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riga/law | law/util.py | human_time_diff | def human_time_diff(*args, **kwargs):
"""
Returns a human readable time difference. The largest unit is days. All *args* and *kwargs* are
passed to ``datetime.timedelta``. Example:
.. code-block:: python
human_time_diff(seconds=1233)
# -> "20 minutes, 33 seconds"
human_time_di... | python | def human_time_diff(*args, **kwargs):
"""
Returns a human readable time difference. The largest unit is days. All *args* and *kwargs* are
passed to ``datetime.timedelta``. Example:
.. code-block:: python
human_time_diff(seconds=1233)
# -> "20 minutes, 33 seconds"
human_time_di... | [
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riga/law | law/util.py | is_file_exists_error | def is_file_exists_error(e):
"""
Returns whether the exception *e* was raised due to an already existing file or directory.
"""
if six.PY3:
return isinstance(e, FileExistsError) # noqa: F821
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return isinstance(e, OSError) and e.errno == 17 | python | def is_file_exists_error(e):
"""
Returns whether the exception *e* was raised due to an already existing file or directory.
"""
if six.PY3:
return isinstance(e, FileExistsError) # noqa: F821
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riga/law | law/util.py | send_mail | def send_mail(recipient, sender, subject="", content="", smtp_host="127.0.0.1", smtp_port=25):
"""
Lightweight mail functionality. Sends an mail from *sender* to *recipient* with *subject* and
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is returned on... | python | def send_mail(recipient, sender, subject="", content="", smtp_host="127.0.0.1", smtp_port=25):
"""
Lightweight mail functionality. Sends an mail from *sender* to *recipient* with *subject* and
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riga/law | law/util.py | open_compat | def open_compat(*args, **kwargs):
"""
Polyfill for python's ``open`` factory, returning the plain ``open`` in python 3, and
``io.open`` in python 2 with a patched ``write`` method that internally handles unicode
conversion of its first argument. All *args* and *kwargs* are forwarded.
"""
if six.... | python | def open_compat(*args, **kwargs):
"""
Polyfill for python's ``open`` factory, returning the plain ``open`` in python 3, and
``io.open`` in python 2 with a patched ``write`` method that internally handles unicode
conversion of its first argument. All *args* and *kwargs* are forwarded.
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riga/law | law/util.py | patch_object | def patch_object(obj, attr, value):
"""
Context manager that temporarily patches an object *obj* by replacing its attribute *attr* with
*value*. The original value is set again when the context is closed.
"""
orig = getattr(obj, attr, no_value)
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yi... | python | def patch_object(obj, attr, value):
"""
Context manager that temporarily patches an object *obj* by replacing its attribute *attr* with
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"""
orig = getattr(obj, attr, no_value)
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riga/law | law/util.py | TeeStream._flush | def _flush(self):
"""
Flushes all registered consumer streams.
"""
for consumer in self.consumers:
if not getattr(consumer, "closed", False):
consumer.flush() | python | def _flush(self):
"""
Flushes all registered consumer streams.
"""
for consumer in self.consumers:
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riga/law | law/util.py | TeeStream._write | def _write(self, *args, **kwargs):
"""
Writes to all registered consumer streams, passing *args* and *kwargs*.
"""
for consumer in self.consumers:
consumer.write(*args, **kwargs) | python | def _write(self, *args, **kwargs):
"""
Writes to all registered consumer streams, passing *args* and *kwargs*.
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riga/law | law/util.py | FilteredStream._write | def _write(self, *args, **kwargs):
"""
Writes to the consumer stream when *filter_fn* evaluates to *True*, passing *args* and
*kwargs*.
"""
if self.filter_fn(*args, **kwargs):
self.stream.write(*args, **kwargs) | python | def _write(self, *args, **kwargs):
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riga/law | law/config.py | Config.get_default | def get_default(self, section, option, default=None, type=None, expandvars=False,
expanduser=False):
"""
Returns the config value defined by *section* and *option*. When either the section or the
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riga/law | law/config.py | Config.get_expanded | def get_expanded(self, *args, **kwargs):
"""
Same as :py:meth:`get_default`, but *expandvars* and *expanduser* arguments are set to
*True* by default.
"""
kwargs.setdefault("expandvars", True)
kwargs.setdefault("expanduser", True)
return self.get_default(*args, **... | python | def get_expanded(self, *args, **kwargs):
"""
Same as :py:meth:`get_default`, but *expandvars* and *expanduser* arguments are set to
*True* by default.
