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Python not recognizing sub module in Jupyter

I have a problem using python module in Jupyter. It was working fine until yesterday. The only new thing is that I updated Seaborn to th elatest version. I do not have the pb when I use Spyder directly.
For exemple, I have a file that would be like :
import numpy as np
import pandas as pd
import scipy
def test_skewn(TimeSeries):
tempTimeSeries = TimeSeries.copy()
temp_Rolling_Perf = (tempTimeSeries / tempTimeSeries.shift(1) -1 ).dropna()
current_skew = scipy.stats.skew(temp_Rolling_Perf.iloc[i:i+Maturity-1])
return(current_skew )
I work perfectly from Spyder but from Jupyter it return :
AttributeError: module 'scipy' has no attribute 'stats'
If I correct it like this :
import numpy as np
import pandas as pd
#import scipy
from scipy.stats import skew, kurtosis
def test_skewness(TimeSeries):
tempTimeSeries = TimeSeries.copy()
temp_Rolling_Perf = (tempTimeSeries / tempTimeSeries.shift(1) -1 ).dropna()
#current_skew = scipy.stats.skew(temp_Rolling_Perf.iloc[i:i+Maturity-1])
current_skew = skew(temp_Rolling_Perf.iloc[i:i+Maturity-1])
return(current_skew )
It works in Jupyter.
It was working with both version before and I am not confortable at all with this pb and I would like to understand where it can come from.

How to import "gleam" package in Python 3?

I'm tyring to import the "gleam" package in Python 3. I have installed the "gleam" package successfully, but still it showing error.
from wtforms import fields
from ggplot import *
from gleam import Page, panels
class ScatterInput(panels.Inputs):
title = fields.StringField(label="Title of plot:")
yvar = fields.SelectField(label="Y axis",
choices=[("beef", "Beef"),
("pork", "Pork")])
smoother = fields.BooleanField(label="Smoothing Curve")
class ScatterPlot(panels.Plot):
name = "Scatter"
def plot(self, inputs):
p = ggplot(meat, aes(x='date', y=inputs.yvar))
if inputs.smoother:
p = p + stat_smooth(color="blue")
p = p + geom_point() + ggtitle(inputs.title)
return p
class ScatterPage(Page):
input = ScatterInput()
output = ScatterPlot()
ScatterPage.run()
Error:
ModuleNotFoundError - Traceback (most> recent call last) in ()
----> 1 import gleam
C:\pythonNJ\lib\site-packages\gleam__init__.py in ()
5 import os
6 import json
----> 7 import urlparse
8 from collections import namedtuple
9
ModuleNotFoundError: No module named 'urlparse'
I looked for the solution and I found that urlparse has been moved to a new module in python 3, which can be imported as
from urllib.parse import urlparse
And I even imported it, but still when I trying to import "gleam" package it shows error of module "urlparse". Can you suggest me how to bypass it (bypassing import urlparse statement and importing gleam package in Python 3).
I know how to import the urlparse but I don't know how to import the gleam package.

You have two possiblities:
Modify source code yourself as you stated inside gleam package, but it could work incorrectly.
Fall back to version of python it works on - so 2.7 it seems, since the modification you mentioned was done with python 3.0 release. It's stated in docs here.

Just do this to get over it:
from:
import urlparser
to:
import urllib.parse

rpy2 in python SyntaxError: invalid syntax for as.ape.AAbin

Im using rpy2 package in python. It's a package for R programming via python. when i use 'as' function in python it consider it a syntax error. It works fine in R. I imported all necessary packages. Is there any command to replace as.apes.
from rpy2.robjects.packages import importrcode
utils = importr('utils')
utils.chooseCRANmirror(ind=1)
base = importr('base')
methods= importr('methods')
packnames = ('ape', 'aphid','methods')
apes= importr("ape")
g1 = as.apes.AAbin("EL---DSD-ILPELLATLARTHDLNK----VGPAHYDLFAKVLM")
g1 = as.apes.AAbin("EL---DSD-ILPELLATLARTHDLNK----VGPAHYDLFAKVLM")
^
SyntaxError: invalid syntax

problem solved! I changed the whole way of calling R in python. I used wrapping,I used my whole R script as follows:
from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
string = """
#paste your script here
"""
powerpack = SignatureTranslatedAnonymousPackage(string, "powerpack")
refer to thepackage documentation for further details.

