├── README.rst ├── sklearnef ├── tree │ ├── tests │ │ └── __init__.py │ ├── headers │ │ └── sklearn │ │ │ ├── __init__.py │ │ │ └── tree │ │ │ └── __init__.py │ ├── __init__.py │ ├── compile.sh │ ├── _diffentropy.pxd │ ├── setup.py │ └── _tree.pxd ├── ensemble │ ├── tests │ │ ├── __init__.py │ │ └── test_ensemble.py │ └── __init__.py ├── build │ └── temp.linux-x86_64-2.7 │ │ └── tmp.o ├── setup.py ├── __init__.py └── .ipynb_checkpoints │ └── Untitled0-checkpoint.ipynb ├── doc ├── numpydoc │ ├── MANIFEST.in │ ├── numpydoc │ │ ├── __init__.py │ │ ├── tests │ │ │ ├── test_linkcode.py │ │ │ ├── test_traitsdoc.py │ │ │ ├── test_phantom_import.py │ │ │ └── test_plot_directive.py │ │ ├── linkcode.py │ │ └── traitsdoc.py │ ├── .travis.yml │ ├── setup.py │ └── README.rst ├── drafts │ └── Notes.odt ├── scipy-sphinx-theme │ ├── test_autodoc.rst │ ├── _static │ │ └── scipyshiny_small.png │ ├── _theme │ │ └── scipy │ │ │ ├── static │ │ │ ├── img │ │ │ │ ├── contents.png │ │ │ │ ├── navigation.png │ │ │ │ ├── scipy-logo.png │ │ │ │ ├── flags │ │ │ │ │ ├── flag-ad.png │ │ │ │ │ ├── flag-ae.png │ │ │ │ │ ├── flag-af.png │ │ │ │ │ ├── flag-ag.png │ │ │ │ │ ├── flag-ai.png │ │ │ │ │ ├── flag-al.png │ │ │ │ │ ├── flag-am.png │ │ │ │ │ ├── flag-ao.png │ │ │ │ │ ├── flag-aq.png │ │ │ │ │ ├── flag-ar.png │ │ │ │ │ ├── flag-as.png │ │ │ │ │ ├── flag-at.png │ │ │ │ │ ├── flag-au.png │ │ │ │ │ ├── flag-aw.png │ │ │ │ │ ├── flag-az.png │ │ │ │ │ ├── flag-ba.png │ │ │ │ │ ├── flag-bb.png │ │ │ │ │ ├── flag-bd.png │ │ │ │ │ ├── flag-be.png │ │ │ │ │ ├── flag-bf.png │ │ │ │ │ ├── flag-bg.png │ │ │ │ │ ├── flag-bh.png │ │ │ │ │ ├── flag-bi.png │ │ │ │ │ ├── flag-bj.png │ │ │ │ │ ├── flag-bl.png │ │ │ │ │ ├── flag-bm.png │ │ │ │ │ ├── flag-bn.png │ │ │ │ │ ├── flag-bo.png │ │ │ │ │ ├── flag-br.png │ │ │ │ │ ├── flag-bs.png │ │ │ │ │ ├── flag-bt.png │ │ │ │ │ ├── flag-bw.png │ │ │ │ │ ├── flag-by.png │ │ │ │ │ ├── flag-bz.png │ │ │ │ │ ├── flag-ca.png │ │ │ │ │ ├── flag-cc.png │ │ │ │ │ ├── flag-cd.png │ │ │ │ │ ├── flag-cf.png │ │ │ │ │ ├── flag-cg.png │ │ │ │ │ ├── flag-ch.png │ │ │ │ │ ├── flag-ci.png │ │ │ │ │ ├── flag-ck.png │ │ │ │ │ ├── flag-cl.png │ │ │ │ │ ├── flag-cm.png │ │ │ │ │ ├── flag-cn.png │ │ │ │ │ ├── flag-co.png │ │ │ │ │ ├── flag-cr.png │ │ │ │ │ ├── flag-cu.png │ │ │ │ │ ├── flag-cv.png │ │ │ │ │ ├── flag-cw.png │ │ │ │ │ ├── flag-cx.png │ │ │ │ │ ├── flag-cy.png │ │ │ │ │ ├── flag-cz.png │ │ │ │ │ ├── flag-de.png │ │ │ │ │ ├── flag-dj.png │ │ │ │ │ ├── flag-dk.png │ │ │ │ │ ├── flag-dm.png │ │ │ │ │ ├── flag-do.png │ │ │ │ │ ├── flag-dz.png │ │ │ │ │ ├── flag-ec.png │ │ │ │ │ ├── flag-ee.png │ │ │ │ │ ├── flag-eg.png │ │ │ │ │ ├── flag-er.png │ │ │ │ │ ├── flag-es.png │ │ │ │ │ ├── flag-et.png │ │ │ │ │ ├── flag-fi.png │ │ │ │ │ ├── flag-fj.png │ │ │ │ │ ├── flag-fk.png │ │ │ │ │ ├── flag-fm.png │ │ │ │ │ ├── flag-fo.png │ │ │ │ │ ├── flag-fr.png │ │ │ │ │ ├── flag-ga.png │ │ │ │ │ ├── flag-gb.png │ │ │ │ │ ├── flag-gd.png │ │ │ │ │ ├── flag-ge.png │ │ │ │ │ ├── flag-gf.png │ │ │ │ │ ├── flag-gg.png │ │ │ │ │ ├── flag-gh.png │ │ │ │ │ ├── flag-gi.png │ │ │ │ │ ├── flag-gl.png │ │ │ │ │ ├── flag-gm.png │ │ │ │ │ ├── flag-gn.png │ │ │ │ │ ├── flag-gq.png │ │ │ │ │ ├── flag-gr.png │ │ │ │ │ ├── flag-gs.png │ │ │ │ │ ├── flag-gt.png │ │ │ │ │ ├── flag-gu.png │ │ │ │ │ ├── flag-gw.png │ │ │ │ │ ├── flag-gy.png │ │ │ │ │ ├── flag-hk.png │ │ │ │ │ ├── flag-hm.png │ │ │ │ │ ├── flag-hn.png │ │ │ │ │ ├── flag-hr.png │ │ │ │ │ ├── flag-ht.png │ │ │ │ │ ├── flag-hu.png │ │ │ │ │ ├── flag-id.png │ │ │ │ │ ├── flag-ie.png │ │ │ │ │ ├── flag-il.png │ │ │ │ │ ├── flag-im.png │ │ │ │ │ ├── flag-in.png │ │ │ │ │ ├── flag-io.png │ │ │ │ │ ├── flag-iq.png │ │ │ │ │ ├── flag-ir.png │ │ │ │ │ ├── flag-is.png │ │ │ │ │ ├── flag-it.png │ │ │ │ │ ├── flag-je.png │ │ │ │ │ ├── flag-jm.png │ │ │ │ │ ├── flag-jo.png │ │ │ │ │ ├── flag-jp.png │ │ │ │ │ ├── flag-ke.png │ │ │ │ │ ├── flag-kg.png │ │ │ │ │ ├── flag-kh.png │ │ │ │ │ ├── flag-ki.png │ │ │ │ │ ├── flag-km.png │ │ │ │ │ ├── flag-kn.png │ │ │ │ │ ├── flag-kp.png │ │ │ │ │ ├── flag-kr.png │ │ │ │ │ ├── flag-kw.png │ │ │ │ │ ├── flag-ky.png │ │ │ │ │ ├── flag-kz.png │ │ │ │ │ ├── flag-la.png │ │ │ │ │ ├── flag-lb.png │ │ │ │ │ ├── flag-lc.png │ │ │ │ │ ├── flag-li.png │ │ │ │ │ ├── flag-lk.png │ │ │ │ │ ├── flag-lr.png │ │ │ │ │ ├── flag-ls.png │ │ │ │ │ ├── flag-lt.png │ │ │ │ │ ├── flag-lu.png │ │ │ │ │ ├── flag-lv.png │ │ │ │ │ ├── flag-ly.png │ │ │ │ │ ├── flag-ma.png │ │ │ │ │ ├── flag-mc.png │ │ │ │ │ ├── flag-md.png │ │ │ │ │ ├── flag-me.png │ │ │ │ │ ├── flag-mf.png │ │ │ │ │ ├── flag-mg.png │ │ │ │ │ ├── flag-mh.png │ │ │ │ │ ├── flag-mk.png │ │ │ │ │ ├── flag-ml.png │ │ │ │ │ ├── flag-mm.png │ │ │ │ │ ├── flag-mn.png │ │ │ │ │ ├── flag-mo.png │ │ │ │ │ ├── flag-mp.png │ │ │ │ │ ├── flag-mq.png │ │ │ │ │ ├── flag-mr.png │ │ │ │ │ ├── flag-ms.png │ │ │ │ │ ├── flag-mt.png │ │ │ │ │ ├── flag-mu.png │ │ │ │ │ ├── flag-mv.png │ │ │ │ │ ├── flag-mw.png │ │ │ │ │ ├── flag-mx.png │ │ │ │ │ ├── flag-my.png │ │ │ │ │ ├── flag-mz.png │ │ │ │ │ ├── flag-na.png │ │ │ │ │ ├── flag-nc.png │ │ │ │ │ ├── flag-ne.png │ │ │ │ │ ├── flag-nf.png │ │ │ │ │ ├── flag-ng.png │ │ │ │ │ ├── flag-ni.png │ │ │ │ │ ├── flag-nl.png │ │ │ │ │ ├── flag-no.png │ │ │ │ │ ├── flag-np.png │ │ │ │ │ ├── flag-nr.png │ │ │ │ │ ├── flag-nu.png │ │ │ │ │ ├── flag-nz.png │ │ │ │ │ ├── flag-om.png │ │ │ │ │ ├── flag-pa.png │ │ │ │ │ ├── flag-pe.png │ │ │ │ │ ├── flag-pf.png │ │ │ │ │ ├── flag-pg.png │ │ │ │ │ ├── flag-ph.png │ │ │ │ │ ├── flag-pk.png │ │ │ │ │ ├── flag-pl.png │ │ │ │ │ ├── flag-pm.png │ │ │ │ │ ├── flag-pn.png │ │ │ │ │ ├── flag-pr.png │ │ │ │ │ ├── flag-ps.png │ │ │ │ │ ├── flag-pt.png │ │ │ │ │ ├── flag-pw.png │ │ │ │ │ ├── flag-py.png │ │ │ │ │ ├── flag-qa.png │ │ │ │ │ ├── flag-re.png │ │ │ │ │ ├── flag-ro.png │ │ │ │ │ ├── flag-rs.png │ │ │ │ │ ├── flag-ru.png │ │ │ │ │ ├── flag-rw.png │ │ │ │ │ ├── flag-sa.png │ │ │ │ │ ├── flag-sb.png │ │ │ │ │ ├── flag-sc.png │ │ │ │ │ ├── flag-sd.png │ │ │ │ │ ├── flag-se.png │ │ │ │ │ ├── flag-sg.png │ │ │ │ │ ├── flag-sh.png │ │ │ │ │ ├── flag-si.png │ │ │ │ │ ├── flag-sj.png │ │ │ │ │ ├── flag-sk.png │ │ │ │ │ ├── flag-sl.png │ │ │ │ │ ├── flag-sm.png │ │ │ │ │ ├── flag-sn.png │ │ │ │ │ ├── flag-so.png │ │ │ │ │ ├── flag-sr.png │ │ │ │ │ ├── flag-st.png │ │ │ │ │ ├── flag-sv.png │ │ │ │ │ ├── flag-sy.png │ │ │ │ │ ├── flag-sz.png │ │ │ │ │ ├── flag-tc.png │ │ │ │ │ ├── flag-td.png │ │ │ │ │ ├── flag-tf.png │ │ │ │ │ ├── flag-tg.png │ │ │ │ │ ├── flag-th.png │ │ │ │ │ ├── flag-tj.png │ │ │ │ │ ├── flag-tk.png │ │ │ │ │ ├── flag-tl.png │ │ │ │ │ ├── flag-tm.png │ │ │ │ │ ├── flag-tn.png │ │ │ │ │ ├── flag-to.png │ │ │ │ │ ├── flag-tr.png │ │ │ │ │ ├── flag-tt.png │ │ │ │ │ ├── flag-tv.png │ │ │ │ │ ├── flag-tw.png │ │ │ │ │ ├── flag-tz.png │ │ │ │ │ ├── flag-ua.png │ │ │ │ │ ├── flag-ug.png │ │ │ │ │ ├── flag-um.png │ │ │ │ │ ├── flag-us.png │ │ │ │ │ ├── flag-uy.png │ │ │ │ │ ├── flag-uz.png │ │ │ │ │ ├── flag-va.png │ │ │ │ │ ├── flag-vc.png │ │ │ │ │ ├── flag-ve.png │ │ │ │ │ ├── flag-vg.png │ │ │ │ │ ├── flag-vi.png │ │ │ │ │ ├── flag-vn.png │ │ │ │ │ ├── flag-vu.png │ │ │ │ │ ├── flag-wf.png │ │ │ │ │ ├── flag-ws.png │ │ │ │ │ ├── flag-ye.png │ │ │ │ │ ├── flag-za.png │ │ │ │ │ ├── flag-zm.png │ │ │ │ │ └── flag-zw.png │ │ │ │ ├── important-icon.png │ │ │ │ ├── scipy_org_logo.gif │ │ │ │ ├── information-icon.png │ │ │ │ ├── person-list-icon.png │ │ │ │ ├── scipycentral_logo.png │ │ │ │ ├── scipyshiny_small.png │ │ │ │ ├── send-email-icon.png │ │ │ │ ├── single-file-icon.png │ │ │ │ ├── transparent-pixel.gif │ │ │ │ ├── external-link-icon.png │ │ │ │ ├── multiple-file-icon.png │ │ │ │ ├── ui-anim_basic_16x16.gif │ │ │ │ ├── glyphicons-halflings.png │ │ │ │ ├── internet-web-browser.png │ │ │ │ ├── person-list-icon-tiny.png │ │ │ │ ├── single-file-list-icon.png │ │ │ │ ├── create-new-account-icon.png │ │ │ │ ├── external-link-list-icon.png │ │ │ │ ├── multiple-file-list-icon.png │ │ │ │ ├── single-file-icon-shrunk.png │ │ │ │ ├── external-link-icon-shrunk.png │ │ │ │ ├── glyphicons-halflings-white.png │ │ │ │ ├── multiple-file-icon-shrunk.png │ │ │ │ ├── single-file-list-icon-tiny.png │ │ │ │ ├── external-link-list-icon-tiny.png │ │ │ │ ├── multiple-file-list-icon-tiny.png │ │ │ │ ├── single-file-list-icon-tiniest.png │ │ │ │ └── external-link-list-icon-tiniest.png │ │ │ ├── less │ │ │ │ ├── spc-footer.less │ │ │ │ ├── spc-rightsidebar.less │ │ │ │ ├── bootstrap │ │ │ │ │ ├── layouts.less │ │ │ │ │ ├── component-animations.less │ │ │ │ │ ├── utilities.less │ │ │ │ │ ├── grid.less │ │ │ │ │ ├── breadcrumbs.less │ │ │ │ │ ├── responsive-768px-979px.less │ │ │ │ │ ├── hero-unit.less │ │ │ │ │ ├── wells.less │ │ │ │ │ ├── responsive-1200px-min.less │ │ │ │ │ ├── close.less │ │ │ │ │ ├── accordion.less │ │ │ │ │ ├── pager.less │ │ │ │ │ ├── media.less │ │ │ │ │ ├── scaffolding.less │ │ │ │ │ ├── responsive.less │ │ │ │ │ ├── thumbnails.less │ │ │ │ │ ├── code.less │ │ │ │ │ ├── alerts.less │ │ │ │ │ ├── bootstrap.less │ │ │ │ │ ├── responsive-utilities.less │ │ │ │ │ ├── tooltip.less │ │ │ │ │ ├── labels-badges.less │ │ │ │ │ ├── modals.less │ │ │ │ │ ├── pagination.less │ │ │ │ │ ├── carousel.less │ │ │ │ │ ├── progress-bars.less │ │ │ │ │ ├── popovers.less │ │ │ │ │ ├── responsive-767px-max.less │ │ │ │ │ └── responsive-navbar.less │ │ │ │ ├── spc-extend.less │ │ │ │ ├── spc-utils.less │ │ │ │ ├── spc-bootstrap.less │ │ │ │ ├── spc-header.less │ │ │ │ └── spc-content.less │ │ │ ├── css │ │ │ │ ├── spc-extend.css │ │ │ │ ├── extend.css │ │ │ │ └── pygments.css │ │ │ └── js │ │ │ │ └── copybutton.js │ │ │ ├── theme.conf │ │ │ └── sourcelink.html │ ├── test_autodoc_3.rst │ ├── test_autodoc_2.rst │ ├── test_autodoc_4.rst │ ├── index.rst │ ├── README.rst │ ├── conf.py │ └── Makefile ├── source │ ├── examples │ │ ├── images │ │ │ ├── density_tree_01.png │ │ │ ├── density_tree_02.png │ │ │ ├── density_example_blobs.png │ │ │ ├── density_example_moons.png │ │ │ ├── density_example_scurve.png │ │ │ ├── density_example_circlenear.png │ │ │ ├── density_example_swissroll.png │ │ │ ├── density_circlesdistant_minimp0.1.png │ │ │ ├── density_circlesdistant_minimp0.5.png │ │ │ ├── density_circlesdistant_minimp1.png │ │ │ ├── density_circlesdistant_minimp2.png │ │ │ ├── density_circlesdistant_minimp_gt.png │ │ │ ├── density_example_circlesdistant.png │ │ │ ├── density_circlesdistant_minimp0.01.png │ │ │ ├── density_circlesdistant_minimp0.05.png │ │ │ └── density_circlesdistant_minimp0.25.png │ │ ├── densitytreeaccuracy.rst │ │ └── sklearndensity.rst │ ├── scripts.rst │ ├── index.rst │ └── installation │ │ └── asroot.rst └── README ├── README.md ├── .gitignore └── bin └── density └── plot_sherwood.py /README.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /sklearnef/tree/tests/__init__.py: 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3 |
4 | {{ _('Show Source') }} 6 |
7 | {%- endif %} 8 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/tests/test_traitsdoc.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import sys 4 | from nose import SkipTest 5 | 6 | def test_import(): 7 | if sys.version_info[0] >= 3: 8 | raise SkipTest("traitsdoc not ported to Python3") 9 | import numpydoc.traitsdoc 10 | 11 | # No tests at the moment... 12 | -------------------------------------------------------------------------------- /sklearnef/ensemble/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | The :mod:`sklearnef.ensemble` module includes ensemble-based methods for 3 | density learning and semi-supervised classification. 4 | """ 5 | 6 | from .forest import DensityForest 7 | from .forest import SemiSupervisedRandomForestClassifier 8 | 9 | __all__ = ["DensityForest", 10 | "SemiSupervisedRandomForestClassifier"] 11 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/tests/test_phantom_import.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import sys 4 | from nose import SkipTest 5 | 6 | def test_import(): 7 | if sys.version_info[0] >= 3: 8 | raise SkipTest("phantom_import not ported to Py3") 9 | 10 | import numpydoc.phantom_import 11 | 12 | # No tests at the moment... 13 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-rightsidebar.less: -------------------------------------------------------------------------------- 1 | @import "bootstrap/variables.less"; 2 | 3 | .spc-rightsidebar { 4 | color: @gray; 5 | .navigation { 6 | padding: @paddingSmall; 7 | font-size: @fontSizeSmall; 8 | } 9 | .navigation .nav-title { 10 | font-weight: bold; 11 | text-transform: uppercase; 12 | } 13 | .navigation li { margin: 5px; } 14 | } -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/tests/test_plot_directive.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import sys 4 | from nose import SkipTest 5 | 6 | def test_import(): 7 | if sys.version_info[0] >= 3: 8 | raise SkipTest("plot_directive not ported to Python 3 (use the one from Matplotlib instead)") 9 | import numpydoc.plot_directive 10 | 11 | # No tests at the moment... 12 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/layouts.less: -------------------------------------------------------------------------------- 1 | // 2 | // Layouts 3 | // -------------------------------------------------- 4 | 5 | 6 | // Container (centered, fixed-width layouts) 7 | .container { 8 | .container-fixed(); 9 | } 10 | 11 | // Fluid layouts (left aligned, with sidebar, min- & max-width content) 12 | .container-fluid { 13 | padding-right: @gridGutterWidth; 14 | padding-left: @gridGutterWidth; 15 | .clearfix(); 16 | } -------------------------------------------------------------------------------- /doc/numpydoc/.travis.yml: -------------------------------------------------------------------------------- 1 | # After changing this file, check it on: 2 | # http://lint.travis-ci.org/ 3 | language: python 4 | python: 5 | - 3.3 6 | - 2.7 7 | before_install: 8 | - pip install --upgrade pip setuptools # Upgrade pip and setuptools to get ones with `wheel` support 9 | - pip install --find-links http://wheels.astropy.org/ --find-links http://wheels2.astropy.org/ --use-wheel --use-mirrors nose numpy matplotlib Sphinx 10 | script: 11 | - python setup.py test 12 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/component-animations.less: -------------------------------------------------------------------------------- 1 | // 2 | // Component animations 3 | // -------------------------------------------------- 4 | 5 | 6 | .fade { 7 | opacity: 0; 8 | .transition(opacity .15s linear); 9 | &.in { 10 | opacity: 1; 11 | } 12 | } 13 | 14 | .collapse { 15 | position: relative; 16 | height: 0; 17 | overflow: hidden; 18 | .transition(height .35s ease); 19 | &.in { 20 | height: auto; 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-extend.less: -------------------------------------------------------------------------------- 1 | //spc extend settings 2 | 3 | body { 4 | background-color: rgb(249,250,245); 5 | } 6 | 7 | .container { 8 | width: 80%; 9 | } 10 | 11 | .main { 12 | background-color: white; 13 | padding: 18px; 14 | -moz-box-shadow: 0 0 3px #888; 15 | -webkit-box-shadow: 0 0 3px #888; 16 | box-shadow: 0 0 3px #888; 17 | } 18 | 19 | @import "spc-header.less"; 20 | @import "spc-content.less"; 21 | @import "spc-rightsidebar.less"; 22 | @import "spc-footer.less"; -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/utilities.less: -------------------------------------------------------------------------------- 1 | // 2 | // Utility classes 3 | // -------------------------------------------------- 4 | 5 | 6 | // Quick floats 7 | .pull-right { 8 | float: right; 9 | } 10 | .pull-left { 11 | float: left; 12 | } 13 | 14 | // Toggling content 15 | .hide { 16 | display: none; 17 | } 18 | .show { 19 | display: block; 20 | } 21 | 22 | // Visibility 23 | .invisible { 24 | visibility: hidden; 25 | } 26 | 27 | // For Affix plugin 28 | .affix { 29 | position: fixed; 30 | } 31 | -------------------------------------------------------------------------------- /sklearnef/tree/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | The :mod:`sklearnef.tree` module includes decision tree-based models for 3 | density learning and semi-supervised classification, as well as some 4 | density classes for further operations on density trees. 