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esafak/mca | src/mca.py | MCA.cos_r | def cos_r(self, N=None): # percent=0.9
"""Return the squared cosines for each row."""
if not hasattr(self, 'F') or self.F.shape[1] < self.rank:
self.fs_r(N=self.rank) # generate F
self.dr = norm(self.F, axis=1)**2
# cheaper than diag(self.F.dot(self.F.T))?
return apply_along_axis(lambda _: _/self.dr, 0... | python | def cos_r(self, N=None): # percent=0.9
"""Return the squared cosines for each row."""
if not hasattr(self, 'F') or self.F.shape[1] < self.rank:
self.fs_r(N=self.rank) # generate F
self.dr = norm(self.F, axis=1)**2
# cheaper than diag(self.F.dot(self.F.T))?
return apply_along_axis(lambda _: _/self.dr, 0... | [
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esafak/mca | src/mca.py | MCA.cos_c | def cos_c(self, N=None): # percent=0.9,
"""Return the squared cosines for each column."""
if not hasattr(self, 'G') or self.G.shape[1] < self.rank:
self.fs_c(N=self.rank) # generate
self.dc = norm(self.G, axis=1)**2
# cheaper than diag(self.G.dot(self.G.T))?
return apply_along_axis(lambda _: _/self.dc,... | python | def cos_c(self, N=None): # percent=0.9,
"""Return the squared cosines for each column."""
if not hasattr(self, 'G') or self.G.shape[1] < self.rank:
self.fs_c(N=self.rank) # generate
self.dc = norm(self.G, axis=1)**2
# cheaper than diag(self.G.dot(self.G.T))?
return apply_along_axis(lambda _: _/self.dc,... | [
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esafak/mca | src/mca.py | MCA.cont_r | def cont_r(self, percent=0.9, N=None):
"""Return the contribution of each row."""
if not hasattr(self, 'F'):
self.fs_r(N=self.rank) # generate F
return apply_along_axis(lambda _: _/self.L[:N], 1,
apply_along_axis(lambda _: _*self.r, 0, self.F[:, :N]**2)) | python | def cont_r(self, percent=0.9, N=None):
"""Return the contribution of each row."""
if not hasattr(self, 'F'):
self.fs_r(N=self.rank) # generate F
return apply_along_axis(lambda _: _/self.L[:N], 1,
apply_along_axis(lambda _: _*self.r, 0, self.F[:, :N]**2)) | [
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esafak/mca | src/mca.py | MCA.cont_c | def cont_c(self, percent=0.9, N=None): # bug? check axis number 0 vs 1 here
"""Return the contribution of each column."""
if not hasattr(self, 'G'):
self.fs_c(N=self.rank) # generate G
return apply_along_axis(lambda _: _/self.L[:N], 1,
apply_along_axis(lambda _: _*self.c, 0, self.G[:, :N]**2)) | python | def cont_c(self, percent=0.9, N=None): # bug? check axis number 0 vs 1 here
"""Return the contribution of each column."""
if not hasattr(self, 'G'):
self.fs_c(N=self.rank) # generate G
return apply_along_axis(lambda _: _/self.L[:N], 1,
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esafak/mca | src/mca.py | MCA.fs_r_sup | def fs_r_sup(self, DF, N=None):
"""Find the supplementary row factor scores.
ncols: The number of singular vectors to retain.
If both are passed, cols is given preference.
"""
if not hasattr(self, 'G'):
self.fs_c(N=self.rank) # generate G
if N and (not isinstance(N, int) or N <= 0):
raise ValueErro... | python | def fs_r_sup(self, DF, N=None):
"""Find the supplementary row factor scores.
ncols: The number of singular vectors to retain.
If both are passed, cols is given preference.
"""
if not hasattr(self, 'G'):
self.fs_c(N=self.rank) # generate G
if N and (not isinstance(N, int) or N <= 0):
raise ValueErro... | [
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esafak/mca | src/mca.py | MCA.fs_c_sup | def fs_c_sup(self, DF, N=None):
"""Find the supplementary column factor scores.
ncols: The number of singular vectors to retain.
If both are passed, cols is given preference.
"""
if not hasattr(self, 'F'):
self.fs_r(N=self.rank) # generate F
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"""Find the supplementary column factor scores.
ncols: The number of singular vectors to retain.
If both are passed, cols is given preference.
"""
if not hasattr(self, 'F'):
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primetang/qrtools | src/qrtools.py | QR.data_recognise | def data_recognise(self, data=None):
"""Returns an unicode string indicating the data type of the data paramater"""
data = data or self.data
data_lower = data.lower()
if data_lower.startswith(u"http://") or data_lower.startswith(u"https://"):
return u'url'
elif data_l... | python | def data_recognise(self, data=None):
"""Returns an unicode string indicating the data type of the data paramater"""
data = data or self.data
data_lower = data.lower()
if data_lower.startswith(u"http://") or data_lower.startswith(u"https://"):
return u'url'
elif data_l... | [
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primetang/qrtools | src/qrtools.py | QR.data_to_string | def data_to_string(self):
"""Returns a UTF8 string with the QR Code's data"""
# FIX-ME: if we don't add the BOM_UTF8 char, QtQR doesn't decode
# correctly; but if we add it, mobile apps don't.-
# Apparently is a zbar bug.
if self.data_type == 'text':
return BOM_UTF8 +... | python | def data_to_string(self):
"""Returns a UTF8 string with the QR Code's data"""
# FIX-ME: if we don't add the BOM_UTF8 char, QtQR doesn't decode
# correctly; but if we add it, mobile apps don't.-
# Apparently is a zbar bug.
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python-visualization/branca | branca/utilities.py | split_six | def split_six(series=None):
"""
Given a Pandas Series, get a domain of values from zero to the 90% quantile
rounded to the nearest order-of-magnitude integer. For example, 2100 is
rounded to 2000, 2790 to 3000.
