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matplotlib / basemap

Plot on map projections (with coastlines and political boundaries) using matplotlib
MIT License
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installation fails on ubuntu 21.04 with Python 3.9.5 #518

Closed thdb-theo closed 2 years ago

thdb-theo commented 3 years ago

I have succesfully install geos, but running sudo python3 setup.py install fails with the following error:

checking for GEOS lib in /root ....
checking for GEOS lib in /root/local ....
checking for GEOS lib in /usr ....
GEOS lib (version 3.9.0) found in /usr
running install
running bdist_egg
running egg_info
running build_src
build_src
building extension "_geoslib" sources
build_src: building npy-pkg config files
creating basemap.egg-info
writing basemap.egg-info/PKG-INFO
writing dependency_links to basemap.egg-info/dependency_links.txt
writing namespace_packages to basemap.egg-info/namespace_packages.txt
writing requirements to basemap.egg-info/requires.txt
writing top-level names to basemap.egg-info/top_level.txt
writing manifest file 'basemap.egg-info/SOURCES.txt'
reading manifest file 'basemap.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'basemap.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.9
creating build/lib.linux-x86_64-3.9/mpl_toolkits
creating build/lib.linux-x86_64-3.9/mpl_toolkits/basemap

. . . .

A bunch of compiler notes and warnings. Then the error:

      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~^
src/_geoslib.c: In function ‘__Pyx_modinit_type_init_code’:
src/_geoslib.c:5678:36: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
 5678 |   __pyx_type_8_geoslib_BaseGeometry.tp_print = 0;
      |                                    ^
src/_geoslib.c:5686:31: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
 5686 |   __pyx_type_8_geoslib_Polygon.tp_print = 0;
      |                               ^
src/_geoslib.c:5694:34: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
 5694 |   __pyx_type_8_geoslib_LineString.tp_print = 0;
      |                                  ^
src/_geoslib.c:5702:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
 5702 |   __pyx_type_8_geoslib_Point.tp_print = 0;
      |                             ^

error: Command "x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-1n6GrT/python3.9-3.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-1n6GrT/python3.9-3.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/distutils/include -I/usr/include/python3.9 -c src/_geoslib.c -o build/temp.linux-x86_64-3.9/src/_geoslib.o -MMD -MF build/temp.linux-x86_64-3.9/src/_geoslib.o.d -msse -msse2 -msse3" failed with exit status 1

########### EXT COMPILER OPTIMIZATION ###########
Platform      : 
  Architecture: x64
  Compiler    : gcc

CPU baseline  : 
  Requested   : 'min'
  Enabled     : SSE SSE2 SSE3
  Flags       : -msse -msse2 -msse3
  Extra checks: none

CPU dispatch  : 
  Requested   : 'max -xop -fma4'
  Enabled     : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_KNM AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
  Generated   : none
CCompilerOpt._cache_write[796] : write cache to path -> /home/theodor/Downloads/basemap/build/temp.linux-x86_64-3.9/ccompiler_opt_cache_ext.py

Installing using pip results in the same error.

molinav commented 3 years ago

It seems that tp_print was removed in CPython 3.9 (see https://bugs.python.org/issue39361), so this error is probably occurring in the conversion of _geoslib.pyx to _geoslib.c.

Are you using the _geoslib.c file from the repo? It might work if you remove the C file to force the generation of this file again by Cython. This _geoslib.c file in the repo is probably super-old and ideally it should be deleted and add Cython as build dependency.

thdb-theo commented 3 years ago

Thanks, that made me able to install, but led to another (possibly related) issue. When importing Basemap i get this error:

>>> from mpl_toolkits.basemap import Basemap
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/theodor/.local/lib/python3.9/site-packages/basemap-1.2.2+dev-py3.9-linux-x86_64.egg/mpl_toolkits/basemap/__init__.py", line 53, in <module>
    import _geoslib
ImportError: libgeos-3.9.1.so: cannot open shared object file: No such file or directory
>>>

I have libgeos-dev 3.9.0-1installed

molinav commented 3 years ago

That looks strange to me, in the original message the output says:

GEOS lib (version 3.9.0) found in /usr

so I would expect basemap to request libgeos-3.9.0.so, which is available in Ubuntu 21.04 under /usr/lib/x86_64-linux-gnu/libgeos-3.9.0.so when you install libgeos-3.9.0 (this package gets installed automatically with libgeos-dev). Do you have several GEOS versions installed?

thdb-theo commented 3 years ago

Thank for your help! I fixed it by removing 3.9.1 and installing 3.9.0.

GeoFelpave commented 3 years ago

Just to add here. The following worked for me without having to altered the version of Python.

sudo apt -y install libgeos-dev pip3 install git+https://github.com/matplotlib/basemap/

molinav commented 2 years ago

@thdb-theo @GeoFelpave I just uploaded preliminary wheel binaries of the future basemap version 1.3.0 (with bundled libgeos_c). In case you are still interested you can try out with (for Python 2.7 and 3.5 to 3.9):

python -m pip install "basemap-data == 1.3.0b1" "basemap == 1.3.0b1"