scimax.info

This is scimax.info, produced by makeinfo version 4.8 from scimax.texi.


File: scimax.info,  Node: Top,  Next: Org-mode,  Up: (dir)

Scimax - The manual
*******************

Scimax is an Emacs starterkit designed for people interested in
reproducible research and publishing. Scimax is just Emacs that has
been configured extensively to make it act like we need it to for
research documentation and publication. The notes below document some
features we have built into scimax.

   Note: The org-mode version of this manual is the preferred version
for reading; it is the most functional version, and the most up to
date. The *Note Top: (scimax)Top. version is also useful though, and
you might prefer that one.

* Menu:

* Org-mode::
* Writing tools::
* Bibliography management::
* Email utilities::
* Contacts::
* Google::
* Magit::
* Project management - projectile::
* Programming::
* RSS feeds::
* Miscellaneous scimax utilities::
* External Packages::
* Scientific notebook::
* ivy/counsel::
* scimax-hydras::
* Appendix::
* Archive::

--- The Detailed Node Listing ---

Org-mode

* Markup shortcuts::
* Block expansions in org-mode::
* LaTeX::
* Better image scaling::
* new speed commands::
* Formatted copy and paste::

LaTeX

* Latex classes that scimax knows about::

Writing tools

* Spell-checking::
* Autoformat::
* Track changes::
* Highlighting and annotation::
* org-ref::
* Publishing (ox-manuscript)::

Publishing (ox-manuscript)

* Manuscript templates::

Bibliography management

* Searching your bibliography files::
* Bibtex entries::
* Bibtex hotkeys::

Bibtex entries

* Article (Article in Journal)::
* InProceedings (Article in Conference Proceedings)::
* InCollection (Article in a Collection)::
* InBook (Chapter or Pages in a Book)::
* Proceedings (Conference Proceedings)::
* Book (Book)::
* Booklet (Booklet (Bound, but no Publisher)): Booklet (Booklet (Bound but no Publisher)).
* PhdThesis (PhD. Thesis): PhdThesis (PhD Thesis).
* MastersThesis (Master's Thesis)::
* TechReport (Technical Report)::
* Manual (Technical Manual)::
* Unpublished (Unpublished)::
* Misc (Miscellaneous)::

Email utilities

* html mail::
* mail merge::

Magit

* Basic magit::
* Intermediate concepts::
* Advanced concepts::

Basic magit

* Create a git repo::
* Clone a repo::
* Check the status of your repo::
* Stage a file::
* Commit a file::
* Diffs::
* See the log::
* Push::
* Pull::
* Run a command-line git command manually::
* Check the output of the git command::
* Keybindings::

Intermediate concepts

* Checkout an older version of a file::
* Search the commit messages for a pattern::
* Revert a commit::
* Tag a version::
* Checkout an existing branch.: Checkout an existing branch.
* Merge two branches::
* Resolving conflicts::
* Fetching::
* Add a remote::
* Stashing::
* Git blame::

Advanced concepts

* Resetting::
* Rebasing::
* Create patches::
* Cherry-picking::
* Apply patches::
* Notes about commits::
* Cherry-picking: Cherry-picking 1.

Programming

* Python::
* Asynchronous Python::
* Jupyter/Ipython::
* Emacs-lisp::

Jupyter/Ipython

* Scimax enhancements to ob-ipython::
* Export org to ipynb::
* Using other kernels - hy::

Miscellaneous scimax utilities

* Open a bash window::
* Open Finder/Explorer::
* words::
* ore::
* org-show::
* org-db::

External Packages

* avy::
* counsel::
* helm::
* swiper::
* undo-tree::

Scientific notebook

* Archive the notebook with git::

ivy/counsel

* counsel-find-file::

Appendix

* Emacs::

Emacs

* Getting help on Emacs functions::
* Getting help on system commands::
* What happens if I press a key?::
* How do I learn shortcuts?::

Archive

* Navigation - navy::
* Hotspots::


File: scimax.info,  Node: Org-mode,  Next: Writing tools,  Prev: Top,  Up: Top

1 Org-mode
**********

scimax provides a lot of customization of org-mode. Here are some of
the more important ones.

* Menu:

* Markup shortcuts::
* Block expansions in org-mode::
* LaTeX::
* Better image scaling::
* new speed commands::
* Formatted copy and paste::


File: scimax.info,  Node: Markup shortcuts,  Next: Block expansions in org-mode,  Up: Org-mode

1.1 Markup shortcuts
====================

scimax defines some shortcuts for org-mode markup. You can select text
and type the shortcut to wrap the region in the markup, or if on a
word, type the shortcut to wrap the word, or type the short cut to
create the markup with the cursor inside it to keep typing.

   Note these modifier keys:

S   shift
M   alt/meta
C   Ctrl
s   super
H   hyper

   Notation like s-b means press super and b together.

markup              keyshortcut   emacs-command
------------------------------------------------------------------------ 
*Bold*              s-b           `org-bold-region-or-point'
_italics_           s-i           `org-italics-region-or-point'
`verbatim'          s-v           `org-verbatim-region-or-point'
`code'              s-c           `org-code-region-or-point'
underline           s-u           `org-underline-region-or-point'
strike              s-+           `org-strikethrough-region-or-point'
_{subscript}        s-            `org-subscript-region-or-point'
^{superscript}      s-=           `org-superscript-region-or-point'
                    s-4           `org-latex-math-region-or-point'
                    C-u s-4       
                    C-u C-u 4     
°                  s-e           `ivy-insert-org-entity'

   Use  `ivy-insert-org-entity' (s-e) for all accented characters.


File: scimax.info,  Node: Block expansions in org-mode,  Next: LaTeX,  Prev: Markup shortcuts,  Up: Org-mode

1.2 Block expansions in org-mode
================================

The following examples show the shortcuts defined in scimax for
expansion. Put your cursor after the shortcut and press tab to expand
them.

     <ip
     #+BEGIN_SRC ipython :session :results output org drawer

     #+END_SRC

     <p
     #+BEGIN_SRC python :results org drawer

     #+END_SRC

     <por
     #+BEGIN_SRC python :results output raw

     #+END_SRC

     <pv
     #+BEGIN_SRC python :results value

     #+END_SRC

     <el
     #+BEGIN_SRC emacs-lisp

     #+END_SRC

     <sh
     #+BEGIN_SRC sh

     #+END_SRC

     <lh
     #+latex_header:

     <lc
     # +latex_class:

     <lco
     #+latex_class_options:

     <ao
     #+attr_org:

     <al
     #+attr_latex:

     <ca
     #+caption:

     <tn
     #+tblname:

     <n
     #+name:

     Here are some convenient table expansions.

     <t
     |  |

     <tt
     |  |   |

     <ttt
     |  |   |   |

     <tttt
     |  |   |   |   |

     <ttttt
     |  |   |   |   |   |

     <tttttt
     |  |   |   |   |   |   |


File: scimax.info,  Node: LaTeX,  Next: Better image scaling,  Prev: Block expansions in org-mode,  Up: Org-mode

1.3 LaTeX
=========

For numbered LaTeX equations, scimax will make sure that the overlays
have correct numbers on them.

* Menu:

* Latex classes that scimax knows about::


File: scimax.info,  Node: Latex classes that scimax knows about,  Up: LaTeX

1.3.1 Latex classes that scimax knows about
-------------------------------------------

Here is a list of installed latex classes.
     (mapcar 'car org-latex-classes)

cmu-memo   gMOS2e   nature   elsarticle   svjour3   revtex4-1   achemso   article-nodefaults   article-no-defaults   article-1   article   report   book


File: scimax.info,  Node: Better image scaling,  Next: new speed commands,  Prev: LaTeX,  Up: Org-mode

1.4 Better image scaling
========================

Image rescaling in org-mode/Emacs used to require an Emacs with
imagemagick support compiled in. This is a problem on Windows. Scimax
support image rescaling with an external imagemagick program called
mogrify. You can rescale the appearance of an image in org-mode by
adding an attribute like this above the figure.

   where resize-option is one of:
N%     to scale the image by a percentage.
N      to set the width, keeping the aspect ratio constant.
xN     to set the height, keeping the aspect ratio constant.
NxM!   to set the width and height, ignoring the aspect ratio.

   Here are some examples.

[image src="./org-show/taskbar.png"]

Figure: An unscaled image.

[image src="./org-show/taskbar.png"]

[image src="./org-show/taskbar.png"]

[image src="./org-show/taskbar.png"]

[image src="./org-show/taskbar.png"]

[image src="./org-show/taskbar.png"]


File: scimax.info,  Node: new speed commands,  Next: Formatted copy and paste,  Prev: Better image scaling,  Up: Org-mode

1.5 new speed commands
======================

scimax defines these new speed commands that are active when the cursor
is on the first character of a headline.

m   Mark the subtree
S   widen
k   kill the subtree
q   jump to a headline with avy
T   org-teleport (move headline)

   The best way to see other speed commands is to put your cursor at
the beginning of a headline and press ?. You can also run
`org-speed-command-help' to see a full list of speed commands.


File: scimax.info,  Node: Formatted copy and paste,  Prev: new speed commands,  Up: Org-mode

1.6 Formatted copy and paste
============================

`ox-clip-formatted-copy' provides a way to copy org-mode with
formatting so it can be pasted into other programs like MS Word and web
browsers. It does this by copying the selected text to the HTML
clipboard.


