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