My code is
from geopandas.tools import sjoin
ref_bts_adm = sjoin(Airport, ref_adm, how='left', op = 'within')
The error message
--------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-10-5c31e9843a8a> in <module>
1 from geopandas.tools import sjoin
----> 2 ref_bts_adm = sjoin(Airport, ref_adm, how='left', op = 'within')
~/.local/lib/python3.6/site-packages/geopandas/tools/sjoin.py in sjoin(left_df, right_df, how, op, lsuffix, rsuffix)
87 _basic_checks(left_df, right_df, how, lsuffix, rsuffix)
88
---> 89 indices = _geom_predicate_query(left_df, right_df, op)
90
91 joined = _frame_join(indices, left_df, right_df, how, lsuffix, rsuffix)
~/.local/lib/python3.6/site-packages/geopandas/tools/sjoin.py in _geom_predicate_query(left_df, right_df, op)
171 # see discussion at https://github.com/geopandas/geopandas/pull/1421
172 predicate = "contains"
--> 173 sindex = left_df.sindex
174 input_geoms = right_df.geometry
175 else:
~/.local/lib/python3.6/site-packages/geopandas/base.py in sindex(self)
2628 [2]])
2629 """
-> 2630 return self.geometry.values.sindex
2631
2632 #property
~/.local/lib/python3.6/site-packages/geopandas/array.py in sindex(self)
307 def sindex(self):
308 if self._sindex is None:
--> 309 self._sindex = _get_sindex_class()(self.data)
310 return self._sindex
311
~/.local/lib/python3.6/site-packages/geopandas/sindex.py in _get_sindex_class()
20 return RTreeIndex
21 raise ImportError(
---> 22 "Spatial indexes require either `rtree` or `pygeos`. "
23 "See installation instructions at https://geopandas.org/install.html"
24 )
ImportError: Spatial indexes require either `rtree` or `pygeos`. See installation instructions at https://geopandas.org/install.html
Basically I have similar error with this
ImportError: Spatial indexes require either `rtree` or `pygeos` in geopanda but rtree is installed
But I don't have sudo right
I had a similar issue and solved it by installing libspatialindex via spack, e.g., spack install libspatialindex (note: this installs the library in your homedir and does not require sudo privileges). Then you can pip install pygeos and rtree, as indicated in the other answers.
Related
The code below is triggering a AttributeError: can't set attribute. I'm still new to programming so am having a difficult time figuring out why this error is occurring. Any help is appreciated.
import cimcb_lite as cb
cv = cb.cross_val.kfold(model=cb.model.PLS_SIMPLS,X=XTknn,
Y=Ytrain,
param_dict={'n_components': [1,2,3,4,5]},
folds=5,
bootnum=100)
cv.run()
seeing this error
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/var/folders/rs/f6nsd1894354_821jj157jnr0000gn/T/ipykernel_30013/1292624611.py in <module>
8
9 # run the cross validation
---> 10 cv.run()
11
/opt/anaconda3/lib/python3.9/site-packages/cimcb_lite/cross_val/kfold.py in run(self)
82 def run(self):
83 """Runs all functions prior to plot."""
---> 84 self.calc_ypred()
85 self.calc_stats()
86 if self.bootnum > 1:
/opt/anaconda3/lib/python3.9/site-packages/cimcb_lite/cross_val/kfold.py in calc_ypred(self)
55 model_i = self.model(**params_i)
56 # Full
---> 57 model_i.train(self.X, self.Y)
58 ypred_full_i = model_i.test(self.X)
59 self.ypred_full.append(ypred_full_i)
/opt/anaconda3/lib/python3.9/site-packages/cimcb_lite/model/PLS_SIMPLS.py in train(self, X, Y)
77 # Calculates and store attributes of PLS SIMPLS
78 Xscores, Yscores, Xloadings, Yloadings, Weights, Beta = self.pls_simpls(X, Y, ncomp=self.n_component)
---> 79 self.model.x_scores_ = Xscores
80 self.model.y_scores_ = Yscores
81 self.model.x_loadings_ = Xloadings
AttributeError: can't set attribute
I want to edit a tree that I got from BEAST2 treeannotator in nexus-format.
Usually I use the module Phylo from Biopython for such work but Phylo.read(r"filename.tree", "nexus") gave me the next exception:
---------------------------------------------------------------------------
NexusError Traceback (most recent call last)
Input In [29], in <cell line: 1>()
----> 1 Phylo.read(r"filename.tree", "nexus")
File ~\miniconda3\lib\site-packages\Bio\Phylo\_io.py:60, in read(file, format, **kwargs)
58 try:
59 tree_gen = parse(file, format, **kwargs)
---> 60 tree = next(tree_gen)
61 except StopIteration:
62 raise ValueError("There are no trees in this file.") from None
File ~\miniconda3\lib\site-packages\Bio\Phylo\_io.py:49, in parse(file, format, **kwargs)
34 """Parse a file iteratively, and yield each of the trees it contains.
35
36 If a file only contains one tree, this still returns an iterable object that
(...)
