separate setup.py with pip installation, add trouble shooting page

python-package/build_trouble_shooting.md

@@ -0,0 +1,48 @@
+XGBoost Python Package Troubleshooting
+======================
+Windows platform
+------------
+The current best solution for installing xgboost on windows machine is building from github. Please go to [windows](/windows/), build with the Visual Studio project file, and install. Additional detailed instruction can be found at this [installation tutorial](https://www.kaggle.com/c/otto-group-product-classification-challenge/forums/t/13043/run-xgboost-from-windows-and-python) from Kaggle Otto Forum.
+
+`pip install xgboost` is **not** tested nor supported in windows platform for now. 
+
+Linux platform (also Mac OS X in general)
+------------
+**Trouble 0**: I see error messages like this when install from github using `python setup.py install`.
+
+    XGBoostLibraryNotFound: Cannot find XGBoost Libarary in the candicate path, did you install compilers and run build.sh in root path?
+    List of candidates:
+    /home/dmlc/anaconda/lib/python2.7/site-packages/xgboost-0.4-py2.7.egg/xgboost/libxgboostwrapper.so
+    /home/dmlc/anaconda/lib/python2.7/site-packages/xgboost-0.4-py2.7.egg/xgboost/../../wrapper/libxgboostwrapper.so
+    /home/dmlc/anaconda/lib/python2.7/site-packages/xgboost-0.4-py2.7.egg/xgboost/./wrapper/libxgboostwrapper.so
+
+**Solution 0**: Please check if you have:
+
+* installed C++ compilers, for example `g++` and `gcc` (Linux) or `clang LLVM` (Mac OS X). Recommended compilers are `g++-5` or newer (Linux and Mac), or `clang` comes with Xcode in Mac OS X. For installting compilers, please refer to your system package management commands, e.g. `apt-get` `yum` or `brew`(Mac).
+* compilers in your `$PATH`. Try typing `gcc` and see if your have it in your path.
+
+**Trouble 1**: I see the same error message in **Trouble 0** when install from `pip install xgboost`.
+
+**Solution 1**: the problem is the same as in **Trouble 0**, please see **Solution 0**.
+
+**Trouble 2**: I see this error message when `pip install xgboost`. It says I have `libxgboostwrapper.so` but it is not valid.
+
+    OSError: /home/dmlc/anaconda/lib/python2.7/site-packages/xgboost/./wrapper/libxgboostwrapper.so: invalid ELF header
+   
+**Solution 2**: Solution is as in 0 and 1 by installing `g++` compiler. The reason for this rare error is that, `pip` ships with a pre-compiled `libxgboostwrapper.so` with Mac for placeholder for allowing `setup.py` to find the right lib path. If a system doesn't compile, it may refer to this placeholder lib and fail. This placeholder `libxgboostwrapper.so` will be automatically removed and correctly generated by the compiling on-the-fly for the system.
+
+**Trouble 3**: My system's `pip` says it can't find a valid `xgboost` installation release on `PyPI`.
+**Solution 3**: Some linux system comes with an old `pip` version. Please update to the latest `pip` by following the official installation document at <http://pip.readthedocs.org/en/stable/installing/>
+
+**Trouble 4**: I tried `python setup.py install` but it says `setuptools` import fail.
+**Solution 4**: Please make sure you have [setuptools](https://pypi.python.org/pypi/setuptools) before installing the python package.
+
+Mac OS X (specific)
+------------
+Most of the troubles and solutions are the same with that in the Linux platform. Mac has the following specific problems.
+
+**Trouble 0**: I successfully installed `xgboost` using github installation/using `pip install xgboost`. But it runs very slow with only single thread, what is going on?
+**Solution 0**: `clang LLVM` compiler on Mac OS X from Xcode doesn't support OpenMP multi-thread. An alternative choice is installing `homebrew` <http://brew.sh/> and `brew install g++-5` which provides multi-thread OpenMP support.
+
+**Trouble 1**: Can I install `clang-omp` for supporting OpenMP without using `gcc`?
+**Solution 1**: it is not support and may have linking errors.

python-package/setup.py

@@ -7,19 +7,6 @@ from setuptools import setup, find_packages
 #import subprocess
 sys.path.insert(0, '.')
 
