% Ebib Manual
% Joost Kremers

<article>

Ebib is a program with which you can manage BibTeX and BibLateX database files without having to edit the raw `.bib` files. It runs in GNU/Emacs, version 24.3 or higher. (Users of GNU/Emacs 23.1 and up can install Ebib 1.x, which is available in the pasture branch on Github or as a zip or tar archive on Github's releases page.)

It should be noted that Ebib is *not* a minor or major mode for editing BibTeX files. It is a program in itself, which just happens to make use of Emacs as a working environment, in the same way that for example Gnus is.


# News #

## Version 2.9, January 2017 ##

- Allow `%s` in the program strings in `ebib-file-associations`, making it possible to pass command line arguments to the program being called.

## 19 December 2016 ##

- Remove support for a separate rc file for Ebib. User configuration should be moved to Emacs' `init.el` file. To keep Ebib customisation in a separate file, simply load it from `init.el`.
- The macro `ebib-key` has also been removed. Simply use `define-key` or any other key binding mechanism to define keys for Ebib. See the section [Modifying Key Bindings](#modifying-key-bindings) for details.

## 7 December 2016 ##

- Upgrade Emacs dependency to 24.4.

## 5 December 2016 ##

- New library `org-ebib`. This defines a new Org link type `ebib:`, which uses the command `org-ebib-open` to open Ebib. The previous commands to do this, `ebib-show-entry` and `ebib-open-org-link` have been removed. `org-ebib` also allows the creation of Org links to Ebib entries with `org-store-link`.
- New citation insertion command `ebib-insert-citation`. This replaces `ebib-insert-bibtex-key`, so please update your key bindings. The new command uses `ivy` for completion if this package is available, so that it is possible to select an entry by typing parts of its author and/or title.


## 7 November 2016 ##

- New tabulated list interface in index buffer. This interface is not based on Emacs' built-in `tabulated-list-mode`, hence sorting cannot be done by clicking on the column headers. Sorting can be done with `<`, `>` (sort ascending and sort descending, respectively, which ask for the column to sort) and `=`, to reset to default sort (which is on the entry key).
- The user option `ebib-index-display-fields` is replaced with `ebib-index-columns`, which has a different format: each element in `ebib-index-columns` describes a column in the tabulated view and consists of a list containing the field name, the column's width and a boolean indicating whether sorting on this column is possible.


## Version 2.8, 26 October 2016 ##

- Changed key bindings: `j` and `k` no longer move up/down in the index, entry and strings buffers; use `p` and `n` instead. Furthermore, `i` now executes `ebib-push-bibtex-key` (used to be `p`), and `I` (capital i) executes `ebib-browse-doi` (used to be `i`).
- In the index buffer, `ebib-search-next` (which used to be bound to `n`) is no longer bound. Instead, `ebib-search` (still bound to `/`) activates a transient map which binds the keys `/` and `RET` to `ebib-search-next`. Any other key disables the transient keymap and is executed normally.
- In the index buffer, `C-u /` repeats the previous search. (This fixes a small bug that has so far gone unnoticed: moving to the top of the databas and calling `ebib-search-next`, as previously suggested in the manual to get around the fact that `ebib-search-next` does not wrap, would not search the first entry.)
- In the entry buffer, `x` is replaced by `k` (`ebib-kill-field-contents`).
- New functions: `ebib-kill-entry` and `ebib-yank-entry` for killing and yanking BibTeX entries. `ebib-kill-entry` deletes the current entry from the database and puts it in the kill ring. `ebib-yank-entry` adds an entry from the kill ring to the current database.


## Version 2.7, 22 September 2016 ##

- Reading list management: add and remove BibTeX entries to an Org reading list.
- Remove options `ebib-notes-identifier-function` and  `ebib-notes-title-function`.
- Add option `ebib-notes-template-specifiers`: allow customisation of the format specs used in `ebib-notes-template`. (This option replaces `ebib-notes-identifier-function` and  `ebib-notes-title-function`).

## Version 2.6.3, 31 August 2016 ##

- Allow storing notes in a single file rather than using one file per note.
- Correct handling of DOIs.
- Add option `ebib-truncate-file-names`: if set (the default), file names added to the `file` field are truncated relative to `ebib-file-search-dirs`.
- Add option `ebib-file-name-mod-function`: modify file paths before storing them in the `file` field.


# Installation #

## Package manager ##

The easiest way to install Ebib is to use Emacs' package manager. Ebib is available as a package from the [Melpa package archive](http://melpa.org/). If you add the Melpa archive to your `package-archive` list, you can install Ebib from the package manager. This will also install the Info file so you can access the Ebib manual within Emacs.

## Debian and Ubuntu ##

Users of Debian 9 or later and Ubuntu 16.10 or later can also use their distro's package manager: `apt-get install elpa-ebib`.

## Manual installation ##

It's also possible to install Ebib manually by downloading the source, compiling it and telling Emacs where to find it. If you prefer this method, then you probably know what you're doing so detailed instructions are omitted here. Just be sure to also install Ebib's dependencies, the [dash](https://github.com/magnars/dash.el) and [parsebib](https://github.com/joostkremers/parsebib) libraries.


## Starting Ebib ##

Once Ebib has been installed and is loaded, you can start it with `M-x ebib`. This command is also used to return to Ebib when you have put the program in the background. You can bind this command to a key sequence by putting something like the following in Emacs' init file:

    (global-set-key "\C-ce" 'ebib)

You can of course choose any key combination you like. (In Emacs, key combinations of `C-c` `<letter>` are reserved for the user, which means that no package may set them.)

You can also call Ebib from an Eshell command line. This in itself is entirely unspectacular (in Eshell, you can invoke any Emacs function), but the nice thing is that you can then provide a filename to load. So, provided a file `references.bib` exists in `~/Work/Papers/`, the following command:

    ~/Work/Papers $ ebib references.bib

starts Ebib and loads the file `references.bib`.


## Upgrading from Ebib 1.x ##

If you upgrade from Ebib 1.x to the current version 2, there are a few things you need to be aware of. First, Ebib 2 does not support Emacs versions below 24.3. If you're on an older version of Emacs, either upgrade Emacs, or do not upgrade Ebib. Ebib 1.x will continue to be available in the `pasture` branch on Github or as a package on the Github releases page, so if for some reason you do not want to upgrade, you can continue to use this branch. Ebib 1.x will continue to be supported with bug fixes and possibly the occasional (small) feature addition, though no major changes will take place.

If you do upgrade, it is important to note that a few customisation options have changed. If you never made any customisations to Ebib, the upgrade should not pose any problems. If you have, however, read on.

The most important change is that the variable `ebib-entry-types` (option "Entry Types") has been removed. Ebib now uses the entry type definitions of the built-in `bibtex-mode`, which means that if you wish to customise the entry types, you should customise `bibtex-BibTeX-entry-alist` or `bibtex-biblatex-entry-alist`.

Secondly, a few user options have been renamed because their types have changed. (Mainly from `symbol` to `string`). The name change means that existing customisations are lost, but it also prevents Ebib from throwing cryptic errors and refusing to run. If you customised any of the following options, you should redo them after upgrading Ebib (and preferably remove the old ones from your init file):

- `ebib-default-entry`: renamed to `ebib-default-entry-type`.
- `ebib-additional-fields`: renamed to `ebib-extra-fields`.
- `ebib-standard-url-field`: renamed to `ebib-url-field`.
- `ebib-standard-file-field`: renamed to `ebib-file-field`.
- `ebib-standard-doi-field`: renamed to `ebib-doi-field`.
- `ebib-biblatex-inheritance`: renamed to `ebib-biblatex-inheritances` (note the `s`).

Note that even if you customised `ebib-biblatex-inheritance`, there is most likely no need to customise its replacement `ebib-biblatex-inheritances`, because the latter is set up with the default inheritance rules that Biblatex defines.