46
47 """
48 with File.as_handle(file) as fp:
---> 49 yield from getattr(supported_formats[format], "parse")(fp, **kwargs)
File ~\miniconda3\lib\site-packages\Bio\Phylo\NexusIO.py:40, in parse(handle)
32 def parse(handle):
33 """Parse the trees in a Nexus file.
34
35 Uses the old Nexus.Trees parser to extract the trees, converts them back to
(...)
38 eventually change Nexus to use the new NewickIO parser directly.)
39 """
---> 40 nex = Nexus.Nexus(handle)
42 # NB: Once Nexus.Trees is modified to use Tree.Newick objects, do this:
43 # return iter(nex.trees)
44 # Until then, convert the Nexus.Trees.Tree object hierarchy:
45 def node2clade(nxtree, node):
File ~\miniconda3\lib\site-packages\Bio\Nexus\Nexus.py:668, in Nexus.__init__(self, input)
665 self.options["gapmode"] = "missing"
667 if input:
--> 668 self.read(input)
669 else:
670 self.read(DEFAULTNEXUS)
File ~\miniconda3\lib\site-packages\Bio\Nexus\Nexus.py:718, in Nexus.read(self, input)
716 break
717 if title in KNOWN_NEXUS_BLOCKS:
--> 718 self._parse_nexus_block(title, contents)
719 else:
720 self._unknown_nexus_block(title, contents)
File ~\miniconda3\lib\site-packages\Bio\Nexus\Nexus.py:759, in Nexus._parse_nexus_block(self, title, contents)
757 for line in block.commandlines:
758 try:
--> 759 getattr(self, "_" + line.command)(line.options)
760 except AttributeError:
761 raise NexusError("Unknown command: %s " % line.command) from None
File ~\miniconda3\lib\site-packages\Bio\Nexus\Nexus.py:1144, in Nexus._translate(self, options)
1142 break
1143 elif c != ",":
-> 1144 raise NexusError("Missing ',' in line %s." % options)
1145 except NexusError:
1146 raise
NexusError: Missing ',' in line 1 AB298157.1_2015_-7.9133750332192605_114.8086828279248, 2 AB298158.1_2007_-8.41698974207…
Using Nexus.read(Nexus(), input=r"filename.tree") gave the same result. Please could anyone help with this? I cannot understand the reason of this error because nexus file looks correct.
The reason is that Biopython cannot read nexus trees with links, constituent from translations & a newick tree. So it is required previously to convert this to the form with full names into the tree (as hereinbelow).
Begin
tree TREE1 = (((your,tree),(in,(the, newick))),format);
End;
P.S. It is allowed in the newick format to surround the label with quotes, & some programmes or scripts add them to those names that have ambiguous characters. But it can lead to exceptions during the following phylogenetic analysis, for instance, in BEAST. I wish you would be careful with this.
I installed pynput module (version 1.7.4) using this command: pip3 install pynput
I tried to import the module in my Jupyter-lab, which always ended up a failure. The error message looks like this:
AttributeError: dlsym(0x7f90f7d0c310, PyObjCObject_New): symbol not found
I tried to find previous questions but could not find one that could help me solve this issue. If someone can help me with dealing with this issue, that would be highly appreciated.
Just in case it would be necessary to figure out my issue, the entire error message is attached below:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/var/folders/l3/gg_2y0zx4zz2rqytp5sctpy80000gn/T/ipykernel_64397/3885633262.py in <module>
----> 1 import pynput
~/opt/anaconda3/envs/GE/lib/python3.9/site-packages/pynput/__init__.py in <module>
38
39
---> 40 from . import keyboard
41 from . import mouse
~/opt/anaconda3/envs/GE/lib/python3.9/site-packages/pynput/keyboard/__init__.py in <module>
29
30
---> 31 backend = backend(__name__)
32 KeyCode = backend.KeyCode
33 Key = backend.Key
~/opt/anaconda3/envs/GE/lib/python3.9/site-packages/pynput/_util/__init__.py in backend(package)
68 for module in modules:
69 try:
---> 70 return importlib.import_module('._' + module, package)
71 except ImportError as e:
72 errors.append(e)
~/opt/anaconda3/envs/GE/lib/python3.9/importlib/__init__.py in import_module(name, package)
125 break
126 level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
128
129
~/opt/anaconda3/envs/GE/lib/python3.9/site-packages/pynput/keyboard/_darwin.py in <module>
49 NSSystemDefined)
50
---> 51 from pynput._util.darwin import (
52 get_unicode_to_keycode_map,
53 keycode_context,
~/opt/anaconda3/envs/GE/lib/python3.9/site-packages/pynput/_util/darwin.py in <module>
58 OBJC = ctypes.PyDLL(objc._objc.__file__)
59
---> 60 OBJC.PyObjCObject_New.restype = ctypes.py_object
61 OBJC.PyObjCObject_New.argtypes = [ctypes.c_void_p, ctypes.c_int, ctypes.c_int]
62
~/opt/anaconda3/envs/GE/lib/python3.9/ctypes/__init__.py in __getattr__(self, name)
393 if name.startswith('__') and name.endswith('__'):
394 raise AttributeError(name)
--> 395 func = self.__getitem__(name)
396 setattr(self, name, func)
397 return func
~/opt/anaconda3/envs/GE/lib/python3.9/ctypes/__init__.py in __getitem__(self, name_or_ordinal)
398
399 def __getitem__(self, name_or_ordinal):
--> 400 func = self._FuncPtr((name_or_ordinal, self))
401 if not isinstance(name_or_ordinal, int):
402 func.__name__ = name_or_ordinal
AttributeError: dlsym(0x7f90f7d0c310, PyObjCObject_New): symbol not found
https://github.com/moses-palmer/pynput/issues/420
The latest Pyobjc breaks pynput. Downgrading it to 7.3 fixes this issue.