5 | """ 6 | 7 | from .tree import SemiSupervisedDecisionTreeClassifier 8 | from .tree import DensityTree 9 | from .tree import GoodnessOfFit 10 | from .tree import MECDF 11 | 12 | __all__ = ["DensityTree", 13 | "SemiSupervisedDecisionTreeClassifier", 14 | "GoodnessOfFit", "MECDF"] 15 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-utils.less: -------------------------------------------------------------------------------- 1 | // LESS Utilities for spc 2 | @import "bootstrap/variables.less"; 3 | 4 | .padding (@top: 0px, @bottom: 0px, @left: 0px, @right: 0px) { 5 | padding-top: @top; 6 | padding-bottom: @bottom; 7 | padding-left: @left; 8 | padding-right: @right; 9 | } 10 | 11 | .margin (@top: 0px, @bottom: 0px, @left: 0px, @right: 0px) { 12 | margin-top: @top; 13 | margin-bottom: @bottom; 14 | margin-left: @left; 15 | margin-right:@right; 16 | } 17 | 18 | .underline { 19 | border-bottom: 1.5px solid @hrBorder; 20 | } 21 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/grid.less: -------------------------------------------------------------------------------- 1 | // 2 | // Grid system 3 | // -------------------------------------------------- 4 | 5 | 6 | // Fixed (940px) 7 | #grid > .core(@gridColumnWidth, @gridGutterWidth); 8 | 9 | // Fluid (940px) 10 | #grid > .fluid(@fluidGridColumnWidth, @fluidGridGutterWidth); 11 | 12 | // Reset utility classes due to specificity 13 | [class*="span"].hide, 14 | .row-fluid [class*="span"].hide { 15 | display: none; 16 | } 17 | 18 | [class*="span"].pull-right, 19 | .row-fluid [class*="span"].pull-right { 20 | float: right; 21 | } 22 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-bootstrap.less: -------------------------------------------------------------------------------- 1 | // spc bootstrap settings 2 | @import "bootstrap/bootstrap.less"; 3 | @import "bootstrap/responsive.less"; 4 | 5 | // google webfont 6 | @import url(http://fonts.googleapis.com/css?family=Open+Sans); 7 | 8 | //Typography 9 | @sansFontFamily: 'Open Sans', sans-serif !important; 10 | @baseFontSize: 13px; 11 | @baseLineHeight: 19px; 12 | 13 | //Colors 14 | @blue: #12567D; 15 | 16 | //Sprites 17 | @iconSpritePath: '../../img/glyphicons-halflings.png'; 18 | @iconWhiteSpritePath: '../../img/glyphicons-halflings-white.png'; -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/breadcrumbs.less: -------------------------------------------------------------------------------- 1 | // 2 | // Breadcrumbs 3 | // -------------------------------------------------- 4 | 5 | 6 | .breadcrumb { 7 | padding: 8px 15px; 8 | margin: 0 0 @baseLineHeight; 9 | list-style: none; 10 | background-color: #f5f5f5; 11 | .border-radius(@baseBorderRadius); 12 | > li { 13 | display: inline-block; 14 | .ie7-inline-block(); 15 | text-shadow: 0 1px 0 @white; 16 | > .divider { 17 | padding: 0 5px; 18 | color: #ccc; 19 | } 20 | } 21 | > .active { 22 | color: @grayLight; 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-header.less: -------------------------------------------------------------------------------- 1 | // settings for 2 | // 1) .header 3 | // header block is found on the top of the website 4 | // spc-navbar, spc-header-searchbar found inside .header 5 | // 2) .spc-navbar 6 | // 3) .spc-header-searchbar 7 | 8 | @import "spc-utils.less"; 9 | 10 | .header { 11 | .margin(@top: 15px, @bottom: 15px); 12 | } 13 | 14 | .spc-navbar { 15 | .margin (@top: 15px, @bottom: 5px); 16 | .nav-pills { 17 | margin-bottom: 0px; 18 | font-size: 12px; 19 | 20 | >li >a { 21 | padding-top: 2.5px; 22 | padding-bottom: 2.5px; 23 | } 24 | } 25 | } -------------------------------------------------------------------------------- /sklearnef/tree/compile.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | VERSION="0.16.1" 4 | 5 | echo '---- CLEAN ----' 6 | rm headers/${VERSION}/_tree.c 7 | rm _tree.so 8 | rm headers/_diffentropy.c 9 | rm _diffentropy.so 10 | 11 | echo '---- COMPILE ----' 12 | cython _diffentropy.pyx -o headers/_diffentropy.c -I headers/ -f 13 | #gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I/usr/include/python2.7 -o _diffentropy.so _diffentropy.c 14 | cython _tree.pyx -o headers/${VERSION}/_tree.c -I headers/ -f 15 | python setup.py build_ext --inplace 16 | 17 | echo '---- RUN ----' 18 | ipython -c "import _tree" 19 | 20 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-768px-979px.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Tablet to desktop 3 | // -------------------------------------------------- 4 | 5 | 6 | @media (min-width: 768px) and (max-width: 979px) { 7 | 8 | // Fixed grid 9 | #grid > .core(@gridColumnWidth768, @gridGutterWidth768); 10 | 11 | // Fluid grid 12 | #grid > .fluid(@fluidGridColumnWidth768, @fluidGridGutterWidth768); 13 | 14 | // Input grid 15 | #grid > .input(@gridColumnWidth768, @gridGutterWidth768); 16 | 17 | // No need to reset .thumbnails here since it's the same @gridGutterWidth 18 | 19 | } 20 | -------------------------------------------------------------------------------- /sklearnef/setup.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | def configuration(parent_package='', top_path=None): 4 | from numpy.distutils.misc_util import Configuration 5 | 6 | libraries = [] 7 | if os.name == 'posix': 8 | libraries.append('m') 9 | 10 | config = Configuration('sklearnef', parent_package, top_path) 11 | 12 | config.add_subpackage("ensemble") 13 | config.add_subpackage("ensemble/tests") 14 | config.add_subpackage("tree") 15 | config.add_subpackage("tree/tests") 16 | 17 | return config 18 | 19 | if __name__ == '__main__': 20 | from numpy.distutils.core import setup 21 | setup(**configuration(top_path='').todict()) 22 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/hero-unit.less: -------------------------------------------------------------------------------- 1 | // 2 | // Hero unit 3 | // -------------------------------------------------- 4 | 5 | 6 | .hero-unit { 7 | padding: 60px; 8 | margin-bottom: 30px; 9 | font-size: 18px; 10 | font-weight: 200; 11 | line-height: @baseLineHeight * 1.5; 12 | color: @heroUnitLeadColor; 13 | background-color: @heroUnitBackground; 14 | .border-radius(6px); 15 | h1 { 16 | margin-bottom: 0; 17 | font-size: 60px; 18 | line-height: 1; 19 | color: @heroUnitHeadingColor; 20 | letter-spacing: -1px; 21 | } 22 | li { 23 | line-height: @baseLineHeight * 1.5; // Reset since we specify in type.less 24 | } 25 | } 26 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/wells.less: -------------------------------------------------------------------------------- 1 | // 2 | // Wells 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base class 7 | .well { 8 | min-height: 20px; 9 | padding: 19px; 10 | margin-bottom: 20px; 11 | background-color: @wellBackground; 12 | border: 1px solid darken(@wellBackground, 7%); 13 | .border-radius(@baseBorderRadius); 14 | .box-shadow(inset 0 1px 1px rgba(0,0,0,.05)); 15 | blockquote { 16 | border-color: #ddd; 17 | border-color: rgba(0,0,0,.15); 18 | } 19 | } 20 | 21 | // Sizes 22 | .well-large { 23 | padding: 24px; 24 | .border-radius(@borderRadiusLarge); 25 | } 26 | .well-small { 27 | padding: 9px; 28 | .border-radius(@borderRadiusSmall); 29 | } 30 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-1200px-min.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Large desktop and up 3 | // -------------------------------------------------- 4 | 5 | 6 | @media (min-width: 1200px) { 7 | 8 | // Fixed grid 9 | #grid > .core(@gridColumnWidth1200, @gridGutterWidth1200); 10 | 11 | // Fluid grid 12 | #grid > .fluid(@fluidGridColumnWidth1200, @fluidGridGutterWidth1200); 13 | 14 | // Input grid 15 | #grid > .input(@gridColumnWidth1200, @gridGutterWidth1200); 16 | 17 | // Thumbnails 18 | .thumbnails { 19 | margin-left: -@gridGutterWidth1200; 20 | } 21 | .thumbnails > li { 22 | margin-left: @gridGutterWidth1200; 23 | } 24 | .row-fluid .thumbnails { 25 | margin-left: 0; 26 | } 27 | 28 | } 29 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/index.rst: -------------------------------------------------------------------------------- 1 | .. scipy-sphinx-theme documentation master file, created by 2 | sphinx-quickstart on Sun Apr 21 11:22:24 2013. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to scipy-sphinx-theme's documentation! 7 | ============================================== 8 | 9 | The theme is under `_theme`, this document contains various test 10 | pages. 11 | 12 | Contents: 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | 17 | README 18 | test_optimize 19 | test_autodoc 20 | test_autodoc_2 21 | test_autodoc_3 22 | test_autodoc_4 23 | 24 | Indices and tables 25 | ================== 26 | 27 | * :ref:`genindex` 28 | * :ref:`modindex` 29 | * :ref:`search` 30 | 31 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/close.less: -------------------------------------------------------------------------------- 1 | // 2 | // Close icons 3 | // -------------------------------------------------- 4 | 5 | 6 | .close { 7 | float: right; 8 | font-size: 20px; 9 | font-weight: bold; 10 | line-height: @baseLineHeight; 11 | color: @black; 12 | text-shadow: 0 1px 0 rgba(255,255,255,1); 13 | .opacity(20); 14 | &:hover, 15 | &:focus { 16 | color: @black; 17 | text-decoration: none; 18 | cursor: pointer; 19 | .opacity(40); 20 | } 21 | } 22 | 23 | // Additional properties for button version 24 | // iOS requires the button element instead of an anchor tag. 25 | // If you want the anchor version, it requires `href="#"`. 26 | button.close { 27 | padding: 0; 28 | cursor: pointer; 29 | background: transparent; 30 | border: 0; 31 | -webkit-appearance: none; 32 | } -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/accordion.less: -------------------------------------------------------------------------------- 1 | // 2 | // Accordion 3 | // -------------------------------------------------- 4 | 5 | 6 | // Parent container 7 | .accordion { 8 | margin-bottom: @baseLineHeight; 9 | } 10 | 11 | // Group == heading + body 12 | .accordion-group { 13 | margin-bottom: 2px; 14 | border: 1px solid #e5e5e5; 15 | .border-radius(@baseBorderRadius); 16 | } 17 | .accordion-heading { 18 | border-bottom: 0; 19 | } 20 | .accordion-heading .accordion-toggle { 21 | display: block; 22 | padding: 8px 15px; 23 | } 24 | 25 | // General toggle styles 26 | .accordion-toggle { 27 | cursor: pointer; 28 | } 29 | 30 | // Inner needs the styles because you can't animate properly with any styles on the element 31 | .accordion-inner { 32 | padding: 9px 15px; 33 | border-top: 1px solid #e5e5e5; 34 | } 35 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | *.egg-info/ 24 | .installed.cfg 25 | *.egg 26 | 27 | # PyInstaller 28 | # Usually these files are written by a python script from a template 29 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 30 | *.manifest 31 | *.spec 32 | 33 | # Installer logs 34 | pip-log.txt 35 | pip-delete-this-directory.txt 36 | 37 | # Unit test / coverage reports 38 | htmlcov/ 39 | .tox/ 40 | .coverage 41 | .coverage.* 42 | .cache 43 | nosetests.xml 44 | coverage.xml 45 | *,cover 46 | 47 | # Translations 48 | *.mo 49 | *.pot 50 | 51 | # Django stuff: 52 | *.log 53 | 54 | # Sphinx documentation 55 | docs/_build/ 56 | 57 | # PyBuilder 58 | target/ 59 | 60 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/pager.less: -------------------------------------------------------------------------------- 1 | // 2 | // Pager pagination 3 | // -------------------------------------------------- 4 | 5 | 6 | .pager { 7 | margin: @baseLineHeight 0; 8 | list-style: none; 9 | text-align: center; 10 | .clearfix(); 11 | } 12 | .pager li { 13 | display: inline; 14 | } 15 | .pager li > a, 16 | .pager li > span { 17 | display: inline-block; 18 | padding: 5px 14px; 19 | background-color: #fff; 20 | border: 1px solid #ddd; 21 | .border-radius(15px); 22 | } 23 | .pager li > a:hover, 24 | .pager li > a:focus { 25 | text-decoration: none; 26 | background-color: #f5f5f5; 27 | } 28 | .pager .next > a, 29 | .pager .next > span { 30 | float: right; 31 | } 32 | .pager .previous > a, 33 | .pager .previous > span { 34 | float: left; 35 | } 36 | .pager .disabled > a, 37 | .pager .disabled > a:hover, 38 | .pager .disabled > a:focus, 39 | .pager .disabled > span { 40 | color: @grayLight; 41 | background-color: #fff; 42 | cursor: default; 43 | } -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-content.less: -------------------------------------------------------------------------------- 1 | @import "spc-utils.less"; 2 | @import "bootstrap/variables.less"; 3 | 4 | .spc-page-title { 5 | h1, h2, h3, h4 { 6 | font-weight: normal; 7 | .underline; 8 | } 9 | } 10 | 11 | //tags -- depricated 12 | // need to design 13 | .tags .btn { 14 | border: none; 15 | font-size: 9.5px; 16 | font-weight: bold; 17 | } 18 | 19 | // search item specific settings 20 | .spc-search-result { 21 | &-title { 22 | h1, h2, h3, h4 { font-weight: normal; } 23 | } 24 | } 25 | 26 | // snippet specific settings 27 | .spc-snippet-header { 28 | margin-bottom: 5px; 29 | } 30 | 31 | .spc-snippet-info { 32 | padding-top: 10px; 33 | 34 | .dl-horizontal { 35 | margin: 5px; 36 | dt { font-weight: normal; } 37 | } 38 | } 39 | 40 | .spc-snippet-body { 41 | padding: 10px; 42 | 43 | .accordion-group { 44 | border: none; 45 | } 46 | 47 | .accordion-heading { 48 | text-transform: uppercase; 49 | font-size: 14px; 50 | border-bottom: 1px solid #e5e5e5; 51 | } 52 | 53 | .accordion-heading .accordion-toggle { 54 | padding-top: 10px; 55 | padding-bottom: 5px; 56 | } 57 | } 58 | -------------------------------------------------------------------------------- /doc/numpydoc/setup.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function 2 | 3 | import sys 4 | import setuptools 5 | from distutils.core import setup 6 | 7 | if sys.version_info[:2] < (2, 6) or (3, 0) <= sys.version_info[0:2] < (3, 3): 8 | raise RuntimeError("Python version 2.6, 2.7 or >= 3.3 required.") 9 | 10 | version = "0.6.dev" 11 | 12 | setup( 13 | name="numpydoc", 14 | packages=["numpydoc"], 15 | version=version, 16 | description="Sphinx extension to support docstrings in Numpy format", 17 | # classifiers from http://pypi.python.org/pypi?%3Aaction=list_classifiers 18 | classifiers=["Development Status :: 3 - Alpha", 19 | "Environment :: Plugins", 20 | "License :: OSI Approved :: BSD License", 21 | "Topic :: Documentation"], 22 | keywords="sphinx numpy", 23 | author="Pauli Virtanen and others", 24 | author_email="pav@iki.fi", 25 | url="https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt", 26 | license="BSD", 27 | requires=["sphinx (>= 1.0.1)"], 28 | package_data={'numpydoc': ['tests/test_*.py']}, 29 | test_suite = 'nose.collector', 30 | ) 31 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/media.less: -------------------------------------------------------------------------------- 1 | // Media objects 2 | // Source: http://stubbornella.org/content/?p=497 3 | // -------------------------------------------------- 4 | 5 | 6 | // Common styles 7 | // ------------------------- 8 | 9 | // Clear the floats 10 | .media, 11 | .media-body { 12 | overflow: hidden; 13 | *overflow: visible; 14 | zoom: 1; 15 | } 16 | 17 | // Proper spacing between instances of .media 18 | .media, 19 | .media .media { 20 | margin-top: 15px; 21 | } 22 | .media:first-child { 23 | margin-top: 0; 24 | } 25 | 26 | // For images and videos, set to block 27 | .media-object { 28 | display: block; 29 | } 30 | 31 | // Reset margins on headings for tighter default spacing 32 | .media-heading { 33 | margin: 0 0 5px; 34 | } 35 | 36 | 37 | // Media image alignment 38 | // ------------------------- 39 | 40 | .media > .pull-left { 41 | margin-right: 10px; 42 | } 43 | .media > .pull-right { 44 | margin-left: 10px; 45 | } 46 | 47 | 48 | // Media list variation 49 | // ------------------------- 50 | 51 | // Undo default ul/ol styles 52 | .media-list { 53 | margin-left: 0; 54 | list-style: none; 55 | } 56 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/scaffolding.less: -------------------------------------------------------------------------------- 1 | // 2 | // Scaffolding 3 | // -------------------------------------------------- 4 | 5 | 6 | // Body reset 7 | // ------------------------- 8 | 9 | body { 10 | margin: 0; 11 | font-family: @baseFontFamily; 12 | font-size: @baseFontSize; 13 | line-height: @baseLineHeight; 14 | color: @textColor; 15 | background-color: @bodyBackground; 16 | } 17 | 18 | 19 | // Links 20 | // ------------------------- 21 | 22 | a { 23 | color: @linkColor; 24 | text-decoration: none; 25 | } 26 | a:hover, 27 | a:focus { 28 | color: @linkColorHover; 29 | text-decoration: underline; 30 | } 31 | 32 | 33 | // Images 34 | // ------------------------- 35 | 36 | // Rounded corners 37 | .img-rounded { 38 | .border-radius(6px); 39 | } 40 | 41 | // Add polaroid-esque trim 42 | .img-polaroid { 43 | padding: 4px; 44 | background-color: #fff; 45 | border: 1px solid #ccc; 46 | border: 1px solid rgba(0,0,0,.2); 47 | .box-shadow(0 1px 3px rgba(0,0,0,.1)); 48 | } 49 | 50 | // Perfect circle 51 | .img-circle { 52 | .border-radius(500px); // crank the border-radius so it works with most reasonably sized images 53 | } 54 | -------------------------------------------------------------------------------- /doc/source/examples/densitytreeaccuracy.rst: -------------------------------------------------------------------------------- 1 | ============================= 2 | DensityTree accuracy examples 3 | ============================= 4 | 5 | All examples were created with the `plot_tree_gauss.py` script shipped with **sklearnef**. 