#
##
## This file is part of pyFormex 2.0 (Mon Sep 14 12:29:05 CEST 2020)
## pyFormex is a tool for generating, manipulating and transforming 3D
## geometrical models by sequences of mathematical operations.
## Home page: http://pyformex.org
## Project page: http://savannah.nongnu.org/projects/pyformex/
## Copyright 2004-2020 (C) Benedict Verhegghe (benedict.verhegghe@ugent.be)
## Distributed under the GNU General Public License version 3 or later.
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program. If not, see http://www.gnu.org/licenses/.
##
"""A collection of miscellaneous utility functions.
The pyformex.utils module contains a wide variety of utilitary functions.
Because there are so many and they are so widely used, the utils module
is imported in the environment where scripts and apps are executed, so
that users can always call the utils functions without explicitely
importing the module.
Module attributes
~~~~~~~~~~~~~~~~~
Attributes
----------
FileTypes: OrderedDict
A collection of :class:`FileType` records. Each FileType instance holds
the definition of a file type, and is accessible from this dict with a
simple mnemonic key. These are the ones that are commonly used in
pyFormex. But users can add their own definitions too, just by creating
an instance of :class:`FileType`.
Examples
--------
>>> for k,v in FileTypes.items(): print(f"{k} = '{v}'")
all = 'All files (*)'
ccx = 'CalCuliX files (*.dat *.inp)'
dcm = 'DICOM images (*.dcm)'
dxf = 'AutoCAD DXF files (*.dxf)'
dxftext = 'Converted AutoCAD files (*.dxftext)'
flavia = 'flavia results (*.flavia.msh *.flavia.res)'
gts = 'GTS files (*.gts)'
gz = 'Compressed files (*.gz *.bz2)'
html = 'Web pages (*.html)'
icon = 'Icons (*.xpm)'
img = 'Images (*.png *.jpg *.jpeg *.eps *.gif *.bmp)'
inp = 'Abaqus or CalCuliX input files (*.inp)'
neu = 'Gambit Neutral files (*.neu)'
obj = 'Wavefront OBJ files (*.obj)'
off = 'Geomview object files (*.off)'
pgf = 'pyFormex geometry files (*.pgf)'
ply = 'Stanford Polygon File Format files (*.ply)'
png = 'PNG images (*.png)'
postproc = 'Postproc scripts (*.post.py)'
pyformex = 'pyFormex scripts (*.py *.pye)'
pyf = 'pyFormex projects (*.pyf)'
pzf = 'pyFormex zip files (*.pzf)'
smesh = 'Tetgen surface mesh files (*.smesh)'
stl = 'STL files (*.stl)'
stlb = 'Binary STL files (*.stl)'
surface = 'Surface models (*.off *.gts *.stl)'
tetsurf = 'Tetgen surface (*.smesh)'
tetgen = 'Tetgen files (*.poly *.smesh *.ele *.face *.edge *.node *.neigh)'
vtk = 'VTK types (*.vtk *.vtp)'
vtp = 'vtkPolyData file (*.vtp)'
"""
import os
import re
import tempfile
import time
import random
from collections import OrderedDict
import pyformex as pf
from pyformex import Path
from pyformex import process
# These are here to re-export them as utils functions
from pyformex.software import Module, External # noqa: F401
from pyformex.config import formatDict # noqa: F401
#_exclude_members_ = ['runCommand']
shuffle = random.shuffle
# Some regular expressions
RE_digits = re.compile(r'(\d+)')
######### WARNINGS ##############
[docs]def rev_lookup(dictionary, value, default=None):
"""Reverse lookup in a dict
Lookup a value in a dict, and return its key (the first match).
Parameters
----------
dictionary: dict
The dict in which to lookup a value
value: anything
The value to lookup in the dict
default: anything
The key to return if the value was not found
Returns
-------
key: anything
The first key in the dict whose value matches the given ``value``,
or ``default`` if no match was found.
"""
for key, val in dictionary.items():
if val==value:
return key
return default
[docs]def warningCategory(category):
"""Return a warning category and its alias
The input can be a category or an alias. Returns both as a tuple
(alias, category).
Invalid values return the default category ('W', Warning).
"""
_warn_category = {'W': Warning, 'U': UserWarning, 'F': FutureWarning}
if category in _warn_category:
alias = category
else:
alias = rev_lookup(_warn_category, category, 'W')
return alias, _warn_category[alias]
[docs]def warningAction(action):
"""Return a warning action and its alias
The input can be an action string or an alias. Returns both as a tuple
(alias, action).
Invalid values return the default action ('i', 'ignore').
"""
_warn_action = {'d': 'default', 'i': 'ignore', 'a': 'always',
'o': 'once', 'e': 'error'}
if action in _warn_action:
alias = action
else:
alias = rev_lookup(_warn_action, action, 'i')
return alias, _warn_action[alias]
[docs]def filterWarning(message, module='', category='U', action='i', save=False):
"""Add a warning message to the warnings filter.
category can be a Warning subclass or a key in the _warn_category dict
If save is True, the filter is saved in the user settings for future
sessions.
"""
import warnings
message = str(message)
if message.isidentifier() or len(message) < 40:
# Avoid short messages hiding longer ones starting with
# the same string. This is because Python filters test whether
# the message starts with the given re.
message = message + '$'
c, category = warningCategory(category)
a, action = warningAction(action)
pf.debug(f"Warning filter: {action} {category.__name__} '{message}' "
f"from module '{module}'", pf.DEBUG.WARNING)
warnings.filterwarnings(action, message, category, module)
if save:
filters = pf.prefcfg['warnings/filters']
newfilter = (message, '', c)
if action != 'i':
newfilter = (*newfilter, a)
filters.add(newfilter)
pf.debug(f"Saved warning filters: {pf.prefcfg['warnings/filters']}",
pf.DEBUG.WARNING)
_saved_warnings = None
[docs]def resetWarningFilters():
"""Reset the warning filters
Reset the warning filters to the Python defaults plus the ones
listed in the 'warnings/filters' configuration variable.
"""
# global _saved_warnings
# import copy
# if _saved_warnings is None:
# _saved_warnings = copy.copy(warnings.filters)
if pf.cfg['warnings/reset']:
warnings.resetwarnings()
#else:
# warnings.filters = _saved_warnings
pf.debug(
"Current warning filters: %s" % pf.cfg['warnings/filters'],
pf.DEBUG.WARNING
)
# We always add the refcfg filters, to avoid having to store them
a = set(pf.prefcfg['warnings/filters'])
b = set(pf.refcfg['warnings/filters'])
for w in a | b:
try:
filterWarning(*w)
except Exception:
pf.debug(
"Error while processing warning filter: %s" % w,
pf.DEBUG.WARNING
)
def warn(message, level=UserWarning, stacklevel=2, uplevel=0, data=None):
import warnings
from pyformex import messages
# pass the data into the message
messages._message_data = data
warnings.warn(message, level, stacklevel+uplevel)
def deprec(message, stacklevel=4, data=None):
warn(message, level=FutureWarning, stacklevel=stacklevel, data=data)
[docs]def warning(message, level=UserWarning, stacklevel=3):
"""Decorator to add a warning to a function.
Adding this decorator to a function will warn the user with the
supplied message when the decorated function gets executed for
the first time in a session.
An option is provided to switch off this warning in future sessions.
Decorating a function is done as follows::
@utils.warning('This is the message shown to the user')
def function(args):
...
"""
import functools
def decorator(func):
def wrapper(*_args, **_kargs):
warn(message, level=level, stacklevel=stacklevel)
# For some reason these messages are not auto-appended to
# the filters for the currently running program
# Therefore we do it here explicitely
filterWarning(message, category=level)
return func(*_args, **_kargs)
functools.update_wrapper(wrapper, func)
return wrapper
return decorator
[docs]def deprecated(message, stacklevel=4):
"""Decorator to deprecate a function
This is like :func:`warning`, but the level is set to FutureWarning.
"""
return warning(message, level=FutureWarning, stacklevel=stacklevel)
[docs]def deprecated_by(old, new, stacklevel=4):
"""Decorator to deprecate a function by another one.
Adding this decorator to a function will warn the user with a
message that the `old` function is deprecated in favor of `new`,
at the first execution of `old`.
See also: :func:`deprecated`.
"""
return deprecated(f"{old} is deprecated: use {new} instead",
stacklevel=stacklevel)
[docs]def deprecated_future():
"""Decorator to warn that a function may be deprecated in future.
See also: :func:`deprecated`.
"""
return deprecated("This functionality is deprecated and will probably "
"be removed in future, unless you explain to the "
"developers why they should retain it.")
