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values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | setupuv | Horn Schunck legacy OpenCV function requires we use these old-fashioned cv matrices, not numpy array | morecvutils/calcOptFlow.py | def setupuv(rc):
"""
Horn Schunck legacy OpenCV function requires we use these old-fashioned cv matrices, not numpy array
"""
if cv is not None:
(r, c) = rc
u = cv.CreateMat(r, c, cv.CV_32FC1)
v = cv.CreateMat(r, c, cv.CV_32FC1)
return (u, v)
else:
return [Non... | def setupuv(rc):
"""
Horn Schunck legacy OpenCV function requires we use these old-fashioned cv matrices, not numpy array
"""
if cv is not None:
(r, c) = rc
u = cv.CreateMat(r, c, cv.CV_32FC1)
v = cv.CreateMat(r, c, cv.CV_32FC1)
return (u, v)
else:
return [Non... | [
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train | Model._init_cat_dict | Initialize a CatDict object, checking for errors. | astrocats/catalog/model.py | def _init_cat_dict(self, cat_dict_class, key_in_self, **kwargs):
"""Initialize a CatDict object, checking for errors.
"""
# Catch errors associated with crappy, but not unexpected data
try:
new_entry = cat_dict_class(self, key=key_in_self, **kwargs)
except CatDictErro... | def _init_cat_dict(self, cat_dict_class, key_in_self, **kwargs):
"""Initialize a CatDict object, checking for errors.
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train | Model._add_cat_dict | Add a CatDict to this Entry if initialization succeeds and it
doesn't already exist within the Entry. | astrocats/catalog/model.py | def _add_cat_dict(self,
cat_dict_class,
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check_for_dupes=True,
**kwargs):
"""Add a CatDict to this Entry if initialization succeeds and it
doesn't already exist within the Entry.
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# Try... | def _add_cat_dict(self,
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"""Add a CatDict to this Entry if initialization succeeds and it
doesn't already exist within the Entry.
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train | pbar | Wrapper for `tqdm` progress bar. | astrocats/catalog/utils/tq_funcs.py | def pbar(iter, desc='', **kwargs):
"""Wrapper for `tqdm` progress bar.
"""
return tqdm(
iter,
desc=('<' + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + '> ' +
desc),
dynamic_ncols=True,
**kwargs) | def pbar(iter, desc='', **kwargs):
"""Wrapper for `tqdm` progress bar.
"""
return tqdm(
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train | pbar_strings | Wrapper for `tqdm` progress bar which also sorts list of strings | astrocats/catalog/utils/tq_funcs.py | def pbar_strings(files, desc='', **kwargs):
"""Wrapper for `tqdm` progress bar which also sorts list of strings
"""
return tqdm(
sorted(files, key=lambda s: s.lower()),
desc=('<' + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + '> ' +
desc),
dynamic_ncols=True,
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"""Wrapper for `tqdm` progress bar which also sorts list of strings
"""
return tqdm(
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desc=('<' + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + '> ' +
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train | _get_task_priority | Get the task `priority` corresponding to the given `task_priority`.
If `task_priority` is an integer or 'None', return it.
If `task_priority` is a str, return the priority of the task it matches.
Otherwise, raise `ValueError`. | astrocats/catalog/catalog.py | def _get_task_priority(tasks, task_priority):
"""Get the task `priority` corresponding to the given `task_priority`.
If `task_priority` is an integer or 'None', return it.
If `task_priority` is a str, return the priority of the task it matches.
Otherwise, raise `ValueError`.
"""
if task_priorit... | def _get_task_priority(tasks, task_priority):
"""Get the task `priority` corresponding to the given `task_priority`.
If `task_priority` is an integer or 'None', return it.
If `task_priority` is a str, return the priority of the task it matches.
Otherwise, raise `ValueError`.
"""
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train | Catalog.import_data | Run all of the import tasks.
This is executed by the 'scripts.main.py' when the module is run as an
executable. This can also be run as a method, in which case default
arguments are loaded, but can be overriden using `**kwargs`. | astrocats/catalog/catalog.py | def import_data(self):
"""Run all of the import tasks.
This is executed by the 'scripts.main.py' when the module is run as an
executable. This can also be run as a method, in which case default
arguments are loaded, but can be overriden using `**kwargs`.
"""
tasks_list ... | def import_data(self):
"""Run all of the import tasks.
This is executed by the 'scripts.main.py' when the module is run as an
executable. This can also be run as a method, in which case default
arguments are loaded, but can be overriden using `**kwargs`.
"""
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train | Catalog.load_task_list | Load the list of tasks in this catalog's 'input/tasks.json' file.
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in. These are placed in an OrderedDict, sorted by the `priority`
parameter, with positive values and then negative values,
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"""Load the list of tasks in this catalog's 'input/tasks.json' file.
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in. These are placed in an OrderedDict, sorted by the `priority`
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train | Catalog.add_entry | Find an existing entry in, or add a new one to, the `entries` dict.
FIX: rename to `create_entry`???
Returns
-------
entries : OrderedDict of Entry objects
newname : str
Name of matching entry found in `entries`, or new entry added to
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FIX: rename to `create_entry`???
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entries : OrderedDict of Entry objects
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train | Catalog.find_entry_name_of_alias | Return the first entry name with the given 'alias' included in its
list of aliases.
Returns
-------
name of matching entry (str) or 'None' if no matches | astrocats/catalog/catalog.py | def find_entry_name_of_alias(self, alias):
"""Return the first entry name with the given 'alias' included in its
list of aliases.