R clump within python with rpy2

My specific issue is exactly the title. I have a large raster processing script in python and need to perform a clump function which I cannot find in gdal / python nor have I figured out how to 'write it' myself.
I am becoming better with python all the time just still newish, but am learning R for this task. (installed R version 3.4.1 (2017-06-30))
I am able to get rpy2 installed within python after spending a little time learning R and through help on Stackoverflow I have been able to perform several 'tests' of rpy2.
The most helpful info in getting rpy2 to respond was to establish where your R is within your python session or script. from another Stack answer. As below:
import os
os.environ['PYTHONHOME'] = r'C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\Scripts'
os.environ['PYTHONPATH'] = r'C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\Lib\site-packages'
os.environ['R_HOME'] = r'C:\Program Files\R\R-3.4.1'
os.environ['R_USER'] = r'C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\Lib\site-packages\rpy2'
However, the main tests listed in the documentation http://rpy.sourceforge.net/rpy2/doc-2.1/html/overview.html I cannot get to work.
import rpy2.robjects.tests
import unittest
# the verbosity level can be increased if needed
tr = unittest.TextTestRunner(verbosity = 1)
suite = rpy2.robjects.tests.suite()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'suite'
However:
import rpy2.robjects as robjects
pi = robjects.r['pi']
pi[0]
works just fine. as do a few other rpy2.robjects tests I have found. I can create string = ''' f <- functions ect ''' and call those from python.
If i use:
python -m 'rpy2.tests'
I get the following error.
r\Scripts>python -m 'rpy2.tests'
r\Scripts\python.exe: No module named 'rpy2
Documentation states: On Python 2.6, this should return that all tests were successful. I am using Python 2.7 and I also tried this in Python 3.3.
My script for clump starts as below:
I do not want to have to actually install the package names each time I run the script as they are already installed in my R Home.
I would like to use my python variables if possible.
I need to figure out why rpy2 does not respond as the documentation indicates, or why I am getting errors. And then after that figure out the correct way to write my clump portion of my python script.
packageNames = ('raster', 'rgdal')
if all(rpackages.isinstalled(x) for x in packageNames):
have_packages = True
else:
have_packages = False
if not have_packages:
utils = rpackages.importr('utils')
utils.chooseCRANmirror(ind=1)
packnames_to_install = [x for x in packageNames if not rpackages.isinstalled(x)]
if len(packnames_to_install) > 0:
utils.install_packages(StrVector(packnames_to_install))
from rpy2.robjects.packages import importr
import rpy2.robjects as robjects
There are several ways I have found to call the raster and clump options from R, however, if I cannot get rpy2 to respond correctly, I am not going to get these to work at all But since several other tests work I am not positive.
raster = robjects.r['raster']
raster = importr('raster')
clump = raster.clump
clump = robjects.r.clump
type(raster.clump)
tempDIR = r"C:\Users\script_out\temp"
slope_recode = os.path.join(tempDIR, "step2b_input.img")
outfile = os.path.join(tempDIR, "Rclumpfile.img")
raster.clump(slope_recode, filename=outfile, direction=4, gaps=True, format='HFA', overwrite=True)
Which results in a large amount of errors.
Traceback (most recent call last):
File "C:/Python27/ArcGIS10.3/Scripts/new_ve_folder/Scripts/rpy2_practice.py", line 97, in <module>
raster.clump(slope_recode, filename=outfile, direction=4, gaps=True, format='HFA', overwrite=True)
File "C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\lib\site-packages\rpy2\robjects\functions.py", line 178, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\lib\site-packages\rpy2\robjects\functions.py", line 106, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'clump' for signature '"character"'
Issues:
testing rpy2 in command line and script (both produce errors, but I am still able to use basic rpy2
importing the R packages so as not to install them each time
finally getting my clump script called correctly
If I have missed something basic, please point me in the right direction. Thanks all.

For your first problem, replace suite = rpy2.robjects.tests.suite() with suite = rpy2.tests.suite().
For your third problem (getting clump to work correctly), you need to create a RasterLayer object in R using the image. I'm not familiar with the raster package, so I can't give you the exact steps.
I will point out the arcpy module is not "pythonic". Normally, strings of filenames are just strings in Python. arcpy is weird in using plain strings to represent objects like map layers.
In your example, slope_recode is just a string. That's why you got the error unable to find an inherited method for function 'clump' for signature '"character"'. It means slope_recode was passed to R as a character value (which it is), and the clump function expects a RasterLayer object. It doesn't know how to handle character values.