##########################################################################
## Running external commands ##
###############################
# Store the outcome of the last command
last_command = None
# TODO: REMOVE THIS SOON. IT WAS FOR COMPATIBILITY ONLY
def _add_old_attributes_with_warning():
@property
def out(self):
warn('system_command', uplevel=2)
return self.stdout
@property
def err(self):
warn('system_command', uplevel=2)
return self.stderr
@property
def sta(self):
warn('system_command', uplevel=2)
return self.returncode
process.DoneProcess.out = out
process.DoneProcess.err = err
process.DoneProcess.sta = sta
if not pf.sphinx:
_add_old_attributes_with_warning()
# REMOVE UNTIL HERE
[docs]def system(args, *, wait=True, verbose=False, **kargs):
"""Execute a command through the operating system.
This is a wrapper around the process.run and process.start functions,
aimed particularly at the pyFormex GUI user:
- there is a common interface for both functions,
- the `verbose` option provides effortless extra feedback,
- the outcome of the last command is saved for later consultation.
Parameters
----------
args: string or sequence of program arguments.
The command to be executed. It is passed together with `**kargs`
to process.run or process.start.
wait: bool
If True (default) the command is executed by process.run, waiting
for the outcome. If False, the command is executed by process.start,
returning immediately and not waiting for the result
verbose: bool
If True, the command and (in case of failure, timeout or error exit)
a report of its outcome, are written to stdout.
**kargs: keyword arguments
Any keyword arguments accepted by :func:`process.run` (if `wait`
is True) or :func:`process.start` (if `wait` is False).
See the Python documentation for :func:`subprocess.run` for full info.
Returns
-------
:class:`DoneProcess` or subprocess.Popen
If `wait` is True, returns a :class:`DoneProcess` with the ourcome of
the command.
If `wait` is False, returns a subprocess.Popen which can be used to
communicate with the started subprocess.
See Also
--------
process.run: run a command and wait for its outcome
process.start: start a subprocess but do not wait for its outcome
command: call :func:`system` with some other defaults
Examples
--------
>>> P = system("pwd")
>>> P.stdout.strip('\\n') == os.getcwd()
True
>>> P = system('true')
>>> P
DoneProcess(args=['true'], returncode=0, stdout='', stderr='')
>>> P = system('false', capture_output=False)
>>> P
DoneProcess(args=['false'], returncode=1)
>>> P = system('False', verbose=True)
Running command: False
DoneProcess report
args: ['False']
Command failed to run!
returncode: 127
<BLANKLINE>
>>> P = system("sleep 5", timeout=1, verbose=True)
Running command: sleep 5
DoneProcess report
args: ['sleep', '5']
returncode: -1
timedout: True
<BLANKLINE>
"""
global last_command
# TODO: REMOVE
if 'raise_error' in kargs:
# Warn about deprecated param
warn('system_command', uplevel=1)
if 'raise_error' in kargs:
v = kargs.pop('raise_error')
if 'check' not in kargs:
kargs['check'] = v
if verbose:
print(f"Running command: {args}")
if wait:
# run command and wait for result
last_command = P = process.run(args, **kargs)
if verbose and (P.failed or P.timedout or P.returncode != 0):
print(P)
else:
# just start the subprocess
P = process.start(args, **kargs)
return P
[docs]def command(cmd, verbose=True, check=True, **kargs):
"""Run an external command in a user friendly way.
This is equivalent with the :func:`system` function but has
verbose=True and check=True options on by default.
"""
return system(cmd, verbose=verbose, check=check, **kargs)
[docs]def killProcesses(pids, signal=15):
"""Send the specified signal to the processes in list
Parameters
----------
pids: list of int
List of process ids to be killed.
signal: int
Signal to be send to the processes. The default (15) will
try to terminate the process in a friendly way.
See ``man kill`` for more values.
"""
for pid in pids:
try:
os.kill(pid, signal)
except Exception:
pf.debug(f"Error in killing of process {pid}", pf.DEBUG.INFO)
[docs]def execSource(script, glob={}):
"""Execute Python code in another thread.
Parameters
----------
script: str
A string containing some executable Python/pyFormex code.
glob: dict, optional
A dict with globals specifying the environment in which the
source code is executed.
"""
pf.interpreter.locals = glob
pf.interpreter.runsource(script, '<input>', 'exec')
##########################################################################
## match multiple patterns
##########################
[docs]def matchMany(regexps, target):
"""Return multiple regular expression matches of the same target string."""
return [re.match(r, target) for r in regexps]
[docs]def matchCount(regexps, target):
"""Return the number of matches of target to regexps."""
return len([_f for _f in matchMany(regexps, target) if _f])
[docs]def matchAny(regexps, target):
"""Check whether target matches any of the regular expressions."""
return matchCount(regexps, target) > 0
[docs]def matchNone(regexps, target):
"""Check whether target matches none of the regular expressions."""
return matchCount(regexps, target) == 0
[docs]def matchAll(regexps, target):
"""Check whether targets matches all of the regular expressions."""
return matchCount(regexps, target) == len(regexps)
##########################################################################
## File types ##
################
FileTypes = OrderedDict()
[docs]class FileType:
"""A class for holding file types and the related filename patterns.
Parameters
----------
key: str
A short and unique mnemonic string, by preference lower case,
that wil be used as lookup key for this FileType definition
in the global :attr:`FileTypes` collection.
text: str
A textual description of the file type.
*suffixes: sequence of str
All remaining parameters are file suffixes that should be used
to filter files that are supposed to be of this type. Any number
of suffixes is allowed. If None are provided, all files will match
the file type.
See Also
--------
FileTypes: the set of FileType's knownd by pyFormex
"""
def __init__(self, key, text, *suffixes):
self.text = text
self.suff = suffixes
FileTypes[key] = self
[docs] def suffixes(self, compr=False):
"""Return a list of file suffixes for the FileType.
Parameters
----------
compr: bool
If True, the file suffixes for compressed files of this type
are automatically added.
Examples
--------
>>> FileTypes['pgf'].suffixes()
['pgf']
>>> FileTypes['pgf'].suffixes(compr=True)
['pgf', 'pgf.gz', 'pgf.bz2']
>>> FileTypes['all'].suffixes()
[]
"""
suff = list(self.suff)
if compr:
compr_types = FileTypes['gz'].suff
suff.extend([f"{s}.{c}" for s in suff for c in compr_types])
return suff
[docs] def patterns(self, compr=False):
"""Return a list with the file patterns matching the FileType.
Parameters
----------
compr: bool
If True, the file suffixes for compressed files of this type
are automatically added.
Examples
--------
>>> FileTypes['pgf'].patterns()
['*.pgf']
>>> FileTypes['pgf'].patterns(compr=True)
['*.pgf', '*.pgf.gz', '*.pgf.bz2']
>>> FileTypes['all'].patterns()
['*']
"""
if self.suff:
return [f"*.{s}" for s in self.suffixes(compr)]
else:
return ['*']
[docs] def desc(self, compr=False):
"""Create a filetype description compatible with Qt Widgets.
Parameters
----------
compr: bool
If True, the file patterns for compressed files are automatically
added.
Returns
-------
str
A string that can be directly used in the Qt File Dialog
widgets to filter the selectable files. This string has the
format::
file type text (*.ext1 *.ext2)
Examples
--------
>>> FileTypes['img'].desc()
'Images (*.png *.jpg *.jpeg *.eps *.gif *.bmp)'
>>> fileDescription('inp')
'Abaqus or CalCuliX input files (*.inp)'
>>> fileDescription('doc')
'DOC files (*.doc)'
>>> fileDescription('*.inp')
'*.inp'
>>> fileDescription('pgf',compr=True)
'pyFormex geometry files (*.pgf *.pgf.gz *.pgf.bz2)'
"""
return f"{self.text} ({' '.join(self.patterns(compr))})"