"""
kwargs.setdefault("expandvars", True)
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riga/law | law/config.py | Config.update | def update(self, data, overwrite=None, overwrite_sections=True, overwrite_options=True):
"""
Updates the currently stored configuration with new *data*, given as a dictionary. When
*overwrite_sections* is *False*, sections in *data* that are already present in the current
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"""
Updates the currently stored configuration with new *data*, given as a dictionary. When
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riga/law | law/config.py | Config.include | def include(self, filename, *args, **kwargs):
"""
Updates the current configc with the config found in *filename*. All *args* and *kwargs* are
forwarded to :py:meth:`update`.
"""
p = self.__class__(filename, skip_defaults=True, skip_fallbacks=True)
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"""
Updates the current configc with the config found in *filename*. All *args* and *kwargs* are
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"""
p = self.__class__(filename, skip_defaults=True, skip_fallbacks=True)
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riga/law | law/config.py | Config.keys | def keys(self, section, prefix=None):
"""
Returns all keys of a *section* in a list. When *prefix* is set, only keys starting with
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"""
return [key for key, _ in self.items(section) if (not prefix or key.startswith(prefix))] | python | def keys(self, section, prefix=None):
"""
Returns all keys of a *section* in a list. When *prefix* is set, only keys starting with
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riga/law | law/config.py | Config.sync_luigi_config | def sync_luigi_config(self, push=True, pull=True, expand=True):
"""
Synchronizes sections starting with ``"luigi_"`` with the luigi configuration parser. First,
when *push* is *True*, options that exist in law but **not** in luigi are stored as defaults
in the luigi config. Then, when *p... | python | def sync_luigi_config(self, push=True, pull=True, expand=True):
"""
Synchronizes sections starting with ``"luigi_"`` with the luigi configuration parser. First,
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riga/law | law/contrib/telegram/notification.py | notify_telegram | def notify_telegram(title, content, token=None, chat=None, mention_user=None, **kwargs):
"""
Sends a telegram notification and returns *True* on success. The communication with the telegram
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riga/law | law/workflow/local.py | LocalWorkflowProxy.complete | def complete(self):
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... | python | def complete(self):
"""
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riga/law | law/workflow/local.py | LocalWorkflowProxy.run | def run(self):
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riga/law | law/decorator.py | factory | def factory(**default_opts):
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.. code-block:: python
@factory(digits=... | python | def factory(**default_opts):
"""
Factory function to create decorators for tasks' run methods. Default options for the decorator
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riga/law | law/decorator.py | log | def log(fn, opts, task, *args, **kwargs):
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defined by the tasks's *log_file* parameter or *default_log_file* attribute. If its value is
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riga/law | law/decorator.py | safe_output | def safe_output(fn, opts, task, *args, **kwargs):
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riga/law | law/decorator.py | delay | def delay(fn, opts, task, *args, **kwargs):
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riga/law | law/decorator.py | notify | def notify(fn, opts, task, *args, **kwargs):
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riga/law | law/decorator.py | timeit | def timeit(fn, opts, task, *args, **kwargs):
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riga/law | law/contrib/wlcg/util.py | get_voms_proxy_user | def get_voms_proxy_user():
"""
Returns the owner of the voms proxy.
"""
out = _voms_proxy_info(["--identity"])[1].strip()
try:
return re.match(r".*\/CN\=([^\/]+).*", out.strip()).group(1)
except:
raise Exception("no valid identity found in voms proxy: {}".format(out)) | python | def get_voms_proxy_user():
"""
Returns the owner of the voms proxy.
"""
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riga/law | law/contrib/wlcg/util.py | check_voms_proxy_validity | def check_voms_proxy_validity(log=False):
"""
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warning will be logged.
"""
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"""
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riga/law | law/contrib/wlcg/util.py | renew_voms_proxy | def renew_voms_proxy(passwd="", vo=None, lifetime="196:00"):
"""
Renews the voms proxy using a password *passwd*, an optional virtual organization name *vo*, and
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Renews the voms proxy using a password *passwd*, an optional virtual organization name *vo*, and
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riga/law | law/contrib/wlcg/util.py | delegate_voms_proxy_glite | def delegate_voms_proxy_glite(endpoint, stdout=None, stderr=None, cache=True):
"""
Delegates the voms proxy via gLite to an *endpoint*, e.g.
``grid-ce.physik.rwth-aachen.de:8443``. *stdout* and *stderr* are passed to the *Popen*
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"""
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riga/law | law/target/formatter.py | get_formatter | def get_formatter(name, silent=False):
"""
Returns the formatter class whose name attribute is *name*. When no class could be found and
*silent* is *True*, *None* is returned. Otherwise, an exception is raised.