File: scimax.info,  Node: Writing tools,  Next: Bibliography management,  Prev: Org-mode,  Up: Top

2 Writing tools
***************

* Menu:

* Spell-checking::
* Autoformat::
* Track changes::
* Highlighting and annotation::
* org-ref::
* Publishing (ox-manuscript)::


File: scimax.info,  Node: Spell-checking,  Next: Autoformat,  Up: Writing tools

2.1 Spell-checking
==================

scimax is configured with flyspell and flycheck on. When you mispell a
word it will be underlined in red, and you will see a message in the
minibuffer that tells you how to fix it (C-;). Type that, and you will
be able to fix the word spelling without losing your place! Not only
that, but the correction will be saved as an abbreviation so it will
auto correct every time you make the mistake again! Note this only
works for single word corrections (i.e. the correction cannot be a two
word correction).

   If the word is correct, you can type M-o s to save the word in your
dictionary so you will not see it as misspelled again.


File: scimax.info,  Node: Autoformat,  Next: Track changes,  Prev: Spell-checking,  Up: Writing tools

2.2 Autoformat
==============

Scimax will auto-format several things for you.

  1. Ordinal numbers, e.g. 1st to 1^st.

  2. Fractions: 1/4 to ¼

  3. Some superscripts, e.g. cm2  to cm^2

  4. Transposed cAps, e.g. tHe to The

   These are controlled by the following variables you can customize
(they default to t):
   * `scimax-autoformat-ordinals'

   * `scimax-autoformat-fractions'

   * `scimax-autoformat-superscript'

   * `scimax-autoformat-transposed-caps'

   To get the autoformatting you have to enable
`scimax-autoformat-mode'. If you want it on all the time, add something
like this to your init files:

     (add-hook 'org-mode-hook 'scimax-autoformat-mode)

   scimax also defines some abbreviations that you can toggle on and
off. The abbreviations are defined in these variables:

  1. Auto-capitalization of weekdays and months, e.g. Monday and June.
       1. `scimax-month-abbreviations'

       2. `scimax-weekday-abbreviations'

  2. Contraction expansion: cant to can not and can't  to can not
       1. `scimax-contraction-abbreviations'

  3. Commonly transposed letters in words: teh to the
       1. `scimax-transposition-abbreviations'

  4. Some common chemicals like co2 to CO_2
       1. `scimax-chemical-formula-abbreviations'

  5. Some convenience symbols like degC to °C and Ang to Å, and some
     names like norskov to Nørskov.
       1. `scimax-misc-abbreviations'

   You should be able to undo any expansion with C-/. Alternatively you
can prevent the expansion by typing C-q after the abbreviation before
the next character is typed.

   These are not on by default. You have to enable them with commands
like the one below in your init file. Use +1 to enable the abbrevs, and
-1 to disable the abbrevs that are defined in the variable.

     (scimax-toggle-abbrevs 'scimax-month-abbreviations +1)

   `scimax-toggle-abbrevs' is an interactive command you can use to
toggle the abbreviations on and off. If you run that command it will
toggle the state of the abbrevs. With a single prefix arg it will turn
them on, and with a double prefix arg turn them off.

   You can see the abbreviations defined with this command
`edit-abbrevs'.


File: scimax.info,  Node: Track changes,  Next: Highlighting and annotation,  Prev: Autoformat,  Up: Writing tools

2.3 Track changes
=================

Scimax provides some support for track changes and edit marks in
org-mode.

   `Add this text' `Delete this'  `A comment'

   The markup is clickable, and clicking on it deletes the markup.

   You can use these commands
   * `em-insert' - insert text at point

   * `em-delete' - mark the selected text for deletion

   * `em-comment' - insert a comment from minibuffer and comment
     history.

   * `em-comment-1' - insert a comment at point with buffer editing,
     and multiline comments.

   * `em-replace' - marks selected text for deletion, inserts new text

   * `em-editmarks' - list all editmarks in an ivy selection buffer.

   On an editmark you can:
   * `em-accept-edit-mark-at-point'

   * `em-reject-edit-mark-at-point'

   * `em-delete-edit-mark-at-point'

   -`em-typo' to mark a `tpyo'

   scimax provides some commands to:
   * `em-accept-all-changes'

   * `em-reject-all-changes'

   You can navigate the editmarks with:
   * `em-next-editmark'

   * `em-previous-editmark'

   Note, for the next commands, you need a working wdiff command.

   You can also create diffs between git commits using helm to select
them.
   * `em-wdiff-git'

   The commands all have key bindings. The prefix key for these is H-e.
     (loop for (char . func) in (cdr em-map) collect (list (char-to-string char) (format "`%s'" func)))

m   `em-comment'
w   `em-wdiff-git'
R   `em-reject-all-changes'
A   `em-accept-all-changes'
j   `em-reject-edit-mark-at-point'
a   `em-accept-edit-mark-at-point'
p   `em-previous-editmark'
n   `em-next-editmark'
o   `org-inlinetask-insert-task'
r   `em-replace'
l   `em-editmarks'
k   `em-delete-editmark-at-point'
d   `em-delete'
i   `em-insert'
c   `em-comment-1'
t   `em-typo'


File: scimax.info,  Node: Highlighting and annotation,  Next: org-ref,  Prev: Track changes,  Up: Writing tools

2.4 Highlighting and annotation
===============================

Scimax provides some support for highlighting, comment overlays, and
edit marks.

   The main way to access the functions is via a hydra menu:
`ov-highlighter/body' that is bound to H-h (hyper-h).

   The highlights are not part of org-mode, and they do not export to
any backend. The highlights should work in any kind of file.


File: scimax.info,  Node: org-ref,  Next: Publishing (ox-manuscript),  Prev: Highlighting and annotation,  Up: Writing tools

2.5 org-ref
===========

org-ref is the answer to citations and bibliographies in scientific
writing. Run `org-ref-help'  and read it.


File: scimax.info,  Node: Publishing (ox-manuscript),  Prev: org-ref,  Up: Writing tools

2.6 *TODO* Publishing (ox-manuscript)
=====================================

The key-binding C-c C-e j should enter the ox-manuscript export menu.
This process differs from the regular export process in a number of
ways. It will detect if bibtex, makeindex, or  makeglossary, and if
minted is used, -shell-escape will automatically be used with pdflatex.
The function `ox-manuscript-latex-pdf-process' handles all of that.

   Additionally, you can generate different outputs of an org-file:

`ox-manuscript-build-submission-manuscript-and-open'
     creates a standalone tex file with embedded bibliography, and
     image extensions stripped, and the pdf file.

`ox-manuscript-make-submission-archive'
     creates a directory containing all the files you normally need for
     submission.

`ox-manuscript-toggle-interactive-build'
     if you are having trouble building a PDF, this will show you what
     happens at each step.


     `ox-manuscript-nobibliography'

`ox-manuscript-texcount'
     Estimate how many words are in your manuscript. For when you are
     limited to a fixed number of words.

* Menu:

* Manuscript templates::


File: scimax.info,  Node: Manuscript templates,  Up: Publishing (ox-manuscript)

2.6.1 Manuscript templates
--------------------------

We have templates prepared for the following manuscripts, proposals and
documents.

     (mapcar (lambda (x) (list (plist-get x :template))) (ox-manuscript-candidates))

ACS Applied Materials and Interfaces
ACS Catalysis
ACS -Industrial & Engineering Chemistry Research
ACS - Journal of Physical Chemistry C
ACS J. Physical Chemistry Letters
AIP - J. Chemical Physics
Annual student review
Physical Review B
Physical Review Letters
CMU ChemE Written Proposal
CMU ChemE Written Qualifier
CMU ChemE Written Qualifier
Int. J. Greenhouse Gas Control - Elsevier
Cover letter for manuscript submission
Nature
NSF Proposal - Biographical sketch
NSF Proposal - Checklist
NSF Proposal - Current and pending
NSF Proposal - data management plan
NSF Proposal - Facilities, Equipment, and other Resources
NSF Proposal - postdoctoral mentoring plan
NSF Proposal - Project description
NSF Proposal - Project summary
NSF Proposal - Statement of work
Response to reviewers
Surface Science - Elsevier
Taylor & Francis Molecular Simulation
Weekly progress report
Wiley - Int. J. Quantum Chemistry

   * `ox-manuscript-new-ivy'

   * `ox-manuscript-new-helm'


File: scimax.info,  Node: Bibliography management,  Next: Email utilities,  Prev: Writing tools,  Up: Top

3 Bibliography management
*************************

Bibliographies in scimax are stored in bibtex files. A bibtex file is a
plain text file containing bibtex entries. Each entry describes an
item. Here is a typical example.

     @article{kitchin-2015-examp,f
       author =         {Kitchin, John R.},
       title =         {Examples of Effective Data Sharing in Scientific Publishing},
       journal =         {ACS Catalysis},
       volume =         {5},
       number =         {6},
       pages =         {3894-3899},
       year =         2015,
       doi =                 {10.1021/acscatal.5b00538},
       url =                 { http://dx.doi.org/10.1021/acscatal.5b00538 },
       keywords =         {DESC0004031, early-career, orgmode, Data sharing },
       eprint =         { http://dx.doi.org/10.1021/acscatal.5b00538 },
     }

   This entry identifies the item as an article, labels it with a key
(kitchin-2015-examp), and describes the details of the item in a series
of key = {value} lines. You can learn more about bibtex here
`http://www.bibtex.org'.