__str__ = desc
# The builtin file types. Only types that are relevant for pyFormex
# should be added here. Users can of course add their own types.
# Some tests
FileType('all', 'All files')
FileType('ccx', 'CalCuliX files', 'dat', 'inp')
FileType('dcm', 'DICOM images', 'dcm')
FileType('dxf', 'AutoCAD DXF files', 'dxf')
FileType('dxftext', 'Converted AutoCAD files', 'dxftext')
FileType('flavia', 'flavia results', 'flavia.msh', 'flavia.res')
FileType('gts', 'GTS files', 'gts')
FileType('gz', 'Compressed files', 'gz', 'bz2')
FileType('html', 'Web pages', 'html')
FileType('icon', 'Icons', 'xpm')
FileType('img', 'Images', 'png', 'jpg', 'jpeg', 'eps', 'gif', 'bmp')
FileType('inp', 'Abaqus or CalCuliX input files', 'inp')
FileType('neu', 'Gambit Neutral files', 'neu')
FileType('obj', 'Wavefront OBJ files', 'obj')
FileType('off', 'Geomview object files', 'off')
FileType('pgf', 'pyFormex geometry files', 'pgf')
FileType('ply', 'Stanford Polygon File Format files', 'ply')
FileType('png', 'PNG images', 'png')
FileType('postproc', 'Postproc scripts', 'post.py')
FileType('pyformex', 'pyFormex scripts', 'py', 'pye')
FileType('pyf', 'pyFormex projects', 'pyf')
FileType('pzf', 'pyFormex zip files', 'pzf')
FileType('smesh', 'Tetgen surface mesh files', 'smesh')
FileType('stl', 'STL files', 'stl')
FileType('stlb', 'Binary STL files', 'stl') # Use only for output
FileType('surface', 'Surface models', 'off', 'gts', 'stl')
FileType('tetsurf', 'Tetgen surface', 'smesh')
FileType('tetgen', 'Tetgen files', 'poly', 'smesh', 'ele', 'face',
'edge', 'node', 'neigh')
FileType('vtk', 'VTK types', 'vtk', 'vtp')
FileType('vtp', 'vtkPolyData file', 'vtp')
[docs]def fileDescription(ftype, compr=False):
"""Return a description of the specified file type(s).
Parameters
----------
ftype: str or list of str
The file type (or types) for which a description is requested.
The case of the string(s) is ignored: it is converted to lower case.
Returns
-------
str of list of str
The file description(s) corresponding with the specified file type(s).
The return value(s) depend(s) on the value of the input string(s) in the
the following way (see Examples below):
- if it is a key in the :attr:`file_description` dict, the
corresponding value is returned;
- if it is a string of only alphanumerical characters: it is interpreted
as a file extension and the corresponding return value is
``FTYPE files (*.ftype)``;
- any other string is returned as as: this allows the user to compose
his filters himself.
Examples
--------
>>> fileDescription('img')
'Images (*.png *.jpg *.jpeg *.eps *.gif *.bmp)'
>>> fileDescription(['stl','all'])
['STL files (*.stl)', 'All files (*)']
>>> fileDescription('inp')
'Abaqus or CalCuliX input files (*.inp)'
>>> fileDescription('doc')
'DOC files (*.doc)'
>>> fileDescription('*.inp')
'*.inp'
>>> fileDescription('pgf',compr=True)
'pyFormex geometry files (*.pgf *.pgf.gz *.pgf.bz2)'
"""
if isinstance(ftype, list):
return [FileTypes[f].desc(compr) for f in ftype]
ftype = ftype.lower()
if ftype in FileTypes:
ret = FileTypes[ftype].desc(compr)
elif ftype.isalnum():
ret = f"{ftype.upper()} files (*.{ftype})"
else:
ret = ftype
return ret
[docs]def fileTypes(ftype, compr=False):
"""Return the list of file extension types for a given type.
Parameters
----------
ftype: str
The file type (see :func:`fileDescription`.
compr: bool,optional
If True, the compressed file types are automatically added.
Returns
-------
list of str
A list of the normalized matching extensions for this type.
Normalized extension do not have the leading dot and are
lower case only.
Examples
--------
>>> fileTypes('pgf')
['pgf']
>>> fileTypes('pgf',compr=True)
['pgf', 'pgf.gz', 'pgf.bz2']
"""
return FileTypes[ftype].suffixes(compr)
[docs]def fileTypesFromFilter(fdesc):
"""Extract the filetypes from a file type descriptor.
A file type descriptor is a string consisting of an initial part
followed by a second part enclosed in parentheses. The second part
is a space separated list of glob patterns. An example
file descriptor is 'file type text (\\*.ext1 \\*.ext2)'.
This is the format as returned by :meth:`FileType.desc`.
Parameters
----------
fdesc: str
A file descriptor string.
compr: bool,optional
If True, the compressed file types are automatically added.
Returns
-------
desc: str
The file type description text.
ext: list of str
A list of the matching extensions for this type. Each string
starts with a '.'.
Examples
--------
>>> fileTypesFromFilter(FileTypes['img'].desc())
['png', 'jpg', 'jpeg', 'eps', 'gif', 'bmp']
>>> fileTypesFromFilter(FileTypes['pgf'].desc(compr=True))
['pgf', 'pgf.gz', 'pgf.bz2']
"""
desc, ext, dummy = re.compile('[()]').split(fdesc)
return [e.lstrip('*').lstrip('.') for e in ext.split(' ')]
##########################################################################
## Filenames ##
###############
# TODO: these should go to path module
[docs]def projectName(fn):
"""Derive a project name from a file name.
The project name is the basename of the file without the extension.
It is equivalent with Path(fn).stem
Examples
--------
>>> projectName('aa/bb/cc.dd')
'cc'
>>> projectName('cc.dd')
'cc'
>>> projectName('cc')
'cc'
"""
return Path(fn).stem
[docs]def findIcon(name):
"""Return the file name for an icon with given name.
Parameters
----------
name: str
Name of the icon: this is the stem fof the filename.
Returns
-------
str
The full path name of an icon file with the specified name, found
in the pyFormex icon folder, or the question mark icon file, if
no match was found.
Examples
--------
>>> print(findIcon('view-xr-yu').relative_to(pf.cfg['pyformexdir']))
icons/view-xr-yu.xpm
>>> print(findIcon('right').relative_to(pf.cfg['pyformexdir']))
icons/64x64/right.png
>>> print(findIcon('xyz').relative_to(pf.cfg['pyformexdir']))
icons/question.xpm
"""
for icondir in pf.cfg['gui/icondirs']:
for icontype in pf.cfg['gui/icontypes']:
fname = icondir / (name+icontype)
if fname.exists():
return fname
return pf.cfg['icondir'] / 'question.xpm'
[docs]def listIconNames(dirs=None, types=None):
"""Return the list of available icons by their name.
Parameters
----------
dirs: list of paths, optional
If specified, only return icons names from these directories.
types: list of strings, optional
List of file suffixes, each starting with a dot. If specified,
Only names of icons having one of these suffixes are returned.
Returns
-------
list of str
A sorted list of the icon names available in the pyFormex icons folder.
Examples
--------
>>> listIconNames()[:4]
['clock', 'dist-angle', 'down', 'down']
>>> listIconNames([pf.cfg['icondir'] / '64x64'])[:4]
['down', 'ff', 'info', 'lamp']
>>> listIconNames(types=['.xpm'])[:4]
['clock', 'dist-angle', 'down', 'far']
"""
if dirs is None:
dirs = pf.cfg['gui/icondirs']
if types is None:
types = pf.cfg['gui/icontypes']
types = ['.+\\'+t for t in types]
icons = []
for icondir in dirs:
files = [Path(f).stem for f in icondir.files() if matchAny(types, f)]
icons.extend(files)
return sorted(icons)
##########################################################################
## File lists ##
################
[docs]def sourceFiles(relative=False, symlinks=True, extended=False):
"""Return the list of pyFormex .py source files.
Parameters
----------
relative: bool
If True, returned filenames are relative to the current directory.
symlinks: bool
If False, files that are symbolic links are retained in the
list. The default is to remove them.
extended: bool
If True, also return the .py files in all the paths in the configured
appdirs and scriptdirs.
Returns
-------
list of str
A list of filenames of .py files in the pyFormex source tree, and,
if ``extended`` is True, .py files in the configured app and script
dirs as well.
"""
path = pf.cfg['pyformexdir']
if relative:
path = path.relative_to(Path.cwd())
files = path.listTree(
listdirs=False, sorted=True, includedirs=pf.cfg['sourcedirs'],
includefiles=['.*[.]py$', 'pyformexrc'],
excludefiles=['[.].*'], # exclude hidden files, like autobackups
symlinks=symlinks)
# Add the one file from vtk_light that is really pyFormex source
onemore = path / "vtk_light" / "__init__.py"
if onemore.exists():
files.append(onemore.relative_to(Path.cwd()))
if extended:
searchdirs = [Path(i[1]) for i in pf.cfg['appdirs'] + pf.cfg['scriptdirs']]
for path in set(searchdirs):
if path.exists():
files += path.listTree(
listdirs=False, sorted=True,
includefiles=['.*[.]py$'], symlinks=symlinks)
return files
[docs]def grepSource(pattern, options='', relative=True):
"""Finds pattern in the pyFormex source files.
Uses the `grep` program to find all occurrences of some specified
pattern text in the pyFormex source .py files (including the examples).
Extra options can be passed to the grep command. See `man grep` for
more info.
Returns the output of the grep command.
