbr_tools/GSEA/ncbr_huse.py
@@ -10,10 +10,10 @@
 __version__ = "1.0.0"
 __copyright__ = "none"
 
-import sys
 import os
 import re
 import subprocess
+import sys
 
 try:
     import MySQLdb
@@ -139,27 +139,19 @@ def pause_for_input(txt, contkey="y", quitkey="q", log=None):
             err_out("User elected to quit.  Exiting...\n", log)
 
         # if none, just return the input
-        if contkey is None:
-            result = answer
-
-        # if there is a contkey, then be sure it is correctly typed
-        elif answer == contkey:
+        if contkey is None or answer == contkey:
             result = answer
 
         else:
             # give them additional help and increment the answer count
-            reminder = "Note: only {} to continue and {} to quit are valid options.\nPlease try again.\n".format(
-                contkey, quitkey
-            )
+            reminder = f"Note: only {contkey} to continue and {quitkey} to quit are valid options.\nPlease try again.\n"
             if answer_cnt == 0:
                 txt = "\n" + txt + "\n" + reminder
 
             # Otherwise 3 strikes and exit from the loop
             if answer_cnt == 2:
                 err_out(
-                    "User failed to continue ({}) or quit ({}) three times in a row.  Exiting...".format(
-                        contkey, quitkey
-                    ),
+                    f"User failed to continue ({contkey}) or quit ({quitkey}) three times in a row.  Exiting...",
                     log,
                 )
 
diff --git a/src/ccbr_tools/__main__.py b/src/ccbr_tools/__main__.py
index 95e931a..976f2a5 100755
--- a/src/ccbr_tools/__main__.py
+++ b/src/ccbr_tools/__main__.py
@@ -2,20 +2,19 @@
 Entry point for CCBR Tools
 """
 
-import click
 import cffconvert.cli.cli
+import click
 
 from .pkg_util import (
+    CustomClickGroup,
     get_project_scripts,
     get_version,
     print_citation,
     repo_base,
-    CustomClickGroup,
 )
 from .send_email import send_email_msg
-from .templates import use_quarto_ext, get_quarto_extensions
 from .software import install as install_software
-
+from .templates import get_quarto_extensions, use_quarto_ext
 
 all_scripts = "All installed tools:\n" + "\n".join(
     [f"  {cmd}" for cmd in get_project_scripts()]
@@ -37,7 +36,6 @@ def cli():
 
     https://ccbr.github.io/Tools/
     """
-    pass
 
 
 @click.command()
diff --git a/src/ccbr_tools/gb2gtf.py b/src/ccbr_tools/gb2gtf.py
index efc8834..117ac4d 100755
--- a/src/ccbr_tools/gb2gtf.py
+++ b/src/ccbr_tools/gb2gtf.py
@@ -9,8 +9,9 @@
 # Usage:python gb2gtf.py sequence.gb  > sequence.gtf
 
 import sys
-from Bio import SeqIO
+
 import Bio
+from Bio import SeqIO
 
 
 def main():
diff --git a/src/ccbr_tools/github.py b/src/ccbr_tools/github.py
index 095dfb5..9c801cf 100644
--- a/src/ccbr_tools/github.py
+++ b/src/ccbr_tools/github.py
@@ -10,6 +10,7 @@
 """
 
 import warnings
+
 from .pkg_util import get_url_json
 
 
@@ -64,7 +65,7 @@ def get_user_info(user_login):
     try:
         user_info = get_url_json(url)
     except ConnectionError as e:
-        warnings.warn(f"Could not retrieve user info for {user_login}. {str(e)}")
+        warnings.warn(f"Could not retrieve user info for {user_login}. {e!s}")
     return user_info
 
 
diff --git a/src/ccbr_tools/homologfinder/hf.py b/src/ccbr_tools/homologfinder/hf.py
index f70e464..7f2f3b5 100755
--- a/src/ccbr_tools/homologfinder/hf.py
+++ b/src/ccbr_tools/homologfinder/hf.py
@@ -25,13 +25,14 @@
 
 import argparse
 import importlib.resources
-import pandas as pd
 import sys
 
+import pandas as pd
+
 
 def exit_w_msg(message):
     """Gracefully exit with proper message"""
-    print("{} : EXITING!!".format(__file__))
+    print(f"{__file__} : EXITING!!")
     print(message)
     sys.exit()
 
@@ -42,7 +43,6 @@ def check_help(parser):
         print(__doc__)
         parser.print_help()
         parser.exit()
-    return
 
 
 def collect_args():
@@ -54,7 +54,7 @@ def collect_args():
 
     # add version
     parser.add_argument(
-        "-v", "--version", action="version", version="%(prog)s {}".format(__version__)
+        "-v", "--version", action="version", version=f"%(prog)s {__version__}"
     )
 
