From 5628354aef57a828343de1b3a23f9ccd2a6be640 Mon Sep 17 00:00:00 2001 From: Aaron Ayres Date: Wed, 13 Jan 2021 13:06:21 -0600 Subject: [PATCH] create new 5.1 folder to hold current docs. Replace current documentation (not in a folder, which used to match contents of 5.0) to now match contents of 5.1 --- 5.1/_modules/apptools/io/file.html | 443 + 5.1/_modules/apptools/io/h5/dict_node.html | 362 + 5.1/_modules/apptools/io/h5/file.html | 671 + 5.1/_modules/apptools/io/h5/table_node.html | 287 + .../_modules/apptools/io/h5/utils.html | 72 +- .../apptools/logger/agent/attachments.html | 235 + .../logger/agent/quality_agent_mailer.html | 244 + .../logger/agent/quality_agent_view.html | 510 + .../apptools/logger/custom_excepthook.html | 165 + 5.1/_modules/apptools/logger/log_point.html | 170 + .../apptools/logger/log_queue_handler.html | 198 + 5.1/_modules/apptools/logger/logger.html | 188 + .../apptools/logger/plugin/logger_plugin.html | 238 + .../logger/plugin/logger_preferences.html | 71 +- .../logger/plugin/logger_service.html | 310 + .../plugin/view/logger_preferences_page.html | 226 + .../logger/plugin/view/logger_view.html | 343 + 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| 18 + .../apptools.naming.object_serializer.rst.txt | 18 + .../api/apptools.naming.py_context.rst.txt | 18 + .../apptools.naming.py_object_factory.rst.txt | 18 + .../api/apptools.naming.pyfs_context.rst.txt | 18 + ...ptools.naming.pyfs_context_factory.rst.txt | 18 + ...aming.pyfs_initial_context_factory.rst.txt | 18 + ...pptools.naming.pyfs_object_factory.rst.txt | 18 + ...apptools.naming.pyfs_state_factory.rst.txt | 18 + .../api/apptools.naming.reference.rst.txt | 18 + .../api/apptools.naming.referenceable.rst.txt | 18 + ...naming.referenceable_state_factory.rst.txt | 18 + 5.1/_sources/api/apptools.naming.rst.txt | 52 + .../api/apptools.naming.state_factory.rst.txt | 18 + .../apptools.naming.trait_defs.api.rst.txt | 18 + ...ls.naming.trait_defs.naming_traits.rst.txt | 18 + .../api/apptools.naming.trait_defs.rst.txt | 24 + .../api/apptools.naming.unique_name.rst.txt | 18 + .../apptools.persistence.file_path.rst.txt | 18 + ...pptools.persistence.project_loader.rst.txt | 18 + 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Source code for apptools.io.file

+# (C) Copyright 2005-2021 Enthought, Inc., Austin, TX
+# All rights reserved.
+#
+# This software is provided without warranty under the terms of the BSD
+# license included in LICENSE.txt and may be redistributed only under
+# the conditions described in the aforementioned license. The license
+# is also available online at http://www.enthought.com/licenses/BSD.txt
+#
+# Thanks for using Enthought open source!
+""" A representation of files and folders in a file system. """
+
+
+# Standard/built-in imports.
+import mimetypes
+import os
+import shutil
+import stat
+
+# Enthought library imports.
+from traits.api import Bool, HasPrivateTraits, Instance, List, Property
+from traits.api import Str
+
+
+
[docs]class File(HasPrivateTraits): + """ A representation of files and folders in a file system. """ + + #### 'File' interface ##################################################### + + # The absolute path name of this file/folder. + absolute_path = Property(Str) + + # The folder's children (for files this is always None). + children = Property(List("File")) + + # The file extension (for folders this is always the empty string). + # + # fixme: Currently the extension includes the '.' (ie. we have '.py' and + # not 'py'). This is because things like 'os.path.splitext' leave the '.' + # on, but I'm not sure that this is a good idea! + ext = Property(Str) + + # Does the file/folder exist? + exists = Property(Bool) + + # Is this an existing file? + is_file = Property(Bool) + + # Is this an existing folder? + is_folder = Property(Bool) + + # Is this a Python package (ie. a folder contaning an '__init__.py' file. + is_package = Property(Bool) + + # Is the file/folder readonly? + is_readonly = Property(Bool) + + # The MIME type of the file (for a folder this will always be + # 'context/unknown' (is that what it should be?)). + mime_type = Property(Str) + + # The last component of the path without the extension. + name = Property(Str) + + # The parent of this file/folder (None if it has no parent). + parent = Property(Instance("File")) + + # The path name of this file/folder. + path = Str + + # A URL reference to the file. + url = Property(Str) + + ########################################################################### + # 'object' interface. + ########################################################################### + + def __init__(self, path, **traits): + """ Creates a new representation of the specified path. """ + + super(File, self).__init__(path=path, **traits) + + def __str__(self): + """ Returns an 'informal' string representation of the object. """ + + return "File(%s)" % self.path + + ########################################################################### + # 'File' interface. + ########################################################################### + + #### Properties ########################################################### + + def _get_absolute_path(self): + """ Returns the absolute path of this file/folder. """ + + return os.path.abspath(self.path) + + def _get_children(self): + """Returns the folder's children. + + Returns None if the path does not exist or is not a folder. + + """ + + if self.is_folder: + children = [] + for name in os.listdir(self.path): + children.append(File(os.path.join(self.path, name))) + + else: + children = None + + return children + + def _get_exists(self): + """ Returns True if the file exists, otherwise False. """ + + return os.path.exists(self.path) + + def _get_ext(self): + """ Returns the file extension. """ + + name, ext = os.path.splitext(self.path) + + return ext + + def _get_is_file(self): + """ Returns True if the path exists and is a file. """ + + return self.exists and os.path.isfile(self.path) + + def _get_is_folder(self): + """ Returns True if the path exists and is a folder. """ + + return self.exists and os.path.isdir(self.path) + + def _get_is_package(self): + """ Returns True if the path exists and is a Python package. """ + + return self.is_folder and "__init__.py" in os.listdir(self.path) + + def _get_is_readonly(self): + """ Returns True if the file/folder is readonly, otherwise False. """ + + # If the File object is a folder, os.access cannot be used because it + # returns True for both read-only and writable folders on Windows + # systems. + if self.is_folder: + + # Mask for the write-permission bits on the folder. If these bits + # are set to zero, the folder is read-only. + WRITE_MASK = 0x92 + permissions = os.stat(self.path)[0] + + if permissions & WRITE_MASK == 0: + readonly = True + else: + readonly = False + + elif self.is_file: + readonly = not os.access(self.path, os.W_OK) + + else: + readonly = False + + return readonly + + def _get_mime_type(self): + """ Returns the mime-type of this file/folder. """ + + mime_type, encoding = mimetypes.guess_type(self.path) + if mime_type is None: + mime_type = "content/unknown" + + return mime_type + + def _get_name(self): + """ Returns the last component of the path without the extension. """ + + basename = os.path.basename(self.path) + + name, ext = os.path.splitext(basename) + + return name + + def _get_parent(self): + """ Returns the parent of this file/folder. """ + + return File(os.path.dirname(self.path)) + + def _get_url(self): + """ Returns the path as a URL. """ + + # Strip out the leading slash on POSIX systems. + return "file:///%s" % self.absolute_path.lstrip("/") + + #### Methods ############################################################## + +
[docs] def copy(self, destination): + """ Copies this file/folder. """ + + # Allow the destination to be a string. + if not isinstance(destination, File): + destination = File(destination) + + if self.is_folder: + shutil.copytree(self.path, destination.path) + + elif self.is_file: + shutil.copyfile(self.path, destination.path)
+ +
[docs] def create_file(self, contents=""): + """ Creates a file at this path. """ + + if self.exists: + raise ValueError("file %s already exists" % self.path) + + f = open(self.path, "w") + f.write(contents) + f.close()
+ +
[docs] def create_folder(self): + """Creates a folder at this path. + + All intermediate folders MUST already exist. + + """ + + if self.exists: + raise ValueError("folder %s already exists" % self.path) + + os.mkdir(self.path)
+ +
[docs] def create_folders(self): + """Creates a folder at this path. + + This will attempt to create any missing intermediate folders. + + """ + + if self.exists: + raise ValueError("folder %s already exists" % self.path) + + os.makedirs(self.path)
+ +
[docs] def create_package(self): + """Creates a package at this path. + + All intermediate folders/packages MUST already exist. + + """ + + if self.exists: + raise ValueError("package %s already exists" % self.path) + + os.mkdir(self.path) + + # Create the '__init__.py' file that actually turns the folder into a + # package! + init = File(os.path.join(self.path, "__init__.py")) + init.create_file()
+ +
[docs] def delete(self): + """Deletes this file/folder. + + Does nothing if the file/folder does not exist. + + """ + + if self.is_folder: + # Try to make sure that everything in the folder is writeable. + self.make_writeable() + + # Delete it! + shutil.rmtree(self.path) + + elif self.is_file: + # Try to make sure that the file is writeable. + self.make_writeable() + + # Delete it! + os.remove(self.path)
+ +
[docs] def make_writeable(self): + """ Attempt to make the file/folder writeable. """ + + if self.is_folder: + # Try to make sure that everything in the folder is writeable + # (i.e., can be deleted!). This comes in especially handy when + # deleting '.svn' directories. + for path, dirnames, filenames in os.walk(self.path): + for name in dirnames + filenames: + filename = os.path.join(path, name) + if not os.access(filename, os.W_OK): + os.chmod(filename, stat.S_IWUSR) + + elif self.is_file: + # Try to make sure that the file is writeable (i.e., can be + # deleted!). + if not os.access(self.path, os.W_OK): + os.chmod(self.path, stat.S_IWUSR)
+ +
[docs] def move(self, destination): + """ Moves this file/folder. """ + + # Allow the destination to be a string. + if not isinstance(destination, File): + destination = File(destination) + + # Try to make sure that everything in the directory is writeable. + self.make_writeable() + + # Move it! + shutil.move(self.path, destination.path)
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+ + \ No newline at end of file diff --git a/5.1/_modules/apptools/io/h5/dict_node.html b/5.1/_modules/apptools/io/h5/dict_node.html new file mode 100644 index 000000000..3aec8a56a --- /dev/null +++ b/5.1/_modules/apptools/io/h5/dict_node.html @@ -0,0 +1,362 @@ + + + + + + + apptools.io.h5.dict_node — Apptools Documentation + + + + + + + + + + + + + + + + + + + +
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Source code for apptools.io.h5.dict_node

+# (C) Copyright 2005-2021 Enthought, Inc., Austin, TX
+# All rights reserved.