"""
opts = options.split(' ')
if '-a' in opts:
opts.remove('-a')
options = ' '.join(opts)
extended = True
else:
extended = False
files = sourceFiles(relative=relative, extended=extended, symlinks=False)
cmd = f"grep {options} '{pattern}' {' '.join(files)}"
P = system(cmd, verbose=True)
if not P.returncode:
return P.stdout
[docs]def moduleList(package='all'):
"""Return a list of all pyFormex modules in a subpackage.
This is like :func:`sourceFiles`, but returns the files in a
Python module syntax.
"""
files = sourceFiles(relative=True)
directory = os.path.split(files[0])[0]
dirlen = len(directory)
if dirlen > 0:
dirlen += 1
# Retain only .py files and convert to Python pkg.module format
modules = [fn[dirlen:].replace('.py', '').replace('/', '.')
for fn in files if fn.endswith('.py')]
if package == 'core':
# only core
modules = [m for m in modules if '.' not in m]
elif package == 'all':
# everything except examples
modules = [m for m in modules if not m.startswith('examples.')
and not m.startswith('scripts.')]
elif package == 'all+ex':
# everything including examples
pass
else:
modules = [m for m in modules if m.startswith(package+'.')]
for i,m in enumerate(modules):
if m.endswith('__init__'):
if m == '__init__':
modules[i] = 'pyformex'
else:
modules[i] = m[:-9]
return modules
[docs]def findModuleSource(module):
"""Find the path of the source file of a module
module is either an imported module (pkg.mod) or a string with the module
name ('pkg.mod'), imported or not.
Returns the source file from which the module was/would be loaded when
imported.
Raises an error if the module can not be imported or
does not have a source file.
"""
import importlib.util
if isinstance(module, str):
spec = importlib.util.find_spec(module)
if spec is None:
raise ImportError(f"Can't find module {module}")
else:
spec = module.__spec__
return spec.origin
[docs]def diskSpace(path, units=None, ndigits=2):
"""Returns the amount of diskspace of a file system.
Parameters
----------
path: :term:`path_like`
A path name inside the file system to be probed.
units: str
If provided, results are reported in this units. See
:meth:`humanSize` for possible values. The default
is to return the number of bytes.
ndigits: int
If provided, and also ``units`` is provided, specifies the number
of decimal digits to report. See :meth:`humanSize` for details.
Returns
-------
total: int | float
The total disk space of the file system containing ``path``.
used: int | float
The used disk space on the file system containing ``path``.
available: int | float
The available disk space on the file system containing ``path``.
Notes
-----
The sum ``used + available`` does not necessarily equal ``total``,
because a file system may (and usually does) have reserved blocks.
"""
stat = os.statvfs(Path(path).resolve())
total = stat.f_blocks * stat.f_frsize
avail = stat.f_bavail * stat.f_frsize
used = (stat.f_blocks - stat.f_bfree) * stat.f_frsize
if units:
total = humanSize(total, units, ndigits)
avail = humanSize(avail, units, ndigits)
used = humanSize(used, units, ndigits)
return total, used, avail
[docs]def humanSize(size, units, ndigits=-1):
"""Convert a number to a human size.
Large numbers are often represented in a more human readable
form using k, M, G prefixes. This function returns the input
size as a number with the specified prefix.
Parameters
----------
size: int or float
A number to be converted to human readable form.
units: str
A string specifying the target units. The first character should
be one of k,K,M,G,T,P,E,Z,Y. 'k' and 'K' are equivalent. A second
character 'i' can be added to use binary (K=1024) prefixes instead of
decimal (k=1000).
ndigits: int, optional
If provided and >=0, the result will be rounded to this number of
decimal digits.
Returns
-------
float
The input value in the specified units and possibly rounded
to ``ndigits``.
Examples
--------
>>> humanSize(1234567890,'k')
1234567.89
>>> humanSize(1234567890,'M',0)
1235.0
>>> humanSize(1234567890,'G',3)
1.235
>>> humanSize(1234567890,'Gi',3)
1.15
"""
size = float(size)
order = '.KMGTPEZY'.find(units[0].upper())
if units[1:2] == 'i':
scale = 1024.
else:
scale = 1000.
size = size / scale**order
if ndigits >= 0:
size = round(size, ndigits)
return size
##########################################################################
## Temporary Files ##
#####################
[docs]class TempDir(tempfile.TemporaryDirectory):
"""A temporary directory that can be used as a context manager.
This is a wrapper around Python's tempfile.TemporaryDirectory,
with the following differences:
- the default value for prefix is set to 'pyf\_',
- it has an extra attribute '.path' returning the directory name as a Path,
- the context manager returns a Path instead of a str.
"""
def __init__(self, suffix=None, prefix='pyf_', dir=None):
super().__init__(suffix, prefix, dir)
@property
def path(self):
return Path(self.name)
def __enter__(self):
return self.path
[docs]def TempFile(*args, **kargs):
"""Return a temporary file that can be used as a context manager.
This is a wrapper around Python's tempfile.NamedTemporaryFile,
with the difference that the returned object has an extra attribute
'.path', returning the file name as a Path.
"""
tmpfile = tempfile.NamedTemporaryFile(*args, **kargs)
tmpfile.path = Path(tmpfile.name)
return tmpfile
##########################################################################
## ZIP Files
#####################
[docs]def zipList(filename):
"""List the files in a zip archive
Returns a list of file names
"""
from zipfile import ZipFile
zfil = ZipFile(filename, 'r')
return zfil.namelist()
###################### locale ###################
[docs]def setSaneLocale(localestring=''):
"""Set a sane local configuration for LC_NUMERIC.
`localestring` is the locale string to be set, e.g. 'en_US.UTF-8' or 'C'
for no locale.
Sets the ``LC_ALL`` locale to the specified string if that is not empty,
and (always) sets ``LC_NUMERIC`` and ``LC_COLLATE`` to 'C'.
Changing the LC_NUMERIC setting is a very bad idea! It makes floating
point values to be read or written with a comma instead of a the decimal
point. Of course this makes input and output files completely incompatible.
You will often not be able to process these files any further and
create a lot of troubles for yourself and other people if you use an
LC_NUMERIC setting different from the standard.
Because we do not want to help you shoot yourself in the foot, this
function always sets ``LC_NUMERIC`` back to a sane 'C' value and we
call this function when pyFormex is starting up.
"""
import locale
if localestring:
locale.setlocale(locale.LC_ALL, localestring)
locale.setlocale(locale.LC_NUMERIC, 'C')
locale.setlocale(locale.LC_COLLATE, 'C')
##########################################################################
## Text conversion tools ##
############################
[docs]def to_str(s):
"""Silently convert bytes to str.
The input is either str or bytes. The output is always str.
"""
if isinstance(s, str):
return s
elif isinstance(s, bytes):
return bytes.decode(s)
else:
raise ValueError("Input should be str or bytes")
[docs]def strNorm(s):
"""Normalize a string.
Text normalization removes all '&' characters and converts it to lower case.
>>> strNorm("&MenuItem")
'menuitem'
"""
return str(s).replace('&', '').lower()
_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?@\[\\\]^_`{|},.:]+')
[docs]def slugify(text, delim='-'):
"""Convert a string into a URL-ready readable ascii text.
Example:
>>> slugify("http://example.com/blog/[Some] _ Article's Title--")
'http-example-com-blog-some-article-s-title'
>>> slugify("&MenuItem")
'menuitem'
"""
import unicodedata
text = str(text)
result = []
for word in _punct_re.split(text.lower()):
word = unicodedata.normalize('NFKD', word).encode('ascii', 'ignore')
if word:
word = to_str(word)
result.append(word)
return delim.join(result)
###################### ReST conversion ###################
if Module.has('docutils', quiet=True):
def rst2html(text, writer='html'):
from docutils.core import publish_string
return publish_string(text, writer_name=writer)
else:
def rst2html(text, writer='html'):
return """.. note:
This is a reStructuredText message, but it is currently displayed
as plain text, because it could not be converted to html.
If you install python-docutils, you will see this text (and other
pyFormex messages) in a much nicer layout!
""" + text
[docs]def forceReST(text, underline=False):
"""Convert a text string to have it recognized as reStructuredText.
Returns the text with two lines prepended: a line with '..'
and a blank line. The text display functions will then recognize the
string as being reStructuredText. Since the '..' starts a comment in
reStructuredText, it will not be displayed.
Furthermore, if `underline` is set True, the first line of the text
will be underlined to make it appear as a header.
"""
if underline:
text = underlineHeader(text)
return "..\n\n" + text
[docs]def framedText(text, padding=[0, 2, 0, 2], border=[1, 2, 1, 2], margin=[0, 0, 0, 0],
borderchar='####', cornerchar=None, width=None, adjust='l'):
"""Create a text with a frame around it.
