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Description: Remove code from Stack Overflow
Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be. These snippets may be
too small to be copyrightable, but removing them to be safe.
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no - one part needs Python 3.6+
--- a/snakemake/io.py
+++ b/snakemake/io.py
@@ -1683,18 +1683,7 @@ def _load_configfile(configpath_or_obj,
except ValueError:
f.seek(0) # try again
try:
- # From https://stackoverflow.com/a/21912744/84349
- class OrderedLoader(yaml.Loader):
- pass
-
- def construct_mapping(loader, node):
- loader.flatten_mapping(node)
- return collections.OrderedDict(loader.construct_pairs(node))
-
- OrderedLoader.add_constructor(
- yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, construct_mapping
- )
- return yaml.load(f, Loader=OrderedLoader)
+ return yaml.full_load(f)
except yaml.YAMLError:
raise WorkflowError(
"Config file is not valid JSON or YAML. "
--- a/snakemake/remote/S3Mocked.py
+++ b/snakemake/remote/S3Mocked.py
@@ -10,6 +10,7 @@ import pickle
import time
import threading
import functools
+import pathlib
# intra-module
from snakemake.remote.S3 import (
@@ -122,26 +123,19 @@ class RemoteObject(S3RemoteObject):
# ====== Helpers =====
-def touch(fname, mode=0o666, dir_fd=None, **kwargs):
- # create lock file faster
- # https://stackoverflow.com/a/1160227
- flags = os.O_CREAT | os.O_APPEND
- with os.fdopen(os.open(fname, flags=flags, mode=mode, dir_fd=dir_fd)) as f:
- os.utime(
- f.fileno() if os.utime in os.supports_fd else fname,
- dir_fd=None if os.supports_fd else dir_fd,
- **kwargs
- )
-
+def touch(fname, mode=0o666):
+ pathlib.Path(fname).touch(mode=mode, exist_ok=True)
@contextmanager
def file_lock(filepath):
lock_file = filepath + ".lock"
- while os.path.isfile(lock_file):
- time.sleep(2)
-
- touch(lock_file)
+ while True:
+ try:
+ pathlib.Path(lock_file).touch(exist_ok=False)
+ break
+ except FileExistsError:
+ time.sleep(2)
try:
yield
--- a/snakemake/utils.py
+++ b/snakemake/utils.py
@@ -487,25 +487,23 @@ def min_version(version):
def update_config(config, overwrite_config):
"""Recursively update dictionary config with overwrite_config.
- See
- https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
- for details.
-
Args:
config (dict): dictionary to update
overwrite_config (dict): dictionary whose items will overwrite those in config
"""
- def _update(d, u):
- for (key, value) in u.items():
- if isinstance(value, collections.abc.Mapping):
- d[key] = _update(d.get(key, {}), value)
+ def nestedupdate(old_d, new_d):
+ for k, v in new_d.items():
+ if isinstance(v, collections.abc.Mapping):
+ if k not in old_d:
+ old_d[k] = {}
+ nestedupdate(old_d[k], v)
else:
- d[key] = value
- return d
+ old_d[k] = v
+
- _update(config, overwrite_config)
+ nestedupdate(config, overwrite_config)
def available_cpu_count():
@@ -514,22 +512,16 @@ def available_cpu_count():
The number of available CPUs can be smaller than the total number of CPUs
when the cpuset(7) mechanism is in use, as is the case on some cluster
systems.
-
- Adapted from https://stackoverflow.com/a/1006301/715090
"""
try:
- with open("/proc/self/status") as f:
- status = f.read()
- m = re.search(r"(?m)^Cpus_allowed:\s*(.*)$", status)
- if m:
- res = bin(int(m.group(1).replace(",", ""), 16)).count("1")
- if res > 0:
- return min(res, multiprocessing.cpu_count())
- except IOError:
- pass
-
- return multiprocessing.cpu_count()
-
+ cpu_count = len(os.sched_getaffinity(0))
+ except Exception:
+ cpu_count = 0
+ if cpu_count == 0:
+ cpu_count = os.cpu_count()
+ if not cpu_count: # None if unknown
+ cpu_count = 1
+ return cpu_count
def argvquote(arg, force=True):
"""Returns an argument quoted in such a way that CommandLineToArgvW
--- a/tests/test_static_remote/S3MockedForStaticTest.py
+++ b/tests/test_static_remote/S3MockedForStaticTest.py
@@ -10,6 +10,7 @@ import pickle
import time
import threading
import functools
+import pathlib
# intra-module
from snakemake.remote.S3 import (
@@ -133,26 +134,20 @@ class RemoteObject(S3RemoteObject):
# ====== Helpers =====
-def touch(fname, mode=0o666, dir_fd=None, **kwargs):
- # create lock file faster
- # https://stackoverflow.com/a/1160227
- flags = os.O_CREAT | os.O_APPEND
- with os.fdopen(os.open(fname, flags=flags, mode=mode, dir_fd=dir_fd)) as f:
- os.utime(
- f.fileno() if os.utime in os.supports_fd else fname,
- dir_fd=None if os.supports_fd else dir_fd,
- **kwargs
- )
+def touch(fname, mode=0o666):
+ pathlib.Path(fname).touch(mode=mode, exist_ok=True)
@contextmanager
def file_lock(filepath):
lock_file = filepath + ".lock"
- while os.path.isfile(lock_file):
- time.sleep(2)
-
- touch(lock_file)
+ while True:
+ try:
+ pathlib.Path(lock_file).touch(exist_ok=False)
+ break
+ except FileExistsError:
+ time.sleep(2)
try:
yield
|