+#
+# This software is provided without warranty under the terms of the BSD
+# license included in LICENSE.txt and may be redistributed only under
+# the conditions described in the aforementioned license. The license
+# is also available online at http://www.enthought.com/licenses/BSD.txt
+#
+# Thanks for using Enthought open source!
+from contextlib import closing
+import json
+
+from numpy import ndarray
+
+from tables import Group as PyTablesGroup
+from tables.nodes import filenode
+
+
+#: The key name which identifies array objects in the JSON dict.
+ARRAY_PROXY_KEY = "__array__"
+NODE_KEY = "node_name"
+
+
+
[docs]class H5DictNode(object): + """Dictionary-like node interface. + + Data for the dict is stored as a JSON file in a PyTables FileNode. This + allows easy storage of Python objects, such as dictionaries and lists of + different data types. + + Note that this is implemented using a group-node assuming that arrays are + valid inputs and will be stored as H5 array nodes. + + Parameters + ---------- + h5_group : H5Group instance + Group node which will be used as a dictionary store. + auto_flush : bool + If True, write data to disk whenever the dict data is altered. + Otherwise, call `flush()` explicitly to write data to disk. + """ + + #: Name of filenode where dict data is stored. + _pyobject_data_node = "_pyobject_data" + + def __init__(self, h5_group, auto_flush=True): + assert self.is_dict_node(h5_group) + + h5_group = self._get_pyt_group(h5_group) + self._h5_group = h5_group + self.auto_flush = auto_flush + + # Load dict data from the file node. + dict_node = getattr(h5_group, self._pyobject_data_node) + with closing(filenode.open_node(dict_node)) as f: + self._pyobject_data = json.loads( + f.read().decode("ascii"), object_hook=self._object_hook + ) + + # -------------------------------------------------------------------------- + # Dictionary interface + # -------------------------------------------------------------------------- + + def __getitem__(self, key): + return self.data[key] + + def __setitem__(self, key, value): + self.data[key] = value + if self.auto_flush: + self.flush() + + def __delitem__(self, key): + del self.data[key] + if self.auto_flush: + self.flush() + + def __contains__(self, key): + return key in self.data + +
[docs] def keys(self): + return self.data.keys()
+ + # -------------------------------------------------------------------------- + # Public interface + # -------------------------------------------------------------------------- + + @property + def data(self): + return self._pyobject_data + + @data.setter + def data(self, new_data_dict): + self._pyobject_data = new_data_dict + if self.auto_flush: + self.flush() + +
[docs] def flush(self): + """ Write buffered data to disk. """ + self._remove_pyobject_node() + self._write_pyobject_node()
+ +
[docs] @classmethod + def add_to_h5file(cls, h5, node_path, data=None, **kwargs): + """Add dict node to an H5 file at the specified path. + + Parameters + ---------- + h5 : H5File + The H5 file where the dictionary data will be stored. + node_path : str + Path to node where data is stored (e.g. '/path/to/my_dict') + data : dict + Data for initialization, if desired. + """ + h5.create_group(node_path) + group = h5[node_path] + + cls._create_pyobject_node(h5._h5, node_path, data=data) + return cls(group, **kwargs)
+ +
[docs] @classmethod + def is_dict_node(cls, pytables_node): + """Return True if PyTables node looks like an H5DictNode. + + NOTE: That this returns False if the node is an `H5DictNode` instance, + since the input node should be a normal PyTables Group node. + """ + # Import here to prevent circular imports + from .file import H5Group + + if isinstance(pytables_node, H5Group): + pytables_node = cls._get_pyt_group(pytables_node) + + if not isinstance(pytables_node, PyTablesGroup): + return False + + return cls._pyobject_data_node in pytables_node._v_children
+ + # -------------------------------------------------------------------------- + # Private interface + # -------------------------------------------------------------------------- + + def _f_remove(self): + """This is called by H5File whenever a node is removed. + + All nodes in `_h5_group` will be removed. + """ + for name in self._h5_group._v_children.keys(): + if name != self._pyobject_data_node: + self._h5_group.