Returns
-------
name of matching entry (str) or 'None' if no matches
"""
if alias in self.aliases:
name = self.aliases[a... | def find_entry_name_of_alias(self, alias):
"""Return the first entry name with the given 'alias' included in its
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Returns
-------
name of matching entry (str) or 'None' if no matches
"""
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train | Catalog.copy_entry_to_entry | Used by `merge_duplicates` | astrocats/catalog/catalog.py | def copy_entry_to_entry(self,
fromentry,
destentry,
check_for_dupes=True,
compare_to_existing=True):
"""Used by `merge_duplicates`
"""
self.log.info("Copy entry object '{}' to '{}'".fo... | def copy_entry_to_entry(self,
fromentry,
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"""Used by `merge_duplicates`
"""
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train | Catalog.merge_duplicates | Merge and remove duplicate entries.
Compares each entry ('name') in `stubs` to all later entries to check
for duplicates in name or alias. If a duplicate is found, they are
merged and written to file. | astrocats/catalog/catalog.py | def merge_duplicates(self):
"""Merge and remove duplicate entries.
Compares each entry ('name') in `stubs` to all later entries to check
for duplicates in name or alias. If a duplicate is found, they are
merged and written to file.
"""
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... | def merge_duplicates(self):
"""Merge and remove duplicate entries.
Compares each entry ('name') in `stubs` to all later entries to check
for duplicates in name or alias. If a duplicate is found, they are
merged and written to file.
"""
if len(self.entries) == 0:
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train | Catalog.load_stubs | Load all events in their `stub` (name, alias, etc only) form.
Used in `update` mode. | astrocats/catalog/catalog.py | def load_stubs(self, log_mem=False):
"""Load all events in their `stub` (name, alias, etc only) form.
Used in `update` mode.
"""
# Initialize parameter related to diagnostic output of memory usage
if log_mem:
import psutil
process = psutil.Process(os.getp... | def load_stubs(self, log_mem=False):
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train | Catalog._delete_entry_file | Delete the file associated with the given entry. | astrocats/catalog/catalog.py | def _delete_entry_file(self, entry_name=None, entry=None):
"""Delete the file associated with the given entry.
"""
if entry_name is None and entry is None:
raise RuntimeError("Either `entry_name` or `entry` must be given.")
elif entry_name is not None and entry is not None:
... | def _delete_entry_file(self, entry_name=None, entry=None):
"""Delete the file associated with the given entry.
"""
if entry_name is None and entry is None:
raise RuntimeError("Either `entry_name` or `entry` must be given.")
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train | Catalog.journal_entries | Write all entries in `entries` to files, and clear. Depending on
arguments and `tasks`.
Iterates over all elements of `entries`, saving (possibly 'burying')
and deleting.
- If ``clear == True``, then each element of `entries` is deleted,
and a `stubs` entry is added | astrocats/catalog/catalog.py | def journal_entries(self,
clear=True,
gz=False,
bury=False,
write_stubs=False,
final=False):
"""Write all entries in `entries` to files, and clear. Depending on
arguments and `tasks`.... | def journal_entries(self,
clear=True,
gz=False,
bury=False,
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train | Catalog.set_preferred_names | Choose between each entries given name and its possible aliases for
the best one. | astrocats/catalog/catalog.py | def set_preferred_names(self):
"""Choose between each entries given name and its possible aliases for
the best one.
"""
if len(self.entries) == 0:
self.log.error("WARNING: `entries` is empty, loading stubs")
self.load_stubs()
task_str = self.get_current_t... | def set_preferred_names(self):
"""Choose between each entries given name and its possible aliases for
the best one.
"""
if len(self.entries) == 0:
self.log.error("WARNING: `entries` is empty, loading stubs")
self.load_stubs()
task_str = self.get_current_t... | [
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train | Catalog._prep_git_add_file_list | Get a list of files which should be added to the given repository.
Notes
-----
* Finds files in the *root* of the given repository path.
* If `file_types` is given, only use those file types.
* If an uncompressed file is above the `size_limit`, it is compressed.
* If a c... | astrocats/catalog/catalog.py | def _prep_git_add_file_list(self,
repo,
size_limit,
fail=True,
file_types=None):
"""Get a list of files which should be added to the given repository.
Notes
-----
... | def _prep_git_add_file_list(self,
repo,
size_limit,
fail=True,
file_types=None):
"""Get a list of files which should be added to the given repository.
Notes
-----
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train | Catalog.load_url | Load the given URL, or a cached-version.
Load page from url or cached file, depending on the current settings.
'archived' mode applies when `args.archived` is true (from
`--archived` CL argument), and when this task has `Task.archived`
also set to True.
'archived' mode:
... | astrocats/catalog/catalog.py | def load_url(self,
url,
fname,
repo=None,
timeout=120,
post=None,
fail=False,
write=True,
json_sort=None,
cache_only=False,
archived_mode=None,
... | def load_url(self,
url,
fname,
repo=None,
timeout=120,
post=None,
fail=False,
write=True,
json_sort=None,
cache_only=False,
archived_mode=None,
... | [
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train | Catalog.download_url | Download text from the given url.
Returns `None` on failure.
Arguments
---------
self
url : str
URL web address to download.
timeout : int
Duration after which URL request should terminate.
fail : bool
If `True`, then an error... | astrocats/catalog/catalog.py | def download_url(self, url, timeout, fail=False, post=None, verify=True):
"""Download text from the given url.
Returns `None` on failure.
Arguments
---------
self
url : str
URL web address to download.
timeout : int
Duration after which U... | def download_url(self, url, timeout, fail=False, post=None, verify=True):
"""Download text from the given url.
Returns `None` on failure.
Arguments
---------
self
url : str
URL web address to download.
timeout : int
Duration after which U... | [
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train | CatDict.append_sources_from | Merge the source alias lists of two CatDicts. | astrocats/catalog/catdict.py | def append_sources_from(self, other):
"""Merge the source alias lists of two CatDicts."""
# Get aliases lists from this `CatDict` and other
self_aliases = self[self._KEYS.SOURCE].split(',')
other_aliases = other[self._KEYS.SOURCE].split(',')
# Store alias to `self`
self[... | def append_sources_from(self, other):
"""Merge the source alias lists of two CatDicts."""