     # add joblist
diff --git a/src/ccbr_tools/hooks/__main__.py b/src/ccbr_tools/hooks/__main__.py
index 55ae98e..729c916 100644
--- a/src/ccbr_tools/hooks/__main__.py
+++ b/src/ccbr_tools/hooks/__main__.py
@@ -3,9 +3,10 @@
 """
 
 import click
+
 from ..pkg_util import (
-    get_version,
     CustomClickGroup,
+    get_version,
 )
 from .detect_absolute_paths import detect_absolute_paths
 from .sync_nextflow_version import sync_nextflow_version
@@ -25,7 +26,6 @@ def cli():
 
     https://ccbr.github.io/Tools/hooks
     """
-    pass
 
 
 cli.add_command(detect_absolute_paths)
diff --git a/src/ccbr_tools/intersect.py b/src/ccbr_tools/intersect.py
index 8f4d375..5f2a4b1 100755
--- a/src/ccbr_tools/intersect.py
+++ b/src/ccbr_tools/intersect.py
@@ -7,7 +7,6 @@
     intersect file1 file2
 """
 
-from __future__ import print_function
 import sys
 
 
diff --git a/src/ccbr_tools/jobby.py b/src/ccbr_tools/jobby.py
index 152eecc..07bfc90 100755
--- a/src/ccbr_tools/jobby.py
+++ b/src/ccbr_tools/jobby.py
@@ -44,9 +44,6 @@
     ```
 """
 
-from .pkg_util import get_version
-from .paths import glob_files
-
 import itertools
 import json
 import os
@@ -55,6 +52,9 @@
 import sys
 import warnings
 
+from .paths import glob_files
+from .pkg_util import get_version
+
 # Graceful imports
 try:
     import pandas as pd
@@ -123,7 +123,7 @@ def parse_time_to_seconds(t: str):
                 s = parts[0]
 
             total_seconds = int(
-                round((int(days) * 86400 + int(h) * 3600 + int(m) * 60 + s))
+                round(int(days) * 86400 + int(h) * 3600 + int(m) * 60 + s)
             )
     except ValueError:
         warnings.warn(f"❌ Invalid time format: {t}. Time will be set to NaN.")
@@ -171,7 +171,7 @@ def extract_jobids_from_file(filepath):
                         job_ids.append(match_nextflow.group(1))
     except FileNotFoundError:
         warnings.warn(f"❌ File not found: {filepath}")
-    return list(sorted(set(job_ids)))  # deduplicate
+    return sorted(set(job_ids))  # deduplicate
 
 
 def list_records(
@@ -242,7 +242,7 @@ def get_sacct_info(
                 # If this is .batch, update resource usage fields
                 if step_type.endswith(".batch"):
                     for resource_field in ("MaxRSS", "AveRSS", "MaxVMSize"):
-                        if resource_field in record_raw and record_raw[resource_field]:
+                        if record_raw.get(resource_field):
                             job_records[base_jobid][resource_field] = record_raw[
                                 resource_field
                             ]
diff --git a/src/ccbr_tools/jobinfo.py b/src/ccbr_tools/jobinfo.py
index 65da9eb..7c65261 100755
--- a/src/ccbr_tools/jobinfo.py
+++ b/src/ccbr_tools/jobinfo.py
@@ -24,12 +24,13 @@
 __email__ = "vishal.koparde@nih.gov"
 
 import argparse
-import subprocess
+import datetime
 import json
 import os
-import datetime
-import time
+import subprocess
 import sys
+import time
+
 import pandas as pd
 
 # SHORT_FIELDS used to display on screen
@@ -45,7 +46,7 @@
 
 def exit_w_msg(message):
     """Gracefully exit with proper message"""
-    print("{} : EXITING!!".format(__file__))
+    print(f"{__file__} : EXITING!!")
     print(message)
     sys.exit()
 
@@ -56,7 +57,6 @@ def check_help(parser):
         print(__doc__)
         parser.print_help()
         parser.exit()
-    return
 
 
 def check_host():
@@ -79,7 +79,7 @@ def collect_args():
 
     # add version
     parser.add_argument(
-        "-v", "--version", action="version", version="%(prog)s {}".format(__version__)
+        "-v", "--version", action="version", version=f"%(prog)s {__version__}"
     )
 