- `adjust`: 'l', 'c' or 'r': makes the text lines be adjusted to the
left, center or right.
>>> print(framedText("Hello World,\\nThis is me calling",adjust='c'))
##########################
## Hello World, ##
## This is me calling ##
##########################
"""
lines = text.splitlines()
maxlen = max([len(l) for l in lines])
if adjust == 'c':
lines = [l.center(maxlen) for l in lines]
elif adjust == 'r':
lines = [l.rjust(maxlen) for l in lines]
else:
lines = [l.ljust(maxlen) for l in lines]
prefix = ' '*margin[3] + borderchar[3]*border[3] + ' '*padding[3]
suffix = ' '*padding[1] + borderchar[1]*border[1] + ' '*margin[1]
width = len(prefix)+maxlen+len(suffix)
s = []
for i in range(margin[0]):
s.append('')
for i in range(border[0]):
s.append(borderchar[0]*width)
for i in range(padding[0]):
s.append(prefix+' '*maxlen+suffix)
for l in lines:
s.append(prefix+("%"+str(maxlen)+"s") % l+suffix)
for i in range(padding[2]):
s.append(prefix+' '*maxlen+suffix)
for i in range(border[2]):
s.append(borderchar[2]*width)
for i in range(margin[2]):
s.append('')
return '\n'.join(s)
[docs]def prefixText(text, prefix):
"""Add a prefix to all lines of a text.
- `text`: multiline string
- `prefix`: string: prefix to insert at the start of all lines of text.
>>> print(prefixText("line1\\nline2","** "))
** line1
** line2
"""
return '\n'.join([prefix+line for line in text.split('\n')])
###################### file conversion ###################
[docs]def dos2unix(infile):
"""Convert a text file to unix line endings."""
return system(f"sed -i 's|$|\\r|' {infile}")
[docs]def unix2dos(infile, outfile=None):
"""Convert a text file to dos line endings."""
return system(f"sed -i 's|\\r||' {infile}")
[docs]def gzip(filename, gzipped=None, remove=True, level=5, compr='gz'):
r"""Compress a file in gzip/bzip2 format.
Parameters
----------
filename: :term:`path_like`
The input file name.
gzipped: :term:`path_like`, optional
The output file name. If not specified, it will be set to
the input file name + '.' + `compr`. An existing output file will be
overwritten.
remove: bool
If True (default), the input file is removed after
successful compression.
level: int 1..9
The gzip/bzip2 compression level.
Higher values result in smaller files, but require longer compression
times. The default of 5 gives already a fairly good compression ratio.
compr: 'gz' | 'bz2'
The compression algorithm to be used.
The default is 'gz' for gzip compression. Setting to 'bz2' will use
bzip2 compression.
Returns
-------
:class:`Path`
The path of the compressed file.
Examples
--------
>>> f = Path('./test_gzip.out')
>>> f.write_text('This is a test\n'*100)
1500
>>> print(f.size())
1500
>>> g = gzip(f)
>>> print(g)
test_gzip.out.gz
>>> print(g.size())
60
>>> f.exists()
False
>>> f = gunzip(g)
>>> f.exists()
True
>>> print(f.read_text().split('\n')[50])
This is a test
>>> g.exists()
False
"""
filename = Path(filename)
if gzipped is None:
gzipped = filename + '.' + compr
if compr == 'gz':
import gzip
gz = gzip.GzipFile(gzipped, 'wb', compresslevel=level)
elif compr == 'bz2':
import bz2
gz = bz2.BZ2File(gzipped, 'wb', compresslevel=level)
else:
raise ValueError("`compr` should be 'gz' or 'bz2'")
with open(filename, 'rb') as fil:
gz.write(fil.read())
gz.close()
if remove:
filename.remove()
return gzipped
[docs]def gunzip(filename, unzipped=None, remove=True, compr='gz'):
"""Uncompress a file in gzip/bzip2 format.
Parameters
----------
filename: :term:`path_like`
The compressed input file name (usually ending in '.gz' or
'.bz2').
unzipped: :term:`path_like`, optional
The output file name. If not provided and `filename` ends with
'.gz' or '.bz2', it will be set to the `filename` with the '.gz' or
'.bz2' removed.
If not provided and `filename` does not end in '.gz' or '.bz2',
or if an empty string is provided, the name of a temporary file is
generated. Since you will normally want to read something from the
decompressed file, this temporary file is not deleted after closing.
It is up to the user to delete it (using the returned file name) when
the file has been dealt with.
remove: bool
If True (default), the input file is removed after successful
decompression. You probably want to set this to False when
decompressing to a temporary file.
compr: 'gz' | 'bz2'
The compression algorithm used in the input file.
If not provided, it is automatically set from the extension of the
`filename` if that is either '.gz' or '.bz2', or else the default 'gz'
is used.
Returns
-------
:class:`Path`
The name of the uncompressed file.
Examples
--------
See `gzip`.
"""
filename = Path(filename)
if filename.suffix in ['.gz', '.bz2']:
compr = filename.suffix[1:]
if compr == 'gz':
import gzip
gz = gzip.GzipFile(filename, 'rb')
elif compr == 'bz2':
import bz2
gz = bz2.BZ2File(filename, 'rb')
else:
raise ValueError("`compr` should be 'gz' or 'bz2'")
if unzipped is None and filename.endswith('.'+compr):
unzipped = filename.without_suffix
if unzipped:
fil = open(unzipped, 'wb')
else:
fil = TempFile(prefix='gunzip-', delete=False)
unzipped = fil.name
fil.write(gz.read())
gz.close()
fil.close()
if remove:
filename.remove()
return unzipped
[docs]class File(object):
"""Transparent file compression.
This class is a context manager providing transparent file compression
and decompression. It is commonly used in a `with` statement, as follows::
with File('filename.ext','w') as f:
f.write('something')
f.write('something more')
This will create an uncompressed file with the specified name, write some
things to the file, and close it. The file can be read back similarly::
with File('filename.ext','r') as f:
for line in f:
print(f)
Because File is a context manager, the file is closed automatically when
leaving the `with` block.
By specifying a filename ending with '.gz' or '.bz2', the file will be
compressed (on writing) or decompressed (on reading) automatically.
The code can just stay the same as above.
Parameters
----------
filename: :term:`path_like`
Path of the file to open.
If the filename ends with '.gz' or '.bz2', transparent (de)compression
will be used, with gzip or bzip2 compression algorithms respectively.
mode: str
File open mode: 'r' for read, 'w' for write or 'a' for
append mode. See also the Python documentation for the
:func:`.open` builtin function.
For compressed files, append mode is not yet available.
compr: 'gz' | 'bz2'
The compression algorithm to be used: gzip or bzip2.
If not provided and the file name ends with '.gz' or '.bz2',
`compr` is set automatically from the extension.
level: int (1..9)
Compression level for gzip/bzip2.
Higher values result in smaller files, but require longer compression
times. The default of 5 gives already a fairly good compression ratio.
delete_temp: bool
If True (default), the temporary files needed to
do the (de)compression are deleted when the File instance is closed.
The File class can also be used outside a ``with`` statement. In that case
the user has to open and close the File himself. The following are more
or less equivalent with the above examples (the ``with`` statement is
better at handling exceptions)::
fil = File('filename.ext','w')
f = fil.open()
f.write('something')
f.write('something more')
fil.close()
This will create an uncompressed file with the specified name, write some
things to the file, and close it. The file can be read back similarly::
fil = File('filename.ext','r')
f = fil.open()
for line in f:
print(f)
fil.close()
"""
def __init__(self, filename, mode, compr=None, level=5, delete_temp=True):
"""Initialize the File instance"""
filename = Path(filename)
if compr is None:
if filename.suffix in ['.gz', '.bz2']:
# A recognized compression format
compr = filename.suffix[1:]
self.name = filename
self.tmpfile = None
self.tmpname = None
self.mode = mode
self.compr = compr
self.level = level
self.delete = delete_temp
self.file = None
[docs] def open(self):
"""Open the File in the requested mode.
This can be used to open a File object outside a `with`
statement. It returns a Python file object that can be used
to read from or write to the File. It performs the following:
- If no compression is used, ope the file in the requested mode.
- For reading a compressed file, decompress the file to a temporary
file and open the temporary file for reading.
- For writing a compressed file, open a tem[porary file for writing.
See the documentation for the :class:`File` class for an example of
its use.