__getattr__(name)._f_remove() + # Remove the dict node + self._remove_pyobject_node() + # Remove the group node + self._h5_group._f_remove() + + def _object_hook(self, dct): + """This gets passed object dictionaries by `json.load(s)` and if it + finds `ARRAY_PROXY_KEY` in the object description it returns the + proxied array object. + """ + if ARRAY_PROXY_KEY in dct: + node_name = dct[NODE_KEY] + return getattr(self._h5_group, node_name)[:] + return dct + + def _remove_pyobject_node(self): + node = getattr(self._h5_group, self._pyobject_data_node) + node._f_remove() + + def _write_pyobject_node(self): + pyt_file = self._h5_group._v_file + node_path = self._h5_group._v_pathname + self._create_pyobject_node(pyt_file, node_path, self.data) + + @classmethod + def _create_pyobject_node(cls, pyt_file, node_path, data=None): + if data is None: + data = {} + + # Stash the array values in their own h5 nodes and return a dictionary + # which is appropriate for JSON serialization. + out_data = cls._handle_array_values(pyt_file, node_path, data) + + kwargs = dict(where=node_path, name=cls._pyobject_data_node) + with closing(filenode.new_node(pyt_file, **kwargs)) as f: + f.write(json.dumps(out_data).encode("ascii")) + + @classmethod + def _get_pyt_group(self, group): + if hasattr(group, "_h5_group"): + group = group._h5_group + return group + + @classmethod + def _array_proxy(cls, pyt_file, group, key, array): + """Stores an array as a normal H5 node and returns the proxy object + which will be serialized to JSON. + + `ARRAY_PROXY_KEY` marks the object dictionary as an array proxy so that + `_object_hook` can recognize it. `NODE_KEY` stores the node name of the + array so that `_object_hook` can load the array data when the dict node + is deserialized. + + """ + if key in group: + pyt_file.remove_node(group, key) + pyt_file.create_array(group, key, array) + return {ARRAY_PROXY_KEY: True, NODE_KEY: key} + + @classmethod + def _handle_array_values(cls, pyt_file, group_path, data): + group = pyt_file.get_node(group_path) + + # Convert numpy array values to H5 array nodes. + out_data = {} + for key in data.keys(): + value = data[key] + if isinstance(value, ndarray): + out_data[key] = cls._array_proxy(pyt_file, group, key, value) + else: + out_data[key] = value + + # Remove stored arrays which are no longer in the data dictionary. + pyt_children = group._v_children + nodes_to_remove = [] + for key in pyt_children.keys(): + if key not in data: + nodes_to_remove.append(key) + + for key in nodes_to_remove: + pyt_file.remove_node(group, key) + + return out_data
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+ + \ No newline at end of file diff --git a/5.1/_modules/apptools/io/h5/file.html b/5.1/_modules/apptools/io/h5/file.html new file mode 100644 index 000000000..76c101bcd --- /dev/null +++ b/5.1/_modules/apptools/io/h5/file.html @@ -0,0 +1,671 @@ + + + + + + + apptools.io.h5.file — Apptools Documentation + + + + + + + + + + + + + + + + + + + +
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Source code for apptools.io.h5.file

+# (C) Copyright 2005-2021 Enthought, Inc., Austin, TX
+# All rights reserved.
+#
+# This software is provided without warranty under the terms of the BSD
+# license included in LICENSE.txt and may be redistributed only under
+# the conditions described in the aforementioned license. The license
+# is also available online at http://www.enthought.com/licenses/BSD.txt
+#
+# Thanks for using Enthought open source!
+from collections import Mapping, MutableMapping
+from functools import partial
+import inspect
+
+import numpy as np
+import tables
+
+from .dict_node import H5DictNode
+from .table_node import H5TableNode
+
+
+
[docs]def get_atom(dtype): + """Return a PyTables Atom for the given dtype or dtype string.""" + return tables.Atom.from_dtype(np.dtype(dtype))
+ + +
[docs]def iterator_length(iterator): + return sum(1 for _ in iterator)
+ + +def _update_wrapped_docstring(wrapped, original=None): + PREAMBLE = """\ +** H5Group wrapper for H5File.{func_name}: ** +Note that the first argument is a nodepath relative to the group, rather than +an absolute path. Below is the original docstring: + +""".format( + func_name=wrapped.__name__ + ) + wrapped.__doc__ = PREAMBLE + inspect.cleandoc(original.__doc__) + return wrapped + + +
[docs]def h5_group_wrapper(original): + return partial(_update_wrapped_docstring, original=original)
+ + +
[docs]class H5File(Mapping): + """File object for HDF5 files. + + This class wraps PyTables to provide a cleaner, but only implements an + interface for accessing arrays. + + Parameters + ---------- + filename : str or a `tables.File` instance + Filename for an HDF5 file, or a PyTables `File` object. + mode : str + Mode to open the file: + + 'r' : Read-only + 'w' : Write; create new file (an existing file would be deleted). + 'a' : Read and write to file; create if not existing + 'r+': Read and write to file; must already exist + + delete_existing : bool + If True, an existing node will be deleted when a `create_*` method is + called. Otherwise, a ValueError will be raise. + auto_groups : bool + If True, `create_array` will automatically create parent groups. + auto_open : bool + If True, open the file automatically on initialization. Otherwise, + you can call `H5File.open()` explicitly after initialization. + chunked : bool + If True, the default behavior of `create_array` will be a chunked + array (see PyTables `create_carray`). + + """ + + exists_error = ( + "'{}' exists in '{}'; set `delete_existing` attribute " + "to True to overwrite existing calculations." + ) + + def __init__( + self, + filename, + mode="r+", + delete_existing=False, + auto_groups=True, + auto_open=True, + h5filters=None, + ): + self.mode = mode + self.delete_existing = delete_existing + self.auto_groups = auto_groups + if h5filters is None: + self.h5filters = tables.Filters( + complib="blosc", complevel=5, shuffle=True + ) + self._h5 = None + + if isinstance(filename, tables.File): + pyt_file = filename + filename = pyt_file.filename + if pyt_file.isopen: + self._h5 = pyt_file + + self.filename = filename + if auto_open: + self.open() + +