"""
formatter = FormatterRegister.formatters.get(name)
if formatter or silent:
... | python | def get_formatter(name, silent=False):
"""
Returns the formatter class whose name attribute is *name*. When no class could be found and
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"""
formatter = FormatterRegister.formatters.get(name)
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riga/law | law/target/formatter.py | find_formatters | def find_formatters(path, silent=True):
"""
Returns a list of formatter classes which would accept the file given by *path*. When no classes
could be found and *silent* is *True*, an empty list is returned. Otherwise, an exception is
raised.
"""
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"""
Returns the formatter class whose name attribute is *name* when *name* is not *AUTO_FORMATTER*.
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riga/law | law/job/base.py | JobArguments.encode_list | def encode_list(cls, value):
"""
Encodes a list *value* into a string via base64 encoding.
"""
encoded = base64.b64encode(six.b(" ".join(str(v) for v in value) or "-"))
return encoded.decode("utf-8") if six.PY3 else encoded | python | def encode_list(cls, value):
"""
Encodes a list *value* into a string via base64 encoding.
"""
encoded = base64.b64encode(six.b(" ".join(str(v) for v in value) or "-"))
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riga/law | law/job/base.py | JobArguments.get_args | def get_args(self):
"""
Returns the list of encoded job arguments. The order of this list corresponds to the
arguments expected by the job wrapper script.
"""
return [
self.task_cls.__module__,
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Returns the list of encoded job arguments. The order of this list corresponds to the
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riga/law | law/contrib/__init__.py | load | def load(*packages):
"""
Loads contrib *packages* and adds members exposed in ``__all__`` to the law main module.
Example:
.. code-block:: python
import law
law.contrib.load("numpy")
print(law.NumpyFormatter)
# -> <class 'law.contrib.numpy.formatter.NumpyFormatter'>
... | python | def load(*packages):
"""
Loads contrib *packages* and adds members exposed in ``__all__`` to the law main module.
Example:
.. code-block:: python
import law
law.contrib.load("numpy")
print(law.NumpyFormatter)
# -> <class 'law.contrib.numpy.formatter.NumpyFormatter'>
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riga/law | law/notification.py | notify_mail | def notify_mail(title, message, recipient=None, sender=None, smtp_host=None, smtp_port=None,
**kwargs):
"""
Mail notification method taking a *title* and a string *message*. *recipient*, *sender*,
*smtp_host* and *smtp_port* default to the configuration values in the [notifications] section.
"""... | python | def notify_mail(title, message, recipient=None, sender=None, smtp_host=None, smtp_port=None,
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"""
Mail notification method taking a *title* and a string *message*. *recipient*, *sender*,
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riga/law | law/patches.py | patch_all | def patch_all():
"""
Runs all patches. This function ensures that a second invocation has no effect.
"""
global _patched
if _patched:
return
_patched = True
patch_default_retcodes()
patch_worker_run_task()
patch_worker_factory()
patch_keepalive_run()
patch_cmdline_p... | python | def patch_all():
"""
Runs all patches. This function ensures that a second invocation has no effect.
"""
global _patched
if _patched:
return
_patched = True
patch_default_retcodes()
patch_worker_run_task()
patch_worker_factory()
patch_keepalive_run()
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riga/law | law/patches.py | patch_default_retcodes | def patch_default_retcodes():
"""
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- already_running: 10
- missing_data: 20
- not_run: 30
- task_failed: 40
- scheduling_error: 50
- unhandled_exception: 60
"""
import luigi.retcodes
... | python | def patch_default_retcodes():
"""
Sets the default luigi return codes in ``luigi.retcodes.retcode`` to:
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- not_run: 30
- task_failed: 40
- scheduling_error: 50
- unhandled_exception: 60
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riga/law | law/patches.py | patch_worker_run_task | def patch_worker_run_task():
"""
Patches the ``luigi.worker.Worker._run_task`` method to store the worker id and the id of its
first task in the task. This information is required by the sandboxing mechanism
"""
_run_task = luigi.worker.Worker._run_task
def run_task(self, task_id):
task... | python | def patch_worker_run_task():
"""
Patches the ``luigi.worker.Worker._run_task`` method to store the worker id and the id of its
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"""
_run_task = luigi.worker.Worker._run_task
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riga/law | law/patches.py | patch_worker_factory | def patch_worker_factory():
"""
Patches the ``luigi.interface._WorkerSchedulerFactory`` to include sandboxing information when
create a worker instance.
"""
def create_worker(self, scheduler, worker_processes, assistant=False):
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"""
Patches the ``luigi.interface._WorkerSchedulerFactory`` to include sandboxing information when
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"""
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riga/law | law/patches.py | patch_keepalive_run | def patch_keepalive_run():
"""
Patches the ``luigi.worker.KeepAliveThread.run`` to immediately stop the keep-alive thread when
running within a sandbox.
