def add_history(self, filename):
"""
Add new history tab
Slot for add_history signal emitted by shell instance
"""
filename = encoding.to_unicode_from_fs(filename)
if filename in self.filenames:
return
editor = codeeditor.CodeEditor(self)
if osp.splitext(filename)[1] == '.py':
language = 'py'
else:
language = 'bat'
editor.setup_editor(linenumbers=False,
language=language,
scrollflagarea=False)
editor.focus_changed.connect(lambda: self.focus_changed.emit())
editor.setReadOnly(True)
color_scheme = self.get_color_scheme()
editor.set_font(self.get_plugin_font(), color_scheme)
editor.toggle_wrap_mode(self.get_option('wrap'))
text, _ = encoding.read(filename)
editor.set_text(text)
editor.set_cursor_position('eof')
self.editors.append(editor)
self.filenames.append(filename)
index = self.tabwidget.addTab(editor, osp.basename(filename))
self.find_widget.set_editor(editor)
self.tabwidget.setTabToolTip(index, filename)
self.tabwidget.setCurrentIndex(index)
def get_filename_text(self, filename):
"""
Read and return content from filename.
Parameters
----------
filename: str
The file path to read.
Returns
-------
str
Content of the filename.
"""
# Avoid a possible error when reading the history file
try:
text, _ = encoding.read(filename)
except (IOError, OSError):
text = "# Previous history could not be read from disk, sorry\n\n"
text = normalize_eols(text)
linebreaks = [m.start() for m in re.finditer('\n', text)]
if len(linebreaks) > MAX_LINES:
text = text[linebreaks[-MAX_LINES - 1] + 1:]
# Avoid an error when trying to write the trimmed text to disk.
# See spyder-ide/spyder#9093.
try:
encoding.write(text, filename)
except (IOError, OSError):
pass
return text
def add_history(self, filename, color_scheme, font, wrap):
"""
Add new history tab.
Args:
filename (str): file to be loaded in a new tab.
"""
filename = encoding.to_unicode_from_fs(filename)
if filename in self.filenames:
return
editor = codeeditor.CodeEditor(self)
if osp.splitext(filename)[1] == '.py':
language = 'py'
else:
language = 'bat'
editor.setup_editor(linenumbers=False,
language=language,
scrollflagarea=False,
show_class_func_dropdown=False)
editor.focus_changed.connect(lambda: self.focus_changed.emit())
editor.setReadOnly(True)
editor.set_font(font, color_scheme)
editor.toggle_wrap_mode(wrap)
text, _ = encoding.read(filename)
editor.set_text(text)
editor.set_cursor_position('eof')
self.editors.append(editor)
self.filenames.append(filename)
index = self.tabwidget.addTab(editor, osp.basename(filename))
self.find_widget.set_editor(editor)
self.tabwidget.setTabToolTip(index, filename)
self.tabwidget.setCurrentIndex(index)
def add_history(self, filename):
"""
Add new history tab
Slot for add_history signal emitted by shell instance
"""
filename = encoding.to_unicode_from_fs(filename)
if filename in self.filenames:
return
editor = codeeditor.CodeEditor(self)
if osp.splitext(filename)[1] == ".py":
language = "py"
else:
language = "bat"
editor.setup_editor(linenumbers=False, language=language, scrollflagarea=False)
editor.focus_changed.connect(lambda: self.focus_changed.emit())
editor.setReadOnly(True)
color_scheme = self.get_color_scheme()
editor.set_font(self.get_plugin_font(), color_scheme)
editor.toggle_wrap_mode(self.get_option("wrap"))
text, _ = encoding.read(filename)
editor.set_text(text)
editor.set_cursor_position("eof")
self.editors.append(editor)
self.filenames.append(filename)
index = self.tabwidget.addTab(editor, osp.basename(filename))
self.find_widget.set_editor(editor)
self.tabwidget.setTabToolTip(index, filename)
self.tabwidget.setCurrentIndex(index)
def add_history(self, filename):
"""
Add new history tab
Slot for add_history signal emitted by shell instance
"""
filename = encoding.to_unicode_from_fs(filename)
if filename in self.filenames:
return
editor = codeeditor.CodeEditor(self)
if osp.splitext(filename)[1] == '.py':
language = 'py'
else:
language = 'bat'
editor.setup_editor(linenumbers=self.get_option('line_numbers'),
language=language,
scrollflagarea=False)
editor.focus_changed.connect(lambda: self.focus_changed.emit())
editor.setReadOnly(True)
color_scheme = self.get_color_scheme()
editor.set_font(self.get_font(), color_scheme)
editor.toggle_wrap_mode(self.get_option('wrap'))
# Avoid a possible error when reading the history file
try:
text, _ = encoding.read(filename)
except (IOError, OSError):
text = "# Previous history could not be read from disk, sorry\n\n"
text = normalize_eols(text)
linebreaks = [m.start() for m in re.finditer('\n', text)]
maxNline = self.get_option('max_entries')
if len(linebreaks) > maxNline:
text = text[linebreaks[-maxNline - 1] + 1:]
