Merge pull request #189 from ndawe/tmva

[MRG] Add TMVA support

.gitattributes

@@ -1 +1,2 @@
 /root_numpy/src/_librootnumpy.cpp binary
+/root_numpy/tmva/src/_libtmvanumpy.cpp binary

.travis.yml

@@ -4,10 +4,12 @@ python:
     - "2.7"
     - "3.4"
 env:
-    - ROOT=v5-34-18
+    - ROOT=v5-34-18 NOTMVA=1
     - ROOT=master
 install: source ci/install.sh
 script: bash ci/test.sh
 after_success:
     - time coveralls
 cache: apt
+notifications:
+    email: false

MANIFEST.in

@@ -1,3 +1,4 @@
+recursive-include examples *.py
 recursive-include root_numpy *.root *.h *.cpp *.pyx *.pxi
 include *.py
 include README.rst

Makefile

@@ -4,10 +4,11 @@ PYTHON := $(shell which python)
 CYTHON := $(shell which cython)
 NOSETESTS := $(shell which nosetests)
 
-CYTHON_PYX := root_numpy/src/_librootnumpy.pyx
-CYTHON_CPP := root_numpy/src/_librootnumpy.cpp
-CYTHON_SRC := $(filter-out $(CYTHON_PYX),$(filter-out $(CYTHON_CPP),$(wildcard root_numpy/src/*)))
-CYTHON_PYX_SRC := $(filter-out $(CYTHON_PYX),$(wildcard root_numpy/src/*.pyx))
+CYTHON_CORE_PYX := root_numpy/src/_librootnumpy.pyx
+CYTHON_TMVA_PYX := root_numpy/tmva/src/_libtmvanumpy.pyx
+CYTHON_CORE_CPP := $(CYTHON_CORE_PYX:.pyx=.cpp)
+CYTHON_TMVA_CPP := $(CYTHON_TMVA_PYX:.pyx=.cpp)
+CYTHON_PYX_SRC := $(filter-out $(CYTHON_CORE_PYX),$(wildcard root_numpy/src/*.pyx))
 
 INTERACTIVE := $(shell ([ -t 0 ] && echo 1) || echo 0)
 
@@ -18,7 +19,7 @@ else
 	OPEN := xdg-open
 endif
 
-all: $(CYTHON_CPP) clean inplace test
+all: clean cython inplace test
 
 clean-pyc:
 	@find . -name "*.pyc" -exec rm {} \;
@@ -34,15 +35,12 @@ clean-html:
 
 clean: clean-build clean-pyc clean-so
 
-$(CYTHON_PYX): $(CYTHON_SRC)
-
-$(CYTHON_CPP): $(CYTHON_PYX)
+.SECONDEXPANSION:
+%.cpp: %.pyx $$(filter-out $$@,$$(wildcard $$(@D)/*))
 	@echo "compiling $< ..."
-	@$(CYTHON) --cplus --fast-fail --line-directives $<
+	$(CYTHON) --cplus --fast-fail --line-directives $<
 
-cython:
-	@echo "compiling $(CYTHON_PYX) ..."
-	$(CYTHON) --cplus --fast-fail --line-directives $(CYTHON_PYX)
+cython: $(CYTHON_CORE_CPP) $(CYTHON_TMVA_CPP)
 
 show-cython: clean-html
 	@tmp=`mktemp -d`; \

ci/install.sh

@@ -6,16 +6,23 @@
 
 set -e
 
+# Install gcc 4.8
 sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
 sudo apt-get -qq update
 sudo apt-get -qq install g++-4.8
 sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 90
 sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90
+
 sudo apt-get -qq install python-nose python-pip
 pip install coverage coveralls
 
 # Install the ROOT binary
-time wget --no-check-certificate https://copy.com/rtIyUdxgjt7h/ci/root_builds/root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64.tar.gz
-time tar zxf root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64.tar.gz
-mv root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64 root
+build=root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64
+if [ ! -z ${NOTMVA+x} ]; then
+    # Use a build without TMVA
+    build+=_notmva
+fi
+time wget --no-check-certificate https://copy.com/rtIyUdxgjt7h/ci/root_builds/${build}.tar.gz
+time tar zxf ${build}.tar.gz
+mv ${build} root
 source root/bin/thisroot.sh

ci/test.sh

@@ -8,10 +8,11 @@ set -e
 
 gcc -dumpversion
 g++ -dumpversion
+ldd --version
 python --version
 python -c "import numpy; print('numpy %s' % numpy.__version__)"
+
 # Check if ROOT and PyROOT work
-#root -l -q
 python -c "import ROOT; ROOT.TBrowser()"
 python -c "from __future__ import print_function; import ROOT; print(ROOT.gROOT.GetVersion())"
 
@@ -20,5 +21,9 @@ export PYTHONPATH=/home/travis/.local/lib/python${TRAVIS_PYTHON_VERSION}/site-pa
 # Install into the user site-packages directory and run tests on that
 time make install-user
 time make test-installed
+
 # Run tests in the local directory with coverage
-time make test-coverage </dev/null
+if [ -z ${NOTMVA+x} ]; then
+    # TMVA is included in this build, so run the coverage
+    time make test-coverage </dev/null
+fi

docs/.gitignore

@@ -1,2 +1,3 @@
 _build
 reference/generated
+auto_examples

docs/Makefile

@@ -54,6 +54,7 @@ show:
 clean:
 	rm -rf $(BUILDDIR)/*
 	rm -rf reference/generated/*
+	rm -rf auto_examples/
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

docs/_static/root_numpy.css

@@ -3,6 +3,11 @@
     list-style: none;
 }
 
+#examples ul {
+    list-style-type: none;
+    list-style: none;
+}
+
 h2.main {
     margin: 0;
     font-style: italic;

docs/conf.py

@@ -40,6 +40,7 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.autosummary',
     'numpydoc',
+    'gen_rst',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/index.rst

@@ -20,3 +20,11 @@ Documentation
    start
    reference/index
 
+Examples
+--------
+
+.. toctree::
+   :maxdepth: 2
+
+   auto_examples/index
+

docs/reference/index.rst

@@ -7,11 +7,14 @@ root_numpy Reference
 :Release: |version|
 :Date: |today|
 
-.. module:: root_numpy
-
 This reference manual details the functions included in root_numpy, describing
 what they are and what they do.
 
+root_numpy
+----------
+
+.. module:: root_numpy
+
 .. autosummary::
    :toctree: generated
 
@@ -39,6 +42,19 @@ what they are and what they do.
    dup_idx
    blockwise_inner_join
 
+root_numpy.tmva
+---------------
+
+.. module:: root_numpy.tmva
+
+.. autosummary::
+   :toctree: generated
+
+   add_classification_events
+   add_regression_events
+   evaluate_reader
+   evaluate_method
+
 .. _conversion_table:
 
 Type Conversion Table
@@ -70,7 +86,3 @@ vector<vector<t> >  np.object
 Variable length arrays (such as ``particletype[nparticle]``) and vectors
 (such as ``vector<int>``) are converted to NumPy arrays of the corresponding
 types. Fixed length arrays are converted to fixed length NumPy array fields.
-
-.. note::
-    Tab completion for numpy.recarray column names (yourdata.<TAB>)
-    is also available with this `numpy extension <https://github.com/piti118/inumpy>`_.