"""
_run = luigi.worker.KeepAliveThread.run
def run(self):
# do not run the keep-alive loop when sandboxed
if os.getenv("LAW_S... | python | def patch_keepalive_run():
"""
Patches the ``luigi.worker.KeepAliveThread.run`` to immediately stop the keep-alive thread when
running within a sandbox.
"""
_run = luigi.worker.KeepAliveThread.run
def run(self):
# do not run the keep-alive loop when sandboxed
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riga/law | law/patches.py | patch_cmdline_parser | def patch_cmdline_parser():
"""
Patches the ``luigi.cmdline_parser.CmdlineParser`` to store the original command line arguments
for later processing in the :py:class:`law.config.Config`.
"""
# store original functions
_init = luigi.cmdline_parser.CmdlineParser.__init__
# patch init
def ... | python | def patch_cmdline_parser():
"""
Patches the ``luigi.cmdline_parser.CmdlineParser`` to store the original command line arguments
for later processing in the :py:class:`law.config.Config`.
"""
# store original functions
_init = luigi.cmdline_parser.CmdlineParser.__init__
# patch init
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riga/law | law/contrib/slack/notification.py | notify_slack | def notify_slack(title, content, attachment_color="#4bb543", short_threshold=40, token=None,
channel=None, mention_user=None, **kwargs):
"""
Sends a slack notification and returns *True* on success. The communication with the slack API
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channel=None, mention_user=None, **kwargs):
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riga/law | examples/workflows/tasks.py | maybe_wait | def maybe_wait(func):
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"""
def wrapper(self, *args, **kwargs):
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time.sleep... | python | def maybe_wait(func):
"""
Wrapper around run() methods that reads the *slow* flag to decide whether to wait some seconds
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riga/law | law/contrib/lsf/job.py | LSFJobManager.parse_query_output | def parse_query_output(cls, out):
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Example output to parse:
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"""
global console_handler
# make sure ... | python | def setup_logging():
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riga/law | law/cli/config.py | execute | def execute(args):
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# just print the file location?
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riga/law | law/cli/config.py | get_config | def get_config(name, expand=False):
"""
Returns the config value that corresponds to *name*, which must have the format
``<section>[.<option>]``. When an option is given and *expand* is *True*, variables are expanded
in the returned value.
"""
cfg = Config.instance()
only_section = "." not i... | python | def get_config(name, expand=False):
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Returns the config value that corresponds to *name*, which must have the format
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riga/law | law/cli/run.py | setup_parser | def setup_parser(sub_parsers):
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Sets up the command line parser for the *run* subprogram and adds it to *sub_parsers*.
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riga/law | law/cli/run.py | execute | def execute(args):
"""
Executes the *run* subprogram with parsed commandline *args*.
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task_family = None
error = None
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parts = args.task_family.rsplit(".", 1)
if len(parts) == 2:
modid, cls_name = parts
... | python | def execute(args):
"""
Executes the *run* subprogram with parsed commandline *args*.
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error = None
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parts = args.task_family.rsplit(".", 1)
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riga/law | law/cli/run.py | read_task_from_index | def read_task_from_index(task_family, index_file=None):
"""
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riga/law | law/cli/cli.py | run | def run():
"""
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"""
# setup the main parser and sub parsers
parser = ArgumentParser(prog="law", description="The law command line tool.")
sub_parsers = parser.add_subparsers(help="sub... | python | def run():
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riga/law | law/job/dashboard.py | cache_by_status | def cache_by_status(func):
"""
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published status to decide if the a new publication is necessary or not. When the status did not
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"""
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riga/law | law/cli/software.py | setup_parser | def setup_parser(sub_parsers):
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riga/law | law/cli/software.py | execute | def execute(args):
"""
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"""
sw_dir = get_sw_dir()
# just print the cache location?
if args.location:
print(sw_dir)
return
# just remove the current software cache?
if args.remove:
remove_software_... | python | def execute(args):
"""
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"""
sw_dir = get_sw_dir()
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riga/law | law/cli/software.py | build_software_cache | def build_software_cache(sw_dir=None):
"""
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modules. *sw_dir* is evaluated with :py:func:`get_sw_dir`.
"""
# ensure the cache is empty
sw_dir = get_sw_dir(sw_dir)
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"""
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riga/law | law/cli/software.py | remove_software_cache | def remove_software_cache(sw_dir=None):
"""
Removes the software cache directory at *sw_dir* which is evaluated with :py:func:`get_sw_dir`.
