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conda-forge / geopandas-feedstock

A conda-smithy repository for geopandas.
BSD 3-Clause "New" or "Revised" License
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'Shell is not a LinearRing' with geopandas, fiona, and Mac High Sierra #31

Closed grahamanderson closed 6 years ago

grahamanderson commented 6 years ago

Hi I'm getting a 'Shell is not a LinearRing' error when using fiona and geopandas. I made a fresh vm with conda for the test below. Any help is appreciated

import geopandas as gpd
import fiona
cdf20 = gpd.read_file('./data/geo/20m-US-counties.geojson')

Gives multiple 'Shell is not a LinearRing' errors.

This below gives the same ''Shell is not a LinearRing' error:

import fiona
import shapely
from shapely.geometry import shape
c = fiona.open("./data/geo/cb_2016_us_division_20m/cb_2016_us_division_20m.shp")
pol = c.next()
shape(pol['geometry'])

__ Mac OS High Sierra (10.13.1) Python 3.62 My Conda List

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backports.functools_lru_cache 1.4                      py36_1    conda-forge
bleach                    2.0.0                    py36_0    conda-forge
boost                     1.65.1                   py36_0    conda-forge
boost-cpp                 1.65.1                        1    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.08.26           ha1e5d58_0
cairo                     1.14.6                        5    conda-forge
certifi                   2017.11.5        py36ha569be9_0
cffi                      1.11.2                   py36_0    conda-forge
chardet                   3.0.4                     <pip>
chardet                   3.0.4                    py36_0    conda-forge
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click                     6.7                      py36_0    conda-forge
click-plugins             1.0.3                    py36_0    conda-forge
cligj                     0.4.0                    py36_0    conda-forge
colormath                 2.1.1                    py36_1    conda-forge
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curl                      7.55.1                        0    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
dash                      0.19.0                    <pip>
dash-core-components      0.14.0                    <pip>
dash-html-components      0.8.0                     <pip>
dash-renderer             0.11.1                    <pip>
DateTime                  4.0.1                     <pip>
decorator                 4.1.2                    py36_0    conda-forge
descartes                 1.1.0                    py36_0    conda-forge
entrypoints               0.2.3                    py36_1    conda-forge
expat                     2.1.0                         3    conda-forge
fiona                     1.7.10                   py36_2    conda-forge
Flask                     0.12.2                    <pip>
Flask-Compress            1.4.0                     <pip>
fontconfig                2.12.1                        6    conda-forge
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gdal                      2.1.3                    py36_7    conda-forge
geocoder                  1.33.0                    <pip>
geopandas                 0.1.1                     <pip>
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icu                       58.2                          0    conda-forge
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idna                      2.6                       <pip>
intel-openmp              2018.0.0             h8158457_8
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ipython                   6.2.1                    py36_0    conda-forge
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ipython_genutils          0.2.0                    py36_0    conda-forge
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jedi                      0.10.2                   py36_0    conda-forge
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Jinja2                    2.10                      <pip>
jpeg                      9b                            2    conda-forge
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jupyter_core              4.4.0                      py_0    conda-forge
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libcxxabi                 4.0.1                hebd6815_0
libdap4                   3.18.3                        2    conda-forge
libedit                   3.1                  hb4e282d_0
libffi                    3.2.1                h475c297_4
libgdal                   2.2.2                         7    conda-forge/label/broken
libgfortran               3.0.1                h93005f0_2
libiconv                  1.15                          0    conda-forge
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libpng                    1.6.28                        2    conda-forge
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jorisvandenbossche commented 6 years ago

@grahamanderson The output of conda list is a bit different than the one you posted in https://github.com/geopandas/geopandas/issues/562#issuecomment-350042573. Did you make this fresh environment in another way?

This line seems a bit suspicous:

libgdal                   2.2.2                         7    conda-forge/label/broken

cc @ocefpaf is the above normal? (I am a bit lost with what the situation is nowadays with gdal vs libgdal)

ocefpaf commented 6 years ago

That is odd. One should not get packages from the broken label without an explicit request :confused:

grahamanderson commented 6 years ago

@jorisvandenbossche and @ocefpaf–– I've been trying a number of different installs...including the broken libgdal. I have been using conda..I could switch to miniconda and try again? Any help is appreciated. With the below install I get the below '...' is for repeating lines

import pandas as pd
import geopandas as gpd
import fiona
div20m = gpd.read_file('./data/geo/cb_2016_us_division_20m')
div20m.head()

Output:

Shell is not a LinearRing
...
IllegalArgumentException: geometries must not contain null elements

Shell is not a LinearRing
Shell is not a LinearRing
...
IllegalArgumentException: geometries must not contain null elements

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/anaconda3/envs/geotest/lib/python3.6/site-packages/IPython/core/formatters.py in __call__(self, obj)
    700                 type_pprinters=self.type_printers,
    701                 deferred_pprinters=self.deferred_printers)
--> 702             printer.pretty(obj)
    703             printer.flush()
    704             return stream.getvalue()

