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Fix dependencies - get from conda #14

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Fix dependencies - get from conda #14

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1ab19c4
google-benchmark from conda
breznak Jun 4, 2020
2ea9c94
Blitz: add to conda env
breznak Jun 4, 2020
b9e36b9
Pythran: install from conda
breznak Jun 4, 2020
253142e
CMake: add conda's include,lib paths
breznak Jun 4, 2020
869ca2d
cmake: fix Numpy detection
breznak Jun 5, 2020
f7fc77a
revert conda paths
breznak Jun 5, 2020
3cb72bc
Revert "google-benchmark from conda"
breznak Jun 5, 2020
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5 changes: 2 additions & 3 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,6 @@ add_executable(${XTENSOR_BENCHMARK_TARGET} ${XTENSOR_BENCHMARK} ${XTENSOR_HEADER

# Mandatory dependencies
# ======================

find_package(xtensor REQUIRED CONFIG)
find_package(xsimd REQUIRED)
find_package(xtl REQUIRED)
Expand Down Expand Up @@ -135,8 +134,8 @@ endif()

if(BENCHMARK_PYTHONIC)
find_package(PythonLibs)
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in conda env, the cmake is still picking wrong python (that may be the reason for Pythran, numpy errors?) :

env:

 $ which python
/home/mmm/.conda/envs/xtensor-benchmark/bin/python
(xtensor-benchmark) mmm@mmm-U2442:~/devel/xtensor-benchmark/build$ python --version
Python 3.7.1

while in cmake (3.8!!):

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so (found version "3.8.2")
-- Found PythonInterp: /usr/bin/python3.8 (found version "3.8.2")

I guess it's with priority of the paths?

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found relevant issue, usnistgov/feasst#2
but even after applying that solution, still detects wrong python

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I really don't get it, I've just tested your branch on my machine and it could detect everything correctly. I'm using conda 4.8.3 (from miniconda) on gentoo.

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@breznak breznak Jun 12, 2020 •
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This is my complete cmake output (for all benchmarks)


(xtensor-benchmark) mmm@mmm-U2442:~/devel/xtensor-benchmark$ cmake . -DBENCHMARK_ALL=ON
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Forcing tests build type to Release
-- Performing Test HAS_CPP14_FLAG
-- Performing Test HAS_CPP14_FLAG - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found Blitz: /home/mmm/devel/.conda/envs/xtensor-benchmark/include  
-- Found Armadillo: /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so (found version "9.200.7") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so (found version "3.8.2") 
-- Found PythonInterp: /usr/bin/python3.8 (found version "3.8.2") 
CMake Error at modules/FindNumpy.cmake:68 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:69 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:70 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:71 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:74 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:77 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:81 (string):
string sub-command REGEX, mode MATCH regex "[0-9]*" matched an empty
string.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:82 (math):
math cannot parse the expression: "(NOTFOUND * 10000) + (NOTFOUND * 100) +
NOTFOUND": syntax error, unexpected exp_TIMES (11).
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindPythran.cmake:43 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:44 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:45 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:46 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:49 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:56 (string):
string sub-command REGEX, mode MATCH regex "[0-9]*" matched an empty
string.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:57 (math):
math cannot parse the expression: "(NOTFOUND * 10000) + (NOTFOUND * 100) +
NOTFOUND": syntax error, unexpected exp_TIMES (11).
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)




COMPILING WITH
======================================


COMPILER        : /usr/bin/c++
FLAGS           :  -Ofast -ffast-math -march=native -pthread

Found xtensor   : /home/mmm/.conda/envs/xtensor-benchmark/include
Found xsimd     : /home/mmm/.conda/envs/xtensor-benchmark/include


Found eigen     : /home/mmm/.conda/envs/xtensor-benchmark/include/eigen3
Found Blitz     : /home/mmm/devel/.conda/envs/xtensor-benchmark/include | /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libblitz.so
Found Armadillo : /home/mmm/devel/.conda/envs/xtensor-benchmark/include | /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so
Found Pythran   :
Using benchmark :  | benchmark::benchmark_main
-- Configuring incomplete, errors occurred!
See also "/home/mmm/devel/xtensor-benchmark/CMakeFiles/CMakeOutput.log".
See also "/home/mmm/devel/xtensor-benchmark/CMakeFiles/CMakeError.log".

