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February 27, 2023 11:06
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napari-pymeshlab error Ubuntu 20.04
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| (napari) genevieve@genevieve-G5-5500:~$ pip install napari-pymeshlab | |
| Collecting napari-pymeshlab | |
| Using cached napari_pymeshlab-0.0.5-py3-none-any.whl (27 kB) | |
| Requirement already satisfied: npe2 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from napari-pymeshlab) (0.6.2) | |
| Requirement already satisfied: numpy in ./anaconda3/envs/napari/lib/python3.10/site-packages (from napari-pymeshlab) (1.24.2) | |
| Collecting pymeshlab | |
| Downloading pymeshlab-2022.2.post2-cp310-cp310-manylinux1_x86_64.whl (56.9 MB) | |
| ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.9/56.9 MB 2.4 MB/s eta 0:00:00 | |
| Requirement already satisfied: rich in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (13.3.1) | |
| Requirement already satisfied: psygnal>=0.3.0 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (0.7.2) | |
| Requirement already satisfied: appdirs in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (1.4.4) | |
| Requirement already satisfied: pydantic in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (1.10.5) | |
| Requirement already satisfied: PyYAML in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (6.0) | |
| Requirement already satisfied: typer in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (0.4.2) | |
| Requirement already satisfied: pytomlpp in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (1.0.11) | |
| Requirement already satisfied: build in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (0.10.0) | |
| Requirement already satisfied: typing-extensions in ./anaconda3/envs/napari/lib/python3.10/site-packages (from psygnal>=0.3.0->npe2->napari-pymeshlab) (4.4.0) | |
| Requirement already satisfied: mypy-extensions in ./anaconda3/envs/napari/lib/python3.10/site-packages (from psygnal>=0.3.0->npe2->napari-pymeshlab) (1.0.0) | |
| Requirement already satisfied: tomli>=1.1.0 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from build->npe2->napari-pymeshlab) (2.0.1) | |
| Requirement already satisfied: pyproject_hooks in ./anaconda3/envs/napari/lib/python3.10/site-packages (from build->npe2->napari-pymeshlab) (1.0.0) | |
| Requirement already satisfied: packaging>=19.0 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from build->npe2->napari-pymeshlab) (23.0) | |
| Requirement already satisfied: markdown-it-py<3.0.0,>=2.1.0 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from rich->npe2->napari-pymeshlab) (2.2.0) | |
| Requirement already satisfied: pygments<3.0.0,>=2.14.0 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from rich->npe2->napari-pymeshlab) (2.14.0) | |
| Requirement already satisfied: click<9.0.0,>=7.1.1 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from typer->npe2->napari-pymeshlab) (8.1.3) | |
| Requirement already satisfied: mdurl~=0.1 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from markdown-it-py<3.0.0,>=2.1.0->rich->npe2->napari-pymeshlab) (0.1.0) | |
| Installing collected packages: pymeshlab, napari-pymeshlab | |
| Successfully installed napari-pymeshlab-0.0.5 pymeshlab-2022.2.post2 | |
| (napari) genevieve@genevieve-G5-5500:~$ ipython | |
| Python 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:20:04) [GCC 11.3.0] | |
| Type 'copyright', 'credits' or 'license' for more information | |
| IPython 8.10.0 -- An enhanced Interactive Python. Type '?' for help. | |
| In [1]: import napari | |
| In [2]: viewer = nap | |
| --------------------------------------------------------------------------- | |
| NameError Traceback (most recent call last) | |
| Cell In[2], line 1 | |
| ----> 1 viewer = nap | |
| NameError: name 'nap' is not defined | |
| In [3]: viewer = napari.Viewer() | |
| Traceback (most recent call last): | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/_command_registry.py", line 33, in resolve | |
| self.function = utils.import_python_name(self.python_name) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/utils.py", line 255, in import_python_name | |
| mod = import_module(module_name) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/importlib/__init__.py", line 126, in import_module | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| File "<frozen importlib._bootstrap>", line 1050, in _gcd_import | |
| File "<frozen importlib._bootstrap>", line 1027, in _find_and_load | |
| File "<frozen importlib._bootstrap>", line 992, in _find_and_load_unlocked | |
| File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed | |
| File "<frozen importlib._bootstrap>", line 1050, in _gcd_import | |
| File "<frozen importlib._bootstrap>", line 1027, in _find_and_load | |
| File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked | |
| File "<frozen importlib._bootstrap>", line 688, in _load_unlocked | |
| File "<frozen importlib._bootstrap_external>", line 883, in exec_module | |
| File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari_pymeshlab/__init__.py", line 5, in <module> | |
| from ._reader import get_mesh_reader, mesh_reader | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari_pymeshlab/_reader.py", line 1, in <module> | |
| import pymeshlab as ml | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/pymeshlab/__init__.py", line 11, in <module> | |
| from .pmeshlab import * | |
| ImportError: /home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/pymeshlab/lib/libQt5Xml.so.5: undefined symbol: _ZdlPvm, version Qt_5 | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py", line 1126, in _open_or_raise_error | |
| added = self._add_layers_with_plugins( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py", line 1216, in _add_layers_with_plugins | |
| layer_data, hookimpl = read_data_with_plugins( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/io.py", line 77, in read_data_with_plugins | |
| res = _npe2.read(paths, plugin, stack=stack) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/_npe2.py", line 55, in read | |
| layer_data, reader = io_utils.read_get_reader( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py", line 66, in read_get_reader | |
| return _read( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py", line 160, in _read | |
| read_func = rdr.exec(kwargs={"path": paths, "stack": stack}) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/contributions/_readers.py", line 52, in exec | |
| callable_ = super().exec(kwargs=kwargs) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/utils.py", line 62, in exec | |
| return self.get_callable(_registry)(*args, **kwargs) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/utils.py", line 72, in get_callable | |
| return _registry.get(self.command) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/_command_registry.py", line 132, in get | |
| return self._commands[id].resolve() | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/_command_registry.py", line 35, in resolve | |
| raise RuntimeError( | |
| RuntimeError: Failed to import command at 'napari_pymeshlab._reader:get_mesh_reader': /home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/pymeshlab/lib/libQt5Xml.so.5: undefined symbol: _ZdlPvm, version Qt_5 | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py", line 830, in _qt_open | |
| self.viewer.open( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py", line 1024, in open | |
| layers = self._open_or_raise_error( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py", line 1135, in _open_or_raise_error | |
| raise ReaderPluginError( | |
| napari.errors.reader_errors.ReaderPluginError: Tried opening with napari-pymeshlab, but failed. | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py", line 1191, in dropEvent | |
| self._qt_open( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py", line 838, in _qt_open | |
| handle_gui_reading( | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/dialogs/qt_reader_dialog.py", line 188, in handle_gui_reading | |
| readers = prepare_remaining_readers(paths, plugin_name, error) | |
| File "/home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/dialogs/qt_reader_dialog.py", line 243, in prepare_remaining_readers | |
| raise ReaderPluginError( | |
| napari.errors.reader_errors.ReaderPluginError: Tried to read /home/genevieve/Downloads/surface-morphometrics-example-data-20230224T062515Z-001/surface-morphometrics-example-data/morphometrics/TF1_ER.ply with plugin napari-pymeshlab, because it was associated with that file extension/because it is the only plugin capable of reading that path, but it gave an error. Try associating a different plugin or installing a different plugin for this kind of file. | |
| If you suspect this is an IPython 8.10.0 bug, please report it at: | |
| https://github.com/ipython/ipython/issues | |
| or send an email to the mailing list at ipython-dev@python.org | |
| You can print a more detailed traceback right now with "%tb", or use "%debug" | |
| to interactively debug it. | |
| Extra-detailed tracebacks for bug-reporting purposes can be enabled via: | |
| %config Application.verbose_crash=True | |
| In [4]: %tb | |
| --------------------------------------------------------------------------- | |
| ImportError Traceback (most recent call last) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/_command_registry.py:33, in CommandHandler.resolve(self) | |
| 32 try: | |
| ---> 33 self.function = utils.import_python_name(self.python_name) | |
| 34 except Exception as e: | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/utils.py:255, in import_python_name(python_name) | |