~/anaconda3/envs/geotest/lib/python3.6/site-packages/IPython/lib/pretty.py in pretty(self, obj)
    393                             if callable(meth):
    394                                 return meth(obj, self, cycle)
--> 395             return _default_pprint(obj, self, cycle)
    396         finally:
    397             self.end_group()

~/anaconda3/envs/geotest/lib/python3.6/site-packages/IPython/lib/pretty.py in _default_pprint(obj, p, cycle)
    508     if _safe_getattr(klass, '__repr__', None) is not object.__repr__:
    509         # A user-provided repr. Find newlines and replace them with p.break_()
--> 510         _repr_pprint(obj, p, cycle)
    511         return
    512     p.begin_group(1, '<')

~/anaconda3/envs/geotest/lib/python3.6/site-packages/IPython/lib/pretty.py in _repr_pprint(obj, p, cycle)
    699     """A pprint that just redirects to the normal repr function."""
    700     # Find newlines and replace them with p.break_()
--> 701     output = repr(obj)
    702     for idx,output_line in enumerate(output.splitlines()):
    703         if idx:

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/core/base.py in __repr__(self)
     78         Yields Bytestring in Py2, Unicode String in py3.
     79         """
---> 80         return str(self)
     81 
     82 

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/core/base.py in __str__(self)
     57 
     58         if compat.PY3:
---> 59             return self.__unicode__()
     60         return self.__bytes__()
     61 

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/core/frame.py in __unicode__(self)
    634             width = None
    635         self.to_string(buf=buf, max_rows=max_rows, max_cols=max_cols,
--> 636                        line_width=width, show_dimensions=show_dimensions)
    637 
    638         return buf.getvalue()

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/core/frame.py in to_string(self, buf, columns, col_space, header, index, na_rep, formatters, float_format, sparsify, index_names, justify, line_width, max_rows, max_cols, show_dimensions)
   1673                                            max_cols=max_cols,
   1674                                            show_dimensions=show_dimensions)
-> 1675         formatter.to_string()
   1676 
   1677         if buf is None:

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in to_string(self)
    596         else:
    597 
--> 598             strcols = self._to_str_columns()
    599             if self.line_width is None:  # no need to wrap around just print
    600                 # the whole frame

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _to_str_columns(self)
    531                 header_colwidth = max(self.col_space or 0,
    532                                       *(self.adj.len(x) for x in cheader))
--> 533                 fmt_values = self._format_col(i)
    534                 fmt_values = _make_fixed_width(fmt_values, self.justify,
    535                                                minimum=header_colwidth,

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _format_col(self, i)
    707         return format_array(values_to_format, formatter,
    708                             float_format=self.float_format, na_rep=self.na_rep,
--> 709                             space=self.col_space, decimal=self.decimal)
    710 
    711     def to_html(self, classes=None, notebook=False, border=None):

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in format_array(values, formatter, float_format, na_rep, digits, space, justify, decimal)
   1812                         space=space, justify=justify, decimal=decimal)
   1813 
-> 1814     return fmt_obj.get_result()
   1815 
   1816 

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in get_result(self)
   1832 
   1833     def get_result(self):
-> 1834         fmt_values = self._format_strings()
   1835         return _make_fixed_width(fmt_values, self.justify)
   1836 

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _format_strings(self)
   1878                 fmt_values.append(float_format(v))
   1879             else:
-> 1880                 fmt_values.append(u' {v}'.format(v=_format(v)))
   1881 
   1882         return fmt_values

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _format(x)
   1860             else:
   1861                 # object dtype
-> 1862                 return u'{x}'.format(x=formatter(x))
   1863 
   1864         vals = self.values

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in <lambda>(x)
   1847         formatter = (
   1848             self.formatter if self.formatter is not None else
-> 1849             (lambda x: pprint_thing(x, escape_chars=('\t', '\r', '\n'))))
   1850 
   1851         def _format(x):

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/printing.py in pprint_thing(thing, _nest_lvl, escape_chars, default_escapes, quote_strings, max_seq_items)
    228         result = fmt.format(thing=as_escaped_unicode(thing))
    229     else:
--> 230         result = as_escaped_unicode(thing)
    231 
    232     return compat.text_type(result)  # always unicode

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/printing.py in as_escaped_unicode(thing, escape_chars)
    191 
    192         try:
--> 193             result = compat.text_type(thing)  # we should try this first
    194         except UnicodeDecodeError:
    195             # either utf-8 or we replace errors

~/anaconda3/envs/geotest/lib/python3.6/site-packages/shapely/geometry/base.py in __str__(self)
    236 
    237     def __str__(self):
--> 238         return self.wkt
    239 
    240     # To support pickling

~/anaconda3/envs/geotest/lib/python3.6/site-packages/shapely/geometry/base.py in wkt(self, **kw)
    365     def wkt(self, **kw):
    366         """WKT representation of the geometry"""
--> 367         return WKTWriter(lgeos, **kw).write(self)
    368 
    369     @property

~/anaconda3/envs/geotest/lib/python3.6/site-packages/shapely/geos.py in write(self, geom)
    360         """Returns WKT string for geometry"""
    361         if geom is None or geom._geom is None:
--> 362             raise ValueError("Null geometry supports no operations")
    363         result = self._lgeos.GEOSWKTWriter_write(self._writer, geom._geom)
    364         text = string_at(result)