Parameters
----------
series: Pandas series, default None
Returns
-----... | python | def split_six(series=None):
"""
Given a Pandas Series, get a domain of values from zero to the 90% quantile
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python-visualization/branca | branca/colormap.py | StepColormap.to_linear | def to_linear(self, index=None):
"""
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index : list of floats, default None
The values corresponding to each color in the output colormap.
It has to be sorted.
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"""
Transforms the StepColormap into a LinearColormap.
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----------
index : list of floats, default None
The values corresponding to each color in the output colormap.
It has to be sorted.
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python-visualization/branca | branca/element.py | Element.add_to | def add_to(self, parent, name=None, index=None):
"""Add element to a parent."""
parent.add_child(self, name=name, index=index)
return self | python | def add_to(self, parent, name=None, index=None):
"""Add element to a parent."""
parent.add_child(self, name=name, index=index)
return self | [
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python-visualization/branca | branca/element.py | Element.to_json | def to_json(self, depth=-1, **kwargs):
"""Returns a JSON representation of the object."""
return json.dumps(self.to_dict(depth=depth, ordered=True), **kwargs) | python | def to_json(self, depth=-1, **kwargs):
"""Returns a JSON representation of the object."""
return json.dumps(self.to_dict(depth=depth, ordered=True), **kwargs) | [
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python-visualization/branca | branca/element.py | Element.save | def save(self, outfile, close_file=True, **kwargs):
"""Saves an Element into a file.
Parameters
----------
outfile : str or file object
The file (or filename) where you want to output the html.
close_file : bool, default True
Whether the file has to be cl... | python | def save(self, outfile, close_file=True, **kwargs):
"""Saves an Element into a file.
Parameters
----------
outfile : str or file object
The file (or filename) where you want to output the html.
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python-visualization/branca | branca/element.py | Link.get_code | def get_code(self):
"""Opens the link and returns the response's content."""
if self.code is None:
self.code = urlopen(self.url).read()
return self.code | python | def get_code(self):
"""Opens the link and returns the response's content."""
if self.code is None:
self.code = urlopen(self.url).read()
return self.code | [
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python-visualization/branca | branca/element.py | Figure._repr_html_ | def _repr_html_(self, **kwargs):
"""Displays the Figure in a Jupyter notebook.
"""
html = self.render(**kwargs)
html = "data:text/html;charset=utf-8;base64," + base64.b64encode(html.encode('utf8')).decode('utf8') # noqa
if self.height is None:
iframe = (
... | python | def _repr_html_(self, **kwargs):
"""Displays the Figure in a Jupyter notebook.
"""
html = self.render(**kwargs)
html = "data:text/html;charset=utf-8;base64," + base64.b64encode(html.encode('utf8')).decode('utf8') # noqa
if self.height is None:
iframe = (
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quiltdata/quilt | compiler/quilt/tools/data_transfer.py | create_s3_session | def create_s3_session():
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quiltdata/quilt | compiler/quilt/imports.py | ModuleFinder.find_module | def find_module(self, fullname, path=None):
"""
Looks up the table based on the module path.
"""
if not fullname.startswith(self._module_name + '.'):
# Not a quilt submodule.
return None
submodule = fullname[len(self._module_name) + 1:]
parts = su... | python | def find_module(self, fullname, path=None):
"""
Looks up the table based on the module path.
"""
if not fullname.startswith(self._module_name + '.'):
# Not a quilt submodule.
return None
submodule = fullname[len(self._module_name) + 1:]
parts = su... | [
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quiltdata/quilt | compiler/quilt/tools/build.py | _have_pyspark | def _have_pyspark():
"""
Check if we're running Pyspark
"""
if _have_pyspark.flag is None:
try:
if PackageStore.get_parquet_lib() is ParquetLib.SPARK:
import pyspark # pylint:disable=W0612
_have_pyspark.flag = True
else:
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"""
Check if we're running Pyspark
"""
if _have_pyspark.flag is None:
try:
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import pyspark # pylint:disable=W0612
_have_pyspark.flag = True
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quiltdata/quilt | compiler/quilt/tools/build.py | _path_hash | def _path_hash(path, transform, kwargs):
"""
Generate a hash of source file path + transform + args
"""
sortedargs = ["%s:%r:%s" % (key, value, type(value))
for key, value in sorted(iteritems(kwargs))]
srcinfo = "{path}:{transform}:{{{kwargs}}}".format(path=os.path.abspath(path),
... | python | def _path_hash(path, transform, kwargs):
"""
Generate a hash of source file path + transform + args
"""
sortedargs = ["%s:%r:%s" % (key, value, type(value))
for key, value in sorted(iteritems(kwargs))]
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quiltdata/quilt | compiler/quilt/tools/build.py | _gen_glob_data | def _gen_glob_data(dir, pattern, child_table):
"""Generates node data by globbing a directory for a pattern"""
dir = pathlib.Path(dir)
matched = False
used_names = set() # Used by to_nodename to prevent duplicate names
# sorted so that renames (if any) are consistently ordered
for filepath in s... | python | def _gen_glob_data(dir, pattern, child_table):
"""Generates node data by globbing a directory for a pattern"""
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used_names = set() # Used by to_nodename to prevent duplicate names
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quiltdata/quilt | compiler/quilt/tools/build.py | _remove_keywords | def _remove_keywords(d):
"""
copy the dict, filter_keywords
Parameters
----------
d : dict
"""
return { k:v for k, v in iteritems(d) if k not in RESERVED } | python | def _remove_keywords(d):
"""
copy the dict, filter_keywords
Parameters
----------
d : dict
"""
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quiltdata/quilt | compiler/quilt/tools/build.py | build_package | def build_package(team, username, package, subpath, yaml_path,
checks_path=None, dry_run=False, env='default'):
"""
Builds a package from a given Yaml file and installs it locally.
