├── .flake8 ├── .gitattributes ├── .github └── workflows │ └── testing.yml ├── .gitignore ├── COPYING ├── Makefile ├── README.md ├── docs ├── example_plugin │ ├── README.md │ ├── pyproject.toml │ ├── setup.cfg │ ├── src │ │ └── pubget_example_plugin │ │ │ └── __init__.py │ ├── tests │ │ ├── run_plugin.py │ │ └── test_example_plugin.py │ └── tox.ini ├── example_queries │ ├── README.md │ ├── fmri_2019.txt │ ├── journal_list_fmri_vbm.txt │ └── pmcids.txt └── module.html.jinja2 ├── pubget.svg ├── pylintrc ├── pyproject.toml ├── setup.cfg ├── setup.py ├── src └── pubget │ ├── __init__.py │ ├── _articles.py │ ├── _authors.py │ ├── _commands.py │ ├── _coordinate_space.py │ ├── _coordinates.py │ ├── _data │ ├── VERSION │ ├── _fit_neuroquery │ │ ├── README.md │ │ ├── app.py │ │ └── requirements.txt │ ├── _fit_neurosynth │ │ ├── README.md │ │ ├── app.py │ │ └── requirements.txt │ └── stylesheets │ │ ├── docbook │ │ ├── AUTHORS │ │ ├── BUGS │ │ ├── COPYING │ │ ├── INSTALL │ │ ├── Makefile │ │ ├── NEWS │ │ ├── NEWS.html │ │ ├── NEWS.xml │ │ ├── README │ │ ├── RELEASE-NOTES.html │ │ ├── RELEASE-NOTES.txt │ │ ├── RELEASE-NOTES.xml │ │ ├── REVISION │ │ ├── TODO │ │ ├── VERSION │ │ ├── VERSION.xsl │ │ ├── assembly │ │ │ ├── README │ │ │ ├── assemble.xsl │ │ │ ├── schema │ │ │ │ ├── assembly51b7.rnc │ │ │ │ └── docbook51b7.rnc │ │ │ ├── topic-maker-chunk.xsl │ │ │ └── topic-maker.xsl │ │ ├── build.xml │ │ ├── catalog.xml │ │ ├── common │ │ │ ├── addns.xsl │ │ │ ├── af.xml │ │ │ ├── am.xml │ │ │ ├── ar.xml │ │ │ ├── as.xml │ │ │ ├── ast.xml │ │ │ ├── autoidx-kimber.xsl │ │ │ ├── autoidx-kosek.xsl │ │ │ ├── az.xml │ │ │ ├── bg.xml │ │ │ ├── bn.xml │ │ │ ├── bn_in.xml │ │ │ ├── bs.xml │ │ │ ├── build.xml │ │ │ ├── ca.xml │ │ │ ├── charmap.xml │ │ │ ├── charmap.xsl │ │ │ ├── common.xml │ │ │ ├── common.xsl │ │ │ ├── cs.xml │ │ │ ├── cy.xml │ │ │ ├── da.xml │ │ │ ├── de.xml │ │ │ ├── el.xml │ │ │ ├── en.xml │ │ │ ├── entities.ent │ │ │ ├── eo.xml │ │ │ ├── es.xml │ │ │ ├── et.xml │ │ │ ├── eu.xml │ │ │ ├── fa.xml │ │ │ ├── fi.xml │ │ │ ├── fr.xml │ │ │ ├── ga.xml │ │ │ ├── gentext.xsl │ │ │ ├── gl.xml │ │ │ ├── gu.xml │ │ │ ├── he.xml │ │ │ ├── hi.xml │ │ │ ├── hr.xml │ │ │ ├── hu.xml │ │ │ ├── id.xml │ │ │ ├── insertfile.xsl │ │ │ ├── is.xml │ │ │ ├── it.xml │ │ │ ├── ja.xml │ │ │ ├── ka.xml │ │ │ ├── kn.xml │ │ │ ├── ko.xml │ │ │ ├── ky.xml │ │ │ ├── l10n.dtd │ │ │ ├── l10n.xml │ │ │ ├── l10n.xsl │ │ │ ├── la.xml │ │ │ ├── labels.xsl │ │ │ ├── lt.xml │ │ │ ├── lv.xml │ │ │ ├── ml.xml │ │ │ ├── mn.xml │ │ │ ├── mr.xml │ │ │ ├── nb.xml │ │ │ ├── nds.xml │ │ │ ├── nl.xml │ │ │ ├── nn.xml │ │ │ ├── olink.xsl │ │ │ ├── or.xml │ │ │ ├── pa.xml │ │ │ ├── pi.xml │ │ │ ├── pi.xsl │ │ │ ├── pl.xml │ │ │ ├── pt.xml │ │ │ ├── pt_br.xml │ │ │ ├── refentry.xml │ │ │ ├── refentry.xsl │ │ │ ├── ro.xml │ │ │ ├── ru.xml │ │ │ ├── sk.xml │ │ │ ├── sl.xml │ │ │ ├── sq.xml │ │ │ ├── sr.xml │ │ │ ├── sr_Latn.xml │ │ │ ├── stripns.xsl │ │ │ ├── subtitles.xsl │ │ │ ├── sv.xml │ │ │ ├── ta.xml │ │ │ ├── table.xsl │ │ │ ├── targetdatabase.dtd │ │ │ ├── targets.xsl │ │ │ ├── te.xml │ │ │ ├── th.xml │ │ │ ├── titles.xsl │ │ │ ├── tl.xml │ │ │ ├── tr.xml │ │ │ ├── uk.xml │ │ │ ├── ur.xml │ │ │ ├── utility.xml │ │ │ ├── utility.xsl │ │ │ ├── vi.xml │ │ │ ├── xh.xml │ │ │ ├── zh.xml │ │ │ ├── zh_cn.xml │ │ │ └── zh_tw.xml │ │ ├── docsrc │ │ │ ├── authors.xml │ │ │ ├── copyright.xml │ │ │ ├── license.xml │ │ │ ├── page.png │ │ │ ├── reference.css │ │ │ ├── reference.xml │ │ │ ├── reference.xml.included │ │ │ └── warranty.xml │ │ ├── eclipse │ │ │ ├── build.xml │ │ │ ├── eclipse.xsl │ │ │ ├── eclipse3.xsl │ │ │ └── profile-eclipse.xsl │ │ ├── epub │ │ │ ├── README │ │ │ ├── bin │ │ │ │ ├── dbtoepub │ │ │ │ ├── lib │ │ │ │ │ └── docbook.rb │ │ │ │ └── xslt │ │ │ │ │ └── obfuscate.xsl │ │ │ └── docbook.xsl │ │ ├── epub3 │ │ │ ├── README │ │ │ ├── build.xml │ │ │ ├── chunk.xsl │ │ │ ├── chunkfast.xsl │ │ │ ├── docbook-epub.css.xml │ │ │ ├── docbook.xsl │ │ │ ├── epub3-chunk-mods.xsl │ │ │ ├── epub3-element-mods.xsl │ │ │ ├── profile-chunk.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── titlepage.templates.xml │ │ │ └── titlepage.templates.xsl │ │ ├── extensions │ │ │ ├── LICENSE.txt │ │ │ ├── NOTICE.txt │ │ │ ├── README.LIBXSLT │ │ │ ├── README.txt │ │ │ ├── build.xml │ │ │ ├── docbook.py │ │ │ ├── lucene-analyzers-3.0.0.jar │ │ │ ├── lucene-core-3.0.0.jar │ │ │ ├── saxon65.jar │ │ │ ├── tagsoup-1.2.1.jar │ │ │ ├── webhelpindexer.jar │ │ │ ├── xalan27.jar │ │ │ └── xslt.py │ │ ├── fo │ │ │ ├── admon.xsl │ │ │ ├── annotations.xsl │ │ │ ├── autoidx-kimber.xsl │ │ │ ├── autoidx-kosek.xsl │ │ │ ├── autoidx-ng.xsl │ │ │ ├── autoidx.xsl │ │ │ ├── autotoc.xsl │ │ │ ├── axf.xsl │ │ │ ├── biblio-iso690.xsl │ │ │ ├── biblio.xsl │ │ │ ├── block.xsl │ │ │ ├── build.xml │ │ │ ├── callout.xsl │ │ │ ├── component.xsl │ │ │ ├── division.xsl │ │ │ ├── docbook.xsl │ │ │ ├── ebnf.xsl │ │ │ ├── fo-rtf.xsl │ │ │ ├── fo.xsl │ │ │ ├── footnote.xsl │ │ │ ├── fop.xsl │ │ │ ├── fop1.xsl │ │ │ ├── formal.xsl │ │ │ ├── glossary.xsl │ │ │ ├── graphics.xsl │ │ │ ├── highlight.xsl │ │ │ ├── htmltbl.xsl │ │ │ ├── index.xsl │ │ │ ├── info.xsl │ │ │ ├── inline.xsl │ │ │ ├── keywords.xsl │ │ │ ├── lists.xsl │ │ │ ├── math.xsl │ │ │ ├── pagesetup.xsl │ │ │ ├── param.xml │ │ │ ├── param.xsl │ │ │ ├── passivetex.xsl │ │ │ ├── pdf2index │ │ │ ├── pi.xml │ │ │ ├── pi.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── ptc.xsl │ │ │ ├── publishers.xsl │ │ │ ├── qandaset.xsl │ │ │ ├── refentry.xsl │ │ │ ├── sections.xsl │ │ │ ├── spaces.xsl │ │ │ ├── synop.xsl │ │ │ ├── table.xml │ │ │ ├── table.xsl │ │ │ ├── task.xsl │ │ │ ├── titlepage.templates.xml │ │ │ ├── titlepage.templates.xsl │ │ │ ├── titlepage.xsl │ │ │ ├── toc.xsl │ │ │ ├── verbatim.xsl │ │ │ ├── xep.xsl │ │ │ └── xref.xsl │ │ ├── highlighting │ │ │ ├── README │ │ │ ├── bourne-hl.xml │ │ │ ├── c-hl.xml │ │ │ ├── cmake-hl.xml │ │ │ ├── common.xsl │ │ │ ├── cpp-hl.xml │ │ │ ├── csharp-hl.xml │ │ │ ├── css21-hl.xml │ │ │ ├── delphi-hl.xml │ │ │ ├── ini-hl.xml │ │ │ ├── java-hl.xml │ │ │ ├── javascript-hl.xml │ │ │ ├── lua-hl.xml │ │ │ ├── m2-hl.xml │ │ │ ├── myxml-hl.xml │ │ │ ├── perl-hl.xml │ │ │ ├── php-hl.xml │ │ │ ├── python-hl.xml │ │ │ ├── ruby-hl.xml │ │ │ ├── sql1999-hl.xml │ │ │ ├── sql2003-hl.xml │ │ │ ├── sql92-hl.xml │ │ │ ├── tcl-hl.xml │ │ │ ├── upc-hl.xml │ │ │ └── xslthl-config.xml │ │ ├── html │ │ │ ├── admon.xsl │ │ │ ├── annotations.xsl │ │ │ ├── autoidx-kimber.xsl │ │ │ ├── autoidx-kosek.xsl │ │ │ ├── autoidx-ng.xsl │ │ │ ├── autoidx.xsl │ │ │ ├── autotoc.xsl │ │ │ ├── biblio-iso690.xsl │ │ │ ├── biblio.xsl │ │ │ ├── block.xsl │ │ │ ├── build.xml │ │ │ ├── callout.xsl │ │ │ ├── changebars.xsl │ │ │ ├── chunk-changebars.xsl │ │ │ ├── chunk-code.xsl │ │ │ ├── chunk-common.xsl │ │ │ ├── chunk.xsl │ │ │ ├── chunker.xsl │ │ │ ├── chunkfast.xsl │ │ │ ├── chunktoc.xsl │ │ │ ├── component.xsl │ │ │ ├── division.xsl │ │ │ ├── docbook.css.xml │ │ │ ├── docbook.xsl │ │ │ ├── ebnf.xsl │ │ │ ├── footnote.xsl │ │ │ ├── formal.xsl │ │ │ ├── glossary.xsl │ │ │ ├── graphics.xsl │ │ │ ├── highlight.xsl │ │ │ ├── html-rtf.xsl │ │ │ ├── html.xsl │ │ │ ├── htmltbl.xsl │ │ │ ├── index.xsl │ │ │ ├── info.xsl │ │ │ ├── inline.xsl │ │ │ ├── its.xsl │ │ │ ├── keywords.xsl │ │ │ ├── lists.xsl │ │ │ ├── maketoc.xsl │ │ │ ├── manifest.xsl │ │ │ ├── math.xsl │ │ │ ├── oldchunker.xsl │ │ │ ├── onechunk.xsl │ │ │ ├── param.xml │ │ │ ├── param.xsl │ │ │ ├── pi.xml │ │ │ ├── pi.xsl │ │ │ ├── profile-chunk-code.xsl │ │ │ ├── profile-chunk.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── profile-onechunk.xsl │ │ │ ├── publishers.xsl │ │ │ ├── qandaset.xsl │ │ │ ├── refentry.xsl │ │ │ ├── sections.xsl │ │ │ ├── synop.xsl │ │ │ ├── table.xsl │ │ │ ├── task.xsl │ │ │ ├── titlepage.templates.xml │ │ │ ├── titlepage.templates.xsl │ │ │ ├── titlepage.xsl │ │ │ ├── toc.xsl │ │ │ ├── verbatim.xsl │ │ │ └── xref.xsl │ │ ├── htmlhelp │ │ │ ├── build.xml │ │ │ ├── htmlhelp-common.xsl │ │ │ ├── htmlhelp.xsl │ │ │ ├── profile-htmlhelp-common.xsl │ │ │ └── profile-htmlhelp.xsl │ │ ├── images │ │ │ ├── annot-close.png │ │ │ ├── annot-open.png │ │ │ ├── blank.png │ │ │ ├── callouts │ │ │ │ ├── 1.gif │ │ │ │ ├── 1.png │ │ │ │ ├── 1.svg │ │ │ │ ├── 10.gif │ │ │ │ ├── 10.png │ │ │ │ ├── 10.svg │ │ │ │ ├── 11.gif │ │ │ │ ├── 11.png │ │ │ │ ├── 11.svg │ │ │ │ ├── 12.gif │ │ │ │ ├── 12.png │ │ │ │ ├── 12.svg │ │ │ │ ├── 13.gif │ │ │ │ ├── 13.png │ │ │ │ ├── 13.svg │ │ │ │ ├── 14.gif │ │ │ │ ├── 14.png │ │ │ │ ├── 14.svg │ │ │ │ ├── 15.gif │ │ │ │ ├── 15.png │ │ │ │ ├── 15.svg │ │ │ │ ├── 16.svg │ │ │ │ ├── 17.svg │ │ │ │ ├── 18.svg │ │ │ │ ├── 19.svg │ │ │ │ ├── 2.gif │ │ │ │ ├── 2.png │ │ │ │ ├── 2.svg │ │ │ │ ├── 20.svg │ │ │ │ ├── 21.svg │ │ │ │ ├── 22.svg │ │ │ │ ├── 23.svg │ │ │ │ ├── 24.svg │ │ │ │ ├── 25.svg │ │ │ │ ├── 26.svg │ │ │ │ ├── 27.svg │ │ │ │ ├── 28.svg │ │ │ │ ├── 29.svg │ │ │ │ ├── 3.gif │ │ │ │ ├── 3.png │ │ │ │ ├── 3.svg │ │ │ │ ├── 30.svg │ │ │ │ ├── 4.gif │ │ │ │ ├── 4.png │ │ │ │ ├── 4.svg │ │ │ │ ├── 5.gif │ │ │ │ ├── 5.png │ │ │ │ ├── 5.svg │ │ │ │ ├── 6.gif │ │ │ │ ├── 6.png │ │ │ │ ├── 6.svg │ │ │ │ ├── 7.gif │ │ │ │ ├── 7.png │ │ │ │ ├── 7.svg │ │ │ │ ├── 8.gif │ │ │ │ ├── 8.png │ │ │ │ ├── 8.svg │ │ │ │ ├── 9.gif │ │ │ │ ├── 9.png │ │ │ │ └── 9.svg │ │ │ ├── caution.gif │ │ │ ├── caution.png │ │ │ ├── caution.svg │ │ │ ├── caution.tif │ │ │ ├── colorsvg │ │ │ │ ├── caution.svg │ │ │ │ ├── home.svg │ │ │ │ ├── important.svg │ │ │ │ ├── next.svg │ │ │ │ ├── note.svg │ │ │ │ ├── prev.svg │ │ │ │ ├── tip.svg │ │ │ │ ├── up.svg │ │ │ │ └── warning.svg │ │ │ ├── draft.png │ │ │ ├── draft.svg │ │ │ ├── home.gif │ │ │ ├── home.png │ │ │ ├── home.svg │ │ │ ├── important.gif │ │ │ ├── important.png │ │ │ ├── important.svg │ │ │ ├── important.tif │ │ │ ├── next.gif │ │ │ ├── next.png │ │ │ ├── next.svg │ │ │ ├── note.gif │ │ │ ├── note.png │ │ │ ├── note.svg │ │ │ ├── note.tif │ │ │ ├── prev.gif │ │ │ ├── prev.png │ │ │ ├── prev.svg │ │ │ ├── tip.gif │ │ │ ├── tip.png │ │ │ ├── tip.svg │ │ │ ├── tip.tif │ │ │ ├── toc-blank.png │ │ │ ├── toc-minus.png │ │ │ ├── toc-plus.png │ │ │ ├── up.gif │ │ │ ├── up.png │ │ │ ├── up.svg │ │ │ ├── warning.gif │ │ │ ├── warning.png │ │ │ ├── warning.svg │ │ │ └── warning.tif │ │ ├── install.sh │ │ ├── javahelp │ │ │ ├── build.xml │ │ │ ├── javahelp.xsl │ │ │ └── profile-javahelp.xsl │ │ ├── lib │ │ │ ├── build.xml │ │ │ └── lib.xsl │ │ ├── log │ │ ├── manpages │ │ │ ├── ChangeLog.20020917 │ │ │ ├── block.xsl │ │ │ ├── build.xml │ │ │ ├── charmap.groff.xsl │ │ │ ├── docbook.xsl │ │ │ ├── endnotes.xsl │ │ │ ├── html-synop.xsl │ │ │ ├── info.xsl │ │ │ ├── inline.xsl │ │ │ ├── lists.xsl │ │ │ ├── other.xsl │ │ │ ├── param.xml │ │ │ ├── param.xsl │ │ │ ├── pi.xml │ │ │ ├── pi.