Category Archives: Software

Mutt on Yosemite

I use Mutt to read and send mail. My recent adventurous switch to Apple’s beta Yosemite system (OS 10.10) created an authentication problem when sending mail. The solution was to add a line to my .muttrc file: set smtp_authenticators=”login”

How to delete zotero data

In case anyone wants to delete the bibliographic data stored on Zotero (the Zotero info doesn’t help at all, as far as I could tell), here is what I did. I had over 5,000 items on Zotero which I wanted to delete. The reason is that I much prefer Bibdesk because it is flexible, fast, convenient, and works well with Textmate, XeLaTeX, and/or TeXShop for processing and pdf production. I couldn’t find a “data delete” button on the Zotero web page. So, I launched the Zotero extension (“add-on”) in Firefox, highlighted all the references in the library with shift-click, dragged them to the trash (or used Delete, I’m not sure anymore), then clicked on Trash and repeated the operation. “Sync” wiped the data on Zotero. Took a little while. Then I removed the Zotero folder left on my machine (Mac: /Users/username/Library/Application Support/Firefox/Profiles/random string/zotero) and whatever preference zotero files I had in /Library/Preferences. As for my Zotero account on the website, I removed it indirectly by deleting the email account associated with it. Cumbersome, but it worked.

Writing tools

These are notes on software tools I use in writing and presentations. I’m posting them for anyone interested in writing, publishing, lecturing. Comments welcome.

I used to write in copybooks, on loose sheets, the back of envelopes, and wrapping paper. The scratching of the pen and the shaping of the ink on the paper helped in thinking, or so I thought. Now I do much of the writing directly on computer and screen. I learned to type when I began to use computers, in my thirties. I’m talking amber screens, a prompt and text only, with a non-visual editor (in spite of its acronym), vi, and mysterious Unix commands that one used to handle files and send them to the printer. Thirty years later, I still remember those commands, the vi ones in particular, and the strings of code I typed to obtain Greek and Hebrew. I also remember I couldn’t think at the screen. This inability to think increased when windows appeared on various machines, for instance the Mac and then on so-called Windows desktop machines. I found the commercial programs very constraining: they lined text up in ways one could do little about, hyphenated things without permission, and made you concerned above all about how things looked. And they cost dearly at every major re-issue, forcing the user to become a kind of renter on contract for an indefinite period of time. I don’t like to be on a leash. I also worried about the archival aspect: would the documents I cared about be readable ten or twenty years from now, given the inexorable change of operating systems and proprietary programs (.doc, .pdf, and others)? Of course one can use TextEdit on the Mac, or even better Bean, which allows you to work on .doc or .docx files without any problem. Spare program though, for the ascetically minded.

I looked for other ways to do things, especially after Unicode encoding became easily accessible, and found that there are tools which are powerful, entirely free, presently fairly easy to install, and highly configurable. They allow complex multi-lingual texts to be beautifully typeset or produced, which is what I’m interested in, while keeping them in the simplest possible original format (.txt or .tex files).

So here is a list of what I have been using for quite a while, with short explanations and examples.

Tools

  1. Free:
    • TeX, a typesetting system designed and mostly written by Donald Knuth. It is presently easy to install, in the default cross-platform distribution called TeX Live. Mac users simply may download and install MacTeX. I use only part of this large distribution, something called XeLaTeX, which makes the high-quality typesetting of most languages a breeze. I’m interested in using LuaLateX, a new flavor promised to a great future but am waiting for its maturing. All of this lies hidden in the bowels of my machine and never fails, in years of use.
    • A highly recommended editor for the Mac: TeXShop. I can type left-to-right and right-to-left languages easily, typeset my source entries by using the included engines (XeLaTeX mostly), look at the pdf produced by it, and navigate from source to pdf with great precision (with the help of its sync mechanism).
    • A bibliographical tool for Mac (Unicode encoding also), BibDesk. It manages any kind of bibliographical data for many applications, not only for TeX or LaTeX above.
    • Fonts: Aside from the fonts that come with the Mac (mostly Hoefler Text), I also use Linux Libertine, TeX Gyre, esp. Pagella and Schola, as well as Latin Modern. Other good fonts rich in special characters are: Gentium and Charis, or Junicode. For Hebrew and Greek, see the high quality SBL Greek and SBL Hebrew.
  2. Not free:
    • another editor for Mac, TextMate. This is overkill for a text editor, since TeXShop is already so good. It is for software writers, not really for me, but I find it has features I miss in TeXShop:
      1. It has project windows (or in TextMate 2, a powerful file browser). In a project containing a number of chapters or articles, I can do a global find and substitute, or simply find passages where I have taken notes or reflected upon some topic. Because I have many texts, I find this extremely useful. I can also easily switch from file to file. This feature is very important when I prepare courses: I have immediate access to grades, lectures, text sources, etc.
      2. TextMate provides “bundles” which are specialized tools: I prepare my courses with “Markdown.” My structured text becomes a html page, with pictures, links, etc., which I project as a html file in class. Or I write this blog and load it in about a second to my WordPress page. And I use the LaTeX bundle (see TeX above).
      3. This LaTeX bundle has special advantages:
        • color syntax: footnotes, quotes, bibliographical references are colored as I prefer.
        • citation completion: while I write, it is enough to remember the name of an author and punch in a key combination. The program searches the BibDesk data files (even though BibDesk application is closed) and presents the possibilities in a window from which you choose what you need. Very convenient to generate commented bibliographies or reference lists for students.
        • structuring the text and navigating it are made very easy: this is a problem in many applications, where one needs to scroll back and forth…
      4. Fonts: I purchased GraecaUBSU (for Greek) and NewJerusalemU (for Hebrew) from Linguist’s Software.

Workflow

  1. For courses:
    • I use TextMate and its Markdown bundle to write text files and transform them into html or pdf files which I either post on the web or project on the screen in class. Other formats are possible. No need for power point presentations.
    • I also provide source texts and fuller lecture notes which I typeset with XeLaTeX (see above) and put on a server and link to the class page (just an example, the course on the notion of sin).
    • Note: I use a portable computer in class, but a desktop to prepare text (larger screen, easier on the eyes). This means I need to backup all of my material in such a way that it is simultaneously identical on the two machines. I use Dropbox for this task. It is free, if use is below 2GB (presently more: 5GB?).
  2. For writing:
    • I write a .tex file in a large project called “Writing” (surprise!). Suffixes like .tex are automatically recognized by either TextMate or TeXShop as files that can be color coded and processed in the proper TeX fashion. My “Writing” project is a bit too large but in fact opens rather quickly. I find it convenient to have everything gathered in one spot so that I can easily do a global search.
    • For examples of how LaTeX works, see the TeXShop website.
    • Last remark: the packaging of text, images, and sounds for public or individual use is changing rapidly. The tools listed above are very flexible in this regard. Most commercial applications are poor competitors.