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Matthew Brett matthew-brett University of Birmingham Birmingham, UK http://matthew.dynevor.org

BIDS/datarray 78

Prototyping numpy arrays with named axes for data management.

jonathan-taylor/stats-lecture-notes 26

Statistics lecture notes

BIDS-numpy/numpy-paper 10

Draft of NumPy paper

jbpoline/bayfmri 10

Bay area fMRI course description

fperez/nipy-notebooks 9

Example notebooks for basic tasks in neuroimaging and statistcs with nipy

biopython/biopython-wheels 6

Automated compilation of Python wheel binary packages for Biopython

fperez/spheredwi 6

Research: representation of functions on the sphere and diffusion-weighted imaging

fperez/datarray-doc 5

Datarray Documentation

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Policies

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Credit for policies

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Typo

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Matthew Brett

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Fill out CILogon etc auth instructions.

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Better comments for cleaned config.

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issue commentjupyterhub/oauthenticator

Stripping domains only for case of single allowed domain?

Ah - thanks - I knew there was a good reason, it's just I hadn't seen it.

But how about my suggestion of allowing a list for strip_idp_domain to cover my use-case?

matthew-brett

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issue openedjupyterhub/oauthenticator

Stripping domains only for case of single allowed domain?

This is just asking for the reasoning behind the logic at https://github.com/jupyterhub/oauthenticator/blob/master/oauthenticator/cilogon.py#L206.

In the CILogon authenticator, you can specify allowed identity provider suffixes in allowed_idps' - in my case these will be['bham.ac.uk', 'student.bham.ac.uk']`.

You can also specify strip_idp_domain, which will strip the username from (e.g. in my case) m.brett@bham.ac.uk to just m.brett. This is what I want.

But the logic specifies that I can only strip_idp_domain if I have exactly one entry in allowed_idps. Why is that a requirement? It's a problem in my case, because I must allow two suffixes to allow for staff and students, but I want the bare username e.g. "m.brett" rather than "m.brett@bham.ac.uk".

Maybe strip_idp_domain could also also allow a list of domains that should be stripped?

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Cleaned config

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pull request commentmatthew-brett/multibuild

Update openblas download from anaconda

Thanks Matti. Restarted.

mattip

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pull request commentmatplotlib/matplotlib

Add a code of conduct link to github

Only to say that, for the Scipy code of conduct (later adopted by Numpy) we struggled with the problem that codes of conduct are often very badly written, in an unpleasant imitation of legal documents, and disheartening, as well as being light on specifics of procedure for reporting adjudication and enforcement. So we did our collective best to be specific, and to make the text as readable and positive as possible.

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Teardown zonal cluster

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pull request commentmatplotlib/matplotlib

Add a code of conduct link to github

@story645 - do you think the Numpy one is OK, then, for Matplotlib (once names have been changed)? I do agree that the code of conduct should provide mechanisms for reporting, and stated procedures for when things go wrong.

dstansby

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Zonal cluster

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Correct authentication command

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Matthew Brett

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Revert "Clarify assumptions for disks in test rig" This reverts commit a966ffff03d5cb3f4084aa87eeb35687b2f98dd7.

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Make changes

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issue commentmatthew-brett/multibuild

Support Python 3.9

It's a bit dangerous to build wheels against the RCs, because the binary interface could still change, though it usually doesn't, I think.

Needed is Manylinux, and a macOS binary installer ...

hugovk

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PR opened data-8/materials-x18

Fix link to little_women data.

Link seems to have changed from earlier editions.

+1 -1

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Publicly available materials that are used in the Data 8X Foundations of Data Science course on EdX in 2018. Generated by data-8/assignments (private).

