From d5072cbcae8ad380c319bddd8085b40524ff7907 Mon Sep 17 00:00:00 2001
From: Michael Hall <michael@mbh.sh>
Date: Fri, 13 May 2022 16:02:04 +1000
Subject: [PATCH] add class for dealing with job names and logs

---
 README.md                                     | 16 ++++++++--------
 {{cookiecutter.profile_name}}/CookieCutter.py |  2 +-
 {{cookiecutter.profile_name}}/slurm_utils.py  |  7 ++++---
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 86feb84..4f2416d 100644
--- a/README.md
+++ b/README.md
@@ -281,11 +281,11 @@ specified as `time="4h30m"`.
 
 Supported (case-insensitive) time units are:
 
--   `w`: week
--   `d`: day
--   `h`: hour
--   `m`: minute
--   `s`: second
+- `w`: week
+- `d`: day
+- `h`: hour
+- `m`: minute
+- `s`: second
 
 However, you may also pass the time in the [slurm
 format](https://slurm.schedmd.com/sbatch.html#OPT_time).
@@ -323,7 +323,7 @@ from the source code root directory. Test options can be configured via
 the pytest configuration file `tests/pytest.ini`.
 
 Test dependencies are listed in `test-environment.yml` and can be
-installed in e.g. a conda environment.
+installed in e.g. a conda environment.
 
 ### Testing on a HPC running SLURM
 
@@ -342,8 +342,8 @@ For local testing the test suite will deploy a docker stack
 `cookiecutter-slurm` that runs two services based on the following
 images:
 
-1.  [quay.io/biocontainers/snakemake](https://quay.io/repository/biocontainers/snakemake?tab=tags)
-2.  [giovtorres/docker-centos7-slurm](https://github.com/giovtorres/docker-centos7-slurm)
+1. [quay.io/biocontainers/snakemake](https://quay.io/repository/biocontainers/snakemake?tab=tags)
+2. [giovtorres/docker-centos7-slurm](https://github.com/giovtorres/docker-centos7-slurm)
 
 The docker stack will be automatically deployed provided that the user
 has installed docker and enabled [docker
diff --git a/{{cookiecutter.profile_name}}/CookieCutter.py b/{{cookiecutter.profile_name}}/CookieCutter.py
index 9f67a94..c2514d0 100644
--- a/{{cookiecutter.profile_name}}/CookieCutter.py
+++ b/{{cookiecutter.profile_name}}/CookieCutter.py
@@ -28,4 +28,4 @@ def get_cluster_logpath() -> str:
 
     @staticmethod
     def get_cluster_jobname() -> str:
-        return "{{cookiecutter.cluster_jobname}}"
\ No newline at end of file
+        return "{{cookiecutter.cluster_jobname}}"
diff --git a/{{cookiecutter.profile_name}}/slurm_utils.py b/{{cookiecutter.profile_name}}/slurm_utils.py
index bd6d190..7a96e75 100644
--- a/{{cookiecutter.profile_name}}/slurm_utils.py
+++ b/{{cookiecutter.profile_name}}/slurm_utils.py
@@ -95,7 +95,7 @@ def format(_pattern, _quote_all=False, **kwargs):  # noqa: A001
 
 #  adapted from Job.format_wildcards in snakemake.jobs
 def format_wildcards(string, job_properties):
-    """ Format a string with variables from the job. """
+    """Format a string with variables from the job."""
 
     class Job(object):
         def __init__(self, job_properties):
@@ -263,7 +263,7 @@ class Time:
         "d": _day_size,
         "w": _week_size,
     }
-    pattern = re.compile(rf'(?P<val>\d+(\.\d*)?|\.\d+)(?P<unit>[a-zA-Z])')
+    pattern = re.compile(rf"(?P<val>\d+(\.\d*)?|\.\d+)(?P<unit>[a-zA-Z])")
 
     def __init__(self, duration: str):
         self.duration = Time._from_str(duration)
@@ -301,7 +301,8 @@ def _from_str(duration: str) -> Union[timedelta, str]:
             unit = m.group("unit").lower()
             if unit not in Time.units:
                 raise InvalidTimeUnitError(
-                    "Unknown unit '{}' in time {}".format(unit, duration))
+                    "Unknown unit '{}' in time {}".format(unit, duration)
+                )
 
             total += float(value) * Time.units[unit]