6 | 7 | Example 01 8 | ========== 9 | 10 | Example where the blobs are perfectly separated. The blue lines denote the chosen splits. 11 | 12 | .. code-block:: bash 13 | 14 | ./plot_tree_gauss.py --seed=10 --min-improvement=1 15 | 16 | Goodness of fit evaluation: 17 | 18 | * maxium error: 0.0157099898541 19 | * mean squared error: 1.96287068935e-05 20 | * mean squared error weighted: 1.43077730335e-06 21 | 22 | .. image:: images/density_tree_02.png 23 | :width: 800px 24 | :align: center 25 | 26 | 27 | Example 02 28 | ========== 29 | 30 | Example where two very close blobs where not separated by the DensityTree. 31 | 32 | .. code-block:: bash 33 | 34 | ./plot_tree_gauss.py --seed=0 --min-improvement=1 35 | 36 | Goodness of fit evaluation: 37 | 38 | * maxium error: 0.037187800654 39 | * mean squared error: 0.000154910423727 40 | * mean squared error weighted: 7.67144729963e-06 41 | 42 | .. image:: images/density_tree_01.png 43 | :width: 800px 44 | :align: center 45 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive.less: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap Responsive v2.3.1 3 | * 4 | * Copyright 2012 Twitter, Inc 5 | * Licensed under the Apache License v2.0 6 | * http://www.apache.org/licenses/LICENSE-2.0 7 | * 8 | * Designed and built with all the love in the world @twitter by @mdo and @fat. 9 | */ 10 | 11 | 12 | // Responsive.less 13 | // For phone and tablet devices 14 | // ------------------------------------------------------------- 15 | 16 | 17 | // REPEAT VARIABLES & MIXINS 18 | // ------------------------- 19 | // Required since we compile the responsive stuff separately 20 | 21 | @import "variables.less"; // Modify this for custom colors, font-sizes, etc 22 | @import "mixins.less"; 23 | 24 | 25 | // RESPONSIVE CLASSES 26 | // ------------------ 27 | 28 | @import "responsive-utilities.less"; 29 | 30 | 31 | // MEDIA QUERIES 32 | // ------------------ 33 | 34 | // Large desktops 35 | @import "responsive-1200px-min.less"; 36 | 37 | // Tablets to regular desktops 38 | @import "responsive-768px-979px.less"; 39 | 40 | // Phones to portrait tablets and narrow desktops 41 | @import "responsive-767px-max.less"; 42 | 43 | 44 | // RESPONSIVE NAVBAR 45 | // ------------------ 46 | 47 | // From 979px and below, show a button to toggle navbar contents 48 | @import "responsive-navbar.less"; 49 | -------------------------------------------------------------------------------- /doc/source/scripts.rst: -------------------------------------------------------------------------------- 1 | ============================== 2 | Scripts shipped with sklearnef 3 | ============================== 4 | 5 | **sklearnef** comes with a small number of examples scripts to visualize its functionality. 6 | 7 | *bin/density/* 8 | 9 | ``plot_ensemble_gauss.py`` 10 | 11 | Learn simple random Gaussian blobs distributions with DensityForest. 12 | 13 | ``plot_ensemble_sklearn.py`` 14 | 15 | Learn the typical sklearn example distributions with DensityForest. 16 | 17 | ``plot_sherwood.py`` 18 | 19 | Learn the Sherwood library's distributions with DensityForest. 20 | 21 | ``plot_tree_gauss.py`` 22 | 23 | Learn simple random Gaussian blobs distributions with DensityTrees and check their accuracy. 24 | 25 | ``plot_tree_sklearn.py`` 26 | 27 | Learn the typical sklearn example distributions with DensityTrees and check their accuracy. 28 | 29 | *bin/semisupervised/* 30 | 31 | ``plot_ensemble_gauss.py`` 32 | 33 | Classify samples from partially labelled blobs with SemiSupervisedRandomForestClassifiers. 34 | 35 | ``plot_ensemble_sklearn.py`` 36 | 37 | Classify the typical sklearn examples with SemiSupervisedRandomForestClassifiers. 38 | 39 | ``plot_tree_gauss.py`` 40 | 41 | Classify samples from partially labelled blobs with SemiSupervisedDecicionTreeClassifiers. 42 | 43 | 44 | -------------------------------------------------------------------------------- /doc/source/index.rst: -------------------------------------------------------------------------------- 1 | ========= 2 | sklearnef 3 | ========= 4 | 5 | :Release: |release| 6 | :Date: |today| 7 | 8 | **sklearnef** is an extension library for `sklearn `_, providing density and semi-supervised forests written in Python. 9 | 10 | Installation 11 | ============ 12 | 13 | .. toctree:: 14 | :maxdepth: 1 15 | 16 | installation/virtualenvironement 17 | 18 | 19 | Examples 20 | ======== 21 | 22 | .. toctree:: 23 | :glob: 24 | :maxdepth: 1 25 | 26 | examples/* 27 | 28 | Reference 29 | ========= 30 | 31 | .. toctree:: 32 | :maxdepth: 1 33 | 34 | scripts 35 | 36 | :mod:`sklearn.ensemble`: Ensemble methods (decision forests) 37 | ------------------------------------------------------------ 38 | 39 | .. automodule:: sklearnef.ensemble 40 | 41 | .. currentmodule:: sklearnef 42 | 43 | .. autosummary:: 44 | :toctree: generated/ 45 | 46 | ensemble.DensityForest 47 | ensemble.SemiSupervisedRandomForestClassifier 48 | 49 | :mod:`sklearn.tree`: Decision trees 50 | ----------------------------------- 51 | 52 | .. automodule:: sklearnef.tree 53 | 54 | .. currentmodule:: sklearnef 55 | 56 | .. autosummary:: 57 | :toctree: generated/ 58 | 59 | tree.DensityTree 60 | tree.SemiSupervisedDecisionTreeClassifier 61 | tree.GoodnessOfFit 62 | tree.MECDF 63 | 64 | 65 | 66 | 67 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/README.rst: -------------------------------------------------------------------------------- 1 | scipy-sphinx-theme 2 | ================== 3 | 4 | `Sphinx `__ theme for `Scipy `__. 5 | 6 | 7 | Theme options 8 | ------------- 9 | 10 | The theme takes the followin options in the `html_options` 11 | configuration variable: 12 | 13 | - ``edit_link`` 14 | 15 | ``True`` or ``False``. Determines if an "edit this page" link is displayed 16 | in the left sidebar. 17 | 18 | - ``rootlinks`` 19 | 20 | List of tuples ``(url, link_name)`` to show in the beginning of the 21 | breadcrumb list on the top left. You can override it by defining an 22 | `edit_link` block in ``searchbox.html``. 23 | 24 | - ``sidebar`` 25 | 26 | One of ``"left"``, ``"right"``, ``"none"``. Defines where the sidebar 27 | should appear. 28 | 29 | - ``scipy_org_logo`` 30 | 31 | ``True`` or ``False``. Whether to plaster the scipy.org logo on top. 32 | 33 | You can use your own logo by overriding the :attr:`layout.html:header` 34 | block. 35 | 36 | - ``navigation_links`` 37 | 38 | ``True`` or ``False``. Whether to display "next", "prev", "index", etc. 39 | links. 40 | 41 | The following blocks are defined: 42 | 43 | - ``layout.html:header`` 44 | 45 | Block at the top of the page, for logo etc. 46 | 47 | - ``searchbox.html:edit_link`` 48 | 49 | Edit link HTML code to paste in the left sidebar, if `edit_link` is enabled. 50 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/thumbnails.less: -------------------------------------------------------------------------------- 1 | // 2 | // Thumbnails 3 | // -------------------------------------------------- 4 | 5 | 6 | // Note: `.thumbnails` and `.thumbnails > li` are overriden in responsive files 7 | 8 | // Make wrapper ul behave like the grid 9 | .thumbnails { 10 | margin-left: -@gridGutterWidth; 11 | list-style: none; 12 | .clearfix(); 13 | } 14 | // Fluid rows have no left margin 15 | .row-fluid .thumbnails { 16 | margin-left: 0; 17 | } 18 | 19 | // Float li to make thumbnails appear in a row 20 | .thumbnails > li { 21 | float: left; // Explicity set the float since we don't require .span* classes 22 | margin-bottom: @baseLineHeight; 23 | margin-left: @gridGutterWidth; 24 | } 25 | 26 | // The actual thumbnail (can be `a` or `div`) 27 | .thumbnail { 28 | display: block; 29 | padding: 4px; 30 | line-height: @baseLineHeight; 31 | border: 1px solid #ddd; 32 | .border-radius(@baseBorderRadius); 33 | .box-shadow(0 1px 3px rgba(0,0,0,.055)); 34 | .transition(all .2s ease-in-out); 35 | } 36 | // Add a hover/focus state for linked versions only 37 | a.thumbnail:hover, 38 | a.thumbnail:focus { 39 | border-color: @linkColor; 40 | .box-shadow(0 1px 4px rgba(0,105,214,.25)); 41 | } 42 | 43 | // Images and captions 44 | .thumbnail > img { 45 | display: block; 46 | max-width: 100%; 47 | margin-left: auto; 48 | margin-right: auto; 49 | } 50 | .thumbnail .caption { 51 | padding: 9px; 52 | color: @gray; 53 | } 54 | -------------------------------------------------------------------------------- /doc/README: -------------------------------------------------------------------------------- 1 | Building the HTML documentation 2 | ############################### 3 | 4 | IMPORTANT: Make sure that module is importable i.e. python -c 'import sklearnef' 5 | 6 | Run 7 | 8 | sphinx-build -aE -b html source/ build/ 9 | 10 | , then edit .rst files belong to Python classes 11 | 12 | source/generated/*.rst 13 | 14 | by removing the line 15 | 16 | .. automethod:: __init__ 17 | 18 | and adding the line 19 | 20 | :toctree: generated/ 21 | 22 | beneath each ".. autosummary::" command. 23 | 24 | If inherited members should be documented (e.g. cdf() and pdf() methods), add them manually. 25 | 26 | Finally rerun the build 27 | 28 | sphinx-build -aE -b html source/ build/ 29 | 30 | Module members do not show up (sphinx 1.3.x) 31 | ############################################ 32 | Since sphinx 1.3.0, the dedault option for autodoc is to not show IMPORTED members. 33 | Can this be fixed? Only I see right now is using: pip install sphinx==1.2.3 34 | 35 | @see: https://github.com/sphinx-doc/sphinx/pull/1892 36 | 37 | 38 | Enabling the search box 39 | ####################### 40 | 41 | Remove 42 | 43 | scipy-sphinx-theme/_theme/scipy/searchbox.html 44 | 45 | from the scipy template, as it somehow overrides the search box with a custom link to edit the .rst files in-place online. 46 | 47 | 48 | Generate the API documentation files 49 | #################################### 50 | 51 | Run 52 | 53 | sphinx-apidoc -efF -H MedPy -A "Oskar Maier" -V 0.2 -R 1 -o generated/ ../../medpy/medpy/ 54 | 55 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/code.less: -------------------------------------------------------------------------------- 1 | // 2 | // Code (inline and blocK) 3 | // -------------------------------------------------- 4 | 5 | 6 | // Inline and block code styles 7 | code, 8 | pre { 9 | padding: 0 3px 2px; 10 | #font > #family > .monospace; 11 | font-size: @baseFontSize - 2; 12 | color: @grayDark; 13 | .border-radius(3px); 14 | } 15 | 16 | // Inline code 17 | code { 18 | padding: 2px 4px; 19 | color: #d14; 20 | background-color: #f7f7f9; 21 | border: 1px solid #e1e1e8; 22 | white-space: nowrap; 23 | } 24 | 25 | // Blocks of code 26 | pre { 27 | display: block; 28 | padding: (@baseLineHeight - 1) / 2; 29 | margin: 0 0 @baseLineHeight / 2; 30 | font-size: @baseFontSize - 1; // 14px to 13px 31 | line-height: @baseLineHeight; 32 | word-break: break-all; 33 | word-wrap: break-word; 34 | white-space: pre; 35 | white-space: pre-wrap; 36 | background-color: #f5f5f5; 37 | border: 1px solid #ccc; // fallback for IE7-8 38 | border: 1px solid rgba(0,0,0,.15); 39 | .border-radius(@baseBorderRadius); 40 | 41 | // Make prettyprint styles more spaced out for readability 42 | &.prettyprint { 43 | margin-bottom: @baseLineHeight; 44 | } 45 | 46 | // Account for some code outputs that place code tags in pre tags 47 | code { 48 | padding: 0; 49 | color: inherit; 50 | white-space: pre; 51 | white-space: pre-wrap; 52 | background-color: transparent; 53 | border: 0; 54 | } 55 | } 56 | 57 | // Enable scrollable blocks of code 58 | .pre-scrollable { 59 | max-height: 340px; 60 | overflow-y: scroll; 61 | } -------------------------------------------------------------------------------- /doc/source/installation/asroot.rst: -------------------------------------------------------------------------------- 1 | ============================ 2 | Installing sklearnef as root 3 | ============================ 4 | 5 | **Note: Not valid yet!** 6 | 7 | * Requirements? Which numpy version? Which scipy version? Whicht sklearn version? 8 | * buntu provides: http://packages.ubuntu.com/python-sklearn sklearn version. 9 | * I require maybe already the 0.16? Maybe a little bit older would also be possible? 10 | * What about the build-essential? Required? 11 | 12 | .. note:: 13 | 14 | All installation instructions are for Ubuntu, but they should be simmilar for other distributions. 15 | 16 | When installed with root privileges, **sklearnef** will be available for all uses of your machine. 