Returns the name of the package.
"""
def find(key, value):
"""
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Builds a package from a given Yaml file and installs it locally.
Returns the name of the package.
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quiltdata/quilt | registry/quilt_server/mail.py | send_comment_email | def send_comment_email(email, package_owner, package_name, commenter):
"""Send email to owner of package regarding new comment"""
link = '{CATALOG_URL}/package/{owner}/{pkg}/comments'.format(
CATALOG_URL=CATALOG_URL, owner=package_owner, pkg=package_name)
subject = "New comment on {package_owner}/{p... | python | def send_comment_email(email, package_owner, package_name, commenter):
"""Send email to owner of package regarding new comment"""
link = '{CATALOG_URL}/package/{owner}/{pkg}/comments'.format(
CATALOG_URL=CATALOG_URL, owner=package_owner, pkg=package_name)
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quiltdata/quilt | compiler/quilt/tools/core.py | hash_contents | def hash_contents(contents):
"""
Creates a hash of key names and hashes in a package dictionary.
"contents" must be a GroupNode.
"""
assert isinstance(contents, GroupNode)
result = hashlib.sha256()
def _hash_int(value):
result.update(struct.pack(">L", value))
def _hash_str(st... | python | def hash_contents(contents):
"""
Creates a hash of key names and hashes in a package dictionary.
"contents" must be a GroupNode.
"""
assert isinstance(contents, GroupNode)
result = hashlib.sha256()
def _hash_int(value):
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quiltdata/quilt | compiler/quilt/tools/core.py | find_object_hashes | def find_object_hashes(root, meta_only=False):
"""
Iterator that returns hashes of all of the file and table nodes.
:param root: starting node
"""
stack = [root]
while stack:
obj = stack.pop()
if not meta_only and isinstance(obj, (TableNode, FileNode)):
for objhash i... | python | def find_object_hashes(root, meta_only=False):
"""
Iterator that returns hashes of all of the file and table nodes.
:param root: starting node
"""
stack = [root]
while stack:
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quiltdata/quilt | registry/quilt_server/analytics.py | _send_event_task | def _send_event_task(args):
"""
Actually sends the MixPanel event. Runs in a uwsgi worker process.
"""
endpoint = args['endpoint']
json_message = args['json_message']
_consumer_impl.send(endpoint, json_message) | python | def _send_event_task(args):
"""
Actually sends the MixPanel event. Runs in a uwsgi worker process.
"""
endpoint = args['endpoint']
json_message = args['json_message']
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quiltdata/quilt | registry/quilt_server/analytics.py | AsyncConsumer.send | def send(self, endpoint, json_message):
"""
Queues the message to be sent.
"""
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"""
Queues the message to be sent.
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quiltdata/quilt | compiler/quilt/tools/main.py | main | def main(args=None):
"""Build and run parser
:param args: cli args from tests
"""
parser = argument_parser()
args = parser.parse_args(args)
# If 'func' isn't present, something is misconfigured above or no (positional) arg was given.
if not hasattr(args, 'func'):
args = parser.pars... | python | def main(args=None):
"""Build and run parser
:param args: cli args from tests
"""
parser = argument_parser()
args = parser.parse_args(args)
# If 'func' isn't present, something is misconfigured above or no (positional) arg was given.
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quiltdata/quilt | compiler/quilt/tools/util.py | is_identifier | def is_identifier(string):
"""Check if string could be a valid python identifier
:param string: string to be tested
:returns: True if string can be a python identifier, False otherwise
:rtype: bool
"""
matched = PYTHON_IDENTIFIER_RE.match(string)
return bool(matched) and not keyword.iskeywo... | python | def is_identifier(string):
"""Check if string could be a valid python identifier
:param string: string to be tested
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:rtype: bool
"""
matched = PYTHON_IDENTIFIER_RE.match(string)
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quiltdata/quilt | compiler/quilt/tools/util.py | fs_link | def fs_link(path, linkpath, linktype='soft'):
"""Create a hard or soft link of `path` at `linkpath`
Works on Linux/OSX/Windows (Vista+).
:param src: File or directory to be linked
:param dest: Path of link to create
:param linktype: 'soft' or 'hard'
"""
global WIN_SOFTLINK
global WIN_H... | python | def fs_link(path, linkpath, linktype='soft'):
"""Create a hard or soft link of `path` at `linkpath`
Works on Linux/OSX/Windows (Vista+).
:param src: File or directory to be linked
:param dest: Path of link to create
:param linktype: 'soft' or 'hard'
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quiltdata/quilt | compiler/quilt/tools/util.py | FileWithReadProgress.read | def read(self, size=-1):
"""Read bytes and update the progress bar."""
buf = self._fd.read(size)
self._progress_cb(len(buf))
return buf | python | def read(self, size=-1):
"""Read bytes and update the progress bar."""
buf = self._fd.read(size)
self._progress_cb(len(buf))
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.create_dirs | def create_dirs(self):
"""
Creates the store directory and its subdirectories.