"""
if not self.compr:
# Open an uncompressed file:
# - just open the file with specified mode
self.file = open(self.name, self.mode)
elif self.mode[0:1] in 'ra':
# Open a compressed file in read or append mode:
# - first decompress file
self.tmpname = gunzip(self.name, unzipped='', remove=False)
# - then open the decompressed file in read/append mode
self.file = open(self.tmpname, self.mode)
else:
# Open a compressed file in write mode
# - open a temporary file (to be compressed after closing)
self.tmpfile = TempFile(prefix='File-', mode=self.mode, delete=False)
self.tmpname = self.tmpfile.name
self.file = self.tmpfile.file
return self.file
# this is needed to make this a context manager
__enter__ = open
[docs] def close(self):
"""Close the File.
This can be used to close the File if it was not opened using a
`with` statement. It performs the following:
- The underlying file object is closed.
- If the file was opened in write or append mode and compression is
requested, the file is compressed.
- If a temporary file was in use and delete_temp is True,
the temporary file is deleted.
See the documentation for the :class:`File` class for an example of
its use.
"""
self.file.close()
if self.compr and self.mode[0:1] in 'wa':
# compress the resulting file
gzip(self.tmpname, gzipped=self.name, remove=True,
compr=self.compr, level=self.level)
if self.tmpname and self.delete:
Path(self.tmpname).remove()
def __exit__(self, exc_type, exc_value, traceback):
"""Close the File
"""
if exc_type is None:
self.close()
return True
else:
# An exception occurred
if self.file:
self.file.close()
if self.tmpfile:
self.tmpfile.close()
if self.tmpname and self.delete:
Path(self.tmpname).remove()
return False
[docs] def reopen(self, mode='r'):
"""Reopen the file, possibly in another mode.
This allows e.g. to read back data from a just saved file
without having to destroy the File instance.
Returns the open file object.
"""
self.close()
self.mode = mode
return self.open()
# These two functions are undocumented for a reason. Believe me! BV
def splitme(s): # noqa: E302
return s[::2], s[1::2]
def mergeme(s1, s2): # noqa: E302
return ''.join([a+b for a, b in zip(s1, s2)])
[docs]def timeEval(s, glob=None):
"""Return the time needed for evaluating a string.
s is a string with a valid Python instructions.
The string is evaluated using Python's eval() and the difference
in seconds between the current time before and after the evaluation
is printed. The result of the evaluation is returned.
This is a simple method to measure the time spent in some operation.
It should not be used for microlevel instructions though, because
the overhead of the time calls. Use Python's timeit module to measure
microlevel execution time.
"""
start = time.time()
res = eval(s, glob)
stop = time.time()
print(f"Timed evaluation: {stop-start} seconds")
return res
[docs]def countLines(fn):
"""Return the number of lines in a text file."""
P = system(["wc", fn])
if P.returncode == 0:
return int(P.stdout.split()[0])
else:
return 0
##########################################################################
## Miscellaneous ##
###############################
[docs]def userName():
"""Find the name of the user."""
import getpass
return getpass.getuser()
[docs]def isString(o):
"""Test if an object is a string (ascii or unicode)"""
return isinstance(o, (str, bytes))
[docs]def isFile(o):
"""Test if an object is a file"""
import io
return isinstance(o, io.IOBase)
[docs]def is_script(appname):
"""Checks whether an application name is rather a script name"""
return str(appname).endswith('.py') or str(appname).endswith('.pye')
def is_app(appname):
return not is_script(appname)
[docs]def getDocString(scriptfile):
"""Return the docstring from a script file.
This actually returns the first multiline string (delimited by
triple double quote characters) from the file.
It does relies on the script file being structured properly and
indeed including a doctring at the beginning of the file.
"""
fil = open(scriptfile, 'r')
s = fil.read()
i = s.find('"""')
if i >= 0:
j = s.find('"""', i+1)
if j >= i+3:
return s[i+3:j]
return ''
[docs]def hsorted(l):
"""Sort a list of strings in human order.
When human sort a list of strings, they tend to interprete the
numerical fields like numbers and sort these parts numerically,
instead of the lexicographic sorting by the computer.
Returns the list of strings sorted in human order.
Example:
>>> hsorted(['a1b','a11b','a1.1b','a2b','a1'])
['a1', 'a1.1b', 'a1b', 'a2b', 'a11b']
"""
def human(s):
s = RE_digits.split(s)+['0']
return list(zip(s[0::2], [int(i) for i in s[1::2]]))
return sorted(l, key=human)
[docs]def numsplit(s):
"""Split a string in numerical and non-numerical parts.
Returns a series of substrings of s. The odd items do not contain
any digits. The even items only contain digits.
Joined together, the substrings restore the original.
The number of items is always odd: if the string ends or starts with a
digit, the first or last item is an empty string.
Example:
>>> print(numsplit("aa11.22bb"))
['aa', '11', '.', '22', 'bb']
>>> print(numsplit("11.22bb"))
['', '11', '.', '22', 'bb']
>>> print(numsplit("aa11.22"))
['aa', '11', '.', '22', '']
"""
return RE_digits.split(s)
[docs]def splitDigits(s, pos=-1):
"""Split a string at a sequence of digits.
The input string is split in three parts, where the second part is
a contiguous series of digits. The second argument specifies at which
numerical substring the splitting is done. By default (pos=-1) this is
the last one.
Returns a tuple of three strings, any of which can be empty. The
second string, if non-empty is a series of digits. The first and last
items are the parts of the string before and after that series.
Any of the three return values can be an empty string.
If the string does not contain any digits, or if the specified splitting
position exceeds the number of numerical substrings, the second and
third items are empty strings.
Example:
>>> splitDigits('abc123')
('abc', '123', '')
>>> splitDigits('123')
('', '123', '')
>>> splitDigits('abc')
('abc', '', '')
>>> splitDigits('abc123def456fghi')
('abc123def', '456', 'fghi')
>>> splitDigits('abc123def456fghi',0)
('abc', '123', 'def456fghi')
>>> splitDigits('123-456')
('123-', '456', '')
>>> splitDigits('123-456',2)
('123-456', '', '')
>>> splitDigits('')
('', '', '')
"""
g = numsplit(s)
n = len(g)
i = 2*pos
if i >= -n and i+1 < n:
if i >= 0:
i += 1
return ''.join(g[:i]), g[i], ''.join(g[i+1:])
else:
return s, '', ''
[docs]class NameSequence(object):
"""A class for autogenerating sequences of names.
Sequences of names are autogenerated by combining a fixed part with
a numeric part. The latter is incremented at each creation of a new
name (by the next() function).
Parameters
----------
name: str
Base of the names to be generated. The name is split in three parts
(prefix, numeric, suffix), where numeric only contains digits and
suffix does not contain any digits. Thus, numeric is the last numeric
part in the string. The prefix and suffix are invariable parts, while
the numeric part will be incremented starting from the value in the
provided name.
Use ``ext`` if the variable part is not the last numeric part of name.
If ``name`` does not contain any numeric part, it is split as a file
name in stem and suffix, and '-0' is appended to the stem.
If ``name`` is empty, it will be replaced with '0'.
ext: str, optional
If provided, this is an invariable string added to the suffix from
``name`` to construct the full name template. This may contain
numeric parts, allowing the variable numeric part at any place
in the full template.
Examples
--------
>>> N = NameSequence('obj')
>>> [ next(N) for i in range(3) ]
['obj-0', 'obj-1', 'obj-2']
>>> N.peek()
'obj-3'
>>> next(N), next(N)
('obj-3', 'obj-4')
>>> N.template
'obj-%d'
>>> N = NameSequence('obj-005')
>>> [ next(N) for i in range(3) ]
['obj-005', 'obj-006', 'obj-007']
>>> N = NameSequence('abc.98')
>>> [ next(N) for i in range(3) ]
['abc.98', 'abc.99', 'abc.100']
>>> N = NameSequence('abc-8x.png')
>>> [ next(N) for i in range(3) ]
['abc-8x.png', 'abc-9x.png', 'abc-10x.png']
>>> N.template
'abc-%01dx.png'
>>> N.glob()
'abc-*x.png'
>>> next(NameSequence('abc','.png'))
'abc-0.png'
>>> next(NameSequence('abc.png'))
'abc-0.png'
>>> N = NameSequence('/home/user/abc23','5.png')
>>> [ next(N) for i in range(2) ]
['/home/user/abc235.png', '/home/user/abc245.png']
>>> N = NameSequence('')
>>> next(N), next(N)
('0', '1')
>>> N = NameSequence('12')
>>> next(N), next(N)
('12', '13')
"""
def __init__(self, name, ext=''):
"""Create a new NameSequence from name,ext."""
prefix, number, suffix = splitDigits(name)
if len(number) > 0:
self.nr = int(number)
format = "%%0%dd" % len(number)
else:
self.nr = 0
if name:
p = Path(name)
prefix, suffix = p.stem, p.suffix
format = "-%d"
else:
prefix = suffix = ''
format = "%d"
self.template = prefix+format+suffix+ext
def __next__(self):
"""Return the next name in the sequence"""
fn = self.template % self.nr
self.nr += 1
return fn
next = __next__
[docs] def peek(self):
"""Return the next name in the sequence without incrementing."""
return self.template % self.nr
[docs] def glob(self):
"""Return a UNIX glob pattern for the generated names.
