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Merge branch 'releases' into debian-experimental
* releases: (970 commits) REF _fit_newton use np.asarray(hess) REF: _fit_newton, add ridge_factor option, default 1e-10 REF: _fit_newton add Ridge correction to Hessian, see also statsmodels#953 Bug comment: commented out code, weigths don't sum to 1 see statsmodels#1845 CLN: TST cleanup comment, unused code. REF: "is" None (not ==) BUG: fix if alpha is scalar, TST: try standardized REF: NegativeBinomial fit_regularized, try regularized Poisson for start_params DOC: add comment in notes about not penalizing NegBin shape parameter [skip ci] TST: TestNegativeBinomialL1Compatability use desired as start_params TST: adjust test, precision and start_params (failure on TravisCI) BUG: NegativeBinomial fix aic, bic for 'geometric', adjust tests REF add k_extra to NegativeBinomial, don't count it in df_model, df_resid TST explicitely define k_extra in test class CLN: a few cosmetic changes TST fix negbin geometric test for fit_regularized CLN L1NegativeBinomialResults rename closes statsmodels#1615, remove redundant `__init__` BUG NegativeBinomial add fit_regularized closes statsmodels#1453 closes statsmodels#1454 adjust test to handle extra parameter REF: has_constant remove special code in linear_model, is moved to data Fix const_idx with multiple const, more tests ...
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@@ -48,3 +48,5 @@ help | |
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| # Project specific | ||
| statsmodels/version.py | ||
| cythonize.dat | ||
| statsmodels.egg-info/ | ||
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| # Adapted from M. Brett's .yaml file for nipy: | ||
| # https://github.com/nipy/nipy/blob/master/.travis.yml | ||
| # | ||
| # We pretend to be erlang because we can't use the python support in | ||
| # travis-ci; it uses virtualenvs, they do not have numpy, scipy, matplotlib, | ||
| # and it is impractical to build them | ||
| language: erlang | ||
| notifications: | ||
| email: | ||
| - statsmodels-commits@googlegroups.com | ||
| env: | ||
| # Enable python 2 and python 3 builds. Python3.2 available in Ubuntu 12.04. | ||
| - PYTHON=python PYSUF='' | ||
| - PYTHON=python3 PYSUF=3 | ||
| install: | ||
| - sudo apt-get update | ||
| - sudo apt-get install $PYTHON-dev | ||
| - sudo apt-get install $PYTHON-numpy | ||
| - sudo apt-get install $PYTHON-scipy | ||
| - sudo apt-get install $PYTHON-setuptools | ||
| - sudo apt-get install $PYTHON-nose | ||
| # Cython needs manual install under Python 3 | ||
| - if [ "${PYSUF}" == "3" ]; then | ||
| wget http://cython.org/release/Cython-0.17.1.tar.gz ; | ||
| tar xfvz Cython-0.17.1.tar.gz ; | ||
| cd Cython-0.17.1 ; | ||
| sudo python3 setup.py install ; | ||
| cd .. ; | ||
| else | ||
| sudo apt-get install cython ; | ||
| fi | ||
| - echo ${DISTRIB_CODENAME} | ||
| - wget -O- http://neuro.debian.net/lists/precise.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list | ||
| - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9 | ||
| - sudo apt-get update -qq | ||
| - sudo apt-get install $PYTHON-dateutil | ||
| - sudo apt-get --no-install-recommends install $PYTHON-pandas | ||
| - sudo apt-get --no-install-recommends install $PYTHON-pandas-lib | ||
| - sudo easy_install$PYSUF -U patsy | ||
| - if [ "${PYSUF}" != "3" ]; then sudo pip install coverage; fi | ||
| - if [ "${PYSUF}" != "3" ]; then sudo pip install coveralls; fi | ||
| script: | ||
| - SRCDIR=$PWD | ||
| - sudo $PYTHON setup.py install | ||