   If you know the DOI I recommend you use `doi-add-bibtex-entry' as
much as possible to add bibtex entries to your bibliography files. This
will add properly formatted and cleaned entries and download the pdf if
it knows how. You may also find `crossref-add-bibtex-entry' useful if
you have a freeform citation and want to search for it.

   In a bibtex file, `org-ref-bibtex-hydra/body' will give you a menu
of options to do things on an entry including:

  1. Search pubmed, WebOfScience (wos), wos-citing, wos-related,
     crossref, and google scholar using the DOI or title of the entry.

  2. Clean the entry, replace non-ascii characters, sort the entry
     fields, or change the case of the title.

  3. Update the entry or fields using the doi.

  4. Open the notes, pdf, or url associated with the entry.

  5. Email the entry to someone

  6. Copy or cut the entry to paste somewhere

  7. Copy a formatted bibliography entry

  8. Add tags to an entry

  9. Add a new entry

   `org-ref-bibtex-file/body' provides menu access to bibtex file
functions:
  1. `bibtex-validate' - Checks if the file is syntactically valid, and
     for duplicate keys.

  2. `bibtex-sort-buffer'

  3. `bibtex-reformat'

  4. `bibtex-count-entries'

  5. `org-ref-build-full-bibliography'

* Menu:

* Searching your bibliography files::
* Bibtex entries::
* Bibtex hotkeys::


File: scimax.info,  Node: Searching your bibliography files,  Next: Bibtex entries,  Up: Bibliography management

3.1 Searching your bibliography files
=====================================

I like `helm-bibtex'. You type C-SPC to mark multiple entries. Type TAB
to see what actions you can perform on the entries.

   See `org-ref-help' for information on using org-ref to insert
citations.


File: scimax.info,  Node: Bibtex entries,  Next: Bibtex hotkeys,  Prev: Searching your bibliography files,  Up: Bibliography management

3.2 Bibtex entries
==================

Here are the bibtex entry types and fields you should use. You can add
extra fields like keywords, doi, url, notes, etc... to each entry.
Usually they will be ignored by bibtex, but they are useful for you.
Note that biblatex (https://www.ctan.org/pkg/biblatex?lang=en) is
considered a more powerful bibliography formatting tool, but we use
bibtex because that is what most of the publishers we use support.

     (loop for (type doc required crossref optional) in bibtex-BibTeX-entry-alist
           do
           (princ (format "\n*** %s (%s)\n" type doc))
           (princ "\n**** Required fields\n\n")
           (loop for field in required
                 do
                 (princ (format "- %s" (car field)))
                 (message "%s" field)
                 (if (>= (length field) 2)
                     (princ (format " :: %s\n" (nth 1 field)))
                   (princ "\n")))

           (princ "\n**** Optional if Crossref present but otherwise required fields\n\n")
           (loop for field in crossref
                 do
                 (princ (format "- %s" (car field)))
                 (if (>= (length field) 2)
                     (princ (format " :: %s\n" (nth 1 field)))
                   (princ "\n")))
           (princ "\n**** Optional fields\n\n")
           (loop for field in optional
                 do
                 (princ (format "- %s" (car field)))
                 (if (>= (length field) 2)
                     (princ (format " :: %s\n" (nth 1 field)))
                   (princ "\n"))))

* Menu:

* Article (Article in Journal)::
* InProceedings (Article in Conference Proceedings)::
* InCollection (Article in a Collection)::
* InBook (Chapter or Pages in a Book)::
* Proceedings (Conference Proceedings)::
* Book (Book)::
* Booklet (Booklet (Bound, but no Publisher)): Booklet (Booklet (Bound but no Publisher)).
* PhdThesis (PhD. Thesis): PhdThesis (PhD Thesis).
* MastersThesis (Master's Thesis)::
* TechReport (Technical Report)::
* Manual (Technical Manual)::
* Unpublished (Unpublished)::
* Misc (Miscellaneous)::


File: scimax.info,  Node: Article (Article in Journal),  Next: InProceedings (Article in Conference Proceedings),  Up: Bibtex entries

3.2.1 Article (Article in Journal)
----------------------------------

  1. Required fields

        * author

        * title Title of the article (BibTeX converts it to lowercase)

  2. Optional if Crossref present but otherwise required fields

        * journal

        * year

  3. Optional fields

    volume
          Volume of the journal

    number
          Number of the journal (only allowed if entry contains volume)

    pages
          Pages in the journal


          month


          note


File: scimax.info,  Node: InProceedings (Article in Conference Proceedings),  Next: InCollection (Article in a Collection),  Prev: Article (Article in Journal),  Up: Bibtex entries

3.2.2 InProceedings (Article in Conference Proceedings)
-------------------------------------------------------

  1. Required fields

        * author

        * title Title of the article in proceedings (BibTeX converts it
          to lowercase)

  2. Optional if Crossref present but otherwise required fields

    booktitle
          Name of the conference proceedings


          year

  3. Optional fields

        * editor

        * volume Volume of the conference proceedings in the series

        * number Number of the conference proceedings in a small series
          (overwritten by volume)

        * series Series in which the conference proceedings appeared

        * pages Pages in the conference proceedings

        * month

        * address

        * organization Sponsoring organization of the conference

        * publisher Publishing company, its location

        * note


File: scimax.info,  Node: InCollection (Article in a Collection),  Next: InBook (Chapter or Pages in a Book),  Prev: InProceedings (Article in Conference Proceedings),  Up: Bibtex entries

3.2.3 InCollection (Article in a Collection)
--------------------------------------------

  1. Required fields

        * author

        * title Title of the article in book (BibTeX converts it to
          lowercase)

        * booktitle Name of the book

  2. Optional if Crossref present but otherwise required fields

        * publisher

        * year

  3. Optional fields

        * editor

        * volume Volume of the book in the series

        * number Number of the book in a small series (overwritten by
          volume)

        * series Series in which the book appeared

        * type Word to use instead of "chapter"

        * chapter Chapter in the book

        * pages Pages in the book

        * edition Edition of the book as a capitalized English word

        * month

        * address

        * note


File: scimax.info,  Node: InBook (Chapter or Pages in a Book),  Next: Proceedings (Conference Proceedings),  Prev: InCollection (Article in a Collection),  Up: Bibtex entries

3.2.4 InBook (Chapter or Pages in a Book)
-----------------------------------------

  1. Required fields

    author
          nil

    editor
          nil

    title
          Title of the book

    chapter
          Chapter in the book

  2. Optional if Crossref present but otherwise required fields

        * publisher

        * year

  3. Optional fields

    volume
          Volume of the book in the series

    number
          Number of the book in a small series (overwritten by volume)

    series
          Series in which the book appeared

    type
          Word to use instead of "chapter"


          address

    edition
          Edition of the book as a capitalized English word


          month

    pages
          Pages in the book


          note


File: scimax.info,  Node: Proceedings (Conference Proceedings),  Next: Book (Book),  Prev: InBook (Chapter or Pages in a Book),  Up: Bibtex entries

3.2.5 Proceedings (Conference Proceedings)
------------------------------------------

  1. Required fields

    title
          Title of the conference proceedings


          year

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

    booktitle
          Title of the proceedings for cross references


          editor

    volume
          Volume of the conference proceedings in the series

    number
          Number of the conference proceedings in a small series
          (overwritten by volume)

    series
          Series in which the conference proceedings appeared


          address


          month

    organization
          Sponsoring organization of the conference

    publisher
          Publishing company, its location


          note


File: scimax.info,  Node: Book (Book),  Next: Booklet (Booklet (Bound but no Publisher)),  Prev: Proceedings (Conference Proceedings),  Up: Bibtex entries

3.2.6 Book (Book)
-----------------

  1. Required fields

    author
          nil

    editor
          nil

    title
          Title of the book

  2. Optional if Crossref present but otherwise required fields

        * publisher

        * year

  3. Optional fields

    volume
          Volume of the book in the series

    number
          Number of the book in a small series (overwritten by volume)

    series
          Series in which the book appeared


          address

    edition
          Edition of the book as a capitalized English word


          month


          note


File: scimax.info,  Node: Booklet (Booklet (Bound but no Publisher)),  Next: PhdThesis (PhD Thesis),  Prev: Book (Book),  Up: Bibtex entries

3.2.7 Booklet (Booklet (Bound, but no Publisher))
-------------------------------------------------

  1. Required fields

    title
          Title of the booklet (BibTeX converts it to lowercase)

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

        * author

        * howpublished The way in which the booklet was published

        * address

        * month

        * year

        * note


File: scimax.info,  Node: PhdThesis (PhD Thesis),  Next: MastersThesis (Master's Thesis),  Prev: Booklet (Booklet (Bound but no Publisher)),  Up: Bibtex entries

3.2.8 PhdThesis (PhD. Thesis)
-----------------------------

  1. Required fields

        * author

        * title Title of the PhD. thesis

        * school School where the PhD. thesis was written

        * year

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

    type
          Type of the PhD. thesis

    address
          Address of the school (if not part of field "school") or
          country


          month


          note


File: scimax.info,  Node: MastersThesis (Master's Thesis),  Next: TechReport (Technical Report),  Prev: PhdThesis (PhD Thesis),  Up: Bibtex entries

3.2.9 MastersThesis (Master's Thesis)
-------------------------------------

  1. Required fields

        * author

        * title Title of the master's thesis (BibTeX converts it to
          lowercase)