ValueError: Null geometry supports no operations

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/anaconda3/envs/geotest/lib/python3.6/site-packages/IPython/core/formatters.py in __call__(self, obj)
    343             method = get_real_method(obj, self.print_method)
    344             if method is not None:
--> 345                 return method()
    346             return None
    347         else:

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/core/frame.py in _repr_html_(self)
    667 
    668             return self.to_html(max_rows=max_rows, max_cols=max_cols,
--> 669                                 show_dimensions=show_dimensions, notebook=True)
    670         else:
    671             return None

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/core/frame.py in to_html(self, buf, columns, col_space, header, index, na_rep, formatters, float_format, sparsify, index_names, justify, bold_rows, classes, escape, max_rows, max_cols, show_dimensions, notebook, decimal, border)
   1732                                            decimal=decimal)
   1733         # TODO: a generic formatter wld b in DataFrameFormatter
-> 1734         formatter.to_html(classes=classes, notebook=notebook, border=border)
   1735 
   1736         if buf is None:

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in to_html(self, classes, notebook, border)
    732                                       border=border)
    733         if hasattr(self.buf, 'write'):
--> 734             html_renderer.write_result(self.buf)
    735         elif isinstance(self.buf, compat.string_types):
    736             with open(self.buf, 'w') as f:

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in write_result(self, buf)
   1206         indent += self.indent_delta
   1207         indent = self._write_header(indent)
-> 1208         indent = self._write_body(indent)
   1209 
   1210         self.write('</table>', indent)

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _write_body(self, indent)
   1362         fmt_values = {}
   1363         for i in range(min(len(self.columns), self.max_cols)):
-> 1364             fmt_values[i] = self.fmt._format_col(i)
   1365 
   1366         # write values

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _format_col(self, i)
    707         return format_array(values_to_format, formatter,
    708                             float_format=self.float_format, na_rep=self.na_rep,
--> 709                             space=self.col_space, decimal=self.decimal)
    710 
    711     def to_html(self, classes=None, notebook=False, border=None):

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in format_array(values, formatter, float_format, na_rep, digits, space, justify, decimal)
   1812                         space=space, justify=justify, decimal=decimal)
   1813 
-> 1814     return fmt_obj.get_result()
   1815 
   1816 

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in get_result(self)
   1832 
   1833     def get_result(self):
-> 1834         fmt_values = self._format_strings()
   1835         return _make_fixed_width(fmt_values, self.justify)
   1836 

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _format_strings(self)
   1878                 fmt_values.append(float_format(v))
   1879             else:
-> 1880                 fmt_values.append(u' {v}'.format(v=_format(v)))
   1881 
   1882         return fmt_values

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in _format(x)
   1860             else:
   1861                 # object dtype
-> 1862                 return u'{x}'.format(x=formatter(x))
   1863 
   1864         vals = self.values

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/format.py in <lambda>(x)
   1847         formatter = (
   1848             self.formatter if self.formatter is not None else
-> 1849             (lambda x: pprint_thing(x, escape_chars=('\t', '\r', '\n'))))
   1850 
   1851         def _format(x):

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/printing.py in pprint_thing(thing, _nest_lvl, escape_chars, default_escapes, quote_strings, max_seq_items)
    228         result = fmt.format(thing=as_escaped_unicode(thing))
    229     else:
--> 230         result = as_escaped_unicode(thing)
    231 
    232     return compat.text_type(result)  # always unicode

~/anaconda3/envs/geotest/lib/python3.6/site-packages/pandas/io/formats/printing.py in as_escaped_unicode(thing, escape_chars)
    191 
    192         try:
--> 193             result = compat.text_type(thing)  # we should try this first
    194         except UnicodeDecodeError:
    195             # either utf-8 or we replace errors

~/anaconda3/envs/geotest/lib/python3.6/site-packages/shapely/geometry/base.py in __str__(self)
    236 
    237     def __str__(self):
--> 238         return self.wkt
    239 
    240     # To support pickling

~/anaconda3/envs/geotest/lib/python3.6/site-packages/shapely/geometry/base.py in wkt(self, **kw)
    365     def wkt(self, **kw):
    366         """WKT representation of the geometry"""
--> 367         return WKTWriter(lgeos, **kw).write(self)
    368 
    369     @property

~/anaconda3/envs/geotest/lib/python3.6/site-packages/shapely/geos.py in write(self, geom)
    360         """Returns WKT string for geometry"""
    361         if geom is None or geom._geom is None:
--> 362             raise ValueError("Null geometry supports no operations")
    363         result = self._lgeos.GEOSWKTWriter_write(self._writer, geom._geom)
    364         text = string_at(result)