I'm using conda 4.8.3 (from miniconda) on gentoo.

I'm also on conda 4.8.3, Ubuntu 20.04 LTS.
The use of system python would be the main cause, then the other conda-installed libs get missing.

My cmake is 3.16.0

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@JohanMabille JohanMabille Jun 12, 2020 •
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can you pass -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX to the cmake command? (and check that it is correctly set in CMakeCache.txt efter running cmake).

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sure.
The err is the same.
Setup:

git clean -xdf
cmake . -DBENCHMARK_ALL=ON -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX 
echo $CONDA_PREFIX
> /home/mmm/.conda/envs/xtensor-benchmark 

#validate
$ grep 'PREFIX' CMakeCache.txt
CMAKE_INSTALL_PREFIX:PATH=/home/mmm/.conda/envs/xtensor-benchmark

Cmake Output:

$ echo $CONDA_PREFIX
/home/mmm/.conda/envs/xtensor-benchmark
(xtensor-benchmark) mmm@mmm-U2442:~/devel/xtensor-benchmark$ cmake . -DBENCHMARK_ALL=ON -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX 
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Forcing tests build type to Release
-- Performing Test HAS_CPP14_FLAG
-- Performing Test HAS_CPP14_FLAG - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found Blitz: /home/mmm/devel/.conda/envs/xtensor-benchmark/include  
-- Found Armadillo: /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so (found version "9.200.7") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so (found version "3.8.2") 
-- Found PythonInterp: /usr/bin/python3.8 (found version "3.8.2") 
CMake Error at modules/FindNumpy.cmake:68 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:69 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:70 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:71 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:74 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:77 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:81 (string):
string sub-command REGEX, mode MATCH regex "[0-9]*" matched an empty
string.
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindNumpy.cmake:82 (math):
math cannot parse the expression: "(NOTFOUND * 10000) + (NOTFOUND * 100) +
NOTFOUND": syntax error, unexpected exp_TIMES (11).
Call Stack (most recent call first):
CMakeLists.txt:137 (find_package)


CMake Error at modules/FindPythran.cmake:43 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:44 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:45 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:46 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:49 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:56 (string):
string sub-command REGEX, mode MATCH regex "[0-9]*" matched an empty
string.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:57 (math):
math cannot parse the expression: "(NOTFOUND * 10000) + (NOTFOUND * 100) +
NOTFOUND": syntax error, unexpected exp_TIMES (11).
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)




COMPILING WITH
======================================


COMPILER        : /usr/bin/c++
FLAGS           :  -Ofast -ffast-math -march=native -pthread

Found xtensor   : /home/mmm/.conda/envs/xtensor-benchmark/include
Found xsimd     : /home/mmm/.conda/envs/xtensor-benchmark/include


Found eigen     : /home/mmm/.conda/envs/xtensor-benchmark/include/eigen3
Found Blitz     : /home/mmm/devel/.conda/envs/xtensor-benchmark/include | /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libblitz.so
Found Armadillo : /home/mmm/devel/.conda/envs/xtensor-benchmark/include | /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so
Found Pythran   :
Using benchmark :  | benchmark::benchmark_main
-- Configuring incomplete, errors occurred!
See also "/home/mmm/devel/xtensor-benchmark/CMakeFiles/CMakeOutput.log".
See also "/home/mmm/devel/xtensor-benchmark/CMakeFiles/CMakeError.log".

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@JohanMabille JohanMabille Jun 23, 2020 •
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We got a hint for a similar problem with xtensor-python, can you pass the -DPYTHON_EXECUTABLE:FILEPATH=path_to_python to the cmake command line and see if it fixes the issue?

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Thanks @JohanMabille , I guess it helps a bit - thanks to that it: finds NumPy, uses correct Python (3.7), BUT python libs now mismatch (3.8)! Is there a similar setting for pythonlibs?