        * school School where the master's thesis was written

        * year

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

    type
          Type of the master's thesis (if other than "Master's thesis")

    address
          Address of the school (if not part of field "school") or
          country


          month


          note


File: scimax.info,  Node: TechReport (Technical Report),  Next: Manual (Technical Manual),  Prev: MastersThesis (Master's Thesis),  Up: Bibtex entries

3.2.10 TechReport (Technical Report)
------------------------------------

  1. Required fields

        * author

        * title Title of the technical report (BibTeX converts it to
          lowercase)

        * institution Sponsoring institution of the report

        * year

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

    type
          Type of the report (if other than "technical report")

    number
          Number of the technical report


          address


          month


          note


File: scimax.info,  Node: Manual (Technical Manual),  Next: Unpublished (Unpublished),  Prev: TechReport (Technical Report),  Up: Bibtex entries

3.2.11 Manual (Technical Manual)
--------------------------------

  1. Required fields

    title
          Title of the manual

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

        * author

        * organization Publishing organization of the manual

        * address

        * edition Edition of the manual as a capitalized English word

        * month

        * year

        * note


File: scimax.info,  Node: Unpublished (Unpublished),  Next: Misc (Miscellaneous),  Prev: Manual (Technical Manual),  Up: Bibtex entries

3.2.12 Unpublished (Unpublished)
--------------------------------

  1. Required fields

        * author

        * title Title of the unpublished work (BibTeX converts it to
          lowercase)

        * note

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

        * month

        * year


File: scimax.info,  Node: Misc (Miscellaneous),  Prev: Unpublished (Unpublished),  Up: Bibtex entries

3.2.13 Misc (Miscellaneous)
---------------------------

  1. Required fields

  2. Optional if Crossref present but otherwise required fields

  3. Optional fields

        * author

        * title Title of the work (BibTeX converts it to lowercase)

        * howpublished The way in which the work was published

        * month

        * year

        * note


File: scimax.info,  Node: Bibtex hotkeys,  Prev: Bibtex entries,  Up: Bibliography management

3.3 Bibtex hotkeys
==================

Scimax provides hotkeys for when your cursor is on the @ at the
beginning of an entry. Here are the currently defined hotkeys.

     (require 'bibtex-hotkeys)
     (loop for (key . desc) in bibtex-hotkeys collect (list key desc))

y   Paste last entry
w   Move entry down
T   Title-case article
S   Sentence-case title
s   Move entry up
F   Jump to field with avy
?   Show hotkeys
p   Jump to previous entry
n   Jump to next entry
I   Inspect
l   Clean entry
k   Kill the entry
f   Copy formatted
e   Email entry
c   Copy entry
b   Open in browser


File: scimax.info,  Node: Email utilities,  Next: Contacts,  Prev: Bibliography management,  Up: Top

4 Email utilities
*****************

`email-buffer'
     email the whole buffer

`email-region'
     emails selected region

`email-heading'
     email the current heading, including properties, deadlines, etc...

`email-heading-body'
     email just the body of the current heading

`email-bibtex-entry'
     email the bibtex entry at point

* Menu:

* html mail::
* mail merge::


File: scimax.info,  Node: html mail,  Next: mail merge,  Up: Email utilities

4.1 html mail
=============

You can send html email from org-mode.

   From an org-file run `org-mime'. You will be prompted for the scope
to send, which is either the whole buffer, the heading you are in, or
the selected region. Then you will select how to make the email: html
will export the text to html and put it in an email, and htmlize will
use the htmlize library to generate the html.

   Alternatively, you may want to type org-mode directly in an email
buffer. Use `org-mime-compose-mail' to do that.


File: scimax.info,  Node: mail merge,  Prev: html mail,  Up: Email utilities

4.2 mail merge
==============

scimax provides some tools to do a mail merge in org-mode. The idea is
to run `mail-merge-make-headings' with a template and data-source to
generate a series of org-mode headings that are the messages. You can
inspect these, edit them if needed, and then run `mail-merge' to
actually send them. Each heading will be tagged as sent, and marked
DONE.


File: scimax.info,  Node: Contacts,  Next: Google,  Prev: Email utilities,  Up: Top

5 Contacts
**********

scimax provides a emacs-lisp library to interface with a contact
database written in org-mode.

   First, add some org-files to the variable `contacts-files'. Any
headline in these files that has an EMAIL property will be considered a
contact. Then, you can search your database with `ivy-contacts' or
`helm-contacts'. There are a variety of actions to choose from ranging
from inserting email addresses, copying properties, opening contact
urls, etc...

   See `contacts-help' for more information.


File: scimax.info,  Node: Google,  Next: Magit,  Prev: Contacts,  Up: Top

6 Google
********

google-this (https://github.com/Malabarba/emacs-google-this) is
installed in scimax. You can use these commands to search for things
from Emacs:

   C-c / SPC        `google-this-region' C-c / a
`google-this-ray' C-c / c
`google-this-translate-query-or-region' C-c / e
`google-this-error' C-c / f                `google-this-forecast' C-c /
g                `google-this-lucky-search' C-c / i
`google-this-lucky-and-insert-url' C-c / l
`google-this-line' C-c / m                `google-maps' C-c / n
      `google-this-noconfirm' C-c / r
`google-this-cpp-reference' C-c / s                `google-this-symbol'
C-c / t                `google-this' C-c / w
`google-this-word' C-c / <return>        `google-this-search'


File: scimax.info,  Node: Magit,  Next: Project management - projectile,  Prev: Google,  Up: Top

7 Magit
*******

Magit is a front-end for git version control. There is a good manual
here: *Note info:magit#Top: (magit)Top.

* Menu:

* Basic magit::
* Intermediate concepts::
* Advanced concepts::


File: scimax.info,  Node: Basic magit,  Next: Intermediate concepts,  Up: Magit

7.1 Basic magit
===============

* Menu:

* Create a git repo::
* Clone a repo::
* Check the status of your repo::
* Stage a file::
* Commit a file::
* Diffs::
* See the log::
* Push::
* Pull::
* Run a command-line git command manually::
* Check the output of the git command::
* Keybindings::


File: scimax.info,  Node: Create a git repo,  Next: Clone a repo,  Up: Basic magit

7.1.1 Create a git repo
-----------------------

*Note info:magit#Repository setup: (magit)Repository setup.  You can
create a git repo with M-x magit-init. This will create a git-repo in
the current directory.

     (magit-init)

   `magit-init'


File: scimax.info,  Node: Clone a repo,  Next: Check the status of your repo,  Prev: Create a git repo,  Up: Basic magit

7.1.2 Clone a repo
------------------

*Note info:magit#Repository setup: (magit)Repository setup.

   M-x magit-clone

   This will prompt you for a repo, which is either a url, or a path,
and a path to clone it to.

   `magit-clone'


File: scimax.info,  Node: Check the status of your repo,  Next: Stage a file,  Prev: Clone a repo,  Up: Basic magit

7.1.3 Check the status of your repo
-----------------------------------

*Note info:magit#Status buffer: (magit)Status buffer.

   Run M-x magit-status to see the status of your repo.

   Press "g" in the window to refresh it.

   press "n" (next) or "p" (previous) to navigate in this window.

   `magit-status'


File: scimax.info,  Node: Stage a file,  Next: Commit a file,  Prev: Check the status of your repo,  Up: Basic magit

7.1.4 Stage a file
------------------

*Note info:magit#Staging and unstaging: (magit)Staging and unstaging.

   In the magit-status window, put your cursor on an unstaged file and
press "s".

   If you press TAB on the file, it will expand to show the changes
that are unstaged. Deletions show in red, and additions in green. The
changes are in "hunks".

   You can unstage a file with "u"


File: scimax.info,  Node: Commit a file,  Next: Diffs,  Prev: Stage a file,  Up: Basic magit

7.1.5 Commit a file
-------------------

*Note info:magit#Initiating a commit: (magit)Initiating a commit.

   *Note info:magit#Editing commit messages: (magit)Editing commit
messages.

   In the magit-status window with some files that are staged, press
"c", review the options, and probably press "c" again. Enter a commit
message and type "C-c C-c" to commit it, or "C-c C-k" to cancel it.


File: scimax.info,  Node: Diffs,  Next: See the log,  Prev: Commit a file,  Up: Basic magit

7.1.6 Diffs
-----------

*Note info:magit#Diffing: (magit)Diffing.

   From the magit-status window, press "d" then "d" to see what has
changed.


File: scimax.info,  Node: See the log,  Next: Push,  Prev: Diffs,  Up: Basic magit

7.1.7 See the log
-----------------

*Note info:magit#Logging: (magit)Logging.

   In the magit-status window press "l", review the options, and press
"l" again.

   If you want to see only the commits that affected a file, in the
magit-status window press "l" then "=f", enter the filename, and then
press "l" again.


File: scimax.info,  Node: Push,  Next: Pull,  Prev: See the log,  Up: Basic magit

7.1.8 Push
----------

*Note info:magit#Pushing: (magit)Pushing.

   In the magit-status window press "P" then "p".

   Note that tags don't normally get pushed, but there are options ("T"
to push a tag, and "t" to push all tags).


File: scimax.info,  Node: Pull,  Next: Run a command-line git command manually,  Prev: Push,  Up: Basic magit

7.1.9 Pull
----------

*Note info:magit#Pulling: (magit)Pulling.  In the magit-status window
press "F" then "p".