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── refentry.xsl │ │ │ ├── synop.xsl │ │ │ ├── table.xsl │ │ │ ├── tbl.xsl │ │ │ └── utility.xsl │ │ ├── params │ │ │ ├── abstract.notitle.enabled.xml │ │ │ ├── abstract.properties.xml │ │ │ ├── abstract.title.properties.xml │ │ │ ├── activate.external.olinks.xml │ │ │ ├── active.toc.xml │ │ │ ├── ade.extensions.xml │ │ │ ├── admon.graphics.extension.xml │ │ │ ├── admon.graphics.path.xml │ │ │ ├── admon.graphics.xml │ │ │ ├── admon.style.xml │ │ │ ├── admon.textlabel.xml │ │ │ ├── admonition.properties.xml │ │ │ ├── admonition.title.properties.xml │ │ │ ├── alignment.xml │ │ │ ├── annotate.toc.xml │ │ │ ├── annotation.css.xml │ │ │ ├── annotation.graphic.close.xml │ │ │ ├── annotation.graphic.open.xml │ │ │ ├── annotation.js.xml │ │ │ ├── annotation.support.xml │ │ │ ├── appendix.autolabel.xml │ │ │ ├── arbortext.extensions.xml │ │ │ ├── article.appendix.title.properties.xml │ │ │ ├── author.othername.in.middle.xml │ │ │ ├── autolayout-file.xml │ │ │ ├── autolink.index.see.xml │ │ │ ├── autotoc.label.in.hyperlink.xml │ │ │ ├── autotoc.label.separator.xml │ │ │ ├── axf.extensions.xml │ │ │ ├── banner.before.navigation.xml │ │ │ ├── base.dir.xml │ │ │ ├── biblioentry.item.separator.xml │ │ │ ├── biblioentry.properties.xml │ │ │ ├── bibliography.collection.xml │ │ │ ├── bibliography.numbered.xml │ │ │ ├── bibliography.style.xml │ │ │ ├── blockquote.properties.xml │ │ │ ├── blurb.on.titlepage.enabled.xml │ │ │ ├── body.attributes.xml │ │ │ ├── body.bg.color.xml │ │ │ ├── body.end.indent.xml │ │ │ ├── body.font.family.xml │ │ │ ├── body.font.master.xml │ │ │ ├── body.font.size.xml │ │ │ ├── body.margin.bottom.xml │ │ │ ├── body.margin.inner.xml │ │ │ ├── body.margin.outer.xml │ │ │ ├── body.margin.top.xml │ │ │ ├── body.start.indent.xml │ │ │ ├── bookmarks.collapse.xml │ │ │ ├── bridgehead.in.toc.xml │ │ │ ├── bullet.image.xml │ │ │ ├── callout.defaultcolumn.xml │ │ │ ├── callout.graphics.extension.xml │ │ │ ├── callout.graphics.number.limit.xml │ │ │ ├── callout.graphics.path.xml │ │ │ ├── callout.graphics.xml │ │ │ ├── callout.icon.size.xml │ │ │ ├── callout.list.table.xml │ │ │ ├── callout.properties.xml │ │ │ ├── callout.unicode.font.xml │ │ │ ├── callout.unicode.number.limit.xml │ │ │ ├── callout.unicode.start.character.xml │ │ │ ├── callout.unicode.xml │ │ │ ├── calloutlist.properties.xml │ │ │ ├── callouts.extension.xml │ │ │ ├── chapter.autolabel.xml │ │ │ ├── chunk.append.xml │ │ │ ├── chunk.first.sections.xml │ │ │ ├── chunk.quietly.xml │ │ │ ├── chunk.section.depth.xml │ │ │ ├── chunk.sections.xml │ │ │ ├── chunk.separate.lots.xml │ │ │ ├── chunk.toc.xml │ │ │ ├── chunk.tocs.and.lots.has.title.xml │ │ │ ├── chunk.tocs.and.lots.xml │ │ │ ├── chunked.filename.prefix.xml │ │ │ ├── chunker.output.cdata-section-elements.xml │ │ │ ├── chunker.output.doctype-public.xml │ │ │ ├── chunker.output.doctype-system.xml │ │ │ ├── chunker.output.encoding.xml │ │ │ ├── chunker.output.indent.xml │ │ │ ├── chunker.output.media-type.xml │ │ │ ├── chunker.output.method.xml │ │ │ ├── chunker.output.omit-xml-declaration.xml │ │ │ ├── chunker.output.standalone.xml │ │ │ ├── citerefentry.link.xml │ │ │ ├── collect.xref.targets.xml │ │ │ ├── column.count.back.xml │ │ │ ├── column.count.body.xml │ │ │ ├── column.count.front.xml │ │ │ ├── column.count.index.xml │ │ │ ├── column.count.lot.xml │ │ │ ├── column.count.titlepage.xml │ │ │ ├── column.gap.back.xml │ │ │ ├── column.gap.body.xml │ │ │ ├── column.gap.front.xml │ │ │ ├── column.gap.index.xml │ │ │ ├── column.gap.lot.xml │ │ │ ├── column.gap.titlepage.xml │ │ │ ├── compact.list.item.spacing.xml │ │ │ ├── component.label.includes.part.label.xml │ │ │ ├── component.title.properties.xml │ │ │ ├── component.titlepage.properties.xml │ │ │ ├── contrib.inline.enabled.xml │ │ │ ├── crop.mark.bleed.xml │ │ │ ├── crop.mark.offset.xml │ │ │ ├── crop.mark.width.xml │ │ │ ├── crop.marks.xml │ │ │ ├── css.decoration.xml │ │ │ ├── css.stylesheet.dir.xml │ │ │ ├── css.stylesheet.xml │ │ │ ├── current.docid.xml │ │ │ ├── currentpage.marker.xml │ │ │ ├── custom.css.source.xml │ │ │ ├── default.float.class.xml │ │ │ ├── default.image.width.xml │ │ │ ├── default.table.frame.xml │ │ │ ├── default.table.rules.xml │ │ │ ├── default.table.width.xml │ │ │ ├── default.units.xml │ │ │ ├── dialogue.properties.xml │ │ │ ├── dingbat.font.family.xml │ │ │ ├── disable.collapsible.xml │ │ │ ├── disable.incremental.xml │ │ │ ├── docbook.css.link.xml │ │ │ ├── docbook.css.source.xml │ │ │ ├── double.sided.xml │ │ │ ├── draft.mode.xml │ │ │ ├── draft.watermark.image.xml │ │ │ ├── drama.properties.xml │ │ │ ├── dry-run.xml │ │ │ ├── dynamic.toc.xml │ │ │ ├── ebnf.assignment.xml │ │ │ ├── ebnf.statement.terminator.xml │ │ │ ├── ebnf.table.bgcolor.xml │ │ │ ├── ebnf.table.border.xml │ │ │ ├── eclipse.autolabel.xml │ │ │ ├── eclipse.plugin.id.xml │ │ │ ├── eclipse.plugin.name.xml │ │ │ ├── eclipse.plugin.provider.xml │ │ │ ├── editedby.enabled.xml │ │ │ ├── email.delimiters.enabled.xml │ │ │ ├── email.mailto.enabled.xml │ │ │ ├── emphasis.propagates.style.xml │ │ │ ├── entry.propagates.style.xml │ │ │ ├── epub.autolabel.xml │ │ │ ├── equation.number.properties.xml │ │ │ ├── equation.properties.xml │ │ │ ├── example.properties.xml │ │ │ ├── exsl.node.set.available.xml │ │ │ ├── feedback.href.xml │ │ │ ├── feedback.link.text.xml │ │ │ ├── feedback.with.ids.xml │ │ │ ├── figure.properties.xml │ │ │ ├── filename-prefix.xml │ │ │ ├── firstterm.only.link.xml │ │ │ ├── foil.footer.properties.xml │ │ │ ├── foil.header.properties.xml │ │ │ ├── foil.master.properties.xml │ │ │ ├── foil.page-sequence.properties.xml │ │ │ ├── foil.properties.xml │ │ │ ├── foil.region-after.properties.xml │ │ │ ├── foil.region-before.properties.xml │ │ │ ├── foil.region-body.properties.xml │ │ │ ├── foil.subtitle.properties.xml │ │ │ ├── foil.title.master.xml │ │ │ ├── foil.title.properties.xml │ │ │ ├── foil.title.size.xml │ │ │ ├── foilgroup.properties.xml │ │ │ ├── foilgroup.toc.xml │ │ │ ├── footer.column.widths.xml │ │ │ ├── footer.content.properties.xml │ │ │ ├── footer.hr.xml │ │ │ ├── footer.rule.xml │ │ │ ├── footer.table.height.xml │ │ │ ├── footer.table.properties.xml │ │ │ ├── footers.on.blank.pages.xml │ │ │ ├── footnote.font.size.xml │ │ │ ├── footnote.mark.properties.xml │ │ │ ├── footnote.number.format.xml │ │ │ ├── footnote.number.symbols.xml │ │ │ ├── footnote.properties.xml │ │ │ ├── footnote.sep.leader.properties.xml │ │ │ ├── fop.extensions.xml │ │ │ ├── fop1.extensions.xml │ │ │ ├── force.blank.pages.xml │ │ │ ├── formal.object.properties.xml │ │ │ ├── formal.procedures.xml │ │ │ ├── formal.title.placement.xml │ │ │ ├── formal.title.properties.xml │ │ │ ├── funcsynopsis.decoration.xml │ │ │ ├── funcsynopsis.style.xml │ │ │ ├── function.parens.xml │ │ │ ├── generate.consistent.ids.xml │ │ │ ├── generate.copyright.xml │ │ │ ├── generate.css.header.xml │ │ │ ├── generate.foilgroup.numbered.toc.xml │ │ │ ├── generate.foilgroup.toc.xml │ │ │ ├── generate.handoutnotes.xml │ │ │ ├── generate.id.attributes.xml │ │ │ ├── generate.index.xml │ │ │ ├── generate.legalnotice.link.xml │ │ │ ├── generate.manifest.xml │ │ │ ├── generate.meta.abstract.xml │ │ │ ├── generate.page.number.xml │ │ │ ├── generate.pubdate.xml │ │ │ ├── generate.revhistory.link.xml │ │ │ ├── generate.section.toc.level.xml │ │ │ ├── generate.speakernotes.xml │ │ │ ├── generate.titlepage.xml │ │ │ ├── generate.toc.xml │ │ │ ├── glossary.as.blocks.xml │ │ │ ├── glossary.collection.xml │ │ │ ├── glossary.sort.xml │ │ │ ├── glossdef.block.properties.xml │ │ │ ├── glossdef.list.properties.xml │ │ │ ├── glossentry.list.item.properties.xml │ │ │ ├── glossentry.show.acronym.xml │ │ │ ├── glosslist.as.blocks.xml │ │ │ ├── glossterm.auto.link.xml │ │ │ ├── glossterm.block.properties.xml │ │ │ ├── glossterm.list.properties.xml │ │ │ ├── glossterm.separation.xml │ │ │ ├── glossterm.width.xml │ │ │ ├── graphic.default.extension.xml │ │ │ ├── graphical.admonition.properties.xml │ │ │ ├── graphics.dir.xml │ │ │ ├── graphicsize.extension.xml │ │ │ ├── graphicsize.use.img.src.path.xml │ │ │ ├── handoutnotes.properties.xml │ │ │ ├── header.column.widths.xml │ │ │ ├── header.content.properties.xml │ │ │ ├── header.hr.xml │ │ │ ├── header.rule.xml │ │ │ ├── header.table.height.xml │ │ │ ├── header.table.properties.xml │ │ │ ├── headers.on.blank.pages.xml │ │ │ ├── hidetoc.image.xml │ │ │ ├── highlight.default.language.xml │ │ │ ├── highlight.source.xml │ │ │ ├── highlight.xslthl.config.xml │ │ │ ├── home.image.xml │ │ │ ├── html.append.xml │ │ │ ├── html.base.xml │ │ │ ├── html.cellpadding.xml │ │ │ ├── html.cellspacing.xml │ │ │ ├── html.cleanup.xml │ │ │ ├── html.ext.xml │ │ │ ├── html.extra.head.links.xml │ │ │ ├── html.head.legalnotice.link.multiple.xml │ │ │ ├── html.head.legalnotice.link.types.xml │ │ │ ├── html.longdesc.link.xml │ │ │ ├── html.longdesc.xml │ │ │ ├── html.script.type.xml │ │ │ ├── html.script.xml │ │ │ ├── html.stylesheet.type.xml │ │ │ ├── html.stylesheet.xml │ │ │ ├── htmlhelp.alias.file.xml │ │ │ ├── htmlhelp.autolabel.xml │ │ │ ├── htmlhelp.button.back.xml │ │ │ ├── htmlhelp.button.forward.xml │ │ │ ├── htmlhelp.button.hideshow.xml │ │ │ ├── htmlhelp.button.home.url.xml │ │ │ ├── htmlhelp.button.home.xml │ │ │ ├── htmlhelp.button.jump1.title.xml │ │ │ ├── htmlhelp.button.jump1.url.xml │ │ │ ├── htmlhelp.button.jump1.xml │ │ │ ├── htmlhelp.button.jump2.title.xml │ │ │ ├── htmlhelp.button.jump2.url.xml │ │ │ ├── htmlhelp.button.jump2.xml │ │ │ ├── htmlhelp.button.locate.xml │ │ │ ├── htmlhelp.button.next.xml │ │ │ ├── htmlhelp.button.options.xml │ │ │ ├── htmlhelp.button.prev.xml │ │ │ ├── htmlhelp.button.print.xml │ │ │ ├── htmlhelp.button.refresh.xml │ │ │ ├── htmlhelp.button.stop.xml │ │ │ ├── htmlhelp.button.zoom.xml │ │ │ ├── htmlhelp.chm.xml │ │ │ ├── htmlhelp.default.topic.xml │ │ │ ├── htmlhelp.display.progress.xml │ │ │ ├── htmlhelp.encoding.xml │ │ │ ├── htmlhelp.enhanced.decompilation.xml │ │ │ ├── htmlhelp.enumerate.images.xml │ │ │ ├── htmlhelp.force.map.and.alias.xml │ │ │ ├── htmlhelp.hhc.binary.xml │ │ │ ├── htmlhelp.hhc.folders.instead.books.xml │ │ │ ├── htmlhelp.hhc.section.depth.xml │ │ │ ├── htmlhelp.hhc.show.root.xml │ │ │ ├── htmlhelp.hhc.width.xml │ │ │ ├── htmlhelp.hhc.xml │ │ │ ├── htmlhelp.hhk.xml │ │ │ ├── htmlhelp.hhp.tail.xml │ │ │ ├── htmlhelp.hhp.window.xml │ │ │ ├── htmlhelp.hhp.windows.xml │ │ │ ├── htmlhelp.hhp.xml │ │ │ ├── htmlhelp.map.file.xml │ │ │ ├── htmlhelp.only.xml │ │ │ ├── htmlhelp.remember.window.position.xml │ │ │ ├── htmlhelp.show.advanced.search.xml │ │ │ ├── htmlhelp.show.favorities.xml │ │ │ ├── htmlhelp.show.menu.xml │ │ │ ├── htmlhelp.show.toolbar.text.xml │ │ │ ├── htmlhelp.title.xml │ │ │ ├── htmlhelp.use.hhk.xml │ │ │ ├── htmlhelp.window.geometry.xml │ │ │ ├── hyphenate.verbatim.characters.xml │ │ │ ├── hyphenate.verbatim.xml │ │ │ ├── hyphenate.xml │ │ │ ├── id.warnings.xml │ │ │ ├── ignore.image.scaling.xml │ │ │ ├── img.src.path.xml │ │ │ ├── index.div.title.properties.xml │ │ │ ├── index.entry.properties.xml │ │ │ ├── index.links.to.section.xml │ │ │ ├── index.method.xml │ │ │ ├── index.number.separator.xml │ │ │ ├── index.on.role.xml │ │ │ ├── index.on.type.xml │ │ │ ├── index.page.number.properties.xml │ │ │ ├── index.prefer.titleabbrev.xml │ │ │ ├── index.preferred.page.properties.xml │ │ │ ├── index.range.separator.xml │ │ │ ├── index.term.separator.xml │ │ │ ├── informal.object.properties.xml │ │ │ ├── informalequation.properties.xml │ │ │ ├── informalexample.properties.xml │ │ │ ├── informalfigure.properties.xml │ │ │ ├── informaltable.properties.xml │ │ │ ├── inherit.keywords.xml │ │ │ ├── inlinestagedir.properties.xml │ │ │ ├── inner.region.content.properties.xml │ │ │ ├── insert.link.page.number.xml │ │ │ ├── insert.olink.page.number.xml │ │ │ ├── insert.olink.pdf.frag.xml │ │ │ ├── insert.xref.page.number.para.xml │ │ │ ├── insert.xref.page.number.xml │ │ │ ├── itemizedlist.label.properties.xml │ │ │ ├── itemizedlist.label.width.xml │ │ │ ├── itemizedlist.properties.xml │ │ │ ├── javahelp.encoding.xml │ │ │ ├── keep.relative.image.uris.xml │ │ │ ├── keyboard.nav.xml │ │ │ ├── l10n.gentext.default.language.xml │ │ │ ├── l10n.gentext.language.xml │ │ │ ├── l10n.gentext.use.xref.language.xml │ │ │ ├── l10n.lang.value.rfc.compliant.xml │ │ │ ├── label.from.part.xml │ │ │ ├── line-height.xml │ │ │ ├── line.properties.xml │ │ │ ├── linegroup.properties.xml │ │ │ ├── linenumbering.everyNth.xml │ │ │ ├── linenumbering.extension.xml │ │ │ ├── linenumbering.separator.xml │ │ │ ├── linenumbering.width.xml │ │ │ ├── link.mailto.url.xml │ │ │ ├── link.to.self.for.mediaobject.xml │ │ │ ├── list.block.properties.xml │ │ │ ├── list.block.spacing.xml │ │ │ ├── list.item.spacing.xml │ │ │ ├── make.clean.html.xml │ │ │ ├── make.graphic.viewport.xml │ │ │ ├── make.index.markup.xml │ │ │ ├── make.single.year.ranges.xml │ │ │ ├── make.valid.html.xml │ │ │ ├── make.year.ranges.xml │ │ │ ├── man.authors.section.enabled.xml │ │ │ ├── man.base.url.for.relative.links.xml │ │ │ ├── man.break.after.slash.xml │ │ │ ├── man.charmap.enabled.xml │ │ │ ├── man.charmap.subset.profile.english.xml │ │ │ ├── man.charmap.subset.profile.xml │ │ │ ├── man.charmap.uri.xml │ │ │ ├── man.charmap.use.subset.xml │ │ │ ├── man.copyright.section.enabled.xml │ │ │ ├── man.endnotes.are.numbered.xml │ │ │ ├── man.endnotes.list.enabled.xml │ │ │ ├── man.endnotes.list.heading.xml │ │ │ ├── man.font.funcprototype.xml │ │ │ ├── man.font.funcsynopsisinfo.xml │ │ │ ├── man.font.links.xml │ │ │ ├── man.font.table.headings.xml │ │ │ ├── man.font.table.title.xml │ │ │ ├── man.funcsynopsis.style.xml │ │ │ ├── man.hyphenate.computer.inlines.xml │ │ │ ├── man.hyphenate.filenames.xml │ │ │ ├── man.hyphenate.urls.xml │ │ │ ├── man.hyphenate.xml │ │ │ ├── man.indent.blurbs.xml │ │ │ ├── man.indent.lists.xml │ │ │ ├── man.indent.refsect.xml │ │ │ ├── man.indent.verbatims.xml │ │ │ ├── man.indent.width.xml │ │ │ ├── man.justify.xml │ │ │ ├── man.output.base.dir.xml │ │ │ ├── man.output.better.ps.enabled.xml │ │ │ ├── man.output.encoding.xml │ │ │ ├── man.output.in.separate.dir.xml │ │ │ ├── man.output.lang.in.name.enabled.xml │ │ │ ├── man.output.manifest.enabled.xml │ │ │ ├── man.output.manifest.filename.xml │ │ │ ├── man.output.quietly.xml │ │ │ ├── man.output.subdirs.enabled.xml │ │ │ ├── man.segtitle.suppress.xml │ │ │ ├── man.string.subst.map.local.post.xml │ │ │ ├── man.string.subst.map.local.pre.xml │ │ │ ├── man.string.subst.map.xml │ │ │ ├── man.subheading.divider.enabled.xml │ │ │ ├── man.subheading.divider.xml │ │ │ ├── man.table.footnotes.divider.xml │ │ │ ├── man.th.extra1.suppress.xml │ │ │ ├── man.th.extra2.max.length.xml │ │ │ ├── man.th.extra2.suppress.xml │ │ │ ├── man.th.extra3.max.length.xml │ │ │ ├── man.th.extra3.suppress.xml │ │ │ ├── man.th.title.max.length.xml │ │ │ ├── manifest.in.base.dir.xml │ │ │ ├── manifest.xml │ │ │ ├── manual.toc.xml │ │ │ ├── margin.note.float.type.xml │ │ │ ├── margin.note.properties.xml │ │ │ ├── margin.note.title.properties.xml │ │ │ ├── margin.note.width.xml │ │ │ ├── mark.optional.procedure.steps.xml │ │ │ ├── marker.section.level.xml │ │ │ ├── menuchoice.menu.separator.xml │ │ │ ├── menuchoice.separator.xml │ │ │ ├── minus.image.xml │ │ │ ├── mml.embedding.mode.fo.xml │ │ │ ├── mml.embedding.mode.xml │ │ │ ├── monospace.font.family.xml │ │ │ ├── monospace.properties.xml │ │ │ ├── monospace.verbatim.font.width.xml │ │ │ ├── monospace.verbatim.properties.xml │ │ │ ├── multiframe.bottom.bgcolor.xml │ │ │ ├── multiframe.navigation.height.xml │ │ │ ├── multiframe.top.bgcolor.xml │ │ │ ├── multiframe.xml │ │ │ ├── nav.separator.xml │ │ │ ├── nav.table.summary.xml │ │ │ ├── navbgcolor.xml │ │ │ ├── navbodywidth.xml │ │ │ ├── navig.graphics.extension.xml │ │ │ ├── navig.graphics.path.xml │ │ │ ├── navig.graphics.xml │ │ │ ├── navig.showtitles.xml │ │ │ ├── navtocwidth.xml │ │ │ ├── next.image.xml │ │ │ ├── no.home.image.xml │ │ │ ├── no.next.image.xml │ │ │ ├── no.prev.image.xml │ │ │ ├── no.toc.image.xml │ │ │ ├── no.up.image.xml │ │ │ ├── nominal.image.depth.xml │ │ │ ├── nominal.image.width.xml │ │ │ ├── nominal.table.width.xml │ │ │ ├── nongraphical.admonition.properties.xml │ │ │ ├── normal.para.spacing.xml │ │ │ ├── olink.base.uri.xml │ │ │ ├── olink.debug.xml │ │ │ ├── olink.doctitle.xml │ │ │ ├── olink.fragid.xml │ │ │ ├── olink.lang.fallback.sequence.xml │ │ │ ├── olink.outline.ext.xml │ │ │ ├── olink.properties.xml │ │ │ ├── olink.pubid.xml │ │ │ ├── olink.resolver.xml │ │ │ ├── olink.sysid.xml │ │ │ ├── orderedlist.label.properties.xml │ │ │ ├── orderedlist.label.width.xml │ │ │ ├── orderedlist.properties.xml │ │ │ ├── othercredit.like.author.enabled.xml │ │ │ ├── outer.region.content.properties.xml │ │ │ ├── output-root.xml │ │ │ ├── output.indent.xml │ │ │ ├── overlay.js.xml │ │ │ ├── overlay.logo.xml │ │ │ ├── overlay.xml │ │ │ ├── page.height.portrait.xml │ │ │ ├── page.height.xml │ │ │ ├── page.margin.bottom.xml │ │ │ ├── page.margin.inner.xml │ │ │ ├── page.margin.outer.xml │ │ │ ├── page.margin.top.xml │ │ │ ├── page.orientation.xml │ │ │ ├── page.width.portrait.xml │ │ │ ├── page.width.xml │ │ │ ├── pages.template.xml │ │ │ ├── paper.type.xml │ │ │ ├── para.propagates.style.xml │ │ │ ├── para.properties.xml │ │ │ ├── part.autolabel.xml │ │ │ ├── passivetex.extensions.xml │ │ │ ├── pgwide.properties.xml │ │ │ ├── phrase.propagates.style.xml │ │ │ ├── pixels.per.inch.xml │ │ │ ├── plus.image.xml │ │ │ ├── poetry.properties.xml │ │ │ ├── points.per.em.xml │ │ │ ├── preface.autolabel.xml │ │ │ ├── prefer.internal.olink.xml │ │ │ ├── preferred.mediaobject.role.xml │ │ │ ├── prev.image.xml │ │ │ ├── procedure.properties.xml │ │ │ ├── process.empty.source.toc.xml │ │ │ ├── process.source.toc.xml │ │ │ ├── profile.arch.xml │ │ │ ├── profile.attribute.xml │ │ │ ├── profile.audience.xml │ │ │ ├── profile.condition.xml │ │ │ ├── profile.conformance.xml │ │ │ ├── profile.lang.xml │ │ │ ├── profile.os.xml │ │ │ ├── profile.outputformat.xml │ │ │ ├── profile.revision.xml │ │ │ ├── profile.revisionflag.xml │ │ │ ├── profile.role.xml │ │ │ ├── profile.security.xml │ │ │ ├── profile.separator.xml │ │ │ ├── profile.status.xml │ │ │ ├── profile.userlevel.xml │ │ │ ├── profile.value.xml │ │ │ ├── profile.vendor.xml │ │ │ ├── profile.wordsize.xml │ │ │ ├── publishers.properties.xml │ │ │ ├── punct.honorific.xml │ │ │ ├── qanda.defaultlabel.xml │ │ │ ├── qanda.in.toc.xml │ │ │ ├── qanda.inherit.numeration.xml │ │ │ ├── qanda.nested.in.toc.xml │ │ │ ├── qanda.title.level1.properties.xml │ │ │ ├── qanda.title.level2.properties.xml │ │ │ ├── qanda.title.level3.properties.xml │ │ │ ├── qanda.title.level4.properties.xml │ │ │ ├── qanda.title.level5.properties.xml │ │ │ ├── qanda.title.level6.properties.xml │ │ │ ├── qanda.title.properties.xml │ │ │ ├── qandadiv.autolabel.xml │ │ │ ├── rebuild-all.xml │ │ │ ├── refclass.suppress.xml │ │ │ ├── refentry.date.profile.enabled.xml │ │ │ ├── refentry.date.profile.xml │ │ │ ├── refentry.generate.name.xml │ │ │ ├── refentry.generate.title.xml │ │ │ ├── refentry.manual.fallback.profile.xml │ │ │ ├── refentry.manual.profile.enabled.xml │ │ │ ├── refentry.manual.profile.xml │ │ │ ├── refentry.meta.get.quietly.xml │ │ │ ├── refentry.pagebreak.xml │ │ │ ├── refentry.separator.xml │ │ │ ├── refentry.source.fallback.profile.xml │ │ │ ├── refentry.source.name.profile.enabled.xml │ │ │ ├── refentry.source.name.profile.xml │ │ │ ├── refentry.source.name.suppress.xml │ │ │ ├── refentry.title.properties.xml │ │ │ ├── refentry.version.profile.enabled.xml │ │ │ ├── refentry.version.profile.xml │ │ │ ├── refentry.version.suppress.xml │ │ │ ├── refentry.xref.manvolnum.xml │ │ │ ├── reference.autolabel.xml │ │ │ ├── region.after.extent.xml │ │ │ ├── region.before.extent.xml │ │ │ ├── region.inner.extent.xml │ │ │ ├── region.inner.properties.xml │ │ │ ├── region.outer.extent.xml │ │ │ ├── region.outer.properties.xml │ │ │ ├── revhistory.table.cell.properties.xml │ │ │ ├── revhistory.table.properties.xml │ │ │ ├── revhistory.title.properties.xml │ │ │ ├── root.filename.xml │ │ │ ├── root.properties.xml │ │ │ ├── rootid.xml │ │ │ ├── runinhead.default.title.end.punct.xml │ │ │ ├── runinhead.title.end.punct.xml │ │ │ ├── running.foot.properties.xml │ │ │ ├── s5.controls.xml │ │ │ ├── s5.defaultview.xml │ │ │ ├── s5.opera.css.xml │ │ │ ├── s5.outline.css.xml │ │ │ ├── s5.path.prefix.xml │ │ │ ├── s5.print.css.xml │ │ │ ├── s5.slides.css.xml │ │ │ ├── s5.slides.js.xml │ │ │ ├── sans.font.family.xml │ │ │ ├── saxon.callouts.xml │ │ │ ├── saxon.character.representation.xml │ │ │ ├── saxon.linenumbering.xml │ │ │ ├── saxon.tablecolumns.xml │ │ │ ├── script.dir.xml │ │ │ ├── section.autolabel.max.depth.xml │ │ │ ├── section.autolabel.xml │ │ │ ├── section.container.element.xml │ │ │ ├── section.label.includes.component.label.xml │ │ │ ├── section.level1.properties.xml │ │ │ ├── section.level2.properties.xml │ │ │ ├── section.level3.properties.xml │ │ │ ├── section.level4.properties.xml │ │ │ ├── section.level5.properties.xml │ │ │ ├── section.level6.properties.xml │ │ │ ├── section.properties.xml │ │ │ ├── section.title.level1.properties.xml │ │ │ ├── section.title.level2.properties.xml │ │ │ ├── section.title.level3.properties.xml │ │ │ ├── section.title.level4.properties.xml │ │ │ ├── section.title.level5.properties.xml │ │ │ ├── section.title.level6.properties.xml │ │ │ ├── section.title.properties.xml │ │ │ ├── segmentedlist.as.table.xml │ │ │ ├── sequential.links.xml │ │ │ ├── shade.verbatim.style.xml │ │ │ ├── shade.verbatim.xml │ │ │ ├── show.bookmarks.xml │ │ │ ├── show.comments.xml │ │ │ ├── show.foil.number.xml │ │ │ ├── show.revisionflag.xml │ │ │ ├── showtoc.image.xml │ │ │ ├── side.float.properties.xml │ │ │ ├── side.region.precedence.xml │ │ │ ├── sidebar.float.type.xml │ │ │ ├── sidebar.float.width.xml │ │ │ ├── sidebar.properties.xml │ │ │ ├── sidebar.title.properties.xml │ │ │ ├── simplesect.in.toc.xml │ │ │ ├── slide.font.family.xml │ │ │ ├── slide.title.font.family.xml │ │ │ ├── slides.js.xml │ │ │ ├── slides.properties.xml │ │ │ ├── slides.titlepage.author.properties.xml │ │ │ ├── slides.titlepage.authorgroup.properties.xml │ │ │ ├── slides.titlepage.corpauthor.properties.xml │ │ │ ├── slides.titlepage.master.properties.xml │ │ │ ├── slides.titlepage.pubdate.properties.xml │ │ │ ├── slides.titlepage.region-body.properties.xml │ │ │ ├── slides.titlepage.subtitle.properties.xml │ │ │ ├── slides.titlepage.title.properties.xml │ │ │ ├── slidy.duration.xml │ │ │ ├── slidy.path.prefix.xml │ │ │ ├── slidy.slidy.css.xml │ │ │ ├── slidy.slidy.js.xml │ │ │ ├── slidy.user.css.xml │ │ │ ├── spacing.paras.xml │ │ │ ├── speaker.properties.xml │ │ │ ├── speakernote.properties.xml │ │ │ ├── speakernotes.properties.xml │ │ │ ├── stagedir.properties.xml │ │ │ ├── subscript.properties.xml │ │ │ ├── superscript.properties.xml │ │ │ ├── suppress.footer.navigation.xml │ │ │ ├── suppress.header.navigation.xml │ │ │ ├── suppress.homepage.title.xml │ │ │ ├── suppress.navigation.xml │ │ │ ├── svg.embedding.mode.fo.xml │ │ │ ├── svg.embedding.mode.xml │ │ │ ├── symbol.font.family.xml │ │ │ ├── table.borders.with.css.xml │ │ │ ├── table.caption.properties.xml │ │ │ ├── table.cell.border.color.xml │ │ │ ├── table.cell.border.style.xml │ │ │ ├── table.cell.border.thickness.xml │ │ │ ├── table.cell.padding.xml │ │ │ ├── table.entry.padding.xml │ │ │ ├── table.footnote.number.format.xml │ │ │ ├── table.footnote.number.symbols.xml │ │ │ ├── table.footnote.properties.xml │ │ │ ├── table.frame.border.color.xml │ │ │ ├── table.frame.border.style.xml │ │ │ ├── table.frame.border.thickness.xml │ │ │ ├── table.properties.xml │ │ │ ├── table.spacer.image.xml │ │ │ ├── table.table.properties.xml │ │ │ ├── tablecolumns.extension.xml │ │ │ ├── target.database.document.xml │ │ │ ├── targets.filename.xml │ │ │ ├── task.properties.xml │ │ │ ├── template.xml │ │ │ ├── tex.math.delims.xml │ │ │ ├── tex.math.file.xml │ │ │ ├── tex.math.in.alt.xml │ │ │ ├── text.home.xml │ │ │ ├── text.next.xml │ │ │ ├── text.prev.xml │ │ │ ├── text.toc.xml │ │ │ ├── text.up.xml │ │ │ ├── textbgcolor.xml │ │ │ ├── textdata.default.encoding.xml │ │ │ ├── textinsert.extension.xml │ │ │ ├── title.font.family.xml │ │ │ ├── title.margin.left.xml │ │ │ ├── titlefoil.html.xml │ │ │ ├── toc.bg.color.xml │ │ │ ├── toc.blank.graphic.xml │ │ │ ├── toc.blank.image.xml │ │ │ ├── toc.blank.text.xml │ │ │ ├── toc.hide.show.xml │ │ │ ├── toc.html.xml │ │ │ ├── toc.image.xml │ │ │ ├── toc.indent.width.xml │ │ │ ├── toc.leader.properties.xml │ │ │ ├── toc.line.properties.xml │ │ │ ├── toc.list.type.xml │ │ │ ├── toc.margin.properties.xml │ │ │ ├── toc.max.depth.xml │ │ │ ├── toc.pointer.graphic.xml │ │ │ ├── toc.pointer.image.xml │ │ │ ├── toc.pointer.text.xml │ │ │ ├── toc.row.height.xml │ │ │ ├── toc.section.depth.xml │ │ │ ├── toc.spacer.graphic.xml │ │ │ ├── toc.spacer.image.xml │ │ │ ├── toc.spacer.text.xml │ │ │ ├── toc.width.xml │ │ │ ├── ua.js.xml │ │ │ ├── ulink.footnotes.xml │ │ │ ├── ulink.hyphenate.chars.xml │ │ │ ├── ulink.hyphenate.xml │ │ │ ├── ulink.show.xml │ │ │ ├── ulink.target.xml │ │ │ ├── up.image.xml │ │ │ ├── use.embed.for.svg.xml │ │ │ ├── use.extensions.xml │ │ │ ├── use.id.as.filename.xml │ │ │ ├── use.id.function.xml │ │ │ ├── use.local.olink.style.xml │ │ │ ├── use.role.as.xrefstyle.xml │ │ │ ├── use.role.for.mediaobject.xml │ │ │ ├── use.svg.xml │ │ │ ├── user.css.xml │ │ │ ├── variablelist.as.blocks.xml │ │ │ ├── variablelist.as.table.xml │ │ │ ├── variablelist.max.termlength.xml │ │ │ ├── variablelist.term.break.after.xml │ │ │ ├── variablelist.term.properties.xml │ │ │ ├── variablelist.term.separator.xml │ │ │ ├── verbatim.properties.xml │ │ │ ├── webhelp.autolabel.xml │ │ │ ├── webhelp.base.dir.xml │ │ │ ├── webhelp.common.dir.xml │ │ │ ├── webhelp.default.topic.xml │ │ │ ├── webhelp.include.search.tab.xml │ │ │ ├── webhelp.indexer.language.xml │ │ │ ├── webhelp.start.filename.xml │ │ │ ├── webhelp.tree.cookie.id.xml │ │ │ ├── wordml.template.xml │ │ │ ├── wrap.slidecontent.xml │ │ │ ├── writing.mode.xml │ │ │ ├── xbCollapsibleLists.js.xml │ │ │ ├── xbDOM.js.xml │ │ │ ├── xbLibrary.js.xml │ │ │ ├── xbStyle.js.xml │ │ │ ├── xep.extensions.xml │ │ │ ├── xep.index.item.properties.xml │ │ │ ├── xref.label-page.separator.xml │ │ │ ├── xref.label-title.separator.xml │ │ │ ├── xref.properties.xml │ │ │ ├── xref.title-page.separator.xml │ │ │ ├── xref.with.number.and.title.xml │ │ │ └── xsl1.1.bookmarks.xml │ │ ├── profiling │ │ │ ├── profile-mode.xsl │ │ │ ├── profile.xsl │ │ │ ├── strip-attributes.xsl │ │ │ └── xsl2profile.xsl │ │ ├── roundtrip │ │ │ ├── blocks-spec.xml │ │ │ ├── blocks2dbk.dtd │ │ │ ├── blocks2dbk.xsl │ │ │ ├── dbk2ooo.xsl │ │ │ ├── dbk2pages.xsl │ │ │ ├── dbk2wordml.xsl │ │ │ ├── dbk2wp.xsl │ │ │ ├── normalise-common.xsl │ │ │ ├── normalise2sections.xsl │ │ │ ├── pages2normalise.xsl │ │ │ ├── param.xml │ │ │ ├── param.xsl │ │ │ ├── sections-spec.xml │ │ │ ├── sections2blocks.xsl │ │ │ ├── specifications.xml │ │ │ ├── template-pages.xml │ │ │ ├── template.xml │ │ │ └── wordml2normalise.xsl │ │ ├── slides │ │ │ ├── README │ │ │ ├── RELEASE-NOTES.xml │ │ │ ├── common │ │ │ │ └── common.xsl │ │ │ ├── doc │ │ │ │ ├── slides.xml │ │ │ │ └── user.css │ │ │ ├── fo │ │ │ │ ├── param.xml │ │ │ │ ├── param.xsl │ │ │ │ ├── plain-titlepage.xml │ │ │ │ ├── plain-titlepage.xsl │ │ │ │ └── plain.xsl │ │ │ ├── images │ │ │ │ ├── callouts │ │ │ │ │ ├── 1.png │ │ │ │ │ ├── 1.svg │ │ │ │ │ ├── 10.png │ │ │ │ │ ├── 10.svg │ │ │ │ │ ├── 11.png │ │ │ │ │ ├── 11.svg │ │ │ │ │ ├── 12.png │ │ │ │ │ ├── 12.svg │ │ │ │ │ ├── 13.png │ │ │ │ │ ├── 13.svg │ │ │ │ │ ├── 14.png │ │ │ │ │ ├── 14.svg │ │ │ │ │ ├── 15.png │ │ │ │ │ ├── 15.svg │ │ │ │ │ ├── 16.png │ │ │ │ │ ├── 16.svg │ │ │ │ │ ├── 17.png │ │ │ │ │ ├── 17.svg │ │ │ │ │ ├── 18.png │ │ │ │ │ ├── 18.svg │ │ │ │ │ ├── 19.png │ │ │ │ │ ├── 19.svg │ │ │ │ │ ├── 2.png │ │ │ │ │ ├── 2.svg │ │ │ │ │ ├── 20.png │ │ │ │ │ ├── 20.svg │ │ │ │ │ ├── 21.png │ │ │ │ │ ├── 21.svg │ │ │ │ │ ├── 22.png │ │ │ │ │ ├── 22.svg │ │ │ │ │ ├── 23.png │ │ │ │ │ ├── 23.svg │ │ │ │ │ ├── 24.png │ │ │ │ │ ├── 24.svg │ │ │ │ │ ├── 25.png │ │ │ │ │ ├── 25.svg │ │ │ │ │ ├── 26.png │ │ │ │ │ ├── 26.svg │ │ │ │ │ ├── 27.png │ │ │ │ │ ├── 27.svg │ │ │ │ │ ├── 28.png │ │ │ │ │ ├── 28.svg │ │ │ │ │ ├── 29.png │ │ │ │ │ ├── 29.svg │ │ │ │ │ ├── 3.png │ │ │ │ │ ├── 3.svg │ │ │ │ │ ├── 30.png │ │ │ │ │ ├── 30.svg │ │ │ │ │ ├── 4.png │ │ │ │ │ ├── 4.svg │ │ │ │ │ ├── 5.png │ │ │ │ │ ├── 5.svg │ │ │ │ │ ├── 6.png │ │ │ │ │ ├── 6.svg │ │ │ │ │ ├── 7.png │ │ │ │ │ ├── 7.svg │ │ │ │ │ ├── 8.png │ │ │ │ │ ├── 8.svg │ │ │ │ │ ├── 9.png │ │ │ │ │ ├── 9.svg │ │ │ │ │ └── gen.sh │ │ │ │ ├── face1.gif │ │ │ │ ├── face2.gif │ │ │ │ ├── face3.gif │ │ │ │ └── face4.gif │ │ │ ├── locatingrules.xml │ │ │ ├── s5 │ │ │ │ ├── index-osf.html │ │ │ │ ├── index-xoxo.html │ │ │ │ ├── pix │ │ │ │ │ ├── S501.jpg │ │ │ │ │ ├── S502.jpg │ │ │ │ │ ├── S503.jpg │ │ │ │ │ ├── S504.jpg │ │ │ │ │ ├── mememe01.png │ │ │ │ │ ├── mememe02.png │ │ │ │ │ ├── mememe03.png │ │ │ │ │ ├── mememe04.png │ │ │ │ │ ├── mememe05.png │ │ │ │ │ └── s5filemap.png │ │ │ │ └── ui │ │ │ │ │ ├── bg-shade.png │ │ │ │ │ ├── default │ │ │ │ │ ├── blank.gif │ │ │ │ │ ├── bodybg.gif │ │ │ │ │ ├── framing.css │ │ │ │ │ ├── iepngfix.htc │ │ │ │ │ ├── notes.css │ │ │ │ │ ├── opera.css │ │ │ │ │ ├── outline.css │ │ │ │ │ ├── pretty.css │ │ │ │ │ ├── print.css │ │ │ │ │ ├── s5-core.css │ │ │ │ │ ├── slides.css │ │ │ │ │ └── slides.js │ │ │ │ │ └── s5-notes.html │ │ │ ├── schema │ │ │ │ ├── relaxng │ │ │ │ │ ├── admonitions.rng │ │ │ │ │ ├── annotations.rng │ │ │ │ │ ├── bibliography.rng │ │ │ │ │ ├── callouts.rng │ │ │ │ │ ├── calstbl.rng │ │ │ │ │ ├── core.rng │ │ │ │ │ ├── docbook.rng │ │ │ │ │ ├── docbook1.rng │ │ │ │ │ ├── ebnf.rng │ │ │ │ │ ├── error.rng │ │ │ │ │ ├── glossary.rng │ │ │ │ │ ├── gui.rng │ │ │ │ │ ├── hier.rng │ │ │ │ │ ├── htmltbl.rng │ │ │ │ │ ├── index.rng │ │ │ │ │ ├── keyboard.rng │ │ │ │ │ ├── markup.rng │ │ │ │ │ ├── math.rng │ │ │ │ │ ├── mathml.rng │ │ │ │ │ ├── msgset.rng │ │ │ │ │ ├── os.rng │ │ │ │ │ ├── pool.rng │ │ │ │ │ ├── product.rng │ │ │ │ │ ├── programming.rng │ │ │ │ │ ├── qandaset.rng │ │ │ │ │ ├── refentry.rng │ │ │ │ │ ├── refsect1.rng │ │ │ │ │ ├── sect1.rng │ │ │ │ │ ├── slides.rnc │ │ │ │ │ ├── slides.rng │ │ │ │ │ ├── svg.rng │ │ │ │ │ ├── tasks.rng │ │ │ │ │ ├── technical.rng │ │ │ │ │ ├── toc.rng │ │ │ │ │ ├── topic.rng │ │ │ │ │ └── xlink.rng │ │ │ │ └── xsd │ │ │ │ │ ├── admonitions.xsd │ │ │ │ │ ├── annotations.xsd │ │ │ │ │ ├── bibliography.xsd │ │ │ │ │ ├── callouts.xsd │ │ │ │ │ ├── calstbl.xsd │ │ │ │ │ ├── core.xsd │ │ │ │ │ ├── db.xsd │ │ │ │ │ ├── docbook.xsd │ │ │ │ │ ├── docbook1.xsd │ │ │ │ │ ├── ebnf.xsd │ │ │ │ │ ├── error.xsd │ │ │ │ │ ├── glossary.xsd │ │ │ │ │ ├── gui.xsd │ │ │ │ │ ├── hier.xsd │ │ │ │ │ ├── htmltbl.xsd │ │ │ │ │ ├── index.xsd │ │ │ │ │ ├── keyboard.xsd │ │ │ │ │ ├── markup.xsd │ │ │ │ │ ├── math.xsd │ │ │ │ │ ├── mathml.xsd │ │ │ │ │ ├── msgset.xsd │ │ │ │ │ ├── os.xsd │ │ │ │ │ ├── pool.xsd │ │ │ │ │ ├── product.xsd │ │ │ │ │ ├── programming.xsd │ │ │ │ │ ├── qandaset.xsd │ │ │ │ │ ├── refentry.xsd │ │ │ │ │ ├── refsect1.xsd │ │ │ │ │ ├── sect1.xsd │ │ │ │ │ ├── slides.xsd │ │ │ │ │ ├── svg.xsd │ │ │ │ │ ├── tasks.xsd │ │ │ │ │ ├── technical.xsd │ │ │ │ │ ├── toc.xsd │ │ │ │ │ ├── topic.xsd │ │ │ │ │ ├── xlink.xsd │ │ │ │ │ ├── xlink1.xsd │ │ │ │ │ └── xml.xsd │ │ │ ├── slidy │ │ │ │ ├── .htaccess │ │ │ │ ├── Overview.html │ │ │ │ ├── Overview.xhtml │ │ │ │ ├── blank.html │ │ │ │ ├── graphics │ │ │ │ │ ├── bullet-fold-dim.gif │ │ │ │ │ ├── bullet-fold-dim.png │ │ │ │ │ ├── bullet-fold.gif │ │ │ │ │ ├── bullet-fold.png │ │ │ │ │ ├── bullet-nofold-dim.gif │ │ │ │ │ ├── bullet-nofold-dim.png │ │ │ │ │ ├── bullet-nofold.gif │ │ │ │ │ ├── bullet-nofold.png │ │ │ │ │ ├── bullet-unfold-dim.gif │ │ │ │ │ ├── bullet-unfold-dim.png │ │ │ │ │ ├── bullet-unfold.gif │ │ │ │ │ ├── bullet-unfold.png │ │ │ │ │ ├── bullet.png │ │ │ │ │ ├── example.png │ │ │ │ │ ├── example.svg │ │ │ │ │ ├── face1.gif │ │ │ │ │ ├── face2.gif │ │ │ │ │ ├── face3.gif │ │ │ │ │ ├── face4.gif │ │ │ │ │ ├── fold-bright.gif │ │ │ │ │ ├── fold-dim.bmp │ │ │ │ │ ├── fold-dim.gif │ │ │ │ │ ├── fold.bmp │ │ │ │ │ ├── fold.gif │ │ │ │ │ ├── icon-blue.png │ │ │ │ │ ├── keys2.jpg │ │ │ │ │ ├── nofold-dim.bmp │ │ │ │ │ ├── nofold-dim.gif │ │ │ │ │ ├── nofold.bmp │ │ │ │ │ ├── unfold-bright.gif │ │ │ │ │ ├── unfold-dim.bmp │ │ │ │ │ ├── unfold-dim.gif │ │ │ │ │ ├── unfold.bmp │ │ │ │ │ ├── unfold.gif │ │ │ │ │ ├── w3c-logo-blue.gif │ │ │ │ │ ├── w3c-logo-blue.svg │ │ │ │ │ ├── w3c-logo-slanted.jpg │ │ │ │ │ ├── w3c-logo-white.gif │ │ │ │ │ └── w3c-logo-white.svg │ │ │ │ ├── help │ │ │ │ │ ├── .htaccess │ │ │ │ │ ├── help.html │ │ │ │ │ ├── help.html.ca │ │ │ │ │ ├── help.html.de │ │ │ │ │ ├── help.html.en │ │ │ │ │ ├── help.html.es │ │ │ │ │ ├── help.html.fr │ │ │ │ │ ├── help.html.hu │ │ │ │ │ ├── help.html.nl │ │ │ │ │ ├── help.html.pl │ │ │ │ │ ├── help.html.pt-br │ │ │ │ │ ├── help.html.pt_br │ │ │ │ │ ├── help.html.sv │ │ │ │ │ └── help.pt-br.html │ │ │ │ ├── scripts │ │ │ │ │ ├── .htaccess │ │ │ │ │ ├── slidy.js │ │ │ │ │ └── slidy.js.gz │ │ │ │ └── styles │ │ │ │ │ ├── .htaccess │ │ │ │ │ ├── slidy.css │ │ │ │ │ └── w3c-blue.css │ │ │ ├── tools │ │ │ │ └── dbs3-upgrade.xsl │ │ │ └── xhtml │ │ │ │ ├── param.xml │ │ │ │ ├── param.xsl │ │ │ │ ├── plain-titlepage.xml │ │ │ │ ├── plain-titlepage.xsl │ │ │ │ ├── plain.xsl │ │ │ │ ├── s5.xsl │ │ │ │ └── slidy.xsl │ │ ├── template │ │ │ ├── titlepage.xml │ │ │ └── titlepage.xsl │ │ ├── tests │ │ │ ├── refentry.007.ns.xml │ │ │ └── refentry.007.xml │ │ ├── tools │ │ │ ├── bin │ │ │ │ └── docbook-xsl-update │ │ │ ├── build-shared.xml │ │ │ ├── lib │ │ │ │ ├── ant-contrib-1.0b3.jar │ │ │ │ ├── calabash.jar │ │ │ │ ├── commons-codec-1.3.jar │ │ │ │ ├── commons-httpclient-3.1.jar │ │ │ │ ├── commons-logging-1.1.1.jar │ │ │ │ ├── isorelax.jar │ │ │ │ ├── jing.jar │ │ │ │ ├── jython.jar │ │ │ │ ├── saxon.jar │ │ │ │ ├── saxon9-ant.jar │ │ │ │ ├── saxon9he.jar │ │ │ │ ├── xalan.jar │ │ │ │ ├── xercesImpl.jar │ │ │ │ ├── xml-apis.jar │ │ │ │ └── xmlresolver.jar │ │ │ ├── licenses │ │ │ │ ├── jing │ │ │ │ │ ├── copying.html │ │ │ │ │ ├── isorelax.copying.txt │ │ │ │ │ └── xerces.copying.txt │ │ │ │ └── saxon │ │ │ │ │ ├── CERN.txt │ │ │ │ │ ├── JAMESCLARK.txt │ │ │ │ │ ├── LEGAL.txt │ │ │ │ │ ├── LICENSE.txt │ │ │ │ │ ├── THAI.txt │ │ │ │ │ └── UNICODE.txt │ │ │ └── make │ │ │ │ ├── Makefile.DocBook │ │ │ │ ├── Makefile.combine │ │ │ │ └── Makefile.docParam │ │ ├── webhelp │ │ │ ├── LICENSE │ │ │ ├── Makefile.sample │ │ │ ├── build.properties │ │ │ ├── build.xml │ │ │ ├── docs │ │ │ │ ├── ch01.html │ │ │ │ ├── ch02.html │ │ │ │ ├── ch02s01.html │ │ │ │ ├── ch02s02.html │ │ │ │ ├── ch02s02s01.html │ │ │ │ ├── ch02s03.html │ │ │ │ ├── ch02s04.html │ │ │ │ ├── ch02s05.html │ │ │ │ ├── ch03.html │ │ │ │ ├── ch03s01.html │ │ │ │ ├── ch03s02.html │ │ │ │ ├── ch03s02s01.html │ │ │ │ ├── ch04.html │ │ │ │ ├── ch05.html │ │ │ │ ├── ch05s01.html │ │ │ │ ├── ch05s02.html │ │ │ │ ├── common │ │ │ │ │ ├── browserDetect.js │ │ │ │ │ ├── css │ │ │ │ │ │ ├── ie.css │ │ │ │ │ │ └── positioning.css │ │ │ │ │ ├── images │ │ │ │ │ │ ├── admon │ │ │ │ │ │ │ ├── caution.png │ │ │ │ │ │ │ ├── important.png │ │ │ │ │ │ │ ├── note.png │ │ │ │ │ │ │ ├── tip.png │ │ │ │ │ │ │ └── warning.png │ │ │ │ │ │ ├── callouts │ │ │ │ │ │ │ ├── 1.png │ │ │ │ │ │ │ ├── 10.png │ │ │ │ │ │ │ ├── 11.png │ │ │ │ │ │ │ ├── 12.png │ │ │ │ │ │ │ ├── 13.png │ │ │ │ │ │ │ ├── 14.png │ │ │ │ │ │ │ ├── 15.png │ │ │ │ │ │ │ ├── 16.png │ │ │ │ │ │ │ ├── 17.png │ │ │ │ │ │ │ ├── 18.png │ │ │ │ │ │ │ ├── 19.png │ │ │ │ │ │ │ ├── 2.png │ │ │ │ │ │ │ ├── 20.png │ │ │ │ │ │ │ ├── 21.png │ │ │ │ │ │ │ ├── 22.png │ │ │ │ │ │ │ ├── 23.png │ │ │ │ │ │ │ ├── 24.png │ │ │ │ │ │ │ ├── 25.png │ │ │ │ │ │ │ ├── 26.png │ │ │ │ │ │ │ ├── 27.png │ │ │ │ │ │ │ ├── 28.png │ │ │ │ │ │ │ ├── 29.png │ │ │ │ │ │ │ ├── 3.png │ │ │ │ │ │ │ ├── 30.png │ │ │ │ │ │ │ ├── 4.png │ │ │ │ │ │ │ ├── 5.png │ │ │ │ │ │ │ ├── 6.png │ │ │ │ │ │ │ ├── 7.png │ │ │ │ │ │ │ ├── 8.png │ │ │ │ │ │ │ └── 9.png │ │ │ │ │ │ ├── header-bg.gif │ │ │ │ │ │ ├── header-bg.png │ │ │ │ │ │ ├── highlight-blue.gif │ │ │ │ │ │ ├── highlight-yellow.gif │ │ │ │ │ │ ├── loading.gif │ │ │ │ │ │ ├── logo.png │ │ │ │ │ │ ├── next-arrow.png │ │ │ │ │ │ ├── previous-arrow.png │ │ │ │ │ │ ├── search-icon.png │ │ │ │ │ │ ├── showHideTreeIcons.png │ │ │ │ │ │ ├── sidebar.png │ │ │ │ │ │ ├── starsSmall.png │ │ │ │ │ │ └── toc-icon.png │ │ │ │ │ ├── jquery │ │ │ │ │ │ ├── jquery-1.7.2.min.js │ │ │ │ │ │ ├── jquery-ui-1.8.2.custom.min.js │ │ │ │ │ │ ├── jquery.cookie.js │ │ │ │ │ │ ├── jquery.ui.all.js │ │ │ │ │ │ ├── layout │ │ │ │ │ │ │ └── jquery.layout.js │ │ │ │ │ │ ├── theme-redmond │ │ │ │ │ │ │ ├── images │ │ │ │ │ │ │ │ ├── ui-anim_basic_16x16.gif │ │ │ │ │ │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ │ │ │ │ │ ├── ui-bg_flat_55_fbec88_40x100.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_75_d0e5f5_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_85_dfeffc_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_95_fef1ec_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_gloss-wave_55_5c9ccc_500x100.png │ │ │ │ │ │ │ │ ├── ui-bg_inset-hard_100_f5f8f9_1x100.png │ │ │ │ │ │ │ │ ├── ui-bg_inset-hard_100_fcfdfd_1x100.png │ │ │ │ │ │ │ │ ├── ui-icons_217bc0_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_469bdd_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_6da8d5_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_cd0a0a_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_d8e7f3_256x240.png │ │ │ │ │ │ │ │ └── ui-icons_f9bd01_256x240.png │ │ │ │ │ │ │ ├── jquery-ui-1.8.2.custom.css │ │ │ │ │ │ │ └── jquery-ui-1.8.21.custom.css │ │ │ │ │ │ └── treeview │ │ │ │ │ │ │ ├── images │ │ │ │ │ │ │ ├── file.gif │ │ │ │ │ │ │ ├── folder-closed.gif │ │ │ │ │ │ │ ├── folder-closed2.gif │ │ │ │ │ │ │ ├── folder.gif │ │ │ │ │ │ │ ├── folder2.gif │ │ │ │ │ │ │ ├── minus.gif │ │ │ │ │ │ │ ├── plus.gif │ │ │ │ │ │ │ ├── treeview-black-line.gif │ │ │ │ │ │ │ ├── treeview-black.gif │ │ │ │ │ │ │ ├── treeview-default-line.gif │ │ │ │ │ │ │ ├── treeview-default.gif │ │ │ │ │ │ │ ├── treeview-famfamfam-line.gif │ │ │ │ │ │ │ ├── treeview-famfamfam.gif │ │ │ │ │ │ │ ├── treeview-gray-line.gif │ │ │ │ │ │ │ ├── treeview-gray.gif │ │ │ │ │ │ │ ├── treeview-red-line.gif │ │ │ │ │ │ │ └── treeview-red.gif │ │ │ │ │ │ │ ├── jquery.treeview.css │ │ │ │ │ │ │ └── jquery.treeview.min.js │ │ │ │ │ ├── main.js │ │ │ │ │ └── splitterInit.js │ │ │ │ ├── favicon.ico │ │ │ │ ├── images │ │ │ │ │ └── sample.jpg │ │ │ │ ├── index.html │ │ │ │ ├── ix01.html │ │ │ │ └── search │ │ │ │ │ ├── default.props │ │ │ │ │ ├── en-us.props │ │ │ │ │ ├── es-es.props │ │ │ │ │ ├── htmlFileInfoList.js │ │ │ │ │ ├── index-1.js │ │ │ │ │ ├── index-2.js │ │ │ │ │ ├── index-3.js │ │ │ │ │ ├── ja-jp.props │ │ │ │ │ ├── l10n.js │ │ │ │ │ ├── nwSearchFnt.js │ │ │ │ │ ├── punctuation.props │ │ │ │ │ └── stemmers │ │ │ │ │ ├── de_stemmer.js │ │ │ │ │ ├── en_stemmer.js │ │ │ │ │ └── fr_stemmer.js │ │ │ ├── docsrc │ │ │ │ ├── images │ │ │ │ │ └── sample.jpg │ │ │ │ ├── readme.xml │ │ │ │ └── xinclude-test.xml │ │ │ ├── template │ │ │ │ ├── common │ │ │ │ │ ├── browserDetect.js │ │ │ │ │ ├── css │ │ │ │ │ │ ├── ie.css │ │ │ │ │ │ └── positioning.css │ │ │ │ │ ├── images │ │ │ │ │ │ ├── admon │ │ │ │ │ │ │ ├── caution.png │ │ │ │ │ │ │ ├── important.png │ │ │ │ │ │ │ ├── note.png │ │ │ │ │ │ │ ├── tip.png │ │ │ │ │ │ │ └── warning.png │ │ │ │ │ │ ├── callouts │ │ │ │ │ │ │ ├── 1.png │ │ │ │ │ │ │ ├── 10.png │ │ │ │ │ │ │ ├── 11.png │ │ │ │ │ │ │ ├── 12.png │ │ │ │ │ │ │ ├── 13.png │ │ │ │ │ │ │ ├── 14.png │ │ │ │ │ │ │ ├── 15.png │ │ │ │ │ │ │ ├── 16.png │ │ │ │ │ │ │ ├── 17.png │ │ │ │ │ │ │ ├── 18.png │ │ │ │ │ │ │ ├── 19.png │ │ │ │ │ │ │ ├── 2.png │ │ │ │ │ │ │ ├── 20.png │ │ │ │ │ │ │ ├── 21.png │ │ │ │ │ │ │ ├── 22.png │ │ │ │ │ │ │ ├── 23.png │ │ │ │ │ │ │ ├── 24.png │ │ │ │ │ │ │ ├── 25.png │ │ │ │ │ │ │ ├── 26.png │ │ │ │ │ │ │ ├── 27.png │ │ │ │ │ │ │ ├── 28.png │ │ │ │ │ │ │ ├── 29.png │ │ │ │ │ │ │ ├── 3.png │ │ │ │ │ │ │ ├── 30.png │ │ │ │ │ │ │ ├── 4.png │ │ │ │ │ │ │ ├── 5.png │ │ │ │ │ │ │ ├── 6.png │ │ │ │ │ │ │ ├── 7.png │ │ │ │ │ │ │ ├── 8.png │ │ │ │ │ │ │ └── 9.png │ │ │ │ │ │ ├── header-bg.gif │ │ │ │ │ │ ├── header-bg.png │ │ │ │ │ │ ├── highlight-blue.gif │ │ │ │ │ │ ├── highlight-yellow.gif │ │ │ │ │ │ ├── loading.gif │ │ │ │ │ │ ├── logo.png │ │ │ │ │ │ ├── next-arrow.png │ │ │ │ │ │ ├── previous-arrow.png │ │ │ │ │ │ ├── search-icon.png │ │ │ │ │ │ ├── showHideTreeIcons.png │ │ │ │ │ │ ├── sidebar.png │ │ │ │ │ │ ├── starsSmall.png │ │ │ │ │ │ └── toc-icon.png │ │ │ │ │ ├── jquery │ │ │ │ │ │ ├── jquery-1.7.2.min.js │ │ │ │ │ │ ├── jquery-ui-1.8.2.custom.min.js │ │ │ │ │ │ ├── jquery.cookie.js │ │ │ │ │ │ ├── jquery.ui.all.js │ │ │ │ │ │ ├── layout │ │ │ │ │ │ │ └── jquery.layout.js │ │ │ │ │ │ ├── theme-redmond │ │ │ │ │ │ │ ├── images │ │ │ │ │ │ │ │ ├── ui-anim_basic_16x16.gif │ │ │ │ │ │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ │ │ │ │ │ ├── ui-bg_flat_55_fbec88_40x100.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_75_d0e5f5_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_85_dfeffc_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_95_fef1ec_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_gloss-wave_55_5c9ccc_500x100.png │ │ │ │ │ │ │ │ ├── ui-bg_inset-hard_100_f5f8f9_1x100.png │ │ │ │ │ │ │ │ ├── ui-bg_inset-hard_100_fcfdfd_1x100.png │ │ │ │ │ │ │ │ ├── ui-icons_217bc0_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_469bdd_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_6da8d5_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_cd0a0a_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_d8e7f3_256x240.png │ │ │ │ │ │ │ │ └── ui-icons_f9bd01_256x240.png │ │ │ │ │ │ │ ├── jquery-ui-1.8.2.custom.css │ │ │ │ │ │ │ └── jquery-ui-1.8.21.custom.css │ │ │ │ │ │ └── treeview │ │ │ │ │ │ │ ├── images │ │ │ │ │ │ │ ├── file.gif │ │ │ │ │ │ │ ├── folder-closed.gif │ │ │ │ │ │ │ ├── folder-closed2.gif │ │ │ │ │ │ │ ├── folder.gif │ │ │ │ │ │ │ ├── folder2.gif │ │ │ │ │ │ │ ├── minus.gif │ │ │ │ │ │ │ ├── plus.gif │ │ │ │ │ │ │ ├── treeview-black-line.gif │ │ │ │ │ │ │ ├── treeview-black.gif │ │ │ │ │ │ │ ├── treeview-default-line.gif │ │ │ │ │ │ │ ├── treeview-default.gif │ │ │ │ │ │ │ ├── treeview-famfamfam-line.gif │ │ │ │ │ │ │ ├── treeview-famfamfam.gif │ │ │ │ │ │ │ ├── treeview-gray-line.gif │ │ │ │ │ │ │ ├── treeview-gray.gif │ │ │ │ │ │ │ ├── treeview-red-line.gif │ │ │ │ │ │ │ └── treeview-red.gif │ │ │ │ │ │ │ ├── jquery.treeview.css │ │ │ │ │ │ │ └── jquery.treeview.min.js │ │ │ │ │ ├── main.js │ │ │ │ │ └── splitterInit.js │ │ │ │ ├── favicon.ico │ │ │ │ └── search │ │ │ │ │ ├── default.props │ │ │ │ │ ├── en-us.props │ │ │ │ │ ├── es-es.props │ │ │ │ │ ├── ja-jp.props │ │ │ │ │ ├── nwSearchFnt.js │ │ │ │ │ ├── punctuation.props │ │ │ │ │ └── stemmers │ │ │ │ │ ├── de_stemmer.js │ │ │ │ │ ├── en_stemmer.js │ │ │ │ │ └── fr_stemmer.js │ │ │ └── xsl │ │ │ │ ├── titlepage.templates.xml │ │ │ │ ├── titlepage.templates.xsl │ │ │ │ ├── webhelp-common.xsl │ │ │ │ └── webhelp.xsl │ │ ├── website │ │ │ ├── autolayout.xsl │ │ │ ├── build.xml │ │ │ ├── chunk-common.xsl │ │ │ ├── chunk-tabular.xsl │ │ │ ├── chunk-website.xsl │ │ │ ├── head.xsl │ │ │ ├── makefile-dep.xsl │ │ │ ├── olink.xsl │ │ │ ├── param.xml │ │ │ ├── param.xsl │ │ │ ├── rss.xsl │ │ │ ├── tabular.xsl │ │ │ ├── toc-tabular.xsl │ │ │ ├── toc.xsl │ │ │ ├── website-common.xsl │ │ │ ├── website-targets.xsl │ │ │ ├── website.xsl │ │ │ └── xbel.xsl │ │ ├── xhtml-1_1 │ │ │ ├── admon.xsl │ │ │ ├── annotations.xsl │ │ │ ├── autoidx-kimber.xsl │ │ │ ├── autoidx-kosek.xsl │ │ │ ├── autoidx-ng.xsl │ │ │ ├── autoidx.xsl │ │ │ ├── autotoc.xsl │ │ │ ├── biblio-iso690.xsl │ │ │ ├── biblio.xsl │ │ │ ├── block.xsl │ │ │ ├── build.xml │ │ │ ├── callout.xsl │ │ │ ├── changebars.xsl │ │ │ ├── chunk-changebars.xsl │ │ │ ├── chunk-code.xsl │ │ │ ├── chunk-common.xsl │ │ │ ├── chunk.xsl │ │ │ ├── chunker.xsl │ │ │ ├── chunkfast.xsl │ │ │ ├── chunktoc.xsl │ │ │ ├── component.xsl │ │ │ ├── division.xsl │ │ │ ├── docbook.css.xml │ │ │ ├── docbook.xsl │ │ │ ├── ebnf.xsl │ │ │ ├── footnote.xsl │ │ │ ├── formal.xsl │ │ │ ├── glossary.xsl │ │ │ ├── graphics.xsl │ │ │ ├── highlight.xsl │ │ │ ├── html-rtf.xsl │ │ │ ├── html.xsl │ │ │ ├── htmltbl.xsl │ │ │ ├── index.xsl │ │ │ ├── info.xsl │ │ │ ├── inline.xsl │ │ │ ├── its.xsl │ │ │ ├── keywords.xsl │ │ │ ├── lists.xsl │ │ │ ├── maketoc.xsl │ │ │ ├── manifest.xsl │ │ │ ├── math.xsl │ │ │ ├── oldchunker.xsl │ │ │ ├── onechunk.xsl │ │ │ ├── param.xsl │ │ │ ├── pi.xsl │ │ │ ├── profile-chunk-code.xsl │ │ │ ├── profile-chunk.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── profile-onechunk.xsl │ │ │ ├── publishers.xsl │ │ │ ├── qandaset.xsl │ │ │ ├── refentry.xsl │ │ │ ├── sections.xsl │ │ │ ├── synop.xsl │ │ │ ├── table.xsl │ │ │ ├── task.xsl │ │ │ ├── titlepage.templates.xsl │ │ │ ├── titlepage.xsl │ │ │ ├── toc.xsl │ │ │ ├── verbatim.xsl │ │ │ └── xref.xsl │ │ ├── xhtml │ │ │ ├── admon.xsl │ │ │ ├── annotations.xsl │ │ │ ├── autoidx-kimber.xsl │ │ │ ├── autoidx-kosek.xsl │ │ │ ├── autoidx-ng.xsl │ │ │ ├── autoidx.xsl │ │ │ ├── autotoc.xsl │ │ │ ├── biblio-iso690.xsl │ │ │ ├── biblio.xsl │ │ │ ├── block.xsl │ │ │ ├── build.xml │ │ │ ├── callout.xsl │ │ │ ├── changebars.xsl │ │ │ ├── chunk-changebars.xsl │ │ │ ├── chunk-code.xsl │ │ │ ├── chunk-common.xsl │ │ │ ├── chunk.xsl │ │ │ ├── chunker.xsl │ │ │ ├── chunkfast.xsl │ │ │ ├── chunktoc.xsl │ │ │ ├── component.xsl │ │ │ ├── division.xsl │ │ │ ├── docbook-no-doctype.xsl │ │ │ ├── docbook.css.xml │ │ │ ├── docbook.xsl │ │ │ ├── ebnf.xsl │ │ │ ├── footnote.xsl │ │ │ ├── formal.xsl │ │ │ ├── glossary.xsl │ │ │ ├── graphics.xsl │ │ │ ├── highlight.xsl │ │ │ ├── html-rtf.xsl │ │ │ ├── html.xsl │ │ │ ├── htmltbl.xsl │ │ │ ├── index.xsl │ │ │ ├── info.xsl │ │ │ ├── inline.xsl │ │ │ ├── its.xsl │ │ │ ├── keywords.xsl │ │ │ ├── lists.xsl │ │ │ ├── maketoc.xsl │ │ │ ├── manifest.xsl │ │ │ ├── math.xsl │ │ │ ├── oldchunker.xsl │ │ │ ├── onechunk.xsl │ │ │ ├── param.xsl │ │ │ ├── pi.xsl │ │ │ ├── profile-chunk-code.xsl │ │ │ ├── profile-chunk.