# Get aliases lists from this `CatDict` and other
self_aliases = self[self._KEYS.SOURCE].split(',')
other_aliases = other[self._KEYS.SOURCE].split(',')
# Store alias to `self`
self[... | [
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train | Task.current_task | Name of current action for progress-bar output.
The specific task string is depends on the configuration via `args`.
Returns
-------
ctask : str
String representation of this task. | astrocats/catalog/task.py | def current_task(self, args):
"""Name of current action for progress-bar output.
The specific task string is depends on the configuration via `args`.
Returns
-------
ctask : str
String representation of this task.
"""
ctask = self.nice_name if self.n... | def current_task(self, args):
"""Name of current action for progress-bar output.
The specific task string is depends on the configuration via `args`.
Returns
-------
ctask : str
String representation of this task.
"""
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train | Task.load_archive | Whether previously archived data should be loaded. | astrocats/catalog/task.py | def load_archive(self, args):
"""Whether previously archived data should be loaded.
"""
import warnings
warnings.warn("`Task.load_archive()` is deprecated! "
"`Catalog.load_url` handles the same functionality.")
return self.archived or args.archived | def load_archive(self, args):
"""Whether previously archived data should be loaded.
"""
import warnings
warnings.warn("`Task.load_archive()` is deprecated! "
"`Catalog.load_url` handles the same functionality.")
return self.archived or args.archived | [
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train | get_sha | Use `git rev-parse HEAD <REPO>` to get current SHA. | astrocats/catalog/gitter.py | def get_sha(path=None, log=None, short=False, timeout=None):
"""Use `git rev-parse HEAD <REPO>` to get current SHA.
"""
# git_command = "git rev-parse HEAD {}".format(repo_name).split()
# git_command = "git rev-parse HEAD".split()
git_command = ["git", "rev-parse"]
if short:
git_command.... | def get_sha(path=None, log=None, short=False, timeout=None):
"""Use `git rev-parse HEAD <REPO>` to get current SHA.
"""
# git_command = "git rev-parse HEAD {}".format(repo_name).split()
# git_command = "git rev-parse HEAD".split()
git_command = ["git", "rev-parse"]
if short:
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train | git_add_commit_push_all_repos | Add all files in each data repository tree, commit, push.
Creates a commit message based on the current catalog version info.
If either the `git add` or `git push` commands fail, an error will be
raised. Currently, if `commit` fails an error *WILL NOT* be raised
because the `commit` command will retu... | astrocats/catalog/gitter.py | def git_add_commit_push_all_repos(cat):
"""Add all files in each data repository tree, commit, push.
Creates a commit message based on the current catalog version info.
If either the `git add` or `git push` commands fail, an error will be
raised. Currently, if `commit` fails an error *WILL NOT* be ra... | def git_add_commit_push_all_repos(cat):
"""Add all files in each data repository tree, commit, push.
Creates a commit message based on the current catalog version info.
If either the `git add` or `git push` commands fail, an error will be
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train | git_pull_all_repos | Perform a 'git pull' in each data repository.
> `git pull -s recursive -X theirs` | astrocats/catalog/gitter.py | def git_pull_all_repos(cat, strategy_recursive=True, strategy='theirs'):
"""Perform a 'git pull' in each data repository.
> `git pull -s recursive -X theirs`
"""
# raise RuntimeError("THIS DOESNT WORK YET!")
log = cat.log
log.debug("gitter.git_pull_all_repos()")
log.warning("WARNING: using ... | def git_pull_all_repos(cat, strategy_recursive=True, strategy='theirs'):
"""Perform a 'git pull' in each data repository.
> `git pull -s recursive -X theirs`
"""
# raise RuntimeError("THIS DOESNT WORK YET!")
log = cat.log
log.debug("gitter.git_pull_all_repos()")
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train | git_clone_all_repos | Perform a 'git clone' for each data repository that doesnt exist. | astrocats/catalog/gitter.py | def git_clone_all_repos(cat):
"""Perform a 'git clone' for each data repository that doesnt exist.
"""
log = cat.log
log.debug("gitter.git_clone_all_repos()")
all_repos = cat.PATHS.get_all_repo_folders()
out_repos = cat.PATHS.get_repo_output_folders()
for repo in all_repos:
log.info... | def git_clone_all_repos(cat):
"""Perform a 'git clone' for each data repository that doesnt exist.
"""
log = cat.log
log.debug("gitter.git_clone_all_repos()")
all_repos = cat.PATHS.get_all_repo_folders()
out_repos = cat.PATHS.get_repo_output_folders()
for repo in all_repos:
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train | git_reset_all_repos | Perform a 'git reset' in each data repository. | astrocats/catalog/gitter.py | def git_reset_all_repos(cat, hard=True, origin=False, clean=True):
"""Perform a 'git reset' in each data repository.
"""
log = cat.log
log.debug("gitter.git_reset_all_repos()")
all_repos = cat.PATHS.get_all_repo_folders()
for repo in all_repos:
log.warning("Repo in: '{}'".format(repo))
... | def git_reset_all_repos(cat, hard=True, origin=False, clean=True):
"""Perform a 'git reset' in each data repository.
"""
log = cat.log
log.debug("gitter.git_reset_all_repos()")
all_repos = cat.PATHS.get_all_repo_folders()
for repo in all_repos:
log.warning("Repo in: '{}'".format(repo))
... | [
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train | git_status_all_repos | Perform a 'git status' in each data repository. | astrocats/catalog/gitter.py | def git_status_all_repos(cat, hard=True, origin=False, clean=True):
"""Perform a 'git status' in each data repository.
"""
log = cat.log
log.debug("gitter.git_status_all_repos()")
all_repos = cat.PATHS.get_all_repo_folders()
for repo_name in all_repos:
log.info("Repo in: '{}'".format(re... | def git_status_all_repos(cat, hard=True, origin=False, clean=True):
"""Perform a 'git status' in each data repository.