# Avoid an error when trying to write the trimmed text to
# disk.
# See issue 9093
try:
encoding.write(text, filename)
except (IOError, OSError):
pass
editor.set_text(text)
editor.set_cursor_position('eof')
self.editors.append(editor)
self.filenames.append(filename)
index = self.tabwidget.addTab(editor, osp.basename(filename))
self.find_widget.set_editor(editor)
self.tabwidget.setTabToolTip(index, filename)
self.tabwidget.setCurrentIndex(index)
def add_history(self, filename):
"""
Add new history tab
Slot for add_history signal emitted by shell instance
"""
filename = encoding.to_unicode_from_fs(filename)
if filename in self.filenames:
return
editor = codeeditor.CodeEditor(self)
if osp.splitext(filename)[1] == '.py':
language = 'py'
else:
language = 'bat'
editor.setup_editor(linenumbers=self.get_option('line_numbers'),
language=language,
scrollflagarea=False)
editor.focus_changed.connect(lambda: self.focus_changed.emit())
editor.setReadOnly(True)
color_scheme = self.get_color_scheme()
editor.set_font( self.get_plugin_font(), color_scheme )
editor.toggle_wrap_mode( self.get_option('wrap') )
# Avoid a possible error when reading the history file
try:
text, _ = encoding.read(filename)
except (IOError, OSError):
text = "# Previous history could not be read from disk, sorry\n\n"
text = normalize_eols(text)
linebreaks = [m.start() for m in re.finditer('\n', text)]
maxNline = self.get_option('max_entries')
if len(linebreaks) > maxNline:
text = text[linebreaks[-maxNline - 1] + 1:]
# Avoid an error when trying to write the trimmed text to
# disk.
# See issue 9093
try:
encoding.write(text, filename)
except (IOError, OSError):
pass
editor.set_text(text)
editor.set_cursor_position('eof')
self.editors.append(editor)
self.filenames.append(filename)
index = self.tabwidget.addTab(editor, osp.basename(filename))
self.find_widget.set_editor(editor)
self.tabwidget.setTabToolTip(index, filename)
self.tabwidget.setCurrentIndex(index)
def load_and_translate(self,
sbmlfile,
pythonfile,
editor,
set_current=True):
"""
Read filename as combine archive, unzip, translate, reconstitute in
Python, and create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
widgeteditor = editor.editorstacks[0]
sbmlfile = str(sbmlfile)
widgeteditor.starting_long_process.emit(_("Loading %s...") % sbmlfile)
text, enc = encoding.read(sbmlfile)
sbmlstr = te.readFromFile(sbmlfile)
try:
transtext = str(te.sbmlToAntimony(sbmlstr))
except Exception as e:
transtext = """*********************WARNING*********************
Failed to translate the SBML model to Antimony string.
Please check that the SBML file is valid.
*********************WARNING*********************"""
transtext = transtext + "\n\n" + str(e)
text = "import tellurium as te\n\nr = te.loada('''\n" + transtext + "''')"
finfo = widgeteditor.create_new_editor(pythonfile,
enc,
text,
set_current,
new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
widgeteditor.ending_long_process.emit("")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(
self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name, QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, sbmlfile
def handle_get_file_code(self, filename, save_all=True):
"""
Return the bytes that compose the file.
Bytes are returned instead of str to support non utf-8 files.
"""
editorstack = self.get_editorstack()
if save_all and CONF.get('editor', 'save_all_before_run', True):
editorstack.save_all(save_new_files=False)
editor = self.get_editor(filename)
if editor is None:
# Load it from file instead
text, _enc = encoding.read(filename)
return text
return editor.toPlainText()
def get_file_language(filename, text=None):
"""Get file language from filename"""
ext = osp.splitext(filename)[1]
if ext.startswith('.'):
ext = ext[1:] # file extension with leading dot
language = ext
if not ext:
if text is None:
text, _enc = encoding.read(filename)
for line in text.splitlines():
if not line.strip():
continue
if line.startswith('#!'):
shebang = line[2:]
if 'python' in shebang:
language = 'python'
else:
break
return language
def import_data(self, filenames=None):
"""Import data from text file."""
