PyInstaller

PyInstaller

Whats this:
http://www.pyinstaller.org/
https://mborgerson.com/creating-an-executable-from-a-python-script

Take a look at this:

https://www.digitalocean.com/community/tutorials/how-to-package-and-distribute-python-applications

My first python package on pypi - mspy

Have you heard about http://www.mmass.org/?
It's a python application (with a GUI) for processing and visualizing mass spectrometric data.
Unfortunately, development is discontinued (the latest release was  Jul 1, 2013)*. Unfortunately since there are a few cool features in mMass:

• mzXML file access
• peak detection and deisotoping
• recalibration
• ...

Since mMass, at the first glance is code of good quality, and algorithms are separated from the GUI, it was relatively easy to create a python package containing the algorithm part**. This part is now available as package here:

https://pypi.python.org/pypi/mspy

(Windows 64 version for the start)

so
pip install mspy
will do.

The sources of the package is now here:
https://github.com/wolski/mspy

There are no unit tests (I did not find any, if I will be using mspy I will be adding some).


* Martin Strohalm, PhD. the developer of mMass is now, according to his linked in profile, at Thermo Fischer in Bremen developing I guess some super cool software in C# for the Thermo Orbitrap Mass-specs.

** Although the author specified in the setup.py file is Martin Strohalm at pypi I am missleadingly specified as the author!?

Resharper C++ and findMFBase

Finally got findMFBase
build in with VS. (see my previous post about findMFBase).

The generated .vcproj's build the unit tests shipped with findMFBase.
I have an academic licence of C++ Resharper and would like to put this software to some use.

The problem is that C++ ReSharper seems not to be aware of the header files of findMFBase (a header only library).

As long as I am in the .cpp file everything seems fine but if I open an header than the #include statements pointing to other header files within the findMFBase library are marked in red.

I did the cmake glob trick to have the header files included in the project.

file(GLOB Demo_HEADERS "sql/*.sql" "include/*.h" "include/**/*.h" "include/**/**/*.h"

 "include/**/**/**/*.h" "src/**/*.h" "src/**/**/*.h" ".travis.yml")

add_library(headers SHARED ${Demo_HEADERS} Dummy.cpp)

But as already said Resharper C++ is not aware of them.

I did post the problem also at the C++ ReSharper forum. Curious what they reply? Hopefully they are not going recommend to use clion because of cmake (Visual Studio is so much cooler).

Building findMFBase on windows for VisualStudio

I am trying to build the project https://github.com/findMF/findMFBase 

on windows. (for details of linux build check the .travis.yml file and take a look at Travis build results).

Since, cmake's find_boost does not work on windows, and also setting Boost_DIR in CMake GUI does not work I needed to add to the topmost CMakeLists.txt file

set(BOOST_ROOT "C:/boost/boost_1_57_0/")

Likely you boost installation is somewhere else so adjust it.

I did download prebuild boost libraries from here:

http://sourceforge.net/projects/boost/files/boost-binaries/1.57.0/

And also renamed the lib_win64... directory (the containing the .lib files) into lib/

Than I did run (in PowerShell):

mkdir findMFBaseBuild
cd findMFBaseBuild

cmake ..\findMFBase -G "Visual Studio 12 2013 Win64"

(Since I have VS 2013 community edition installed)

Than I open the generated sln in VS and build the ALL_BUILD project.

What I struggled with when building on windows was the following (now fixed)

Some projects are build but the first project having a dependency on data_time fails with

fatal error LNK1104: cannot open file 'libboost_date_time-vc120-mt-gd-1_59.lib'

I did a search for liboost_*.lib vs. boost_*.lib which returns some discussions on Stackoverflow pointing too:

SET( USE_STATIC_BOOST ON)
set(Boost_USE_STATIC_LIBS ${USE_STATIC_BOOST})

Which does not solve the problem. Finally I find this entry: 

http://stackoverflow.com/questions/28887680/linking-boost-library-with-boost-use-static-lib-off-on-windows

So the solution:
add_definitions( -DBOOST_ALL_NO_LIB )

For more detail see http://www.boost.org/doc/libs/1_57_0/libs/config/doc/html/index.html

Virtualenv on windows and building python packages

using now conda to manage virtual envs on windows (update 19/12/2015)

http://uoa-eresearch.github.io/eresearch-cookbook/recipe/2014/11/20/conda/

for interop with pycharm see:

http://stackoverflow.com/questions/28390961/using-anaconda-within-pycharm

Very helpful (notice got it running only with python 2.7):

http://www.tylerbutler.com/2012/05/how-to-install-python-pip-and-virtualenv-on-windows-with-powershell/

Once you have set up the virtual env and you want to use it in a new powershell just edit the shortcut to PS so that :
Target: %SystemRoot%\syswow64\WindowsPowerShell\v1.0\powershell.exe -ExecutionPolicy Unrestricted
Start In: %HOMEDRIVE%%HOMEPATH%

Creating virtual environment:
Import-Module virtualenvwrapper
New-VirtualEnvironment applicake

Loading a virtual env:

Import-Module virtualenvwrapper 
(not sure if it is actually necessary?)