ValueError: Null geometry supports no operations

Here is my current (not working) conda list

appnope                   0.1.0                    py36_0    conda-forge
backports                 1.0                      py36_1    conda-forge
backports.functools_lru_cache 1.4                      py36_1    conda-forge
bleach                    2.0.0                    py36_0    conda-forge
boost                     1.65.1                   py36_0    conda-forge
boost-cpp                 1.65.1                        1    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.11.5                     0    conda-forge
cairo                     1.14.6                        5    conda-forge
certifi                   2017.11.5                py36_0    conda-forge
click                     6.7                      py36_0    conda-forge
click-plugins             1.0.3                    py36_0    conda-forge
cligj                     0.4.0                    py36_0    conda-forge
curl                      7.55.1                        0    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
decorator                 4.1.2                    py36_0    conda-forge
descartes                 1.1.0                    py36_0    conda-forge
entrypoints               0.2.3                    py36_1    conda-forge
expat                     2.1.0                         3    conda-forge
fiona                     1.7.10                   py36_2    conda-forge
fontconfig                2.12.1                        6    conda-forge
freetype                  2.7                           2    conda-forge
freexl                    1.0.4                         0    conda-forge
gdal                      2.1.4                    py36_2    conda-forge
geopandas                 0.3.0                    py36_0    conda-forge
geos                      3.6.2                         1    conda-forge
geotiff                   1.4.2                         0    conda-forge
gettext                   0.19.8.1                      0    conda-forge
giflib                    5.1.4                         0    conda-forge
glib                      2.51.4                        0    conda-forge
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1                        1    conda-forge
html5lib                  0.999999999              py36_0    conda-forge
icu                       58.2                          0    conda-forge
intel-openmp              2018.0.0             h8158457_8
ipykernel                 4.7.0                    py36_0    conda-forge
ipython                   6.2.1                    py36_0    conda-forge
ipython_genutils          0.2.0                    py36_0    conda-forge
jedi                      0.10.2                   py36_0    conda-forge
jinja2                    2.10                     py36_0    conda-forge
jpeg                      9b                            2    conda-forge
json-c                    0.12.1                        0    conda-forge
jsonschema                2.6.0                    py36_0    conda-forge
jupyter_client            5.1.0                    py36_0    conda-forge
jupyter_contrib_core      0.3.3                    py36_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyter_nbextensions_configurator 0.2.8                    py36_0    conda-forge
kealib                    1.4.7                         4    conda-forge
krb5                      1.14.2                        0    conda-forge
libcxx                    4.0.1                h579ed51_0
libcxxabi                 4.0.1                hebd6815_0
libdap4                   3.18.3                        2    conda-forge
libffi                    3.2.1                         3    conda-forge
libgdal                   2.1.4                         8    conda-forge
libgfortran               3.0.1                h93005f0_2
libiconv                  1.15                          0    conda-forge
libkml                    1.3.0                         4    conda-forge
libnetcdf                 4.4.1.1                      10    conda-forge
libpng                    1.6.28                        2    conda-forge
libpq                     9.6.3                         0    conda-forge
libsodium                 1.0.15                        1    conda-forge
libspatialindex           1.8.5                         1    conda-forge
libspatialite             4.3.0a                       18    conda-forge
libssh2                   1.8.0                         2    conda-forge
libtiff                   4.0.7                         1    conda-forge
libxml2                   2.9.5                         2    conda-forge
markupsafe                1.0                      py36_0    conda-forge
matplotlib                2.1.0                    py36_1    conda-forge
mistune                   0.8.3                      py_0    conda-forge
mkl                       2018.0.1             hfbd8650_4
munch                     2.2.0                    py36_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py36_0    conda-forge
ncurses                   5.9                          10    conda-forge
notebook                  5.2.2                    py36_1    conda-forge
numpy                     1.13.3           py36h2cdce51_0
openjpeg                  2.1.2                         2    conda-forge
openssl                   1.0.2m                        0    conda-forge
pandas                    0.21.0                   py36_0    conda-forge
pandoc                    2.0.4                         0    conda-forge
pandocfilters             1.4.1                    py36_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.3.0                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pip                       9.0.1                    py36_0    conda-forge
pixman                    0.34.0                        1    conda-forge
poppler                   0.61.1                        1    conda-forge
poppler-data              0.4.8                         0    conda-forge
proj4                     4.9.3                         5    conda-forge
prompt_toolkit            1.0.15                   py36_0    conda-forge
psycopg2                  2.7.3.2                  py36_0    conda-forge
ptyprocess                0.5.2                    py36_0    conda-forge
pygments                  2.2.0                    py36_0    conda-forge
pyparsing                 2.2.0                    py36_0    conda-forge
pyproj                    1.9.5.1                  py36_0    conda-forge
pysal                     1.14.3                   py36_0    conda-forge
python                    3.6.3                         1    conda-forge
python-dateutil           2.6.1                    py36_0    conda-forge
pytz                      2017.3                     py_2    conda-forge
pyyaml                    3.12                     py36_1    conda-forge
pyzmq                     16.0.2                   py36_2    conda-forge
readline                  6.2                           0    conda-forge
rtree                     0.8.3                    py36_0    conda-forge
scipy                     1.0.0            py36h1de22e9_0
setuptools                38.2.4                   py36_0    conda-forge
shapely                   1.6.2                    py36_1    conda-forge
simplegeneric             0.8.1                    py36_0    conda-forge
six                       1.11.0                   py36_1    conda-forge
sqlalchemy                1.1.13                   py36_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
terminado                 0.8.1                    py36_0    conda-forge
testpath                  0.3.1                    py36_0    conda-forge
tk                        8.5.19                        2    conda-forge
tornado                   4.5.2                    py36_0    conda-forge
traitlets                 4.3.2                    py36_0    conda-forge
wcwidth                   0.1.7                    py36_0    conda-forge
webencodings              0.5                      py36_0    conda-forge
wheel                     0.30.0                     py_1    conda-forge
xerces-c                  3.2.0                         0    conda-forge
xz                        5.2.3                         0    conda-forge
yaml                      0.1.7                         0    conda-forge
yapf                      0.18.0                     py_0    conda-forge
zeromq                    4.2.1                         1    conda-forge
zlib                      1.2.11                        0    conda-forge
jorisvandenbossche commented 6 years ago