Another thing to note is that four user options have a new default value. First, the default location of the rc file has moved to `~/.emacs.d/ebibrc`, in line with the recommendation to keep all Emacs-related files in `~/.emacs.d`. If you kept an `.ebibrc` file in your home directory, move it to `~/.emacs.d`. Second, a `\documentclass` definition has been added to the user options "Latex Preamble" (`ebib-latex-preamble`) and "Print Preamble" (`ebib-print-preamble`). If you customised one of these, you should add a document class specification, otherwise the LaTeX file won't compile. Third, the option `ebib-save-xrefs-first` now defaults to `t`.

Lastly, if you use Biblatex, make sure to read the section on using Ebib with Biblatex files.


# Getting Started #

A BibTeX database is somewhat of a free-form database. A BibTeX entry consists of a set of field-value pairs. Furthermore, each entry is known by a unique key. The way that Ebib navigates this database is by having two windows, one that contains a list of all the entry keys in the database, and one that contains the fields and values of the currently highlighted entry.

When Ebib is started, the current windows in Emacs are hidden and the Emacs frame is divided into two windows. The top one contains a buffer that is called the *index buffer*, while the lower window contains the *entry buffer*. When a database is loaded, the index buffer holds a list of all the keys in the database plus some additional information for each entry: the author or editor, its year of publication, and the title. You can move through the entries with the cursor keys. In the entry buffer, the fields of the currently highlighted entry are shown, with their values.

This manual first describes Ebib's basic functionality, so that you can get started with it. At times, reference will be made to later sections, where more specific functions are described.

Ebib has a menu through which most functions can be accessed. (Especially some of the lesser used functions can only be accessed through the menu, unless you assign key shortcuts to them, of course.)

You can start Ebib with the command `M-x ebib`. Entering this command hides all the windows in the current Emacs frame and replaces them with two windows: the top one contains the index buffer, the bottom one, taking up the larger part of the screen, contains the entry buffer. The index buffer is named `none`, to indicate that no database has been loaded. If you open a database, or start a new one, the index buffer will carry its name.

You can quit Ebib by typing `q`. You will be asked for confirmation, and you will receive a warning if you happen to have an unsaved database. You can also leave Ebib with the command `z`. However, unlike `q`, which completely quits Ebib, `z` only lowers it, so that it remains active in the background. The `.bib` files that you have opened remain loaded, and you can return to them by typing `M-x ebib` again.


## Opening a `.bib` File ##

Loading a `.bib` file into Ebib is done with the command `o`. Ebib reads the file that you specify, and reports how many entries it found, how many `@string` definitions it found, and whether a `@preamble` was found. Note that when Ebib reads a `.bib` file, it only reads entry types (e.g. `book, article, phdthesis` etc.) that it knows about.  Therefore, you should make sure that all the entry types and fields that your databases use are defined. Ebib uses the entry type definitions of `bibtex.el`, which is fairly complete, but if you use non-standard entry types, you may need to customise `bibtex-bibtex-entry-alist` or `bibtex-biblatex-entry-alist`, depending on which of the two you use.

Every time Ebib reads a `.bib` file, it produces a few log messages. These are written into a special buffer `*Ebib-log*`. If Ebib encounters entry types in the `.bib` file that it doesn't know, a warning will be logged. If Ebib finds something that it cannot parse, it will log an error. If warnings and/or errors occurred during loading, Ebib will issue a message when it finishes loading the `.bib` and direct you to the log buffer.

If Ebib finds entry types in a `.bib` file that are not defined, those entries will still be loaded, but their entry type is displayed using Emacs' `error` face. The most likely case in which this will happen is when you load a Biblatex file without letting Ebib know the file is Biblatex-specific. By default, Ebib assumes that a `.bib` file it loads is a BibTeX file. If you intend to use Biblatex files, make sure to read the section on Biblatex ([Using Biblatex](#using-biblatex)).


## Preloading `.bib` Files ##

Chances are that you will be doing most of your work with one or a few `.bib` files, and you may find yourself opening the same file or files every time you start Ebib. If so, you can tell Ebib to always load specific `.bib` files on startup. To do this, specify the files in Ebib's customisation buffer, under the option "Preload Bib Files" (`ebib-preload-bib-files`).

By default, `.bib` files are searched for in your home directory. Since this is most likely not where you keep the files, you need to specify either the file's full path or a relative path starting from your home directory. Alternatively, you can customise the option "Bib Search Dirs" (`ebib-bib-search-dirs`) to specify one or more directories in which Ebib should search the `.bib` files.


## Navigating a `.bib` File ##

Once you've opened a `.bib` file, all the entries in the file are shown in alphabetical order (sorted by entry key) in the index buffer in the top Ebib window. The first entry is highlighted, meaning it is the current entry. The fields it holds and their values are shown in the entry buffer in the bottom Ebib window. The first field is the type field, which tells you what kind of entry you're dealing with (i.e. `book`, `article`, etc.).

Below the type field, Ebib displays (up to) four sets of fields. The first set are the so-called required fields, the fields that Bib(La)TeX requires to be filled. The second group are the optional fields, which do not have to be filled but which Bib(La)TeX will normally add to the bibliography if they do have a value. The third group is the so-called extra fields. These fields are usually ignored by Bib(La)TeX (note that Bib(La)TeX normally ignores *all* fields it does not know), although there are bibliography styles that treat some of these fields as optional rather than as extra. Extra fields are defined in the user option "Extra Fields" (`ebib-extra-fields`). Lastly, the fourth set of fields shown in the entry buffer are fields that exist in the entry but are not defined as part of the entry type nor as extra fields.

The first two groups of fields are different for each entry type, while the third group is common to all entry types. You can use the extra fields, for example, to add personal comments to the works in your database. Ebib by default defines the following extra fields: `crossref`, `url` (BibTeX only), `annote` (`annotation` for Biblatex), `abstract`, `keywords`, `file`, `timestamp`, and `doi` (BibTeX only). `url` and `doi` are defined only for BibTeX, since Biblatex defines them as optional fields for most entry types. If these are not sufficient for you, you can customise the option "Extra Fields".

To move around in the index buffer, you can use the `up` and `down` cursor keys, `p` and `n` and also the versions with the control key `C-p` and `C-n`. Furthermore, `Space` and `PgDn` move a screenful of entries down, while `b` and `PgUp` move in the other direction. Lastly, `g` and `Home` move to the first entry, while `G` and `End` move to the last one.

Ebib is not restricted to opening just one `.bib` file at a time. You can open more files by just typing `o` again and entering the filename. Ebib numbers the databases: the number of each database is shown in the mode line of the index buffer, directly before the database name. The keys 1--9 provide a quick way of jumping from one database to another. Note that the numbering is dynamic: if you have three databases opened and then close the second, database 3 becomes database 2.

With the `left` and `right` cursor keys, you can move to the previous or next database. These keys wrap, so if you hit the `left` cursor key while the first database is active, you move to the last database. If you are done with a database and want to close it, type `c`. This closes the current database. It does not leave Ebib, and all other databases you have open will remain so.


## Starting a New `.bib` File ##

If you want to start a new `.bib` file from scratch, you cannot just go and enter entries. You first have to give the database a name. So, to start a new database, type `o` first, and give the new file a name. Once you have done this, you can start adding entries to the database.


# Editing the Database #

Of course, being able to open and view `.bib` files is only half the fun. One needs to be able to edit the files as well. Ebib's essential editing facilities are discussed here.


## Adding and Deleting Entries ##

To add an entry to a database, you type `a`. When you do this, Ebib first asks you for an entry key, as every entry must be identified by a unique key. Just type a name for the new entry (say `Jones1998`). Since the entry key must be unique, Ebib will complain if you enter a key that already exists.