"""
if not os.path.isdir(self._path):
os.makedirs(self._path)
for dir_name in [self.OBJ_DIR, self.TMP_OBJ_DIR, self.PKG_DIR, self.CACHE_DIR]:
path = os.path.join(self._path, dir... | python | def create_dirs(self):
"""
Creates the store directory and its subdirectories.
"""
if not os.path.isdir(self._path):
os.makedirs(self._path)
for dir_name in [self.OBJ_DIR, self.TMP_OBJ_DIR, self.PKG_DIR, self.CACHE_DIR]:
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.find_store_dirs | def find_store_dirs(cls):
"""
Returns the primary package directory and any additional ones from QUILT_PACKAGE_DIRS.
"""
store_dirs = [default_store_location()]
extra_dirs_str = os.getenv('QUILT_PACKAGE_DIRS')
if extra_dirs_str:
store_dirs.extend(extra_dirs_st... | python | def find_store_dirs(cls):
"""
Returns the primary package directory and any additional ones from QUILT_PACKAGE_DIRS.
"""
store_dirs = [default_store_location()]
extra_dirs_str = os.getenv('QUILT_PACKAGE_DIRS')
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.find_package | def find_package(cls, team, user, package, pkghash=None, store_dir=None):
"""
Finds an existing package in one of the package directories.
"""
cls.check_name(team, user, package)
dirs = cls.find_store_dirs()
for store_dir in dirs:
store = PackageStore(store_di... | python | def find_package(cls, team, user, package, pkghash=None, store_dir=None):
"""
Finds an existing package in one of the package directories.
"""
cls.check_name(team, user, package)
dirs = cls.find_store_dirs()
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.get_package | def get_package(self, team, user, package, pkghash=None):
"""
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"""
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path = self.package_path(team, user, package)
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return None
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"""
Gets a package from this store.
"""
self.check_name(team, user, package)
path = self.package_path(team, user, package)
if not os.path.isdir(path):
return None
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.install_package | def install_package(self, team, user, package, contents):
"""
Creates a new package in the default package store
and allocates a per-user directory if needed.
"""
self.check_name(team, user, package)
assert contents is not None
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"""
Creates a new package in the default package store
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"""
self.check_name(team, user, package)
assert contents is not None
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.create_package_node | def create_package_node(self, team, user, package, dry_run=False):
"""
Creates a new package and initializes its contents. See `install_package`.
"""
contents = RootNode(dict())
if dry_run:
return contents
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"""
Creates a new package and initializes its contents. See `install_package`.
"""
contents = RootNode(dict())
if dry_run:
return contents
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.iterpackages | def iterpackages(self):
"""
Return an iterator over all the packages in the PackageStore.
"""
pkgdir = os.path.join(self._path, self.PKG_DIR)
if not os.path.isdir(pkgdir):
return
for team in sub_dirs(pkgdir):
for user in sub_dirs(self.team_path(tea... | python | def iterpackages(self):
"""
Return an iterator over all the packages in the PackageStore.
"""
pkgdir = os.path.join(self._path, self.PKG_DIR)
if not os.path.isdir(pkgdir):
return
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.ls_packages | def ls_packages(self):
"""
List packages in this store.
"""
packages = []
pkgdir = os.path.join(self._path, self.PKG_DIR)
if not os.path.isdir(pkgdir):
return []
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for user in sub_dirs(self.team_path(team)):
... | python | def ls_packages(self):
"""
List packages in this store.
"""
packages = []
pkgdir = os.path.join(self._path, self.PKG_DIR)
if not os.path.isdir(pkgdir):
return []
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.team_path | def team_path(self, team=None):
"""
Returns the path to directory with the team's users' package repositories.
"""
if team is None:
team = DEFAULT_TEAM
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"""
Returns the path to directory with the team's users' package repositories.
"""
if team is None:
team = DEFAULT_TEAM
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.user_path | def user_path(self, team, user):
"""
Returns the path to directory with the user's package repositories.
"""
return os.path.join(self.team_path(team), user) | python | def user_path(self, team, user):
"""
Returns the path to directory with the user's package repositories.
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.package_path | def package_path(self, team, user, package):
"""
Returns the path to a package repository.
"""
return os.path.join(self.user_path(team, user), package) | python | def package_path(self, team, user, package):
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.object_path | def object_path(self, objhash):
"""
Returns the path to an object file based on its hash.
"""
return os.path.join(self._path, self.OBJ_DIR, objhash) | python | def object_path(self, objhash):
"""
Returns the path to an object file based on its hash.
"""
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.prune | def prune(self, objs=None):
"""
Clean up objects not referenced by any packages. Try to prune all
objects by default.
"""
if objs is None:
objdir = os.path.join(self._path, self.OBJ_DIR)
objs = os.listdir(objdir)
remove_objs = set(objs)
fo... | python | def prune(self, objs=None):
"""
Clean up objects not referenced by any packages. Try to prune all
objects by default.
"""
if objs is None:
objdir = os.path.join(self._path, self.OBJ_DIR)
objs = os.listdir(objdir)
remove_objs = set(objs)
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.save_dataframe | def save_dataframe(self, dataframe):
"""
Save a DataFrame to the store.