But you did try it in a clean test environment? (in that case it does not matter if your base installation comes from anaconda or miniconda)

ocefpaf commented 6 years ago

@grahamanderson only a clean env would be OK for us to debug this. First of all remove any other channel from you .condarc that is not defaults or conda-forge (even sub-channels, or labels, from like the broken one). Make sure conda-forge is on top of defaults. Then try:

conda create --yes --name TEST python=3.6 geopandas
source activate TEST
<read your file>

This works for me on Linux as expected. Closing this b/c, based on your conda list, this is not an issue with the package but with our channel configuration.

jorisvandenbossche commented 6 years ago

In the comment here https://github.com/geopandas/geopandas/issues/562#issuecomment-350042573, @grahamanderson you seem to indicate that you tested in a clean environment. If so, please indicate here. But indeed as @ocefpaf you have to be careful about the channels.

grahamanderson commented 6 years ago

My .condarc in my Home Directory is 

channels:
  - conda-forge
  - defaults
ssl_verify: true

@ocefpaf I created a new Environment TEST as you specified. I also ran the code directly in python rather than in Jupyter. The below code still gives the error below. Any help is appreciated. FYI, my install was working b/f I upgraded to High Sierra Mac and (currently Geopandas/Fiona works fine on my Ubuntu instance on Google Cloud. Perhaps, other Mac users are going through the same thing? Thankfully, I decided to upgrade my OS post deadline.

# In the terminal Python prompt
import pandas as pd
import geopandas as gpd
import fiona
div20m = gpd.read_file('./data/geo/cb_2016_us_division_20m')
div20m.head()
# Error
Shell is not a LinearRing
Shell is not a LinearRing
Shell is not a LinearRing
Shell is not a LinearRing
Shell is not a LinearRing
IllegalArgumentException: geometries must not contain null elements

My conda list with the the TEST environment is:

(TEST) robert$ conda list
# packages in environment at /Users/robert/anaconda3/envs/TEST:
#
backports                 1.0                      py36_1    conda-forge
backports.functools_lru_cache 1.4                      py36_1    conda-forge
ca-certificates           2017.11.5                     0    conda-forge
certifi                   2017.11.5                py36_0    conda-forge
click                     6.7                      py36_0    conda-forge
click-plugins             1.0.3                    py36_0    conda-forge
cligj                     0.4.0                    py36_0    conda-forge
curl                      7.55.1                        0    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
descartes                 1.1.0                    py36_0    conda-forge
expat                     2.1.0                         3    conda-forge
fiona                     1.7.10                   py36_2    conda-forge
freetype                  2.7                           2    conda-forge
freexl                    1.0.4                         0    conda-forge
gdal                      2.1.3                    py36_7    conda-forge
geopandas                 0.3.0                    py36_0    conda-forge
geos                      3.6.2                         1    conda-forge
giflib                    5.1.4                         0    conda-forge
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1                        1    conda-forge
icu                       58.2                          0    conda-forge
intel-openmp              2018.0.0             h8158457_8
jpeg                      9b                            2    conda-forge
json-c                    0.12.1                        0    conda-forge
kealib                    1.4.7                         4    conda-forge
krb5                      1.14.2                        0    conda-forge
libcxx                    4.0.1                h579ed51_0
libcxxabi                 4.0.1                hebd6815_0
libdap4                   3.18.3                        2    conda-forge
libgfortran               3.0.1                h93005f0_2
libiconv                  1.15                          0    conda-forge
libnetcdf                 4.4.1.1                      10    conda-forge
libpng                    1.6.28                        2    conda-forge
libpq                     9.6.3                         0    conda-forge
libspatialindex           1.8.5                         1    conda-forge
libspatialite             4.3.0a                       18    conda-forge
libssh2                   1.8.0                         2    conda-forge
libtiff                   4.0.9                         0    conda-forge
libxml2                   2.9.5                         2    conda-forge
matplotlib                2.1.0                    py36_1    conda-forge
mkl                       2018.0.1             hfbd8650_4
munch                     2.2.0                    py36_0    conda-forge
ncurses                   5.9                          10    conda-forge
numpy                     1.13.3           py36h2cdce51_0
openjpeg                  2.1.2                         2    conda-forge
openssl                   1.0.2m                        0    conda-forge
pandas                    0.21.0                   py36_0    conda-forge
pcre                      8.39                          0    conda-forge
pip                       9.0.1                    py36_0    conda-forge
proj4                     4.9.3                         5    conda-forge
psycopg2                  2.7.3.2                  py36_0    conda-forge
pyparsing                 2.2.0                    py36_0    conda-forge
pyproj                    1.9.5.1                  py36_0    conda-forge
pysal                     1.14.3                   py36_0    conda-forge
python                    3.6.3                         1    conda-forge
python-dateutil           2.6.1                    py36_0    conda-forge
pytz                      2017.3                     py_2    conda-forge
readline                  6.2                           0    conda-forge
rtree                     0.8.3                    py36_0    conda-forge
scipy                     1.0.0            py36h1de22e9_0
setuptools                38.2.4                   py36_0    conda-forge
shapely                   1.6.2                    py36_1    conda-forge
six                       1.11.0                   py36_1    conda-forge
sqlalchemy                1.1.13                   py36_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
tk                        8.5.19                        2    conda-forge
tornado                   4.5.2                    py36_0    conda-forge
wheel                     0.30.0                     py_1    conda-forge
xerces-c                  3.2.0                         0    conda-forge
xz                        5.2.3                         0    conda-forge
zlib                      1.2.11                        0    conda-forge
ocefpaf commented 6 years ago