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── profile-onechunk.xsl │ │ │ ├── publishers.xsl │ │ │ ├── qandaset.xsl │ │ │ ├── refentry.xsl │ │ │ ├── sections.xsl │ │ │ ├── synop.xsl │ │ │ ├── table.xsl │ │ │ ├── task.xsl │ │ │ ├── titlepage.templates.xml │ │ │ ├── titlepage.templates.xsl │ │ │ ├── titlepage.xsl │ │ │ ├── toc.xsl │ │ │ ├── verbatim.xsl │ │ │ └── xref.xsl │ │ └── xhtml5 │ │ │ ├── README │ │ │ ├── build.xml │ │ │ ├── chunk.xsl │ │ │ ├── chunkfast.xsl │ │ │ ├── docbook.css.xml │ │ │ ├── docbook.xsl │ │ │ ├── html5-chunk-mods.xsl │ │ │ ├── html5-element-mods.xsl │ │ │ ├── onechunk.xsl │ │ │ ├── profile-chunk.xsl │ │ │ ├── profile-docbook.xsl │ │ │ ├── xhtml-docbook.xsl │ │ │ ├── xhtml-profile-docbook.xsl │ │ │ └── xhtml2xhtml5.xsl │ │ ├── table_extraction.xsl │ │ └── text_extraction.xsl │ ├── _data_extraction.py │ ├── _download.py │ ├── _entrez.py │ ├── _fit_neuroquery.py │ ├── _fit_neurosynth.py │ ├── _img_utils.py │ ├── _labelbuddy.py │ ├── _links.py │ ├── _metadata.py │ ├── _model_data.py │ ├── _nimare.py │ ├── _pipeline.py │ ├── _plugins.py │ ├── _table_info.py │ ├── _text.py │ ├── _typing.py │ ├── _utils.py │ ├── _vectorization.py │ ├── _vocabulary.py │ └── _writers.py ├── tests ├── compare_query_vs_pmcid_list.py ├── conftest.py ├── data │ ├── articleset.xml │ ├── make_test_data.py │ ├── text.csv │ ├── vocabulary.csv │ └── vocabulary.csv_voc_mapping_identity.json ├── run_full_pipeline.py ├── test_articles.py ├── test_commands.py ├── test_coordinate_space.py ├── test_coordinates.py ├── test_data_extraction.py ├── test_download.py ├── test_entrez.py ├── test_fit_neuroquery.py ├── test_fit_neurosynth.py ├── test_img_utils.py ├── test_labelbuddy.py ├── test_links.py ├── test_metadata.py ├── test_nimare.py ├── test_pipeline.py ├── test_text.py ├── test_utils.py ├── test_vectorization.py ├── test_vocabulary.py └── test_writers.py ├── tox.ini └── whats_new.md /.flake8: -------------------------------------------------------------------------------- 1 | [flake8] 2 | extend-ignore = E203 -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | src/pubget/_data/stylesheets/docbook/** linguist-vendored 2 | -------------------------------------------------------------------------------- /docs/example_plugin/README.md: -------------------------------------------------------------------------------- 1 | # Example pubget plugin 2 | 3 | This is a plugin that does not do much (it plots the number of downloaded 4 | articles per publication year) to illustrate how to write a plugin and make it 5 | discoverable by pubget, and to be used as a template. 6 | 7 | Plugins are discovered through the `pubget.plugin_actions` entry point 8 | (see the [setuptools documentation on entry 9 | points](https://setuptools.pypa.io/en/latest/userguide/entry_point.html#entry-points-for-plugins)). 10 | 11 | It is defined in the `get_pubget_actions` function (see 12 | `src/pubget_example_plugin/__init__.py`), which is referenced in the 13 | `[options.entry_points]` section of `setup.cfg`. This allows our plugin to be 14 | invoked through the `pubget` command and run as if it were a part of `pubget` 15 | itself. 16 | -------------------------------------------------------------------------------- /docs/example_plugin/pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools", "wheel"] 3 | build-backend = "setuptools.build_meta" 4 | -------------------------------------------------------------------------------- /docs/example_plugin/setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | name = pubget_example_plugin 3 | 4 | [options] 5 | packages = find: 6 | package_dir = 7 | =src 8 | install_requires = 9 | pandas 10 | matplotlib 11 | pubget 12 | python_requires = >=3.7 13 | 14 | [options.extras_require] 15 | dev = 16 | pytest 17 | 18 | [options.packages.find] 19 | where = src 20 | 21 | [options.entry_points] 22 | pubget.plugin_actions = 23 | get_pubget_actions = pubget_example_plugin:get_pubget_actions -------------------------------------------------------------------------------- /docs/example_plugin/tests/run_plugin.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python3 2 | 3 | import subprocess 4 | import tempfile 5 | from pathlib import Path 6 | 7 | with tempfile.TemporaryDirectory(suffix="_pubget") as tmp_dir: 8 | subprocess.run( 9 | [ 10 | "pubget", 11 | "run", 12 | "--plot_pub_dates", 13 | "-q", 14 | "fMRI[Abstract] AND aphasia[Title] " 15 | "AND (2017[PubDate] : 2019[PubDate])", 16 | tmp_dir, 17 | ] 18 | ) 19 | assert ( 20 | Path(tmp_dir) 21 | .joinpath( 22 | "query_49e0abb9869a532a31d37ed788c76780", 23 | "subset_allArticles_examplePluginPubDatesPlot", 24 | "plot.png", 25 | ) 26 | .is_file() 27 | ), "Plugin output not found!" 28 | 29 | print("pubget and plugin ran successfully") 30 | -------------------------------------------------------------------------------- /docs/example_plugin/tests/test_example_plugin.py: -------------------------------------------------------------------------------- 1 | import pandas as pd 2 | import pubget_example_plugin 3 | 4 | 5 | def test_example_plugin(tmp_path): 6 | meta_data = pd.DataFrame( 7 | {"pmcid": [1, 2, 3], "publication_year": [2018, 2020, 2020]} 8 | ) 9 | extracted_data = tmp_path.joinpath("pubget_extractedData") 10 | extracted_data.mkdir() 11 | meta_data.to_csv(extracted_data.joinpath("metadata.csv"), index=False) 12 | out_dir, code = pubget_example_plugin.plot_publication_dates( 13 | extracted_data 14 | ) 15 | assert out_dir.joinpath("plot.png").is_file() 16 | -------------------------------------------------------------------------------- /docs/example_plugin/tox.ini: -------------------------------------------------------------------------------- 1 | [tox] 2 | isolated_build = True 3 | envlist = py 4 | 5 | [testenv] 6 | deps = 7 | pytest 8 | commands = 9 | pytest tests -------------------------------------------------------------------------------- /docs/example_queries/fmri_2019.txt: -------------------------------------------------------------------------------- 1 | fMRI[Title] AND (2019[PubDate] : 2019[PubDate]) -------------------------------------------------------------------------------- /docs/module.html.jinja2: -------------------------------------------------------------------------------- 1 | {% extends "default/module.html.jinja2" %} 2 | 3 | {% block title %}{{ module.modulename }} documentation{% endblock %} 4 | 5 | {% block favicon %} 6 | 7 | {% endblock %} 8 | 9 | {% block nav_title %} 10 |
pubget {{ env.PUBGET_VERSION }}
11 | project logo 12 | {% endblock %} 13 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools", "wheel"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [tool.mypy] 6 | warn_return_any = true 7 | warn_unused_configs = true 8 | warn_unreachable = true 9 | disallow_untyped_defs = true 10 | 11 | [[tool.mypy.overrides]] 12 | module = ["joblib.*", "sklearn.*", "lxml.*", "scipy.*", "pandas.*", "neuroquery.*", "nimare.*", "nibabel.*", "nilearn.*"] 13 | ignore_missing_imports = true 14 | 15 | [tool.black] 16 | line-length = 79 17 | extend-exclude = '/(_data|data)/' 18 | 19 | [tool.isort] 20 | profile = "black" 21 | extend_skip = ["data", "_data"] 22 | skip_gitignore = true 23 | line_length = 79 24 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from pathlib import Path 2 | 3 | from setuptools import setup 4 | 5 | package_dir = Path(__file__).parent.joinpath("src", "pubget") 6 | data_files = [ 7 | str(f.relative_to(package_dir)) 8 | for f in package_dir.joinpath("_data").glob("**/*") 9 | ] 10 | version = package_dir.joinpath("_data", "VERSION").read_text("utf-8").strip() 11 | setup(package_data={"pubget": data_files}, version=version) 12 | -------------------------------------------------------------------------------- /src/pubget/_data/VERSION: -------------------------------------------------------------------------------- 1 | 0.0.9.dev -------------------------------------------------------------------------------- /src/pubget/_data/_fit_neuroquery/README.md: -------------------------------------------------------------------------------- 1 | # NeuroQuery encoding model fitted on data fetched by pubget 2 | 3 | To interactively query the model, run from inside this directory: 4 | 5 | ``` 6 | pip install -r requirements.txt 7 | flask run 8 | ``` 9 | 10 | Then open the adress shown by flask (by default it should be 11 | http://127.0.0.1:5000/) in your web browser. 12 | See the Flask documentation for details. 13 | 14 | To use the model in a Python script, install the `neuroquery` package and load 15 | it from the `neuroquery_model` directory with: 16 | 17 | ``` 18 | from neuroquery import NeuroQueryModel 19 | model = NeuroQueryModel.from_data_dir("neuroquery_model") 20 | ``` 21 | 22 | See the neuroquery documentation for details. 23 | -------------------------------------------------------------------------------- /src/pubget/_data/_fit_neuroquery/requirements.txt: -------------------------------------------------------------------------------- 1 | flask 2 | neuroquery 3 | nilearn 4 | -------------------------------------------------------------------------------- /src/pubget/_data/_fit_neurosynth/README.md: -------------------------------------------------------------------------------- 1 | # NeuroSynth encoding maps obtained from data fetched by pubget 2 | 3 | To interactively query the results, run from inside this directory: 4 | 5 | ``` 6 | pip install -r requirements.txt 7 | flask run 8 | ``` 9 | 10 | Then open the adress shown by flask (by default it should be 11 | http://127.0.0.1:5000/) in your web browser. 12 | See the Flask documentation for details. 13 | -------------------------------------------------------------------------------- /src/pubget/_data/_fit_neurosynth/requirements.txt: -------------------------------------------------------------------------------- 1 | flask>=2.0 2 | numpy 3 | scipy 4 | pandas 5 | nilearn 6 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/AUTHORS: -------------------------------------------------------------------------------- 1 | The DocBook XSL stylesheets are maintained by Norman Walsh, 2 | , and members of the DocBook Project, 3 | 4 | 5 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/BUGS: -------------------------------------------------------------------------------- 1 | To view a list of all open DocBook Project XSL stylesheet bugs: 2 | 3 | http://docbook.sf.net/tracker/xsl/bugs 4 | 5 | To submit a bug report against the stylesheets: 6 | 7 | http://docbook.sf.net/tracker/submit/bug 8 | 9 | To do a full-text search of all DocBook Project issues: 10 | 11 | http://docbook.sf.net/tracker/search 12 | 13 | Discussion about the DocBook Project XSL stylesheets takes place 14 | on the docbook-apps mailing list: 15 | 16 | http://wiki.docbook.org/topic/DocBookAppsMailingList 17 | 18 | Real-time discussion takes place on IRC: 19 | 20 | http://wiki.docbook.org/topic/DocBookIrcChannel 21 | irc://irc.freenode.net/docbook 22 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/RELEASE-NOTES.