     # add joblist
@@ -126,7 +126,7 @@ def collect_args():
     if args.output:
         args.output = os.path.abspath(args.output)
         if not os.access(os.path.dirname(args.output), os.W_OK):
-            msg = "File is not writable: {}".format(args.output)
+            msg = f"File is not writable: {args.output}"
             exit_w_msg(msg)
 
     if args.joblist and args.snakemakelog:
@@ -142,7 +142,7 @@ def collect_args():
         cmd = (
             'grep "external jobid" '
             + args.snakemakelog.name
-            + ' | awk \'{print $NF}\' | sed "s/\'//g" | sed "s/\.//g"'
+            + ' | awk \'{print $NF}\' | sed "s/\'//g" | sed "s/\\.//g"'
         )
         p1 = subprocess.run(cmd, capture_output=True, text=True, shell=True)
         args.joblist = p1.stdout.strip().split("\n")
@@ -292,7 +292,7 @@ def get_jobinfo(args):
                     columns=LONG_FIELDS.split(","),
                 )
         except OSError:
-            msg = "File is not writable: {}".format(args.output)
+            msg = f"File is not writable: {args.output}"
             exit_w_msg(msg)
     return p1_table
 
diff --git a/src/ccbr_tools/paths.py b/src/ccbr_tools/paths.py
index 1c643f4..498ba87 100644
--- a/src/ccbr_tools/paths.py
+++ b/src/ccbr_tools/paths.py
@@ -56,11 +56,9 @@ def get_disk_usage(tree_dict, pipeline_outdir):
     """Get disk usage."""
     try:
         report = next(
-            (
-                item
-                for item in tree_dict
-                if isinstance(item, dict) and item.get("type") == "report"
-            )
+            item
+            for item in tree_dict
+            if isinstance(item, dict) and item.get("type") == "report"
         )
         dir_size = report.get("size", math.nan)
     except StopIteration:  # occurs when there is no report in the tree dict
diff --git a/src/ccbr_tools/peek.py b/src/ccbr_tools/peek.py
index 75cae51..60eaf91 100755
--- a/src/ccbr_tools/peek.py
+++ b/src/ccbr_tools/peek.py
@@ -5,9 +5,8 @@
     peek <file.tsv> [buffer]
 """
 
-from __future__ import print_function
-from pathlib import Path
 import sys
+from pathlib import Path
 
 
 def usage():
@@ -29,7 +28,6 @@ def pargs():
         sys.argv[1]
     except IndexError:
         usage()
-    return
 
 
 def max_string(data):
@@ -43,7 +41,7 @@ def max_string(data):
 
 def print_header(filename, length):
     """Print filenames and divider"""
-    print("# {}".format(filename))
+    print(f"# {filename}")
     print("{}".format("=" * length))
 
 
@@ -75,7 +73,7 @@ def pprint(headlist, data, linelength, fn):
 
         # Calculate spacing for justifying to the right
         insert_spaces = justify(len(column), len(value), linelength, rownumber)
-        print("{} {}{}{}".format(rownumber, column, insert_spaces, value))
+        print(f"{rownumber} {column}{insert_spaces}{value}")
 
 
 def peek(filename, buffer, delim="\t"):
@@ -85,9 +83,9 @@ def peek(filename, buffer, delim="\t"):
     """Peek at the input data."""
     try:
         fh = open(filename, "r")
-    except IOError as e:
+    except OSError as e:
         # File does not exist
-        print("\n{}\nPlease check you filename!\n\n".format(e))
+        print(f"\n{e}\nPlease check you filename!\n\n")
         usage()
 
     headerlist = fh.readline().split(delim)
diff --git a/src/ccbr_tools/pipeline/__init__.py b/src/ccbr_tools/pipeline/__init__.py
index 7af06ee..486f029 100755
--- a/src/ccbr_tools/pipeline/__init__.py
+++ b/src/ccbr_tools/pipeline/__init__.py
@@ -72,7 +72,7 @@ def count_samples(cls, tree_str):
             nsamples = len(sample_names)
         except Exception as err:
             warnings.warn(
-                f"Could not determine number of samples. See original error message below:\n{repr(err)}"
+                f"Could not determine number of samples. See original error message below:\n{err!r}"
             )
         return nsamples, sample_names
 