| 253 module_name, funcname = match.groups() # type: ignore [union-attr] | |
| --> 255 mod = import_module(module_name) | |
| 256 return getattr(mod, funcname) | |
| File ~/anaconda3/envs/napari/lib/python3.10/importlib/__init__.py:126, in import_module(name, package) | |
| 125 level += 1 | |
| --> 126 return _bootstrap._gcd_import(name[level:], package, level) | |
| File <frozen importlib._bootstrap>:1050, in _gcd_import(name, package, level) | |
| File <frozen importlib._bootstrap>:1027, in _find_and_load(name, import_) | |
| File <frozen importlib._bootstrap>:992, in _find_and_load_unlocked(name, import_) | |
| File <frozen importlib._bootstrap>:241, in _call_with_frames_removed(f, *args, **kwds) | |
| File <frozen importlib._bootstrap>:1050, in _gcd_import(name, package, level) | |
| File <frozen importlib._bootstrap>:1027, in _find_and_load(name, import_) | |
| File <frozen importlib._bootstrap>:1006, in _find_and_load_unlocked(name, import_) | |
| File <frozen importlib._bootstrap>:688, in _load_unlocked(spec) | |
| File <frozen importlib._bootstrap_external>:883, in exec_module(self, module) | |
| File <frozen importlib._bootstrap>:241, in _call_with_frames_removed(f, *args, **kwds) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari_pymeshlab/__init__.py:5 | |
| 2 __version__ = "0.0.5" | |
| ----> 5 from ._reader import get_mesh_reader, mesh_reader | |
| 6 from ._writer import write_single_surface #, write_multiple | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari_pymeshlab/_reader.py:1 | |
| ----> 1 import pymeshlab as ml | |
| 3 def get_mesh_reader(path): | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/pymeshlab/__init__.py:11 | |
| 9 os.environ['PATH'] = this_path + os.pathsep + os.environ['PATH'] | |
| ---> 11 from .pmeshlab import * | |
| 12 from .replacer import replace_pymeshlab_filter_names | |
| ImportError: /home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/pymeshlab/lib/libQt5Xml.so.5: undefined symbol: _ZdlPvm, version Qt_5 | |
| The above exception was the direct cause of the following exception: | |
| RuntimeError Traceback (most recent call last) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1126, in ViewerModel._open_or_raise_error(self, paths, kwargs, layer_type, stack) | |
| 1125 try: | |
| -> 1126 added = self._add_layers_with_plugins( | |
| 1127 paths, | |
| 1128 kwargs=kwargs, | |
| 1129 stack=stack, | |
| 1130 plugin=plugin, | |
| 1131 layer_type=layer_type, | |
| 1132 ) | |
| 1133 # plugin failed | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1216, in ViewerModel._add_layers_with_plugins(self, paths, stack, kwargs, plugin, layer_type) | |
| 1215 assert len(paths) == 1 | |
| -> 1216 layer_data, hookimpl = read_data_with_plugins( | |
| 1217 paths, plugin=plugin, stack=stack | |
| 1218 ) | |
| 1220 # glean layer names from filename. These will be used as *fallback* | |
| 1221 # names, if the plugin does not return a name kwarg in their meta dict. | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/io.py:77, in read_data_with_plugins(paths, plugin, stack) | |
| 75 hookimpl: Optional[HookImplementation] | |
| ---> 77 res = _npe2.read(paths, plugin, stack=stack) | |
| 78 if res is not None: | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/_npe2.py:55, in read(paths, plugin, stack) | |
| 54 try: | |
| ---> 55 layer_data, reader = io_utils.read_get_reader( | |
| 56 npe1_path, plugin_name=plugin | |
| 57 ) | |
| 58 return layer_data, _FakeHookimpl(reader.plugin_name) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py:66, in read_get_reader(path, plugin_name, stack) | |
| 65 new_path, new_stack = v1_to_v2(path) | |
| ---> 66 return _read( | |
| 67 new_path, plugin_name=plugin_name, return_reader=True, stack=new_stack | |
| 68 ) | |
| 69 else: | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py:160, in _read(paths, stack, plugin_name, return_reader, _pm) | |
| 159 continue | |
| --> 160 read_func = rdr.exec(kwargs={"path": paths, "stack": stack}) | |
| 161 if read_func is not None: | |
| 162 # if the reader function raises an exception here, we don't try to catch it | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/contributions/_readers.py:52, in ReaderContribution.exec(self, kwargs) | |
| 51 kwargs["path"] = v2_to_v1(kwargs["path"], stack) | |
| ---> 52 callable_ = super().exec(kwargs=kwargs) | |
| 54 if callable_ is None: # pragma: no cover | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/utils.py:62, in Executable.exec(self, args, kwargs, _registry) | |
| 61 kwargs = {} | |
| ---> 62 return self.get_callable(_registry)(*args, **kwargs) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/manifest/utils.py:72, in Executable.get_callable(self, _registry) | |
| 71 _registry = PluginManager.instance().commands | |
| ---> 72 return _registry.get(self.command) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/_command_registry.py:132, in CommandRegistry.get(self, id) | |