"""
log = cat.log
log.debug("gitter.git_status_all_repos()")
all_repos = cat.PATHS.get_all_repo_folders()
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train | clone | Given a list of repositories, make sure they're all cloned.
Should be called from the subclassed `Catalog` objects, passed a list
of specific repository names.
Arguments
---------
all_repos : list of str
*Absolute* path specification of each target repository. | astrocats/catalog/gitter.py | def clone(repo, log, depth=1):
"""Given a list of repositories, make sure they're all cloned.
Should be called from the subclassed `Catalog` objects, passed a list
of specific repository names.
Arguments
---------
all_repos : list of str
*Absolute* path specification of each target rep... | def clone(repo, log, depth=1):
"""Given a list of repositories, make sure they're all cloned.
Should be called from the subclassed `Catalog` objects, passed a list
of specific repository names.
Arguments
---------
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train | _call_command_in_repo | Use `subprocess` to call a command in a certain (repo) directory.
Logs the output (both `stderr` and `stdout`) to the log, and checks the
return codes to make sure they're valid. Raises error if not.
Raises
------
exception `subprocess.CalledProcessError`: if the command fails | astrocats/catalog/gitter.py | def _call_command_in_repo(comm, repo, log, fail=False, log_flag=True):
"""Use `subprocess` to call a command in a certain (repo) directory.
Logs the output (both `stderr` and `stdout`) to the log, and checks the
return codes to make sure they're valid. Raises error if not.
Raises
------
excep... | def _call_command_in_repo(comm, repo, log, fail=False, log_flag=True):
"""Use `subprocess` to call a command in a certain (repo) directory.
Logs the output (both `stderr` and `stdout`) to the log, and checks the
return codes to make sure they're valid. Raises error if not.
Raises
------
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train | Spectrum.sort_func | Logic for sorting keys in a `Spectrum` relative to one another. | astrocats/catalog/spectrum.py | def sort_func(self, key):
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train | Quantity.sort_func | Sorting logic for `Quantity` objects. | astrocats/catalog/quantity.py | def sort_func(self, key):
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train | KeyCollection.vals | Return this class's attribute values (those not stating with '_').
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List of values of internal attributes. Order is effectiely random.
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train | Key.pretty | Return a 'pretty' string representation of this `Key`.
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train | Key.check | Make sure given value is consistent with this `Key` specification.
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Handle for this logger, must be distinct for a distinct logger.
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log : `logging.Logger` object
err_str : str
Error message to be logged and raised.
err_type : `Exception` object
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log : `logging.Logger` object
err_str : str
Error message to be logged and raised.
err_type : `Exception` object
Type of error to raise.
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train | log_memory | Log the current memory usage. | astrocats/catalog/utils/logger.py | def log_memory(log, pref=None, lvl=logging.DEBUG, raise_flag=True):
"""Log the current memory usage.
"""
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import sys
cyc_str = ""
KB = 1024.0
if pref is not None:
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# Linux returns units in Bytes; OSX in kilobytes
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http://docs.opencv.org/trunk/modules/features2d/doc/drawing_function_of_keypoints_and_matches.html | morecvutils/connectedComponents.py | def doblob(morphed, blobdet, img, anno=True):
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http://docs.opencv.org/master/modules/features2d/doc/drawing_function_of_keypoints_and_matches.html
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train | ArgsHandler.load_args | Parse arguments and return configuration settings. | astrocats/catalog/argshandler.py | def load_args(self, args, clargs):
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train | ArgsHandler._setup_argparse | Create `argparse` instance, and setup with appropriate parameters. | astrocats/catalog/argshandler.py | def _setup_argparse(self):
"""Create `argparse` instance, and setup with appropriate parameters.
"""
parser = argparse.ArgumentParser(
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subparsers = parser.add_subparsers(
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train | ArgsHandler._add_parser_arguments_git | Create a sub-parsers for git subcommands. | astrocats/catalog/argshandler.py | def _add_parser_arguments_git(self, subparsers):
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train | ArgsHandler._add_parser_arguments_analyze | Create a parser for the 'analyze' subcommand. | astrocats/catalog/argshandler.py | def _add_parser_arguments_analyze(self, subparsers):
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train | compress_gz | Compress the file with the given name and delete the uncompressed file.
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fname : str
Name of the file to compress and delete.
Returns
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train | draw_flow | draws flow vectors on image
this came from opencv/examples directory
another way: http://docs.opencv.org/trunk/doc/py_tutorials/py_gui/py_drawing_functions/py_drawing_functions.html | morecvutils/cv2draw.py | def draw_flow(img, flow, step=16, dtype=uint8):
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this came from opencv/examples directory
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this came from opencv/examples directory
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train | draw_hsv | mag must be uint8, uint16, uint32 and 2-D
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train | flow2magang | flow dimensions y,x,2 3-D. flow[...,0] is magnitude, flow[...,1] is angle | morecvutils/cv2draw.py | def flow2magang(flow, dtype=uint8):
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flow dimensions y,x,2 3-D. flow[...,0] is magnitude, flow[...,1] is angle
"""
fx, fy = flow[..., 0], flow[..., 1]
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flow dimensions y,x,2 3-D. flow[...,0] is magnitude, flow[...,1] is angle
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fx, fy = flow[..., 0], flow[..., 1]
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train | IOC | dir
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train | IOC_TYPECHECK | Returns the size of given type, and check its suitability for use in an
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Returns the size of given type, and check its suitability for use in an
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train | IOR | An ioctl with read parameters.
size (ctype type or instance)
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"""
An ioctl with read parameters.
size (ctype type or instance)
Type/structure of the argument passed to ioctl's "arg" argument.