-#build on the fly if install in pip
-#otherwise, use build.sh in the parent directory
-
-#ugly solution since pip version transition and the old pip detection method not
-#working. Manually turn on when packing up for pip installation
-if False:
-    if not os.name == 'nt': #if not windows
-        os.system('sh ./xgboost/build-python.sh')
-    else:
-        print('Windows users please use github installation.')
-        sys.exit()
-
-
 CURRENT_DIR = os.path.dirname(__file__)
 
 # We can not import `xgboost.libpath` in setup.py directly since xgboost/__init__.py
@@ -31,10 +18,8 @@ exec(compile(open(libpath_py, "rb").read(), libpath_py, 'exec'), libpath, libpat
 
 LIB_PATH = libpath['find_lib_path']()
 
-#to deploy to pip, please use
+#Please use setup_pip.py for generating and deploying pip installation
-#make pythonpack
+#detailed instruction in setup_pip.py
-#python setup.py register sdist upload
-#and be sure to test it firstly using "python setup.py register sdist upload -r pypitest"
 setup(name='xgboost',
       version=open(os.path.join(CURRENT_DIR, 'xgboost/VERSION')).read().strip(),
       #version='0.4a23',
@@ -47,14 +32,8 @@ setup(name='xgboost',
       maintainer_email='phunter.lau@gmail.com',
       zip_safe=False,
       packages=find_packages(),
-      #don't need this and don't use this, give everything to MANIFEST.in
-      #package_dir = {'':'xgboost'},
-      #package_data = {'': ['*.txt','*.md','*.sh'],
-      #               }
       #this will use MANIFEST.in during install where we specify additional files,
       #this is the golden line
       include_package_data=True,
-      #!!! don't use data_files, otherwise install_data process will copy it to
-      #root directory for some machines, and cause confusions on building
       data_files=[('xgboost', LIB_PATH)],
       url='https://github.com/dmlc/xgboost')

python-package/setup_pip.py

@@ -0,0 +1,58 @@
+# pylint: disable=invalid-name, exec-used
+"""Setup xgboost package."""
+from __future__ import absolute_import
+import sys
+import os
+from setuptools import setup, find_packages
+#import subprocess
+sys.path.insert(0, '.')
+
+#this script is for packing and shipping pip installation
+#it builds xgboost code on the fly and packs for pip
+#please don't use this file for installing from github
+
+if not os.name == 'nt': #if not windows, compile and install
+    os.system('sh ./xgboost/build-python.sh')
+else:
+    print('Windows users please use github installation.')
+    sys.exit()
+
+CURRENT_DIR = os.path.dirname(__file__)
+
+# We can not import `xgboost.libpath` in setup.py directly since xgboost/__init__.py
+# import `xgboost.core` and finally will import `numpy` and `scipy` which are setup
+# `install_requires`. That's why we're using `exec` here.
+libpath_py = os.path.join(CURRENT_DIR, 'xgboost/libpath.py')
+libpath = {'__file__': libpath_py}
+exec(compile(open(libpath_py, "rb").read(), libpath_py, 'exec'), libpath, libpath)
+
+LIB_PATH = libpath['find_lib_path']()
+
+#to deploy to pip, please use
+#make pythonpack
+#python setup.py register sdist upload
+#and be sure to test it firstly using "python setup.py register sdist upload -r pypitest"
+setup(name='xgboost',
+      #version=open(os.path.join(CURRENT_DIR, 'xgboost/VERSION')).read().strip(),
+      version='0.4a24',
+      description=open(os.path.join(CURRENT_DIR, 'README.md')).read(),
+      install_requires=[
+          'numpy',
+          'scipy',
+      ],
+      maintainer='Hongliang Liu',
+      maintainer_email='phunter.lau@gmail.com',
+      zip_safe=False,
+      packages=find_packages(),
+      #don't need this and don't use this, give everything to MANIFEST.in
+      #package_dir = {'':'xgboost'},
+      #package_data = {'': ['*.txt','*.md','*.sh'],
+      #               }
+      #this will use MANIFEST.in during install where we specify additional files,
+      #this is the golden line
+      include_package_data=True,
+      #!!! don't use data_files for creating pip installation,
+      #otherwise install_data process will copy it to
+      #root directory for some machines, and cause confusions on building
+      #data_files=[('xgboost', LIB_PATH)],
+      url='https://github.com/dmlc/xgboost')

python-package/xgboost/libpath.py

@@ -36,9 +36,10 @@ def find_lib_path():
     else:
         dll_path = [os.path.join(p, 'libxgboostwrapper.so') for p in dll_path]
     lib_path = [p for p in dll_path if os.path.exists(p) and os.path.isfile(p)]
+    #From github issues, most of installation errors come from machines w/o compilers
     if len(lib_path) == 0 and not os.environ.get('XGBOOST_BUILD_DOC', False):
         raise XGBoostLibraryNotFound(
             'Cannot find XGBoost Libarary in the candicate path, ' +
-            'did you run build.sh in root path?\n'
+            'did you install compilers and run build.sh in root path?\n'
             'List of candidates:\n' + ('\n'.join(dll_path)))
     return lib_path