In the comment here geopandas/geopandas#562 (comment)

Indeed that does look like a clean env and looks like mine. However, everything works as expected for me. Can you share you data so we can check it?

grahamanderson commented 6 years ago

absolutely :) https://www.dropbox.com/sh/h8s2ozcw0hn899l/AADHAg6hPEmw6VimMckkH5J9a?dl=0

jorisvandenbossche commented 6 years ago

We have had previous reports with a similar error message: https://github.com/geopandas/geopandas/issues/556 and https://github.com/geopandas/geopandas/issues/562, both also on mac (but don't know which version). They solved it by installing through pip .. which seems to indicate it is a conda-forge build issue with fiona / gdal or one of its dependencies

grahamanderson commented 6 years ago

so, to install and empty environment with PIP, should I ? conda create --yes --name PIP_TEST python=3.6 pip install geopandas source activate PIP_TEST

On my end, I'm not even sure how you would run geopandas without Fiona. The two seem intertwined. Perhaos, there is an alternate to fiona-gdal for opening these geo files?

ocefpaf commented 6 years ago

I don't have a Mac to test it but I'll add an extra test with @grahamanderson data on Travis-CI. Let's re-open this then.

ffaristocrat commented 6 years ago

Using the same data as above, this is the whole set of commands I've been running to the same error.

OSX El Capitan 10.11.6 Python 3.6.3

conda create --yes --name GEOTEST python=3.6
source activate GEOTEST
conda install --yes -c conda-forge --override-channels geopandas libgdal osmnx
conda remove --yes geopandas osmnx
pip install geopandas osmnx
python -c "import geopandas as gpd; div20m = gpd.read_file('./Documents/geo/cb_2016_us_division_20m.shp'); div20m.head()"