You can also let Ebib automatically generate entry keys: if you set the customisation option "Autogenerate Keys" (`ebib-autogenerate-keys`), Ebib does not ask you for a key when you add a new entry. Instead, it creates a temporary key (of the form `<new-entry00>`). When you have finished entering the field values for the new entry, Ebib automatically replaces the temporary key with a key that is based on the contents of the `author` (or `editor`), `year` and `title` fields. (It uses the function `bibtex-generate-autokey` for this; see that function's documentation string for customisation options.)

Note that if you should later decide that you want to change the key of an entry, you can do so with the command `E`. So if you have an entry with the key `Jones1998` and you want to add another entry by Jones from 1998, you can call the new one `Jones1998b` and rename the existing one to `Jones1998a`. Similarly, it is possible to let Ebib recreate an autogenerated key by pressing `!`.

Deleting an entry is done in two ways. The key `d` deletes an entry from the database. This command asks for confirmation, because once an entry has been deleted, it cannot be retrieved again. Alternatively, you can use `k`, which kills the current entry, i.e., the entry is deleted from the database and added to the kill ring.

The key `y` lets you yank an entry from the kill ring into the current database. If the first element in the kill ring is not a properly formatted BibTeX entry, the kill ring is simply rotated. This means that you can press `y` again to (try and) add the next element in the kill ring to the database.

In order for `y` to add a BibTeX entry to the database, the kill ring item to be yanked must be a string that constitutes a properly formatted BibTeX entry. Killing an entry from a database will result in such a string (so you can easily move entries from one database to another by killing and then yanking them), but killing a BibTeX entry from another buffer or copying one from an outside source (e.g., a website) is also possible. Furthermore, yanking also works with `@Preamble`, `@String` and `@Comment` definitions.


## Editing Fields Values ##

Editing the field values for an entry is done in the lower of the two Ebib buffers, the so-called entry buffer. You can move focus to the entry buffer and start editing field values by typing the command `e` in the index buffer.

You can move between fields with the same keys that you use to move between entries in the index buffer: the cursor keys `up` and `down`, `p` and `n` or `C-p` and `C-n`. `Space` and `PgDn` move to the next set of fields, while `PgUp` and `b` move to the previous set of fields. `g` and `G`, and `Home` and `End` also work as expected.

Editing a field value can be done with `e`. (In fact, in the entry buffer, `RET` is equivalent to `e`.) For most fields, Ebib simply asks you for a string value in the minibuffer. (Here, `RET` confirms the edit, while `C-g` cancels it.) Although BibTeX requires that field values be surrounded by braces {} (or double quotes "", but Ebib does not use those, even though it can of course handle them when they are used in an existing `.bib` file) you do not need to type these. Ebib adds them when it saves the `.bib` file.

Some fields, however, are handled in a special way. The first of these is the `type` field: if you edit this field, you must enter one of the predefined entry types. Ebib won't allow you to enter anything else. You can use TAB completion in this case. Similarly, if you edit the `crossref` field, Ebib requires that you fill in a key from the database. Here, too, you can use TAB completion. The fields `keywords` and `file` are also treated differently, see [Managing keywords](#managing-keywords) and [Viewing Files](#viewing-files), respectively.

Note that if you're adding a new entry, Ebib automatically puts you in the entry buffer after you've typed the entry key: you don't have to type `e` to move to the entry buffer. When creating a new entry, you should  set the `type` field first, because the `type` field determines which other fields are available for an entry. After editing a field, Ebib puts you on the next field. This is convenient if you're creating a new entry and need to fill out several fields in a row.

If you're done editing the fields of the entry, type `q` to move focus back to the index buffer. (Note: keys may have different functions in the index buffer and the entry buffer. `q` is a typical example: in the entry buffer, it quits editing the entry and moves focus back to the index buffer. In the index buffer, however, `q` quits Ebib.)


## Editing Multiline Values ##

Apart from the `type`, `keywords`, `file` and `crossref` fields, there is another field that Ebib handles in a special way when you edit its value. This is the `annote` field (`annotation` in Biblatex). Most field values normally consist of a single line of text. However, because the `annote` field is meant for creating annotated bibliographies, it would not be very useful if you could only write one line of text in this field. Therefore, when you edit the `annote` field, Ebib puts you in a so-called *multiline edit buffer*. This is essentially a text mode buffer that allows you to enter as much text as you like. To store the text and leave the multiline edit buffer, type `C-c | q`.

If you want to leave the multiline edit buffer without saving the text you have just typed, type `C-c | c`. This command cancels the edit and leaves the multiline edit buffer. The text that is stored in the field you were editing is not altered.

Multiline values are not restricted to the `annote` field. Any field (except the `type` and `crossref` fields) can in fact hold a multiline value. To give a field a multiline value, use `m` instead of `e`. You will again be put in a multiline edit buffer, where you can edit the value. Note that you can use `m` even if a field already has a single line value. Ebib will just make that the first line in the multiline edit buffer.

When a field has a multiline value, only the first line is shown in the entry buffer, for space reasons. To indicate that the value is multiline, a plus sign `+` is placed in front of the value. If you want to see the whole contents of a multiline field, you can use `v`: this will display the contents of the current field in a `*Help*` buffer. This buffer can be dismissed again with `q`. This is quicker than entering the multiline edit buffer just to read the contents of a field and it has the advantage that the other fields stay visible.

By the way, the `e` key is smart about the way an entry must be edited. If you press `e` on a field that already has a multiline value, regardless of the fact whether it is the `annote` field or not, Ebib puts you in a multiline edit buffer. Therefore, you need `m` only if you want to give a field a multiline value when it doesn't have one yet.

For more details on working with multiline edit buffers, see [Multiline Edit Buffers](#multiline-edit-buffers).


## Undefined Fields ##

Bib(la)TeX ignores fields that it does not know, which is a property that can be exploited to add any kind of  information to an entry. Ebib accommodates this by allowing fields with any name, not just the ones that are predefined. Such undefined fields are displayed last in the entry buffer, following the extra fields.

It is even possible to add such fields to an entry by pressing `a` in the entry buffer. This asks for a field name and then a value. If you make heavy use of this option, it may be better to define the relevant fields through the user option "Extra Fields", but undefined fields may be useful when reading or importing BibTeX entries from a different source that contain non-standard fields.

Note that if you delete the contents of an undefined field, the field itself is also deleted. (In fact, the field remains in the database until you close the database, but it will not be saved, so the next time you load the `.bib` file, the field is gone.)


## Hidden Fields ##

Biblatex defines a large number of fields, many of which are optional for most entry types. Displaying all these fields in the entry buffer would not be very practical, because you are most likely interested in only a few of them. For this reason, Ebib defines a (fairly large) number of fields as 'hidden', meaning that they are not shown in the entry buffer. You can make these fields visible with the key `H` in the index buffer. Which fields are treated as hidden is controlled by the option "Hidden Fields" (`ebib-hidden-fields`), which can be customised.

Most of the fields defined as hidden are Biblatex-specific, because BibTeX recognises a much smaller number of fields and there isn't much of a need to hide the lesser used ones. However, the functionality is available: if you wish to use it, just add the relevant fields to the option "Hidden Fields".


## Timestamps ##

Ebib provides the possibility to add a timestamp to every new entry, recording the time it was added to the database. The timestamp is recorded in the (extra) field `timestamp`, which is hidden by default.

You can tell Ebib to create timestamps by setting the option "Use Timestamp" (`ebib-use-timestamp`) in Ebib's customisation buffer. With this option set, a timestamp is included in entries added to the database with `a`. Ebib will also add a timestamp to entries imported from a buffer or merged from a file, and to entries exported to another database or to a file. When importing or exporting entries, existing timestamps will be overwritten. The logic behind this is that the timestamp records the date and time when the entry was added to the database, not when it was first created.