| 131 raise KeyError(f"command {id!r} not registered") | |
| --> 132 return self._commands[id].resolve() | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/npe2/_command_registry.py:35, in CommandHandler.resolve(self) | |
| 34 except Exception as e: | |
| ---> 35 raise RuntimeError( | |
| 36 f"Failed to import command at {self.python_name!r}: {e}" | |
| 37 ) from e | |
| 39 return self.function | |
| RuntimeError: Failed to import command at 'napari_pymeshlab._reader:get_mesh_reader': /home/genevieve/anaconda3/envs/napari/lib/python3.10/site-packages/pymeshlab/lib/libQt5Xml.so.5: undefined symbol: _ZdlPvm, version Qt_5 | |
| The above exception was the direct cause of the following exception: | |
| ReaderPluginError Traceback (most recent call last) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:830, in QtViewer._qt_open(self, filenames, stack, choose_plugin, plugin, layer_type, **kwargs) | |
| 829 try: | |
| --> 830 self.viewer.open( | |
| 831 filenames, | |
| 832 stack=stack, | |
| 833 plugin=plugin, | |
| 834 layer_type=layer_type, | |
| 835 **kwargs, | |
| 836 ) | |
| 837 except ReaderPluginError as e: | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1024, in ViewerModel.open(self, path, stack, plugin, layer_type, **kwargs) | |
| 1022 # no plugin choice was made | |
| 1023 else: | |
| -> 1024 layers = self._open_or_raise_error( | |
| 1025 _path, kwargs, layer_type, _stack | |
| 1026 ) | |
| 1027 added.extend(layers) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1135, in ViewerModel._open_or_raise_error(self, paths, kwargs, layer_type, stack) | |
| 1134 except Exception as e: | |
| -> 1135 raise ReaderPluginError( | |
| 1136 trans._( | |
| 1137 'Tried opening with {plugin}, but failed.', | |
| 1138 deferred=True, | |
| 1139 plugin=plugin, | |
| 1140 ), | |
| 1141 plugin, | |
| 1142 paths, | |
| 1143 ) from e | |
| 1144 # multiple plugins | |
| 1145 else: | |
| ReaderPluginError: Tried opening with napari-pymeshlab, but failed. | |
| The above exception was the direct cause of the following exception: | |
| ReaderPluginError Traceback (most recent call last) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:838, in QtViewer._qt_open(self, filenames, stack, choose_plugin, plugin, layer_type, **kwargs) | |
| 830 self.viewer.open( | |
| 831 filenames, | |
| 832 stack=stack, | |
| (...) | |
| 835 **kwargs, | |
| 836 ) | |
| 837 except ReaderPluginError as e: | |
| --> 838 handle_gui_reading( | |
| 839 filenames, | |
| 840 self, | |
| 841 stack, | |
| 842 e.reader_plugin, | |
| 843 e, | |
| 844 layer_type=layer_type, | |
| 845 **kwargs, | |
| 846 ) | |
| 847 except MultipleReaderError: | |
| 848 handle_gui_reading(filenames, self, stack, **kwargs) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/dialogs/qt_reader_dialog.py:188, in handle_gui_reading(paths, qt_viewer, stack, plugin_name, error, plugin_override, **kwargs) | |
| 161 """Present reader dialog to choose reader and open paths based on result. | |
| 162 | |
| 163 This function is called whenever ViewerModel._open_or_get_error returns | |
| (...) | |
| 185 Dictates whether checkbox to remember choice is unchecked by default | |
| 186 """ | |
| 187 _path = paths[0] | |
| --> 188 readers = prepare_remaining_readers(paths, plugin_name, error) | |
| 189 error_message = str(error) if error else '' | |
| 190 readerDialog = QtReaderDialog( | |
| 191 parent=qt_viewer, | |
| 192 pth=_path, | |
| (...) | |
| 195 persist_checked=not plugin_override, | |
| 196 ) | |
| File ~/anaconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/dialogs/qt_reader_dialog.py:243, in prepare_remaining_readers(paths, plugin_name, error) | |
| 241 # if there's no other readers left, raise the exception | |
| 242 if not readers and error: | |
| --> 243 raise ReaderPluginError( | |
| 244 trans._( | |
| 245 "Tried to read {path_message} with plugin {plugin}, because it was associated with that file extension/because it is the only plugin capable of reading that path, but it gave an error. Try associating a different plugin or installing a different plugin for this kind of file.", | |
| 246 path_message=f"[{paths[0]}, ...]" | |
| 247 if len(paths) > 1 | |
| 248 else paths[0], | |
| 249 plugin=plugin_name, | |
| 250 ), | |
| 251 plugin_name, | |
| 252 paths, | |
| 253 ) from error | |
| 255 return readers | |
| ReaderPluginError: Tried to read /home/genevieve/Downloads/surface-morphometrics-example-data-20230224T062515Z-001/surface-morphometrics-example-data/morphometrics/TF1_ER.ply with plugin napari-pymeshlab, because it was associated with that file extension/because it is the only plugin capable of reading that path, but it gave an error. Try associating a different plugin or installing a different plugin for this kind of file. |
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