"""
storepath = self.temporary_object_path(str(uuid.uuid4()))
# switch parquet lib
parqlib = self.get_parquet_lib()
if isinstance(dataframe, pd.DataFrame):
#parqlib is ParquetLib.... | python | def save_dataframe(self, dataframe):
"""
Save a DataFrame to the store.
"""
storepath = self.temporary_object_path(str(uuid.uuid4()))
# switch parquet lib
parqlib = self.get_parquet_lib()
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.load_numpy | def load_numpy(self, hash_list):
"""
Loads a numpy array.
"""
assert len(hash_list) == 1
self._check_hashes(hash_list)
with open(self.object_path(hash_list[0]), 'rb') as fd:
return np.load(fd, allow_pickle=False) | python | def load_numpy(self, hash_list):
"""
Loads a numpy array.
"""
assert len(hash_list) == 1
self._check_hashes(hash_list)
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.get_file | def get_file(self, hash_list):
"""
Returns the path of the file - but verifies that the hash is actually present.
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Returns the path of the file - but verifies that the hash is actually present.
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.save_metadata | def save_metadata(self, metadata):
"""
Save metadata to the store.
"""
if metadata in (None, {}):
return None
if SYSTEM_METADATA in metadata:
raise StoreException("Not allowed to store %r in metadata" % SYSTEM_METADATA)
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"""
Save metadata to the store.
"""
if metadata in (None, {}):
return None
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raise StoreException("Not allowed to store %r in metadata" % SYSTEM_METADATA)
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.save_package_contents | def save_package_contents(self, root, team, owner, pkgname):
"""
Saves the in-memory contents to a file in the local
package repository.
"""
assert isinstance(root, RootNode)
instance_hash = hash_contents(root)
pkg_path = self.package_path(team, owner, pkgname)
... | python | def save_package_contents(self, root, team, owner, pkgname):
"""
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"""
assert isinstance(root, RootNode)
instance_hash = hash_contents(root)
pkg_path = self.package_path(team, owner, pkgname)
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.add_to_package_numpy | def add_to_package_numpy(self, root, ndarray, node_path, target, source_path, transform, custom_meta):
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"""
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quiltdata/quilt | compiler/quilt/tools/store.py | PackageStore.add_to_package_package_tree | def add_to_package_package_tree(self, root, node_path, pkgnode):
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Adds a package or sub-package tree from an existing package to this package's
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"""
if node_path:
ptr = root
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ptr = ptr.children.setdefa... | python | def add_to_package_package_tree(self, root, node_path, pkgnode):
"""
Adds a package or sub-package tree from an existing package to this package's
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"""
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ptr = root
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quiltdata/quilt | compiler/quilt/__init__.py | _install_interrupt_handler | def _install_interrupt_handler():
"""Suppress KeyboardInterrupt traceback display in specific situations
If not running in dev mode, and if executed from the command line, then
we raise SystemExit instead of KeyboardInterrupt. This provides a clean
exit.
:returns: None if no action is taken, orig... | python | def _install_interrupt_handler():
"""Suppress KeyboardInterrupt traceback display in specific situations
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quiltdata/quilt | compiler/quilt/nodes.py | GroupNode._data_keys | def _data_keys(self):
"""
every child key referencing a dataframe
"""
return [name for name, child in iteritems(self._children) if not isinstance(child, GroupNode)] | python | def _data_keys(self):
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quiltdata/quilt | compiler/quilt/nodes.py | GroupNode._group_keys | def _group_keys(self):
"""
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return [name for name, child in iteritems(self._children) if isinstance(child, GroupNode)] | python | def _group_keys(self):
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quiltdata/quilt | compiler/quilt/nodes.py | GroupNode._data | def _data(self, asa=None):
"""
Merges all child dataframes. Only works for dataframes stored on disk - not in memory.
"""
hash_list = []
stack = [self]
alldfs = True
store = None
while stack:
node = stack.pop()
if isinstance(node, G... | python | def _data(self, asa=None):
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Merges all child dataframes. Only works for dataframes stored on disk - not in memory.
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quiltdata/quilt | compiler/quilt/nodes.py | GroupNode._set | def _set(self, path, value, build_dir=''):
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quiltdata/quilt | registry/quilt_server/views.py | handle_api_exception | def handle_api_exception(error):
"""
Converts an API exception into an error response.
"""
_mp_track(
type="exception",
status_code=error.status_code,
message=error.message,
)
response = jsonify(dict(
message=error.message
))
response.status_code = error.... | python | def handle_api_exception(error):
"""
Converts an API exception into an error response.
"""
_mp_track(
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message=error.message,
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quiltdata/quilt | registry/quilt_server/views.py | api | def api(require_login=True, schema=None, enabled=True,
require_admin=False, require_anonymous=False):
"""
Decorator for API requests.
Handles auth and adds the username as the first argument.
"""
if require_admin:
require_login = True
if schema is not None:
Draft4Validat... | python | def api(require_login=True, schema=None, enabled=True,
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"""
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quiltdata/quilt | registry/quilt_server/views.py | _private_packages_allowed | def _private_packages_allowed():
"""
Checks if the current user is allowed to create private packages.
In the public cloud, the user needs to be on a paid plan.
There are no restrictions in other deployments.
"""
if not HAVE_PAYMENTS or TEAM_ID:
return True
customer = _get_or_creat... | python | def _private_packages_allowed():
"""
Checks if the current user is allowed to create private packages.
In the public cloud, the user needs to be on a paid plan.
There are no restrictions in other deployments.
"""
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quiltdata/quilt | compiler/quilt/tools/command.py | _create_auth | def _create_auth(team, timeout=None):
"""
Reads the credentials, updates the access token if necessary, and returns it.