Note that if this option is unset, the timestamp of an entry is retained when it's imported or exported. Therefore, if you record timestamps and want to im-/export entries without changing their timestamps, temporarily unset this option, which can be done in the menu under “Options”.

Ebib uses the function `format-time-string` to create the timestamp. The format string that Ebib uses can be customised. The default string is `"%a %b` `%e %T %Y"`, which produces a timestamp of the form `"Mon Mar 12 01:03:26 2007"`. This string is not directly suitable for sorting, so if you want to be able to sort on timestamps, you'll need to customise the format string. See the documentation for `format-time-string` on the options that are available. (Alternatively, the default time stamp format can be converted into a sortable time format using `date-to-time`, but currently Ebib is not able to do this automatically.)

Adding timestamps in a format that `date-to-time` can parse makes it possible to list the most recent additions to the database. Ebib provides a function to do this: `ebib-list-recent`, which asks for a number of days and lists the entries that were added since then.


## Copy, Cut (Kill), Paste (Yank), and Delete ##

A few more commands are available when you're in the entry buffer editing field values. The commands `c`, `k` and `y` implement copy, kill and yank: `c` copies the contents of the current field to the kill ring, `k` kills the contents of the current field to the kill ring, and `y` yanks (pastes) the most recently killed text in the kill ring. You can type `y` repeatedly to get the same effect you get in Emacs when you type `M-y` after an initial `C-y`.

Lastly, there is the command `d`, which deletes the contents of the current field without storing the text in the kill ring. (It asks for confirmation, though, just to make sure.)

Note that `y` only works when the current field does not have a value yet. This is to prevent you from accidentally overwriting a field value. If you do want to yank text into a field that already has a value, simply hit `d` first to delete the text.


# Saving a Database #

When you have undertaken any kind of editing action on a database, it is marked as modified, which is indicated in the mode line for the index buffer. A modified database can be saved by typing `s`. This saves the database to the file it was loaded from without asking for confirmation. (It is similar to `C-x C-s` in Emacs.) If you're saving a file for the first time after loading it, Ebib creates a backup file. (Ebib honours `backup-directory-alist` when saving backups. Note that you can also disable backups altogether with the option "Create Backups", `ebib-create-backups`.)

If you want to force-save a database that has not been modified, you can use a prefix argument: `C-u s`. In either case, however, Ebib checks whether the underlying file was modified and warns you if it was. (Ebib does this by storing the `.bib` file’s modification time when reading the file and comparing this time with the modification time when requested to save the file.) If you also want to forego this check, use a double prefix argument: `C-u C-u s`. This saves the file unconditionally.

If you have multiple databases open, have made changes in more than one of them, and want to save all of them without going through each yourself, you can save all databases at once through the menu. You can also save the database to another name, similar to `C-x C-w` in Emacs: the new `.bib` file becomes associated with the database. The command for this is `w`. This command can also be prefixed with `C-u` (or in fact any other prefix argument) in order to overwrite any existing file without asking for confirmation.


# Using Biblatex #

Compared to BibTeX, Biblatex has a greatly expanded number of fields, a somewhat different set of entry types and a much more complex system of field value inheritances. Ebib can handle both kinds of files, provided it is set up for the right “dialect”.


## Setting the BibTeX Dialect ##

Biblatex files use the same `.bib` suffix that BibTeX files use. Whether Ebib interprets a file as a BibTeX or a Biblatex file is determined by the user option “Bibtex Dialect” (`ebib-bibtex-dialect`). Possible values for this option are `BibTeX` and `biblatex`, the default being `BibTeX`. (These values are taken from the variable `bibtex-dialect-list`.)

The dialect specified determines which entry types Ebib recognises and which fields it expects. Reading a file with the wrong dialect setting will most likely result in a series of “Illegal entry type” errors. Note, however, that these entries will still be loaded and displayed, but they will be highlighted with Emacs’ `error` face. Fields that are not defined for the current dialect are displayed as undefined fields (i.e., below all other fields in the entry buffer).

The option “Bibtex Dialect” sets the default dialect, which is the dialect that Ebib gives to newly created `.bib` files and which it assumes for files that are not otherwise specified. If you wish to work with a file that is in a different dialect than what you set as the default, you can set the dialect for this particular file. To do this, load the file and then set the dialect through the menu option «Ebib | BibTeX Dialect» or with the command `M-x ebib-set-dialect`. You only need to do this once for a file, because the setting is saved in the `.bib` file in the local variable block. (If no local variable block exists, one is created.) The setting is actually saved as a file-local value for the variable `bibtex-dialect`, which means that if you should open the file directly in `bibtex-mode`, Emacs will apply the dialect setting as well.

The mode line of the index buffer shows the dialect that Ebib assumes for the current database. Note that this does not necessarily mean that the dialect is set in the `.bib` file: if the file does not have a dialect setting, the mode line shows the default setting.


## Alias Types and Fields ##

The set of entry types defined by Biblatex differs from the set used by BibTeX. Mostly, Biblatex adds new entry types, but there are a few BibTeX entry types that have been dropped. For legacy reasons, Biblatex still recognises these entry types, but it treats them as aliases for some of its own types. The relevant entry types are `@conference` (treated as an alias for `@inproceedings`), `@electronic` (alias for `@online`), `@mastersthesis` (alias for `@thesis` with the `type` field set to 'Master's thesis'), `@phdthesis` (alias for `@thesis` with the `type` field set to 'PhD thesis'), `@techreport` (alias for `@report` with the `type` field set to 'technical report') and `@www` (alias for `@online`). If an entry has such an alias as entry type, Ebib displays the entry type that Biblatex treats it as in the entry buffer. (For example, the entry type alias `phdthesis` is shown as  `phdthesis [==> Thesis]`.)

Similarly, a number of fields are deprecated but still accepted as aliases. These are `address` (alias for `location`), `annote` (alias for `annotation`), `archiveprefix` (for `eprinttype`), `journal` (for `journaltitle`), `key` (for `sortkey`), `pdf` (for `file`), `primaryclass` (for `eprintclass`), and `school` (for `institution`). These aliases are also indicated in the entry buffer, albeit in a slightly different way. For example, if an entry has a `journal` field, its value is shown as the value of the `journaltitle` field; a tag `[<== journal]` is placed after the field value, indicating that the value is actually contained in the journal field. The `journal` field itself is shown as an undefined field (i.e., after all other fields). That is, in such cases, the value is shown twice: once as the `journaltitle` field (among the obligatory fields), and once as the `journal` field. This is done so that you can easily copy the value of the `journal` field to the `journaltitle` field, if you wish to bring your entries into line with Biblatex's conventions.


# The Entries List #

By default, the index buffer displays the list of entries in the database in a table format using the entry key, and the author, year and title fields of each entry. The entries are sorted alphanumerically on the entry key in ascending order.  You can sort the entries on one of the other columns using the keys `<` and `>`. The former performs an ascending sort (smallest to largest, hence the smaller-than sign), the latter a descending sort. They both ask you for the column to sort on. Restoring the default sort can be done with `=`.

The fields that are displayed in the index buffer can be customised with the user option `ebib-index-columns`. Each element in this option describes a column and consists of the field to display (which is also the column label), the width of the column and a flag indicating whether the column can be sorted. You can add or remove fields, or reorder the existing ones.

You can use any BibTeX / BibLaTeX field to define a column in the index buffer. In addition, there are two column labels with a special meaning: `"Entry Key"`, which displays the entry key, and `"Author/Editor"`, which displays the contents of the author field if it is not empty, and the contents of the editor field otherwise.

The first column defined in `ebib-index-colums` is the column on which the entries are sorted by default, i.e., when the database is first opened and when you press `=`. It is not possible to set another column as the default sort key (though you can, of course, sort on them using `<` or `>`).