[docs] def open(self): + if not self.is_open: + self._h5 = tables.open_file(self.filename, mode=self.mode)
+ +
[docs] def close(self): + if self.is_open: + self._h5.close() + self._h5 = None
+ + @property + def root(self): + return self["/"] + + @property + def is_open(self): + return self._h5 is not None + + def __str__(self): + return str(self._h5) + + def __repr__(self): + return repr(self._h5) + + def __contains__(self, node_path): + return node_path in self._h5 + + def __getitem__(self, node_path): + try: + node = self._h5.get_node(node_path) + except tables.NoSuchNodeError: + msg = "Node {0!r} not found in {1!r}" + raise NameError(msg.format(node_path, self.filename)) + return _wrap_node(node) + + def __iter__(self): + return (_wrap_node(n) for n in self._h5.iter_nodes(where="/")) + + def __len__(self): + return iterator_length(self) + +
[docs] def iteritems(self, path="/"): + """ Iterate over node paths and nodes of the h5 file. """ + for node in self._h5.walk_nodes(where=path): + node_path = node._v_pathname + yield node_path, _wrap_node(node)
+ +
[docs] def create_array( + self, + node_path, + array_or_shape, + dtype=None, + chunked=False, + extendable=False, + **kwargs + ): + """Create node to store an array. + + Parameters + ---------- + node_path : str + PyTable node path; e.g. '/path/to/node'. + array_or_shape : array or shape tuple + Array or shape tuple for an array. If given a shape tuple, the + `dtype` parameter must also specified. + dtype : str or numpy.dtype + Data type of array. Only necessary if `array_or_shape` is a shape. + chunked : bool + Controls whether the array is chunked. + extendable : {None | bool} + Controls whether the array is extendable. + kwargs : key/value pairs + Keyword args passed to PyTables `File.create_(c|e)array`. + """ + self._check_node(node_path) + self._assert_valid_path(node_path) + + h5 = self._h5 + + if isinstance(array_or_shape, tuple): + if dtype is None: + msg = "`dtype` must be specified if only given array shape." + raise ValueError(msg) + array = None + dtype = dtype + shape = array_or_shape + else: + array = array_or_shape + dtype = array.dtype.name + shape = array.shape + + path, name = self.split_path(node_path) + if extendable: + shape = (0,) + shape[1:] + atom = get_atom(dtype) + node = h5.create_earray( + path, name, atom, shape, filters=self.h5filters, **kwargs + ) + if array is not None: + node.append(array) + elif chunked: + atom = get_atom(dtype) + node = h5.create_carray( + path, name, atom, shape, filters=self.h5filters, **kwargs + ) + if array is not None: + node[:] = array + else: + if array is None: + array = np.zeros(shape, dtype=dtype) + node = h5.create_array(path, name, array, **kwargs) + return node
+ +
[docs] def create_group(self, group_path, **kwargs): + """Create group. + + Parameters + ---------- + group_path : str + PyTable group path; e.g. '/path/to/group'. + kwargs : key/value pairs + Keyword args passed to PyTables `File.create_group`. + """ + self._check_node(group_path) + self._assert_valid_path(group_path) + path, name = self.split_path(group_path) + self._h5.create_group(path, name, **kwargs) + return self[group_path]
+ +
[docs] def create_dict(self, node_path, data=None, **kwargs): + """Create dict node at the specified path. + + Parameters + ---------- + node_path : str + Path to node where data is stored (e.g. '/path/to/my_dict') + data : dict + Data for initialization, if desired. + """ + self._check_node(node_path) + self._assert_valid_path(node_path) + H5DictNode.add_to_h5file(self, node_path, data=data, **kwargs) + return self[node_path]
+ +
[docs] def create_table(self, node_path, description, **kwargs): + """Create table node at the specified path. + + Parameters + ---------- + node_path : str + Path to node where data is stored (e.g. '/path/to/my_dict') + description : dict or numpy dtype object + The description of the columns in the table. This is either a dict + of column name -> dtype items or a numpy record array dtype. For + more information, see the documentation for Table in pytables. + """ + self._check_node(node_path) + self._assert_valid_path(node_path) + H5TableNode.add_to_h5file(self, node_path, description, **kwargs) + return self[node_path]
+ + def _check_node(self, node_path): + """Check if node exists and create parent groups if necessary. + + Either raise error or delete depending on `delete_existing` attribute. + """ + if self.auto_groups: + path, name = self.split_path(node_path) + self._create_required_groups(path) + + if node_path in self: + if self.delete_existing: + if isinstance(self[node_path], H5Group): + self.remove_group(node_path, recursive=True) + else: + self.remove_node(node_path) + else: + msg = self.exists_error.format(node_path, self.filename) + raise ValueError(msg) + + def _create_required_groups(self, path): + if path not in self: + parent, missing = self.split_path(path) + # Call recursively to ensure that all parent groups exist. + self._create_required_groups(parent) + self.create_group(path) + +