# I have already these environments
Set-VirtualEnvironment engineer
Set-VirtualEnvironment applicake
Set-VirtualEnvironment mspy

Virtual env on linux

source virtenvs/systemmhc/bin/activate

Building native python packages on windows just download:

Microsoft Visual C++ Compiler for Python 2.7

http://www.microsoft.com/en-us/download/details.aspx?id=44266

afterwards you can install numpy by executing
pip install numpy

Some package are more difficult to build because of their dependencies. In such a case visit:
http://www.lfd.uci.edu/~gohlke/pythonlibs/

Building python packages

Just create a folder in the folder create a setup.py file, create a subfolder, place in the subfolder your .py files and an __init__.py file (see my tiny python project cakeme).

install package in user directory  (no virtual env but --user directory):

pip install --user cakeme

install package locally in development mode:

pip install --user -e . (begin in the package directory)

create local whl file

python setup.py bdist_wheel

Register package with pypi.python.org

python setup.py register

Pushing changes in python package to pypi:

python setup.py bdist_wheel upload




How to install a whl file:

pip install some-package.whl

Some more tipps for powershell users:

$env:Path += ";C:\Program Files\Sublime Text 2\"

Calling pwiz build from visual studio

I got this information from Parag and since it might be relevant to many I post it here:

So it means that you can use visual studio as plain text editor when developing pwiz. I might use notepad++ instead.

Classification with R

http://machinelearningmastery.com/linear-classification-in-r/
http://machinelearningmastery.com/feature-selection-with-the-caret-r-package/
http://topepo.github.io/caret/index.html

R markdown to pdf

Rendering from R

rmarkdown::render("specL.Rmd",output_format ="pdf_document", output_file = "SpecL.pdf", clean=FALSE)

Disabling echos and messages for entire document

```{r, include=FALSE}
library(knitr)
opts_chunk$set(echo=FALSE, message=FALSE, warnings=FALSE)

```

Connecting to data with R

pure sql actually

http://www.r-bloggers.com/using-sqlite-in-r/

http://faculty.washington.edu/kenrice/sisg-adv/exampleSQLite.R

ORM with dplyr

I use them as references:

http://rpubs.com/justmarkham/dplyr-tutorial
https://www.youtube.com/watch?v=jWjqLW-u3hc&feature=youtu.be

http://rpubs.com/justmarkham/dplyr-tutorial-part-2
https://www.youtube.com/watch?v=2mh1PqfsXVI&feature=youtu.be

package vignettes

https://cran.r-project.org/web/packages/dplyr/vignettes/

Example how to convert MaxQuant output to plyr using R:

http://rpubs.com/witold/115760

Example how to do a join on floats with errors with dplyr, DBI or sqldf

http://rpubs.com/witold/joinonnumeric

Accessing HDF5 with rhdf5

regarding other possibilities see:
http://stackoverflow.com/questions/15974643/how-to-deal-with-hdf5-files-in-r

rhdf5 package vignette
http://www.bioconductor.org/packages//2.13/bioc/vignettes/rhdf5/inst/doc/rhdf5.pdf

Sentiment analysis with R

To read...

https://sites.google.com/site/miningtwitter/questions/sentiment/sentiment

http://lct-master.org/files/MullenSentimentCourseSlides.pdf

http://andybromberg.com/sentiment-analysis/
http://andybromberg.com/sentiment-analysis-python/

maltcms - getting started

http://maltcms.sourceforge.net/

git clone git://git.code.sf.net/p/maltcms/code
git fetch origin
git checkout release-1.4.0

cd maltcms-code
mvn install


Furthermore, download data from:
http://sourceforge.net/projects/maltcms/files/maltcms/example-data/

in
maltcms-code\maltcms-distribution\target\maltcms-1.4.0-SNAPSHOT-bin\maltcms-1.4.0-SNAPSHOT>

bin\maltcms.bat -Xrunjdwp:transpt=dt_socket,server=y,address=8888,suspend=y -c cfg\pipelines\bipace.mpl -f C:\Users\wolski\prog\maltcms-sampledata\maltcms-example-data\cdf\1D\*.cdf -o testOutput

bin\maltcms.bat -c cfg\pipelines\bipace.mpl -f C:\Users\wolski\prog\maltcms-sampledata\maltcms-example-data\cdf\1D\*.cdf -o testOutput


user information:
http://maltcms.sourceforge.net/maven/maltcms/1.3.2/gettingStarted.html


More information:
http://www.biomedcentral.com/1471-2105/13/214