I'm new to Anaconda. I tried to execute Pytorch Adversarial Neural Network in anaconda. It shows some error that I have no clue. Here is the code that downloads dataset
# MNIST Test dataset and dataloader declaration
test_loader = torch.utils.data.DataLoader(datasets.MNIST('../data', train=False, download=True, transform=transforms.Compose([
transforms.ToTensor(),])),batch_size=1, shuffle=True)
This is the error message I got :
PermissionError Traceback (most recent call last)
<ipython-input-4-59310f6a37f8> in <module>
41
42 # MNIST Test dataset and dataloader declaration
43 test_loader = torch.utils.data.DataLoader(datasets.MNIST('../data', train=False, download=True, transform=transforms.Compose([transforms.ToTensor(),])),batch_size=1, shuffle=True)
44
45 # Define what device we are using
~\anaconda3\lib\site-packages\torchvision\datasets\mnist.py in __init__(self, root,
train,
transform, target_transform, download)
77
78 if download:
79 self.download()
80
81 if not self._check_exists():
~\anaconda3\lib\site-packages\torchvision\datasets\mnist.py in download(self)
138 return
139
140 os.makedirs(self.raw_folder, exist_ok=True)
141 os.makedirs(self.processed_folder, exist_ok=True)
142
~\anaconda3\lib\os.py in makedirs(name, mode, exist_ok)
211 if head and tail and not path.exists(head):
212 try:
213 makedirs(head, exist_ok=exist_ok)
214 except FileExistsError:
215 # Defeats race condition when another thread created the path
~\anaconda3\lib\os.py in makedirs(name, mode, exist_ok)
211 if head and tail and not path.exists(head):
212 try:
213 makedirs(head, exist_ok=exist_ok)
214 except FileExistsError:
215 # Defeats race condition when another thread created the path
~\anaconda3\lib\os.py in makedirs(name, mode, exist_ok)
221 return
222 try:
223 mkdir(name, mode)
224 except OSError:
225 # Cannot rely on checking for EEXIST, since the operating system
PermissionError: [WinError 5] Access is denied: '../data' .
How about changing the '../data' to another directory, like '/Users/***/Downloads/data' or somewhere else.
I am new to using Pandas on Windows and I'm not sure what I am doing wrong here.
My data is located at 'C:\Users\me\data\lending_club\loan.csv'
path = 'C:\\Users\\me\\data\\lending_club\\loan.csv'
pd.read_csv(path)
And I get this error:
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-107-b5792b17a3c3> in <module>()
1 path = 'C:\\Users\\me\\data\\lending_club\\loan.csv'
----> 2 pd.read_csv(path)
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skipfooter, skip_footer, doublequote, delim_whitespace, as_recarray, compact_ints, use_unsigned, low_memory, buffer_lines, memory_map, float_precision)
707 skip_blank_lines=skip_blank_lines)
708
--> 709 return _read(filepath_or_buffer, kwds)
710
711 parser_f.__name__ = name
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds)
447
448 # Create the parser.
--> 449 parser = TextFileReader(filepath_or_buffer, **kwds)
450
451 if chunksize or iterator:
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in __init__(self, f, engine, **kwds)
816 self.options['has_index_names'] = kwds['has_index_names']
817
--> 818 self._make_engine(self.engine)
819
820 def close(self):
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine)
1047 def _make_engine(self, engine='c'):
1048 if engine == 'c':
-> 1049 self._engine = CParserWrapper(self.f, **self.options)
1050 else:
1051 if engine == 'python':
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in __init__(self, src, **kwds)
1693 kwds['allow_leading_cols'] = self.index_col is not False
1694
-> 1695 self._reader = parsers.TextReader(src, **kwds)
1696
1697 # XXX
pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__()
pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()
FileNotFoundError: File b'C:\\Users\\me\\data\\lending_club\\loan.csv' does not exist
EDIT:
I re-installed Anaconda and the error went away. Not sure exactly what was going on but could potentially have been related to the initial install being global vs. user specific in my second install. Thanks for the help everybody!
Just use forward slash('/') instead of backslash('\')
path = 'C:/Users/me/data/lending_club/loan.csv'
Python only access to the current folder's files.
If you want to access files from an other folder, try this :
import sys
sys.path.insert(0, 'C:/Users/myFolder')
Those lines allow your script to access an other folder. Be carrefull, you shoud use slashes /, not backslashes \