"""
return IOC(IOC_READ, type, nr, IOC_TYPECHECK(size)) | def IOR(type, nr, size):
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train | IOW | An ioctl with write parameters.
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"""
An ioctl with write parameters.
size (ctype type or instance)
Type/structure of the argument passed to ioctl's "arg" argument.
"""
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train | IOWR | An ioctl with both read an writes parameters.
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An ioctl with both read an writes parameters.
size (ctype type or instance)
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return IOC(IOC_READ | IOC_WRITE, type, nr, IOC_TYPECHECK(size)) | def IOWR(type, nr, size):
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An ioctl with both read an writes parameters.
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train | _get_last_dirs | Get a path including only the trailing `num` directories.
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last_path : str | astrocats/catalog/analysis.py | def _get_last_dirs(path, num=1):
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last_path : str
"""
head, tail = os.path.split(path)
last_path = str(tail)
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last_path = os.path.join(tail,... | def _get_last_dirs(path, num=1):
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last_path : str
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train | Analysis.analyze | Run the analysis routines determined from the given `args`. | astrocats/catalog/analysis.py | def analyze(self, args):
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"""
self.log.info("Running catalog analysis")
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train | Analysis.count | Analyze the counts of ...things.
Returns
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retvals : dict
Dictionary of 'property-name: counts' pairs for further processing | astrocats/catalog/analysis.py | def count(self):
"""Analyze the counts of ...things.
Returns
-------
retvals : dict
Dictionary of 'property-name: counts' pairs for further processing
"""
self.log.info("Running 'count'")
retvals = {}
# Numbers of 'tasks'
num_tasks =... | def count(self):
"""Analyze the counts of ...things.
Returns
-------
retvals : dict
Dictionary of 'property-name: counts' pairs for further processing
"""
self.log.info("Running 'count'")
retvals = {}
# Numbers of 'tasks'
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train | Analysis._count_tasks | Count the number of tasks, both in the json and directory.
Returns
-------
num_tasks : int
The total number of all tasks included in the `tasks.json` file. | astrocats/catalog/analysis.py | def _count_tasks(self):
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Returns
-------
num_tasks : int
The total number of all tasks included in the `tasks.json` file.
"""
self.log.warning("Tasks:")
tasks, task_names = self.catalog._lo... | def _count_tasks(self):
"""Count the number of tasks, both in the json and directory.
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num_tasks : int
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self.log.warning("Tasks:")
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train | Analysis._count_repo_files | Count the number of files in the data repositories.
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`_IGNORE_FILES` determine which files are ignored in (most) counts.
Returns
-------
repo_files : int
Total number of (non-i... | astrocats/catalog/analysis.py | def _count_repo_files(self):
"""Count the number of files in the data repositories.
`_COUNT_FILE_TYPES` are used to determine which file types are checked
explicitly.
`_IGNORE_FILES` determine which files are ignored in (most) counts.
Returns
-------
repo_files ... | def _count_repo_files(self):
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`_IGNORE_FILES` determine which files are ignored in (most) counts.
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train | Analysis._file_nums_str | Construct a string showing the number of different file types.
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Returns
-------
f_str : str
"""
# 'other' is the difference between all and named
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f_str : str
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train | Analysis._count_files_by_type | Count files in the given path, with the given pattern.
If `ignore = True`, skip files in the `_IGNORE_FILES` list.
Returns
-------
num_files : int | astrocats/catalog/analysis.py | def _count_files_by_type(self, path, pattern, ignore=True):
"""Count files in the given path, with the given pattern.
If `ignore = True`, skip files in the `_IGNORE_FILES` list.
Returns
-------
num_files : int
"""
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num_files : int
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train | Source.bibcode_from_url | Given a URL, try to find the ADS bibcode.
Currently: only `ads` URLs will work, e.g.
Returns
-------
code : str or 'None'
The Bibcode if found, otherwise 'None' | astrocats/catalog/source.py | def bibcode_from_url(cls, url):
"""Given a URL, try to find the ADS bibcode.
Currently: only `ads` URLs will work, e.g.
Returns
-------
code : str or 'None'
The Bibcode if found, otherwise 'None'
"""
try:
code = url.split('/abs/')
... | def bibcode_from_url(cls, url):
"""Given a URL, try to find the ADS bibcode.
Currently: only `ads` URLs will work, e.g.
Returns
-------
code : str or 'None'
The Bibcode if found, otherwise 'None'
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train | Entry._get_save_path | Return the path that this Entry should be saved to. | astrocats/catalog/entry.py | def _get_save_path(self, bury=False):
"""Return the path that this Entry should be saved to."""
filename = self.get_filename(self[self._KEYS.NAME])
# Put objects that shouldn't belong in this catalog in the boneyard
if bury:
outdir = self.catalog.get_repo_boneyard()
... | def _get_save_path(self, bury=False):
"""Return the path that this Entry should be saved to."""
filename = self.get_filename(self[self._KEYS.NAME])
# Put objects that shouldn't belong in this catalog in the boneyard
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train | Entry._ordered | Convert the object into a plain OrderedDict. | astrocats/catalog/entry.py | def _ordered(self, odict):
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ndict = OrderedDict()
if isinstance(odict, CatDict) or isinstance(odict, Entry):
key = odict.sort_func
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train | Entry.get_hash | Return a unique hash associated with the listed keys. | astrocats/catalog/entry.py | def get_hash(self, keys=[]):
"""Return a unique hash associated with the listed keys."""
if not len(keys):
keys = list(self.keys())
string_rep = ''
oself = self._ordered(deepcopy(self))
for key in keys:
string_rep += json.dumps(oself.get(key, ''), sort_ke... | def get_hash(self, keys=[]):
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train | Entry._clean_quantity | Clean quantity value before it is added to entry. | astrocats/catalog/entry.py | def _clean_quantity(self, quantity):
"""Clean quantity value before it is added to entry."""