diff --git a/src/ccbr_tools/pipeline/cache.py b/src/ccbr_tools/pipeline/cache.py
index bc69cb5..a45f8b6 100755
--- a/src/ccbr_tools/pipeline/cache.py
+++ b/src/ccbr_tools/pipeline/cache.py
@@ -81,9 +81,7 @@ def image_cache(sub_args, config):
                 # If local sif does not exist on in cache, print warning
                 # and default to pulling from URI in config/containers/images.json
                 print(
-                    'Warning: Local image "{}" does not exist in singularity cache'.format(
-                        sif
-                    ),
+                    f'Warning: Local image "{sif}" does not exist in singularity cache',
                     file=sys.stderr,
                 )
             else:
@@ -115,10 +113,10 @@ def check_cache(parser, cache, *args, **kwargs):
     elif os.path.isfile(cache):
         # Cache directory exists as file, raise error
         parser.error(
-            """\n\t\x1b[6;37;41mFatal: Failed to provided a valid singularity cache!\x1b[0m
+            f"""\n\t\x1b[6;37;41mFatal: Failed to provided a valid singularity cache!\x1b[0m
         The provided --singularity-cache already exists on the filesystem as a file.
-        Please run {} again with a different --singularity-cache location.
-        """.format(sys.argv[0])
+        Please run {sys.argv[0]} again with a different --singularity-cache location.
+        """
         )
     elif os.path.isdir(cache):
         # Provide cache exists as directory
@@ -130,11 +128,11 @@ def check_cache(parser, cache, *args, **kwargs):
         ):
             # User does NOT own the cache directory, raise error
             parser.error(
-                """\n\t\x1b[6;37;41mFatal: Failed to provided a valid singularity cache!\x1b[0m
+                f"""\n\t\x1b[6;37;41mFatal: Failed to provided a valid singularity cache!\x1b[0m
                 The provided --singularity-cache already exists on the filesystem with a different owner.
                 Singularity strictly enforces that the cache directory is not shared across users.
-                Please run {} again with a different --singularity-cache location.
-                """.format(sys.argv[0])
+                Please run {sys.argv[0]} again with a different --singularity-cache location.
+                """
             )
 
     return cache
diff --git a/src/ccbr_tools/pipeline/hpc.py b/src/ccbr_tools/pipeline/hpc.py
index 3268e31..b6b833c 100755
--- a/src/ccbr_tools/pipeline/hpc.py
+++ b/src/ccbr_tools/pipeline/hpc.py
@@ -9,8 +9,8 @@
 import re
 import shutil
 
-from .cache import get_singularity_cachedir, get_sif_cache_dir
 from ..shell import shell_run
+from .cache import get_sif_cache_dir, get_singularity_cachedir
 
 
 class Cluster:
diff --git a/src/ccbr_tools/pipeline/nextflow.py b/src/ccbr_tools/pipeline/nextflow.py
index c9daa39..5f817de 100755
--- a/src/ccbr_tools/pipeline/nextflow.py
+++ b/src/ccbr_tools/pipeline/nextflow.py
@@ -13,8 +13,8 @@
 from ..pkg_util import msg_box
 from ..shell import shell_run
 from ..templates import use_template
-from .util import copy_config
 from .hpc import get_hpc
+from .util import copy_config
 
 
 def init(output, repo_base, pipeline_name="pipeline"):
@@ -83,9 +83,7 @@ def run(
             prev_arg = arg
     # make sure profile matches biowulf or frce
     profiles = (
-        set(args_dict["-profile"].split(","))
-        if "-profile" in args_dict.keys()
-        else set()
+        set(args_dict["-profile"].split(",")) if "-profile" in args_dict else set()
     )
     if mode == "slurm":
         profiles.add("slurm")
@@ -95,16 +93,16 @@ def run(
         args_dict["-profile"] = ",".join(sorted(profiles))
 
     # use -resume by default, or do not use resume if force_all is True
-    if force_all and "-resume" in args_dict.keys():
+    if force_all and "-resume" in args_dict:
         args_dict.pop("-resume")
-    elif not force_all and "-resume" not in args_dict.keys():
+    elif not force_all and "-resume" not in args_dict:
         args_dict["-resume"] = ""
 
     nextflow_command = " ".join(
         ["nextflow", "run", nextfile_path] + [f"{k} {v}" for k, v in args_dict.items()]
     )
     # Print a preview before launching the actual run
-    if "-preview" not in args_dict.keys():
+    if "-preview" not in args_dict:
         preview_command = (
             (f'bash -c "module load {hpc_modules} && {nextflow_command} -preview"')
             if hpc and hpc_modules
diff --git a/src/ccbr_tools/pipeline/util.py b/src/ccbr_tools/pipeline/util.py
index 231cf73..3fc2c0f 100755
--- a/src/ccbr_tools/pipeline/util.py
+++ b/src/ccbr_tools/pipeline/util.py
@@ -4,20 +4,21 @@
 
 import collections
 import datetime
-import shutil
-import sys
+import glob
 import hashlib
 import json
-import glob
 import os
 import pathlib
 import re
+import shutil
 import stat
 import subprocess
+import sys
 import warnings
+
 import yaml
 
-from ..pkg_util import repo_base, msg
+from ..pkg_util import msg, repo_base
 from .hpc import get_hpcname
 