| # Ubuntu 12.04 installs statsmodels under the wrong path for Python 3 | ||
| - if [ "${PYSUF}" == "3" ]; then | ||
| sudo mv /usr/local/lib/python3.2/dist-packages/statsmodels-*/statsmodels /usr/local/lib/python3.2/dist-packages/statsmodels ; | ||
| sudo rm -rf /usr/lib/python3.2/dist-packages/statsmodels-* ; | ||
| fi | ||
| # statsmodels was installed "system-wide" thus cd under dedicated | ||
| # travis-test/ directory to not try using local version without built extensions | ||
| - mkdir -p "${SRCDIR}/travis-test"; cd "${SRCDIR}/travis-test" | ||
| # Compose a script to run testing with coverage | ||
| - echo 'import statsmodels as sm; a=sm.test(); import sys; sys.exit((len(a.failures)+len(a.errors))>0)' > test.py | ||
| - if [ "${PYSUF}" != "3" ]; then coverage run --rcfile=${SRCDIR}/.travis_coveragerc test.py; else $PYTHON test.py; fi | ||
| after_success: | ||
| - if [ "${PYSUF}" != "3" ]; then coveralls; fi |
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| # Adapted from M. Brett's .yaml file for nipy: | ||
| # https://github.com/nipy/nipy/blob/master/.travis.yml | ||
| # | ||
| # We pretend to be erlang because we can't use the python support in | ||
| # travis-ci; it uses virtualenvs, they do not have numpy, scipy, matplotlib, | ||
| # and it is impractical to build them | ||
| language: erlang | ||
| notifications: | ||
| email: | ||
| - statsmodels-commits@googlegroups.com | ||
| # Travis script that uses miniconda in place of the system installed python | ||
| # versions. Allows substantial flexability for choosing versions of | ||
| # required packages and is simpler to use to test up-to-date scientific Python | ||
| # stack | ||
| language: python | ||
|
|
||
| env: | ||
| # Enable python 2 and python 3 builds. Python3.2 available in Ubuntu 12.04. | ||
| - PYTHON=python PYSUF='' | ||
| - PYTHON=python3 PYSUF=3 | ||
| # Default values for common packages, override as needed | ||
| global: | ||
| - CYTHON=0.20 | ||
| - PATSY=0.2 | ||
| - PANDAS=0.12 | ||
| - MATPLOTLIB=1.3 | ||
| - OPTIONAL= | ||
| - COVERAGE=false | ||
|
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| matrix: | ||
| fast_finish: true | ||
| include: | ||
| - python: 2.7 | ||
| env: | ||
| - PYTHON=2.6 | ||
| - NUMPY="1.6.2=py26_4" | ||
| - SCIPY="0.11.0=np16py26_3" | ||
| - MATPLOTLIB=1.2 | ||
| - python: 2.7 | ||
| env: | ||
| - PYTHON=2.7 | ||
| - NUMPY=1.7 | ||
| - SCIPY=0.12 | ||
| - OPTIONAL=cvxopt | ||
| - COVERAGE=true | ||
| - python: 2.7 | ||
| env: | ||
| - PYTHON=3.3 | ||
| - NUMPY=1.8 | ||
| - SCIPY=0.13 | ||
| - PANDAS=0.13 | ||
| - python: 2.7 | ||
| env: | ||
| - PYTHON=2.7 | ||
| - NUMPY= | ||
| - SCIPY= | ||
| - MATPLOTLIB= | ||
| - PANDAS= | ||
|
|
||
| notifications: | ||
| email: | ||
| on_success: always | ||
|
|
||
| # Setup anaconda | ||
| before_install: | ||
| - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh | ||
| - chmod +x miniconda.sh | ||
| - ./miniconda.sh -b | ||
| - export PATH=/home/travis/miniconda/bin:$PATH | ||
| - conda update --yes --quiet conda | ||
| # Fix for headless TravisCI | ||
| - "export DISPLAY=:99.0" | ||
| - "sh -e /etc/init.d/xvfb start" | ||
| # Avoid noise from matplotlib | ||
| - mkdir $HOME/.config | ||
| - mkdir $HOME/.config/matplotlib | ||
| - SRCDIR=$PWD | ||
| - cp $SRCDIR/tools/matplotlibrc $HOME/.config/matplotlib/matplotlibrc | ||
| # Location for older version of matplotlib | ||
| - if [ ${MATPLOTLIB} = "1.2" ]; then mkdir $HOME/.matplotlib; fi | ||