17 | 18 | To install Python packages from `PyPi `_, we recommend `PIP `_ 19 | 20 | .. code-block:: bash 21 | 22 | sudo apt-get install python-pip 23 | 24 | Furthermore, you'll require ``numpy`` and ``scipy``, which you can either install from the repositories 25 | 26 | .. code-block:: bash 27 | 28 | sudo apt-get install python-numpy python-scipy 29 | 30 | Or via PIP 31 | 32 | .. code-block:: bash 33 | 34 | sudo pip install numpy scipy 35 | 36 | To enable the graph-cut package, we also need the following 37 | 38 | .. code-block:: bash 39 | 40 | sudo apt-get install libboost-python-dev build-essential 41 | 42 | And to enable the loading/saving of various image formats, at least ``nibabel`` and ``pydicom`` should be installed 43 | 44 | .. code-block:: bash 45 | 46 | sudo pip install nibabel pydicom 47 | 48 | Now we can install **MedPy** 49 | 50 | .. code-block:: bash 51 | 52 | sudo pip install medpy 53 | 54 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/alerts.less: -------------------------------------------------------------------------------- 1 | // 2 | // Alerts 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base styles 7 | // ------------------------- 8 | 9 | .alert { 10 | padding: 8px 35px 8px 14px; 11 | margin-bottom: @baseLineHeight; 12 | text-shadow: 0 1px 0 rgba(255,255,255,.5); 13 | background-color: @warningBackground; 14 | border: 1px solid @warningBorder; 15 | .border-radius(@baseBorderRadius); 16 | } 17 | .alert, 18 | .alert h4 { 19 | // Specified for the h4 to prevent conflicts of changing @headingsColor 20 | color: @warningText; 21 | } 22 | .alert h4 { 23 | margin: 0; 24 | } 25 | 26 | // Adjust close link position 27 | .alert .close { 28 | position: relative; 29 | top: -2px; 30 | right: -21px; 31 | line-height: @baseLineHeight; 32 | } 33 | 34 | 35 | // Alternate styles 36 | // ------------------------- 37 | 38 | .alert-success { 39 | background-color: @successBackground; 40 | border-color: @successBorder; 41 | color: @successText; 42 | } 43 | .alert-success h4 { 44 | color: @successText; 45 | } 46 | .alert-danger, 47 | .alert-error { 48 | background-color: @errorBackground; 49 | border-color: @errorBorder; 50 | color: @errorText; 51 | } 52 | .alert-danger h4, 53 | .alert-error h4 { 54 | color: @errorText; 55 | } 56 | .alert-info { 57 | background-color: @infoBackground; 58 | border-color: @infoBorder; 59 | color: @infoText; 60 | } 61 | .alert-info h4 { 62 | color: @infoText; 63 | } 64 | 65 | 66 | // Block alerts 67 | // ------------------------- 68 | 69 | .alert-block { 70 | padding-top: 14px; 71 | padding-bottom: 14px; 72 | } 73 | .alert-block > p, 74 | .alert-block > ul { 75 | margin-bottom: 0; 76 | } 77 | .alert-block p + p { 78 | margin-top: 5px; 79 | } 80 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/bootstrap.less: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap v2.3.1 3 | * 4 | * Copyright 2012 Twitter, Inc 5 | * Licensed under the Apache License v2.0 6 | * http://www.apache.org/licenses/LICENSE-2.0 7 | * 8 | * Designed and built with all the love in the world @twitter by @mdo and @fat. 9 | */ 10 | 11 | // Core variables and mixins 12 | @import "variables.less"; // Modify this for custom colors, font-sizes, etc 13 | @import "mixins.less"; 14 | 15 | // CSS Reset 16 | @import "reset.less"; 17 | 18 | // Grid system and page structure 19 | @import "scaffolding.less"; 20 | @import "grid.less"; 21 | @import "layouts.less"; 22 | 23 | // Base CSS 24 | @import "type.less"; 25 | @import "code.less"; 26 | @import "forms.less"; 27 | @import "tables.less"; 28 | 29 | // Components: common 30 | @import "sprites.less"; 31 | @import "dropdowns.less"; 32 | @import "wells.less"; 33 | @import "component-animations.less"; 34 | @import "close.less"; 35 | 36 | // Components: Buttons & Alerts 37 | @import "buttons.less"; 38 | @import "button-groups.less"; 39 | @import "alerts.less"; // Note: alerts share common CSS with buttons and thus have styles in buttons.less 40 | 41 | // Components: Nav 42 | @import "navs.less"; 43 | @import "navbar.less"; 44 | @import "breadcrumbs.less"; 45 | @import "pagination.less"; 46 | @import "pager.less"; 47 | 48 | // Components: Popovers 49 | @import "modals.less"; 50 | @import "tooltip.less"; 51 | @import "popovers.less"; 52 | 53 | // Components: Misc 54 | @import "thumbnails.less"; 55 | @import "media.less"; 56 | @import "labels-badges.less"; 57 | @import "progress-bars.less"; 58 | @import "accordion.less"; 59 | @import "carousel.less"; 60 | @import "hero-unit.less"; 61 | 62 | // Utility classes 63 | @import "utilities.less"; // Has to be last to override when necessary 64 | -------------------------------------------------------------------------------- /sklearnef/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Extension for the scikit-learn machine learning module for Python 3 | ================================================================= 4 | 5 | sklearnef 6 | --------- 7 | sklearnef extends the random decision forest functionality of sklearn 8 | by un- and semi-supervised random decision forest implementations. 9 | 10 | https://pypi.python.org/pypi/sklearnef/ 11 | https://github.com/loli/sklearnef/ 12 | 13 | 14 | sklearn 15 | ------- 16 | sklearn is a Python module integrating classical machine 17 | learning algorithms in the tightly-knit world of scientific Python 18 | packages (numpy, scipy, matplotlib). 19 | 20 | It aims to provide simple and efficient solutions to learning problems 21 | that are accessible to everybody and reusable in various contexts: 22 | machine-learning as a versatile tool for science and engineering. 23 | 24 | See http://scikit-learn.org for complete documentation. 25 | 26 | 27 | Copyright (C) 2013 Oskar Maier, 28 | 29 | !TODO: Add a license. 30 | """ 31 | import sys 32 | import re 33 | import warnings 34 | 35 | # Make sure that DeprecationWarning within this package always gets printed 36 | warnings.filterwarnings('always', category=DeprecationWarning, 37 | module='^{0}\.'.format(re.escape(__name__))) 38 | 39 | # PEP0440 compatible formatted version, see: 40 | # https://www.python.org/dev/peps/pep-0440/ 41 | # 42 | # Generic release markers: 43 | # X.Y 44 | # X.Y.Z # For bugfix releases 45 | # 46 | # Admissible pre-release markers: 47 | # X.YaN # Alpha release 48 | # X.YbN # Beta release 49 | # X.YrcN # Release Candidate 50 | # X.Y # Final release 51 | # 52 | # Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer. 53 | # 54 | __version__ = '0.1.dev' 55 | __all__ = ['ensemble', 'tree'] 56 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-utilities.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Utility classes 3 | // -------------------------------------------------- 4 | 5 | 6 | // IE10 Metro responsive 7 | // Required for Windows 8 Metro split-screen snapping with IE10 8 | // Source: http://timkadlec.com/2012/10/ie10-snap-mode-and-responsive-design/ 9 | @-ms-viewport{ 10 | width: device-width; 11 | } 12 | 13 | // Hide from screenreaders and browsers 14 | // Credit: HTML5 Boilerplate 15 | .hidden { 16 | display: none; 17 | visibility: hidden; 18 | } 19 | 20 | // Visibility utilities 21 | 22 | // For desktops 23 | .visible-phone { display: none !important; } 24 | .visible-tablet { display: none !important; } 25 | .hidden-phone { } 26 | .hidden-tablet { } 27 | .hidden-desktop { display: none !important; } 28 | .visible-desktop { display: inherit !important; } 29 | 30 | // Tablets & small desktops only 31 | @media (min-width: 768px) and (max-width: 979px) { 32 | // Hide everything else 33 | .hidden-desktop { display: inherit !important; } 34 | .visible-desktop { display: none !important ; } 35 | // Show 36 | .visible-tablet { display: inherit !important; } 37 | // Hide 38 | .hidden-tablet { display: none !important; } 39 | } 40 | 41 | // Phones only 42 | @media (max-width: 767px) { 43 | // Hide everything else 44 | .hidden-desktop { display: inherit !important; } 45 | .visible-desktop { display: none !important; } 46 | // Show 47 | .visible-phone { display: inherit !important; } // Use inherit to restore previous behavior 48 | // Hide 49 | .hidden-phone { display: none !important; } 50 | } 51 | 52 | // Print utilities 53 | .visible-print { display: none !important; } 54 | .hidden-print { } 55 | 56 | @media print { 57 | .visible-print { display: inherit !important; } 58 | .hidden-print { display: none !important; } 59 | } 60 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/tooltip.less: -------------------------------------------------------------------------------- 1 | // 2 | // Tooltips 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base class 7 | .tooltip { 8 | position: absolute; 9 | z-index: @zindexTooltip; 10 | display: block; 11 | visibility: visible; 12 | font-size: 11px; 13 | line-height: 1.4; 14 | .opacity(0); 15 | &.in { .opacity(80); } 16 | &.top { margin-top: -3px; padding: 5px 0; } 17 | &.right { margin-left: 3px; padding: 0 5px; } 18 | &.bottom { margin-top: 3px; padding: 5px 0; } 19 | &.left { margin-left: -3px; padding: 0 5px; } 20 | } 21 | 22 | // Wrapper for the tooltip content 23 | .tooltip-inner { 24 | max-width: 200px; 25 | padding: 8px; 26 | color: @tooltipColor; 27 | text-align: center; 28 | text-decoration: none; 29 | background-color: @tooltipBackground; 30 | .border-radius(@baseBorderRadius); 31 | } 32 | 33 | // Arrows 34 | .tooltip-arrow { 35 | position: absolute; 36 | width: 0; 37 | height: 0; 38 | border-color: transparent; 39 | border-style: solid; 40 | } 41 | .tooltip { 42 | &.top .tooltip-arrow { 43 | bottom: 0; 44 | left: 50%; 45 | margin-left: -@tooltipArrowWidth; 46 | border-width: @tooltipArrowWidth @tooltipArrowWidth 0; 47 | border-top-color: @tooltipArrowColor; 48 | } 49 | &.right .tooltip-arrow { 50 | top: 50%; 51 | left: 0; 52 | margin-top: -@tooltipArrowWidth; 53 | border-width: @tooltipArrowWidth @tooltipArrowWidth @tooltipArrowWidth 0; 54 | border-right-color: @tooltipArrowColor; 55 | } 56 | &.left .tooltip-arrow { 57 | top: 50%; 58 | right: 0; 59 | margin-top: -@tooltipArrowWidth; 60 | border-width: @tooltipArrowWidth 0 @tooltipArrowWidth @tooltipArrowWidth; 61 | border-left-color: @tooltipArrowColor; 62 | } 63 | &.bottom .tooltip-arrow { 64 | top: 0; 65 | left: 50%; 66 | margin-left: -@tooltipArrowWidth; 67 | border-width: 0 @tooltipArrowWidth @tooltipArrowWidth; 68 | border-bottom-color: @tooltipArrowColor; 69 | } 70 | } 71 | -------------------------------------------------------------------------------- /sklearnef/tree/_diffentropy.pxd: -------------------------------------------------------------------------------- 1 | # python imports 2 | 3 | # cython imports 4 | cimport numpy as np 5 | 6 | # extern cdefs: lapack c-wrapped fortran routine definitions 7 | # A = U*D*U**T // http://www.netlib.org/lapack/explore-html/d1/dcd/dsptrf_8f.html 8 | cdef extern void dsptrf_( char *uplo, int *n, double *ap, int *ipiv, int *info ) nogil 9 | 10 | # type definitions 11 | ctypedef np.npy_float32 INTYPE_t # input data type, should be of leass or equl precision that internal data type 12 | ctypedef np.npy_float64 DTYPE_t # data type for internal calculations 13 | ctypedef np.npy_intp SIZE_t # type for indices and counters 14 | 15 | cdef class Diffentropy: 16 | # Dynamically updateable statistical co-variance matrix and log-determinant computation with delayed update 17 | # based on: https://github.com/loli/dynstatcov 18 | # and 19 | # https://github.com/loli/logdet 20 | 21 | # internal structure 22 | cdef DTYPE_t* cov # upper triangular part of the co-variance matrix 23 | cdef DTYPE_t* squaresum # upper triangular part of the sum of all samples outer product 24 | cdef DTYPE_t* sum # sum of all samples 25 | cdef SIZE_t n_samples # number of samples from which the co-variance matrix is computed 26 | cdef SIZE_t n_features # number of elements per samples 27 | cdef SIZE_t n_upper # elements in the upper triangular matrix 28 | 29 | cdef DTYPE_t* __mean # private member 30 | cdef int* __ipiv # private member 31 | cdef double* __covf # private member 32 | 33 | cdef void update_add(self, INTYPE_t* x) nogil # no-gil update method (addition) 34 | cdef void update_sub(self, INTYPE_t* x) nogil # no-gil update method (subtraction) 35 | cdef void reset(self) nogil # reset the class 36 | cdef void compute_covariance_matrix(self) nogil # trigger the computation of the co-variance matrix 37 | cdef DTYPE_t logdet(self) nogil # return the log-determinant of the co-variance matrix -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/conf.py: -------------------------------------------------------------------------------- 1 | needs_sphinx = '1.1' 2 | 3 | extensions = ['sphinx.ext.autodoc', 'sphinx.ext.pngmath', 'numpydoc', 4 | 'sphinx.ext.intersphinx', 'sphinx.ext.coverage', 5 | 'sphinx.ext.autosummary', 'matplotlib.sphinxext.plot_directive'] 6 | 7 | templates_path = ['_templates'] 8 | source_suffix = '.rst' 9 | master_doc = 'index' 10 | project = u'scipy-sphinx-theme' 11 | copyright = u'2013, Surya Kasturi and Pauli Virtanen' 12 | version = '0.1' 13 | release = '0.1' 14 | exclude_patterns = ['_build'] 15 | pygments_style = 'sphinx' 16 | 17 | # -- Options for HTML output --------------------------------------------------- 18 | 19 | html_theme = 'scipy' 20 | html_theme_path = ['_theme'] 21 | #html_logo = '_static/scipyshiny_small.png' 22 | html_static_path = ['_static'] 23 | html_theme_options = { 24 | "edit_link": "true", 25 | "sidebar": "right", 26 | "scipy_org_logo": "false", 27 | "rootlinks": [("http://scipy.org/", "Scipy.org"), 28 | ("http://docs.scipy.org/", "Docs")] 29 | } 30 | 31 | pngmath_latex_preamble = r""" 32 | \usepackage{color} 33 | \definecolor{textgray}{RGB}{51,51,51} 34 | \color{textgray} 35 | """ 36 | pngmath_use_preview = True 37 | pngmath_dvipng_args = ['-gamma 1.5', '-D 96', '-bg Transparent'] 38 | 39 | #------------------------------------------------------------------------------ 40 | # Plot style 41 | #------------------------------------------------------------------------------ 42 | 43 | plot_pre_code = """ 44 | import numpy as np 45 | import scipy as sp 46 | np.random.seed(123) 47 | """ 48 | plot_include_source = True 49 | plot_formats = [('png', 96), 'pdf'] 50 | plot_html_show_formats = False 51 | 52 | import math 53 | phi = (math.sqrt(5) + 1)/2 54 | 55 | font_size = 13*72/96.0 # 13 px 56 | 57 | plot_rcparams = { 58 | 'font.size': font_size, 59 | 'axes.titlesize': font_size, 60 | 'axes.labelsize': font_size, 61 | 'xtick.labelsize': font_size, 62 | 'ytick.labelsize': font_size, 63 | 'legend.fontsize': font_size, 64 | 'figure.figsize': (3*phi, 3), 65 | 'figure.subplot.bottom': 0.2, 66 | 'figure.subplot.left': 0.2, 67 | 'figure.subplot.right': 0.9, 68 | 'figure.subplot.top': 0.85, 69 | 'figure.subplot.wspace': 0.4, 70 | 'text.usetex': False, 71 | } 72 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/labels-badges.less: -------------------------------------------------------------------------------- 1 | // 2 | // Labels and badges 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base classes 7 | .label, 8 | .badge { 9 | display: inline-block; 10 | padding: 2px 4px; 11 | font-size: @baseFontSize * .846; 12 | font-weight: bold; 13 | line-height: 14px; // ensure proper line-height if floated 14 | color: @white; 15 | vertical-align: baseline; 16 | white-space: nowrap; 17 | text-shadow: 0 -1px 0 rgba(0,0,0,.25); 18 | background-color: @grayLight; 19 | } 20 | // Set unique padding and border-radii 21 | .label { 22 | .border-radius(3px); 23 | } 24 | .badge { 25 | padding-left: 9px; 26 | padding-right: 9px; 27 | .border-radius(9px); 28 | } 29 | 30 | // Empty labels/badges collapse 31 | .label, 32 | .badge { 33 | &:empty { 34 | display: none; 35 | } 36 | } 37 | 38 | // Hover/focus state, but only for links 39 | a { 40 | &.label:hover, 41 | &.label:focus, 42 | &.badge:hover, 43 | &.badge:focus { 44 | color: @white; 45 | text-decoration: none; 46 | cursor: pointer; 47 | } 48 | } 49 | 50 | // Colors 51 | // Only give background-color difference to links (and to simplify, we don't qualifty with `a` but [href] attribute) 52 | .label, 53 | .badge { 54 | // Important (red) 55 | &-important { background-color: @errorText; } 56 | &-important[href] { background-color: darken(@errorText, 10%); } 57 | // Warnings (orange) 58 | &-warning { background-color: @orange; } 59 | &-warning[href] { background-color: darken(@orange, 10%); } 60 | // Success (green) 61 | &-success { background-color: @successText; } 62 | &-success[href] { background-color: darken(@successText, 10%); } 63 | // Info (turquoise) 64 | &-info { background-color: @infoText; } 65 | &-info[href] { background-color: darken(@infoText, 10%); } 66 | // Inverse (black) 67 | &-inverse { background-color: @grayDark; } 68 | &-inverse[href] { background-color: darken(@grayDark, 10%); } 69 | } 70 | 71 | // Quick fix for labels/badges in buttons 72 | .btn { 73 | .label, 74 | .badge { 75 | position: relative; 76 | top: -1px; 77 | } 78 | } 79 | .btn-mini { 80 | .label, 81 | .badge { 82 | top: 0; 83 | } 84 | } 85 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # Internal variables. 