remove locale exporters

pcgr/main.py

@@ -130,12 +130,6 @@ def cli():
     optional_other.add_argument("--debug", action="store_true", help="Print full commands to log")
     optional_other.add_argument("--pcgrr_conda", default="pcgrr", help="pcgrr conda env name (default: %(default)s)")
 
-    # Set locale since apptainer on HPC gives warnings
-    #locale_to_use = utils.get_locale()
-    #os.environ["LANGUAGE"] = locale_to_use
-    #os.environ["LANG"] = locale_to_use
-    #os.environ["LC_ALL"] = locale_to_use
-
     # Parse required and optional arguments
     args = parser.parse_args()
     arg_dict = vars(args)

pcgr/utils.py

@@ -210,40 +210,3 @@ def check_tabix_file(fname: str, logger = None) -> bool:
         check_file_exists(tabix_file)
     return(True)
 
-def locale_export():
-    """
-    https://github.com/bcbio/bcbio-nextgen/blob/855c7ae/bcbio/utils.py#L885
-    """
-    locale_to_use = get_locale()
-    return f"export LC_ALL={locale_to_use} && export LANG={locale_to_use} && "
-
-def get_locale():
-    """
-    https://github.com/bcbio/bcbio-nextgen/blob/855c7ae/bcbio/utils.py#L895
-    Looks up available locales on the system to find an appropriate one to pick,
-    defaulting to C.UTF-8 which is globally available on newer systems. Prefers
-    C.UTF-8 and en_US encodings, if available
-    """
-    default_locale = "C.UTF-8"
-    preferred_locales = {"c.utf-8", "c.utf8", "en_us.utf-8", "en_us.utf8"}
-    locale_to_use = None
-    try:
-        locales = subprocess.check_output(["locale", "-a"]).decode(errors="ignore").split("\n")
-    except subprocess.CalledProcessError:
-        locales = []
-    # check for preferred locale
-    for locale in locales:
-        if locale.lower() in preferred_locales:
-            locale_to_use = locale
-            break
-    # if preferred locale not available take first UTF-8 locale
-    if not locale_to_use:
-        for locale in locales:
-            if locale.lower().endswith(("utf-8", "utf8")):
-                locale_to_use = locale
-                break
-    # if locale listing not available, try using the default locale
-    if not locale_to_use:
-        locale_to_use = default_locale
-    return locale_to_use
-