Name formatting for msprime API functions

[ashander]

at least for me the formatting for functions defined here_ has no effect, eg

log from make

``` pdflatex forwards_paper.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./forwards_paper.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) \@input{macros.aux} (./macros.tex) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) No file forwards_paper.aux. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./forwards_paper.out) (./forwards_paper.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) Package natbib Warning: Citation `martin2017human' on page 1 undefined on input line 99. Package natbib Warning: Citation `wakeley2003gene' on page 1 undefined on input line 103. Package natbib Warning: Citation `maruvka2011recovering' on page 1 undefined on input line 103. Package natbib Warning: Citation `bhaskar2014distortion' on page 1 undefined on input line 103. Package natbib Warning: Citation `harris2016genetic' on page 1 undefined on inp ut line 106. Package natbib Warning: Citation `slim' on page 1 undefined on input line 106. Package natbib Warning: Citation `Sanjak2017-ko' on page 1 undefined on input l ine 108. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 109. Package natbib Warning: Citation `haller2017flexible' on page 1 undefined on in put line 126. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 126. Package natbib Warning: Citation `haller2017flexible' on page 1 undefined on in put line 129. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 131. Package natbib Warning: Citation `Hernandez2015-wf' on page 1 undefined on inpu t line 131. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 133. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Package natbib Warning: Citation `kelleher2016efficient' on page 2 undefined on input line 155. Package natbib Warning: Citation `peng2005simupop' on page 2 undefined on input line 177. Package natbib Warning: Citation `fwdpp' on page 2 undefined on input line 177. Package natbib Warning: Citation `Neuhauser1997-nn' on page 2 undefined on inpu t line 211. [2] Package natbib Warning: Citation `Tange2011a' on page 3 undefined on input line 237. LaTeX Warning: Reference `fig:runtimes_selection' on page 3 undefined on input line 244. LaTeX Warning: Reference `fig:runtimes_selection' on page 3 undefined on input line 248. LaTeX Warning: Reference `fig:relative_speedup_selection' on page 3 undefined o n input line 249. LaTeX Warning: Reference `fig:relative_speedup_selection' on page 3 undefined o n input line 250. LaTeX Warning: Reference `fig:runtimes_selection' on page 3 undefined on input line 251. LaTeX Warning: Reference `sfig:rawspeed_nosel' on page 3 undefined on input lin e 257. LaTeX Warning: Reference `fig:runtimes_selection' on page 3 undefined on input line 258. LaTeX Warning: Reference `sfig:speedup_nosel' on page 3 undefined on input line 259. LaTeX Warning: Reference `fig:relative_speedup_selection' on page 3 undefined o n input line 260. LaTeX Warning: Reference `sfig:rawspeed_nosel' on page 3 undefined on input lin e 262. LaTeX Warning: Reference `sfig:speedup_nosel' on page 3 undefined on input line 263. LaTeX Warning: Reference `fig:runtimes_selection' on page 3 undefined on input line 281. LaTeX Warning: Reference `fig:runtimes_selection' on page 3 undefined on input line 281. Package natbib Warning: Citation `griffiths1991two' on page 3 undefined on inpu t line 301. Package natbib Warning: Citation `griffiths1997ancestral' on page 3 undefined o n input line 301. Package natbib Warning: Citation `wiuf1997number' on page 3 undefined on input line 305. Package natbib Warning: Citation `wiuf1999ancestry' on page 3 undefined on inpu t line 305. Package natbib Warning: Citation `marjoram2006coalescent' on page 3 undefined o n input line 305. Package natbib Warning: Citation `wilton2015smc' on page 3 undefined on input l ine 305. Package natbib Warning: Citation `morin2006netgen' on page 3 undefined on input line 308. Package natbib Warning: Citation `mcgill2013graphml' on page 3 undefined on inp ut line 308. Package natbib Warning: Citation `kelleher2016efficient' on page 3 undefined on input line 311. LaTeX Warning: Reference `fig:example_tree_sequence' on page 3 undefined on inp ut line 320. Package natbib Warning: Citation `kelleher2016efficient' on page 3 undefined on input line 322. [3] [4 <./sims/rawspeed.pdf>] [5 <./sims/speedup.pdf>] LaTeX Warning: Reference `fig:example_tree_sequence' on page 6 undefined on inp ut line 333. LaTeX Warning: Reference `fig:example_tree_sequence' on page 6 undefined on inp ut line 361. Package natbib Warning: Citation `kelleher2016efficient' on page 6 undefined on input line 382. [6 <./example_tree_sequence.pdf>] LaTeX Warning: Reference `fig:example_tree_sequence' on page 7 undefined on inp ut line 387. LaTeX Warning: Reference `fig:example_tree_sequence' on page 7 