"""
sw_dir = get_sw_dir(sw_dir)
if os.path.exists(sw_dir):
shutil.rmtree(sw_dir) | python | def remove_software_cache(sw_dir=None):
"""
Removes the software cache directory at *sw_dir* which is evaluated with :py:func:`get_sw_dir`.
"""
sw_dir = get_sw_dir(sw_dir)
if os.path.exists(sw_dir):
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riga/law | law/cli/software.py | reload_dependencies | def reload_dependencies(force=False):
"""
Reloads all python modules that law depends on. Currently, this is just *luigi* and *six*.
Unless *force* is *True*, multiple calls to this function will not have any effect.
"""
global _reloaded_deps
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return
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"""
Reloads all python modules that law depends on. Currently, this is just *luigi* and *six*.
Unless *force* is *True*, multiple calls to this function will not have any effect.
"""
global _reloaded_deps
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riga/law | law/cli/software.py | use_software_cache | def use_software_cache(sw_dir=None, reload_deps=False):
"""
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:py:func:`get_sw_dir`. When *reload_deps* is *True*, :py:func:`reload_dependencies` is invoked.
"""
sw_dir = get_sw_dir(sw_dir)
if os.path.... | python | def use_software_cache(sw_dir=None, reload_deps=False):
"""
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sw_dir = get_sw_dir(sw_dir)
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riga/law | law/cli/software.py | get_sw_dir | def get_sw_dir(sw_dir=None):
"""
Returns the software directory defined in the ``config.software_dir`` config. When *sw_dir* is
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"""
if sw_dir is None:
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sw_dir = os.path.expandvars(os.p... | python | def get_sw_dir(sw_dir=None):
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riga/law | law/contrib/root/formatter.py | GuardedTFile | def GuardedTFile(*args, **kwargs):
"""
Factory function that lazily creates the guarded TFile class, and creates and returns an
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"""
global guarded_tfile_cls
if not guarded_tf... | python | def GuardedTFile(*args, **kwargs):
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Factory function that lazily creates the guarded TFile class, and creates and returns an
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riga/law | law/workflow/base.py | workflow_property | def workflow_property(func):
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riga/law | law/workflow/base.py | cached_workflow_property | def cached_workflow_property(func=None, attr=None, setter=True):
"""
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riga/law | law/workflow/base.py | BaseWorkflowProxy.complete | def complete(self):
"""
Custom completion check that invokes the task's *workflow_complete* if it is callable, or
just does the default completion check otherwise.
"""
if callable(self.task.workflow_complete):
return self.task.workflow_complete()
else:
... | python | def complete(self):
"""
Custom completion check that invokes the task's *workflow_complete* if it is callable, or
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"""
if callable(self.task.workflow_complete):
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riga/law | law/workflow/base.py | BaseWorkflowProxy.requires | def requires(self):
"""
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"""
reqs = OrderedDict()
reqs.update(self.task.workflow_requires())
return reqs | python | def requires(self):
"""
Returns the default workflow requirements in an ordered dictionary, which is updated with
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reqs = OrderedDict()
reqs.update(self.task.workflow_requires())
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riga/law | law/workflow/base.py | BaseWorkflowProxy.output | def output(self):
"""
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"""
if self.task.target_collection_cls is not None:
cls = self.task.tar... | python | def output(self):
"""
Returns the default workflow outputs in an ordered dictionary. At the moment this is just
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"""
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riga/law | law/workflow/base.py | BaseWorkflowProxy.threshold | def threshold(self, n=None):
"""
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"""
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riga/law | law/workflow/base.py | BaseWorkflowProxy.get_prefixed_config | def get_prefixed_config(self, section, option, **kwargs):
"""
TODO.
"""
cfg = Config.instance()
default = cfg.get_expanded(section, option, **kwargs)
return cfg.get_expanded(section, "{}_{}".format(self.workflow_type, option),
default=default, **kwargs) | python | def get_prefixed_config(self, section, option, **kwargs):
"""
TODO.
"""
cfg = Config.instance()
default = cfg.get_expanded(section, option, **kwargs)
return cfg.get_expanded(section, "{}_{}".format(self.workflow_type, option),
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alexandrovteam/pyimzML | pyimzml/ImzMLParser.py | getionimage | def getionimage(p, mz_value, tol=0.1, z=1, reduce_func=sum):
"""
Get an image representation of the intensity distribution
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"""
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alexandrovteam/pyimzML | pyimzml/ImzMLParser.py | ImzMLParser.__iter_read_spectrum_meta | def __iter_read_spectrum_meta(self):
"""
This method should only be called by __init__. Reads the data formats, coordinates and offsets from
the .imzML file and initializes the respective attributes. While traversing the XML tree, the per-spectrum
metadata is pruned, i.e. the <spectrumLi... | python | def __iter_read_spectrum_meta(self):
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alexandrovteam/pyimzML | pyimzml/ImzMLParser.py | ImzMLParser.get_physical_coordinates | def get_physical_coordinates(self, i):
"""
For a pixel index i, return the real-world coordinates in nanometers.