# Searching #

## Simple Searches ##

Ebib provides several search methods. First of all, in the index buffer, the normal Emacs incremental searches, `C-s` and `C-r`, can be used to search entry keys. Once you've found the key you're searching, you must hit `RET` to quit the search and again `RET` to make the entry you found active: Ebib does not update the entry buffer during incremental search. If you make frequent use of this option, you may want to make the cursor visible in the Ebib buffers. Unset the customisation option "Hide Cursor" (`ebib-hide-cursor`) to do so.

The contents of the entries can be searched with `/`. This command (`ebib-search`) searches for a string (more precisely, a regular expression) starting from the current entry (i.e., *not* from the first entry) and will display the entry with the first occurrence of the search string that it finds. All the occurrences of the search string in that entry are highlighted.

Ebib searches all the fields of each entry. It is not possible with `/` to specify the fields to search. Note that if the search term is found in a field with a multiline value, Ebib will highlight the `+` sign that is displayed in front of the field value. When the search term is found, Ebib gives a message saying so, similarly if the search term was not found.

A search term may of course appear more than once in the database. To search for the next occurrence, type `/` again (or, alternatively type `RET`). This continues searching for the search term in the rest of the database. Again, the first entry found to contain the search string is displayed. Note that the search does not wrap: if the end of the database is reached, Ebib stops searching and informs you that no further occurrence of the search string was found. If you want to continue searching from the top, type `g` and then continue the search with `/` or `RET`.

Note that once you've started a search with `/`, Ebib activates a transient key map called `ebib-search-map`. It is this map that holds the bindings of `/` and `RET` to continue searching after the current entry and of the key `g` to jump to the top of the database. You can, of course, bind or rebind keys in this map.

Exiting a search (i.e., getting rid of the transient key map) is done by pressing any key other than `/`, `RET` or `g`. The search is ended and the command associated with this key is executed normally. If you want to repeat a previous search, you can pass a prefix argument to `/`. So typing `C-u /` (or any other prefix argument) starts searching for the previous search string again.


## Filters ##

Ebib also has a much more sophisticated search mechanism that makes use of *filters*. A filter is basically a search expression that selects entries from the current database. When you apply a filter to a database, only the entries that match are shown. With filters, you can, for example, select all entries from a database that contain the string "Jones" in their `author` field. A filter can be as complex as you want: you can select all entries that do *not* contain "Jones" in the `author` field, or all entries that contain "Jones" in either the `author` or the `editor` field, or all entries that contain "Jones" in the `author` field, and "symbiotic hibernation" in the `keyword` field, etc. Basically, the filter can consist of an arbitary number of search criteria combined with the logical operators `and`, `or` and `not`.


### Simple Selection ###

Creating a filter is simple: press `&`, and Ebib will ask you for a field to select on, and for a regular expression to select with. So if you want to select all entries that contain "Jones" in the `author` field, you press `&` and type `author` as the field and `Jones` as the regexp to filter on. Ebib then runs this filter on the database, and only shows those entries that match the filter. To indicate that a filter is active, the active filter is displayed in the mode line of index buffer. (The filter can be displayed in Lisp form, if you prefer: customise "Filters Display As Lisp" to do so.)

If you don't want to filter on one specific field but rather want to select all entries that match a certain regexp in any field, you can type `any` as the field to filter on. So specifying `any` as the field and `Jones` as the regexp will give you all entries that have a field that contains "Jones" in them.

Note that you can also select items based on their entry type. In order to do that, you need to specify `=type=` as the field to search, which is the field name in which Ebib stores the entry type internally. (There is also a "normal" field called `type`, hence the equal signs.) If you search the `=type=` field, only exact matches are returned, so if you search for `book`, only the entries that are of type `book` are returned, not those of type `inbook`. You can use TAB completion in this case, by the way.

If you specify the `keywords` field, the keywords associated with your database are available for TAB completion as well. Though you can enter any search term, of course.


### Complex Filters ###

Once you have a filter on your database, you can refine or extend it. For example, suppose you have a filter selecting all entries with "Jones" in the `author` field and want to add all entries that have "Jones" in the editor field to your selection. In this case you need to do a logical `or` operation: you want to select an entry if it contains "Jones" in the `author` field (which you already did) *or* if it contains "Jones" in the `editor` field.

A short sidenote: the first impulse in a case like this might be to use `and` instead of `or`: after all, you want to select all entries that contain "Jones" in the `author` field *and* all entries that contain "Jones" in the `editor` field. However, the filter that you build up is used to test each entry *individually* whether it meets the selection criterion. An entry meets the criterion if it contains "Jones" in the `author` field *or* if it contains "Jones" in the `editor` field. Therefore, `or` is the required operator in this case. If you would use `and`, you would only get those entries that contain "Jones" in both the `author` *and* `editor` fields.

To perform a logical `or` operation, press the key `|`. As before, you will be asked which field you want to filter on, and which regexp you want to filter with. Ebib will then update the index buffer.

It is also possible to perform a logical `and` on the filter. Use this if you want to select those entries that contain "Jones" in the `author` field and e.g. "symbiotic hibernation" in the `keyword` field. A logical `and` operation is done with the key `&`. (Note: this is the same key that is used to create the filter. In fact, you can create a filter with `|` as well: when used in an unfiltered database, `&` and `|` are equivalent. They are only different when a filter is already active.)

Both the `&` and `|` commands can be used with the negative prefix argument `M--` (or `C-u -`, which is identical). In this case, the search criterion is negated. That is, the negative prefix argument performs a logical `not` operation on the search criterion. For example, if you want to select all entries from a database that do *not* contain "Jones" in the `author` field, you can do this by typing `M-- &` and then filling out the relevant field and regexp.

There is another way of performing a logical `not` operation, which is only available when a filter is active: by pressing the key `~`, you invert the current filter. That is, if you have a filtered database with all the entries containing "Jones" in the `author` or in the `editor` field, and you press `~`, the selection is inverted, and now contains all entries that do *not* have "Jones" in the `author` or `editor` field.

Although `~` and the negative prefix argument to `&` or `|` both perform logical `not` operations, they are *not* equivalent: `~` negates the entire filter built up so far, while the negative prefix argument only negates the single selection criterion you enter with it.

When a filter is active, the filter itself is displayed at the top of the index buffer. If the index window is too small to display the entire filter (which can easily happen if Ebib is set to split the frame vertically rather than horizontally), you can press `F v` (uppercase `F`, small `v`), which will display the filter in the minibuffer.

To cancel the filter and return to the normal view of the database, press `F c`. For convenience, this action is also available with `c`, which normally closes a database. If a filter is active, however, it simply cancels the filter. (If you find this behaviour confusing, you can rebind the `c` key to the function `ebib-close-database`. See [Modifying Key Bindings](#modifying-key-bindings) for details.)


### Storing and Saving Filters ###

When you cancel a filter, it is automatically stored so that it can be reapplied later. To reapply a filter, type `F L`. This will reapply the last used filter regardless of which database you're in. That is, you can use this to search more than one database without having to type the filter over and over.

However, Ebib only stores one filter this way. If you want to store more filters, you have to name them. You can store the currently active filter or the last used filter with `F s`. Ebib will ask you for a name for the filter in order to identify it later. By default, filter names are case-insensitive, but if you prefer to use case-sensitive filter names, you can unset the option "Filters Ignore Case". When Ebib is closed, all stored filters are saved to a file and they're automatically reloaded when you open Ebib again. Stored filters are not associated with a particular database: once a filter is stored, it is available to all databases.

You can apply a stored filter with `F a`. This will ask for the name of a filter and apply it to the current database. You can extend the filter in the normal way, though the changes will not be stored automatically. To store it, type `F s` again. You can store the extended filter under the old name, in which case Ebib will ask you for confirmation, or under a new name, which will store it as a new filter, keeping the old one.