11 | PAPEROPT_a4 = -D latex_paper_size=a4 12 | PAPEROPT_letter = -D latex_paper_size=letter 13 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 14 | # the i18n builder cannot share the environment and doctrees with the others 15 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 16 | 17 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext all css 18 | 19 | all: html 20 | 21 | css: $(wildcard _theme/scipy/static/css/*.css) 22 | 23 | _theme/scipy/static/css/%.css: _theme/scipy/static/less/%.less 24 | lessc $^ > $@.new 25 | mv -f $@.new $@ 26 | 27 | help: 28 | @echo "Please use \`make ' where is one of" 29 | @echo " html to make standalone HTML files" 30 | @echo " dirhtml to make HTML files named index.html in directories" 31 | @echo " singlehtml to make a single large HTML file" 32 | @echo " pickle to make pickle files" 33 | @echo " json to make JSON files" 34 | @echo " htmlhelp to make HTML files and a HTML help project" 35 | @echo " qthelp to make HTML files and a qthelp project" 36 | @echo " devhelp to make HTML files and a Devhelp project" 37 | @echo " epub to make an epub" 38 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 39 | @echo " latexpdf to make LaTeX files and run them through pdflatex" 40 | @echo " text to make text files" 41 | @echo " man to make manual pages" 42 | @echo " texinfo to make Texinfo files" 43 | @echo " info to make Texinfo files and run them through makeinfo" 44 | @echo " gettext to make PO message catalogs" 45 | @echo " changes to make an overview of all changed/added/deprecated items" 46 | @echo " linkcheck to check all external links for integrity" 47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)" 48 | 49 | clean: 50 | -rm -rf $(BUILDDIR)/* 51 | 52 | html: 53 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 54 | @echo 55 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 56 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/modals.less: -------------------------------------------------------------------------------- 1 | // 2 | // Modals 3 | // -------------------------------------------------- 4 | 5 | // Background 6 | .modal-backdrop { 7 | position: fixed; 8 | top: 0; 9 | right: 0; 10 | bottom: 0; 11 | left: 0; 12 | z-index: @zindexModalBackdrop; 13 | background-color: @black; 14 | // Fade for backdrop 15 | &.fade { opacity: 0; } 16 | } 17 | 18 | .modal-backdrop, 19 | .modal-backdrop.fade.in { 20 | .opacity(80); 21 | } 22 | 23 | // Base modal 24 | .modal { 25 | position: fixed; 26 | top: 10%; 27 | left: 50%; 28 | z-index: @zindexModal; 29 | width: 560px; 30 | margin-left: -280px; 31 | background-color: @white; 32 | border: 1px solid #999; 33 | border: 1px solid rgba(0,0,0,.3); 34 | *border: 1px solid #999; /* IE6-7 */ 35 | .border-radius(6px); 36 | .box-shadow(0 3px 7px rgba(0,0,0,0.3)); 37 | .background-clip(padding-box); 38 | // Remove focus outline from opened modal 39 | outline: none; 40 | 41 | &.fade { 42 | .transition(e('opacity .3s linear, top .3s ease-out')); 43 | top: -25%; 44 | } 45 | &.fade.in { top: 10%; } 46 | } 47 | .modal-header { 48 | padding: 9px 15px; 49 | border-bottom: 1px solid #eee; 50 | // Close icon 51 | .close { margin-top: 2px; } 52 | // Heading 53 | h3 { 54 | margin: 0; 55 | line-height: 30px; 56 | } 57 | } 58 | 59 | // Body (where all modal content resides) 60 | .modal-body { 61 | position: relative; 62 | overflow-y: auto; 63 | max-height: 400px; 64 | padding: 15px; 65 | } 66 | // Remove bottom margin if need be 67 | .modal-form { 68 | margin-bottom: 0; 69 | } 70 | 71 | // Footer (for actions) 72 | .modal-footer { 73 | padding: 14px 15px 15px; 74 | margin-bottom: 0; 75 | text-align: right; // right align buttons 76 | background-color: #f5f5f5; 77 | border-top: 1px solid #ddd; 78 | .border-radius(0 0 6px 6px); 79 | .box-shadow(inset 0 1px 0 @white); 80 | .clearfix(); // clear it in case folks use .pull-* classes on buttons 81 | 82 | // Properly space out buttons 83 | .btn + .btn { 84 | margin-left: 5px; 85 | margin-bottom: 0; // account for input[type="submit"] which gets the bottom margin like all other inputs 86 | } 87 | // but override that for button groups 88 | .btn-group .btn + .btn { 89 | margin-left: -1px; 90 | } 91 | // and override it for block buttons as well 92 | .btn-block + .btn-block { 93 | margin-left: 0; 94 | } 95 | } 96 | -------------------------------------------------------------------------------- /doc/numpydoc/README.rst: -------------------------------------------------------------------------------- 1 | .. image:: https://travis-ci.org/numpy/numpydoc.png?branch=master 2 | :target: https://travis-ci.org/numpy/numpydoc/ 3 | 4 | ===================================== 5 | numpydoc -- Numpy's Sphinx extensions 6 | ===================================== 7 | 8 | Numpy's documentation uses several custom extensions to Sphinx. These 9 | are shipped in this ``numpydoc`` package, in case you want to make use 10 | of them in third-party projects. 11 | 12 | The following extensions are available: 13 | 14 | - ``numpydoc``: support for the Numpy docstring format in Sphinx, and add 15 | the code description directives ``np:function``, ``np-c:function``, etc. 16 | that support the Numpy docstring syntax. 17 | 18 | - ``numpydoc.traitsdoc``: For gathering documentation about Traits attributes. 19 | 20 | - ``numpydoc.plot_directive``: Adaptation of Matplotlib's ``plot::`` 21 | directive. Note that this implementation may still undergo severe 22 | changes or eventually be deprecated. 23 | 24 | See `A Guide to NumPy/SciPy Documentation `_ 25 | for how to write docs that use this extension. 26 | 27 | 28 | numpydoc 29 | ======== 30 | 31 | Numpydoc inserts a hook into Sphinx's autodoc that converts docstrings 32 | following the Numpy/Scipy format to a form palatable to Sphinx. 33 | 34 | Options 35 | ------- 36 | 37 | The following options can be set in conf.py: 38 | 39 | - numpydoc_use_plots: bool 40 | 41 | Whether to produce ``plot::`` directives for Examples sections that 42 | contain ``import matplotlib``. 43 | 44 | - numpydoc_show_class_members: bool 45 | 46 | Whether to show all members of a class in the Methods and Attributes 47 | sections automatically. 48 | ``True`` by default. 49 | 50 | - numpydoc_show_inherited_class_members: bool 51 | 52 | Whether to show all inherited members of a class in the Methods and Attributes 53 | sections automatically. If it's false, inherited members won't shown. 54 | ``True`` by default. 55 | 56 | - numpydoc_class_members_toctree: bool 57 | 58 | Whether to create a Sphinx table of contents for the lists of class 59 | methods and attributes. If a table of contents is made, Sphinx expects 60 | each entry to have a separate page. 61 | ``True`` by default. 62 | 63 | - numpydoc_edit_link: bool (DEPRECATED -- edit your HTML template instead) 64 | 65 | Whether to insert an edit link after docstrings. 66 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/css/spc-extend.css: -------------------------------------------------------------------------------- 1 | body { 2 | background-color: #f9faf5; 3 | } 4 | .container { 5 | width: 80%; 6 | } 7 | .main { 8 | background-color: white; 9 | padding: 18px; 10 | -moz-box-shadow: 0 0 3px #888; 11 | -webkit-box-shadow: 0 0 3px #888; 12 | box-shadow: 0 0 3px #888; 13 | } 14 | .underline { 15 | border-bottom: 1.5px solid #eeeeee; 16 | } 17 | .header { 18 | margin-top: 15px; 19 | margin-bottom: 15px; 20 | margin-left: 0px; 21 | margin-right: 0px; 22 | } 23 | .spc-navbar { 24 | margin-top: 15px; 25 | margin-bottom: 5px; 26 | margin-left: 0px; 27 | margin-right: 0px; 28 | } 29 | .spc-navbar .nav-pills { 30 | margin-bottom: 0px; 31 | font-size: 12px; 32 | } 33 | .spc-navbar .nav-pills > li > a { 34 | padding-top: 2.5px; 35 | padding-bottom: 2.5px; 36 | } 37 | .underline { 38 | border-bottom: 1.5px solid #eeeeee; 39 | } 40 | .spc-page-title h1, 41 | .spc-page-title h2, 42 | .spc-page-title h3, 43 | .spc-page-title h4 { 44 | font-weight: normal; 45 | border-bottom: 1.5px solid #eeeeee; 46 | } 47 | .tags .btn { 48 | border: none; 49 | font-size: 9.5px; 50 | font-weight: bold; 51 | } 52 | .spc-search-result-title h1, 53 | .spc-search-result-title h2, 54 | .spc-search-result-title h3, 55 | .spc-search-result-title h4 { 56 | font-weight: normal; 57 | } 58 | .spc-snippet-header { 59 | margin-bottom: 5px; 60 | } 61 | .spc-snippet-info { 62 | padding-top: 10px; 63 | } 64 | .spc-snippet-info .dl-horizontal { 65 | margin: 5px; 66 | } 67 | .spc-snippet-info .dl-horizontal dt { 68 | font-weight: normal; 69 | } 70 | .spc-snippet-body { 71 | padding: 10px; 72 | } 73 | .spc-snippet-body .accordion-group { 74 | border: none; 75 | } 76 | .spc-snippet-body .accordion-heading { 77 | text-transform: uppercase; 78 | font-size: 14px; 79 | border-bottom: 1px solid #e5e5e5; 80 | } 81 | .spc-snippet-body .accordion-heading .accordion-toggle { 82 | padding-top: 10px; 83 | padding-bottom: 5px; 84 | } 85 | .spc-rightsidebar { 86 | color: #555555; 87 | } 88 | .spc-rightsidebar .navigation { 89 | padding: 2px 10px; 90 | font-size: 11.9px; 91 | } 92 | .spc-rightsidebar .navigation .nav-title { 93 | font-weight: bold; 94 | text-transform: uppercase; 95 | } 96 | .spc-rightsidebar .navigation li { 97 | margin: 5px; 98 | } 99 | .footer { 100 | padding: 5px; 101 | font-size: small; 102 | } 103 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/css/extend.css: -------------------------------------------------------------------------------- 1 | .container { 2 | width: 80%; 3 | } 4 | .navbar1 { 5 | padding-bottom: 10px; 6 | } 7 | .navbar1 .nav-pills { 8 | margin-bottom: 0px; 9 | font-size: 12px; 10 | } 11 | .navbar1 .nav-pills > li > a { 12 | padding-top: 2.5px; 13 | padding-bottom: 2.5px; 14 | } 15 | .navbar1 .dropdown.dropdown-menu { 16 | padding: 0px; 17 | } 18 | .header { 19 | padding-top: 30px; 20 | padding-bottom: 18px; 21 | } 22 | .SearchBar .form-search { 23 | margin-bottom: 0px; 24 | } 25 | .SearchBar .input-append input { 26 | height: 12px; 27 | } 28 | body { 29 | font-family: Segoe UI; 30 | background-color: #f9faf7; 31 | } 32 | .main { 33 | background-color: white; 34 | padding: 18px; 35 | -moz-box-shadow: 0 0 3px #888; 36 | -webkit-box-shadow: 0 0 3px #888; 37 | box-shadow: 0 0 3px #888; 38 | } 39 | .MainHeader h1 { 40 | font-weight: normal; 41 | } 42 | .content .contentTitle h4 { 43 | font-size: 18px; 44 | font-weight: normal; 45 | } 46 | .content .meta { 47 | font-size: small; 48 | } 49 | .tags .btn { 50 | border: none; 51 | font-size: 10px; 52 | font-weight: bold; 53 | } 54 | .navigation { 55 | font-size: 12px; 56 | padding-bottom: 12px; 57 | } 58 | .navigation .nav-title { 59 | color: #333333; 60 | font-family: "Segoe UI semibold"; 61 | font-size: 16px; 62 | text-transform: uppercase; 63 | } 64 | .navigation li { 65 | margin: 5px; 66 | } 67 | .snippetHeader { 68 | margin-bottom: 5px; 69 | } 70 | .snippetHeader .snippetTitle { 71 | font-size: 21px; 72 | line-height: 40px; 73 | border-bottom: 1px solid #e5e5e5; 74 | display: block; 75 | color: #333333; 76 | } 77 | .snippetInfo { 78 | padding-top: 10px; 79 | } 80 | .snippetInfo .dl-horizontal { 81 | margin: 5px; 82 | } 83 | .snippet-body { 84 | padding: 10px; 85 | } 86 | .snippet-body .accordion-group { 87 | border: none; 88 | } 89 | .snippet-body .accordion-heading { 90 | text-transform: uppercase; 91 | font-size: 14px; 92 | border-bottom: 1px solid #e5e5e5; 93 | } 94 | .snippet-body .accordion-heading .accordion-toggle { 95 | padding-top: 10px; 96 | padding-bottom: 5px; 97 | } 98 | .SearchResult { 99 | padding: 10px; 100 | padding-top: 0px; 101 | } 102 | .SearchResult .PageTitle { 103 | font-size: 21px; 104 | line-height: 40px; 105 | border-bottom: 1px solid #e5e5e5; 106 | padding-bottom: 5px; 107 | display: block; 108 | color: #333333; 109 | } 110 | .footer { 111 | padding: 10px; 112 | } 113 | .footer-inside { 114 | border-top: 1px solid #e5e5e5; 115 | padding: 10px; 116 | } 117 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/linkcode.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | linkcode 4 | ~~~~~~~~ 5 | 6 | Add external links to module code in Python object descriptions. 7 | 8 | :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. 9 | :license: BSD, see LICENSE for details. 10 | 11 | """ 12 | from __future__ import division, absolute_import, print_function 13 | 14 | import warnings 15 | import collections 16 | 17 | warnings.warn("This extension has been accepted to Sphinx upstream. " 18 | "Use the version from there (Sphinx >= 1.2) " 19 | "https://bitbucket.org/birkenfeld/sphinx/pull-request/47/sphinxextlinkcode", 20 | FutureWarning, stacklevel=1) 21 | 22 | 23 | from docutils import nodes 24 | 25 | from sphinx import addnodes 26 | from sphinx.locale import _ 27 | from sphinx.errors import SphinxError 28 | 29 | class LinkcodeError(SphinxError): 30 | category = "linkcode error" 31 | 32 | def doctree_read(app, doctree): 33 | env = app.builder.env 34 | 35 | resolve_target = getattr(env.config, 'linkcode_resolve', None) 36 | if not isinstance(env.config.linkcode_resolve, collections.Callable): 37 | raise LinkcodeError( 38 | "Function `linkcode_resolve` is not given in conf.py") 39 | 40 | domain_keys = dict( 41 | py=['module', 'fullname'], 42 | c=['names'], 43 | cpp=['names'], 44 | js=['object', 'fullname'], 45 | ) 46 | 47 | for objnode in doctree.traverse(addnodes.desc): 48 | domain = objnode.get('domain') 49 | uris = set() 50 | for signode in objnode: 51 | if not isinstance(signode, addnodes.desc_signature): 52 | continue 53 | 54 | # Convert signode to a specified format 55 | info = {} 56 | for key in domain_keys.get(domain, []): 57 | value = signode.get(key) 58 | if not value: 59 | value = '' 60 | info[key] = value 61 | if not info: 62 | continue 63 | 64 | # Call user code to resolve the link 65 | uri = resolve_target(domain, info) 66 | if not uri: 67 | # no source 68 | continue 69 | 70 | if uri in uris or not uri: 71 | # only one link per name, please 72 | continue 73 | uris.add(uri) 74 | 75 | onlynode = addnodes.only(expr='html') 76 | onlynode += nodes.reference('', '', internal=False, refuri=uri) 77 | onlynode[0] += nodes.inline('', _('[source]'), 78 | classes=['viewcode-link']) 79 | signode += onlynode 80 | 81 | def setup(app): 82 | app.connect('doctree-read', doctree_read) 83 | app.add_config_value('linkcode_resolve', None, '') 84 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/js/copybutton.js: -------------------------------------------------------------------------------- 1 | // Copyright 2014 PSF. Licensed under the PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2 2 | // File originates from the cpython source found in Doc/tools/sphinxext/static/copybutton.js 3 | 4 | $(document).ready(function() { 5 | /* Add a [>>>] button on the top-right corner of code samples to hide 6 | * the >>> and ... prompts and the output and thus make the code 7 | * copyable. */ 8 | var div = $('.highlight-python .highlight,' + 9 | '.highlight-python3 .highlight') 10 | var pre = div.find('pre'); 11 | 12 | // get the styles from the current theme 13 | pre.parent().parent().css('position', 'relative'); 14 | var hide_text = 'Hide the prompts and output'; 15 | var show_text = 'Show the prompts and output'; 16 | var border_width = pre.css('border-top-width'); 17 | var border_style = pre.css('border-top-style'); 18 | var border_color = pre.css('border-top-color'); 19 | var button_styles = { 20 | 'cursor':'pointer', 'position': 'absolute', 'top': '0', 'right': '0', 21 | 'border-color': border_color, 'border-style': border_style, 22 | 'border-width': border_width, 'color': border_color, 'text-size': '75%', 23 | 'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em', 24 | 'border-radius': '0 3px 0 0' 25 | } 26 | 27 | // create and add the button to all the code blocks that contain >>> 28 | div.each(function(index) { 29 | var jthis = $(this); 30 | if (jthis.find('.gp').length > 0) { 31 | var button = $('>>>'); 32 | button.css(button_styles) 33 | button.attr('title', hide_text); 34 | jthis.prepend(button); 35 | } 36 | // tracebacks (.gt) contain bare text elements that need to be 37 | // wrapped in a span to work with .nextUntil() (see later) 38 | jthis.find('pre:has(.gt)').contents().filter(function() { 39 | return ((this.nodeType == 3) && (this.data.trim().length > 0)); 40 | }).wrap(''); 41 | }); 42 | 43 | // define the behavior of the button when it's clicked 44 | $('.copybutton').toggle( 45 | function() { 46 | var button = $(this); 47 | button.parent().find('.go, .gp, .gt').hide(); 48 | button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden'); 49 | button.css('text-decoration', 'line-through'); 50 | button.attr('title', show_text); 51 | }, 52 | function() { 53 | var button = $(this); 54 | button.parent().find('.go, .gp, .gt').show(); 55 | button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible'); 56 | button.css('text-decoration', 'none'); 57 | button.attr('title', hide_text); 58 | }); 59 | }); 60 | 61 | -------------------------------------------------------------------------------- /doc/source/examples/sklearndensity.rst: -------------------------------------------------------------------------------- 1 | ============================================== 2 | DensityForest examples (sklearn distributions) 3 | ============================================== 4 | 5 | DensityForest examples on data distributions from the sklearn library created with the `plot_ensemble_sklearn.py` script shipped with **sklearnef**. 6 | 7 | Learning the densities of various distributions 8 | =============================================== 9 | 10 | Learning the density of various distributions. All examples were generated with ``minimum_improvement=0.1``, only the *blobs* examples used a value of ``0.5``. The integral over the learned density is always 1.0. 