conda list

# packages in environment at /Users/civisemployee/anaconda3/envs/GEOTEST:
#
altair                    1.2.1                      py_0    conda-forge
appnope                   0.1.0                    py36_0    conda-forge
asn1crypto                0.22.0                   py36_0    conda-forge
backports                 1.0                      py36_1    conda-forge
backports.functools_lru_cache 1.4                      py36_1    conda-forge
bleach                    2.0.0                    py36_0    conda-forge
boost                     1.65.1                   py36_0    conda-forge
boost-cpp                 1.65.1                        1    conda-forge
branca                    0.2.0                      py_1    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.08.26           ha1e5d58_0  
cairo                     1.14.6                        5    conda-forge
certifi                   2017.11.5        py36ha569be9_0  
cffi                      1.11.2                   py36_0    conda-forge
chardet                   3.0.4                    py36_0    conda-forge
click                     6.7                      py36_0    conda-forge
click-plugins             1.0.3                    py36_0    conda-forge
cligj                     0.4.0                    py36_0    conda-forge
cryptography              2.1.4                    py36_0    conda-forge
curl                      7.55.1                        0    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
decorator                 4.1.2                    py36_0    conda-forge
descartes                 1.1.0                    py36_0    conda-forge
entrypoints               0.2.3                    py36_1    conda-forge
expat                     2.1.0                         3    conda-forge
fiona                     1.7.10           py36h42caba7_0  
folium                    0.5.0                      py_0    conda-forge
fontconfig                2.12.1                        6    conda-forge
freetype                  2.7                           2    conda-forge
freexl                    1.0.4                         0    conda-forge
gdal                      2.2.3                    py36_0    conda-forge
geopandas                 0.3.0                     <pip>
geopy                     1.11.0                   py36_0    conda-forge
geos                      3.6.2                         1    conda-forge
geotiff                   1.4.2                         0    conda-forge
gettext                   0.19.8.1                      0    conda-forge
giflib                    5.1.4                         0    conda-forge
glib                      2.51.4                        0    conda-forge
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1                        1    conda-forge
html5lib                  1.0.1                      py_0    conda-forge
icu                       58.2                          0    conda-forge
idna                      2.6                      py36_1    conda-forge
intel-openmp              2018.0.0             h8158457_8  
ipykernel                 4.7.0                    py36_0    conda-forge
ipython                   6.2.1                    py36_0    conda-forge
ipython_genutils          0.2.0                    py36_0    conda-forge
jedi                      0.10.2                   py36_0    conda-forge
jinja2                    2.10                     py36_0    conda-forge
jpeg                      9b                            2    conda-forge
json-c                    0.12.1                        0    conda-forge
jsonschema                2.6.0                    py36_0    conda-forge
jupyter_client            5.1.0                    py36_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
kealib                    1.4.7                         4    conda-forge
krb5                      1.14.2                        0    conda-forge
libcxx                    4.0.1                h579ed51_0  
libcxxabi                 4.0.1                hebd6815_0  
libdap4                   3.18.3                        2    conda-forge
libedit                   3.1                  hb4e282d_0  
libffi                    3.2.1                h475c297_4  
libgdal                   2.2.3                         1    conda-forge
libgfortran               3.0.1                h93005f0_2  
libiconv                  1.15                          0    conda-forge
libkml                    1.3.0                         4    conda-forge
libnetcdf                 4.4.1.1                      10    conda-forge
libpng                    1.6.28                        2    conda-forge
libpq                     9.6.3                         0    conda-forge
libsodium                 1.0.15                        1    conda-forge
libspatialindex           1.8.5                         1    conda-forge
libspatialite             4.3.0a                       18    conda-forge
libssh2                   1.8.0                         2    conda-forge
libtiff                   4.0.7                         1    conda-forge
libxml2                   2.9.5                         2    conda-forge
markupsafe                1.0                      py36_0    conda-forge
matplotlib                2.1.1                    py36_0    conda-forge
mistune                   0.8.3                      py_0    conda-forge
mkl                       2018.0.1             hfbd8650_4  
munch                     2.2.0                    py36_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py36_0    conda-forge
ncurses                   6.0                  hd04f020_2  
networkx                  2.0                      py36_1    conda-forge
notebook                  5.2.2                    py36_1    conda-forge
numpy                     1.13.3           py36h2cdce51_0  
openjpeg                  2.3.0                         1    conda-forge
openssl                   1.0.2n               hdbc3d79_0  
osmnx                     0.6                       <pip>
pandas                    0.21.0                   py36_0    conda-forge
pandoc                    2.0.4                         0    conda-forge
pandocfilters             1.4.1                    py36_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.3.0                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pip                       9.0.1            py36h1555ced_4  
pixman                    0.34.0                        1    conda-forge
poppler                   0.61.1                        2    conda-forge
poppler-data              0.4.8                         0    conda-forge
proj4                     4.9.3                         5    conda-forge
prompt_toolkit            1.0.15                   py36_0    conda-forge
psycopg2                  2.7.3.2                  py36_0    conda-forge
ptyprocess                0.5.2                    py36_0    conda-forge
pycparser                 2.18                     py36_0    conda-forge
pygments                  2.2.0                    py36_0    conda-forge
pyopenssl                 17.4.0                   py36_0    conda-forge
pyparsing                 2.2.0                    py36_0    conda-forge
pyproj                    1.9.5.1                  py36_0    conda-forge
pysal                     1.14.3                   py36_0    conda-forge
pysocks                   1.6.7                    py36_0    conda-forge
python                    3.6.3                         1    conda-forge
python-dateutil           2.6.1                    py36_0    conda-forge
pytz                      2017.3                     py_2    conda-forge
pyzmq                     16.0.2                   py36_2    conda-forge
readline                  6.2                           2  
requests                  2.18.4                   py36_1    conda-forge
rtree                     0.8.3                    py36_0    conda-forge
scipy                     1.0.0            py36h1de22e9_0  
setuptools                36.5.0           py36h2134326_0  
shapely                   1.6.3                    py36_0    conda-forge
simplegeneric             0.8.1                    py36_0    conda-forge
six                       1.11.0                   py36_1    conda-forge
sqlalchemy                1.1.13                   py36_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
terminado                 0.8.1                    py36_0    conda-forge
testpath                  0.3.1                    py36_0    conda-forge
tk                        8.5.19                        2    conda-forge
tornado                   4.5.2                    py36_0    conda-forge
traitlets                 4.3.2                    py36_0    conda-forge
urllib3                   1.22                     py36_0    conda-forge
vega                      0.4.4                    py36_1    conda-forge
vincent                   0.4.4                    py36_0    conda-forge
wcwidth                   0.1.7                    py36_0    conda-forge
webencodings              0.5                      py36_0    conda-forge
wheel                     0.30.0           py36h5eb2c71_1  
xerces-c                  3.2.0                         0    conda-forge
xz                        5.2.3                h0278029_2  
zeromq                    4.2.1                         1    conda-forge
zlib                      1.2.11               hf3cbc9b_2
ocefpaf commented 6 years ago

@ffaristocrat you fiona is coming from defaults. Mixing packages like that is a no-no.

ffaristocrat commented 6 years ago

When I do the install of geopandas from conda-forge as above, it's installing the defaults version of fiona even though I'm doing override channels.