value = quantity.get(QUANTITY.VALUE, '').strip()
error = quantity.get(QUANTITY.E_VALUE, '').strip()
unit = quantity.get(QUANTITY.U_VALUE, '').strip()
kind = quantity.get(QUANTITY.KIND, ''... | def _clean_quantity(self, quantity):
"""Clean quantity value before it is added to entry."""
value = quantity.get(QUANTITY.VALUE, '').strip()
error = quantity.get(QUANTITY.E_VALUE, '').strip()
unit = quantity.get(QUANTITY.U_VALUE, '').strip()
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train | Entry._convert_odict_to_classes | Convert `OrderedDict` into `Entry` or its derivative classes. | astrocats/catalog/entry.py | def _convert_odict_to_classes(self,
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clean=False,
merge=True,
pop_schema=True,
compare_to_existing=True,
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train | Entry._check_cat_dict_source | Check that a source exists and that a quantity isn't erroneous. | astrocats/catalog/entry.py | def _check_cat_dict_source(self, cat_dict_class, key_in_self, **kwargs):
"""Check that a source exists and that a quantity isn't erroneous."""
# Make sure that a source is given
source = kwargs.get(cat_dict_class._KEYS.SOURCE, None)
if source is None:
raise CatDictError(
... | def _check_cat_dict_source(self, cat_dict_class, key_in_self, **kwargs):
"""Check that a source exists and that a quantity isn't erroneous."""
# Make sure that a source is given
source = kwargs.get(cat_dict_class._KEYS.SOURCE, None)
if source is None:
raise CatDictError(
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train | Entry._add_cat_dict | Add a `CatDict` to this `Entry`.
CatDict only added if initialization succeeds and it
doesn't already exist within the Entry. | astrocats/catalog/entry.py | def _add_cat_dict(self,
cat_dict_class,
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check_for_dupes=True,
compare_to_existing=True,
**kwargs):
"""Add a `CatDict` to this `Entry`.
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train | Entry.init_from_file | Construct a new `Entry` instance from an input file.
The input file can be given explicitly by `path`, or a path will
be constructed appropriately if possible.
Arguments
---------
catalog : `astrocats.catalog.catalog.Catalog` instance
The parent catalog object of wh... | astrocats/catalog/entry.py | def init_from_file(cls,
catalog,
name=None,
path=None,
clean=False,
merge=True,
pop_schema=True,
ignore_keys=[],
compare_to_existing=Tru... | def init_from_file(cls,
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name=None,
path=None,
clean=False,
merge=True,
pop_schema=True,
ignore_keys=[],
compare_to_existing=Tru... | [
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train | Entry.add_alias | Add an alias, optionally 'cleaning' the alias string.
Calls the parent `catalog` method `clean_entry_name` - to apply the
same name-cleaning as is applied to entry names themselves.
Returns
-------
alias : str
The stored version of the alias (cleaned or not). | astrocats/catalog/entry.py | def add_alias(self, alias, source, clean=True):
"""Add an alias, optionally 'cleaning' the alias string.
Calls the parent `catalog` method `clean_entry_name` - to apply the
same name-cleaning as is applied to entry names themselves.
Returns
-------
alias : str
... | def add_alias(self, alias, source, clean=True):
"""Add an alias, optionally 'cleaning' the alias string.
Calls the parent `catalog` method `clean_entry_name` - to apply the
same name-cleaning as is applied to entry names themselves.
Returns
-------
alias : str
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train | Entry.add_error | Add an `Error` instance to this entry. | astrocats/catalog/entry.py | def add_error(self, value, **kwargs):
"""Add an `Error` instance to this entry."""
kwargs.update({ERROR.VALUE: value})
self._add_cat_dict(Error, self._KEYS.ERRORS, **kwargs)
return | def add_error(self, value, **kwargs):
"""Add an `Error` instance to this entry."""
kwargs.update({ERROR.VALUE: value})
self._add_cat_dict(Error, self._KEYS.ERRORS, **kwargs)
return | [
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train | Entry.add_photometry | Add a `Photometry` instance to this entry. | astrocats/catalog/entry.py | def add_photometry(self, compare_to_existing=True, **kwargs):
"""Add a `Photometry` instance to this entry."""
self._add_cat_dict(
Photometry,
self._KEYS.PHOTOMETRY,
compare_to_existing=compare_to_existing,
**kwargs)
return | def add_photometry(self, compare_to_existing=True, **kwargs):
"""Add a `Photometry` instance to this entry."""
self._add_cat_dict(
Photometry,
self._KEYS.PHOTOMETRY,
compare_to_existing=compare_to_existing,
**kwargs)
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train | Entry.merge_dupes | Merge two entries that correspond to the same entry. | astrocats/catalog/entry.py | def merge_dupes(self):
"""Merge two entries that correspond to the same entry."""
for dupe in self.dupe_of:
if dupe in self.catalog.entries:
if self.catalog.entries[dupe]._stub:
# merge = False to avoid infinite recursion
self.catalog.l... | def merge_dupes(self):
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train | Entry.add_quantity | Add an `Quantity` instance to this entry. | astrocats/catalog/entry.py | def add_quantity(self,
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source,
check_for_dupes=True,
compare_to_existing=True,
**kwargs):
"""Add an `Quantity` instance to this entry."""
success = True
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success = True
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train | Entry.add_self_source | Add a source that refers to the catalog itself.
For now this points to the Open Supernova Catalog by default. | astrocats/catalog/entry.py | def add_self_source(self):
"""Add a source that refers to the catalog itself.
For now this points to the Open Supernova Catalog by default.
"""
return self.add_source(
bibcode=self.catalog.OSC_BIBCODE,
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"""Add a source that refers to the catalog itself.
For now this points to the Open Supernova Catalog by default.
