remove umask calls (#234)

* remove umask calls

* add umask setting to job files

src/OSmOSE/Spectrogram.py

@@ -31,8 +31,8 @@
 from OSmOSE.utils.core_utils import (
     chmod_if_needed,
     get_timestamp_of_audio_file,
+    get_umask,
     safe_read,
-    set_umask,
 )
 from OSmOSE.utils.path_utils import make_path
 
@@ -479,7 +479,6 @@ def __build_path(
             dry: `bool`, optional
                 If set to True, will not create the folders and just return the file path.
         """
-        set_umask()
         processed_path = self.path / OSMOSE_PATH.spectrogram
         audio_foldername = f"{self.spectro_duration!s}_{self.dataset_sr!s}"
         self.audio_path = self.path / OSMOSE_PATH.raw_audio / audio_foldername
@@ -803,6 +802,7 @@ def initialize(
                                 --batch-ind-min {i_min}\
                                 --batch-ind-max {i_max}\
                                 --concat {self.concat}\
+                                --umask {get_umask()}\
                                 {'--verbose' if self.verbose else ''}",
                         jobname=f"reshape_{batch}",
                         preset="low",
@@ -822,7 +822,8 @@ def initialize(
         if not self.__local:
             self.jb.build_job_file(
                 script_path=Path(inspect.getfile(merge_timestamp_csv)).resolve(),
-                script_args=f"--input-files {self.audio_path}",
+                script_args=f"--input-files {self.audio_path}\
+                        --umask {get_umask()}",
                 jobname="merge_timestamp",
                 preset="low",
                 mem="30G",
@@ -899,6 +900,7 @@ def initialize(
                             --hp-filter-min-freq {self.hp_filter_min_freq}\
                             --batch-ind-min {i_min}\
                             --batch-ind-max {i_max}\
+                            --umask {get_umask()}\
                             --output-file {self.path / OSMOSE_PATH.statistics / f'SummaryStats_{i_min}.csv'}",
                         jobname="OSmOSE_get_zscore_params",
                         preset="low",
@@ -1121,7 +1123,6 @@ def process_file(
             self.save_for_LTAS = save_for_LTAS
 
         else:
-            set_umask()
             try:
                 if clean_adjust_folder and (
                     (

src/OSmOSE/cluster/audio_reshaper.py

@@ -1,3 +1,4 @@
+import os
 from argparse import ArgumentParser
 from pathlib import Path
 
@@ -8,7 +9,7 @@
 
 from OSmOSE.config import DPDEFAULT, FPDEFAULT
 from OSmOSE.utils.audio_utils import get_all_audio_files
-from OSmOSE.utils.core_utils import chmod_if_needed, set_umask
+from OSmOSE.utils.core_utils import chmod_if_needed
 from OSmOSE.utils.path_utils import make_path
 from OSmOSE.utils.timestamp_utils import to_timestamp
 
@@ -31,6 +32,7 @@ def reshape(
     verbose: bool = False,
     overwrite: bool = True,
     threshold: int = 5,
+    umask: int = 0o002,
 ):
     """Reshape all audio files in the folder to be of the specified duration and/or sampling rate.
 
@@ -89,11 +91,16 @@ def reshape(
 
     threshold : int, optional
         Integer from 0 to 100 to filter out segments with a number of sample inferior to (threshold * spectrogram duration * new_sr)
+
+    umask : int, optional
+        The umask to apply on the created files permissions. Default is 0o002.
+
     """
-    set_umask()
     segment_duration = pd.Timedelta(seconds=segment_size)
     msg_log = ""
 
+    os.umask(umask)
+
     # validation for threshold
     if not (0 <= threshold <= 100):
         raise ValueError(
@@ -458,6 +465,12 @@ def reshape(
         default=-1,
         help="Sampling rate",
     )
+    parser.add_argument(
+        "--umask",
+        type=int,
+        default=0o002,
+        help="Umask to apply on the created files permissions.",
+    )
 
     args = parser.parse_args()
 
@@ -486,4 +499,5 @@ def reshape(
         verbose=args.verbose,
         overwrite=args.overwrite,
         threshold=args.threshold,
+        umask=args.umask,
     )

src/OSmOSE/cluster/compute_statistics.py

@@ -1,13 +1,14 @@
 import argparse
 import csv
+import os
 import sys
 from pathlib import Path
 
 import numpy as np
 import soundfile as sf
 from scipy import signal
 
-from OSmOSE.utils.core_utils import get_timestamp_of_audio_file, set_umask
+from OSmOSE.utils.core_utils import get_timestamp_of_audio_file
 
 
 def Write_zscore_norma_params(
@@ -17,6 +18,7 @@ def Write_zscore_norma_params(
     hp_filter_min_freq: int,
     batch_ind_min: int = 0,
     batch_ind_max: int = -1,
+    umask: int = 0o002,
 ):
     """Computes the normalization parameters for the Zscore normalisation of the dataset and writes it to a csv.
 
