From 079e647e16a3ad2776e451a7568c25732c459d6c Mon Sep 17 00:00:00 2001
From: Matthew K Defenderfer <mdefende@uab.edu>
Date: Fri, 27 Dec 2024 19:33:20 -0600
Subject: [PATCH 1/3] add main functions to cli __init__ import
---
src/rc_gpfs/cli/__init__.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/rc_gpfs/cli/__init__.py b/src/rc_gpfs/cli/__init__.py
index e69de29..fcbd7b1 100644
--- a/src/rc_gpfs/cli/__init__.py
+++ b/src/rc_gpfs/cli/__init__.py
@@ -0,0 +1,2 @@
+from .convert_to_parquet import convert_to_parquet
+from .split_log import split_log
\ No newline at end of file
--
GitLab
From 29f20525719f255b4d1e3d7c86f9751302a24eba Mon Sep 17 00:00:00 2001
From: Matthew K Defenderfer <mdefende@uab.edu>
Date: Fri, 27 Dec 2024 19:52:59 -0600
Subject: [PATCH 2/3] add extra % to correctly escape the % character in raw
text
---
src/rc_gpfs/cli/convert_to_parquet.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/rc_gpfs/cli/convert_to_parquet.py b/src/rc_gpfs/cli/convert_to_parquet.py
index 28b5895..e684935 100644
--- a/src/rc_gpfs/cli/convert_to_parquet.py
+++ b/src/rc_gpfs/cli/convert_to_parquet.py
@@ -44,8 +44,8 @@ def parse_args():
slurm.add_argument('-p','--partition', type=str, default='amd-hdr100')
slurm.add_argument('-t','--time',type=str,default='02:00:00')
slurm.add_argument('-m','--mem',type=str,default='16G')
- slurm.add_argument('--slurm-log-dir',type=Path,default='./out',
- help='Output log directory. If the directory does not exist, it will be created automatically. Logs will be named convert_%A_%a to differentiate amongs job IDs and task IDs')
+ slurm.add_argument('--slurm-log-dir',type=Path, default='./out',
+ help='Output log directory. If the directory does not exist, it will be created automatically. Logs will be named convert_%%A_%%a to differentiate amongs job IDs and task IDs')
interpreter = slurm.add_mutually_exclusive_group()
interpreter.add_argument('--python-path',type=Path,
help="Path to Python interpreter to use for conversion. This interpreter should have access to a pandas library, preferably version >=2.0. If not specified, the path to the active python3 interpreter will be used.")
@@ -76,7 +76,7 @@ convert-to-parquet -o {output_dir} ${{log}}
def setup_slurm_logs(slurm_log_dir):
slurm_log_dir = slurm_log_dir.absolute()
slurm_log_dir.mkdir(exist_ok = True,parents=True,mode = 0o2770)
- out_log,err_log = [slurm_log_dir.joinpath('convert_%A_%a.out'),slurm_log_dir.joinpath('convert_%A_%a.err')]
+ out_log,err_log = [str(slurm_log_dir.joinpath('convert_%A_%a.out')),str(slurm_log_dir.joinpath('convert_%A_%a.err'))]
slurm_logs = {'output_log':out_log,'error_log':err_log}
return slurm_logs
--
GitLab
From 650203a37f037078721eefbb71460d159cb69825 Mon Sep 17 00:00:00 2001
From: Matthew K Defenderfer <mdefende@uab.edu>
Date: Fri, 27 Dec 2024 20:18:38 -0600
Subject: [PATCH 3/3] remove imports from init until I can figure out how to
reduce import time
---
src/rc_gpfs/__init__.py | 2 --
1 file changed, 2 deletions(-)
diff --git a/src/rc_gpfs/__init__.py b/src/rc_gpfs/__init__.py
index 039b8a2..e69de29 100644
--- a/src/rc_gpfs/__init__.py
+++ b/src/rc_gpfs/__init__.py
@@ -1,2 +0,0 @@
-from .compute import *
-from .process import *
\ No newline at end of file
--
GitLab