undefined on inp ut line 394. LaTeX Warning: Reference `ss:simplify' on page 7 undefined on input line 463. [7] [8 <./wf-before-after.pdf>] LaTeX Warning: Reference `fig:wf-trees' on page 9 undefined on input line 558. LaTeX Warning: Reference `fig:wf-trees' on page 9 undefined on input line 577. LaTeX Warning: Float too large for page by 60.35172pt on input line 627. Package natbib Warning: Citation `hudson1983properties' on page 9 undefined on input line 642. Package natbib Warning: Citation `kelleher2016efficient' on page 9 undefined on input line 643. LaTeX Warning: Reference `ss:simplify_algorithm' on page 9 undefined on input l ine 644. LaTeX Warning: Reference `fig:method_diagram' on page 9 undefined on input line 659. LaTeX Warning: Reference `fig:simplify_state' on page 9 undefined on input line 661. LaTeX Warning: Reference `fig:method_diagram' on page 9 undefined on input line 673. LaTeX Warning: Reference `fig:method_diagram' on page 9 undefined on input line 673. [9] [10 <./method_diagram.pdf>] Package natbib Warning: Citation `kelleher2016efficient' on page 11 undefined o n input line 732. [11 <./simplify-state-diagram.pdf>] LaTeX Warning: Reference `fig:simplify_complexity' on page 12 undefined on inpu t line 769. LaTeX Warning: Reference `eqn:edge_bound' on page 12 undefined on input line 80 0. LaTeX Warning: Reference `eqn:edge_bound' on page 12 undefined on input line 80 0. LaTeX Warning: Reference `fig:simplify_complexity' on page 12 undefined on inpu t line 819. LaTeX Warning: Reference `fig:simplify_complexity' on page 12 undefined on inpu t line 828. Package natbib Warning: Citation `numpy_C_api' on page 12 undefined on input li ne 870. [12] [13 <./sims/num_edges_50.pdf> <./sims/simplify_timings.pdf>] Package natbib Warning: Citation `hdf5' on page 14 undefined on input line 879. Package natbib Warning: Citation `fwdpp' on page 14 undefined on input line 890 . Package natbib Warning: Citation `aberer2013rapid' on page 14 undefined on inpu t line 923. Package natbib Warning: Citation `padhukasahasram2008exploring' on page 14 unde fined on input line 926. Package natbib Warning: Citation `kelleher2016efficient' on page 14 undefined o n input line 943. Package natbib Warning: Citation `wilkins2004separation' on page 14 undefined o n input line 958. Package natbib Warning: Citation `barton2002neutral' on page 14 undefined on in put line 959. Package natbib Warning: Citation `cox2002stepping' on page 14 undefined on inpu t line 959. Package natbib Warning: Citation `lawrie2017accelerating' on page 14 undefined on input line 964. Package natbib Warning: Citation `Sawyer1992-jw' on page 14 undefined on input line 965. [14] Package natbib Warning: Citation `liberman2014little' on page 15 undefined on i nput line 973. No file forwards_paper.bbl. [15] [16] pdfTeX warning (ext4): destination with the same i dentifier (name{figure.1}) has been already used, duplicate ignored \relax l.1172 selection.} pdfTeX warning (ext4): destination with the same identifi er (name{figure.1}) has been already used, duplicate ignored \relax l.1172 selection.} pdfTeX warning (ext4): destination with the same id entifier (name{figure.2}) has been already used, duplicate ignored \relax l.1179 ...er the run times tracking the pedigree.} LaTeX Warning: Reference `sfig:rawspeed_nosel' on page 17 undefined on input li ne 1179. pdfTeX warning (ext4): destination with the same identifier (name{figure.2}) ha s been already used, duplicate ignored \relax l.1179 ...er the run times tracking the pedigree.} LaTeX Warning: Reference `sfig:rawspeed_nosel' on page 17 undefined on input li ne 1179. Package natbib Warning: There were undefined citations. [17 <./sims/rawspeed_nosel.pdf>] [18 <./sims/speedup_nosel.pdf>] (./forwards_paper.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on forwards_paper.pdf (18 pages, 614087 bytes). Transcript written on forwards_paper.log. bibtex forwards_paper.aux This is BibTeX, Version 0.99d (TeX Live 2016/Debian) The top-level auxiliary file: forwards_paper.aux The style file: plainnat.bst Database file #1: references.bib Warning--I didn't find a database entry for "numpy_C_api" Warning--I didn't find a database entry for "hdf5" Warning--empty note in Hernandez2015-wf (There were 3 warnings) while ( pdflatex forwards_paper.tex; grep -q "Rerun to get" forwards_paper.log ) do true ; done This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./forwards_paper.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. 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Package natbib Warning: Citation `wakeley2003gene' on page 1 undefined on input line 103. Package natbib Warning: Citation `maruvka2011recovering' on page 1 undefined on input line 103. Package natbib Warning: Citation `bhaskar2014distortion' on page 1 undefined on input line 103. Package natbib Warning: Citation `harris2016genetic' on page 1 undefined on inp ut line 106. Package natbib Warning: Citation `slim' on page 1 undefined on input line 106. Package natbib Warning: Citation `Sanjak2017-ko' on page 1 undefined on input l ine 108. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 109. Package natbib Warning: Citation `haller2017flexible' on page 1 undefined on in put line 126. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 126. Package natbib Warning: Citation `haller2017flexible' on page 1 undefined on in put line 129. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 131. Package natbib Warning: Citation `Hernandez2015-wf' on page 1 undefined on inpu t line 131. Package natbib Warning: Citation `fwdpp' on page 1 undefined on input line 133. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Package natbib Warning: Citation `kelleher2016efficient' on page 2 undefined on input line 155. Package natbib Warning: Citation `peng2005simupop' on page 2 undefined on input line 177. Package natbib Warning: Citation `fwdpp' on page 2 undefined on input line 177. Package natbib Warning: Citation `Neuhauser1997-nn' on page 2 undefined on inpu t line 211. [2] Package natbib Warning: Citation `Tange2011a' on page 3 undefined on input line 237. Package natbib Warning: Citation `griffiths1991two' on page 3 undefined on inpu t line 301. Package natbib Warning: Citation `griffiths1997ancestral' on page 3 undefined o n input line 301. Package natbib Warning: Citation `wiuf1997number' on page 3 undefined on input line 305. 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[7] [8 <./wf-before-after.pdf>] LaTeX Warning: Float too large for page by 60.35172pt on input line 627. Package natbib Warning: Citation `hudson1983properties' on page 9 undefined on input line 642. Package natbib Warning: Citation `kelleher2016efficient' on page 9 undefined on input line 643. [9] [10 <./method_diagram.pdf>] Package natbib Warning: Citation `kelleher2016efficient' on page 11 undefined o n input line 732. [11 <./simplify-state-diagram.pdf>] Package natbib Warning: Citation `numpy_C_api' on page 12 undefined on input li ne 870. [12] [13 <./sims/num_edges_50.pdf> <./sims/simplify_timings.pdf>] Package natbib Warning: Citation `hdf5' on page 14 undefined on input line 879. Package natbib Warning: Citation `fwdpp' on page 14 undefined on input line 890 . Package natbib Warning: Citation `aberer2013rapid' on page 14 undefined on inpu t line 923. Package natbib Warning: Citation `padhukasahasram2008exploring' on page 14 unde fined on input line 926. Package natbib Warning: Citation `kelleher2016efficient' on page 14 undefined o n input line 943. Package natbib Warning: Citation `wilkins2004separation' on page 14 undefined o n input line 958. Package natbib Warning: Citation `barton2002neutral' on page 14 undefined on in put line 959. Package natbib Warning: Citation `cox2002stepping' on page 14 undefined on inpu t line 959. Package natbib Warning: Citation `lawrie2017accelerating' on page 14 undefined on input line 964. Package natbib Warning: Citation `Sawyer1992-jw' on page 14 undefined on input line 965. [14] Package natbib Warning: Citation `liberman2014little' on page 15 undefined on i nput line 973. (./forwards_paper.bbl [15] [16]) [17] [18] pdfTeX warning (ext4): destination with the same i dentifier (name{figure.1}) has been already used, duplicate ignored \relax l.1172 selection.} pdfTeX warning (ext4): destination with the same identifi er (name{figure.1}) has been already used, duplicate ignored \relax l.1172 selection.} pdfTeX warning (ext4): destination with the same id entifier (name{figure.2}) has been already used, duplicate ignored \relax l.1179 ...er the run times tracking the pedigree.} pdfTeX warning (ext4): destin ation with the same identifier (name{figure.2}) has been already used, duplicat e ignored \relax l.1179 ...er the run times tracking the pedigree.} Package natbib Warning: There were undefined citations. [19 <./sims/rawspeed_nosel.pdf>] [20 <./sims/speedup_nosel.pdf>] (./forwards_paper.aux Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on forwards_paper.pdf (20 pages, 631496 bytes). Transcript written on forwards_paper.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./forwards_paper.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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Transcript written on forwards_paper.log. rm forwards_paper.aux forwards_paper.bbl ```

[petrelharp]

I think that's fine... but would be fine with a different display if you think it better.

[ashander]

Cool. I guess the current formatting is to ensure the functions are normal text in mathmode but they're mostly (entirely?) used in plain text. I'll maybe suggest something

[jeromekelleher]

I just stuck in a very basic version using macros so that we can change the style easily later if we want. Maybe camelCase would be more appropriate (e.g., addNode)? I'm also fine with some other display form if you like.