File: scimax.info,  Node: Run a command-line git command manually,  Next: Check the output of the git command,  Prev: Pull,  Up: Basic magit

7.1.10 Run a command-line git command manually
----------------------------------------------

*Note info:magit#Running Git manually: (magit)Running Git manually.  In
the magit-status window, type "!" to get the popup and choose what you
want to do (e.g. where to run the command, etc... You do not need to
type "git" in the command. Note you can also run a shell command from
this interface.


File: scimax.info,  Node: Check the output of the git command,  Next: Keybindings,  Prev: Run a command-line git command manually,  Up: Basic magit

7.1.11 Check the output of the git command
------------------------------------------

Press "$"


File: scimax.info,  Node: Keybindings,  Prev: Check the output of the git command,  Up: Basic magit

7.1.12 Keybindings
------------------

*Note info:magit#Keystroke Index: (magit)Keystroke Index.


File: scimax.info,  Node: Intermediate concepts,  Next: Advanced concepts,  Prev: Basic magit,  Up: Magit

7.2 Intermediate concepts
=========================

* Menu:

* Checkout an older version of a file::
* Search the commit messages for a pattern::
* Revert a commit::
* Tag a version::
* Checkout an existing branch.: Checkout an existing branch.
* Merge two branches::
* Resolving conflicts::
* Fetching::
* Add a remote::
* Stashing::
* Git blame::


File: scimax.info,  Node: Checkout an older version of a file,  Next: Search the commit messages for a pattern,  Up: Intermediate concepts

7.2.1 Checkout an older version of a file
-----------------------------------------

Use M-x magit-checkout-file select the branch, or enter a revision, and
then choose a file.

   `magit-checkout-file'

   `magit-find-file' `magit-find-file-other-window'


File: scimax.info,  Node: Search the commit messages for a pattern,  Next: Revert a commit,  Prev: Checkout an older version of a file,  Up: Intermediate concepts

7.2.2 Search the commit messages for a pattern
----------------------------------------------

In a magit-status window press "l =g" enter a pattern to grep for, and
then press "l".


File: scimax.info,  Node: Revert a commit,  Next: Tag a version,  Prev: Search the commit messages for a pattern,  Up: Intermediate concepts

7.2.3 Revert a commit
---------------------

*Note info:magit#Reverting: (magit)Reverting.

   Got to the log, select the commit and type "V" then "V".


File: scimax.info,  Node: Tag a version,  Next: Checkout an existing branch,  Prev: Revert a commit,  Up: Intermediate concepts

7.2.4 Tag a version
-------------------

*Note info:magit#Tagging: (magit)Tagging.

   press "t" in the magit-status window. You can then create a tag,
annotate it, delete tags, and prune them.


File: scimax.info,  Node: Checkout an existing branch,  Next: Merge two branches,  Prev: Tag a version,  Up: Intermediate concepts

7.2.5 Checkout an existing branch.
----------------------------------

*Note info:magit#The branch popup: (magit)The branch popup.

   In the magit-status window press "b" then "b" and choose the branch.

   To checkout a new branch, in the magit-status window press "b" then
"c". Choose the branch to start from then a name for the new branch.


File: scimax.info,  Node: Merge two branches,  Next: Resolving conflicts,  Prev: Checkout an existing branch,  Up: Intermediate concepts

7.2.6 Merge two branches
------------------------

*Note info:magit#Merging: (magit)Merging.

   In the magit-status window press "m", then "m" and select the branch
to merge into the current one.


File: scimax.info,  Node: Resolving conflicts,  Next: Fetching,  Prev: Merge two branches,  Up: Intermediate concepts

7.2.7 *TODO* Resolving conflicts
--------------------------------

*Note info:magit#Resolving conflicts: (magit)Resolving conflicts.

   You will probably also want to get familiar with *Note
info:ediff#Top: (ediff)Top.

   On a file in a magit-status window, press "e" to enter the 3-window
ediff view. The A window is the version at HEAD, the B window is what
is in the index, and the C window is the current version.


File: scimax.info,  Node: Fetching,  Next: Add a remote,  Prev: Resolving conflicts,  Up: Intermediate concepts

7.2.8 Fetching
--------------

*Note info:magit#Fetching: (magit)Fetching.

   In the magit-status window press "f".


File: scimax.info,  Node: Add a remote,  Next: Stashing,  Prev: Fetching,  Up: Intermediate concepts

7.2.9 Add a remote
------------------

*Note info:magit#Remotes: (magit)Remotes.

   M-x magit-remote-add then enter an alias, and the url.


File: scimax.info,  Node: Stashing,  Next: Git blame,  Prev: Add a remote,  Up: Intermediate concepts

7.2.10 Stashing
---------------

*Note info:magit#Stashing: (magit)Stashing.

   Press "z" in the magit-status window


File: scimax.info,  Node: Git blame,  Prev: Stashing,  Up: Intermediate concepts

7.2.11 *TODO* Git blame
-----------------------


File: scimax.info,  Node: Advanced concepts,  Prev: Intermediate concepts,  Up: Magit

7.3 Advanced concepts
=====================

* Menu:

* Resetting::
* Rebasing::
* Create patches::
* Cherry-picking::
* Apply patches::
* Notes about commits::
* Cherry-picking: Cherry-picking 1.


File: scimax.info,  Node: Resetting,  Next: Rebasing,  Up: Advanced concepts

7.3.1 Resetting
---------------

*Note info:magit#Resetting: (magit)Resetting.


File: scimax.info,  Node: Rebasing,  Next: Create patches,  Prev: Resetting,  Up: Advanced concepts

7.3.2 Rebasing
--------------

*Note info:magit#Rebasing: (magit)Rebasing.

  1. Interactve rebasing

     Open the log, select the oldest commit you want to rebase on then
     press "r" and then "i". Use M-p and M-n to move commits around.
     Press "s" on any commits you want to squash into the commit above
     it. C-c C-c will start the commands.

     From the magit-status on unpushed commits, you can also press "r"
     to get the rebase popup.

  2. Reword a commit message

     "r w" allows you to reword the commit message.


File: scimax.info,  Node: Create patches,  Next: Cherry-picking,  Prev: Rebasing,  Up: Advanced concepts

7.3.3 Create patches
--------------------

*Note info:magit#Creating and sending patches: (magit)Creating and
sending patches.

   In magit-status window, press "W"

   "W p" creates patches "W r" makes a pull request. This just creates
an email with information in it. It is not a GitHUB request, and it is
only useful if there is a public, external copy of the repo.


File: scimax.info,  Node: Cherry-picking,  Next: Apply patches,  Prev: Create patches,  Up: Advanced concepts

7.3.4 Cherry-picking
--------------------

*Note info:magit#Cherry picking: (magit)Cherry picking.

   Press "A"


File: scimax.info,  Node: Apply patches,  Next: Notes about commits,  Prev: Cherry-picking,  Up: Advanced concepts

7.3.5 Apply patches
-------------------

*Note info:magit#Applying patches: (magit)Applying patches.


File: scimax.info,  Node: Notes about commits,  Next: Cherry-picking 1,  Prev: Apply patches,  Up: Advanced concepts

7.3.6 Notes about commits
-------------------------

*Note info:magit#Notes: (magit)Notes.

   Press "T" to attach a note.

   A typical use of notes is to supplement a commit message without
changing the         commit itself. Notes can be shown by git log along
with the original         commit message. To distinguish these notes
from the message stored in         the commit object, the notes are
indented like the message, after an         unindented line saying
"Notes (<refname>):" (or "Notes:" for         refs/notes/commits).


File: scimax.info,  Node: Cherry-picking 1,  Prev: Notes about commits,  Up: Advanced concepts

7.3.7 Cherry-picking
--------------------

*Note info:magit#Cherry picking: (magit)Cherry picking.


File: scimax.info,  Node: Project management - projectile,  Next: Programming,  Prev: Magit,  Up: Top

8 Project management - projectile
*********************************

`https://github.com/bbatsov/projectile' for project management. A
project is basically a directory under version control, e.g. git.

   Projectile makes it easy to jump to projects, find files in
projects, search projects, etc...

C-c p p   Switch to a project
C-c p k   Kill project buffers

   You can see all the key bindings with C-c p C-h.

   While in a project, you may want to try:

   `helm-projectile-grep' or `counsel-git-grep' to search all project
files for a phrase.


File: scimax.info,  Node: Programming,  Next: RSS feeds,  Prev: Project management - projectile,  Up: Top

9 Programming
*************

* Menu:

* Python::
* Asynchronous Python::
* Jupyter/Ipython::
* Emacs-lisp::


File: scimax.info,  Node: Python,  Next: Asynchronous Python,  Up: Programming

9.1 Python
==========

   * scimax is setup with `elpy-mode'.

   * `pydoc' provides nice, hyperlinked documentation for python.


File: scimax.info,  Node: Asynchronous Python,  Next: Jupyter/Ipython,  Prev: Python,  Up: Programming

9.2 Asynchronous Python
=======================

You can run python blocks asynchronously with M-x
`org-babel-async-execute:python' with the cursor in a code block. This
will allow you to keep typing, and show you a buffer with the progress
of your code block. When it is done, the results will be inserted into
the buffer where it belongs when the job is done. A temporary hash mark
will go in the results.