11 | 12 | .. code-block:: bash 13 | 14 | ./plot_ensemble_sklearn.py {circles_distant,circles_near,moons,blobs,s_curve,swiss_roll} --min-improvement={.1,.5} 15 | 16 | 17 | .. image:: images/density_example_circlesdistant.png 18 | :width: 400px 19 | 20 | .. image:: images/density_example_circlenear.png 21 | :width: 400px 22 | 23 | .. image:: images/density_example_moons.png 24 | :width: 400px 25 | 26 | .. image:: images/density_example_blobs.png 27 | :width: 400px 28 | 29 | .. image:: images/density_example_scurve.png 30 | :width: 400px 31 | 32 | .. image:: images/density_example_swissroll.png 33 | :width: 400px 34 | 35 | 36 | The influence of the ``min_improvement`` parameter 37 | ================================================== 38 | 39 | The min_improvement parameter, which restricts the tree growth based on the information gain, is the most important lever to train DensityForests. The following examples should give an idea on how it influences the learned distribution. 40 | 41 | The first image denotes the training data, i.e. the distribution of the training datapoints whose density distribution we want to learn. The remaining images show the learned distributions for different ``min_improvement`` values: {2.00,1.00,0.50,0.25,0.10,0.05,0.01}. Stopping the tree growth to early fails to capture the finer details, while a too low value fragments the density into many narrow Gaussians. 42 | 43 | .. code-block:: bash 44 | 45 | ./plot_ensemble_sklearn.py circles_distant --min-improvement={2.00,1.00,0.50,0.25,0.10,0.05,0.01} 46 | 47 | .. image:: images/density_circlesdistant_minimp_gt.png 48 | :width: 300px 49 | 50 | .. image:: images/density_circlesdistant_minimp2.png 51 | :width: 300px 52 | 53 | .. image:: images/density_circlesdistant_minimp1.png 54 | :width: 300px 55 | 56 | .. image:: images/density_circlesdistant_minimp0.5.png 57 | :width: 300px 58 | 59 | .. image:: images/density_circlesdistant_minimp0.25.png 60 | :width: 300px 61 | 62 | .. image:: images/density_circlesdistant_minimp0.1.png 63 | :width: 300px 64 | 65 | .. image:: images/density_circlesdistant_minimp0.05.png 66 | :width: 300px 67 | 68 | .. image:: images/density_circlesdistant_minimp0.01.png 69 | :width: 300px 70 | 71 | 72 | 73 | -------------------------------------------------------------------------------- /sklearnef/ensemble/tests/test_ensemble.py: -------------------------------------------------------------------------------- 1 | """ 2 | Testing for the ensemble module (sklearnef.ensemble). 3 | """ 4 | 5 | import numpy as np 6 | 7 | from sklearn.utils.testing import assert_array_equal 8 | from sklearn.utils.testing import assert_array_almost_equal 9 | from sklearn.utils.testing import assert_almost_equal 10 | from sklearn.utils.testing import assert_equal 11 | from sklearn.utils.testing import assert_in 12 | from sklearn.utils.testing import assert_raises 13 | from sklearn.utils.testing import assert_greater 14 | from sklearn.utils.testing import assert_greater_equal 15 | from sklearn.utils.testing import assert_less 16 | from sklearn.utils.testing import assert_true, assert_false 17 | from sklearn.utils.testing import raises 18 | 19 | from sklearn import datasets 20 | 21 | from sklearnef.ensemble import SemiSupervisedRandomForestClassifier, DensityForest 22 | 23 | # ---------- Datasets ---------- 24 | # load the iris dataset, randomly permute it and mask some as unsupervised 25 | iris = datasets.load_iris() 26 | rng = np.random.RandomState(1) 27 | perm = rng.permutation(iris.target.size) 28 | iris.data = iris.data[perm] 29 | iris.target = iris.target[perm] 30 | iris.target_semisup = np.copy(iris.target) 31 | iris.target_semisup[np.random.randint(0, 2, iris.target_semisup.shape[0]) == 0] = -1 32 | 33 | DATASETS = { 34 | "iris": {"X": iris.data, "y": iris.target}, 35 | "iris_semisup": {"X": iris.data, "y": iris.target_semisup}, 36 | } 37 | 38 | # ---------- Definitions ---------- 39 | SEMISCLF_FORESTS = { 40 | "SemiSupervisedRandomForestClassifier": SemiSupervisedRandomForestClassifier 41 | } 42 | 43 | UNSCLF_FORESTS = { 44 | "DensityForest": DensityForest 45 | } 46 | 47 | ALL_FORESTS = dict() 48 | ALL_FORESTS.update(SEMISCLF_FORESTS) 49 | ALL_FORESTS.update(UNSCLF_FORESTS) 50 | 51 | # ---------- Test imports ---------- 52 | 53 | # ---------- Set-ups -------- 54 | 55 | # ---------- Tests ---------- 56 | def test_class_labels(): 57 | """Test if the correct class labels are returned.""" 58 | X = DATASETS["iris_semisup"]["X"] 59 | y = np.copy(DATASETS["iris_semisup"]["y"]) 60 | 61 | # default labels 62 | labels = np.unique(y)[1:] 63 | clf = SemiSupervisedRandomForestClassifier(random_state=2) 64 | clf.fit(X, y) 65 | 66 | _confirm_only_a_in_b(labels, clf.predict(X), "Predicted continuous labels are wrong.") 67 | _confirm_only_a_in_b(labels, clf.transduced_labels_, "Transduced continuous labels are wrong.") 68 | 69 | # far apart labels 70 | for l in labels: 71 | y[l == y] += l*100 72 | labels = np.unique(y)[1:] 73 | clf = SemiSupervisedRandomForestClassifier(random_state=2) 74 | clf.fit(X, y) 75 | 76 | _confirm_only_a_in_b(labels, clf.predict(X), "Predicted apart labels are wrong.") 77 | _confirm_only_a_in_b(labels, clf.transduced_labels_, "Transduced apart labels are wrong.") 78 | 79 | # ---------- Helpers ---------- 80 | def _confirm_only_a_in_b(a, b, msg=None): 81 | print a, b 82 | occurences = np.zeros(b.shape[0], dtype=np.bool) 83 | for l in a: 84 | occurences += l == b 85 | assert_true(np.all(occurences), msg=msg) 86 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/pagination.less: -------------------------------------------------------------------------------- 1 | // 2 | // Pagination (multiple pages) 3 | // -------------------------------------------------- 4 | 5 | // Space out pagination from surrounding content 6 | .pagination { 7 | margin: @baseLineHeight 0; 8 | } 9 | 10 | .pagination ul { 11 | // Allow for text-based alignment 12 | display: inline-block; 13 | .ie7-inline-block(); 14 | // Reset default ul styles 15 | margin-left: 0; 16 | margin-bottom: 0; 17 | // Visuals 18 | .border-radius(@baseBorderRadius); 19 | .box-shadow(0 1px 2px rgba(0,0,0,.05)); 20 | } 21 | .pagination ul > li { 22 | display: inline; // Remove list-style and block-level defaults 23 | } 24 | .pagination ul > li > a, 25 | .pagination ul > li > span { 26 | float: left; // Collapse white-space 27 | padding: 4px 12px; 28 | line-height: @baseLineHeight; 29 | text-decoration: none; 30 | background-color: @paginationBackground; 31 | border: 1px solid @paginationBorder; 32 | border-left-width: 0; 33 | } 34 | .pagination ul > li > a:hover, 35 | .pagination ul > li > a:focus, 36 | .pagination ul > .active > a, 37 | .pagination ul > .active > span { 38 | background-color: @paginationActiveBackground; 39 | } 40 | .pagination ul > .active > a, 41 | .pagination ul > .active > span { 42 | color: @grayLight; 43 | cursor: default; 44 | } 45 | .pagination ul > .disabled > span, 46 | .pagination ul > .disabled > a, 47 | .pagination ul > .disabled > a:hover, 48 | .pagination ul > .disabled > a:focus { 49 | color: @grayLight; 50 | background-color: transparent; 51 | cursor: default; 52 | } 53 | .pagination ul > li:first-child > a, 54 | .pagination ul > li:first-child > span { 55 | border-left-width: 1px; 56 | .border-left-radius(@baseBorderRadius); 57 | } 58 | .pagination ul > li:last-child > a, 59 | .pagination ul > li:last-child > span { 60 | .border-right-radius(@baseBorderRadius); 61 | } 62 | 63 | 64 | // Alignment 65 | // -------------------------------------------------- 66 | 67 | .pagination-centered { 68 | text-align: center; 69 | } 70 | .pagination-right { 71 | text-align: right; 72 | } 73 | 74 | 75 | // Sizing 76 | // -------------------------------------------------- 77 | 78 | // Large 79 | .pagination-large { 80 | ul > li > a, 81 | ul > li > span { 82 | padding: @paddingLarge; 83 | font-size: @fontSizeLarge; 84 | } 85 | ul > li:first-child > a, 86 | ul > li:first-child > span { 87 | .border-left-radius(@borderRadiusLarge); 88 | } 89 | ul > li:last-child > a, 90 | ul > li:last-child > span { 91 | .border-right-radius(@borderRadiusLarge); 92 | } 93 | } 94 | 95 | // Small and mini 96 | .pagination-mini, 97 | .pagination-small { 98 | ul > li:first-child > a, 99 | ul > li:first-child > span { 100 | .border-left-radius(@borderRadiusSmall); 101 | } 102 | ul > li:last-child > a, 103 | ul > li:last-child > span { 104 | .border-right-radius(@borderRadiusSmall); 105 | } 106 | } 107 | 108 | // Small 109 | .pagination-small { 110 | ul > li > a, 111 | ul > li > span { 112 | padding: @paddingSmall; 113 | font-size: @fontSizeSmall; 114 | } 115 | } 116 | // Mini 117 | .pagination-mini { 118 | ul > li > a, 119 | ul > li > span { 120 | padding: @paddingMini; 121 | font-size: @fontSizeMini; 122 | } 123 | } 124 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/carousel.less: -------------------------------------------------------------------------------- 1 | // 2 | // Carousel 3 | // -------------------------------------------------- 4 | 5 | 6 | .carousel { 7 | position: relative; 8 | margin-bottom: @baseLineHeight; 9 | line-height: 1; 10 | } 11 | 12 | .carousel-inner { 13 | overflow: hidden; 14 | width: 100%; 15 | position: relative; 16 | } 17 | 18 | .carousel-inner { 19 | 20 | > .item { 21 | display: none; 22 | position: relative; 23 | .transition(.6s ease-in-out left); 24 | 25 | // Account for jankitude on images 26 | > img, 27 | > a > img { 28 | display: block; 29 | line-height: 1; 30 | } 31 | } 32 | 33 | > .active, 34 | > .next, 35 | > .prev { display: block; } 36 | 37 | > .active { 38 | left: 0; 39 | } 40 | 41 | > .next, 42 | > .prev { 43 | position: absolute; 44 | top: 0; 45 | width: 100%; 46 | } 47 | 48 | > .next { 49 | left: 100%; 50 | } 51 | > .prev { 52 | left: -100%; 53 | } 54 | > .next.left, 55 | > .prev.right { 56 | left: 0; 57 | } 58 | 59 | > .active.left { 60 | left: -100%; 61 | } 62 | > .active.right { 63 | left: 100%; 64 | } 65 | 66 | } 67 | 68 | // Left/right controls for nav 69 | // --------------------------- 70 | 71 | .carousel-control { 72 | position: absolute; 73 | top: 40%; 74 | left: 15px; 75 | width: 40px; 76 | height: 40px; 77 | margin-top: -20px; 78 | font-size: 60px; 79 | font-weight: 100; 80 | line-height: 30px; 81 | color: @white; 82 | text-align: center; 83 | background: @grayDarker; 84 | border: 3px solid @white; 85 | .border-radius(23px); 86 | .opacity(50); 87 | 88 | // we can't have this transition here 89 | // because webkit cancels the carousel 90 | // animation if you trip this while 91 | // in the middle of another animation 92 | // ;_; 93 | // .transition(opacity .2s linear); 94 | 95 | // Reposition the right one 96 | &.right { 97 | left: auto; 98 | right: 15px; 99 | } 100 | 101 | // Hover/focus state 102 | &:hover, 103 | &:focus { 104 | color: @white; 105 | text-decoration: none; 106 | .opacity(90); 107 | } 108 | } 109 | 110 | // Carousel indicator pips 111 | // ----------------------------- 112 | .carousel-indicators { 113 | position: absolute; 114 | top: 15px; 115 | right: 15px; 116 | z-index: 5; 117 | margin: 0; 118 | list-style: none; 119 | 120 | li { 121 | display: block; 122 | float: left; 123 | width: 10px; 124 | height: 10px; 125 | margin-left: 5px; 126 | text-indent: -999px; 127 | background-color: #ccc; 128 | background-color: rgba(255,255,255,.25); 129 | border-radius: 5px; 130 | } 131 | .active { 132 | background-color: #fff; 133 | } 134 | } 135 | 136 | // Caption for text below images 137 | // ----------------------------- 138 | 139 | .carousel-caption { 140 | position: absolute; 141 | left: 0; 142 | right: 0; 143 | bottom: 0; 144 | padding: 15px; 145 | background: @grayDark; 146 | background: rgba(0,0,0,.75); 147 | } 148 | .carousel-caption h4, 149 | .carousel-caption p { 150 | color: @white; 151 | line-height: @baseLineHeight; 152 | } 153 | .carousel-caption h4 { 154 | margin: 0 0 5px; 155 | } 156 | .carousel-caption p { 157 | margin-bottom: 0; 158 | } 159 | -------------------------------------------------------------------------------- /sklearnef/tree/setup.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | import numpy 4 | import sklearn 5 | from numpy.distutils.misc_util import Configuration 6 | 7 | #cython _tree.pyx -o headers/0.16.1/_tree.c -I headers/ 8 | 9 | def configuration(parent_package="", top_path=None): 10 | config = Configuration("tree", parent_package, top_path) 11 | libraries = [] 12 | if os.name == 'posix': 13 | libraries.append('m') 14 | 15 | # check for pre-compiled versions for the encountered sklearn version 16 | if not os.path.isdir("{}/headers/{}".format(os.path.dirname(os.path.realpath(__file__)), sklearn.__version__)) or \ 17 | not os.path.isfile("{}/headers/{}/_tree.c".format(os.path.dirname(os.path.realpath(__file__)), sklearn.__version__)): 18 | raise Exception(\ 19 | """sklearnef holds no pre-compiled _tree.c for your current scikit-learn version ({version}). 20 | Please download the corresponding header file from \ 21 | https://raw.githubusercontent.com/scikit-learn/scikit-learn/{version}/sklearn/tree/_tree.pxd, 22 | place it in sklearnef/tree/headers/sklearn/tree/ and compile _tree.pyx with cython using \ 23 | 'cython _tree.pyx -o headers/{version}/_tree.c -I headers/'. Then re-run \ 24 | the installation of sklearnef.""".format(version=sklearn.__version__)) 25 | 26 | config.add_extension("_diffentropy", 27 | sources=["headers/_diffentropy.c"], 28 | include_dirs=[numpy.get_include()], 29 | libraries=libraries + ['lapack', 'blas'], 30 | extra_compile_args=["-O3"]) 31 | 32 | config.add_extension("_tree", 33 | sources=["headers/{version}/_tree.c".format(version=sklearn.__version__)], 34 | include_dirs=[numpy.get_include()], 35 | libraries=libraries, 36 | extra_compile_args=["-O3"]) 37 | 38 | config.add_subpackage("tests") 39 | 40 | return config 41 | 42 | # def __fetch_sklearn_tree_header_file(): 43 | # SKLEARN_REP_TREE_HEADER = "https://raw.githubusercontent.com/scikit-learn/scikit-learn/{version}/sklearn/tree/_tree.pxd" 44 | # tmpdir = tempfile.mktemp(prefix="sklearnef") 45 | # tree_header = "{dir}_tree_{version}.pxd".format(dir=tmpdir, 46 | # version=sklearn.__version__) 47 | # urllib.URLopener().retrieve(SKLEARN_REP_TREE_HEADER.format(sklearn.__version__), 48 | # tree_header) 49 | # 50 | # if not os.path.isfile(tree_header): 51 | # raise Exception("Failed to download the required sklearn headers for your \ 52 | # sklearn version ({version} from {url}.".format( 53 | # version=sklearn.__version__, 54 | # url=SKLEARN_REP_TREE_HEADER.format(sklearn.__version__))) 55 | # return tmpdir 56 | # 57 | # def __clean_tmpdir(tmpdir): 58 | # tree_header = "{dir}_tree_{version}.pxd".format(dir=tmpdir, 59 | # version=sklearn.