[docs] def remove_node(self, node_path): + """Remove node + + Parameters + ---------- + node_path : str + PyTable node path; e.g. '/path/to/node'. + """ + node = self[node_path] + if isinstance(node, H5Group): + msg = "{!r} is a group. Use `remove_group` to remove group nodes." + raise ValueError(msg.format(node.pathname)) + node._f_remove()
+ +
[docs] def remove_group(self, group_path, **kwargs): + """Remove group + + Parameters + ---------- + group_path : str + PyTable group path; e.g. '/path/to/group'. + """ + self[group_path]._h5_group._g_remove(**kwargs)
+ + @classmethod + def _assert_valid_path(self, node_path): + if "attrs" in node_path.split("/"): + raise ValueError("'attrs' is an invalid node name.") + +
[docs] @classmethod + def split_path(cls, node_path): + """Split node path returning the base path and node name. + + For example: '/path/to/node' will return '/path/to' and 'node' + + Parameters + ---------- + node_path : str + PyTable node path; e.g. '/path/to/node'. + """ + i = node_path.rfind("/") + if i == 0: + return "/", node_path[1:] + else: + return node_path[:i], node_path[i + 1:]
+ +
[docs] @classmethod + def join_path(cls, *args): + """Join parts of an h5 path. + + For example, the 3 argmuments 'path', 'to', 'node' will return + '/path/to/node'. + + Parameters + ---------- + args : str + Parts of path to be joined. + """ + path = "/".join(part.strip("/") for part in args) + if not path.startswith("/"): + path = "/" + path + return path
+ + +
[docs]class H5Attrs(MutableMapping): + """An attributes dictionary for an h5 node. + + This intercepts `__setitem__` so that python sequences can be converted to + numpy arrays. This helps preserve the readability of our HDF5 files by + other (non-python) programs. + """ + + def __init__(self, node_attrs): + self._node_attrs = node_attrs + + def __delitem__(self, key): + del self._node_attrs[key] + + def __getitem__(self, key): + return self._node_attrs[key] + + def __iter__(self): + return iter(self.keys()) + + def __len__(self): + return len(self._node_attrs._f_list()) + + def __setitem__(self, key, value): + if isinstance(value, tuple) or isinstance(value, list): + value = np.array(value) + self._node_attrs[key] = value + +
[docs] def get(self, key, default=None): + return default if key not in self else self[key]
+ +
[docs] def keys(self): + return self._node_attrs._f_list()
+ +
[docs] def values(self): + return [self[k] for k in self.keys()]
+ +
[docs] def items(self): + return [(k, self[k]) for k in self.keys()]
+ + +
[docs]class H5Group(Mapping): + """A group node in an H5File. + + This is a thin wrapper around PyTables' Group object to expose attributes + and maintain the dict interface of H5File. + """ + + def __init__(self, pytables_group): + self._h5_group = pytables_group + self.attrs = H5Attrs(self._h5_group._v_attrs) + + def __contains__(self, node_path): + return node_path in self._h5_group + + def __str__(self): + return str(self._h5_group) + + def __repr__(self): + return repr(self._h5_group) + + def __getitem__(self, node_path): + parts = node_path.split("/") + # PyTables stores children as attributes + node = self._h5_group.__getattr__(parts[0]) + node = _wrap_node(node) + if len(parts) == 1: + return node + else: + return node["/".join(parts[1:])] + + def __iter__(self): + return (_wrap_node(c) for c in self._h5_group) + + def __len__(self): + return iterator_length(self) + + @property + def pathname(self): + return self._h5_group._v_pathname + + @property + def name(self): + return self._h5_group._v_name + + @property + def filename(self): + return self._h5_group._v_file.filename + + @property + def root(self): + return _wrap_node(self._h5_group._v_file.root) + + @property + def children_names(self): + return list(self._h5_group._v_children.keys()) + + @property + def subgroup_names(self): + return list(self._h5_group._v_groups.keys()) + +
[docs] def iter_groups(self): + """ Iterate over `H5Group` nodes that are children of this group. """ + groups = self._h5_group._v_groups + + # not using the groups.values() method here, because groups is a + # `proxydict` object whose .values() method is non-lazy. Related: + # PyTables/PyTables#784. + return (_wrap_node(groups[group_name]) for group_name in groups)
+ +
[docs] @h5_group_wrapper(H5File.create_group) + def create_group(self, group_subpath, delete_existing=False, **kwargs): + return self._delegate_to_h5file( + "create_group", + group_subpath, + delete_existing=delete_existing, + **kwargs + )
+ +
[docs] @h5_group_wrapper(H5File.remove_group) + def remove_group(self, group_subpath, **kwargs): + return self._delegate_to_h5file( + "remove_group", group_subpath, **kwargs + )
+ +