A NameSequence is often used as a generator for file names.
The glob() method returns a pattern that can be used in a
UNIX-like shell command to select all the generated file names.
"""
m = re.match(r'(.*)%\d*d(.*)', self.template)
if m:
return f"{m.group(1)}*{ m.group(2)}"
else:
raise ValueError("Invalid template")
[docs]def globFiles(pattern, sort=hsorted):
"""Return a (sorted) list of files matching a filename pattern.
A function may be specified to sort/filter the list of file names.
The function should take a list of filenames as input. The output
of the function is returned. The default sort function will sort
the filenames in a human order. This will sort numeric fields in
order of increasing numbers instead of alphanumerically.
Examples
--------
>>> globFiles('pyformex/o*.py')
['pyformex/olist.py', 'pyformex/options.py']
"""
import glob
files = glob.glob(pattern)
if callable(sort):
files = sort(files)
return files
################### automatic naming of objects ##########################
_autoname = {}
[docs]def autoName(clas):
"""Return the autoname class instance for objects of type clas.
This allows for objects of a certain class to be automatically
named throughout pyFormex.
Parameters
----------
clas: str or class or object
The object class name. If a str, it is the class name. If a class,
the name is found from it. If an object, the name is taken from
the object's class. In all cases the name is converted to lower
case
Returns
-------
NameSequence instance
A NameSequence that will generate subsequent names corresponding
with the specified class.
Examples
--------
>>> from pyformex.formex import Formex
>>> F = Formex()
>>> print(next(autoName(Formex)))
formex-0
>>> print(next(autoName(F)))
formex-1
>>> print(next(autoName('Formex')))
formex-2
"""
if isinstance(clas, str):
name = clas
else:
try:
name = clas.__name__
except Exception:
try:
name = clas.__class__.__name__
except Exception:
raise ValueError("Expected an instance, class or string")
name = name.lower()
if name not in _autoname:
_autoname[name] = NameSequence(name+'-0')
return _autoname[name]
[docs]def prefixDict(d, prefix=''):
"""Prefix all the keys of a dict with the given prefix.
Parameters
----------
d: dict
A dict where all keys are strings.
prefix: str
A string to prepend to all keys in the dict.
Returns
-------
dict
A dict with the same contents as the input, but where all keys
have been prefixed with the given prefix string.
Examples
--------
>>> prefixDict({'a':0,'b':1},'p_')
{'p_a': 0, 'p_b': 1}
"""
return dict([(prefix+k, d[k]) for k in d])
[docs]def subDict(d, prefix='', strip=True):
"""Return a dict with the items whose key starts with prefix.
Parameters
----------
d: dict
A dict where all the keys are strings.
prefix: str
The string that is to be found at the start of the keys.
strip: bool
If True (default), the prefix is stripped from the keys.
Returns
-------
dict
A dict with all the items from ``d`` whose key starts
with ``prefix``. The keys in the returned dict will have the prefix
stripped off, unless strip=False is specified.
Examples
--------
>>> subDict({'p_a':0,'q_a':1,'p_b':2}, 'p_')
{'a': 0, 'b': 2}
>>> subDict({'p_a':0,'q_a':1,'p_b':2}, 'p_', strip=False)
{'p_a': 0, 'p_b': 2}
"""
if strip:
return dict([(k.replace(prefix, '', 1), d[k]) for k in d if k.startswith(prefix)])
else:
return dict([(k, d[k]) for k in d if k.startswith(prefix)])
[docs]def selectDict(d, keys, remove=False):
"""Return a dict with the items whose key is in keys.
Parameters
----------
d: dict
The dict to select items from.
keys: set of str
The keys to select from ``d``. This can be a set or list of key
values, or another dict, or any object having the ``key in object``
interface.
remove: bool
If True, the selected keys are removed from the input dict.
Returns
-------
dict
A dict with all the items from ``d`` whose key is in ``keys``.
See Also
--------
removeDict: the complementary operation, returns items not in ``keys``.
Examples
--------
>>> d = dict([(c,c*c) for c in range(4)])
>>> selectDict(d,[2,0])
{0: 0, 2: 4}
>>> print(d)
{0: 0, 1: 1, 2: 4, 3: 9}
>>> selectDict(d,[2,0,6],remove=True)
{0: 0, 2: 4}
>>> print(d)
{1: 1, 3: 9}
"""
keys = set(d) & set(keys)
sel = dict([(k, d[k]) for k in keys])
if remove:
for k in keys:
del d[k]
return sel
[docs]def removeDict(d, keys):
"""Return a dict with the specified keys removed.
Parameters
----------
d: dict
The dict to select items from.
keys: set of str
The keys to select from ``d``. This can be a set or list of key
values, or another dict, or any object having the ``key in object``
interface.
Returns
-------
dict
A dict with all the items from ``d`` whose key is not in ``keys``.
See Also
--------
selectDict: the complementary operation returning the items in ``keys``
Examples
--------
>>> d = dict([(c,c*c) for c in range(6)])
>>> removeDict(d,[4,0])
{1: 1, 2: 4, 3: 9, 5: 25}
"""
return dict([(k, d[k]) for k in set(d)-set(keys)])
[docs]def refreshDict(d, src):
"""Refresh a dict with values from another dict.
The values in the dict d are update with those in src.
Unlike the dict.update method, this will only update existing keys
but not add new keys.
"""
d.update(selectDict(src, d))
[docs]def inverseDict(d):
"""Return the inverse of a dictionary.
Returns a dict with keys and values interchanged.
Example:
>>> inverseDict({'a':0,'b':1})
{0: 'a', 1: 'b'}
"""
return dict([(d[k], k) for k in d])
[docs]def selectDictValues(d, values):
"""Return the keys in a dict which have a specified value
- `d`: a dict where all the keys are strings.
- `values`: a list/set of values.
The return value is a list with all the keys from d whose value
is in keys.
Example:
>>> d = dict([(c,c*c) for c in range(6)])
>>> selectDictValues(d,range(10))
[0, 1, 2, 3]
"""
return [k for k in d if d[k] in values]
[docs]def dictStr(d, skipkeys=[]):
"""Convert a dict to a string.
This is much like dict.__str__, but formats all keys as
strings and prints the items with the keys sorted.
This function is can be used as replacement for the __str__
method od dict-like classes.
A list of strings skipkeys kan be specified, to suppress the
printing of some special key values.
Example:
>>> dictStr({'a':0, 'b':1, 'c':2}, ['b'])
"{'a': 0, 'c': 2}"
"""
s = ["'%s': %r" % (k, d[k]) for k in d if k not in skipkeys]
return '{' + ', '.join(sorted(s)) + '}'
[docs]class DictDiff():
"""A class to compute the difference between two dictionaries
Parameters
----------
current_dict: dict
past_dict: dict
The differences are reported as sets of keys:
- items added
- items removed
- keys same in both but changed values
- keys same in both and unchanged values
"""
def __init__(self, current_dict, past_dict):
self.current_dict, self.past_dict = current_dict, past_dict
self.current_keys, self.past_keys = [
set(d.keys()) for d in (current_dict, past_dict)
]
self.intersect = self.current_keys.intersection(self.past_keys)
[docs] def added(self):
"""Return the keys in current_dict but not in past_dict"""
return self.current_keys - self.intersect
[docs] def removed(self):
"""Return the keys in past_dict but not in current_dict"""
return self.past_keys - self.intersect
[docs] def changed(self):
"""Return the keys for which the value has changed"""
return set(o for o in self.intersect
if self.past_dict[o] != self.current_dict[o])
[docs] def unchanged(self):
"""Return the keys with same value in both dicts"""
return set(o for o in self.intersect
if self.past_dict[o] == self.current_dict[o])
[docs] def equal(self):
"""Return True if both dicts are equivalent"""
return len(self.added() | self.removed() | self.changed()) == 0
[docs] def report(self):
"""Create a reports of the differences"""
return(f"""Dict difference report:
(1) items added : {', '.join(self.added())}
(2) items removed : {', '.join(self.removed())}
(3) keys same in both but changed values : {', '.join(self.changed())}
(4) keys same in both and unchanged values : {', '.join(self.unchanged())}
""")
[docs]def listFonts(mono=False):
"""List the fonts known to the system.