 
@@ -139,13 +140,9 @@ def permissions(parser, path, *args, **kwargs):
         str: Returns absolute path if it exists and permissions are correct.
     """
     if not exists(path):
-        parser.error(
-            "Path '{}' does not exists! Failed to provide valid input.".format(path)
-        )
+        parser.error(f"Path '{path}' does not exists! Failed to provide valid input.")
     if not os.access(path, *args, **kwargs):
-        parser.error(
-            "Path '{}' exists, but cannot read path due to permissions!".format(path)
-        )
+        parser.error(f"Path '{path}' exists, but cannot read path due to permissions!")
 
     return os.path.abspath(path)
 
@@ -266,17 +263,13 @@ def require(cmds, suggestions, path=None):
         if not available:
             error = True
             err(
-                """\x1b[6;37;41m\n\tFatal: {} is not in $PATH and is required during runtime!
-            └── Solution: please 'module load {}' and run again!\x1b[0m""".format(
-                    cmds[i], suggestions[i]
-                )
+                f"""\x1b[6;37;41m\n\tFatal: {cmds[i]} is not in $PATH and is required during runtime!
+            └── Solution: please 'module load {suggestions[i]}' and run again!\x1b[0m"""
             )
 
     if error:
         fatal()
 
-    return
-
 
 def safe_copy(source, target, resources=[]):
     """
@@ -360,9 +353,7 @@ def check_python_version(MIN_PYTHON=(3, 11)):
     try:
         assert sys.version_info >= MIN_PYTHON
         print(
-            "Python version: {0}.{1}.{2}".format(
-                sys.version_info.major, sys.version_info.minor, sys.version_info.micro
-            )
+            f"Python version: {sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}"
         )
     except AssertionError:
         exit(
@@ -485,7 +476,7 @@ def rename(filename):
 
     if not converted:
         raise NameError(
-            """\n\tFatal: Failed to rename provided input '{}'!
+            f"""\n\tFatal: Failed to rename provided input '{filename}'!
         Cannot determine the extension of the user provided input file.
         Please rename the file list above before trying again.
         Here is example of acceptable input file extensions:
@@ -494,7 +485,7 @@ def rename(filename):
           sampleName_1.fastq.gz       sampleName_2.fastq.gz
         Please also check that your input files are gzipped?
         If they are not, please gzip them before proceeding again.
-        """.format(filename)
+        """
         )
 
     return renamed_filename
diff --git a/src/ccbr_tools/pkg_util.py b/src/ccbr_tools/pkg_util.py
index 50f4fa5..d1dbca9 100755
--- a/src/ccbr_tools/pkg_util.py
+++ b/src/ccbr_tools/pkg_util.py
@@ -2,18 +2,19 @@
 Miscellaneous utility functions for the package
 """
 
-import click
 import datetime
-import importlib.resources
 import importlib.metadata
+import importlib.resources
 import os
 import pathlib
-import requests
-from time import localtime, strftime
-import tomllib
 import uuid
+from time import localtime, strftime
 from urllib.parse import urlparse
 
+import click
+import requests
+import tomllib
+
 
 class CustomClickGroup(click.Group):
     def format_epilog(self, ctx, formatter):
@@ -156,7 +157,7 @@ def msg_box(splash, errmsg=None):
     """
     msg("-" * (len(splash) + 4))
     msg(f"| {splash} |")
-    msg(("-" * (len(splash) + 4)))
+    msg("-" * (len(splash) + 4))
     if errmsg:
         click.echo("\n" + errmsg, err=True)
 
diff --git a/src/ccbr_tools/send_email.py b/src/ccbr_tools/send_email.py
index 3d41143..f63fb8c 100644
--- a/src/ccbr_tools/send_email.py
+++ b/src/ccbr_tools/send_email.py
@@ -5,9 +5,9 @@
 Intended to run from biowulf
 """
 
-from email.message import EmailMessage
 import os
 import smtplib
+from email.message import EmailMessage
 
 
 def send_email_msg(
diff --git a/src/ccbr_tools/software.py b/src/ccbr_tools/software.py
index 4f4bdec..c8696f2 100644
--- a/src/ccbr_tools/software.py
+++ b/src/ccbr_tools/software.py
@@ -1,6 +1,6 @@
 from .pipeline.hpc import Cluster
 from .shell import shell_run
-from .versions import match_semver, get_major_minor_version
+from .versions import get_major_minor_version, match_semver
 
 
 class Software:
@@ -88,7 +88,7 @@ def bash(software: Software, hpc: Cluster, branch_tag=None):
 
 class PythonTool(Software):
     def __init__(self, name, version):
-        super(PythonTool, self).__init__(name, version)
+        super().__init__(name, version)
         self.repo_name = name.replace("ccbr_", "")
 
     def install(self, hpc: Cluster, branch_tag=None):
@@ -103,7 +103,7 @@ def url(self):
 
 class BashTool(Software):
     def __init__(self, name, version):
-        super(BashTool, self).__init__(name, version)
+        super().__init__(name, version)
 