[docs] @h5_group_wrapper(H5File.create_array) + def create_array( + self, + node_subpath, + array_or_shape, + dtype=None, + chunked=False, + extendable=False, + **kwargs + ): + return self._delegate_to_h5file( + "create_array", + node_subpath, + array_or_shape, + dtype=dtype, + chunked=chunked, + extendable=extendable, + **kwargs + )
+ +
[docs] @h5_group_wrapper(H5File.create_table) + def create_table(self, node_subpath, description, *args, **kwargs): + return self._delegate_to_h5file( + "create_table", node_subpath, description, *args, **kwargs + )
+ +
[docs] @h5_group_wrapper(H5File.create_dict) + def create_dict(self, node_subpath, data=None, **kwargs): + return self._delegate_to_h5file( + "create_dict", node_subpath, data=data, **kwargs + )
+ +
[docs] @h5_group_wrapper(H5File.remove_node) + def remove_node(self, node_subpath, **kwargs): + return self._delegate_to_h5file("remove_node", node_subpath, **kwargs)
+ + def _delegate_to_h5file( + self, function_name, node_subpath, *args, **kwargs + ): + delete_existing = kwargs.pop("delete_existing", False) + h5 = H5File(self._h5_group._v_file, delete_existing=delete_existing) + group_path = h5.join_path(self.pathname, node_subpath) + func = getattr(h5, function_name) + return func(group_path, *args, **kwargs)
+ + +def _wrap_node(node): + """ Wrap PyTables node object, if necessary. """ + if isinstance(node, tables.Group): + if H5DictNode.is_dict_node(node): + node = H5DictNode(node) + else: + node = H5Group(node) + elif H5TableNode.is_table_node(node): + node = H5TableNode(node) + return node +
+ +
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+ + \ No newline at end of file diff --git a/5.1/_modules/apptools/io/h5/table_node.html b/5.1/_modules/apptools/io/h5/table_node.html new file mode 100644 index 000000000..fd8c25ba8 --- /dev/null +++ b/5.1/_modules/apptools/io/h5/table_node.html @@ -0,0 +1,287 @@ + + + + + + + apptools.io.h5.table_node — Apptools Documentation + + + + + + + + + + + + + + + + + + + +
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+ +

Source code for apptools.io.h5.table_node

+# (C) Copyright 2005-2021 Enthought, Inc., Austin, TX
+# All rights reserved.
+#
+# This software is provided without warranty under the terms of the BSD
+# license included in LICENSE.txt and may be redistributed only under
+# the conditions described in the aforementioned license. The license
+# is also available online at http://www.enthought.com/licenses/BSD.txt
+#
+# Thanks for using Enthought open source!
+import numpy as np
+
+from tables.table import Table as PyTablesTable
+
+
+class _TableRowAccessor(object):
+    """A simple object which provides read access to the rows in a Table."""
+
+    def __init__(self, h5_table):
+        self._h5_table = h5_table
+
+    def __getitem__(self, key):
+        return self._h5_table[key]
+
+
+
[docs]class H5TableNode(object): + """A wrapper for PyTables Table nodes. + + Parameters + ---------- + node : tables.Table instance + An H5 node which is a pytables.Table or H5TableNode instance + """ + + def __init__(self, node): + # Avoid a circular import + from .file import H5Attrs + + assert self.is_table_node(node) + self._h5_table = node._h5_table if hasattr(node, "_h5_table") else node + self.attrs = H5Attrs(self._h5_table._v_attrs) + + # -------------------------------------------------------------------------- + # Creation methods + # -------------------------------------------------------------------------- + +
[docs] @classmethod + def add_to_h5file(cls, h5, node_path, description, **kwargs): + """Add table node to an H5 file at the specified path. + + Parameters + ---------- + h5 : H5File + The H5 file where the table node will be stored. + node_path : str + Path to node where data is stored (e.g. '/path/to/my_table') + description : list of tuples or numpy dtype object + The description of the columns in the table. This is either a list + of (column name, dtype, [, shape or itemsize]) tuples or a numpy + record array dtype. For more information, see the documentation for + `Table` in PyTables. + **kwargs : dict + Additional keyword arguments to pass to pytables.File.create_table + """ + if isinstance(description, (tuple, list)): + description = np.dtype(description) + + cls._create_pytables_node(h5, node_path, description, **kwargs) + node = h5[node_path] + + return cls(node)
+ +
[docs] @classmethod + def is_table_node(cls, pytables_node): + """Return True if pytables_node is a pytables.Table or a H5TableNode. + """ + return isinstance(pytables_node, (PyTablesTable, H5TableNode))
+ + # -------------------------------------------------------------------------- + # Public interface + # -------------------------------------------------------------------------- + +
[docs] def append(self, data): + """Add some data to the table. + + Parameters + ---------- + data : dict + A dictionary of column name -> values items + """ + rows = list(zip(*[data[name] for name in self.keys()])) + self._h5_table.append(rows)