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neuroquery/pubget/12d1451cf846757968f80f6c71ce5bbfc44d18a1/src/pubget/_data/stylesheets/docbook/RELEASE-NOTES.html -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/REVISION: -------------------------------------------------------------------------------- 1 | 10010 2 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/TODO: -------------------------------------------------------------------------------- 1 | The "to do" list for the DocBook Project XSL stylesheets is 2 | maintained at Sourceforge. To view a list of all open feature 3 | requests for the stylesheets: 4 | 5 | http://docbook.sf.net/tracker/xsl/requests 6 | 7 | To submit a feature request against the stylesheets: 8 | 9 | http://docbook.sf.net/tracker/submit/request 10 | 11 | To do a full-text search of all DocBook Project issues: 12 | 13 | http://docbook.sf.net/tracker/search 14 | 15 | Discussion about the DocBook Project XSL stylesheets takes place 16 | on the docbook-apps mailing list: 17 | 18 | http://wiki.docbook.org/topic/DocBookAppsMailingList 19 | 20 | Real-time discussion takes place on IRC: 21 | 22 | http://wiki.docbook.org/topic/DocBookIrcChannel 23 | irc://irc.freenode.net/docbook 24 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/catalog.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/docsrc/authors.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | WalshNorman 5 | 6 | 7 | 8 | The DocBook Project 9 | 10 | 11 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/docsrc/copyright.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 1999-2007 4 | Norman Walsh 5 | 6 | 7 | 2003 8 | Jiří Kosek 9 | 10 | 11 | 2004-2007 12 | Steve Ball 13 | 14 | 15 | 2001-2007 16 | The DocBook Project 17 | 18 | 19 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/docsrc/page.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neuroquery/pubget/12d1451cf846757968f80f6c71ce5bbfc44d18a1/src/pubget/_data/stylesheets/docbook/docsrc/page.png -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/docsrc/warranty.xml: -------------------------------------------------------------------------------- 1 | Warranty 3 | THE SOFTWARE IS PROVIDED AS IS, 4 | WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT 5 | LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR 6 | PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL NORMAN WALSH OR ANY 7 | OTHER CONTRIBUTOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 8 | WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT 9 | OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 10 | THE SOFTWARE. 11 | 12 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/eclipse/build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Building profiling version of Eclipse stylesheet... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/epub/bin/xslt/obfuscate.xsl: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/epub3/build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Building EPUB3 titlepage... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/epub3/docbook.xsl: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | ]> 6 | 7 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/extensions/NOTICE.txt: -------------------------------------------------------------------------------- 1 | The webhelpindexer is released under the Apache 2.0 license and 2 | includes software from other projects. 3 | 4 | The webhelpindexer was originally developed by N. Quaine and released 5 | under a MIT/BSD-style license. See LICENSE.txt. 6 | 7 | This product includes software developed by The Apache Software 8 | Foundation (http://www.apache.org/). See LICENSE.txt. 9 | 10 | This product also includes software released as part of the Snowball 11 | project maintained by Martin Porter and Richard Boulton released under 12 | a BSD-style license: http://snowball.tartarus.org/ 13 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/extensions/README.LIBXSLT: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neuroquery/pubget/12d1451cf846757968f80f6c71ce5bbfc44d18a1/src/pubget/_data/stylesheets/docbook/extensions/README.LIBXSLT -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/extensions/README.txt: -------------------------------------------------------------------------------- 1 | See webhelp/docs/index.html for more information about the webhelp 2 | indexer and the webhelp output format. 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Use a processor that works with the extension: Saxon 6 or Xalan-J. 3 | 2. Add the latest version of xslthl-2.X.X.jar to your classpath. 4 | 3. Set the highlight.source parameter to 1. 5 | 4. Import into your customization one of the following stylesheet module: 6 | * html/highlight.xsl 7 | * xhtml/highlight.xsl 8 | * xhtml-1_1/highlight.xsl 9 | * fo/highlight.xsl 10 | 5. Use that customiztion layer. 11 | 12 | 13 | Note: Saxon 8.5 or later is also supported, but since it is an XSLT 2.0 14 | processor it is not guaranteed to work with DocBook-XSL in all 15 | circumstances. 16 | 17 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/html/autoidx-ng.xsl: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 14 | 15 | 16 | 17 | 18 | kosek 19 | 20 | 21 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/htmlhelp/build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Building profiling version of HTML Help stylesheet... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- 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/src/pubget/_data/stylesheets/docbook/lib/build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Building XSLT library... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neuroquery/pubget/12d1451cf846757968f80f6c71ce5bbfc44d18a1/src/pubget/_data/stylesheets/docbook/log -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/footer.rule.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | footer.rule 9 | boolean 10 | 11 | 12 | footer.rule 13 | Rule over footers? 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | Description 23 | 24 | If non-zero, a rule will be drawn above the page footers. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/generate.index.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | generate.index 9 | boolean 10 | 11 | 12 | generate.index 13 | Do you want an index? 14 | 15 | 16 | 17 | 18 | 19 | 20 | Description 21 | 22 | Specify if an index should be generated. 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/header.rule.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | header.rule 9 | boolean 10 | 11 | 12 | header.rule 13 | Rule under headers? 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | Description 23 | 24 | If non-zero, a rule will be drawn below the page headers. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/home.image.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | home.image 9 | filename 10 | 11 | 12 | home.image 13 | Home image 14 | 15 | 16 | 17 | 18 | active/nav-home.png 19 | 20 | 21 | 22 | Description 23 | 24 | Specifies the filename of the home navigation icon. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/htmlhelp.chm.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | htmlhelp.chm 9 | string 10 | 11 | 12 | htmlhelp.chm 13 | Filename of output HTML Help file. 14 | 15 | 16 | 17 | 18 | htmlhelp.chm 19 | 20 | 21 | 22 | Description 23 | 24 | Set the name of resulting CHM file 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/line-height.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | line-height 9 | string 10 | 11 | 12 | line-height 13 | Specify the line-height property 14 | 15 | 16 | 17 | 18 | normal 19 | 20 | 21 | 22 | Description 23 | 24 | Sets the line-height property. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/next.image.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | next.image 9 | filename 10 | 11 | 12 | next.image 13 | Right-arrow image 14 | 15 | 16 | 17 | 18 | active/nav-next.png 19 | 20 | 21 | 22 | Description 23 | 24 | Specifies the filename of the right-pointing navigation arrow. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/olink.pubid.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | olink.pubid 9 | string 10 | 11 | 12 | olink.pubid 13 | Names the public identifier portion of an OLink resolver query 14 | 15 | 16 | 17 | 18 | pubid 19 | 20 | 21 | 22 | Description 23 | 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/olink.resolver.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | olink.resolver 9 | string 10 | 11 | 12 | olink.resolver 13 | The root name of the OLink resolver (usually a script) 14 | 15 | 16 | 17 | /cgi-bin/olink 18 | 19 | 20 | Description 21 | FIXME: 22 | 23 | 24 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/olink.sysid.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | olink.sysid 9 | string 10 | 11 | 12 | olink.sysid 13 | Names the system identifier portion of an OLink resolver query 14 | 15 | 16 | 17 | 18 | sysid 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/prev.image.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | prev.image 9 | filename 10 | 11 | 12 | prev.image 13 | Left-arrow image 14 | 15 | 16 | 17 | 18 | active/nav-prev.png 19 | 20 | 21 | 22 | Description 23 | 24 | Specifies the filename of the left-pointing navigation arrow. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/sequential.links.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | sequential.links 9 | boolean 10 | 11 | 12 | sequential.links 13 | Make sequentional links? 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | Description 23 | FIXME 24 | 25 | 26 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/table.entry.padding.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | table.entry.padding 9 | length 10 | 11 | 12 | table.entry.padding 13 | 14 | 15 | 16 | 17 | 18 | 2pt 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/template.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | [[NAME]] 9 | 10 | 11 | 12 | [[NAME]] 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/text.home.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | text.home 9 | string 10 | 11 | 12 | text.home 13 | Home 14 | 15 | 16 | 17 | 18 | Home 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/text.next.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | text.next 9 | string 10 | 11 | 12 | text.next 13 | FIXME: 14 | 15 | 16 | 17 | 18 | Next 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/text.prev.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | text.prev 9 | string 10 | 11 | 12 | text.prev 13 | FIXME: 14 | 15 | 16 | 17 | 18 | Prev 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/text.toc.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | text.toc 9 | string 10 | 11 | 12 | text.toc 13 | FIXME: 14 | 15 | 16 | 17 | 18 | ToC 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/text.up.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | text.up 9 | string 10 | 11 | 12 | text.up 13 | FIXME: 14 | 15 | 16 | 17 | 18 | Up 19 | 20 | 21 | 22 | Description 23 | 24 | FIXME: 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/toc.html.