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Pull request review commentmatthew-brett/multibuild

Friendly error when curl HTTP errors downloading macOS python

 function install_mac_cpython {     local py_inst=$(pyinst_fname_for_version $py_version $py_osx_ver)     local inst_path=$DOWNLOADS_SDIR/$py_inst     mkdir -p $DOWNLOADS_SDIR-    curl $MACPYTHON_URL/$py_stripped/${py_inst} > $inst_path+    # catch 404 and other curl errors+    set +e

Sorry to return to this when my mind is cluttered with other stuff, but can't you do something on the lines of:

curl -L https://no.site/index.html > bar || (retval=$? && if [ "$retval" == 6 ]; then echo "Could not resolve host"; fi)

?

robbuckley

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My exercise for R

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Clarify assumptions for disks in test rig

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Show gcloud utility

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Generalize cluster name

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Remove stray copy of vars.sh

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Matthew Brett

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Make explicit that deployment is template Remarks to help use of testing YaML files for storage.

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Clean commented lines from YaML

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NFS server needs to be variable-completed in order to get disk name.

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Set up kubernetes environment.

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Matthew Brett

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Update notes on scaling

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pull request commentmatthew-brett/multibuild

update openblas download from anaconda

Getting a build failure - ?for PyPy - where it's trying to access https://anaconda.org/multibuild-wheels-staging/openblas-libs/v0.3.10/download/openblas-v0.3.10-manylinux2014_x86_64.tar.gz - that doesn't exist. Actually, I can't see that file at https://anaconda.org/multibuild-wheels-staging/openblas-libs/files - did I miss it? If not, should it exist?

mattip

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Refactoring disk name into vars.sh

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robbuckley

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bump python 2.7 latest to 2.7.18

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robbuckley

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fix build matrix

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Matthew Brett

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Update .travis.yml Co-authored-by: Andrew Murray <3112309+radarhere@users.noreply.github.com>

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Merge pull request #351 from robbuckley/py2718 MRG: Update python 2.7 to 2.7.18 Very minor changes over 2.7.17, but a couple are worth having for anyone still using 2.7 see https://github.com/python/cpython/blob/2.7/Misc/NEWS.d/2.7.18rc1.rst

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PR merged matthew-brett/multibuild

Update python 2.7 to 2.7.18

very minor changes over 2.7.17, but a couple are worth having for anyone still using 2.7 see https://github.com/python/cpython/blob/2.7/Misc/NEWS.d/2.7.18rc1.rst

+6 -9

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robbuckley

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pull request commentmatthew-brett/multibuild

Update python 2.7 to 2.7.18

Yes - thanks for the reminder.

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Comments on variable substitution.

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Comment on variable filling

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Comment on Docker image source

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issue commentmatthew-brett/multibuild

LAPACK library is not found for linux builds

@mattip - sorry to ping you at once - but I'm a bit out of date on Lapack now - any thoughts?

MarkWieczorek

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issue commentmatthew-brett/multibuild

Does multibuild work with versioneer?

Yes - a new issue would be good. I'm a little out of the loop on LAPACK these days - when you submit the issue, I'll @ mention Mattip - who has done the most recent work on that.

MarkWieczorek

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Updated comment [ci skip]

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Updated Python version [ci skip]

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Matthew Brett

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Merge pull request #9 from radarhere/patch-1 MRG: Updated comment As of c6a009e#diff-f36d243f9dd7dad91d339286d74fd515, it is no longer 3.8rc1, just 3.8

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Updated comment

As of https://github.com/matthew-brett/trusty/commit/c6a009eedb557f4157e5428b4093133a4e99363d#diff-f36d243f9dd7dad91d339286d74fd515, it is no longer 3.8rc1, just 3.8

+2 -2

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Updated comment

Great - thanks.

radarhere

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issue commentmatthew-brett/multibuild

Does multibuild work with versioneer?

Sorry for the comment-and-run - but just in case it helps debugging - I seem to remember that there is a problem with versioneer and submodules. The standard way to use multibuild is with your project as a submodule of your wheel-building repo. I wonder if you get any goodness from removing your project as a submodule, and then git cloning it in your travis.yml instead?

MarkWieczorek

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pull request commentmatthew-brett/trusty

Updated comment

Well spotted. Any chance of fixing the README while you're there?

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Drop 3.4 testing Not compatibile with requirements: ``` pyrsistent requires Python '>=3.5' ```

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Default CRAN repo; comment disable workspace save.

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Matthew Brett

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Make Python 3 default virtualenv.

