6 files were added to this release more than 14 days after its initial publication. Inspect the release files before installing.
Introduction
This package contains Python bindings for a large part of the OpenMS library (http://www.open-ms.de) for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).
The pyOpenMS package runs - like OpenMS - on Windows, Linux and OSX.
Installation
We provide binary packages for Python 2.6 and 2.7 on Windows (64 bit) and Linux 64 bit which makes the installation very straightforward with pip. For other platforms, please refer to the compilation instructions.
Binary installation
On linux machines you can install pyopenms with:
$ easy_install pyopenms
For other systems first ensure that your pip is up to date, then install the pyopenms wheel:
$ pip install -U pip $ pip install -U wheel $ pip install pyopenms
Source installation
Download the latest OpenMS source from SVN (following the OpenMS documentation), configure and build.
Install Qt and then start with the dependencies of OpenMS itself:
$ svn co https://open-ms.svn.sourceforge.net/svnroot/open-ms/contrib $ cmake .
Now you have to install the dependencies of pyOpenMS:
Install Python (2.6 or 2.7)
Install numpy (On OSX, numpy should already be installed. On GNU/Linux there should be packages for numpy (e.g. python-numpy for Ubuntu/Debian). On Windows, you can install it from Christoph Gohlkes webpage).
Install setuptools, see the setuptools PyPI page .
Use setuptools to install pip, autowrap and nose:
$ easy_install pip $ pip install autowrap $ pip install nose
Configure and build pyOpenMS:
$ svn co https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS $ cmake -DPYOPENMS=ON . $ make pyopenms_bdist_egg
This should build a file like pyopenms-1.10.1-py2.7-linux-x86_64.egg the folder ./pyOpenMS/dist of your build directory which you can distribute or install it from there:
$ cd pyOpenMS/dist $ easy_install pyopenms-1.10.1-py-2.7-linux-x86_64.egg
Testing
pyOpenMS provides unittests, they are found under ./pyOpenMS/tests/ and can be executed using nosetests:
$ python run_nose.py
License
pyOpenMS is published under the 3-clause BSD licence, see ./pyOpenMS/License.txt
Documentation
pyOpenMS follows the OpenMS documentation very closely. Additionally, there is also a pyOpenMS Manual available. The online manual contains a complete record of every wrapped class and function while the documentation of the corresponding class or function can be inferred from the OpenMS online documentation.
3 maintainers
Metadata
3 maintainers
Release files for pyopenms 2.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Files added late
6 files were uploaded more than 14 days after the first file in this release.
While project maintainers occasionally add legitimate files to an existing release, late additions can also indicate a security compromise.
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Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| pyopenms-2.0.post0-cp27-none-win_amd64.whl | CPython 2.7 | none | Windows x86-64 | Details |
| pyopenms-2.0.0-py3.4-linux-x86_64.egg | Legacy Egg format | - | - | Details |
| pyopenms-2.0.0-py2.7-linux-x86_64.egg | Legacy Egg format | - | - | Details |
| pyopenms-2.0.0-py2.6-linux-x86_64.egg | Legacy Egg format | - | - | Details |
| pyopenms-2.0-cp27-none-macosx_10_10_intel.whl | CPython 2.7 | none | macOS 10.10+ Intel (x86-64, i386) | Details |
| pyopenms-2.0-cp27-none-macosx_10_9_intel.whl | CPython 2.7 | none | macOS 10.9+ Intel (x86-64, i386) | Details |
Total release size: 147.1 MB
Release files / pyopenms-2.0.post0-cp27-none-win_amd64.whl
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| Download URL | pyopenms-2.0.post0-cp27-none-win_amd64.whl |
|---|---|
| Size | 26.1 MB |
| Tags | CPython 2.7 Windows x86-64 |
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Release files / pyopenms-2.0.0-py3.4-linux-x86_64.egg
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| Download URL | pyopenms-2.0.0-py3.4-linux-x86_64.egg |
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Release files / pyopenms-2.0.0-py2.7-linux-x86_64.egg
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| Download URL | pyopenms-2.0.0-py2.7-linux-x86_64.egg |
|---|---|
| Size | 17.1 MB |
| Tags | Egg |
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Release files / pyopenms-2.0.0-py2.6-linux-x86_64.egg
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| Download URL | pyopenms-2.0.0-py2.6-linux-x86_64.egg |
|---|---|
| Size | 17.7 MB |
| Tags | Egg |
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| Download URL | pyopenms-2.0-cp27-none-macosx_10_10_intel.whl |
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| Size | 34.6 MB |
| Tags | CPython 2.7 macOS 10.10+ Intel (x86-64, i386) |
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File added late
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While project maintainers occasionally add legitimate files to an existing release, late additions can also indicate a security compromise.
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| Download URL | pyopenms-2.0-cp27-none-macosx_10_9_intel.whl |
|---|---|
| Size | 34.6 MB |
| Tags | CPython 2.7 macOS 10.9+ Intel (x86-64, i386) |
|
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