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | toc.html 9 | filename 10 | 11 | 12 | toc.html 13 | Name of ToC HTML file 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | Description 23 | 24 | Sets the filename used for the table of contents page. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/toc.image.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | toc.image 9 | filename 10 | 11 | 12 | toc.image 13 | ToC image 14 | 15 | 16 | 17 | 18 | active/nav-toc.png 19 | 20 | 21 | 22 | Description 23 | 24 | Specifies the filename of the ToC navigation icon. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/params/up.image.xml: -------------------------------------------------------------------------------- 1 | 7 | 8 | up.image 9 | filename 10 | 11 | 12 | up.image 13 | Up-arrow image 14 | 15 | 16 | 17 | 18 | active/nav-up.png 19 | 20 | 21 | 22 | Description 23 | 24 | Specifies the filename of the upward-pointing navigation arrow. 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/profiling/strip-attributes.xsl: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | 7 | 8 | 9 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/roundtrip/blocks-spec.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/roundtrip/param.xsl: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 15 | 16 | 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/slides/README: -------------------------------------------------------------------------------- 1 | $Id: README 9639 2012-10-22 18:41:00Z stefan $ 2 | 3 | README for the DocBook Slides distribution 4 | 5 | For a more detailed manual on Slides, please see the doc 6 | directory. 7 | 8 | For information about open DocBook Slides bugs and 9 | pending feature requests, see the following: 10 | 11 | http://sourceforge.net/search/?group_artifact_id=373747&type_of_search=artifact&group_id=21935&words=slides 12 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/slides/common/common.xsl: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/slides/doc/user.css: -------------------------------------------------------------------------------- 1 | .face_container {margin-left: 4em; position: relative;} 2 | .face_first {position: static; vertical-align: bottom;} 3 | .face_other {position: absolute; left: 0; top: 0;} 4 | 5 | .left {float: left;} 6 | .right {float: right;} 7 | -------------------------------------------------------------------------------- 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You may obtain a copy of the 3 | License at http://www.mozilla.org/MPL/ 4 | 5 | Software distributed under the License is distributed on an "AS IS" basis, 6 | WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the 7 | specific language governing rights and limitations under the License. 8 | 9 | The Original Code is all Saxon modules labelled with a notice referring to this license. 10 | 11 | The Initial Developer of the Original Code is Michael Kay, except where otherwise specified in an individual module. 12 | 13 | Portions created by other named contributors are copyright as identified in the relevant module. 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DEF36=Next 37 | DEF37=Prev 38 | DEF38=Home 39 | DEF39=Motive 40 | DEF40=Inc 41 | DEF41=Copyright 42 | DEF42=All 43 | DEF43=rights 44 | DEF44=reserved 45 | DEF45=Up -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/docs/search/es-es.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neuroquery/pubget/12d1451cf846757968f80f6c71ce5bbfc44d18a1/src/pubget/_data/stylesheets/docbook/webhelp/docs/search/es-es.props -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/docs/search/ja-jp.props: -------------------------------------------------------------------------------- 1 | J01=\\u306B -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/docs/search/l10n.js: -------------------------------------------------------------------------------- 1 | 2 | //Resource strings for localization 3 | var localeresource = new Object; 4 | localeresource["search_no_results"]="Your search returned no results."; 5 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/docs/search/punctuation.props: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neuroquery/pubget/12d1451cf846757968f80f6c71ce5bbfc44d18a1/src/pubget/_data/stylesheets/docbook/webhelp/docs/search/punctuation.props -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/docsrc/images/sample.jpg: -------------------------------------------------------------------------------- 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5 | Some search words for testing 6 | arsenal, arsenic, buy, say, by, vary, try, sky, nucleus, day, key, currency, currencies, build.xml 7 |
8 |
9 | Some search words for testing (inflected) 10 | arsenal, arsenic, buys, says, varies, tries, skies, nuclei, days, keys, currencies, build.xml 11 |
12 | 13 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/template/common/css/ie.css: -------------------------------------------------------------------------------- 1 | .statustext{ 2 | filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=1) 3 | progid:DXImageTransform.Microsoft.BasicImage(opacity=.5); 4 | width: 100%; 5 | height: 30px; 6 | right: -5px; 7 | top:105px; 8 | /* left: 280px; */ /* change to -12px; when sidebar is collapsed */ 9 | } 10 | 11 | body #content{ 12 | /* padding-top: 136px;*/ 13 | } 14 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/webhelp/template/common/images/admon/caution.png: -------------------------------------------------------------------------------- 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/src/pubget/_data/stylesheets/docbook/webhelp/xsl/webhelp.xsl: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/website/build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Building Website parameters... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/website/chunk-tabular.xsl: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/website/chunk-website.xsl: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/website/website-targets.xsl: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | 7 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/xhtml5/build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Building HTML5 stylesheet... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /src/pubget/_data/stylesheets/docbook/xhtml5/docbook.xsl: -------------------------------------------------------------------------------- 1 | 2 | 4 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/pubget/_plugins.py: -------------------------------------------------------------------------------- 1 | """Utilities for loading pubget plug-in functionality.""" 2 | 3 | from typing import Any, Dict, List 4 | 5 | import importlib_metadata 6 | 7 | 8 | def get_plugin_actions() -> Dict[str, List[Any]]: 9 | """Load entry points from all pubget plugins. 10 | 11 | See https://setuptools.pypa.io/en/latest/userguide/entry_point.html 12 | """ 13 | all_actions: Dict[str, List[Any]] = { 14 | "pipeline_steps": [], 15 | "commands": [], 16 | } 17 | for entry_point in importlib_metadata.entry_points().select( 18 | group="pubget.plugin_actions" 19 | ): 20 | plugin_actions = entry_point.load()() 21 | for kind, steps in all_actions.items(): 22 | steps.extend(plugin_actions.get(kind, [])) 23 | return all_actions 24 | -------------------------------------------------------------------------------- /tests/data/text.csv: -------------------------------------------------------------------------------- 1 | pmcid,title,keywords,abstract,body 2 | 123,,,,brain brains memory the words 3 | 456,,,,brains auditory cortex 4 | 789,,,, 5 | -------------------------------------------------------------------------------- /tests/data/vocabulary.csv: -------------------------------------------------------------------------------- 1 | auditory cortex 2 | brain 3 | brains 4 | memory 5 | motor 6 | visual memory 7 | -------------------------------------------------------------------------------- /tests/data/vocabulary.csv_voc_mapping_identity.json: -------------------------------------------------------------------------------- 1 | {"brains": "brain"} 2 | -------------------------------------------------------------------------------- /tests/test_pipeline.py: -------------------------------------------------------------------------------- 1 | from unittest.mock import Mock 2 | 3 | from pubget import _pipeline, _typing 4 | 5 | 6 | def test_stop_pipeline(): 7 | all_steps = Mock(), Mock(), Mock() 8 | for step in all_steps: 9 | step.run.return_value = None, 0 10 | all_steps[1].run.side_effect = _typing.StopPipeline("fatal error") 11 | pipeline = _pipeline.Pipeline(all_steps) 12 | pipeline.run(Mock()) 13 | for step in all_steps[:2]: 14 | assert step.run.called 15 | assert not all_steps[2].called 16 | -------------------------------------------------------------------------------- /tests/test_text.py: -------------------------------------------------------------------------------- 1 | from unittest.mock import Mock 2 | 3 | from lxml import etree 4 | 5 | from pubget import _text 6 | 7 | 8 | def test_text_extractor_transform_failure(monkeypatch): 9 | """Transforming the article to extract text is allowed to fail.""" 10 | extractor = _text.TextExtractor() 11 | monkeypatch.setattr( 12 | etree, "XSLT", Mock(return_value=Mock(side_effect=ValueError)) 13 | ) 14 | assert extractor.extract(Mock(), Mock(), {}) == {} 15 | -------------------------------------------------------------------------------- /tests/test_writers.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import pandas as pd 3 | 4 | from pubget import _writers 5 | 6 | 7 | def test_csv_writer(tmp_path): 8 | output_file = tmp_path.joinpath("myoutput.csv") 9 | writer = _writers.CSVWriter(("A", "B", "C"), "mydata", output_file) 10 | with writer: 11 | writer.write({"mydata": {"A": "a1", "B": 1}}) 12 | df = pd.DataFrame( 13 | [{"A": "a2", "C": 20.5}, {"A": "a3", "B": 3, "C": 30.5}] 14 | ) 15 | assert np.isnan(df.at[0, "B"]) 16 | assert df.at[0, "B"] is not None 17 | writer.write({"mydata": df}) 18 | writer.write({"otherdata": df}) 19 | result = pd.read_csv(output_file, na_values=[""], keep_default_na=False) 20 | assert result.shape == (3, 3) 21 | assert result.isnull().sum().sum() == 2 22 | assert result.at[2, "C"] == 30.5 23 | -------------------------------------------------------------------------------- /tox.ini: -------------------------------------------------------------------------------- 1 | [tox] 2 | envlist = py{37,310}-latest,py37-old,py38-nimare 3 | 4 | [testenv] 5 | deps = 6 | pytest 7 | commands = 8 | pytest tests 9 | 10 | [testenv:py37-old] 11 | deps = 12 | pytest 13 | numpy>=1.16,<1.17 14 | pandas>=0.24,<0.25 15 | scikit-learn>=0.21,<0.22 16 | joblib>=0.17,<0.18 17 | scipy<=1.1.0 18 | importlib_metadata>=3.6,<3.7 19 | commands = 20 | pytest tests 21 | 22 | [testenv:py38-nimare] 23 | deps = 24 | pytest 25 | nimare 26 | commands = 27 | pytest tests 28 | 29 | [testenv:run_plugin] 30 | deps = 31 | docs/example_plugin 32 | setenv = 33 | NEUROQUERY_DATA_DIR = {toxworkdir}/neuroquery_data 34 | commands = 35 | python docs/example_plugin/tests/run_plugin.py 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