| - if [ ${MATPLOTLIB} = "1.2" ]; then cp ${SRCDIR}/tools/matplotlibrc $HOME/.matplotlib/matplotlibrc; fi | ||
| # Build package list to avoid empty package=versions; only needed for versioned pacakges | ||
| - PKGS="python=${PYTHON}" | ||
| - PKGS="${PKGS} numpy"; if [ ${NUMPY} ]; then PKGS="${PKGS}=${NUMPY}"; fi | ||
| - PKGS="${PKGS} scipy"; if [ ${SCIPY} ]; then PKGS="${PKGS}=${SCIPY}"; fi | ||
| - PKGS="${PKGS} patsy"; if [ ${PATSY} ]; then PKGS="${PKGS}=${PATSY}"; fi | ||
| - PKGS="${PKGS} pandas"; if [ ${PANDAS} ]; then PKGS="${PKGS}=${PANDAS}"; fi | ||
| - PKGS="${PKGS} Cython"; if [ ${CYTHON} ]; then PKGS="${PKGS}=${CYTHON}"; fi | ||
| - PKGS="${PKGS} matplotlib"; if [ ${MATPLOTLIB} ]; then PKGS="${PKGS}=${MATPLOTLIB}"; fi | ||
|
|
||
| # Install packages | ||
| install: | ||
| - sudo apt-get update | ||
| - sudo apt-get install $PYTHON-dev | ||
| - sudo apt-get install $PYTHON-numpy | ||
| - sudo apt-get install $PYTHON-scipy | ||
| - sudo apt-get install $PYTHON-setuptools | ||
| - sudo apt-get install $PYTHON-nose | ||
| # Cython needs manual install under Python 3 | ||
| - if [ "${PYSUF}" == "3" ]; then | ||
| wget http://cython.org/release/Cython-0.17.1.tar.gz ; | ||
| tar xfvz Cython-0.17.1.tar.gz ; | ||
| cd Cython-0.17.1 ; | ||
| sudo python3 setup.py install ; | ||
| cd .. ; | ||
| else | ||
| sudo apt-get install cython ; | ||
| fi | ||
| - echo ${DISTRIB_CODENAME} | ||
| - wget -O- http://neuro.debian.net/lists/precise.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list | ||
| - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9 | ||
| - sudo apt-get update -qq | ||
| - sudo apt-get install $PYTHON-dateutil | ||
| - sudo apt-get --no-install-recommends install $PYTHON-pandas | ||
| - sudo apt-get --no-install-recommends install $PYTHON-pandas-lib | ||
| - sudo easy_install$PYSUF -U patsy | ||
| - conda create --yes --quiet -n statsmodels-test ${PKGS} ${OPTIONAL} dateutil nose pip pyyaml setuptools | ||
| - source activate statsmodels-test | ||
| - if [ ${COVERAGE} = true ]; then pip install coverage coveralls; fi | ||
| - python setup.py install | ||
|
|
||
| script: | ||
| - sudo $PYTHON setup.py install | ||
| # Ubuntu 12.04 installs statsmodels under the wrong path for Python 3 | ||
| - if [ "${PYSUF}" == "3" ]; then | ||
| sudo mv /usr/local/lib/python3.2/dist-packages/statsmodels-*/statsmodels /usr/local/lib/python3.2/dist-packages/statsmodels ; | ||
| sudo rm -rf /usr/lib/python3.2/dist-packages/statsmodels-* ; | ||
| fi | ||
| # For some reason, Python 3 will try to work with the build directory. Get out of folder to avoid breakage | ||
| - cd ../ | ||
| - sudo $PYTHON -c "import statsmodels as sm; a=sm.test(); import sys; sys.exit((len(a.failures)+len(a.errors))>0)" | ||
| - SRCDIR=$PWD | ||
| - python setup.py install | ||
| - mkdir -p "${SRCDIR}/travis-test"; cd "${SRCDIR}/travis-test" | ||
| # Show versions | ||
| - python -c 'import statsmodels.api as sm; sm.show_versions();' | ||
| # Compose a script to run testing with coverage | ||
| - echo 'import statsmodels as sm; a=sm.test(); import sys; sys.exit((len(a.failures)+len(a.errors))>0)' > test.py | ||
| - if [ ${COVERAGE} = true ]; then coverage run --rcfile=${SRCDIR}/.travis_coveragerc test.py; else python test.py; fi | ||
|
|
||
| after_success: | ||
| # Coverage only for 2.7 | ||
| - if [ ${COVERAGE} = true ]; then coveralls --rcfile=${SRCDIR}/.travis_coveragerc; fi |
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| [run] | ||
| branch = True | ||
| include = | ||
| */statsmodels/* |
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