This is equivalent to multiplying the image coordinates of the given pixel with the pixel size.
:param i: the pixel index
:return: a tuple of x and y coordinates.
... | python | def get_physical_coordinates(self, i):
"""
For a pixel index i, return the real-world coordinates in nanometers.
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:param i: the pixel index
:return: a tuple of x and y coordinates.
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alexandrovteam/pyimzML | pyimzml/ImzMLParser.py | ImzMLParser.getspectrum | def getspectrum(self, index):
"""
Reads the spectrum at specified index from the .ibd file.
:param index:
Index of the desired spectrum in the .imzML file
Output:
mz_array: numpy.ndarray
Sequence of m/z values representing the horizontal axis of the des... | python | def getspectrum(self, index):
"""
Reads the spectrum at specified index from the .ibd file.
:param index:
Index of the desired spectrum in the .imzML file
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alexandrovteam/pyimzML | pyimzml/ImzMLParser.py | ImzMLParser.get_spectrum_as_string | def get_spectrum_as_string(self, index):
"""
Reads m/z array and intensity array of the spectrum at specified location
from the binary file as a byte string. The string can be unpacked by the struct
module. To get the arrays as numbers, use getspectrum
:param index:
... | python | def get_spectrum_as_string(self, index):
"""
Reads m/z array and intensity array of the spectrum at specified location
from the binary file as a byte string. The string can be unpacked by the struct
module. To get the arrays as numbers, use getspectrum
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alexandrovteam/pyimzML | pyimzml/ImzMLWriter.py | ImzMLWriter._read_mz | def _read_mz(self, mz_offset, mz_len, mz_enc_len):
'''reads a mz array from the currently open ibd file'''
self.ibd.seek(mz_offset)
data = self.ibd.read(mz_enc_len)
self.ibd.seek(0, 2)
data = self.mz_compression.decompress(data)
return tuple(np.fromstring(data, dtype=self... | python | def _read_mz(self, mz_offset, mz_len, mz_enc_len):
'''reads a mz array from the currently open ibd file'''
self.ibd.seek(mz_offset)
data = self.ibd.read(mz_enc_len)
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alexandrovteam/pyimzML | pyimzml/ImzMLWriter.py | ImzMLWriter._get_previous_mz | def _get_previous_mz(self, mzs):
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if the mz array was not previously written, write to disk first'''
mzs = tuple(mzs) # must be hashable
if mzs in self.lru_cache:
return self.lru_cache[mzs]
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'''given an mz array, return the mz_data (disk location)
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mzs = tuple(mzs) # must be hashable
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alexandrovteam/pyimzML | pyimzml/ImzMLWriter.py | ImzMLWriter.addSpectrum | def addSpectrum(self, mzs, intensities, coords, userParams=[]):
"""
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:param mz:
mz array
:param intensities:
intensity array
:param coords:
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* 3-tuple of x, y, and z ... | python | def addSpectrum(self, mzs, intensities, coords, userParams=[]):
"""
Add a mass spectrum to the file.
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mz array
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intensity array
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alexandrovteam/pyimzML | pyimzml/ImzMLWriter.py | ImzMLWriter.finish | def finish(self):
'''alias of close()'''
self.ibd.close()
self._write_xml()
self.xml.close() | python | def finish(self):
'''alias of close()'''
self.ibd.close()
self._write_xml()
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michaeljoseph/changes | changes/__init__.py | initialise | def initialise():
"""
Detects, prompts and initialises the project.
Stores project and tool configuration in the `changes` module.
"""
global settings, project_settings
# Global changes settings
settings = Changes.load()
# Project specific settings
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"""
Detects, prompts and initialises the project.
Stores project and tool configuration in the `changes` module.