The file that Ebib uses to store filters is `~/.emacs.d/ebib-filters`, although that can of course be customised (see the option "Filters Default File"). As mentioned, stored filters are saved automatically when Ebib closes, but you can also save them manually with `F S`. Note that if there are no stored filters when Ebib is closed (or when you press `F S`), the file is deleted.

You can also save your filters to a different file with `F w`. Such a filter file can be reloaded later with `F l`. If you load filters from a file while you still have stored filters, you are asked if you want to replace them completely or if you want to add the new filters to the existing ones. In the latter case, however, filters whose name conflict with existing filters are not loaded. (Ebib will log a message about this when this happens.)

To see what filters are currently stored, use `F V`. If you want to rename a filter, you can do so with `F R`.

Note that cancelling a filter with `F c` does not delete it from the list of stored filters, it will remain available for later application. If you want to delete a filter from the list of stored filters, use `F d`. You can also delete all stored filters with `F D`. These deletion commands do not ask for confirmation, but if you delete any filters by accident, you can reload them from `~/.emacs.d/ebib-filters` with `F l`.


### Special Filters ###

Filters are essentially Lisp expressions that consist of the functions `and`, `or`, and `not`, together with a special macro `contains`. However, filters are not limited to these forms. They can essentially contain any Lisp expression. It is not possible to create such special filters interactively, but it is possible to write such filters and put them in a filter file, or to write a function that creates a special filter.

A filter is a Lisp expression that should return either `t` or `nil`, indicating whether the entry being tested matches the filter or not. The contents of the entry is available in a variable `entry`. This variable is given a value by the function that runs the filter, but it is not passed as an argument. Rather, it is a local dynamic variable, which means that the file that defines the filter function should have the variable `lexical-binding` set to `nil`.

The value of `entry` is an alist of fields and their values. These include the fields `=key=` and `=type=` for the entry key and type:

```
(("author" . "{Noam Chomsky}")
 ("title" . "{Syntactic Structures}")
 ("publisher" . "{The Hague: Mouton}")
 ("year" . "{1957}")
 ("remark" . "{copy}")
 ("timestamp" . "{2007-12-30}")
 ("file" . "{c/Chomsky1957.pdf}")
 ("=type=" . "book")
 ("=key=" . "Chomsky1957"))
```

### An Example: Listing Recent Additions ###

One special filter is included with Ebib. It filters recent additions to the database. The command that creates the filter is `ebib-list-recent`:

``` lisp
(defun ebib-list-recent (days)
  "List entries created in the last DAYS days."
  (interactive "nNumber of days: ")
  ;; save the database's current filter, if there is one.
  (let ((filter (ebib-db-get-filter ebib--cur-db)))
    (when filter (setq ebib--filters-last-filter filter))) 
  (let*
      ;; calculate the from-date in Emacs' time format
      ((date (time-subtract (current-time) (days-to-time days)))
       ;; create a Lisp expression that will function as the filter
       (filter `(ebib--newer-than (quote ,date))))
    ;; install it as the curretn database's filter
    (ebib-db-set-filter filter ebib--cur-db)
    ;; update the display, so that only filtered entries are visible
    (ebib--redisplay)))
```

First, this function saves the current filter if there is one. It then creates a date in Emacs’ internal time format by subtracting the number of days provided by the user from the current date and uses this date to create a Lisp expression which is then installed as the filter for the current database. A call to `ebib--redisplay` then updates the display, taking the filter into account.

The function `ebib--newer-than` is defined as follows:

``` lisp
(defun ebib--newer-than (date)
  "Function for use in filters.
Return t if the entry being tested is newer than DATE.  DATE must
be a list of the format returned by `current-time' and is
compared to the timestamp of the entry being tested.  If the
entry has no timestamp, or a timestamp that cannot be converted
into a date representation, return nil."
  (let ((timestamp (cdr (assoc-string "timestamp" entry))))
    (when (and timestamp
               (setq timestamp (ignore-errors (date-to-time timestamp))))
      (time-less-p date timestamp))))
```

This function obtains the time stamp of the entry being tested from the variable `entry` and then tries to convert it to Emacs’ time format. If successful, it compares this time to the date passed as an argument and returns `t` if the latter precedes the former.


### Properties of Filtered Databases ###

When a filter is active, there are a few things that are not possible or function differently. First, it is not possible to add or delete entries, either interactively or by merging or exporting. Exporting from a filtered database or saving a filtered database is also disabled. Editing existing entries is possible, however. Note that if the entry doesn't match the filter anymore after the edit, it doesn't disappear from view. For that, you need to reapply the filter with `F r`.

It is also possible to mark entries. Marked entries stay marked when you cancel the filter, so in order to do something with all the entries matching a filter, you can mark them all in the filter view with `M`, then cancel the filter and perform an action on them.

If a database has an active filter, the save command is disabled, because it would not be clear whether you want to save the entire database or just the filtered entries. If you want to save only the filtered entries to a file, you can use the command `w` (or the menu option "Save Database As"). This also saves the `@string`, `@preamble` and `@comments`, as well as any file-local variables, so you will have a self-contained `.bib` file with only the filtered entries. In order to save the entire database, you need to cancel the filter. After saving, you can reapply the filter with `F L`, of course.

One final note: of all the filter-related commands, `~`, `F c`, `F r`, `F s` and `F v` are only available when a filter is active. The other commands operate on the stored filters and can be used when no filter is active.


# Accessing BibTeX Databases outside Ebib #

When you're in a text buffer, you can insert a citation with the command `ebib-insert-citation`. This command asks for a key and inserts a citation with that key in a (user-selectable) form that is appropriate for the current buffer. By default, this is set up for LaTeX and  [Pandoc](http://johnmacfarlane.net/pandoc/) Markdown buffers, and for [Org mode](http://orgmode.org).

When you invoke `ebib-insert-citation`, Emacs prompts you for a key from the database(s) associated with the current buffer and for a citation command to use. You can use TAB completion when typing the key. If you have the `ivy` package installed, however, Ebib uses a more sophisticated method: instead of typing just the key, you can type (parts of) the author name, publication year and title in order to find the reference you wish to cite.

You can define different citation commands for each type of file that you use. That is, you can have one set of citation commands for LaTeX files, another set for Org files, etc. For LaTeX buffers, the only citation command that has been predefined is `cite`, which inserts a citation of the form `\cite[arg]{key}`. You may want to define more commands.

For Markdown buffers, three commands have been predefined: `text`, which inserts a citation of the form `@Jones1992`,  `paren`, which inserts a citation of the form `[@Jones1992]` and `year`, which inserts `[-@Jones1992]`. Since these are the only types of citations that Pandoc Markdown knows, you shouldn't need to change anything.

In Org buffers, citations are inserted in the form `[[ebib:<key>][<description>]]`. You are prompted for the description, which you have to provide yourself, unless you use the `ivy` package, in which case a default description is provided, which you can accept by pressing `ENTER`. If you use this type of Org link, you may want to load the `org-ebib` package, which allows you to open Ebib with `org-open-at-point` (by default bound to `C-c C-o`). This package also enables you to create Org links to Ebib entries with `org-store-link`.

Ebib also provides a way to insert citations into a buffer from within Ebib. If you're in the index buffer and press `i`, Ebib asks you for a buffer to insert the citation into (which defaults to the buffer you started Ebib from, or the buffer you previously inserted an entry into), a citation command and also any optional arguments, and then inserts a citation at the current cursor position in the buffer you've supplied.

