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Subsections

Presentation/communication

Text processing: LaTeX

Basic LaTeX:

\documentclass{class}, e.g., article, letter, book, others (see AASTeX below, which provides aastex and emulateapj)
Preamble
- package setup: \usepackage{package}, e.g. graphicx, amsmath, hyperref, color
- command aliases, e.g., \newcommand{\mh}[0]{[M/H]}
\begin{document}
\section{title}, \subsection{subtitle}, \subsubsection{subtitle}
text formatting: \textit, \textbf, etc
math mode (e.g., reference: $ and $$, superscript, subscript, greek letters, math symbols, etc. (note use in iPython notebooks!)

various environments: itemize, enumerate, figure, table, tabular, center, equation, e.g.:

Figures with \usepackage{graphicx}, /textbackslash includegraphics

\begin{itemize} % Use enumerate for numbered list
\item Item 1
\item Item 2
\end{itemize}

\begin{figure}
\includegraphics[width=0.5 \textwidth]{cfig.pdf}
\caption{caption here}
\label{fig:cfig} (see below)
\end{figure}

Refer to Figure in the text to automatically get the correct number!

\begin{table}
\begin{tabular}{llcr}
obj1 & data1 & text1 & number1 \\
obj2 & data2 & text2 & number2 \\
\end{tabular}
\label{tab:data}
\end{table}

Refer to Table in the text to automatically get the correct number!

\end{document}

AASTeX: documentclass for astronomical publications, e.g., aastex, emulateapj. deluxetable environment for tables (including multi-page).

labels: to allow for arbitrary moving/addition/deletion of figures, tables, sections, etc., do not build in numbering into the text. Instead use the \label{labelname} command to label each entity, and automatically reference the correct numerical identification using \ref{labelname}. Note that using these will require two passes through latex, to register the labels correctly. Note that, in the figure environment, the label command must come after the caption command!

references: Instead of building in explicit references in text, perhaps repeating multiple times, and then adding full reference in reference section, use bibitems: create the reference once, give it an identifier, and reference it in the text by the identifier using \citep, \citet, \citealt (the natbib package provides an extension beyond the standard LaTeX commands). You can create the bibitem manually (\bibitem{identifier} reference), or, better yet, use BiBTeX reference information (available from ADS!) and automatically create the bibitems.

manual bibitem: \begin{thebibliography}, \bibitem...., \end{thebibliography}
bibtex: create reffile.bib file with bibtex entries, use \bibliography{reffile} in latex file, then latex file, bibtex, latex file, latex file to put it all together. See discussion on ADS; for astronomical journal reference style, you may want to use the apj bibliography style, using the apj.bst file.

Refer to an article inline (with year in parenthesis) using \citet{id}. Refer
to an article where author and year are both in parenthees using \citep{id}.

\bibliography{ref} % at end of document

"compiling" LateX / pdflatex. Can use a makefile to simplify! Using bibtex, sequence is: prepare a doc.text file with the document and a ref.bib file with a bunch of BibTeX entries (e.g., from ADS), then:

pdflatex doc
bibtex doc
pdflatex doc
pdflatex doc

latex editors: kile. On line resources for sharing/editing/viewing LaTeX: sharelatex, authorea, overleaf, etc.

spell checking: aspell, hunspell. ALWAYS SPELL CHECK YOUR DOCUMENTS

$\begin{shaded} \textit{ Be able to easily create a complete LaTeX file that incl... ...nd section cross-referencing. Be able to do these things quickly. } \end{shaded}$

Introduction to makefiles

Introduction to makefiles (see, e.g., the GNU documentations or someone else's explanations. Explicit commands, variable filenames, rules.

Standard rules.

Standard targets: install, objs, etc.

HTML

Structure of an HTML document: <command></command> structure, <HTML><BODY [bgcolor=]>,

Basic HTML text processing: text will appear continuously in a browser regardless of how it is entered in the HTML source file, unless there are command directives: the width of the text will adapt to the width of the browser. Various text directives:

<Hn> Headings in different font sizes (1 is largest) </Hn>
<P> Force a line break with vertical paragraph space
<BR> Force a line break without extra vertical space
  Force small horizonal space
<UL>/<OL> Unordered list / ordered (numbered) list (end with </UL> or </OL>
- <LI> : individual list element
Font commands
- <I> italic </I>
- <B> bold </B>
- <FONT [color=]> general font command

HTML links:

<A HREF=address> active text </A> : sets up a link
<A NAME=label> : sets a lable in a HTML file, can be directly skipped to using address#label format

HTML tables:

<TABLE [BORDER=]>: start a table
<TR> : start a new row
<TD [COLSPAN=]> : start a new column
</TABLE> : end table

HTML figures:

<IMG SRC={file} [WIDTH=] [HEIGHT=]> : force size using WIDTH= and/or HEIGHT=, usually only one of these, as this will automatically preserve aspect ratio
If at all possible, use file format that most browsers know how to display inline: GIF, JPG, PNG

comments in HTML files:

All of these can be combined, e.g., a table of figure thumbnails with links to full size figures:

	<TABLE BORDER=2>
	<TR> <TD> <A HREF=fig11.jpg> <IMG SRC=fig11.jpg WIDTH=200> </A>
	<TR> <TD> <A HREF=fig12.jpg> <IMG SRC=fig12.jpg WIDTH=200> </A>
	<TR> <TD> <A HREF=fig21.jpg> <IMG SRC=fig21.jpg WIDTH=200> </A>
	<TR> <TD> <A HREF=fig22.jpg> <IMG SRC=fig22.jpg WIDTH=200> </A>
	</TABLE>

Frames, CSS, and much much more!

$\begin{shaded} \textit{ Understand how to write a basic HTML page, including lists, figures, tables, and hyperlinks, and be able to do so quickly. } \end{shaded}$

A web server is a network program that runs on a server machine, and interprets/delivers web pages as requested. Standard web requests are http://{machinename/address}/{file|directory}. One the web server, the {file|directory} is interpreted as a relative path to some document root directory. If the requested address is a directory, the web server will look for a file named index.html in that directory and, if it exists, will use the contents of that file; if it doesn't exist, it will show the directory listing of the directory.

Web server at NMSU uses /home/httpd/html as the document root, and all users have a directory /home/httpd/html/{username}, so web requests to http://astronomy.nmsu.edu/{username} will look for files in this directory. Note that this directory is located on the disk server, so it is not a great location to put large files; if you want to provide access to large files, or even whole directories, located on a disk on your machine, consider the use of symbolic links ...

Collaboration

email/listservers : value as email archive/ risk of junk mail. Be aware of reply-all! Listservers as archives. Listserver options: digest delivery.

file size and format (e.g., for plots): deliver files so as to make it as easy as possible for audience to read/view/digest them!

web pages: very useful as hierarchical source of information, with figures

wiki : centralized set of user-editable web pages, with many other features.

iPython notebooks

Next: Programming Up: AY575 class notes Previous: Working in a Unix

Jon Holtzman 2015-12-11