"""
global settings, project_settings
# Global changes settings
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michaeljoseph/changes | changes/packaging.py | build_distributions | def build_distributions(context):
"""Builds package distributions"""
rmtree('dist', ignore_errors=True)
build_package_command = 'python setup.py clean sdist bdist_wheel'
result = shell.dry_run(build_package_command, context.dry_run)
packages = Path('dist').files() if not context.dry_run else "nothi... | python | def build_distributions(context):
"""Builds package distributions"""
rmtree('dist', ignore_errors=True)
build_package_command = 'python setup.py clean sdist bdist_wheel'
result = shell.dry_run(build_package_command, context.dry_run)
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michaeljoseph/changes | changes/packaging.py | install_package | def install_package(context):
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"""Attempts to install the sdist and wheel."""
if not context.dry_run and build_distributions(context):
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venv.create_venv(tmp_dir=tmp_dir)
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michaeljoseph/changes | changes/packaging.py | upload_package | def upload_package(context):
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michaeljoseph/changes | changes/packaging.py | install_from_pypi | def install_from_pypi(context):
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"""Attempts to install your package from pypi."""
tmp_dir = venv.create_venv()
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michaeljoseph/changes | changes/probe.py | report_and_raise | def report_and_raise(probe_name, probe_result, failure_msg):
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log.info('%s? %s' % (probe_name, probe_result))
if not probe_result:
raise exceptions.ProbeException(failure_msg)
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michaeljoseph/changes | changes/probe.py | has_metadata | def has_metadata(python_module):
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init_path = '{}/__init__.py'.format(python_module)
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michaeljoseph/changes | changes/probe.py | probe_project | def probe_project(python_module):
"""
Check if the project meets `changes` requirements.
Complain and exit otherwise.
"""
log.info('Checking project for changes requirements.')
return (
has_tools()
and has_setup()
and has_metadata(python_module)
and has_test_runne... | python | def probe_project(python_module):
"""
Check if the project meets `changes` requirements.
Complain and exit otherwise.
"""
log.info('Checking project for changes requirements.')
return (
has_tools()
and has_setup()
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and has_test_runne... | [
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michaeljoseph/changes | changes/flow.py | publish | def publish(context):
"""Publishes the project"""
commit_version_change(context)
if context.github:
# github token
project_settings = project_config(context.module_name)
if not project_settings['gh_token']:
click.echo('You need a GitHub token for changes to create a rele... | python | def publish(context):
"""Publishes the project"""
commit_version_change(context)
if context.github:
# github token
project_settings = project_config(context.module_name)
if not project_settings['gh_token']:
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michaeljoseph/changes | changes/flow.py | perform_release | def perform_release(context):
"""Executes the release process."""
try:
run_tests()
if not context.skip_changelog:
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increment_version(context)
build_distributions(context)
install_package(context)
upload_package(context)
... | python | def perform_release(context):
"""Executes the release process."""
try:
run_tests()
if not context.skip_changelog:
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increment_version(context)
build_distributions(context)
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upload_package(context)
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michaeljoseph/changes | changes/attributes.py | extract_attribute | def extract_attribute(module_name, attribute_name):
"""Extract metatdata property from a module"""
with open('%s/__init__.py' % module_name) as input_file:
for line in input_file:
if line.startswith(attribute_name):
return ast.literal_eval(line.split('=')[1].strip()) | python | def extract_attribute(module_name, attribute_name):
"""Extract metatdata property from a module"""
with open('%s/__init__.py' % module_name) as input_file:
for line in input_file:
if line.startswith(attribute_name):
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michaeljoseph/changes | changes/attributes.py | replace_attribute | def replace_attribute(module_name, attribute_name, new_value, dry_run=True):
"""Update a metadata attribute"""
init_file = '%s/__init__.py' % module_name
_, tmp_file = tempfile.mkstemp()
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for line in input_f... | python | def replace_attribute(module_name, attribute_name, new_value, dry_run=True):
"""Update a metadata attribute"""
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michaeljoseph/changes | changes/attributes.py | has_attribute | def has_attribute(module_name, attribute_name):
"""Is this attribute present?"""
init_file = '%s/__init__.py' % module_name
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[attribute_name in init_line for init_line in open(init_file).readlines()]
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"""Is this attribute present?"""
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michaeljoseph/changes | changes/prompt.py | choose_labels | def choose_labels(alternatives):
"""
Prompt the user select several labels from the provided alternatives.
At least one label must be selected.
:param list alternatives: Sequence of options that are available to select from
:return: Several selected labels
"""
if not alternatives:
... | python | def choose_labels(alternatives):
"""
Prompt the user select several labels from the provided alternatives.
At least one label must be selected.
:param list alternatives: Sequence of options that are available to select from
:return: Several selected labels
"""
if not alternatives:
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michaeljoseph/changes | changes/cli.py | work_in | def work_in(dirname=None):
"""
Context manager version of os.chdir. When exited, returns to the working
directory prior to entering.