   You can make this the default behavior by adding this to your init
file:

     (add-to-list 'org-ctrl-c-ctrl-c-hook 'org-babel-async-execute:python)


File: scimax.info,  Node: Jupyter/Ipython,  Next: Emacs-lisp,  Prev: Asynchronous Python,  Up: Programming

9.3 Jupyter/Ipython
===================

If you like sessions in Python, the ob-ipython library is better than
the default ob-python in org-mode.

   Pygments doesn't support ipython out of the box for some reason,
which is a problem if you want to export your src block to LaTeX.
scimax fixes this for you and automatically installs this if you don't
already have it.

   ob-ipython allows you to use Ipython magic commands in your src
blocks. Here is a protypical Ipython src block with a line magic.

     %time print("hello world")
     a = 6

     hello world
     CPU times: user 32 µs, sys: 5 µs, total: 37 µs
     Wall time: 39.8 µs

   And a block with cell magic.

     %%timeit
     7

   * `ob-ipython-inspect' seems to be broken

   * `org-babel-switch-to-session' will open the IPython REPL.

   M-x `ob-ipython-interrupt-kernel' M-x `ob-ipython-kill-kernel'

* Menu:

* Scimax enhancements to ob-ipython::
* Export org to ipynb::
* Using other kernels - hy::


File: scimax.info,  Node: Scimax enhancements to ob-ipython,  Next: Export org to ipynb,  Up: Jupyter/Ipython

9.3.1 Scimax enhancements to ob-ipython
---------------------------------------

We have made a few improvements to ob-ipython. Inline images are
supported now similar to how they are supported in the Jupyter
notebook. You specify the %matplotlib inline magic, and then plots will
appear "inline" along with any output from your cell block. The plots
are saved in a directory ipython-inline-images in filenames derived
from and md5 hash of the image. You can have more than one image, and
you also get the output from your block, similar to the way the Jupyter
notebook behaves.

   You need a header like this, i.e. you need to specify the results as
output, and for them to be in a drawer so that org-mode can display the
file links.

     #+BEGIN_SRC ipython :session :results output drawer

     print('Hello world!')

     %matplotlib inline
     import matplotlib.pyplot as plt
     import numpy as np

     x = np.linspace(0, 20 * np.pi, 200)
     y = np.exp(-0.1 * x) * np.sin(x)
     plt.plot(x, y)
     plt.xlabel('x')
     plt.ylabel('y')
     plt.title('Decaying sin wave')

     # new plot
     plt.figure()
     y2 = np.exp(-0.1 * x) * np.cos(x)
     plt.plot(x, y2)
     plt.xlabel('x')
     plt.ylabel('y')
     plt.title('Decaying cosine')

   Hello world!  [image src="ipython-inline-images/ob-ipython-16d0b561f004e2fd3ff8cba4dfd648b1.png"] [image src="ipython-inline-images/ob-ipython-4c47a49cc1cb84980ecbb91aef2e5b20.png"]

   It also works with :results set to value.

     %matplotlib inline
     import matplotlib.pyplot as plt
     import numpy as np

     x = np.linspace(0, 20 * np.pi, 200)
     y = np.exp(-0.1 * x) * np.sin(x)
     plt.plot(x, y)
     plt.xlabel('x')
     plt.ylabel('y')
     plt.title('Decaying sin wave')

     a = 5
     b = 6
     a + b

   11 [image src="ipython-inline-images/ob-ipython-16d0b561f004e2fd3ff8cba4dfd648b1.png"]

   We also support HTML and Latex outputs like this. The results will
contain an HTML or LaTeX block. As with the Jupyter notebook

     from IPython.display import HTML, Latex

     HTML('H<sub>2</sub>O')

   and

     Latex('H$_2$O')

   As with the Jupyter notebook, only the last returned cell is
rendered.

  1. Asynchronous evaluation

     We finally have asynchronous execution of ipython blocks. This
     allows you to run a block, and keep working in Emacs. A temporary
     string is inserted into the results which is replaced when the
     code is done running. This command will make a clickable link to
     interrupt the kernel, or cancel the cell running. This will put
     names on every src block if they are not already named.

          import time
          time.sleep(5)
          #print(8)

          %matplotlib inline
          import matplotlib.pyplot as plt
          import numpy as np

          x = np.linspace(0, 20 * np.pi, 200)
          y1 = np.exp(-0.1 * x) * np.sin(x)
          y2 = np.exp(-0.1 * x) * np.cos(x)
          plt.plot(y1, y2)
          plt.xlabel('x')
          plt.ylabel('y')
          plt.title('Decaying spiral')

     [image src="ipython-inline-images/ob-ipython-f7122a4c0570fc3bf4ef580b97d5c1ae.png"]

     You can run all the blocks asynchronously with
     `org-babel-execute-ipython-buffer-async'. You can clear the queue
     `org-babel-async-ipython-clear-queue'.


File: scimax.info,  Node: Export org to ipynb,  Next: Using other kernels - hy,  Prev: Scimax enhancements to ob-ipython,  Up: Jupyter/Ipython

9.3.2 Export org to ipynb
-------------------------

Finally, we can export org-mode files to Jupyter notebooks with the
ox-ipynb library. If you load the library, there is a new export option
in the export menu with the letter "n". Or you can use
`ox-ipynb-export-to-ipynb-file-and-open'.


File: scimax.info,  Node: Using other kernels - hy,  Prev: Export org to ipynb,  Up: Jupyter/Ipython

9.3.3 Using other kernels - hy
------------------------------

Amazing. You can use other language kernels with ob-ipython.

   scimax provides the jupyter-hy src block to run hylang in src
blocks. The required :session and :kernel headers are automatically
provided.

     (print "hello world")
     (import time)
     (print (time.asctime))

     hello world
     Fri Jun 10 10:21:24 2016


File: scimax.info,  Node: Emacs-lisp,  Prev: Jupyter/Ipython,  Up: Programming

9.4 Emacs-lisp
==============

   * `lispy-mode' is just amazing.

   * `scimax-org-eldoc' will generate documentation on elisp libraries
     in an org-mode format.


File: scimax.info,  Node: RSS feeds,  Next: Miscellaneous scimax utilities,  Prev: Programming,  Up: Top

10 RSS feeds
************

It is a major challenge to keep up with the scientific literature.
`elfeed' is the package we use in scimax for that. It aggregates RSS
feeds and provides a pretty easy way to consume them, capture them in
to org-mode, search them, and do things with them. scimax preconfigures
elfeed with some python, and emacs feeds, and you can easily add new
feeds:

     (add-to-list 'elfeed-feeds "http://feeds.feedburner.com/acs/accacs")

   or if you want entries from a feed to be automatically tagged, e.g.
anything from Nature magazine could be tagged with nature:

     (add-to-list 'elfeed-feeds '("http://feeds.nature.com/nchem/rss/current" nature))

   Elfeed is configured to run every half hour after Emacs is started.

   On an entry you can type:
e   email entry to someone
c   capture the entry to org-mode
d   add bibtex entry

   In the list of entries you can type:
f,j   marks entry as read
o     open the entry
b     open browser to entry url
s     start a search query (see `https://github.com/skeeto/elfeed#filter-syntax')


File: scimax.info,  Node: Miscellaneous scimax utilities,  Next: External Packages,  Prev: RSS feeds,  Up: Top

11 Miscellaneous scimax utilities
*********************************

* Menu:

* Open a bash window::
* Open Finder/Explorer::
* words::
* ore::
* org-show::
* org-db::


File: scimax.info,  Node: Open a bash window,  Next: Open Finder/Explorer,  Up: Miscellaneous scimax utilities

11.1 Open a bash window
=======================

`bash' will open an external bash terminal in the current working
directory.


File: scimax.info,  Node: Open Finder/Explorer,  Next: words,  Prev: Open a bash window,  Up: Miscellaneous scimax utilities

11.2 Open Finder/Explorer
=========================

`explorer' and `finder' will open a Windows Explorer or Mac Finder
window in the current working directory.


File: scimax.info,  Node: words,  Next: ore,  Prev: Open Finder/Explorer,  Up: Miscellaneous scimax utilities

11.3 words
==========

Try out `words-hydra/body' on a selection or word. I bound it to
\\[words-hydra/body].


File: scimax.info,  Node: ore,  Next: org-show,  Prev: words,  Up: Miscellaneous scimax utilities

11.4 ore
========

This command: `ore' tells you about the org-element your point is on.
It gives some hints on commands you can use on the element, and
provides a way for you to write your own notes.


File: scimax.info,  Node: org-show,  Next: org-db,  Prev: ore,  Up: Miscellaneous scimax utilities

11.5 org-show
=============

This is a simple library to make simple presentations in org-mode. See
`org-show-help' for an example use.


File: scimax.info,  Node: org-db,  Prev: org-show,  Up: Miscellaneous scimax utilities

11.6 org-db
===========

`org-db' is an org-mode database. When it is active every org-mode file
you visit will be indexed into a sqlite database. In each file, each
headline with its title, tags and properties are stored, and every link
in each file is stored.

   This becomes useful because you can then search all of your
org-files and jump to different locations.

`org-db-open-heading'
     Jump to a heading

`org-db-contacts'
     jump to a heading with an email property

`org-db-open-file'
     open a file in the db

`org-db-open-recent-file'
     open a list of recent files from the db

`org-db-locations'
     open a heading with an address property

   You can add a lot of files with `org-db-index'.