Both methods use the same sets of citation commands, which are defined in the user option `ebib-citation-commands`. You can customise this option, as discussed below, [Defining Citation Commands](#defining-citation-commands). For LaTeX, only the `\cite` command is set up by default, so you may want to add some commands. For example, this is what I use:

```
(setq ebib-citation-commands
      '((any
         (("cite"        "\\cite%<[%A]%>[%A]{%(%K%,)}")
          ("text"        "\\textcite%<[%A]%>[%A]{%(%K%,)}")
          ("paren"       "\\parencite%<[%A]%>[%A]{%(%K%,)}")
          ("author"      "\\citeauthor%<[%A]%>{%(%K%,)}")
          ("possauthor"  "\\possciteauthor%<[%A]%>{%K}")
          ("posstext"    "\\posstextcite%<[%A]%>{%K}")
          ("posscite"    "\\posscite%<[%A]%>{%K}")
          ("year"        "\\citeyear%<[%A]%>[%A]{%K}")))
        (org-mode
         (("ebib"        "[[ebib:%K][%D]]")))
        (markdown-mode
         (("text"        "@%K%< [%A]%>")
          ("paren"       "[%(%<%A %>@%K%<, %A%>%; )]")
          ("year"        "[-@%K%< %A%>]")))))
```

Calling Ebib from a text mode buffer has another small advantage. If point is on a BibTeX key when Ebib is called, it jumps to that entry in your database. This allows you to quickly check a reference in your text. Ebib will search the entry in the current database, or, if you're calling Ebib from a LaTeX file and there is a `\bibliography` or `\addbibresource` command in the file, in the databases in these commands, if they are opened in Ebib, [Associating a Database with a LaTeX File](#associating-a-database-with-a-latex-file) below for details.

There is one more command that can be useful: `ebib-create-bib-from-bbl` creates a `.bib` file from the `.bbl` file associated with the LaTeX document in the current buffer. This makes it easy to create a `.bib` file containing just the BibTeX entries that are used in the document. Note, however, that this command does not add cross-referenced entries to the newly created `.bib` file, nor does it add `@String` definitions and the `@Preamble`. So make sure to add those after using `ebib-create-bib-from-bbl`.


## Key Bindings ##

Of course, the easiest way to use the commands discussed here is to bind them to a key sequence. For example, the following binds `C-c b` to `ebib-insert-citation` in AUCTeX's LaTeX mode:

```
(define-key 'LaTeX-mode-map "\C-cb" 'ebib-insert-citation)
```

Note that commands of the form `C-c <letter>` are reserved for the user, and should therefore not be set by any package. For this reasons, Ebib does not set this command itself.

`ebib-insert-citation` recognises the major mode of the buffer it is called from and uses this information to determine which kinds of citations to insert. So you can bind the `ebib-insert-citation` to the same key sequence in every text mode in which you use citations and Ebib will do the right thing.


## Defining Citation Commands ##

As mentioned, you should probably set up some citation commands if you use Ebib with LaTeX documents. The customisation option that allows you to do this is "Citation Commands".

Citation commands are defined for specific major modes. You can also define commands for all modes under the heading `any`. (By default, this option is used for LaTeX commands, since there is more than one Emacs mode for (La)TeX). Each command consists of an identifier, which you type when Ebib prompts you for a citation command, plus a format string, which is used to create the actual citation command.

The identifier should be a simple string which you can type easily when Ebib asks you for a citation command (TAB completion is available, though). The format string can contain a few directives, which are used to add the citation key and any optional arguments. The following directives are recognised:

`%K`
:    the entry key to be inserted.

`%A`
:    an argument, for which the user is prompted.

`%<...%>`
:    optional material surrounding a `%A` directive.

`%(...%<sep>)`
:    a so-called *repeater*, which contains material that can be repeated.
     If present, the repeater must contain the entry key directive `%K`.

`%D`
:   a description, for which the user is prompted. Mainly for use in Org citations.

In the simplest case, the format string contains just a `%K` directive: `\cite{%K}`. In this case, `%K` is replaced with the citation key and the result inserted. Usually, however, citation commands allow for optional arguments that are formatted as pre- or postnotes to the citation. For example, using the `natbib` package, you have citation commands available of the form:

    \citet[cf.][p. 50]{Jones1992}

In order to be able to insert such citations, the format string must contain `%A` directives:

    \citet[%A][%A]{%K}

With such a format string, Ebib asks the user to provide text for the two arguments and inserts it at the locations specified by the directives. Of course, it is possible to leave the arguments empty (by just hitting `RET`). With the format string above, this would yield the following citation in the LaTeX buffer:

    \citet[][]{Jones1992}

The empty brackets are completely harmless, because LaTeX will simply ignore the empty arguments. However, you may prefer for the brackets not to appear if the arguments are empty. In that case, you can wrap the brackets and the `%A` directives in a `%<...%>` pair:

    \citet%<[%A]%>%<[%A]%>{%K}

Now, if you leave the arguments empty, Ebib produces the following citation:

    \citet{Jones1992}

Note however, that this format string is problematic. If you fill out the first argument but not the second, Ebib produces the wrong format string:

    \citet[cf.]{Jones1992}

If only one optional argument is provided, `natbib` assumes that it is a postnote, while what you intended is actually a prenote. Therefore, it is best not to make the second argument optional:

    \citet%<[%A]%>[%A]{%K}

This way, the second pair of brackets is always inserted, regardless of whether you provide a second argument or not.

`Natbib` commands also accept multiple citation keys. When you call `ebib-insert-citation` from within a LaTeX buffer, you can only provide one key, but when you're in Ebib, you can mark multiple entry keys and then use `i` to insert them to a buffer. In this case, Ebib asks you for a separator and then inserts all keys into the position of `%K`:

    \citet{Jones1992,Haddock2004}

It is, however, also possible to specify in the format string that a certain sequence can be repeated and how the different elements should be separated. This is done by wrapping that portion of the format string that can be repeated in a `%(...%)` pair. Normally, you'll want to provide a separator, which is done by placing it between the `%` and the closing parenthesis:

    \citet[%A][%A]{%(%K%,)}

This format string says that the directive `%K` can be repeated and that multiple keys must be separated with a comma. The advantage of this is that you are no longer asked to provide a separator.

It is also possible to put `%A` directives in the repeating part. This is useful for `biblatex` package, which has so-called *multicite* commands that take the following form:

    \footcites[cf.][p. 50]{Jones1992}[][p. 201]{Haddock2004}

Multicite commands can take more than one citation key in braces `{}` and each of those citation keys can take two optional arguments in brackets `[]`. In order to get such citations, you can provide the following format string:

    \footcites%(%<[%A]%>[%A]{%K}%)

Here, the entire sequence of two optional arguments and the obligatory citation key is wrapped in `%(...%)`, so that Ebib knows it can be repeated. If you now mark multiple entries in Ebib, press `p` and select the `footcites` command, Ebib will put all the keys in the citation, asking you for two arguments for each citation key.

Of course it is also possible to combine parts that are repeated with parts that are not repeated. In fact, that already happens in the previous example, because the part `\footcites` is not repeated. But the part that is not repeated may contain `%A` directives as well:

    \footcites%<(%A)%>(%A)%(%<[%A]%>[%A]{%K}%)

Multicite commands in `biblatex` take two additional arguments surrounded with parentheses. These are pre- and postnotes for the entire sequence of citations. They can be accommodated as shown.

Lastly, a citation command can also contain a `%D` directive. This is mainly for use in Org citations, which take the form `[[ebib:<key>][<description>]]`. The description is not an argument to the citation command but the string that will be displayed in the Org buffer.


## Associating a Database with a LaTeX File ##

The commands `ebib-insert-citation` and `ebib-entry-summary` must consult the database or databases loaded in Ebib, and Ebib tries to be smart about which database(s) to consult. Usually, a LaTeX file has a `\bibliography` command somewhere toward the end, or an `\addbibresource` command in the preamble, which names the `.bib` file or files that contain the bibliography entries. If you consult a BibTeX database from within a LaTeX file, Ebib first looks for one of these commands, reads the names of the `.bib` file(s) from it, and then sees if those files happen to be open. If they are, Ebib uses them to let you pick an entry key (in the case of `ebib-insert-entry-key`) or to search for the entry (in the case of `ebib-entry-summary`).