@@ -42,8 +44,7 @@ def Write_zscore_norma_params(
         The last file of the list to be processed. Default is -1, meaning the entire list is processed.
 
     """
-    set_umask()
-
+    os.umask(umask)
     all_files = sorted(Path(input_dir).glob("*wav"))
     # If batch_ind_max is -1, we go to the end of the list.
     wav_list = all_files[
@@ -123,6 +124,12 @@ def Write_zscore_norma_params(
         default=-1,
         help="The last file to consider. -1 means consider all files from ind-min. Default is -1",
     )
+    parser.add_argument(
+        "--umask",
+        type=int,
+        default=0o002,
+        help="Umask to apply on the created files permissions.",
+    )
 
     args = parser.parse_args()
 
@@ -132,4 +139,5 @@ def Write_zscore_norma_params(
         hp_filter_min_freq=args.hp_filter_min_freq,
         batch_ind_min=args.batch_ind_min,
         batch_ind_max=args.batch_ind_max,
+        umask=args.umask,
     )

src/OSmOSE/cluster/merge_timestamp_csv.py

@@ -6,7 +6,8 @@
 import pandas as pd
 
 
-def merge_timestamp_csv(input_files: str):
+def merge_timestamp_csv(input_files: str, umask: int):
+    os.umask(umask)
     input_dir_path = Path(input_files)
 
     list_conca_timestamps = []
@@ -36,6 +37,12 @@ def merge_timestamp_csv(input_files: str):
         "-i",
         help="The files to be reshaped, as either the path to a directory containing audio files and a timestamp.csv or a list of filenames all in the same directory alongside a timestamp.csv.",
     )
+    parser.add_argument(
+        "--umask",
+        type=int,
+        default=0o002,
+        help="Umask to apply on the created files permissions.",
+    )
 
     args = parser.parse_args()
 
@@ -45,4 +52,4 @@ def merge_timestamp_csv(input_files: str):
         else args.input_files
     )
 
-    files = merge_timestamp_csv(input_files=input_files)
+    files = merge_timestamp_csv(input_files=input_files, umask=args.umask)

src/OSmOSE/cluster/resample.py

@@ -4,7 +4,6 @@
 from pathlib import Path
 
 from OSmOSE.utils.audio_utils import get_all_audio_files
-from OSmOSE.utils.core_utils import set_umask
 
 
 def resample(
@@ -31,7 +30,6 @@ def resample(
             The index of the last file of the batch. The default is -1, meaning the last file of the input directory.
 
     """
-    set_umask()
     if platform.system() == "Windows":
         print("Sox is unavailable on Windows")
         return

src/OSmOSE/job.py

@@ -15,7 +15,7 @@
 import tomlkit
 
 from OSmOSE.config import DPDEFAULT, FPDEFAULT
-from OSmOSE.utils.core_utils import chmod_if_needed, read_config, set_umask
+from OSmOSE.utils.core_utils import chmod_if_needed, read_config
 
 JOB_CONFIG_TEMPLATE = namedtuple(
     "job_config",
@@ -277,7 +277,6 @@ def build_job_file(
             The path to the created job file.
 
         """
-        set_umask()
         if "Presets" in self.__config.keys():
             if preset and preset.lower() not in self.__config["Presets"].keys():
                 raise ValueError(
@@ -551,7 +550,7 @@ def list_jobs(self):
                 delta = (
                     datetime.fromtimestamp(
                         time.mktime(
-                            time.localtime(job_info["outfile"].stat().st_ctime)
+                            time.localtime(job_info["outfile"].stat().st_ctime),
                         ),
                     )
                     - created_at

src/OSmOSE/utils/core_utils.py

@@ -526,10 +526,6 @@ def check_n_files(
     return len(bad_files)
 
 
-def set_umask():
-    os.umask(0o002)
-
-
 def get_files(path, extensions):
     all_files = []
     for ext in extensions:
@@ -873,3 +869,10 @@ def change_owner_group(path: Path, owner_group: str) -> None:
         )
         glc.logger.error(message)
         raise PermissionError(message) from e
+
+
+def get_umask() -> int:
+    """Return the current umask."""
+    umask = os.umask(0)
+    os.umask(umask)
+    return umask