     def install(self, hpc: Cluster, branch_tag=None):
         """Return the install command."""
@@ -112,7 +112,7 @@ def install(self, hpc: Cluster, branch_tag=None):
 
 class Nextflow(Software):
     def __init__(self, name, version):
-        super(Nextflow, self).__init__(name.upper(), version)
+        super().__init__(name.upper(), version)
 
     def path(self, hpc: Cluster):
         """Return the installation path."""
@@ -130,7 +130,7 @@ def install(self, hpc: Cluster, branch_tag=None):
 
 class Snakemake(Software):
     def __init__(self, name, version):
-        super(Snakemake, self).__init__(name.upper(), version)
+        super().__init__(name.upper(), version)
 
     def path(self, hpc: Cluster):
         """Return the installation path."""
diff --git a/src/ccbr_tools/spooker.py b/src/ccbr_tools/spooker.py
index 2891d0a..2f66886 100644
--- a/src/ccbr_tools/spooker.py
+++ b/src/ccbr_tools/spooker.py
@@ -9,17 +9,18 @@
 See [](`~ccbr_tools.spooker.spooker`) for the main function
 """
 
-import click
 import gzip
 import json
 import os
 import pathlib
 
-from .paths import get_tree, load_tree, get_disk_usage, glob_files
+import click
+
+from .jobby import jobby
+from .paths import get_disk_usage, get_tree, glob_files, load_tree
 from .pipeline import count_pipeline_samples
 from .pipeline.hpc import Cluster, list_modules, parse_modules
 from .pkg_util import get_random_string, get_timestamp
-from .jobby import jobby
 from .shell import get_groups, shell_run
 
 
diff --git a/src/ccbr_tools/versions.py b/src/ccbr_tools/versions.py
index 9777570..325dce0 100644
--- a/src/ccbr_tools/versions.py
+++ b/src/ccbr_tools/versions.py
@@ -6,8 +6,8 @@
 import re
 import warnings
 
-from .shell import shell_run
 from .pkg_util import get_url_json
+from .shell import shell_run
 
 
 def get_current_hash():
diff --git a/tests/test_cli.py b/tests/test_cli.py
index fafa01b..f30371b 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,9 +1,10 @@
-from ccbr_tools.shell import shell_run
-
 import os
 import pathlib
+
 import pytest
 
+from ccbr_tools.shell import shell_run
+
 is_ci = (
     os.environ.get("CI", "false") == "true"
 )  # Set CI to false if not in a CI environment
diff --git a/tests/test_gb2gtf.py b/tests/test_gb2gtf.py
index e07af49..4a8a2b3 100644
--- a/tests/test_gb2gtf.py
+++ b/tests/test_gb2gtf.py
@@ -1,6 +1,6 @@
 import pytest
 
-import ccbr_tools.gb2gtf as gb2gtf
+from ccbr_tools import gb2gtf
 from ccbr_tools.shell import exec_in_context
 
 
diff --git a/tests/test_github.py b/tests/test_github.py
index 74c3d5e..54c8eec 100644
--- a/tests/test_github.py
+++ b/tests/test_github.py
@@ -1,6 +1,7 @@
-from ccbr_tools.github import print_contributor_images, get_user_info
 import pytest
 
+from ccbr_tools.github import get_user_info, print_contributor_images
+
 
 def test_print_contributor_images():
     """Test print contributor images."""
diff --git a/tests/test_gsea.py b/tests/test_gsea.py
index 517bbc4..819f8fe 100644
--- a/tests/test_gsea.py
+++ b/tests/test_gsea.py
@@ -1,9 +1,9 @@
-from ccbr_tools.shell import shell_run
+import sys
 
 import pytest
-import sys
 
-import ccbr_tools.GSEA.ncbr_huse as ncbr_huse
+from ccbr_tools.GSEA import ncbr_huse
+from ccbr_tools.shell import shell_run
 
 
 def test_help_deg():
diff --git a/tests/test_gsea_cli.py b/tests/test_gsea_cli.py
index 04f85b6..009517e 100644
--- a/tests/test_gsea_cli.py
+++ b/tests/test_gsea_cli.py
@@ -3,8 +3,8 @@
 import pandas as pd
 import pytest
 
-import ccbr_tools.GSEA.deg2gs as deg2gs
 import ccbr_tools.GSEA.multitext2excel as mt2excel
+from ccbr_tools.GSEA import deg2gs
 
 
 def test_deg2gs_gsea_pipeliner(tmp_path, mocker):
diff --git a/tests/test_homologfinder.py b/tests/test_homologfinder.py
index 2f60469..69ccaa8 100644
--- a/tests/test_homologfinder.py
+++ b/tests/test_homologfinder.py
@@ -1,6 +1,6 @@
 import argparse
 