"""
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train | Entry.add_source | Add a `Source` instance to this entry. | astrocats/catalog/entry.py | def add_source(self, allow_alias=False, **kwargs):
"""Add a `Source` instance to this entry."""
if not allow_alias and SOURCE.ALIAS in kwargs:
err_str = "`{}` passed in kwargs, this shouldn't happen!".format(
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self._log.error(err_str)
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"""Add a `Source` instance to this entry."""
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err_str = "`{}` passed in kwargs, this shouldn't happen!".format(
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train | Entry.add_model | Add a `Model` instance to this entry. | astrocats/catalog/entry.py | def add_model(self, allow_alias=False, **kwargs):
"""Add a `Model` instance to this entry."""
if not allow_alias and MODEL.ALIAS in kwargs:
err_str = "`{}` passed in kwargs, this shouldn't happen!".format(
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self._log.error(err_str)
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train | Entry.add_spectrum | Add a `Spectrum` instance to this entry. | astrocats/catalog/entry.py | def add_spectrum(self, compare_to_existing=True, **kwargs):
"""Add a `Spectrum` instance to this entry."""
spec_key = self._KEYS.SPECTRA
# Make sure that a source is given, and is valid (nor erroneous)
source = self._check_cat_dict_source(Spectrum, spec_key, **kwargs)
if source i... | def add_spectrum(self, compare_to_existing=True, **kwargs):
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train | Entry.check | Check that the entry has the required fields. | astrocats/catalog/entry.py | def check(self):
"""Check that the entry has the required fields."""
# Make sure there is a schema key in dict
if self._KEYS.SCHEMA not in self:
self[self._KEYS.SCHEMA] = self.catalog.SCHEMA.URL
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train | Entry.get_aliases | Retrieve the aliases of this object as a list of strings.
Arguments
---------
includename : bool
Include the 'name' parameter in the list of aliases. | astrocats/catalog/entry.py | def get_aliases(self, includename=True):
"""Retrieve the aliases of this object as a list of strings.
Arguments
---------
includename : bool
Include the 'name' parameter in the list of aliases.
"""
# empty list if doesnt exist
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includename : bool
Include the 'name' parameter in the list of aliases.
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train | Entry.get_entry_text | Retrieve the raw text from a file. | astrocats/catalog/entry.py | def get_entry_text(self, fname):
"""Retrieve the raw text from a file."""
if fname.split('.')[-1] == 'gz':
with gz.open(fname, 'rt') as f:
filetext = f.read()
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return filet... | def get_entry_text(self, fname):
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train | Entry.get_source_by_alias | Given an alias, find the corresponding source in this entry.
If the given alias doesn't exist (e.g. there are no sources), then a
`ValueError` is raised.
Arguments
---------
alias : str
The str-integer (e.g. '8') of the target source.
Returns
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"""Given an alias, find the corresponding source in this entry.
If the given alias doesn't exist (e.g. there are no sources), then a
`ValueError` is raised.
Arguments
---------
alias : str
The str-integer (e.g. '8') of t... | def get_source_by_alias(self, alias):
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train | Entry.get_stub | Get a new `Entry` which contains the 'stub' of this one.
The 'stub' is only the name and aliases.
Usage:
-----
To convert a normal entry into a stub (for example), overwrite the
entry in place, i.e.
>>> entries[name] = entries[name].get_stub()
Returns
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The 'stub' is only the name and aliases.
Usage:
-----
To convert a normal entry into a stub (for example), overwrite the
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>>> entries[name] = entries[name].get_st... | def get_stub(self):
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train | Entry.is_erroneous | Check if attribute has been marked as being erroneous. | astrocats/catalog/entry.py | def is_erroneous(self, field, sources):
"""Check if attribute has been marked as being erroneous."""
if self._KEYS.ERRORS in self:
my_errors = self[self._KEYS.ERRORS]
for alias in sources.split(','):
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bib_err... | def is_erroneous(self, field, sources):
"""Check if attribute has been marked as being erroneous."""
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train | Entry.is_private | Check if attribute is private. | astrocats/catalog/entry.py | def is_private(self, key, sources):
"""Check if attribute is private."""
# aliases are always public.
if key == ENTRY.ALIAS:
return False
return all([
SOURCE.PRIVATE in self.get_source_by_alias(x)
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]) | def is_private(self, key, sources):
"""Check if attribute is private."""
# aliases are always public.
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train | Entry.sanitize | Sanitize the data (sort it, etc.) before writing it to disk.
Template method that can be overridden in each catalog's subclassed
`Entry` object. | astrocats/catalog/entry.py | def sanitize(self):
"""Sanitize the data (sort it, etc.) before writing it to disk.
Template method that can be overridden in each catalog's subclassed
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"""
name = self[self._KEYS.NAME]
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train | Entry.save | Write entry to JSON file in the proper location.
Arguments
---------
bury : bool
final : bool
If this is the 'final' save, perform additional sanitization and
cleaning operations. | astrocats/catalog/entry.py | def save(self, bury=False, final=False):
"""Write entry to JSON file in the proper location.
Arguments
---------
bury : bool
final : bool
If this is the 'final' save, perform additional sanitization and
cleaning operations.
"""
outdir, f... | def save(self, bury=False, final=False):
"""Write entry to JSON file in the proper location.
Arguments
---------
bury : bool
final : bool
If this is the 'final' save, perform additional sanitization and
cleaning operations.
"""
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train | Entry.sort_func | Used to sort keys when writing Entry to JSON format.
Should be supplemented/overridden by inheriting classes. | astrocats/catalog/entry.py | def sort_func(self, key):
"""Used to sort keys when writing Entry to JSON format.