__version__) 60 | # os.unlink(tree_header) 61 | # try: 62 | # os.rmdir(tmpdir) 63 | # except OSError as e: 64 | # warnings.warn("Failed to remove temporary directory '{dir}'. \ 65 | # Reason: {err}.".format(dir=tmpdir, err=e)) 66 | 67 | if __name__ == "__main__": 68 | from numpy.distutils.core import setup 69 | setup(**configuration().todict()) 70 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/progress-bars.less: -------------------------------------------------------------------------------- 1 | // 2 | // Progress bars 3 | // -------------------------------------------------- 4 | 5 | 6 | // ANIMATIONS 7 | // ---------- 8 | 9 | // Webkit 10 | @-webkit-keyframes progress-bar-stripes { 11 | from { background-position: 40px 0; } 12 | to { background-position: 0 0; } 13 | } 14 | 15 | // Firefox 16 | @-moz-keyframes progress-bar-stripes { 17 | from { background-position: 40px 0; } 18 | to { background-position: 0 0; } 19 | } 20 | 21 | // IE9 22 | @-ms-keyframes progress-bar-stripes { 23 | from { background-position: 40px 0; } 24 | to { background-position: 0 0; } 25 | } 26 | 27 | // Opera 28 | @-o-keyframes progress-bar-stripes { 29 | from { background-position: 0 0; } 30 | to { background-position: 40px 0; } 31 | } 32 | 33 | // Spec 34 | @keyframes progress-bar-stripes { 35 | from { background-position: 40px 0; } 36 | to { background-position: 0 0; } 37 | } 38 | 39 | 40 | 41 | // THE BARS 42 | // -------- 43 | 44 | // Outer container 45 | .progress { 46 | overflow: hidden; 47 | height: @baseLineHeight; 48 | margin-bottom: @baseLineHeight; 49 | #gradient > .vertical(#f5f5f5, #f9f9f9); 50 | .box-shadow(inset 0 1px 2px rgba(0,0,0,.1)); 51 | .border-radius(@baseBorderRadius); 52 | } 53 | 54 | // Bar of progress 55 | .progress .bar { 56 | width: 0%; 57 | height: 100%; 58 | color: @white; 59 | float: left; 60 | font-size: 12px; 61 | text-align: center; 62 | text-shadow: 0 -1px 0 rgba(0,0,0,.25); 63 | #gradient > .vertical(#149bdf, #0480be); 64 | .box-shadow(inset 0 -1px 0 rgba(0,0,0,.15)); 65 | .box-sizing(border-box); 66 | .transition(width .6s ease); 67 | } 68 | .progress .bar + .bar { 69 | .box-shadow(~"inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15)"); 70 | } 71 | 72 | // Striped bars 73 | .progress-striped .bar { 74 | #gradient > .striped(#149bdf); 75 | .background-size(40px 40px); 76 | } 77 | 78 | // Call animation for the active one 79 | .progress.active .bar { 80 | -webkit-animation: progress-bar-stripes 2s linear infinite; 81 | -moz-animation: progress-bar-stripes 2s linear infinite; 82 | -ms-animation: progress-bar-stripes 2s linear infinite; 83 | -o-animation: progress-bar-stripes 2s linear infinite; 84 | animation: progress-bar-stripes 2s linear infinite; 85 | } 86 | 87 | 88 | 89 | // COLORS 90 | // ------ 91 | 92 | // Danger (red) 93 | .progress-danger .bar, .progress .bar-danger { 94 | #gradient > .vertical(#ee5f5b, #c43c35); 95 | } 96 | .progress-danger.progress-striped .bar, .progress-striped .bar-danger { 97 | #gradient > .striped(#ee5f5b); 98 | } 99 | 100 | // Success (green) 101 | .progress-success .bar, .progress .bar-success { 102 | #gradient > .vertical(#62c462, #57a957); 103 | } 104 | .progress-success.progress-striped .bar, .progress-striped .bar-success { 105 | #gradient > .striped(#62c462); 106 | } 107 | 108 | // Info (teal) 109 | .progress-info .bar, .progress .bar-info { 110 | #gradient > .vertical(#5bc0de, #339bb9); 111 | } 112 | .progress-info.progress-striped .bar, .progress-striped .bar-info { 113 | #gradient > .striped(#5bc0de); 114 | } 115 | 116 | // Warning (orange) 117 | .progress-warning .bar, .progress .bar-warning { 118 | #gradient > .vertical(lighten(@orange, 15%), @orange); 119 | } 120 | .progress-warning.progress-striped .bar, .progress-striped .bar-warning { 121 | #gradient > .striped(lighten(@orange, 15%)); 122 | } 123 | -------------------------------------------------------------------------------- /sklearnef/tree/_tree.pxd: -------------------------------------------------------------------------------- 1 | # Authors: Oskar Maier 2 | # 3 | # Licence: BSD 3 clause !TODO: Change! 4 | 5 | # See _tree.pyx for details. 6 | 7 | import numpy as np 8 | cimport numpy as np 9 | cimport sklearn.tree._tree 10 | import sklearn.tree._tree 11 | 12 | #cdef extern from *: 13 | ctypedef np.npy_float32 DTYPE_t # Type of X 14 | ctypedef np.npy_float64 DOUBLE_t # Type of y, sample_weight 15 | ctypedef np.npy_intp SIZE_t # Type for indices and counters 16 | ctypedef np.npy_int32 INT32_t # Signed 32 bit integer 17 | ctypedef np.npy_uint32 UINT32_t # Unsigned 32 bit integer 18 | 19 | # Import external extension types (with associated PXD files) 20 | from sklearn.tree._tree cimport Criterion, Splitter, SplitRecord 21 | from sklearnef.tree._diffentropy cimport Diffentropy 22 | 23 | # Define external extension types (without associated PXD files) 24 | cdef extern class sklearn.tree._tree.ClassificationCriterion(Criterion): 25 | cdef SIZE_t* n_classes 26 | cdef SIZE_t label_count_stride 27 | cdef double* label_count_left 28 | cdef double* label_count_right 29 | cdef double* label_count_total 30 | cdef extern class sklearn.tree._tree.Entropy(ClassificationCriterion): 31 | pass 32 | 33 | cdef extern class sklearn.tree._tree.BaseDenseSplitter(Splitter): 34 | cdef DTYPE_t* X 35 | cdef SIZE_t X_sample_stride 36 | cdef SIZE_t X_fx_stride 37 | cdef extern class sklearn.tree._tree.BestSplitter(BaseDenseSplitter): 38 | pass 39 | 40 | # ============================================================================= 41 | # Criterion 42 | # ============================================================================= 43 | 44 | cdef class UnSupervisedClassificationCriterion(Criterion): 45 | # Internal structures 46 | cdef DTYPE_t* X # pointer to the training data; will become obsolute, when I've implemented sort(S) without re-copying the memory 47 | cdef SIZE_t X_stride # the X_stride; is this the same as n_features... might just be, then I can remove the second and use this in __reduce__ 48 | cdef SIZE_t n_samples # might not be required, as only used in __cinit__ and __reduce__ 49 | cdef SIZE_t n_features # might not be required, as only used in __cinit__ and __reduce__ 50 | cdef DTYPE_t min_improvement# minimal improvement of a split to consider it 51 | cdef DTYPE_t normalization_entropy # the node's initial entropy / logdet stored for normalization purposes 52 | cdef Diffentropy covr # dynamically updateable covariance matrix (right) 53 | cdef Diffentropy covl # dynamically updateable covariance matrix (left) 54 | # !TODO: Above, some of the member vars could be removed in the future. 55 | # The number of 'effective' prior observations (default = 0). 56 | #cdef DTYPE_t effprior 57 | # The variance of the effective observations (default = 900). 58 | #cdef DTYPE_t effpriorvar 59 | 60 | # Methods 61 | cdef void init2(self, DTYPE_t* X, SIZE_t X_stride, 62 | DOUBLE_t* sample_weight, double weighted_n_samples, 63 | SIZE_t* samples, SIZE_t start, SIZE_t end) nogil 64 | 65 | cdef class SemiSupervisedClassificationCriterion(UnSupervisedClassificationCriterion): 66 | # Internal structures 67 | cdef DTYPE_t supervised_weight # balancing weight 68 | cdef ClassificationCriterion criterion_supervised # supervised split quality criterion 69 | 70 | # Methods 71 | cdef void init3(self, DTYPE_t* X, SIZE_t X_stride, DOUBLE_t* y, SIZE_t y_stride, 72 | DOUBLE_t* sample_weight, double weighted_n_samples, 73 | SIZE_t* samples, SIZE_t start, SIZE_t end) nogil 74 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/popovers.less: -------------------------------------------------------------------------------- 1 | // 2 | // Popovers 3 | // -------------------------------------------------- 4 | 5 | 6 | .popover { 7 | position: absolute; 8 | top: 0; 9 | left: 0; 10 | z-index: @zindexPopover; 11 | display: none; 12 | max-width: 276px; 13 | padding: 1px; 14 | text-align: left; // Reset given new insertion method 15 | background-color: @popoverBackground; 16 | -webkit-background-clip: padding-box; 17 | -moz-background-clip: padding; 18 | background-clip: padding-box; 19 | border: 1px solid #ccc; 20 | border: 1px solid rgba(0,0,0,.2); 21 | .border-radius(6px); 22 | .box-shadow(0 5px 10px rgba(0,0,0,.2)); 23 | 24 | // Overrides for proper insertion 25 | white-space: normal; 26 | 27 | // Offset the popover to account for the popover arrow 28 | &.top { margin-top: -10px; } 29 | &.right { margin-left: 10px; } 30 | &.bottom { margin-top: 10px; } 31 | &.left { margin-left: -10px; } 32 | } 33 | 34 | .popover-title { 35 | margin: 0; // reset heading margin 36 | padding: 8px 14px; 37 | font-size: 14px; 38 | font-weight: normal; 39 | line-height: 18px; 40 | background-color: @popoverTitleBackground; 41 | border-bottom: 1px solid darken(@popoverTitleBackground, 5%); 42 | .border-radius(5px 5px 0 0); 43 | 44 | &:empty { 45 | display: none; 46 | } 47 | } 48 | 49 | .popover-content { 50 | padding: 9px 14px; 51 | } 52 | 53 | // Arrows 54 | // 55 | // .arrow is outer, .arrow:after is inner 56 | 57 | .popover .arrow, 58 | .popover .arrow:after { 59 | position: absolute; 60 | display: block; 61 | width: 0; 62 | height: 0; 63 | border-color: transparent; 64 | border-style: solid; 65 | } 66 | .popover .arrow { 67 | border-width: @popoverArrowOuterWidth; 68 | } 69 | .popover .arrow:after { 70 | border-width: @popoverArrowWidth; 71 | content: ""; 72 | } 73 | 74 | .popover { 75 | &.top .arrow { 76 | left: 50%; 77 | margin-left: -@popoverArrowOuterWidth; 78 | border-bottom-width: 0; 79 | border-top-color: #999; // IE8 fallback 80 | border-top-color: @popoverArrowOuterColor; 81 | bottom: -@popoverArrowOuterWidth; 82 | &:after { 83 | bottom: 1px; 84 | margin-left: -@popoverArrowWidth; 85 | border-bottom-width: 0; 86 | border-top-color: @popoverArrowColor; 87 | } 88 | } 89 | &.right .arrow { 90 | top: 50%; 91 | left: -@popoverArrowOuterWidth; 92 | margin-top: -@popoverArrowOuterWidth; 93 | border-left-width: 0; 94 | border-right-color: #999; // IE8 fallback 95 | border-right-color: @popoverArrowOuterColor; 96 | &:after { 97 | left: 1px; 98 | bottom: -@popoverArrowWidth; 99 | border-left-width: 0; 100 | border-right-color: @popoverArrowColor; 101 | } 102 | } 103 | &.bottom .arrow { 104 | left: 50%; 105 | margin-left: -@popoverArrowOuterWidth; 106 | border-top-width: 0; 107 | border-bottom-color: #999; // IE8 fallback 108 | border-bottom-color: @popoverArrowOuterColor; 109 | top: -@popoverArrowOuterWidth; 110 | &:after { 111 | top: 1px; 112 | margin-left: -@popoverArrowWidth; 113 | border-top-width: 0; 114 | border-bottom-color: @popoverArrowColor; 115 | } 116 | } 117 | 118 | &.left .arrow { 119 | top: 50%; 120 | right: -@popoverArrowOuterWidth; 121 | margin-top: -@popoverArrowOuterWidth; 122 | border-right-width: 0; 123 | border-left-color: #999; // IE8 fallback 124 | border-left-color: @popoverArrowOuterColor; 125 | &:after { 126 | right: 1px; 127 | border-right-width: 0; 128 | border-left-color: @popoverArrowColor; 129 | bottom: -@popoverArrowWidth; 130 | } 131 | } 132 | 133 | } 134 | -------------------------------------------------------------------------------- /sklearnef/.ipynb_checkpoints/Untitled0-checkpoint.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "metadata": { 3 | "name": "" 4 | }, 5 | "nbformat": 3, 6 | "nbformat_minor": 0, 7 | "worksheets": [ 8 | { 9 | "cells": [ 10 | { 11 | "cell_type": "code", 12 | "collapsed": false, 13 | "input": [ 14 | "%load_ext cythonmagic" 15 | ], 16 | "language": "python", 17 | "metadata": {}, 18 | "outputs": [ 19 | { 20 | "output_type": "stream", 21 | "stream": "stdout", 22 | "text": [ 23 | "The cythonmagic extension is already loaded. To reload it, use:\n", 24 | " %reload_ext cythonmagic\n" 25 | ] 26 | } 27 | ], 28 | "prompt_number": 3 29 | }, 30 | { 31 | "cell_type": "code", 32 | "collapsed": false, 33 | "input": [ 34 | "%%cython\n", 35 | "\n", 36 | "cdef int a = 0\n", 37 | "for i in range(10):\n", 38 | " a += i\n", 39 | "print a" 40 | ], 41 | "language": "python", 42 | "metadata": {}, 43 | "outputs": [ 44 | { 45 | "output_type": "stream", 46 | "stream": "stdout", 47 | "text": [ 48 | "45\n" 49 | ] 50 | } 51 | ], 52 | "prompt_number": 5 53 | }, 54 | { 55 | "cell_type": "code", 56 | "collapsed": false, 57 | "input": [ 58 | "%%cython\n", 59 | "\n", 60 | "cimport sklearn.tree._tree\n", 61 | "import sklearn.tree._tree\n", 62 | "from sklearn.tree._tree cimport Criterion" 63 | ], 64 | "language": "python", 65 | "metadata": {}, 66 | "outputs": [ 67 | { 68 | "output_type": "stream", 69 | "stream": "stderr", 70 | "text": [ 71 | "\n", 72 | "Error compiling Cython file:\n", 73 | "------------------------------------------------------------\n", 74 | "...\n", 75 | "\n", 76 | "cimport sklearn.tree._tree\n", 77 | " ^\n", 78 | "------------------------------------------------------------\n", 79 | "\n", 80 | "/home/maier/.cache/ipython/cython/_cython_magic_864d50feb114e2794c5d81fb6eba4cb8.pyx:2:8: 'sklearn/tree/_tree.pxd' not found\n", 81 | "\n", 82 | "Error compiling Cython file:\n", 83 | "------------------------------------------------------------\n", 84 | "...\n", 85 | "\n", 86 | "cimport sklearn.tree._tree\n", 87 | "from sklearn.tree._tree cimport Criterion\n", 88 | "^\n", 89 | "------------------------------------------------------------\n", 90 | "\n", 91 | "/home/maier/.cache/ipython/cython/_cython_magic_864d50feb114e2794c5d81fb6eba4cb8.pyx:3:0: 'Criterion.pxd' not found\n", 92 | "\n", 93 | "Error compiling Cython file:\n", 94 | "------------------------------------------------------------\n", 95 | "...\n", 96 | "\n", 97 | "cimport sklearn.tree._tree\n", 98 | "from sklearn.tree._tree cimport Criterion\n", 99 | " ^\n", 100 | "------------------------------------------------------------\n", 101 | "\n", 102 | "/home/maier/.cache/ipython/cython/_cython_magic_864d50feb114e2794c5d81fb6eba4cb8.pyx:3:32: Name 'Criterion' not declared in module 'sklearn.tree._tree'\n" 103 | ] 104 | } 105 | ], 106 | "prompt_number": 14 107 | }, 108 | { 109 | "cell_type": "code", 110 | "collapsed": false, 111 | "input": [ 112 | "Criterion" 113 | ], 114 | "language": "python", 115 | "metadata": {}, 116 | "outputs": [ 117 | { 118 | "metadata": {}, 119 | "output_type": "pyout", 120 | "prompt_number": 10, 121 | "text": [ 122 | "sklearn.tree._tree.Criterion" 123 | ] 124 | } 125 | ], 126 | "prompt_number": 10 127 | }, 128 | { 129 | "cell_type": "code", 130 | "collapsed": false, 131 | "input": [], 132 | "language": "python", 133 | "metadata": {}, 134 | "outputs": [] 135 | } 136 | ], 137 | "metadata": {} 138 | } 139 | ] 140 | } -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/css/pygments.css: -------------------------------------------------------------------------------- 1 | /* Styling for the source code listings: (mostly from pygments)*/ 2 | 3 | .highlight pre{ 4 | overflow: auto; 5 | padding: 5px; 6 | background-color: #ffffff; 7 | color: #333333; 8 | border: 1px solid #ac9; 9 | border-left: none; 10 | border-right: none; 11 | } 12 | 13 | /* Styling for pre elements: from http://perishablepress.com/press/2009/11/09/perfect-pre-tags/ */ 14 | /* no vertical scrollbars for IE 6 */ 15 | * html pre { 16 | padding-bottom:25px; 17 | overflow-y:hidden; 18 | overflow:visible; 19 | overflow-x:auto 20 | } 21 | /* no vertical scrollbars for IE 7 */ 22 | *:first-child+html pre { 23 | padding-bottom:25px; 24 | overflow-y:hidden; 25 | overflow:visible; 26 | overflow-x:auto 27 | } 28 | 29 | div#spc-section-body td.linenos pre { 30 | padding: 5px 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#800080 } /* Literal.String.Regex */ 81 | .highlight .s1 { color: #800080 } /* Literal.String.Single */ 82 | .highlight .ss { color: #800080 } /* Literal.String.Symbol */ 83 | .highlight .bp { color: #407090 } /* Name.Builtin.Pseudo */ 84 | .highlight .vc { color: #000000 } /* Name.Variable.Class */ 85 | .highlight .vg { color: #000000 } /* Name.Variable.Global */ 86 | .highlight .vi { color: #000000 } /* Name.Variable.Instance */ 87 | .highlight .il { color: #008080 } /* Literal.Number.Integer.Long */ 88 | -------------------------------------------------------------------------------- /bin/density/plot_sherwood.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """Plot an example of Microsoft sherwood library.""" 4 | 5 | # build-in modules 6 | import argparse 7 | 8 | # third-party modules 9 | import numpy 10 | import matplotlib.pyplot as plt 11 | 12 | # path changes 13 | 14 | # own modules 15 | from sklearnef.ensemble import DensityForest 16 | 17 | # information 18 | __author__ = "Oskar Maier" 19 | __version__ = "r0.1.2, 2015-05-18" 20 | __email__ = "oskar.maier@googlemail.com" 21 | __status__ = "Release" 22 | __description__ = """ 23 | Plot an example of Microsofts sherwood library. 24 | """ 25 | 26 | # code 27 | def main(): 28 | args = getArguments(getParser()) 29 | 30 | numpy.random.seed(args.seed) 31 | 32 | # parse dataset 33 | data = numpy.genfromtxt(args.dataset) 34 | if not 2 == data.ndim: 35 | raise Exception("Can only plot 2D datasets.") 