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Disable Cmd-F1 screen mirror shortcut

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op Python snippet

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Jupyter in spell

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Fix rebuild_chapter script

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issue commentnumpy/numpy

PyPy has gone missing.

Isn't the URL fixed in latest multibuild 'devel'?

charris

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issue commentnumpy/numpy

aarch64 manylinux wheel and wrong pagesize

You can always re-upload the wheels with a new build tag : https://github.com/MacPython/wiki/wiki/Build-Tags

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Test get_cmake

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Andrew Murray

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Fixed running test_library_builders for build_multilinux

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Andrew Murray

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Install cmake instead if cmake28 cannot be found in yum

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Andrew Murray

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Skip building xz on manylinux

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Andrew Murray

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Deprecated get_cmake, renaming it to get_modern_cmake

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Andrew Murray

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Added ensure_xz instead of always skipping on manylinux

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Matthew Brett

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Merge pull request #342 from radarhere/cmake MRG: Install cmake instead if cmake28 cannot be found in yum When attempting to build on aarch64, I find that cmake28 is not found. However, cmake does exist. So this PR adds `get_modern_cmake` that searches for cmake28, and if it is not found, then use cmake instead.

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PR merged matthew-brett/multibuild

Install cmake instead if cmake28 cannot be found in yum

When attempting to build on aarch64, I find that cmake28 is not found. However, cmake does exist.

So this PR changes get_cmake to search for cmake28, and if it is not found, then use cmake instead.

+24 -11

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radarhere

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pull request commentmatthew-brett/multibuild

Install cmake instead if cmake28 cannot be found in yum

OK - thanks - let's do it.

radarhere

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pull request commentmatthew-brett/multibuild

Install cmake instead if cmake28 cannot be found in yum

Testing now, I agree, cmake28 exists on Manylinux 1 and 2010, but not 2014. On 2010 yum install cmake28 is identical to bare cmake in effect - installing cmake 2.8.12. So I think it is true that get_modern_cmake installs CMake >= 2.8 for all Manylinux versions (and macOS).

OK to put a comment in the function? Then I'm all OK with this. Any other thoughts?

radarhere

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pull request commentnumpy/numpy-tutorials

Fully automate dev setup with Gitpod

Just as a meta point - over at JupyterLab, we were worrying that it might be unhealthy for the ecosystem if Microsoft Visual Studio Code starts to dominate in the online notebook market. Is that a reason to prefer Gitpod, regardless of convenience? I believe that Gitpod is based on Theia, with a wider governance governance community than VSCode.

melissawm

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Filip Sund

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Documentation error.

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Matthew Brett

commit sha 52321496a0d98f1f698fd3ed81f680d740202553

Merge pull request #35 from FSund/euler2mat_doc_fix MRG: Documentation error in transforms3d.euler.euler2mat Fixes #34

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issue closedmatthew-brett/transforms3d

euler2mat documentation says it can return 4x4

According to the transforms3d.euler.euler2mat documentation it returns

mat : array-like shape (3, 3) or (4, 4)

But as far as I can see it will only return 3x3.

    M = np.eye(3)
    if repetition:
        M[i, i] = cj
        M[i, j] = sj*si
        M[i, k] = sj*ci
        M[j, i] = sj*sk
        M[j, j] = -cj*ss+cc
        M[j, k] = -cj*cs-sc
        M[k, i] = -sj*ck
        M[k, j] = cj*sc+cs
        M[k, k] = cj*cc-ss
    else:
        M[i, i] = cj*ck
        M[i, j] = sj*sc-cs
        M[i, k] = sj*cc+ss
        M[j, i] = cj*sk
        M[j, j] = sj*ss+cc
        M[j, k] = sj*cs-sc
        M[k, i] = -sj
        M[k, j] = cj*si
        M[k, k] = cj*ci
    return M

Is this an error in the docs, or the code, or is there something I'm not seeing?

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FSund

pull request commentmatthew-brett/transforms3d

Documentation error in transforms3d.euler.euler2mat

Great - thank you.

FSund

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issue commentmatthew-brett/transforms3d

euler2mat documentation says it can return 4x4

Oops - yes - looks like a documentation error. Do you have any interest in a little pull request to fix that?