"""
url = get_registry_url(team)
contents = _load_auth()
auth = contents.get(url)
if auth is not None:
# If the access token expires within a minute, update it.
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"""
Reads the credentials, updates the access token if necessary, and returns it.
"""
url = get_registry_url(team)
contents = _load_auth()
auth = contents.get(url)
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quiltdata/quilt | compiler/quilt/tools/command.py | _create_session | def _create_session(team, auth):
"""
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quiltdata/quilt | compiler/quilt/tools/command.py | _get_session | def _get_session(team, timeout=None):
"""
Creates a session or returns an existing session.
"""
global _sessions # pylint:disable=C0103
session = _sessions.get(team)
if session is None:
auth = _create_auth(team, timeout)
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"""
Creates a session or returns an existing session.
"""
global _sessions # pylint:disable=C0103
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quiltdata/quilt | compiler/quilt/tools/command.py | _check_team_login | def _check_team_login(team):
"""
Disallow simultaneous public cloud and team logins.
"""
contents = _load_auth()
for auth in itervalues(contents):
existing_team = auth.get('team')
if team and team != existing_team:
raise CommandException(
"Can't log in as... | python | def _check_team_login(team):
"""
Disallow simultaneous public cloud and team logins.
"""
contents = _load_auth()
for auth in itervalues(contents):
existing_team = auth.get('team')
if team and team != existing_team:
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quiltdata/quilt | compiler/quilt/tools/command.py | _check_team_exists | def _check_team_exists(team):
"""
Check that the team registry actually exists.
"""
if team is None:
return
hostname = urlparse(get_registry_url(team)).hostname
try:
socket.gethostbyname(hostname)
except IOError:
try:
# Do we have internet?
so... | python | def _check_team_exists(team):
"""
Check that the team registry actually exists.
"""
if team is None:
return
hostname = urlparse(get_registry_url(team)).hostname
try:
socket.gethostbyname(hostname)
except IOError:
try:
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quiltdata/quilt | compiler/quilt/tools/command.py | login_with_token | def login_with_token(refresh_token, team=None):
"""
Authenticate using an existing token.
"""
# Get an access token and a new refresh token.
_check_team_id(team)
auth = _update_auth(team, refresh_token)
url = get_registry_url(team)
contents = _load_auth()
contents[url] = auth
_s... | python | def login_with_token(refresh_token, team=None):
"""
Authenticate using an existing token.
"""
# Get an access token and a new refresh token.
_check_team_id(team)
auth = _update_auth(team, refresh_token)
url = get_registry_url(team)
contents = _load_auth()
contents[url] = auth
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quiltdata/quilt | compiler/quilt/tools/command.py | generate | def generate(directory, outfilename=DEFAULT_BUILDFILE):
"""
Generate a build-file for quilt build from a directory of
source files.
"""
try:
buildfilepath = generate_build_file(directory, outfilename=outfilename)
except BuildException as builderror:
raise CommandException(str(bui... | python | def generate(directory, outfilename=DEFAULT_BUILDFILE):
"""
Generate a build-file for quilt build from a directory of
source files.
"""
try:
buildfilepath = generate_build_file(directory, outfilename=outfilename)
except BuildException as builderror:
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quiltdata/quilt | compiler/quilt/tools/command.py | build | def build(package, path=None, dry_run=False, env='default', force=False, build_file=False):
"""
Compile a Quilt data package, either from a build file or an existing package node.
:param package: short package specifier, i.e. 'team:user/pkg'
:param path: file path, git url, or existing package node
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"""
Compile a Quilt data package, either from a build file or an existing package node.
:param package: short package specifier, i.e. 'team:user/pkg'
:param path: file path, git url, or existing package node
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quiltdata/quilt | compiler/quilt/tools/command.py | build_from_node | def build_from_node(package, node):
"""
Compile a Quilt data package from an existing package node.
"""
team, owner, pkg, subpath = parse_package(package, allow_subpath=True)
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store = PackageStore()
pkg_root = get_or_create_package(store, team, owner, pkg, subpath)
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"""
Compile a Quilt data package from an existing package node.
"""
team, owner, pkg, subpath = parse_package(package, allow_subpath=True)
_check_team_id(team)
store = PackageStore()
pkg_root = get_or_create_package(store, team, owner, pkg, subpath)
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quiltdata/quilt | compiler/quilt/tools/command.py | build_from_path | def build_from_path(package, path, dry_run=False, env='default', outfilename=DEFAULT_BUILDFILE):
"""
Compile a Quilt data package from a build file.
Path can be a directory, in which case the build file will be generated automatically.
"""
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"""
Compile a Quilt data package from a build file.
Path can be a directory, in which case the build file will be generated automatically.
