Hey François,
I have been installing the latest version of Polymer in my Linux system from the Forum. Unfortunately I am getting this error (given below) when executing the final make command.
Do you know how to fix this error? Awaiting your reply.
Best, Vishnu
(polymer) hypso@atmospheric-tower:~/Desktop/Polymer/polymer-v4.17beta2$ make
python setup.py build_ext --inplace
Compiling polymer/clut.pyx because it changed.
Compiling polymer/neldermead.pyx because it changed.
Compiling polymer/polymer_main.pyx because it changed.
Compiling polymer/water.pyx because it changed.
[1/4] Cythonizing polymer/clut.pyx
/home/hypso/anaconda3/envs/polymer/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /home/hypso/Desktop/Polymer/polymer-v4.17beta2/polymer/clut.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[2/4] Cythonizing polymer/neldermead.pyx
/home/hypso/anaconda3/envs/polymer/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /home/hypso/Desktop/Polymer/polymer-v4.17beta2/polymer/neldermead.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[3/4] Cythonizing polymer/polymer_main.pyx
/home/hypso/anaconda3/envs/polymer/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /home/hypso/Desktop/Polymer/polymer-v4.17beta2/polymer/polymer_main.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
from libc.math cimport nan, exp, log, abs, sqrt, isnan
from cpython.exc cimport PyErr_CheckSignals
import pandas as pd
from pathlib import Path
from neldermead cimport NelderMeadMinimizer, dot
^
------------------------------------------------------------
polymer/polymer_main.pyx:10:0: 'neldermead.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from libc.math cimport nan, exp, log, abs, sqrt, isnan
from cpython.exc cimport PyErr_CheckSignals
import pandas as pd
from pathlib import Path
from neldermead cimport NelderMeadMinimizer, dot
^
------------------------------------------------------------
polymer/polymer_main.pyx:10:0: 'neldermead/NelderMeadMinimizer.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from libc.math cimport nan, exp, log, abs, sqrt, isnan
from cpython.exc cimport PyErr_CheckSignals
import pandas as pd
from pathlib import Path
from neldermead cimport NelderMeadMinimizer, dot
^
------------------------------------------------------------
polymer/polymer_main.pyx:10:0: 'neldermead/dot.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from cpython.exc cimport PyErr_CheckSignals
import pandas as pd
from pathlib import Path
from neldermead cimport NelderMeadMinimizer, dot
from water cimport WaterModel
^
------------------------------------------------------------
polymer/polymer_main.pyx:11:0: 'water.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from cpython.exc cimport PyErr_CheckSignals
import pandas as pd
from pathlib import Path
from neldermead cimport NelderMeadMinimizer, dot
from water cimport WaterModel
^
------------------------------------------------------------
polymer/polymer_main.pyx:11:0: 'water/WaterModel.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
'W_dR2_Rprime_noglint2': W_dR2_Rprime_noglint2,
'W_dR2_Rprime_noglint2_norm': W_dR2_Rprime_noglint2_norm,
'polymer_3_5': polymer_3_5,
}
cdef class F(NelderMeadMinimizer):
^
------------------------------------------------------------
polymer/polymer_main.pyx:39:13: First base of 'F' is not an extension type
Error compiling Cython file:
------------------------------------------------------------
...
cdef float[:] Rprime
cdef float[:] Rprime_noglint
cdef float[:] Tmol
cdef float[:] wav
cdef WaterModel w
^
------------------------------------------------------------
polymer/polymer_main.pyx:49:9: 'WaterModel' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# 3) calculate rho_w_mod_cov from the Jacobian matrix of the model
# (eq 55 - 58 of E3UB)
# rho_w_mod_cov = d_rw_x . f.cov . d_rw_x'
# [NbxNb] [NbxNp] [NpxNp] [NpxNb]
dot(d_rw_x_cov, d_rw_x, self.f.cov, 0)
^
------------------------------------------------------------
polymer/polymer_main.pyx:647:20: 'dot' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
# 3) calculate rho_w_mod_cov from the Jacobian matrix of the model
# (eq 55 - 58 of E3UB)
# rho_w_mod_cov = d_rw_x . f.cov . d_rw_x'
# [NbxNb] [NbxNp] [NpxNp] [NpxNb]
dot(d_rw_x_cov, d_rw_x, self.f.cov, 0)
dot(rho_w_mod_cov, d_rw_x_cov, d_rw_x, 1)
^
------------------------------------------------------------
polymer/polymer_main.pyx:648:20: 'dot' is not a constant, variable or function identifier
Traceback (most recent call last):
File "setup.py", line 34, in <module>
ext_modules=cythonize(
File "/home/hypso/anaconda3/envs/polymer/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/home/hypso/anaconda3/envs/polymer/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: polymer/polymer_main.pyx
make: *** [makefile:9: main] Error 1