title = _("Import data")
if filenames is None:
if self.filename is None:
basedir = getcwd_or_home()
else:
basedir = osp.dirname(self.filename)
filenames, _selfilter = getopenfilenames(self, title, basedir,
iofunctions.load_filters)
if not filenames:
return
elif is_text_string(filenames):
filenames = [filenames]
for filename in filenames:
self.filename = to_text_string(filename)
if os.name == "nt":
self.filename = remove_backslashes(self.filename)
ext = osp.splitext(self.filename)[1].lower()
if ext not in iofunctions.load_funcs:
buttons = QMessageBox.Yes | QMessageBox.Cancel
answer = QMessageBox.question(
self, title,
_("<b>Unsupported file extension '%s'</b><br><br>"
"Would you like to import it anyway "
"(by selecting a known file format)?") % ext, buttons)
if answer == QMessageBox.Cancel:
return
formats = list(iofunctions.load_extensions.keys())
item, ok = QInputDialog.getItem(self, title,
_('Open file as:'), formats, 0,
False)
if ok:
ext = iofunctions.load_extensions[to_text_string(item)]
else:
return
load_func = iofunctions.load_funcs[ext]
# 'import_wizard' (self.setup_io)
if is_text_string(load_func):
# Import data with import wizard
error_message = None
try:
text, _encoding = encoding.read(self.filename)
base_name = osp.basename(self.filename)
editor = ImportWizard(
self,
text,
title=base_name,
varname=fix_reference_name(base_name))
if editor.exec_():
var_name, clip_data = editor.get_data()
self.editor.new_value(var_name, clip_data)
except Exception as error:
error_message = str(error)
else:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
QApplication.processEvents()
error_message = self.shellwidget.load_data(self.filename, ext)
QApplication.restoreOverrideCursor()
QApplication.processEvents()
if error_message is not None:
QMessageBox.critical(
self, title,
_("<b>Unable to load '%s'</b>"
"<br><br>"
"The error message was:<br>%s") %
(self.filename, error_message))
self.refresh_table()
def import_data(self, filenames=None):
"""Import data from text file."""
title = _("Import data")
if filenames is None:
if self.filename is None:
basedir = getcwd_or_home()
else:
basedir = osp.dirname(self.filename)
filenames, _selfilter = getopenfilenames(self, title, basedir,
iofunctions.load_filters)
if not filenames:
return
elif is_text_string(filenames):
filenames = [filenames]
for filename in filenames:
self.filename = to_text_string(filename)
ext = osp.splitext(self.filename)[1].lower()
if ext not in iofunctions.load_funcs:
buttons = QMessageBox.Yes | QMessageBox.Cancel
answer = QMessageBox.question(self, title,
_("<b>Unsupported file extension '%s'</b><br><br>"
"Would you like to import it anyway "
"(by selecting a known file format)?"
) % ext, buttons)
if answer == QMessageBox.Cancel:
return
formats = list(iofunctions.load_extensions.keys())
item, ok = QInputDialog.getItem(self, title,
_('Open file as:'),
formats, 0, False)
if ok:
ext = iofunctions.load_extensions[to_text_string(item)]
else:
return
load_func = iofunctions.load_funcs[ext]
# 'import_wizard' (self.setup_io)
if is_text_string(load_func):
# Import data with import wizard
error_message = None
try:
text, _encoding = encoding.read(self.filename)
base_name = osp.basename(self.filename)
editor = ImportWizard(self, text, title=base_name,
varname=fix_reference_name(base_name))
if editor.exec_():
var_name, clip_data = editor.get_data()
self.editor.new_value(var_name, clip_data)
except Exception as error:
error_message = str(error)
else:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
QApplication.processEvents()
error_message = self.shellwidget.load_data(self.filename, ext)
self.shellwidget._kernel_reply = None
QApplication.restoreOverrideCursor()
QApplication.processEvents()
if error_message is not None:
QMessageBox.critical(self, title,
_("<b>Unable to load '%s'</b>"
"<br><br>Error message:<br>%s"
) % (self.filename, error_message))
self.refresh_table()
def load_and_translate(self,
inputfile,
pythonfile,
editor,
action,
set_current=True):
"""
If the input is COMBINE archive, read filename as combine archive,
unzip, translate, reconstitute in Python or PhrasedML, and create an
editor instance and return it
If the input is SED-ML file, read filename as SED-ML file, translate
it to Python, and create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
inputfile = str(inputfile)
text, enc = encoding.read(inputfile)
if action == 'c2p':
fformat = '.py'
text = Translatecombine2P(inputfile)