Parameters
----------
mono: bool
If True, only returns the monospace fonts. Default is to return all
fonts.
Returns
-------
list of :class:`Path`
A list of the font files found on the system.
Notes
-----
This uses the 'fc-list' command from the fontconfig package and will
produce a warning if fontconfig is not installed.
"""
cmd = "fc-list : file | sed 's|.*file=||;s|:||'"
P = system(cmd, shell=True)
if P.returncode:
warning("fc-list could not find your font files.\n"
"Maybe you do not have fontconfig installed?")
fonts = []
else:
fonts = sorted([Path(f.strip()) for f in P.stdout.split('\n')])
if len(fonts[0]) <= 1:
fonts = fonts[1:]
if mono:
fonts = [f for f in fonts if is_valid_mono_font(f)]
return fonts
[docs]def is_valid_mono_font(fontfile):
"""Filter valid monotype fonts
Parameters
----------
fontfile: Path
Path of a font file.
Returns
-------
bool
True if the provided font file has a .ttf suffix, is a fixed width
font and the font basename is not listed in the 'fonts/ignore'
configuration variable.
"""
from pyformex import freetype as ft
return fontfile.suffix == '.ttf' and \
fontfile.name not in pf.cfg['fonts/ignore'] and \
ft.Face(fontfile).is_fixed_width
[docs]def defaultMonoFont():
"""Return a default monospace font for the system."""
fonts = listFonts(mono=True)
if not fonts:
raise ValueError("I could not find any monospace font file on your system")
for f in fonts:
if f.endswith('DejaVuSansMono.ttf'):
return f
return fonts[0]
@deprecated_by('utils.listAllFonts','utils.listFonts')
def listAllFonts():
return listFonts()
[docs]def listMonoFonts():
"""List only the monospace fonts
See Also
--------
listFonts
"""
return listFonts(mono=True)
###########################################################################
def execFile(f, *args, **kargs):
with open(f, 'r') as fil:
return exec(compile(fil.read(), f, 'exec'), *args, **kargs)
def procInfo():
print('module name: %s' % __name__)
print('parent process: %s' % os.getppid())
print('process id: %s' % os.getpid())
[docs]def interrogate(item):
"""Print useful information about item."""
info = OrderedDict()
if hasattr(item, '__name__'):
info["NAME: "] = item.__name__
if hasattr(item, '__class__'):
info["CLASS: "] = item.__class__.__name__
info["ID: "] = id(item)
info["TYPE: "] = type(item)
info["VALUE: "] = repr(item)
info["CALLABLE:"] = callable(item)
if hasattr(item, '__doc__'):
doc = getattr(item, '__doc__')
doc = doc.strip() # Remove leading/trailing whitespace.
firstline = doc.split('\n')[0]
info["DOC: "] = firstline
for k in info:
print(f"{k} {info[k]}")
[docs]def memory_report(keys=None):
"""Return info about memory usage"""
import gc
gc.collect()
P = system('cat /proc/meminfo')
res = {}
for line in str(P.stdout).split('\n'):
try:
k, v = line.split(':')
k = k.strip()
v = v.replace('kB', '').strip()
res[k] = int(v)
except Exception:
break
res['MemUsed'] = res['MemTotal'] - res['MemFree'] - res['Buffers'] - res['Cached']
if keys:
res = selectDict(res, keys)
return res
def memory_diff(mem0, mem1, tag=None):
m0 = mem0['MemUsed']/1024.
m1 = mem1['MemUsed']/1024.
m2 = m1 - m0
m3 = mem1['MemFree']/1024.
print(f"{m0:10.1f} MB before; {m1:10.1f} MB after; "
f"{m2:10.1f} MB used; {m3:10.1f} MB free; {tag}")
_mem_state = None
def memory_track(tag=None, since=None):
global _mem_state
if since is None:
since = _mem_state
new_mem_state = memory_report()
if tag and _mem_state is not None:
memory_diff(since, new_mem_state, tag)
_mem_state = new_mem_state
return _mem_state
[docs]def totalMemSize(o, handlers={}, verbose=False):
"""Return the approximate total memory footprint of an object.
This function returns the approximate total memory footprint of an
object and all of its contents.
Automatically finds the contents of the following builtin containers and
their subclasses: tuple, list, deque, dict, set and frozenset.
To search other containers, add handlers to iterate over their contents:
handlers = {SomeContainerClass: iter,
OtherContainerClass: OtherContainerClass.get_elements}
Adapted from http://code.activestate.com/recipes/577504/
"""
from sys import getsizeof, stderr
from itertools import chain
from pyformex.collections import deque
try:
from reprlib import repr
except ImportError:
pass
def dict_handler(d):
return chain.from_iterable(d.items())
all_handlers = {
tuple: iter,
list: iter,
deque: iter,
dict: dict_handler,
set: iter,
frozenset: iter,
}
all_handlers.update(handlers) # user handlers take precedence
seen = set() # track which object id's have already been seen
default_size = getsizeof(0) # estimate sizeof object without __sizeof__
def sizeof(o):
if id(o) in seen: # do not double count the same object
return 0
seen.add(id(o))
s = getsizeof(o, default_size)
if verbose:
print(s, type(o), repr(o), file=stderr)
for typ in all_handlers:
if isinstance(o, typ):
handler = all_handlers[typ]
s += sum([sizeof(i) for i in handler(o)])
break
return s
return sizeof(o)
# TODO: this is not a good way of computing memory usage
def vmSize():
return 0
# raise RuntimeError("From utils.vmSize")
# return int(os.popen('ps h o vsize %s' % os.getpid()).read().strip())
def memUsed():
return memory_report()['MemUsed']
def memory_used():
rsskb = int(re.search(r'^VmRSS:\s+(\d+) kb$',
open('/proc/self/status', 'r').read(),
flags=re.IGNORECASE | re.MULTILINE).group(1))
return rsskb
###########################################################################
#### Deprecated #####
is_pyFormex = is_script
@deprecated_by('utils.runCommand', 'utils.command')
def runCommand(cmd, timeout=None, shell=True, **kargs):
P = command(cmd, timeout=timeout, shell=shell, **kargs)
return P.returncode, P.stdout.rstrip('\n')
@deprecated_by('utils.removeTree', 'Path.removeTree')
def removeTree(path, top=True):
Path(path).removeTree(top)
@deprecated_by('utils.removeFile', 'Path.remove')
def removeFile(filename):
Path(filename).remove()
@deprecated_by('utils.mtime', 'Path.mtime')
def mtime(fn):
return os.stat(fn).st_mtime
@deprecated_by('utils.listDirs', 'Path.dirs')
def listDirs(path):
return Path(path).dirs()
@deprecated_by('utils.listFiles', 'Path.files')
def listFiles(path):
return Path(path).files()
@deprecated_by('utils.splitFilename', 'Path')
def splitFilename(path, *args, **kargs):
p = Path(path)
return p.parent, p.stem, p.suffix
@deprecated_by('utils.listTree', 'Path.listTree')
def listTree(path, *args, **kargs):
return Path(path).listTree(*args, **kargs)
@deprecated_by('utils.tempName', 'Path.TempFile')
def tempName(*args, **kargs):
return tempfile.mkstemp(*args, **kargs)[1]
@deprecated_by('utils.changeExt', 'Path.with_suffix')
def changeExt(path, ext, accept_ext=None, reject_ext=None):
p = Path(path)
oldext = p.suffix
if ((accept_ext and oldext not in accept_ext)
or (reject_ext and oldext in reject_ext)):
return str(p) + ext
else:
return str(p.with_suffix(ext))
@deprecated_by('utils.normalizeFileType', 'Path.ftype')
def normalizeFileType(ftype):
return ftype.lower().lstrip('.')
@deprecated_by('utils.fileTypeFromExt', 'Path.ftype or Path.filetype')
def fileTypeFromExt(fname):
return Path(fname).filetype()
@deprecated_by('utils.fileTypeComprFromExt', 'Path.ftype_compr')
def fileTypeComprFromExt(fname):
return Path(fname).ftype_compr()
@deprecated_by('utils.fileSize', 'Path.size')
def fileSize(fn):
return Path(fn).size
#### Removed ####
# tildeExpand = os.path.expanduser
# splitExt: replaced with fileSuffix
# listDir: was only used in listDirs & listFiles
# prefixFiles: use: [ prefix / f for f in files ]
# unPrefixFiles: use: [ f.relative_to(prefix) for f in files ]
# fileName: use: dir / (name+ext)
# fileSuffix: use Path.filetype
# currentScript
### End