+ + def __getitem__(self, col_or_cols): + """Return one or more columns of data from the table. + + Parameters + ---------- + col_or_cols : str or list of str + A single column name or a list of column names + + Return + ------ + data : ndarray + An array of column data with the column order matching that of + `col_or_cols`. + """ + if isinstance(col_or_cols, str): + return self._h5_table.col(col_or_cols) + + column_data = [self._h5_table.col(name) for name in col_or_cols] + return np.column_stack(column_data) + + @property + def ix(self): + """Return an object which provides access to row data.""" + return _TableRowAccessor(self._h5_table) + +
[docs] def keys(self): + return self._h5_table.colnames
+ +
[docs] def to_dataframe(self): + """Return table data as a pandas `DataFrame`. + + XXX: This does not work if the table contains a multidimensional column + + This method requires pandas to have been installed in the environment. + """ + from pandas import DataFrame + + # Slicing rows gives a numpy struct array, which DataFrame understands. + return DataFrame(self.ix[:])
+ + # -------------------------------------------------------------------------- + # Object interface + # -------------------------------------------------------------------------- + + def __repr__(self): + return repr(self._h5_table) + + def __len__(self): + return self._h5_table.nrows + + # -------------------------------------------------------------------------- + # Private interface + # -------------------------------------------------------------------------- + + def _f_remove(self): + """Implement the PyTables `Node._f_remove` method so that H5File + doesn't choke when trying to remove our node. + """ + self._h5_table._f_remove() + self._h5_table = None + + @classmethod + def _create_pytables_node(cls, h5, node_path, description, **kwargs): + path, name = h5.split_path(node_path) + pyt_file = h5._h5 + pyt_file.create_table(path, name, description, **kwargs)
+
+ +
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+ +
+ + \ No newline at end of file diff --git a/_modules/apptools/undo/action/redo_action.html b/5.1/_modules/apptools/io/h5/utils.html similarity index 51% rename from _modules/apptools/undo/action/redo_action.html rename to 5.1/_modules/apptools/io/h5/utils.html index 34960ff83..8629bb69c 100644 --- a/_modules/apptools/undo/action/redo_action.html +++ b/5.1/_modules/apptools/io/h5/utils.html @@ -4,7 +4,7 @@ - apptools.undo.action.redo_action — Apptools Documentation + apptools.io.h5.utils — Apptools Documentation @@ -76,56 +76,44 @@
-

Source code for apptools.undo.action.redo_action

-# ------------------------------------------------------------------------------
-# Copyright (c) 2007, Riverbank Computing Limited
+  

Source code for apptools.io.h5.utils

+# (C) Copyright 2005-2021 Enthought, Inc., Austin, TX
 # All rights reserved.
 #
 # This software is provided without warranty under the terms of the BSD
-# license included in enthought/LICENSE.txt and may be redistributed only
-# under the conditions described in the aforementioned license.  The license
+# license included in LICENSE.txt and may be redistributed only under
+# the conditions described in the aforementioned license. The license
 # is also available online at http://www.enthought.com/licenses/BSD.txt
-# Thanks for using Enthought open source!
 #
-# Author: Riverbank Computing Limited
-# Description: <Enthought undo package component>
-# ------------------------------------------------------------------------------
-
-# Local imports.
-from .abstract_command_stack_action import AbstractCommandStackAction
-
-
-
[docs]class RedoAction(AbstractCommandStackAction): - """An action that redos the last command undone of the active command - stack. - """ - - ########################################################################### - # 'Action' interface. - ########################################################################### - -
[docs] def perform(self, event): - """ Perform the action. """ +# Thanks for using Enthought open source! +from contextlib import contextmanager - self.undo_manager.redo()
+from .file import H5File - ########################################################################### - # 'AbstractUndoAction' interface. - ########################################################################### - def _update_action(self): - """ Update the state of the action. """ +
[docs]@contextmanager +def open_h5file(filename, mode="r+", **kwargs): + """Context manager for reading an HDF5 file as an H5File object. - name = self.undo_manager.redo_name + Parameters + ---------- + filename : str + HDF5 file name. + mode : str + Mode to open the file: - if name: - name = "&Redo " + name - self.enabled = True - else: - name = "&Redo" - self.enabled = False + 'r' : Read-only + 'w' : Write; create new file (an existing file would be deleted). + 'a' : Read and write to file; create if not existing + 'r+': Read and write to file; must already exist - self.name = name
+ See `H5File` for additional keyword arguments. + """ + h5 = H5File(filename, mode=mode, **kwargs) + try: + yield h5 + finally: + h5.close()
@@ -162,10 +150,10 @@

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