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quiltdata/quilt | compiler/quilt/tools/command.py | log | def log(package):
"""
List all of the changes to a package on the server.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
response = session.get(
"{url}/api/log/{owner}/{pkg}/".format(
url=get_registry_url(team),
owner=owner,
... | python | def log(package):
"""
List all of the changes to a package on the server.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
response = session.get(
"{url}/api/log/{owner}/{pkg}/".format(
url=get_registry_url(team),
owner=owner,
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quiltdata/quilt | compiler/quilt/tools/command.py | push | def push(package, is_public=False, is_team=False, reupload=False, hash=None):
"""
Push a Quilt data package to the server
"""
team, owner, pkg, subpath = parse_package(package, allow_subpath=True)
_check_team_id(team)
session = _get_session(team)
store, pkgroot = PackageStore.find_package(t... | python | def push(package, is_public=False, is_team=False, reupload=False, hash=None):
"""
Push a Quilt data package to the server
"""
team, owner, pkg, subpath = parse_package(package, allow_subpath=True)
_check_team_id(team)
session = _get_session(team)
store, pkgroot = PackageStore.find_package(t... | [
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quiltdata/quilt | compiler/quilt/tools/command.py | version_list | def version_list(package):
"""
List the versions of a package.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
response = session.get(
"{url}/api/version/{owner}/{pkg}/".format(
url=get_registry_url(team),
owner=owner,
pkg=p... | python | def version_list(package):
"""
List the versions of a package.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
response = session.get(
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url=get_registry_url(team),
owner=owner,
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quiltdata/quilt | compiler/quilt/tools/command.py | version_add | def version_add(package, version, pkghash, force=False):
"""
Add a new version for a given package hash.
Version format needs to follow PEP 440.
Versions are permanent - once created, they cannot be modified or deleted.
"""
team, owner, pkg = parse_package(package)
session = _get_session(te... | python | def version_add(package, version, pkghash, force=False):
"""
Add a new version for a given package hash.
Version format needs to follow PEP 440.
Versions are permanent - once created, they cannot be modified or deleted.
"""
team, owner, pkg = parse_package(package)
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quiltdata/quilt | compiler/quilt/tools/command.py | tag_list | def tag_list(package):
"""
List the tags of a package.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
response = session.get(
"{url}/api/tag/{owner}/{pkg}/".format(
url=get_registry_url(team),
owner=owner,
pkg=pkg
)... | python | def tag_list(package):
"""
List the tags of a package.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
response = session.get(
"{url}/api/tag/{owner}/{pkg}/".format(
url=get_registry_url(team),
owner=owner,
pkg=pkg
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quiltdata/quilt | compiler/quilt/tools/command.py | tag_add | def tag_add(package, tag, pkghash):
"""
Add a new tag for a given package hash.
Unlike versions, tags can have an arbitrary format, and can be modified
and deleted.
When a package is pushed, it gets the "latest" tag.
"""
team, owner, pkg = parse_package(package)
session = _get_session(... | python | def tag_add(package, tag, pkghash):
"""
Add a new tag for a given package hash.
Unlike versions, tags can have an arbitrary format, and can be modified
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When a package is pushed, it gets the "latest" tag.
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quiltdata/quilt | compiler/quilt/tools/command.py | install_via_requirements | def install_via_requirements(requirements_str, force=False):
"""
Download multiple Quilt data packages via quilt.xml requirements file.
"""
if requirements_str[0] == '@':
path = requirements_str[1:]
if os.path.isfile(path):
yaml_data = load_yaml(path)
if 'packages... | python | def install_via_requirements(requirements_str, force=False):
"""
Download multiple Quilt data packages via quilt.xml requirements file.
"""
if requirements_str[0] == '@':
path = requirements_str[1:]
if os.path.isfile(path):
yaml_data = load_yaml(path)
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quiltdata/quilt | compiler/quilt/tools/command.py | access_list | def access_list(package):
"""
Print list of users who can access a package.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
lookup_url = "{url}/api/access/{owner}/{pkg}/".format(url=get_registry_url(team), owner=owner, pkg=pkg)
response = session.get(lookup_url)
... | python | def access_list(package):
"""
Print list of users who can access a package.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
lookup_url = "{url}/api/access/{owner}/{pkg}/".format(url=get_registry_url(team), owner=owner, pkg=pkg)
response = session.get(lookup_url)
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] | 651853e7e89a8af86e0ff26167e752efa5878c12 | https://github.com/quiltdata/quilt/blob/651853e7e89a8af86e0ff26167e752efa5878c12/compiler/quilt/tools/command.py#L1061-L1074 | train |
quiltdata/quilt | compiler/quilt/tools/command.py | delete | def delete(package):
"""
Delete a package from the server.
Irreversibly deletes the package along with its history, tags, versions, etc.
"""
team, owner, pkg = parse_package(package)
answer = input(
"Are you sure you want to delete this package and its entire history? "
"Type '... | python | def delete(package):
"""
Delete a package from the server.
Irreversibly deletes the package along with its history, tags, versions, etc.