"""
curdir = os.getcwd()
try:
if dirname is not None:
os.chdir(dirname)
requests_cache.configure(expire_after=60 * 10 * 10)
ch... | python | def work_in(dirname=None):
"""
Context manager version of os.chdir. When exited, returns to the working
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"""
curdir = os.getcwd()
try:
if dirname is not None:
os.chdir(dirname)
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michaeljoseph/changes | changes/cli.py | stage | def stage(draft, discard, repo_directory, release_name, release_description):
"""
Stages a release
"""
with work_in(repo_directory):
if discard:
stage_command.discard(release_name, release_description)
else:
stage_command.stage(draft, release_name, release_descrip... | python | def stage(draft, discard, repo_directory, release_name, release_description):
"""
Stages a release
"""
with work_in(repo_directory):
if discard:
stage_command.discard(release_name, release_description)
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michaeljoseph/changes | changes/changelog.py | generate_changelog | def generate_changelog(context):
"""Generates an automatic changelog from your commit messages."""
changelog_content = [
'\n## [%s](%s/compare/%s...%s)\n\n'
% (
context.new_version,
context.repo_url,
context.current_version,
context.new_version,
... | python | def generate_changelog(context):
"""Generates an automatic changelog from your commit messages."""
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% (
context.new_version,
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michaeljoseph/changes | changes/util.py | extract | def extract(dictionary, keys):
"""
Extract only the specified keys from a dict
:param dictionary: source dictionary
:param keys: list of keys to extract
:return dict: extracted dictionary
"""
return dict((k, dictionary[k]) for k in keys if k in dictionary) | python | def extract(dictionary, keys):
"""
Extract only the specified keys from a dict
:param dictionary: source dictionary
:param keys: list of keys to extract
:return dict: extracted dictionary
"""
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michaeljoseph/changes | changes/util.py | extract_arguments | def extract_arguments(arguments, long_keys, key_prefix='--'):
"""
:param arguments: dict of command line arguments
"""
long_arguments = extract(arguments, long_keys)
return dict(
[(key.replace(key_prefix, ''), value) for key, value in long_arguments.items()]
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"""
:param arguments: dict of command line arguments
"""
long_arguments = extract(arguments, long_keys)
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michaeljoseph/changes | changes/vcs.py | tag_and_push | def tag_and_push(context):
"""Tags your git repo with the new version number"""
tag_option = '--annotate'
if probe.has_signing_key(context):
tag_option = '--sign'
shell.dry_run(
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)
sh... | python | def tag_and_push(context):
"""Tags your git repo with the new version number"""
tag_option = '--annotate'
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tag_option = '--sign'
shell.dry_run(
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michaeljoseph/changes | changes/shell.py | dry_run | def dry_run(command, dry_run):
"""Executes a shell command unless the dry run option is set"""
if not dry_run:
cmd_parts = command.split(' ')
# http://plumbum.readthedocs.org/en/latest/local_commands.html#run-and-popen
return local[cmd_parts[0]](cmd_parts[1:])
else:
log.info(... | python | def dry_run(command, dry_run):
"""Executes a shell command unless the dry run option is set"""
if not dry_run:
cmd_parts = command.split(' ')
# http://plumbum.readthedocs.org/en/latest/local_commands.html#run-and-popen
return local[cmd_parts[0]](cmd_parts[1:])
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michaeljoseph/changes | changes/config.py | project_config | def project_config():
"""Deprecated"""
project_name = curdir
config_path = Path(join(project_name, PROJECT_CONFIG_FILE))
if not exists(config_path):
store_settings(DEFAULTS.copy())
return DEFAULTS
return toml.load(io.open(config_path)) or {} | python | def project_config():
"""Deprecated"""
project_name = curdir
config_path = Path(join(project_name, PROJECT_CONFIG_FILE))
if not exists(config_path):
store_settings(DEFAULTS.copy())
return DEFAULTS
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michaeljoseph/changes | changes/version.py | increment | def increment(version, major=False, minor=False, patch=True):
"""
Increment a semantic version
:param version: str of the version to increment
:param major: bool specifying major level version increment
:param minor: bool specifying minor level version increment
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Increment a semantic version
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michaeljoseph/changes | changes/version.py | increment_version | def increment_version(context):
"""Increments the __version__ attribute of your module's __init__."""
attributes.replace_attribute(
context.module_name, '__version__', context.new_version, dry_run=context.dry_run
)
log.info(
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"""Increments the __version__ attribute of your module's __init__."""
attributes.replace_attribute(
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"__init__",
"."
] | train | https://github.com/michaeljoseph/changes/blob/a8beb409671c58cdf28ee913bad0a5c7d5374ade/changes/version.py#L59-L67 |
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