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"""
if key == self._KEYS.SCHEMA:
return 'aaa'
if key == self._KEYS.NAME:
return 'aab'
if key == self._KEYS.S... | def sort_func(self, key):
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"""
if key == self._KEYS.SCHEMA:
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train | set_pd_mag_from_counts | Set photometry dictionary from a counts measurement. | astrocats/catalog/photometry.py | def set_pd_mag_from_counts(photodict,
c='',
ec='',
lec='',
uec='',
zp=DEFAULT_ZP,
sig=DEFAULT_UL_SIGMA):
"""Set photometry dictionary from a counts measur... | def set_pd_mag_from_counts(photodict,
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zp=DEFAULT_ZP,
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train | set_pd_mag_from_flux_density | Set photometry dictionary from a flux density measurement.
`fd` is assumed to be in microjanskys. | astrocats/catalog/photometry.py | def set_pd_mag_from_flux_density(photodict,
fd='',
efd='',
lefd='',
uefd='',
sig=DEFAULT_UL_SIGMA):
"""Set photometry dictionary from a flux density me... | def set_pd_mag_from_flux_density(photodict,
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train | Photometry._check | Check that entry attributes are legal. | astrocats/catalog/photometry.py | def _check(self):
"""Check that entry attributes are legal."""
# Run the super method
super(Photometry, self)._check()
err_str = None
has_flux = self._KEYS.FLUX in self
has_flux_dens = self._KEYS.FLUX_DENSITY in self
has_u_flux = self._KEYS.U_FLUX in self
... | def _check(self):
"""Check that entry attributes are legal."""
# Run the super method
super(Photometry, self)._check()
err_str = None
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has_flux_dens = self._KEYS.FLUX_DENSITY in self
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train | Photometry.sort_func | Specify order for attributes. | astrocats/catalog/photometry.py | def sort_func(self, key):
"""Specify order for attributes."""
if key == self._KEYS.TIME:
return 'aaa'
if key == self._KEYS.MODEL:
return 'zzy'
if key == self._KEYS.SOURCE:
return 'zzz'
return key | def sort_func(self, key):
"""Specify order for attributes."""
if key == self._KEYS.TIME:
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if key == self._KEYS.MODEL:
return 'zzy'
if key == self._KEYS.SOURCE:
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train | run_migrations_offline | Run migrations in 'offline' mode.
This configures the context with just a URL
and not an Engine, though an Engine is acceptable
here as well. By skipping the Engine creation
we don't even need a DBAPI to be available.
Calls to context.execute() here emit the given string to the
script output. | ziggurat_foundations/migrations/env.py | def run_migrations_offline():
"""Run migrations in 'offline' mode.
This configures the context with just a URL
and not an Engine, though an Engine is acceptable
here as well. By skipping the Engine creation
we don't even need a DBAPI to be available.
Calls to context.execute() here emit the g... | def run_migrations_offline():
"""Run migrations in 'offline' mode.
This configures the context with just a URL
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here as well. By skipping the Engine creation
we don't even need a DBAPI to be available.
Calls to context.execute() here emit the g... | [
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] | ergo/ziggurat_foundations | python | https://github.com/ergo/ziggurat_foundations/blob/9eeec894d08e8d7defa60ddc04b63f69cd4cbeba/ziggurat_foundations/migrations/env.py#L51-L71 | [
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train | run_migrations_online | Run migrations in 'online' mode.
In this scenario we need to create an Engine
and associate a connection with the context. | ziggurat_foundations/migrations/env.py | def run_migrations_online():
"""Run migrations in 'online' mode.
In this scenario we need to create an Engine
and associate a connection with the context.
"""
engine = create_engine(get_url())
connection = engine.connect()
context.configure(
connection=connection,
target_m... | def run_migrations_online():
"""Run migrations in 'online' mode.
In this scenario we need to create an Engine
and associate a connection with the context.
"""
engine = create_engine(get_url())
connection = engine.connect()
context.configure(
connection=connection,
target_m... | [
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] | ergo/ziggurat_foundations | python | https://github.com/ergo/ziggurat_foundations/blob/9eeec894d08e8d7defa60ddc04b63f69cd4cbeba/ziggurat_foundations/migrations/env.py#L74-L95 | [
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train | UserResourcePermissionService.by_resource_user_and_perm | return all instances by user name, perm name and resource id
:param user_id:
:param perm_name:
:param resource_id:
:param db_session:
:return: | ziggurat_foundations/models/services/user_resource_permission.py | def by_resource_user_and_perm(
cls, user_id, perm_name, resource_id, db_session=None
):
"""
return all instances by user name, perm name and resource id
:param user_id:
:param perm_name:
:param resource_id:
:param db_session:
:return:
"""
... | def by_resource_user_and_perm(
cls, user_id, perm_name, resource_id, db_session=None
):
"""
return all instances by user name, perm name and resource id
:param user_id:
:param perm_name:
:param resource_id:
:param db_session:
:return:
"""
... | [
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] | ergo/ziggurat_foundations | python | https://github.com/ergo/ziggurat_foundations/blob/9eeec894d08e8d7defa60ddc04b63f69cd4cbeba/ziggurat_foundations/models/services/user_resource_permission.py#L27-L44 | [
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train | Library.tdSensor | Get the next sensor while iterating.
:return: a dict with the keys: protocol, model, id, datatypes. | tellcore/library.py | def tdSensor(self):
"""Get the next sensor while iterating.
:return: a dict with the keys: protocol, model, id, datatypes.
"""
protocol = create_string_buffer(20)
model = create_string_buffer(20)
sid = c_int()
datatypes = c_int()
self._lib.tdSensor(proto... | def tdSensor(self):
"""Get the next sensor while iterating.
:return: a dict with the keys: protocol, model, id, datatypes.
"""
protocol = create_string_buffer(20)
model = create_string_buffer(20)
sid = c_int()
datatypes = c_int()
self._lib.tdSensor(proto... | [
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] | erijo/tellcore-py | python | https://github.com/erijo/tellcore-py/blob/7a1eb53e12ef039a2350933e502633df7560f6a8/tellcore/library.py#L409-L423 | [
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