pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/License.txt

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+-------------------------------------------------------------------------------
+                     pyopenms -- Python wrapper for OpenMS
+-------------------------------------------------------------------------------
+
+Copyright (C) 2011-2017 -- Uwe Schmitt
+
+This software is released under a three-clause BSD license:
+ * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+ * Neither the name of any author or any participating institution
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+For a full list of authors, refer to the file AUTHORS.
+--------------------------------------------------------------------------
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
+INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+-------------------------------------------------------------------------------
+
+The source code of pyOpenMS is available via
+                                      http://github.com/uweschmitt/pyOpenMS
+
+-------------------------------------------------------------------------------
+
+pyOpenMS depends on the following third party libraries which are included:
+
+
+    Open-MS
+        - URL: http://www.open-ms.de
+
+    Qt 4
+        - URL: http://trolltech.com/downloads/opensource
+
+    If you want to build pyopenms on Microsoft Windows:
+
+    Microsoft Visual C Runtime from Visual C++ 2008 Redistributable Package:
+
+        - URL: http://www.microsoft.com
+
+

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/__init__.py

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+from __future__ import print_function
+from __future__ import absolute_import
+
+from .sysinfo import *
+from .version import version as __version__
+
+import os
+here = os.path.abspath(os.path.dirname(__file__))
+os.environ["OPENMS_DATA_PATH"] = os.path.join(here, "share/OpenMS")
+
+import sys
+if sys.platform.startswith("linux"):
+    # load local shared libries before we import pyopenms.so, else
+    # those are not found. setting LD_LIBRARY_PATH does not work,
+    # see: http://stackoverflow.com/questions/1178094
+    import ctypes
+    ctypes.cdll.LoadLibrary(os.path.join(here, "libOpenSwathAlgo.so"))
+    ctypes.cdll.LoadLibrary(os.path.join(here, "libOpenMS.so"))
+    ctypes.cdll.LoadLibrary(os.path.join(here, "libSuperHirn.so"))
+
+try:
+    from .all_modules import *
+    from .python_extras import *
+except Exception as e:
+    print("\n")
+    print("="*70)
+    print("\n")
+    print("maybe you miss some libraries. please run ldd (on linux) or")
+    print("dependency walker (on windows) on ")
+    print("\n")
+    print(os.path.join(here, "pyopenms.so"))
+    print("\n")
+    try:
+        import PyQt4.QtCore
+    except:
+        pass
+    else:
+        from .qt_version_info import info
+
+        info = "\n    ".join(info.split("\n"))
+
+        print("""When building pyopenms qmake said:
+
+    %s
+PYQT has version %s
+
+Maybe this causes a conflict.  You can test this by importing pyopenms
+first and then import PyQt4.QtCore.
+        """ % (info, PyQt4.QtCore.PYQT_VERSION_STR) )
+    print("="*70)
+    print("\n")
+    raise e
+
+del os, here, sys

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/all_modules.py

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+from .pyopenms_1 import *
+from .pyopenms_2 import *
+from .pyopenms_3 import *
+from .pyopenms_4 import *

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/docompile.py

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+# Python script to compile Cython to C++
+# 
+# this script compiles the *.pyx infile (pyopenms/pyopenms.pyx) to .cpp
+# 
+# It can be run in the build process of pyopenms when manual changes to the pyx
+# files need to be made (not recommended!).
+# 
+# == taken from autowrap/Main.py run(), lower part
+from __future__ import print_function
+
+infile  = "pyopenms/pyopenms.pyx"
+
+import cPickle
+persisted_data_path = "include_dir.bin"
+autowrap_include_dirs = cPickle.load(open(persisted_data_path, "rb"))
+# autowrap_include_dirs = ['/usr/local/lib/python2.7/dist-packages/autowrap/data_files/boost', '/usr/local/lib/python2.7/dist-packages/autowrap/data_files', '/path/to/pyOpenMS/pxds', 'from Map cimport Map as _Map']
+
+
+from Cython.Compiler.Main import compile, CompilationOptions
+from Cython.Compiler.Options import directive_defaults
+directive_defaults["boundscheck"] = False
+directive_defaults["wraparound"] = False
+
+options = dict(include_path=autowrap_include_dirs,
+               compiler_directives=directive_defaults,
+               #output_dir=".",
+               #gdb_debug=True,
+               cplus=True)
+
+print("Compiling with Cython the file", infile)
+print("Using include_path", autowrap_include_dirs)
+options = CompilationOptions(**options)
+compile(infile, options=options)
+print("Success!")
+

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/python_extras.py

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+class SimpleOpenMSSpectraFactory:
+
+    @staticmethod
+    def getSpectrumAccessOpenMSPtr(exp):
+      is_cached = False
+
+      for i in range(exp.size()):
+        for dp in exp[i].getDataProcessing():
+          if dp.metaValueExists("cached_data"):
+            is_cached = True
+
+      for chrom in exp.getChromatograms():
+        for dp in chrom.getDataProcessing():
+          if dp.metaValueExists("cached_data"):
+            is_cached = True
+
+      if is_cached:
+        return SpectrumAccessOpenMSCached( exp.getLoadedFilePath() )
+      else:
+        return SpectrumAccessOpenMS( exp )
+
+

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/qt_version_info.py

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+info='QMake version 2.01a\nUsing Qt version 4.8.7 in /usr/lib/x86_64-linux-gnu\n'
+