   When active, every time you save an org-file it will be added to a
queue to be indexed during idle time.


File: scimax.info,  Node: External Packages,  Next: Scientific notebook,  Prev: Miscellaneous scimax utilities,  Up: Top

12 External Packages
********************

These are external packages that are included in scimax and might be
useful for you.

* Menu:

* avy::
* counsel::
* helm::
* swiper::
* undo-tree::


File: scimax.info,  Node: avy,  Next: counsel,  Up: External Packages

12.1 avy
========

avy lets you jump to things in Emacs. See
`https://github.com/abo-abo/avy'

   There are a lot of avy commands. Click this to see them:
`(apropos-command "^avy")'

   We use a lot of them in *Note Navigation - navy::.


File: scimax.info,  Node: counsel,  Next: helm,  Prev: avy,  Up: External Packages

12.2 counsel
============

This is for completing stuff. See
`http://oremacs.com/2015/04/09/counsel-completion/'

   In particular, scimax sets these keybindings:

   ("M-x" . counsel-M-x) ("C-x b" . ivy-switch-buffer) ("C-x C-f" .
counsel-find-file) ("C-h f" . counsel-describe-function) ("C-h v" .
counsel-describe-variable) ("C-h i" . counsel-info-lookup-symbol) ("H-c
r" . ivy-resume) ("H-c l" . counsel-load-library) ("H-c g" .
counsel-git-grep) ("H-c a" . counsel-ag) ("H-c p" . counsel-pt)


File: scimax.info,  Node: helm,  Next: swiper,  Prev: counsel,  Up: External Packages

12.3 helm
=========

Helm is another completion tool. See
`https://github.com/emacs-helm/helm'

   Type C-c h C-h to see the helm key bindings. There are so many good
things in there!


File: scimax.info,  Node: swiper,  Next: undo-tree,  Prev: helm,  Up: External Packages

12.4 swiper
===========

This is a powerful search tool in Emacs. See
`https://github.com/abo-abo/swiper'

   C-s is bound to `counsel-grep-or-swiper' for searching.


File: scimax.info,  Node: undo-tree,  Prev: swiper,  Up: External Packages

12.5 undo-tree
==============

There are a few undo features:

C-/     undo the last action
C-x u   use the undo-tree (q to quit)


File: scimax.info,  Node: Scientific notebook,  Next: ivy/counsel,  Prev: External Packages,  Up: Top

13 Scientific notebook
**********************

scimax provides a scientific notebook capability. Each "notebook" is
actually collection of org-files in a "project". A project is the set
of files in a directory that is under git version control. Each project
should have a master file (the default is README.org, but you can
customize `nb-master-file' to change this). The master file contains
what ever you want, but typically it links to other documents in the
project and provides an overview of the project.

   You are basically free to structure the notebook however you want.
You have all the freedom of org-mode at your fingers to document your
work.

   We leverage projectile (http://projectile.readthedocs.io/en/latest/)
for project management in the notebook. We use magit (https://magit.vc)
for version control.

   Use `nb-new' to create a new project. You will be prompted for a
name, which must be a valid directory name. The directory will be
created in `nb-notebook-directory'. Note that all git repos will be
considered projects, so it is not necessary to use `nb-new'. It just
automates a few things for you.

   Use `nb-open' to open a project. This will open the project to your
master file. Previously visited projects are remembered by projectile
and should be shown in an ivy completion minibuffer for selection.

   Probably you will keep your projects separate from your agenda
files, but you still would like to see what tasks the project has? Use
`nb-agenda' while in your project, and it will show you all the tasks
in the org-files associated with the project.

   Here are some other interesting commands you may want to use.

`counsel-git-grep'
     grep for a string in the project

`projectile-find-file'
     jump to a file in the project

`projectile-switch-to-buffer'
     switch to a project buffer

`projectile-kill-buffers'
     kill all the buffers associated with the project

   These commands help you navigate to a headline.

`ivy-org-jump-to-heading'
     in the current file

`ivy-org-jump-to-heading-in-directory'
     in the current directory

`ivy-org-jump-to-project-headline'
     in the project

`counsel-org-tag'
     add/remove tags on a headline

   You can manage the version control with *Note Magit::. There are
also keyboard shortcuts for version control. Type C-x v C-h to see them.

   * `vc-next-action' will do the next logical thing for vc, e.g. add
     or commit.

   * `vc-diff' will show you what has changed in the buffer since the
     last commit.

   * `vc-print-log' will show you the vc log.

   scimax defines these additional key bindings:

C-x v p   git push
C-x v P   git pull

* Menu:

* Archive the notebook with git::


File: scimax.info,  Node: Archive the notebook with git,  Up: Scientific notebook

13.1 Archive the notebook with git
==================================

Sometimes you may want a zip file of your notebook. You can use the
`nb-archive' command to create a zip file of the current state of your
notebook. This can be useful to back up versions of your project, send
copies to collaborators who don't use git, or to create archives for
data sharing and supporting information.

   Note that only files under version control are archived, and only
the current committed state is archived. So, uncommitted files and
changes will not be included.


File: scimax.info,  Node: ivy/counsel,  Next: scimax-hydras,  Prev: Scientific notebook,  Up: Top

14 ivy/counsel
**************

scimax currently uses ivy extensively for completion, and enables
`ivy-mode' and `counsel-mode'. The default matching behavior is
`ivy-regex-ignore-order'.

   When you get an ivy minibuffer, start typing to select what you
want, and when it is highlighted, press enter.

   There are a couple of nuances though.

  1. To eliminate matches use ! pattern, but you can only use one of
     these, and it comes last.

   I have extended the `ivy-minibuffer-map' to enable the following:

  1. M-spc will show the actions, and spc to resume the selection
     process.

  2. C-RET to perform the action and move to the next candidate, and
     C-u C-RET to perform the action and move to the previous candidate.

  3. M-RET will perform the default action on every candidate from the
     current selection to the end of the candidates. C-u M-RET does
     that from the current candidate to the beginning.

  4. s-RET quits the selection buffer with no action.

  5. ? shows you the keymap.

   In the ivy selection buffer
M-spc           Show the actions
spc             resume
RET             Default action and exit
C-RET           Default action and move to next line
C-u C-RET       Default action and move to previous line
M-RET           Default action on each candidate from current to end
C-u M-RET       Default action on each candidate from current to beginning
C-u C-u M-RET   Default action on all candidates
s-RET           quit with no action
?               show keymap help

   I use Hyper-c as a prefix map for a these commands.

H-c r   `ivy-resume'
H-c l   `counsel-load-library'
H-c a   `counsel-ag'

* Menu:

* counsel-find-file::


File: scimax.info,  Node: counsel-find-file,  Up: ivy/counsel

14.1 counsel-find-file
======================

Here are some additional actions we define for `counsel-find-file'.

a     attach to email
c     copy relative path
4     Open in new window
5/f   Open in new frame
C     Copy absolute path
d     open in dired
D     Delete file
e     open in external app
p     insert relative path
P     insert absolute path
l     relative org link
L     absolute org link
r     rename file


File: scimax.info,  Node: scimax-hydras,  Next: Appendix,  Prev: ivy/counsel,  Up: Top

15 scimax-hydras
****************

Scimax uses a central hydra to launch a key-driven menu of commonly
used commands.

     (describe-function 'scimax/body)

     scimax/body is an interactive Lisp closure in `scimax-hydra.el'.

     It is bound to <f12>.

     (scimax/body)

     For more information check the manuals.

     Create a hydra with no body and the heads:

     "a":    ‘(scimax-open-hydra scimax-applications/body)’,
     "b":    ‘(scimax-open-hydra scimax-buffers/body)’,
     "e":    ‘(scimax-open-hydra scimax-errors/body)’,
     "f":    ‘(scimax-open-hydra scimax-files/body)’,
     "g":    ‘(scimax-open-hydra scimax-google/body)’,
     "h":    ‘(scimax-open-hydra scimax-help/body)’,
     "i":    ‘(scimax-open-hydra scimax-insert/body)’,
     "j":    ‘(scimax-open-hydra scimax-jump/body)’,
     "k":    ‘(scimax-open-hydra scimax-bookmarks/body)’,
     "l":    ‘(scimax-open-hydra scimax-lisp/body)’,
     "m":    ‘(scimax-open-hydra scimax-minor-modes/body)’,
     "n":    ‘(scimax-open-hydra scimax-navigation/body)’,
     "o":    ‘(scimax-open-hydra scimax-org/body)’,
     "p":    ‘(scimax-open-hydra hydra-projectile/body)’,
     "r":    ‘(scimax-open-hydra scimax-registers/body)’,
     "s":    ‘(scimax-open-hydra scimax-search/body)’,
     "t":    ‘(scimax-open-hydra scimax-text/body)’,
     "v":    ‘(scimax-open-hydra scimax-version-control/body)’,
     "w":    ‘(scimax-open-hydra scimax-windows/body)’,
     "z":    ‘(scimax-open-hydra scimax-settings/body)’,
     ",":    ‘scimax-hydra-pop’,
     "x":    ‘counsel-M-x’,
     "<return>":    ‘save-buffer’,
     "/":    ‘undo-tree-undo’,
     "\":    ‘undo-tree-redo’,
     "*":    ‘(switch-to-buffer "*scratch*")’,
     "?":    ‘scimax-hydra-help’,
     ".":    ‘scimax-dispatch-mode-hydra’,
     "q":    ‘nil’

     The body can be accessed via ‘scimax/body’.