zipextloctemp, sbmlloclisttemp, sedmlloclisttemp = manifestsearch(
inputfile)
elif action == 'c2pwp':
fformat = '_phrasedml.py'
text = Translatecombine2WP(inputfile)
zipextloctemp, sbmlloclisttemp, sedmlloclisttemp = manifestsearch(
inputfile)
elif action == 's2p':
fname = os.path.basename(inputfile)
temp = '"End of code generated by Import SED-ML plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + fname + '"\n\n'
text = te.sedmlToPython(inputfile) + temp
else:
fname = os.path.basename(inputfile)
temp = '"End of code generated by Import SED-ML with PhrasedML plugin ' + time.strftime(
'%m/%d/%Y') + '"\n"Extracted from ' + fname + '"'
text = "import tellurium as te\n\nphrasedmlStr = '''" + pl.convertFile(
inputfile
) + "'''\n\nte.executeSEDML(te.sedml.tephrasedml.phrasedml.convertString(phrasedmlStr))\n\n" + temp
if action == 'c2p' or action == 'c2pwp':
for i in range(len(text)):
widgeteditor = editor.editorstacks[0]
widgeteditor.starting_long_process.emit(
_("Loading %s...") % inputfile)
sedmlfname = os.path.basename(sedmlloclisttemp[i])
finfo = widgeteditor.create_new_editor(
os.path.splitext(sedmlfname)[0] + fformat,
enc,
text[i],
set_current,
new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
widgeteditor.ending_long_process.emit("")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text[i]):
if action == 'c2p':
name = os.path.basename(
os.path.splitext(sedmlfname)[0] + fformat)
else:
name = os.path.basename(pythonfile[:-3] + fformat)
QMessageBox.warning(
self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name, QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
else:
widgeteditor = editor.editorstacks[0]
widgeteditor.starting_long_process.emit(
_("Loading %s...") % inputfile)
finfo = widgeteditor.create_new_editor(pythonfile,
enc,
text,
set_current,
new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
widgeteditor.ending_long_process.emit("")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(
self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name, QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, inputfile
def import_data(self, filenames=None):
"""Import data from text file"""
title = _("Import data")
if filenames is None:
if self.filename is None:
basedir = getcwd()
else:
basedir = osp.dirname(self.filename)
filenames, _selfilter = getopenfilenames(self, title, basedir,
iofunctions.load_filters)
if not filenames:
return
elif is_text_string(filenames):
filenames = [filenames]
for filename in filenames:
self.filename = to_text_string(filename)
ext = osp.splitext(self.filename)[1].lower()
if ext not in iofunctions.load_funcs:
buttons = QMessageBox.Yes | QMessageBox.Cancel
answer = QMessageBox.question(
self, title,
_("<b>Unsupported file extension '%s'</b><br><br>"
"Would you like to import it anyway "
"(by selecting a known file format)?") % ext, buttons)
if answer == QMessageBox.Cancel:
return
formats = list(iofunctions.load_extensions.keys())
item, ok = QInputDialog.getItem(self, title,
_('Open file as:'), formats, 0,
False)
if ok:
ext = iofunctions.load_extensions[to_text_string(item)]
else:
return
load_func = iofunctions.load_funcs[ext]
# 'import_wizard' (self.setup_io)
if is_text_string(load_func):
# Import data with import wizard
error_message = None
try:
text, _encoding = encoding.read(self.filename)
if self.is_internal_shell:
self.editor.import_from_string(text)
else:
base_name = osp.basename(self.filename)
editor = ImportWizard(
self,
text,
title=base_name,
varname=fix_reference_name(base_name))
if editor.exec_():
var_name, clip_data = editor.get_data()
monitor_set_global(self._get_sock(), var_name,
clip_data)
except Exception as error:
error_message = str(error)
else:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
QApplication.processEvents()
if self.is_internal_shell:
namespace, error_message = load_func(self.filename)
interpreter = self.shellwidget.interpreter
for key in list(namespace.keys()):
new_key = fix_reference_name(
key, blacklist=list(interpreter.namespace.keys()))
if new_key != key:
namespace[new_key] = namespace.pop(key)
if error_message is None:
interpreter.namespace.update(namespace)
else:
error_message = monitor_load_globals(
self._get_sock(), self.filename, ext)
QApplication.restoreOverrideCursor()
QApplication.processEvents()
if error_message is not None:
QMessageBox.critical(
self, title,
_("<b>Unable to load '%s'</b>"
"<br><br>Error message:<br>%s") %
(self.filename, error_message))
self.refresh_table()
