Category Archives: Uncategorized

sphinx raise a WARNING: Duplicate explicit target name:

Posted on April 24, 2020 by Thomas Cokelaer

Sphinx is a great tool for developers who want to write nice documentation about their software. I actually use it also to take notes or write about other stuff. From time to time I have a warning such as : … Continue reading →

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pypi upload failed due to non-existent authentication information

Posted on December 27, 2018 by Thomas Cokelaer

After trying to upload a package on Pypi website using python setup.py sdist upload I got this error message: Submitting dist/XXX-0.7.5.tar.gz to https://upload.pypi.org/legacy/ Upload failed (403): Invalid or non-existent authentication information. error: Upload failed (403): Invalid or non-existent authentication information.Submitting … Continue reading →

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git synchronisation of a forked repository

Posted on October 12, 2016 by Thomas Cokelaer

Let us assume you have forked a repository (from https://github.com/project/repository_name). You now have a local version at a given time of the repository repository_name. git pull https://github.com/project/repository_name cd repository_namegit pull https://github.com/project/repository_name cd repository_name Time flyes and you come back to … Continue reading →

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Starting with docker and creating an image with ipython

Posted on May 14, 2015 by Thomas Cokelaer

On my fedora box, I followed the instructions from the official web page: https://docs.docker.com/installation/fedora/ sudo yum -y install docker sudo systemctl start docker sudo systemctl enable docker sudo docker run -i -t fedora /bin/bashsudo yum -y install docker sudo systemctl … Continue reading →

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How to update a forked repository (github)

Posted on December 11, 2014 by Thomas Cokelaer

I followed those steps and it worked like a charm using github interface assuming there was no changes between the fork and main repository Open your fork on GitHub. Click on Pull Requests. Click on New Pull Request. By default, … Continue reading →

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Moving from SVN to git: $Id:$ equivalent

Posted on December 11, 2014 by Thomas Cokelaer

In SVN (and CVS), you could include special strings such as $Id:$$Id:$ and after a commit, the revision number would appear after “Id:”, which was a convenient way to retrieve the revision for instance in a print statement. Apparently, with … Continue reading →

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Migrating from a Subversion repository to GitHub

Posted on August 16, 2014 by Thomas Cokelaer

I’ve just moved a SVN repository to github. I was a bit afraid of spending time and lost the history but fortunately, I came upon this great post http://www.samaxes.com/2013/11/move-from-svn-to-git/ , followed the instructions and it worked almost like a charm. … Continue reading →

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perl: define a module to be called in another script

Posted on June 9, 2014 by Thomas Cokelaer

First, define a module. The module must be in a path reachable by perl (e.g., local directory). Then, to make a script a valid package, you need to proceed as follows: Rename the perl script with the extension .pm It … Continue reading →

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R package dependencies: difference between imports, depends, suggests, enhances

Posted on July 31, 2013 by Thomas Cokelaer

When you want to assemble R codes into a package, you will need to write a file called DESCRIPTION. This file contains some metadata and keywords to be used and some keywords are definitely confusing (at least to me). Here … Continue reading →

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Python: ValueError: unknown locale: UTF-8

Posted on June 13, 2013 by Thomas Cokelaer

When installing bioservices (a python package) using pip or easy_install, I got this error Mac OS X 10.7 – Lion: ValueError: unknown locale: UTF-8ValueError: unknown locale: UTF-8 Although the installation is successful, the error will appear as soon as we … Continue reading →

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