In any case, I went back, added fiona to the install with geopandas and libgdal and got the same error.

jorisvandenbossche commented 6 years ago

So it seems the --override-channels is not really doing what you want. Can you try with setting conda-forge as the first channel in condarc? (you can always change it back afterwards)

In any case, I went back, added fiona to the install with geopandas and libgdal and got the same error.

to be clear, you mean you also installed it with pip?

ffaristocrat commented 6 years ago

Used conda to do the install. I did

conda config --add channels conda-forge

killed the env and restarted the whole thing and it still installed the wrong fiona, same with libgdal, numpy, scipy & libgfortran. You have to install them specifically to get it to the right flavor from conda-forge.

Current workflow

source deactivate
conda env remove --yes --name GEOTEST
conda create --yes --name GEOTEST python=3.6
source activate GEOTEST
conda install --yes -c conda-forge --override-channels geopandas libgdal fiona numpy scipy libgfortran
python -c "import geopandas as gpd; div20m = gpd.read_file('cb_2016_us_division_20m.shp');"
conda remove --yes geopandas
pip install geopandas
python -c "import geopandas as gpd; div20m = gpd.read_file('cb_2016_us_division_20m.shp');"
conda list

Same error still. Trying to walk through with the debugger to see where it's failing exactly.

Edit: I'm doing the test before and after I uninstall/pip install geopandas to see if that's making a difference.

ffaristocrat commented 6 years ago

It seems like the problem is with shapely. If I remove geopandas, fiona and shapely via conda and then pip install them instead, the one line test works.

source deactivate
conda env remove --yes --name GEOTEST
conda create --yes --name GEOTEST python=3.6
source activate GEOTEST
conda install --yes -c conda-forge --override-channels geopandas libgdal fiona numpy scipy libgfortran libgfortran
conda remove --yes geopandas fiona shapely
pip install fiona shapely geopandas
python -c "import geopandas as gpd; div20m = gpd.read_file('cb_2016_us_division_20m.shp');"
conda list

I'm going to see if everything else works.

ffaristocrat commented 6 years ago

After I pip install osmnx and run the little bit of code that sent me down this rabbit hole in the first place, that also works on OSX now.

abe732 commented 6 years ago

Yep, what @ffaristocrat said works for me too. Had to remove shapely, fiona and geopandas via conda and then install back with pip. Same original problem. Hope this helps the next person who runs into this!

ocefpaf commented 6 years ago

Note that we are seeing some incompatibilities in the latest OS X system and shapely. I cannot reproduce that using the OS X VM available in Travis-CI and I do not own a mac to research this further.

Using pip works b/c they are static linked, this suggests that latest OS X may have a system wide geos installed, not sure. If so, the patch we have to find conda geos is not working :unamused:

TL;DR I have no idea what the issue really is and I do not have the tools to fix it.

jorisvandenbossche commented 6 years ago

@ocefpaf are there things that people with a mac (where the issue manifests) can do to help? Eg is there a way they can check which geos installation shapely finds?

I also don't have a mac, so can't help out.

ocefpaf commented 6 years ago

Eg is there a way they can check which geos installation shapely finds?

One could try to dig into shapely's code and see what is the look up path for geos. In theory the latest version should always check for conda first, but I never confirmed that.

jorisvandenbossche commented 6 years ago

I know you have shapely._buildcfg.get_geos_config(), but not sure that gives what you want in this case (we use that in geopandas to find the geos to build against (to use the same that shapely is build against)).

ocefpaf commented 6 years ago

get_geos_config('--prefix') should help. Ideally we everything under the sun there would be better. The options are: --prefix, --version, --libs, --clibs, --cclibs, --static-clibs, --static-cclibs, --cflags, --ldflags, --includes, and --jtsport.

grahamanderson commented 6 years ago

@ffaristocrat's solution worked for me :) Thank you.

biancaglez commented 6 years ago

@ffaristocrat Thanks! This partially worked for me!

I had a similar issue with these errors: Shell is not a linear ring and ModuleNotFoundError: No module named 'osmnx'.

I used your suggested process of uninstalling and pip installing shapely, geopandas, and fiona. I then tried to run the script again and then the no module error came up. I then pip installed osmnx and avoided the conda installation. This made my installation and the suggested code on github page work. Thanks again!

pip install osmnx

ocefpaf commented 6 years ago

I finally found someone with a Mac willing to help me debug this and our conclusion is that geos from homebrew can interfere with shapely when installed, affecting all packages that use shapely. We did have a patch to avoid this but somehow homebrew's geos is still getting in the way.

Either way this is not a bug with the conda package or geopandas so I'm closing this.

If you experience this issue and must use conda try to remove any previous installation of geos you may have.