FSund

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Fix Hacking ref.

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Matthew Brett

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Rename bibcheck target

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Matthew Brett

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References for MC, Hacking

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Pull request review commentmatthew-brett/multibuild

Update python 2.7 to 2.7.18

 matrix:     # OSX builds     - os: osx       env:-        - MB_PYTHON_VERSION=2.7+        - MB_PYTHON_VERSION=2.7.17 # 2.7.18 doesnt have a 10.6 build         - MB_PYTHON_OSX_VER=10.6         - TEST_BUILDS=1         - OPENSSL_ROOT=openssl-1.0.2u         - OPENSSL_HASH=ecd0c6ffb493dd06707d38b14bb4d8c2288bb7033735606569d8f90f89669d16-    - os: osx-      env:-        - MB_PYTHON_VERSION=2.7-        - MB_PYTHON_OSX_VER=10.9-        - TEST_BUILDS=1

I agree - I think there's no need to remove this job. But otherwise, I think it's good to go. Any other thoughts?

robbuckley

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Update .travis.yml Co-authored-by: Andrew Murray <3112309+radarhere@users.noreply.github.com>

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Remove make check-bib Biber not installed, and would pull in TeXlive.

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Fix bibliography, run make check before main build

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BF: work round setuptools 50.0 bug See https://github.com/pypa/setuptools/issues/2352 and https://github.com/pypa/setuptools/blob/17cb9d6bf249cefe653d3bdb712582409035a7db/CHANGES.rst#v5000

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Kroese MC article

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issue closednumpy/numpy

Can not run Python script in powerbi desktop

<!-- Please describe the issue in detail here, and fill in the fields below --> I have create csv file named "dataset" and write a python script to import it to Powerbi desktop. When I get data in powerbi desktop and paste above script, PBI show the error as following: "Details: "ADO.NET: Python script error. C:\Users\Admin\anaconda3\lib\site-packages\numpy_init.py:140: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service from . import distributor_init Traceback (most recent call last): File "PythonScriptWrapper.PY", line 2, in <module> import os, pandas, matplotlib File "C:\Users\Admin\anaconda3\lib\site-packages\pandas_init.py", line 17, in <module> "Unable to import required dependencies:\n" + "\n".join(missing_dependencies) ImportError: Unable to import required dependencies"_

Reproducing code example:

<!-- A short code example that reproduces the problem/missing feature. It should be self-contained, i.e., possible to run as-is via 'python myproblem.py' --> My python script is: "import pandas as pd import numpy as np import matplotlib from matplotlib import pyplot as plt df = pd.read_csv(r'C:\Users\Admin\Desktop\Python\Python_to_powerbi\Dataset.csv') print(df)"

And I also attach my csv file. https://github.com/thuantv-vp/Python-and-powerbi/blob/master/Dataset.csv For more information I use Anaconda with python version is 3.7.4 and Numpy version is 1.18.1 Matplotlib is also installed

Please help me to fix this integration error. Many [thanks]

<< import pandas as pd
import numpy as np
import matplotlib
from matplotlib import pyplot as plt
df = pd.read_csv(r'C:\Users\Admin\Desktop\Python\Python_to_powerbi\Dataset.csv')
print(df)>>

<!-- Remove these sections for a feature request -->

Error message:

<!-- If you are reporting a segfault please include a GDB traceback, which you can generate by following https://github.com/numpy/numpy/blob/master/doc/source/dev/development_environment.rst#debugging -->

<!-- Full error message, if any (starting from line Traceback: ...) -->

Numpy/Python version information:

<!-- Output from 'import sys, numpy; print(numpy.version, sys.version)' -->

closed time in 23 days

thuantv-vp

issue commentnumpy/numpy

Can not run Python script in powerbi desktop

Closing for now, please do reopen if you believe this is due to Numpy.

thuantv-vp

comment created time in 23 days

issue commentnumpy/numpy

Can not run Python script in powerbi desktop

Are you sure this is a Numpy problem? What do you get if you start Python again, and do just import numpy?

thuantv-vp

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pull request commentmatthew-brett/multibuild