   So, instead of C-x C-f to open a file (which still works by the way)
you can simply type: f12 ff. Or instead of C-x C-s to save the file,
type f12 RET. Each hydra will show you a hint in the minibuffer on
which keys do what.


File: scimax.info,  Node: Appendix,  Next: Archive,  Prev: scimax-hydras,  Up: Top

16 Appendix
***********

`scimax-help' will open this document.

* Menu:

* Emacs::


File: scimax.info,  Node: Emacs,  Up: Appendix

16.1 Emacs
==========

Emacs is described as "self-documenting", and it provides a lot of
introspective ways to access documentation. A classic way to access
help is via "info" pages. These are hyperlinked documents containing a
lot of detail about Emacs and its libraries.

   Emacs-manual: *Note Top: (Emacs)Top.

n   goto next page
u   up a node
d   Main directory
?   list of keys and commands
q   quit

Table 16.1: Type these keys to do some basic navigation in an Info page.

   Emacs libraries: *Note Top: (dir)Top.  Emacs-lisp manual: *Note Top:
(elisp)Top.

   org-mode manual: *Note Top: (org)Top.

* Menu:

* Getting help on Emacs functions::
* Getting help on system commands::
* What happens if I press a key?::
* How do I learn shortcuts?::


File: scimax.info,  Node: Getting help on Emacs functions,  Next: Getting help on system commands,  Up: Emacs

16.1.1 Getting help on Emacs functions
--------------------------------------

To get help on functions use: `counsel-describe-function' and on
variables use `counsel-describe-variable'.

   If you do not know exactly what you are looking for try:
`helm-apropos'. This covers commands, functions, variables, faces,
classes, and some other things.


File: scimax.info,  Node: Getting help on system commands,  Next: What happens if I press a key?,  Prev: Getting help on Emacs functions,  Up: Emacs

16.1.2 Getting help on system commands
--------------------------------------

If you have man pages installed (Linux/Mac for sure, maybe on windows)
you can access them easily via Emacs. I like to read man pages in Emacs
with `helm-man-woman' although `man' is also good.

   Note while on a man page you can use these keys:

   m       Prompt to retrieve a new manpage.  r       Retrieve
reference in SEE ALSO section.  M-n   Jump to next manpage in circular
list.  M-p   Jump to previous manpage in circular list.  n       Jump
to next manpage section.  p       Jump to previous manpage section.  g
    Go to a manpage section.  s       Jumps to the SEE ALSO manpage
section.  q       Deletes the manpage window, bury its buffer.  k
Deletes the manpage window, kill its buffer.  ?       Prints this help
text.

   scimax also defines a link for man pages.

   Manpage for BSDTAR(1) (BSDTAR(1)%20)


File: scimax.info,  Node: What happens if I press a key?,  Next: How do I learn shortcuts?,  Prev: Getting help on system commands,  Up: Emacs

16.1.3 What happens if I press a key?
-------------------------------------

The `describe-key' function will prompt you for a key sequence or you
can click on a menu item to see what it does.

   The `describe-mode' function will provide a full list of all the
keybindings in the current buffer.

   In org-mode the `ore' command will give you information about the
org-element under your cursor, including some commands that you can use
at the point. You can also customize this by adding your own notes
(click on User documentation in the help buffer).


File: scimax.info,  Node: How do I learn shortcuts?,  Prev: What happens if I press a key?,  Up: Emacs

16.1.4 How do I learn shortcuts?
--------------------------------

If you use the menus, they will often have the shortcut in the menu.

   The help functions usually show you if a shortcut is defined for a
command.

   If you really want to define your own keys, see `define-key' and
`global-set-key'.

   Make yourself some notes in org-mode using
`emacs-keybinding-command-tooltip-mode'.


File: scimax.info,  Node: Archive,  Prev: Appendix,  Up: Top

17 Archive
**********

* Menu:

* Navigation - navy::
* Hotspots::


File: scimax.info,  Node: Navigation - navy,  Next: Hotspots,  Up: Archive

17.1 Navigation - navy
======================

`navy' opens a hydra for navigation. The following keys are bound to
commands that do something in the following senses

j   left
l   right
i   up
k   down

   The default mode is character mode, and you can change the mode with
single characters, include a word mode (w), sentence (s), paragraph
(p), page (g), line (n) and sexp (x) mode. These modes allow you
navigate forward and backward by those elements. They also define
binding

   I have tried to make the following keys consistent:

;   avy-goto-char-2
'   avy-goto-line
<   goto point-min
>   goto point-max

   There are some useful bindings in `navy' also.
r   counsel-git-grep
o   helm-org-agenda-files-headings
a   swiper-all


File: scimax.info,  Node: Hotspots,  Prev: Navigation - navy,  Up: Archive

17.2 Hotspots
=============

`hotspots' is a helm command that provides easy access to a variety of
locations including user-defined commands, locations, org-agenda files,
recent files, and bookmarks.

   You customize `scimax-user-hotspot-commands' and
`scimax-user-hotspot-locations'.

   I bind this to a key like "f9" and set it up to easily open my mail,
calendar and other things. For example, here is part of my setup.

     (setq scimax-user-hotspot-commands
           '(("Mail" . (lambda ()
                         (browse-url "https://www.google.com/gmail")))
             ("Calendar" . (lambda ()
                             (browse-url "https://www.google.com/calendar/render")))
             ("Contacts" . ivy-contacts)
             ("RSS" . elfeed)
             ("Twitter" . twit)
             ("Agenda" . (lambda () (org-agenda "" "w")))
             ("CV" . (lambda ()
                       (org-open-file
                        "/Users/jkitchin/Dropbox/CMU/CV and bios/kitchin_cv.docx" '(16))))))



Tag Table:
Node: Top73
Node: Org-mode3674
Node: Markup shortcuts4025
Node: Block expansions in org-mode5478
Node: LaTeX6659
Node: Latex classes that scimax knows about6949
Node: Better image scaling7352
Node: new speed commands8397
Node: Formatted copy and paste8992
Node: Writing tools9357
Node: Spell-checking9629
Node: Autoformat10384
Node: Track changes12675
Node: Highlighting and annotation14552
Node: org-ref15062
Node: Publishing (ox-manuscript)15326
Node: Manuscript templates16562
Node: Bibliography management17840
Node: Searching your bibliography files20396
Node: Bibtex entries20791
Node: Article (Article in Journal)23047
Node: InProceedings (Article in Conference Proceedings)23694
Node: InCollection (Article in a Collection)24781
Node: InBook (Chapter or Pages in a Book)25809
Node: Proceedings (Conference Proceedings)26766
Node: Book (Book)27718
Node: Booklet (Booklet (Bound but no Publisher))28472
Node: PhdThesis (PhD Thesis)29055
Node: MastersThesis (Master's Thesis)29701
Node: TechReport (Technical Report)30440
Node: Manual (Technical Manual)31145
Node: Unpublished (Unpublished)31729
Node: Misc (Miscellaneous)32202
Node: Bibtex hotkeys32673
Node: Email utilities33358
Node: html mail33844
Node: mail merge34439
Node: Contacts34900
Node: Google35511
Node: Magit36325
Node: Basic magit36626
Node: Create a git repo37004
Node: Clone a repo37338
Node: Check the status of your repo37698
Node: Stage a file38131
Node: Commit a file38643
Node: Diffs39133
Node: See the log39374
Node: Push39779
Node: Pull40096
Node: Run a command-line git command manually40323
Node: Check the output of the git command40861
Node: Keybindings41110
Node: Intermediate concepts41311
Node: Checkout an older version of a file41771
Node: Search the commit messages for a pattern42170
Node: Revert a commit42519
Node: Tag a version42816
Node: Checkout an existing branch43142
Node: Merge two branches43622
Node: Resolving conflicts43960
Node: Fetching44502
Node: Add a remote44735
Node: Stashing44980
Node: Git blame45204
Node: Advanced concepts45337
Node: Resetting45624
Node: Rebasing45784
Node: Create patches46428
Node: Cherry-picking46906
Node: Apply patches47133
Node: Notes about commits47353
Node: Cherry-picking 148009
Node: Project management - projectile48207
Node: Programming48863
Node: Python49081
Node: Asynchronous Python49293
Node: Jupyter/Ipython49961
Node: Scimax enhancements to ob-ipython51050
Node: Export org to ipynb54487
Node: Using other kernels - hy54924
Node: Emacs-lisp55420
Node: RSS feeds55669
Node: Miscellaneous scimax utilities56839
Node: Open a bash window57122
Node: Open Finder/Explorer57363
Node: words57653
Node: ore57877
Node: org-show58180
Node: org-db58419
Node: External Packages59335
Node: avy59652
Node: counsel59963
Node: helm60547
Node: swiper60821
Node: undo-tree61079
Node: Scientific notebook61288
Node: Archive the notebook with git64094
Node: ivy/counsel64738
Node: counsel-find-file66521
Node: scimax-hydras67009
Node: Appendix69297
Node: Emacs69468
Ref: orgcb46ac769834
Node: Getting help on Emacs functions70274
Node: Getting help on system commands70735
Node: What happens if I press a key?71788
Node: How do I learn shortcuts?72491
Node: Archive72989
Node: Navigation - navy73121
Node: Hotspots73938

End Tag Table