-import ccbr_tools.homologfinder.hf as hf
+from ccbr_tools.homologfinder import hf
 from ccbr_tools.shell import shell_run
 
 
diff --git a/tests/test_hooks.py b/tests/test_hooks.py
index 414a514..00a08e6 100644
--- a/tests/test_hooks.py
+++ b/tests/test_hooks.py
@@ -7,8 +7,8 @@
 import pytest
 from click.testing import CliRunner
 
-from ccbr_tools.hooks import detect_absolute_paths as hooks
 import ccbr_tools.hooks.__main__ as hooks_main
+from ccbr_tools.hooks import detect_absolute_paths as hooks
 from ccbr_tools.hooks.sync_nextflow_version import (
     sync_nextflow_version,
     update_manifest_version,
diff --git a/tests/test_intersect.py b/tests/test_intersect.py
index d582943..cbe1c28 100644
--- a/tests/test_intersect.py
+++ b/tests/test_intersect.py
@@ -1,4 +1,5 @@
 import pytest
+
 import ccbr_tools.intersect
 from ccbr_tools.shell import exec_in_context
 
diff --git a/tests/test_jobby.py b/tests/test_jobby.py
index 45d4741..e520045 100644
--- a/tests/test_jobby.py
+++ b/tests/test_jobby.py
@@ -1,20 +1,21 @@
 import gzip
 import os
-import numpy as np
-import pandas as pd
 import pickle
 import pprint
+
+import numpy as np
+import pandas as pd
 import pytest
 
 from ccbr_tools.jobby import (
-    jobby,
-    parse_time_to_seconds,
-    parse_mem_to_gb,
     extract_jobids_from_file,
-    list_records,
-    records_to_df,
     format_df,
     get_job_logs,
+    jobby,
+    list_records,
+    parse_mem_to_gb,
+    parse_time_to_seconds,
+    records_to_df,
 )
 from ccbr_tools.pipeline.hpc import get_hpcname
 from ccbr_tools.shell import shell_run
diff --git a/tests/test_jobinfo.py b/tests/test_jobinfo.py
index db757c7..19485fa 100644
--- a/tests/test_jobinfo.py
+++ b/tests/test_jobinfo.py
@@ -1,10 +1,11 @@
 import argparse
 import json
 import sys
+
 import pytest
 
+from ccbr_tools.jobinfo import check_host, get_jobinfo, mem2gb, time2sec
 from ccbr_tools.shell import shell_run
-from ccbr_tools.jobinfo import get_jobinfo, check_host, mem2gb, time2sec
 
 
 def test_jobinfo_cli():
diff --git a/tests/test_module_list.py b/tests/test_module_list.py
index ceec912..571f5ee 100644
--- a/tests/test_module_list.py
+++ b/tests/test_module_list.py
@@ -1,5 +1,5 @@
+from ccbr_tools.pipeline.hpc import is_loaded, parse_modules
 from ccbr_tools.shell import shell_run
-from ccbr_tools.pipeline.hpc import parse_modules, is_loaded
 
 
 def test_module_list_cli():
diff --git a/tests/test_nextflow.py b/tests/test_nextflow.py
index 916dc4b..8e9cd19 100644
--- a/tests/test_nextflow.py
+++ b/tests/test_nextflow.py
@@ -1,10 +1,11 @@
 import os
 import pathlib
-import pytest
 import subprocess
 
-from ccbr_tools.pipeline.nextflow import run, init
-from ccbr_tools.pipeline.hpc import Biowulf, FRCE
+import pytest
+
+from ccbr_tools.pipeline.hpc import FRCE, Biowulf
+from ccbr_tools.pipeline.nextflow import init, run
 from ccbr_tools.shell import exec_in_context
 
 
diff --git a/tests/test_peek.py b/tests/test_peek.py
index fa50c2f..4223f82 100644
--- a/tests/test_peek.py
+++ b/tests/test_peek.py
@@ -1,4 +1,4 @@
-import ccbr_tools.peek as peek
+from ccbr_tools import peek
 from ccbr_tools.shell import exec_in_context
 
 
diff --git a/tests/test_pipeline_cache.py b/tests/test_pipeline_cache.py
index 1a0f170..a65ddda 100644
--- a/tests/test_pipeline_cache.py
+++ b/tests/test_pipeline_cache.py
@@ -1,10 +1,10 @@
 import argparse
 
 from ccbr_tools.pipeline.cache import (
+    check_cache,
     get_sif_cache_dir,
     get_singularity_cachedir,
     image_cache,
-    check_cache,
 )
 
 
diff --git a/tests/test_pipeline_util.py b/tests/test_pipeline_util.py
index 80c5054..d41a68a 100644
--- a/tests/test_pipeline_util.py
+++ b/tests/test_pipeline_util.py
@@ -3,13 +3,13 @@
 import pathlib
 