CMake output below

$ git clean -xdf
Removing CMakeCache.txt
Removing CMakeFiles/
(xtensor-benchmark) mmm@mmm-U2442:~/devel/xtensor-benchmark$ cmake . -DBENCHMARK_ALL=ON -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DPYTHON_EXECUTABLE:FILEPATH=`which python` 
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Forcing tests build type to Release
-- Performing Test HAS_CPP14_FLAG
-- Performing Test HAS_CPP14_FLAG - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found Blitz: /home/mmm/devel/.conda/envs/xtensor-benchmark/include  
-- Found Armadillo: /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so (found version "9.200.7") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so (found version "3.8.2") 
-- Found PythonInterp: /home/mmm/.conda/envs/xtensor-benchmark/bin/python (found version "3.7.1") 
-- Found NumPy: version "1.18.5" /home/mmm/.conda/envs/xtensor-benchmark/lib/python3.7/site-packages/numpy/core/include
CMake Error at modules/FindPythran.cmake:43 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:44 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:45 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:46 (list):
list GET given empty list
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:49 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:56 (string):
string sub-command REGEX, mode MATCH regex "[0-9]*" matched an empty
string.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)


CMake Error at modules/FindPythran.cmake:57 (math):
math cannot parse the expression: "(NOTFOUND * 10000) + (NOTFOUND * 100) +
NOTFOUND": syntax error, unexpected exp_TIMES (11).
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)




COMPILING WITH
======================================


COMPILER        : /usr/bin/c++
FLAGS           :  -Ofast -ffast-math -march=native -pthread

Found xtensor   : /home/mmm/.conda/envs/xtensor-benchmark/include
Found xsimd     : /home/mmm/.conda/envs/xtensor-benchmark/include


Found eigen     : /home/mmm/.conda/envs/xtensor-benchmark/include/eigen3
Found Blitz     : /home/mmm/devel/.conda/envs/xtensor-benchmark/include | /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libblitz.so
Found Armadillo : /home/mmm/devel/.conda/envs/xtensor-benchmark/include | /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so
Found Pythran   :
Using benchmark :  | benchmark::benchmark_main
-- Configuring incomplete, errors occurred!
See also "/home/mmm/devel/xtensor-benchmark/CMakeFiles/CMakeOutput.log".
See also "/home/mmm/devel/xtensor-benchmark/CMakeFiles/CMakeError.log".

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It seems like you can pass a -DPYTHON_LIBRARIES=path_to_python_lib option (or DPYTHON_LIBRARY for very olf version of cmake, i.e. < 3) to cmake. Let's hope it fixes the problem for good!

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Unfortunately, no. We're able to set the correct pythonlibs path, but it is still somehow overriden by python 3.8?!

-- Found Blitz: /home/mmm/devel/.conda/envs/xtensor-benchmark/include  
-- Found Armadillo: /home/mmm/devel/.conda/envs/xtensor-benchmark/lib/libarmadillo.so (found version "9.200.7") 
-- Found PythonLibs: /home/mmm/.conda/envs/xtensor-benchmark/lib/python3.7 (found version "3.8.2") 
-- Found PythonInterp: /home/mmm/.conda/envs/xtensor-benchmark/bin/python (found version "3.7.1") 
-- Found NumPy: version "1.18.5" /home/mmm/.conda/envs/xtensor-benchmark/lib/python3.7/site-packages/numpy/core/include
CMake Error at modules/FindPythran.cmake:43 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:138 (find_package)

I tried to go the other way and install py3.8, but conda env has some unresolvable dependency conflicts and is unable to do that.

find_package(NumPy)
find_package(Pythran)
find_package(Numpy)
find_package(Pythran )
link_directories(${Pythran_INCLUDE_DIRS})
target_compile_definitions(${XTENSOR_BENCHMARK_TARGET} PRIVATE HAS_PYTHONIC=1 ENABLE_PYTHON_MODULE=1 USE_BOOST_SIMD=1)
target_include_directories(${XTENSOR_BENCHMARK_TARGET} PRIVATE
Expand Down
11 changes: 6 additions & 5 deletions environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,15 @@ channels:
- conda-forge
- defaults
dependencies:
- eigen
- conda-forge::benchmark
- conda-forge::libblitz
- conda-forge::pythran
- eigen>=3.0
- armadillo
- xsimd
- xtensor
- xtl
- cmake
- cmake>=3.1
- gmp
- numpy
- python
- pip:
- pythran
- python>=3.0