36 | 37 | # train forest 38 | clf = DensityForest(n_estimators=args.n_trees, 39 | random_state=args.seed, 40 | min_samples_leaf=2, 41 | n_jobs=-1, 42 | max_depth=args.max_depth, 43 | max_features=args.max_features, 44 | min_improvement=args.min_improvement) 45 | clf.fit(data) 46 | 47 | # generate plot grid 48 | xrange = (data[:,0].min() - data[:,0].std(), data[:,0].max() + data[:,0].std()) 49 | yrange = (data[:,1].min() - data[:,1].std(), data[:,1].max() + data[:,1].std()) 50 | xresolution = (xrange[1] - xrange[0]) / float(args.resolution) 51 | yresolution = (yrange[1] - yrange[0]) / float(args.resolution) 52 | 53 | grid = numpy.mgrid[xrange[0]:xrange[1]:xresolution,yrange[0]:yrange[1]:yresolution] 54 | x, y = grid 55 | x = numpy.unique(x) 56 | y = numpy.unique(y) 57 | 58 | # apply forest 59 | X = numpy.swapaxes(grid.reshape(2, numpy.product(grid.shape[1:])), 0, 1) 60 | z = clf.predict_proba(X) 61 | 62 | # first plot: gt 63 | plt.subplot(2, 1, 1, axisbg='k') 64 | plt.scatter(data[:, 0], data[:, 1], c='w', alpha=.3, edgecolors='none') 65 | 66 | plt.xlim(min(x),max(x)) 67 | plt.ylim(min(y),max(y)) 68 | plt.title('GT: {}'.format(args.dataset)) 69 | 70 | # second plot: prediction 71 | plt.subplot(2, 1, 2) 72 | im = plt.imshow(z.reshape((x.size,y.size)).T, extent=[min(x),max(x),min(y),max(y)], interpolation='none', cmap=plt.cm.afmhot, aspect='auto', origin='lower') #'auto' 73 | plt.colorbar() 74 | 75 | plt.xlim(min(x),max(x)) 76 | plt.ylim(min(y),max(y)) 77 | plt.title('Learned density: {}'.format(args.dataset)) 78 | 79 | plt.show() 80 | 81 | def getArguments(parser): 82 | "Provides additional validation of the arguments collected by argparse." 83 | args = parser.parse_args() 84 | if args.max_features is not None and args.max_features not in ['auto', 'sqrt' 'log2']: 85 | args.max_features = int(args.max_features) 86 | return args 87 | 88 | def getParser(): 89 | "Creates and returns the argparse parser object." 90 | parser = argparse.ArgumentParser(description=__description__) 91 | parser.add_argument('dataset', help='One of the sharewood density example datasets (a text file containing a table).') 92 | parser.add_argument('--n-trees', default=10, type=int, help='The number of trees to train.') 93 | parser.add_argument('--max-depth', default=None, type=int, help='The maximum tree depth.') 94 | parser.add_argument('--max-features', default='auto', help='The number of features to consider at each split. Can be an integer or one of auto, sqrt and log2') 95 | parser.add_argument('--min-improvement', default=-5.0, type=float, help='Minimum information gain required to consider another split. Note that the information gain can take on negative values in some situations.') 96 | parser.add_argument('--seed', default=None, type=int, help='The random seed to use. Fix to an integer to create reproducible results.') 97 | parser.add_argument('-r', '--resolution', dest='resolution', type=int, default=200, help='Plot resolution (points-per-dimension).') 98 | return parser 99 | 100 | if __name__ == "__main__": 101 | main() 102 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/traitsdoc.py: -------------------------------------------------------------------------------- 1 | """ 2 | ========= 3 | traitsdoc 4 | ========= 5 | 6 | Sphinx extension that handles docstrings in the Numpy standard format, [1] 7 | and support Traits [2]. 8 | 9 | This extension can be used as a replacement for ``numpydoc`` when support 10 | for Traits is required. 11 | 12 | .. [1] http://projects.scipy.org/numpy/wiki/CodingStyleGuidelines#docstring-standard 13 | .. [2] http://code.enthought.com/projects/traits/ 14 | 15 | """ 16 | from __future__ import division, absolute_import, print_function 17 | 18 | import inspect 19 | import os 20 | import pydoc 21 | import collections 22 | 23 | from . import docscrape 24 | from . import docscrape_sphinx 25 | from .docscrape_sphinx import SphinxClassDoc, SphinxFunctionDoc, SphinxDocString 26 | 27 | from . import numpydoc 28 | 29 | from . import comment_eater 30 | 31 | class SphinxTraitsDoc(SphinxClassDoc): 32 | def __init__(self, cls, modulename='', func_doc=SphinxFunctionDoc): 33 | if not inspect.isclass(cls): 34 | raise ValueError("Initialise using a class. Got %r" % cls) 35 | self._cls = cls 36 | 37 | if modulename and not modulename.endswith('.'): 38 | modulename += '.' 39 | self._mod = modulename 40 | self._name = cls.__name__ 41 | self._func_doc = func_doc 42 | 43 | docstring = pydoc.getdoc(cls) 44 | docstring = docstring.split('\n') 45 | 46 | # De-indent paragraph 47 | try: 48 | indent = min(len(s) - len(s.lstrip()) for s in docstring 49 | if s.strip()) 50 | except ValueError: 51 | indent = 0 52 | 53 | for n,line in enumerate(docstring): 54 | docstring[n] = docstring[n][indent:] 55 | 56 | self._doc = docscrape.Reader(docstring) 57 | self._parsed_data = { 58 | 'Signature': '', 59 | 'Summary': '', 60 | 'Description': [], 61 | 'Extended Summary': [], 62 | 'Parameters': [], 63 | 'Returns': [], 64 | 'Raises': [], 65 | 'Warns': [], 66 | 'Other Parameters': [], 67 | 'Traits': [], 68 | 'Methods': [], 69 | 'See Also': [], 70 | 'Notes': [], 71 | 'References': '', 72 | 'Example': '', 73 | 'Examples': '', 74 | 'index': {} 75 | } 76 | 77 | self._parse() 78 | 79 | def _str_summary(self): 80 | return self['Summary'] + [''] 81 | 82 | def _str_extended_summary(self): 83 | return self['Description'] + self['Extended Summary'] + [''] 84 | 85 | def __str__(self, indent=0, func_role="func"): 86 | out = [] 87 | out += self._str_signature() 88 | out += self._str_index() + [''] 89 | out += self._str_summary() 90 | out += self._str_extended_summary() 91 | for param_list in ('Parameters', 'Traits', 'Methods', 92 | 'Returns','Raises'): 93 | out += self._str_param_list(param_list) 94 | out += self._str_see_also("obj") 95 | out += self._str_section('Notes') 96 | out += self._str_references() 97 | out += self._str_section('Example') 98 | out += self._str_section('Examples') 99 | out = self._str_indent(out,indent) 100 | return '\n'.join(out) 101 | 102 | def looks_like_issubclass(obj, classname): 103 | """ Return True if the object has a class or superclass with the given class 104 | name. 105 | 106 | Ignores old-style classes. 107 | """ 108 | t = obj 109 | if t.__name__ == classname: 110 | return True 111 | for klass in t.__mro__: 112 | if klass.__name__ == classname: 113 | return True 114 | return False 115 | 116 | def get_doc_object(obj, what=None, config=None): 117 | if what is None: 118 | if inspect.isclass(obj): 119 | what = 'class' 120 | elif inspect.ismodule(obj): 121 | what = 'module' 122 | elif isinstance(obj, collections.Callable): 123 | what = 'function' 124 | else: 125 | what = 'object' 126 | if what == 'class': 127 | doc = SphinxTraitsDoc(obj, '', func_doc=SphinxFunctionDoc, config=config) 128 | if looks_like_issubclass(obj, 'HasTraits'): 129 | for name, trait, comment in comment_eater.get_class_traits(obj): 130 | # Exclude private traits. 131 | if not name.startswith('_'): 132 | doc['Traits'].append((name, trait, comment.splitlines())) 133 | return doc 134 | elif what in ('function', 'method'): 135 | return SphinxFunctionDoc(obj, '', config=config) 136 | else: 137 | return SphinxDocString(pydoc.getdoc(obj), config=config) 138 | 139 | def setup(app): 140 | # init numpydoc 141 | numpydoc.setup(app, get_doc_object) 142 | 143 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-767px-max.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Landscape phone to desktop/tablet 3 | // -------------------------------------------------- 4 | 5 | 6 | @media (max-width: 767px) { 7 | 8 | // Padding to set content in a bit 9 | body { 10 | padding-left: 20px; 11 | padding-right: 20px; 12 | } 13 | // Negative indent the now static "fixed" navbar 14 | .navbar-fixed-top, 15 | .navbar-fixed-bottom, 16 | .navbar-static-top { 17 | margin-left: -20px; 18 | margin-right: -20px; 19 | } 20 | // Remove padding on container given explicit padding set on body 21 | .container-fluid { 22 | padding: 0; 23 | } 24 | 25 | // TYPOGRAPHY 26 | // ---------- 27 | // Reset horizontal dl 28 | .dl-horizontal { 29 | dt { 30 | float: none; 31 | clear: none; 32 | width: auto; 33 | text-align: left; 34 | } 35 | dd { 36 | margin-left: 0; 37 | } 38 | } 39 | 40 | // GRID & CONTAINERS 41 | // ----------------- 42 | // Remove width from containers 43 | .container { 44 | width: auto; 45 | } 46 | // Fluid rows 47 | .row-fluid { 48 | width: 100%; 49 | } 50 | // Undo negative margin on rows and thumbnails 51 | .row, 52 | .thumbnails { 53 | margin-left: 0; 54 | } 55 | .thumbnails > li { 56 | float: none; 57 | margin-left: 0; // Reset the default margin for all li elements when no .span* classes are present 58 | } 59 | // Make all grid-sized elements block level again 60 | [class*="span"], 61 | .uneditable-input[class*="span"], // Makes uneditable inputs full-width when using grid sizing 62 | .row-fluid [class*="span"] { 63 | float: none; 64 | display: block; 65 | width: 100%; 66 | margin-left: 0; 67 | .box-sizing(border-box); 68 | } 69 | .span12, 70 | .row-fluid .span12 { 71 | width: 100%; 72 | .box-sizing(border-box); 73 | } 74 | .row-fluid [class*="offset"]:first-child { 75 | margin-left: 0; 76 | } 77 | 78 | // FORM FIELDS 79 | // ----------- 80 | // Make span* classes full width 81 | .input-large, 82 | .input-xlarge, 83 | .input-xxlarge, 84 | input[class*="span"], 85 | select[class*="span"], 86 | textarea[class*="span"], 87 | .uneditable-input { 88 | .input-block-level(); 89 | } 90 | // But don't let it screw up prepend/append inputs 91 | .input-prepend input, 92 | .input-append input, 93 | .input-prepend input[class*="span"], 94 | .input-append input[class*="span"] { 95 | display: inline-block; // redeclare so they don't wrap to new lines 96 | width: auto; 97 | } 98 | .controls-row [class*="span"] + [class*="span"] { 99 | margin-left: 0; 100 | } 101 | 102 | // Modals 103 | .modal { 104 | position: fixed; 105 | top: 20px; 106 | left: 20px; 107 | right: 20px; 108 | width: auto; 109 | margin: 0; 110 | &.fade { top: -100px; } 111 | &.fade.in { top: 20px; } 112 | } 113 | 114 | } 115 | 116 | 117 | 118 | // UP TO LANDSCAPE PHONE 119 | // --------------------- 120 | 121 | @media (max-width: 480px) { 122 | 123 | // Smooth out the collapsing/expanding nav 124 | .nav-collapse { 125 | -webkit-transform: translate3d(0, 0, 0); // activate the GPU 126 | } 127 | 128 | // Block level the page header small tag for readability 129 | .page-header h1 small { 130 | display: block; 131 | line-height: @baseLineHeight; 132 | } 133 | 134 | // Update checkboxes for iOS 135 | input[type="checkbox"], 136 | input[type="radio"] { 137 | border: 1px solid #ccc; 138 | } 139 | 140 | // Remove the horizontal form styles 141 | .form-horizontal { 142 | .control-label { 143 | float: none; 144 | width: auto; 145 | padding-top: 0; 146 | text-align: left; 147 | } 148 | // Move over all input controls and content 149 | .controls { 150 | margin-left: 0; 151 | } 152 | // Move the options list down to align with labels 153 | .control-list { 154 | padding-top: 0; // has to be padding because margin collaspes 155 | } 156 | // Move over buttons in .form-actions to align with .controls 157 | .form-actions { 158 | padding-left: 10px; 159 | padding-right: 10px; 160 | } 161 | } 162 | 163 | // Medias 164 | // Reset float and spacing to stack 165 | .media .pull-left, 166 | .media .pull-right { 167 | float: none; 168 | display: block; 169 | margin-bottom: 10px; 170 | } 171 | // Remove side margins since we stack instead of indent 172 | .media-object { 173 | margin-right: 0; 174 | margin-left: 0; 175 | } 176 | 177 | // Modals 178 | .modal { 179 | top: 10px; 180 | left: 10px; 181 | right: 10px; 182 | } 183 | .modal-header .close { 184 | padding: 10px; 185 | margin: -10px; 186 | } 187 | 188 | // Carousel 189 | .carousel-caption { 190 | position: static; 191 | } 192 | 193 | } 194 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-navbar.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Navbar 3 | // -------------------------------------------------- 4 | 5 | 6 | // TABLETS AND BELOW 7 | // ----------------- 8 | @media (max-width: @navbarCollapseWidth) { 9 | 10 | // UNFIX THE TOPBAR 11 | // ---------------- 12 | // Remove any padding from the body 13 | body { 14 | padding-top: 0; 15 | } 16 | // Unfix the navbars 17 | .navbar-fixed-top, 18 | .navbar-fixed-bottom { 19 | position: static; 20 | } 21 | .navbar-fixed-top { 22 | margin-bottom: @baseLineHeight; 23 | } 24 | .navbar-fixed-bottom { 25 | margin-top: @baseLineHeight; 26 | } 27 | .navbar-fixed-top .navbar-inner, 28 | .navbar-fixed-bottom .navbar-inner { 29 | padding: 5px; 30 | } 31 | .navbar .container { 32 | width: auto; 33 | padding: 0; 34 | } 35 | // Account for brand name 36 | .navbar .brand { 37 | padding-left: 10px; 38 | padding-right: 10px; 39 | margin: 0 0 0 -5px; 40 | } 41 | 42 | // COLLAPSIBLE NAVBAR 43 | // ------------------ 44 | // Nav collapse clears brand 45 | .nav-collapse { 46 | clear: both; 47 | } 48 | // Block-level the nav 49 | .nav-collapse .nav { 50 | float: none; 51 | margin: 0 0 (@baseLineHeight / 2); 52 | } 53 | .nav-collapse .nav > li { 54 | float: none; 55 | } 56 | .nav-collapse .nav > li > a { 57 | margin-bottom: 2px; 58 | } 59 | .nav-collapse .nav > .divider-vertical { 60 | display: none; 61 | } 62 | .nav-collapse .nav .nav-header { 63 | color: @navbarText; 64 | text-shadow: none; 65 | } 66 | // Nav and dropdown links in navbar 67 | .nav-collapse .nav > li > a, 68 | .nav-collapse .dropdown-menu a { 69 | padding: 9px 15px; 70 | font-weight: bold; 71 | color: @navbarLinkColor; 72 | .border-radius(3px); 73 | } 74 | // Buttons 75 | .nav-collapse .btn { 76 | padding: 4px 10px 4px; 77 | font-weight: normal; 78 | .border-radius(@baseBorderRadius); 79 | } 80 | .nav-collapse .dropdown-menu li + li a { 81 | margin-bottom: 2px; 82 | } 83 | .nav-collapse .nav > li > a:hover, 84 | .nav-collapse .nav > li > a:focus, 85 | .nav-collapse .dropdown-menu a:hover, 86 | .nav-collapse .dropdown-menu a:focus { 87 | background-color: @navbarBackground; 88 | } 89 | .navbar-inverse .nav-collapse .nav > li > a, 90 | .navbar-inverse .nav-collapse .dropdown-menu a { 91 | color: @navbarInverseLinkColor; 92 | } 93 | .navbar-inverse .nav-collapse .nav > li > a:hover, 94 | .navbar-inverse .nav-collapse .nav > li > a:focus, 95 | .navbar-inverse .nav-collapse .dropdown-menu a:hover, 96 | .navbar-inverse .nav-collapse .dropdown-menu a:focus { 97 | background-color: @navbarInverseBackground; 98 | } 99 | // Buttons in the navbar 100 | .nav-collapse.in .btn-group { 101 | margin-top: 5px; 102 | padding: 0; 103 | } 104 | // Dropdowns in the navbar 105 | .nav-collapse .dropdown-menu { 106 | position: static; 107 | top: auto; 108 | left: auto; 109 | float: none; 110 | display: none; 111 | max-width: none; 112 | margin: 0 15px; 113 | padding: 0; 114 | background-color: transparent; 115 | border: none; 116 | .border-radius(0); 117 | .box-shadow(none); 118 | } 119 | .nav-collapse .open > .dropdown-menu { 120 | display: block; 121 | } 122 | 123 | .nav-collapse .dropdown-menu:before, 124 | .nav-collapse .dropdown-menu:after { 125 | display: none; 126 | } 127 | .nav-collapse .dropdown-menu .divider { 128 | display: none; 129 | } 130 | .nav-collapse .nav > li > .dropdown-menu { 131 | &:before, 132 | &:after { 133 | display: none; 134 | } 135 | } 136 | // Forms in navbar 137 | .nav-collapse .navbar-form, 138 | .nav-collapse .navbar-search { 139 | float: none; 140 | padding: (@baseLineHeight / 2) 15px; 141 | margin: (@baseLineHeight / 2) 0; 142 | border-top: 1px solid @navbarBackground; 143 | border-bottom: 1px solid @navbarBackground; 144 | .box-shadow(~"inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1)"); 145 | } 146 | .navbar-inverse .nav-collapse .navbar-form, 147 | .navbar-inverse .nav-collapse .navbar-search { 148 | border-top-color: @navbarInverseBackground; 149 | border-bottom-color: @navbarInverseBackground; 150 | } 151 | // Pull right (secondary) nav content 152 | .navbar .nav-collapse .nav.pull-right { 153 | float: none; 154 | margin-left: 0; 155 | } 156 | // Hide everything in the navbar save .brand and toggle button */ 157 | .nav-collapse, 158 | .nav-collapse.collapse { 159 | overflow: hidden; 160 | height: 0; 161 | } 162 | // Navbar button 163 | .navbar .btn-navbar { 164 | display: block; 165 | } 166 | 167 | // STATIC NAVBAR 168 | // ------------- 169 | .navbar-static .navbar-inner { 170 | padding-left: 10px; 171 | padding-right: 10px; 172 | } 173 | 174 | 175 | } 176 | 177 | 178 | // DEFAULT DESKTOP 179 | // --------------- 180 | 181 | @media (min-width: @navbarCollapseDesktopWidth) { 182 | 183 | // Required to make the collapsing navbar work on regular desktops 184 | .nav-collapse.collapse { 185 | height: auto !important; 186 | overflow: visible !important; 187 | } 188 | 189 | } 190 | --------------------------------------------------------------------------------