 from ccbr_tools.pipeline.util import (
-    copy_config,
-    get_tmp_dir,
     _get_file_mtime,
+    copy_config,
+    exists,
     get_genomes_dict,
+    get_tmp_dir,
     md5sum,
     permissions,
-    exists,
     which,
 )
 from ccbr_tools.pkg_util import repo_base
diff --git a/tests/test_pkg_util.py b/tests/test_pkg_util.py
index 472e24c..333135b 100644
--- a/tests/test_pkg_util.py
+++ b/tests/test_pkg_util.py
@@ -1,6 +1,7 @@
-from ccbr_tools.pkg_util import repo_base, get_url_json
 import pytest
 
+from ccbr_tools.pkg_util import get_url_json, repo_base
+
 
 def test_repo_base():
     """Test repo base."""
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index eab6147..9551ea2 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -1,5 +1,5 @@
-from ccbr_tools.shell import shell_run
 from ccbr_tools.pipeline.hpc import get_hpcname
+from ccbr_tools.shell import shell_run
 
 
 def test_scripts_help():
diff --git a/tests/test_shell.py b/tests/test_shell.py
index efcab90..aee702e 100644
--- a/tests/test_shell.py
+++ b/tests/test_shell.py
@@ -1,4 +1,4 @@
-from ccbr_tools.shell import shell_run, exec_in_context, concat_newline
+from ccbr_tools.shell import concat_newline, exec_in_context, shell_run
 
 
 def test_exec():
diff --git a/tests/test_software.py b/tests/test_software.py
index 5a85185..01e5913 100644
--- a/tests/test_software.py
+++ b/tests/test_software.py
@@ -1,14 +1,14 @@
+import pytest
+
+from ccbr_tools.pipeline.hpc import Biowulf
+from ccbr_tools.shell import exec_in_context
 from ccbr_tools.software import (
+    FINAL_PERMISSIONS,
+    LATEST_SYMLINK,
+    SET_SYMLINK,
     Software,
     install,
-    SET_SYMLINK,
-    LATEST_SYMLINK,
-    FINAL_PERMISSIONS,
 )
-from ccbr_tools.pipeline.hpc import Biowulf
-from ccbr_tools.shell import exec_in_context
-
-import pytest
 
 
 def test_python():
diff --git a/tests/test_spooker.py b/tests/test_spooker.py
index 1687640..e44751a 100644
--- a/tests/test_spooker.py
+++ b/tests/test_spooker.py
@@ -1,8 +1,8 @@
-import pytest
 import gzip
 import json
 import subprocess
 
+import pytest
 
 from ccbr_tools.spooker import spooker
 
@@ -30,9 +30,7 @@ def test_spooker(data_dir_rel):
         "pipeline_version": "0.1.0",
         "sample_names": [],
     }
-    actual = {
-        k: v for k, v in spook_dat["pipeline_metadata"].items() if k in expected.keys()
-    }
+    actual = {k: v for k, v in spook_dat["pipeline_metadata"].items() if k in expected}
     assert actual == expected
 
 
@@ -74,9 +72,7 @@ def test_spooker_cli(data_dir_rel):
         "sample_names": [],
     }
     actual_meta = {
-        k: v
-        for k, v in spook_dat["pipeline_metadata"].items()
-        if k in expected_meta.keys()
+        k: v for k, v in spook_dat["pipeline_metadata"].items() if k in expected_meta
     }
     assert expected_meta == actual_meta
     assert spook_dat.keys() == {
diff --git a/tests/test_templates.py b/tests/test_templates.py
index 78eead7..81bd640 100644
--- a/tests/test_templates.py
+++ b/tests/test_templates.py
@@ -1,9 +1,10 @@
 import os
 import pathlib
+
 import pytest
 
-from ccbr_tools.templates import read_template, use_template, use_quarto_ext
 from ccbr_tools.pipeline.hpc import get_hpc
+from ccbr_tools.templates import read_template, use_quarto_ext, use_template
 
 
 def test_read_template():
diff --git a/tests/test_versions.py b/tests/test_versions.py
index 109ca2a..ce8de34 100644
--- a/tests/test_versions.py
+++ b/tests/test_versions.py
@@ -1,14 +1,14 @@
 import pytest
 
 from ccbr_tools.versions import (
-    get_releases,
-    get_latest_release_tag,
-    get_latest_release_hash,
-    get_tag_hash,
-    match_semver,
     check_version_increments_by_one,
+    get_latest_release_hash,
+    get_latest_release_tag,
     get_major_minor_version,
+    get_releases,
+    get_tag_hash,
     is_ancestor,
+    match_semver,
 )