"""
team, owner, pkg = parse_package(package)
answer = input(
"Are you sure you want to delete this package and its entire history? "
"Type '... | [
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Irreversibly deletes the package along with its history, tags, versions, etc. | [
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] | 651853e7e89a8af86e0ff26167e752efa5878c12 | https://github.com/quiltdata/quilt/blob/651853e7e89a8af86e0ff26167e752efa5878c12/compiler/quilt/tools/command.py#L1096-L1116 | train |
quiltdata/quilt | compiler/quilt/tools/command.py | search | def search(query, team=None):
"""
Search for packages
"""
if team is None:
team = _find_logged_in_team()
if team is not None:
session = _get_session(team)
response = session.get("%s/api/search/" % get_registry_url(team), params=dict(q=query))
print("* Packages in tea... | python | def search(query, team=None):
"""
Search for packages
"""
if team is None:
team = _find_logged_in_team()
if team is not None:
session = _get_session(team)
response = session.get("%s/api/search/" % get_registry_url(team), params=dict(q=query))
print("* Packages in tea... | [
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"... | Search for packages | [
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] | 651853e7e89a8af86e0ff26167e752efa5878c12 | https://github.com/quiltdata/quilt/blob/651853e7e89a8af86e0ff26167e752efa5878c12/compiler/quilt/tools/command.py#L1118-L1142 | train |
quiltdata/quilt | compiler/quilt/tools/command.py | ls | def ls(): # pylint:disable=C0103
"""
List all installed Quilt data packages
"""
for pkg_dir in PackageStore.find_store_dirs():
print("%s" % pkg_dir)
packages = PackageStore(pkg_dir).ls_packages()
for package, tag, pkghash in sorted(packages):
pri... | python | def ls(): # pylint:disable=C0103
"""
List all installed Quilt data packages
"""
for pkg_dir in PackageStore.find_store_dirs():
print("%s" % pkg_dir)
packages = PackageStore(pkg_dir).ls_packages()
for package, tag, pkghash in sorted(packages):
pri... | [
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... | List all installed Quilt data packages | [
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] | 651853e7e89a8af86e0ff26167e752efa5878c12 | https://github.com/quiltdata/quilt/blob/651853e7e89a8af86e0ff26167e752efa5878c12/compiler/quilt/tools/command.py#L1144-L1152 | train |
quiltdata/quilt | compiler/quilt/tools/command.py | inspect | def inspect(package):
"""
Inspect package details
"""
team, owner, pkg = parse_package(package)
store, pkgroot = PackageStore.find_package(team, owner, pkg)
if pkgroot is None:
raise CommandException("Package {package} not found.".format(package=package))
def _print_children(childr... | python | def inspect(package):
"""
Inspect package details
"""
team, owner, pkg = parse_package(package)
store, pkgroot = PackageStore.find_package(team, owner, pkg)
if pkgroot is None:
raise CommandException("Package {package} not found.".format(package=package))
def _print_children(childr... | [
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",",
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"pkgroot",
"is... | Inspect package details | [
"Inspect",
"package",
"details"
] | 651853e7e89a8af86e0ff26167e752efa5878c12 | https://github.com/quiltdata/quilt/blob/651853e7e89a8af86e0ff26167e752efa5878c12/compiler/quilt/tools/command.py#L1154-L1194 | train |
quiltdata/quilt | compiler/quilt/tools/command.py | load | def load(pkginfo, hash=None):
"""
functional interface to "from quilt.data.USER import PKG"
"""
node, pkgroot, info = _load(pkginfo, hash)
for subnode_name in info.subpath:
node = node[subnode_name]
return node | python | def load(pkginfo, hash=None):
"""
functional interface to "from quilt.data.USER import PKG"
"""
node, pkgroot, info = _load(pkginfo, hash)
for subnode_name in info.subpath:
node = node[subnode_name]
return node | [
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"subnode_name"... | functional interface to "from quilt.data.USER import PKG" | [
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] | 651853e7e89a8af86e0ff26167e752efa5878c12 | https://github.com/quiltdata/quilt/blob/651853e7e89a8af86e0ff26167e752efa5878c12/compiler/quilt/tools/command.py#L1351-L1359 | train |
CalebBell/fluids | fluids/core.py | c_ideal_gas | def c_ideal_gas(T, k, MW):
r'''Calculates speed of sound `c` in an ideal gas at temperature T.
.. math::
c = \sqrt{kR_{specific}T}
Parameters
----------
T : float
Temperature of fluid, [K]
k : float
Isentropic exponent of fluid, [-]
MW : float
Molecular weig... | python | def c_ideal_gas(T, k, MW):
r'''Calculates speed of sound `c` in an ideal gas at temperature T.
.. math::
c = \sqrt{kR_{specific}T}
Parameters
----------
T : float
Temperature of fluid, [K]
k : float
Isentropic exponent of fluid, [-]
MW : float
Molecular weig... | [
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] | r'''Calculates speed of sound `c` in an ideal gas at temperature T.
.. math::
c = \sqrt{kR_{specific}T}
Parameters
----------
T : float
Temperature of fluid, [K]
k : float
Isentropic exponent of fluid, [-]
MW : float
Molecular weight of fluid, [g/mol]
Retur... | [
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] | 57f556752e039f1d3e5a822f408c184783db2828 | https://github.com/CalebBell/fluids/blob/57f556752e039f1d3e5a822f408c184783db2828/fluids/core.py#L82-L123 | train |
CalebBell/fluids | fluids/core.py | Reynolds | def Reynolds(V, D, rho=None, mu=None, nu=None):
r'''Calculates Reynolds number or `Re` for a fluid with the given
properties for the specified velocity and diameter.
.. math::
Re = \frac{D \cdot V}{\nu} = \frac{\rho V D}{\mu}
Inputs either of any of the following sets:
* V, D, density `rh... | python | def Reynolds(V, D, rho=None, mu=None, nu=None):
r'''Calculates Reynolds number or `Re` for a fluid with the given
properties for the specified velocity and diameter.
.. math::
Re = \frac{D \cdot V}{\nu} = \frac{\rho V D}{\mu}
Inputs either of any of the following sets:
* V, D, density `rh... | [
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... | r'''Calculates Reynolds number or `Re` for a fluid with the given
properties for the specified velocity and diameter.
.. math::
Re = \frac{D \cdot V}{\nu} = \frac{\rho V D}{\mu}
Inputs either of any of the following sets:
* V, D, density `rho` and kinematic viscosity `mu`
* V, D, and dyna... | [
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] | 57f556752e039f1d3e5a822f408c184783db2828 | https://github.com/CalebBell/fluids/blob/57f556752e039f1d3e5a822f408c184783db2828/fluids/core.py#L128-L184 | train |
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