MRG: document switch from Rackspace

OK to merge this one?

matthew-brett

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Matthew Brett

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Update Cython code links [skip ci]

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Pull request review commentmatthew-brett/multibuild

MRG: document switch from Rackspace

 Utilities for building on Travis CI and AppVeyor ################################################ +*****************************+Update: Uploads and Rackspace+*****************************++The original Multibuild default was to upload wheels to a Rackspace container,+where Rackspace kindly donated the hosting to the Scikit-learn team.  We had+a URL pointing to the Rackspace container: `http://wheels.scipy.org`.++Rackspace finally stopped subsidizing this container, and the Rackspace of+`http://wheels.scipy.org` is no more. Projects using Multibuild have moved to+using https://anaconda.org/scipy-wheels-nightly/ for weekly uploads and+https://anaconda.org/multibuild-wheels-staging for staging wheels to PyPI.++Another option is to use GitHub for staging --- as do Cython for Travis CI and for+AppVeyor.  Here is the NumPy code (for running on Travis CI) to upload to

Sorry - I did that too fast, and didn't notice that you'd done that above, with basically the same changes.

matthew-brett

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Pull request review commentmatthew-brett/multibuild

MRG: document switch from Rackspace

 Utilities for building on Travis CI and AppVeyor ################################################ +*****************************+Update: Uploads and Rackspace+*****************************++The original Multibuild default was to upload wheels to a Rackspace container,+where Rackspace kindly donated the hosting to the Scikit-learn team.  We had+a URL pointing to the Rackspace container: `http://wheels.scipy.org`.++Rackspace finally stopped subsidizing this container, and the Rackspace of+`http://wheels.scipy.org` is no more. Projects using Multibuild have moved to+using https://anaconda.org/scipy-wheels-nightly/ for weekly uploads and+https://anaconda.org/multibuild-wheels-staging for staging wheels to PyPI.++Another option is to use GitHub for staging --- as do Cython for Travis CI and for+AppVeyor.  Here is the NumPy code (for running on Travis CI) to upload to

No - that was an accident of copy-paste from the Github interface. I've put them back now.

matthew-brett

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Update Cython code links

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commit sha 6b3db57e7f1f5255740493a19b3aea32bb9d17e7

Apply suggestions from review Thanks @hugovk Co-authored-by: Hugo van Kemenade <hugovk@users.noreply.github.com>

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issue commentMacPython/numexpr-wheels

Move away from rackspace

Documented via https://github.com/matthew-brett/multibuild/pull/350 - please have a look?

mattip

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PR opened matthew-brett/multibuild

MRG: document switch from Rackspace

Thanks to @mattip.

+32 -19

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Document switch from Rackspace Thanks to @mattip

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issue commentscipy/scipy

Use manylinux2014 to get aarch64/ppc64le support

As I remember it, when I uploaded Intell-architecture Numpy wheels for previous releases, it found someone whose pipeline depended on the fact that Numpy was installing from source for an older release. I suspect this is very unusual.

hrw

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issue commentMacPython/numexpr-wheels

Move away from rackspace

Thanks Matti - yes - I will use this link from now on - and will put it into the README for Multibuild.

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Efron not Bayesian

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issue commentmatthew-brett/multibuild

wheels.scipy.org server not found

Ah - no - sorry - we haven't got round to documenting this yet, but the Rackspace account is now closed (they stopped subsidizing it).

Most of us have now moved to hosting wheels on Anaconda.org space.

A useful Numpy thread is here: https://mail.python.org/pipermail/numpy-discussion/2020-August/080915.html

Summarizing: Numpy has some example machinery for uploading to the Anaconda.org space:

https://github.com/MacPython/numpy-wheels/blob/master/azure/posix.yml#L87

@mattip - sorry - I bet I'm just being lazy here - but can you comment on permissions for the Anaconda upload?

robbmcleod

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pull request commentmatthew-brett/multibuild

Install cmake instead if cmake28 cannot be found in yum

Ah - that's interesting - I thought this was a fix for the very old cmake on manylinux1 - but not so?

I also thought that it was somewhat equivalent in practice to asking for a cmake >= 2.8 - also not so?

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