I got this all to work with the below code.
import warnings
os.environ['PATH'] = os.path.join(scriptPath, 'path\\my_VE\\R\\R-3.4.2\\bin\\x64')
os.environ['PYTHONHOME'] = os.path.join(scriptPath, 'path\\my_VE\\Scripts\\64bit')
os.environ['PYTHONPATH'] = os.path.join(scriptPath, 'path\\my_VE\\Lib\\site-packages')
os.environ['R_HOME'] = os.path.join(scriptPath, 'path\\my_VE\\R\\R-3.4.2')
os.environ['R_USER'] = os.path.join(scriptPath, 'path\\my_VE\\Scripts\\new_ve_folder\\Scripts\\rpy2')
#
import platform
z = platform.architecture()
print(z)
## above will confirm you are working on 64 bit
gc.collect()
## this code snippit will tell you which library is being Read
command = 'Rscript'
cmd = [command, '-e', ".libPaths()"]
print(cmd)
x = subprocess.Popen(cmd, shell=True)
x.wait()
import rpy2.robjects.packages as rpackages
import rpy2.robjects as robjects
from rpy2.robjects import r
import rpy2.interactive.packages
from rpy2.robjects import lib
from rpy2.robjects.lib import grid
# # grab r packages
print("loading packages from R")
## fails at this point with the following error
## Error: cannot allocate vector of size 232.6 Mb when working with large rasters
rpy2.robjects.packages.importr('raster')
rpy2.robjects.packages.importr('rgdal')
rpy2.robjects.packages.importr('sp')
rpy2.robjects.packages.importr('utils')
# rpy2.robjects.packages.importr('memory')
# rpy2.robjects.packages.importr('dplyr')
rpy2.robjects.packages.importr('data.table')
grid.activate()
# set python variables for R code names
raster = robjects.r['raster']
writeRaster = robjects.r['writeRaster']
# setwd = robjects.r['setwd']
clump = robjects.r['clump']
# head = robjects.r['head']
crs = robjects.r['crs']
dim = robjects.r['dim']
projInfo = robjects.r['projInfo']
slope_recode = os.path.join(tempDIR, "_lope_recode.img")
outfile = os.path.join(tempDIR, "Rclumpfile.img")
recode = raster(slope_recode) # this is taking the image and reading it into R raster package
## https://stackoverflow.com/questions/47399682/clear-r-memory-using-rpy2
gc.collect() # No noticeable effect on memory usage
time.sleep(2)
gc.collect() # Finally, memory usage drops
R = robjects.r
R('memory.limit()')
R('memory.limit(size = 65535)')
R('memory.limit()')
print"starting Clump with rpy2"
clump(recode, filename=outfile, direction=4, gaps="True", format="HFA")
final = raster(outfile)
final = crs("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0,-0,-0,-0,0 +no_defs")
print ("clump file created, CRS accurate, next step")

Rpy2 not finding package

I'm using Rpy2 on windows 7 64 and having trouble loading a package:
in R:
using(mi)
in python:
from rpy2.robjects.packages import importr
mi=importr('mi')
---------------------------------------------------------------------------
RRuntimeError Traceback (most recent call last)
<ipython-input-30-2d393a6df544> in <module>()
----> 1 mi=importr('mi')
C:\Anaconda\lib\site-packages\rpy2\robjects\packages.pyc in importr(name, lib_loc, robject_translations, signature_translation, suppress_messages, on_conflict, data)
397 if _package_has_namespace(rname,
398 _system_file(package = rname)):
--> 399 env = _get_namespace(rname)
400 version = _get_namespace_version(rname)[0]
401 exported_names = set(_get_namespace_exports(rname))
RRuntimeError: Error in loadNamespace(name) : there is no package called 'm
Any suggestions?

I had a similar problem:
rpy2.rinterface.RRuntimeError: Error in loadNamespace(name) : there is no package called speedglm
I noticed that the issue is that rpy2 does not know the location of all R libraries. In my case, typing (in R)
.libPaths()
gave me
[1] "/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4"
[2] "/usr/lib64/R/library"
[3] "/usr/share/R/library"
While, typing (in Python 3)
import rpy2.rinterface
rpy2.rinterface.set_initoptions((b'rpy2', b'--no-save', b'--no-restore', b'--quiet'))
from rpy2.robjects.packages import importr
base = importr('base')
print(base._libPaths())
gave me only
[1] "/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4"
I couldn't find a way to append the other two paths to base._libpath(). If you find a way to do it, please let me know. I used another workaround:
import rpy2
import rpy2.robjects as RObjects
from rpy2.robjects.packages import importr
utils = importr("utils")
d = {'print.me': 'print_dot_me', 'print_me': 'print_uscore_me'}
try:
thatpackage = importr('speedglm', robject_translations = d, lib_loc = "/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4")
except:
try:
thatpackage = importr('speedglm', robject_translations = d, lib_loc = "/usr/lib64/R/library")
except:
thatpackage = importr('speedglm', robject_translations = d, lib_loc = "/usr/share/R/library")
This works. I hope other people who have the same problem find this useful.

For me, in importr, the argument lib_loc inside it worked, putting the first path that appears in the output of .libPaths() in R, like:
importr('name package', lib_loc="/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4"),
where the path is the path in the output example of the #Nbarjest answer.

In python: Check the version of R being used by rpy2
import rpy2.robjects as robjects
robjects.r['version']
Check your rpy2 library location
base = importr('base')
print(base._libPaths())
In R: Check your R library location for this version of r
.libPaths()
copy the library installed in your version of r to the folder used by rpy2.

I also have this problem,and i copy the package i need to base._libPaths() ,here , and it works.
import rpy2.robjects as objects
from rpy2.robjects.packages import importer
base = importr('base')
base._libPaths()[0]

I had a similar problem. I had to uninstall R and reinstall it with admin rights, then reinstall the R package while running R with admin rights, so it would install to the standard library location (not a personal library). Then add R to the PATH variable, and reinstall rpy2.

This is was cross-posted, and answered, on the issue tracker for rpy2: https://bitbucket.org/rpy2/rpy2/issue/265/windows-error-in-loadnamespace