Of course, it may be the case that the LaTeX file is actually part of a bigger project, and that only the master file contains a `\bibliography` or `\addbibresource` command. To accommodate for this, Ebib checks whether the (buffer-local) variable `TeX-master` is set to a filename. If it is, it reads that file and tries to find the relevant command there. (Note: `TeX-master` is an AUCTeX variable, which is used to keep track of multi-file projects. If you don't use AUCTeX, this functionality doesn't work, and Ebib will only check the current file for a `\bibliography` or `\addbibresource` command.)

Note that if one of the `.bib` files in the `\bibliography` or `\addbibresource` command isn't loaded, Ebib issues a warning message about this, and continues to check for the next `.bib` file. These warning messages appear in the minibuffer, but are probably directly overwritten again by further messages or prompts Ebib produces, so check the `*Messages*` buffer if Ebib doesn't seem to be able to find an entry that you're sure is in one of your databases.

Another thing to keep in mind is that Ebib only looks for a `\bibliography` or `\addbibresource` command once: the first time either `ebib-insert-bibtex-entry` or `ebib-entry-summary` is called. It stores the result of this search and uses it the next time either of these commands is used. Therefore, if you make a change to the bibliography command, you must reload the file (use `M-x revert-buffer` or `C-x C-v RET`) to make sure Ebib rereads the bibliography command.

If no `\bibliography` or `\addbibresource` command is found at all, either in the LaTeX file itself, or in the master file, Ebib simply consults the current database, i.e. the database that was active when Ebib was lowered with `z`. This is also what Ebib does for Org mode or Pandoc Markdown files, since they do not have the equivalent of a bibliography command. (Note, however, that you can set `ebib-local-bibtex-filenames` to a list of `.bib` files in the file-local variable section of a file.)


# Cross-referencing #

Both BibTeX and Biblatex have a cross-referencing facility. Suppose you have an entry `Jones1998`, which appeared in a book that is also in your database, say under `Miller1998`. You can tell Bib(La)TeX that `Jones1998` is contained in `Miller1998` by putting `Miller1998` in the `crossref` field. When Bib(La)TeX finds such a cross-reference, all the fields of `Jones1998` that don't have a value inherit their values from `Miller1998`. At the very least, this saves you some typing, but more importantly, if two or more entries cross-reference the same entry, Bib(La)TeX automatically includes the cross-referenced entry in the bibliography (and puts a reduced reference in the cross-referencing entries).

When you fill in the `crossref` field in Ebib, Ebib displays the values of the cross-referenced entry in the entry buffer. To indicate that they are just inherited values, they are marked with `ebib-crossref-face`, which by default inherits from `font-lock-comment-face`. (You can customise it, of course. See the customisation option "Crossref Face".) These values are merely displayed for convenience: they cannot be edited. (They can be copied, however).

BibTeX inheritance mechanism is rather crude: cross-referencing entries simply inherit the fields of the same name from the cross-referenced entry. Biblatex's mechanism is more sophisticated. Biblatex inheritance rules depend on the field and on the types of the cross-referencing *and* the cross-referenced entry. Thus it is possible to specify that the `inbook` entry type can inherit a `maintitle` field from the `title` field if the cross-referenced entry is of type `mvbook`, and a `booktitle` field if the cross-referenced entry is of type `book`. The inheritance scheme for Biblatex is defined by the option "Biblatex Inheritances", which is set up with the default inheritance relations defined by Biblatex, but which can be customised if needed.

If you're viewing an entry that has a cross-reference and you want to go to the cross-referenced entry you can type `C`. This command reads the value of the `crossref` field and then displays that entry. If you want to do the reverse, i.e., see if the current entry is cross-referenced by any other entries, you can use the same key `C`: if you type `C` on an entry that does not have a cross-reference, Ebib makes the key of the current entry the current search string and searches for its first occurrence after the current entry. Note that after Ebib has jumped to the first cross-referencing entry, you cannot type `C` again to find the next one. (Instead, it would take you back to the cross-referenced entry.) In order to find the next cross-referencing entry, you have to type `n`, as with a normal search. (Also, if the cross-referenced entry appears alphabetically before the cross-referencing entry, you need to type `g` and then `/`.)

Note that if you want to use Bib(La)TeX's cross-referencing options, the option "Save Xrefs first" needs to be set (which it is by default). This tells Ebib to save all entries with a `crossref` field first in the `.bib` file. Without this, cross-referencing will not work reliably.


# Marking Entries #

Commands in the index buffer generally operate on one single entry, or on all entries. For some commands, however, it may sometimes be useful to perform them on more than one entry, but not necessarily all of them. This can be achieved by selecting entries. You can select the entries you want to perform a command on with the key `m`. This selects (or unselects) the current entry. Selected entries are highlighted. (Note that the face properties of selected entries can be customised through the customisation option "Selected Face".)

Commands for which it makes sense automatically operate on all marked entries if there are any. Of the commands discussed so far, these are `d` to delete entries and `p` to push entries to a LaTeX buffer. (Note that Ebib creates a single citation command with commas separating the entry keys.)

The command `M` unmarks all entries or, if there are no marked entries, marks all entries in the current database.


# Printing the Database #

Sometimes it may be useful to have a `.pdf` file or print-out of your database. Although Ebib does not actually do the printing itself, it can create a LaTeX file for you that you can compile and print. In fact, there are two ways of doing this.

The print options are available in the Ebib menu when the index buffer is active. You can print the entries as index cards or as a bibliography.

If you print your entries as a bibliography, Ebib creates a simple LaTeX document that essentially contains a `\nocite{*}` command followed by a `\bibliography` command referring to the `.bib` file belonging to the current database. You can then run the usual sequence of LaTeX, BibTeX, LaTeX, LaTeX on this file, creating a document containing a list of all the references in your database.

If you choose to print as index cards, Ebib also creates a LaTeX file. However, instead of simply providing a `\nocite{*}` command, this file contains a `tabular` environment for each entry in the database listing all the fields of that entry and their values.

The entries are separated by a `\bigskip`, but if you set the option `Print Newpage` in the customisation buffer (or in the Print menu), the entries are separated by a `\newpage`, so that every entry is on a separate page. The latter option is useful when printing actual index cards (though you'd probably have to change the page size with the `geometry` package as well).

By default, the index cards only show single-line field values. That is, multiline values are normally excluded. If you want to include multiline values in the print-out, you have to set the option `Print Multiline` in the Options menu or in Ebib's customisation buffer. With this option set, Ebib includes all multiline values in the LaTeX file that it creates. Note however that Ebib does not change anything about the formatting of the text in a multiline value. So if you plan to make (heavy) use of this option, make sure that the way you type your text conforms to LaTeX's conventions (e.g. empty lines to mark paragraphs, etc.) and doesn't contain any characters such as `&` that are illegal in LaTeX. (Or, alternatively, use LaTeX code in your multiline fields.)

As mentioned, when you "print" the database, Ebib really just creates a LaTeX file. More precisely, it creates a temporary buffer and writes the LaTeX code into it, and then saves the contents of that buffer to a file. After it has done that, Ebib lowers itself and instruct Emacs to open the file in a buffer, which will then be properly set up as a LaTeX buffer. From there you can run LaTeX and view the result.

Before doing all this, Ebib asks you which file to write to. Be careful with this: since this is supposed to be a temporary file, Ebib simply assumes that if you provide a filename of an existing file, it can overwrite that file without warning!

A better way to tell Ebib which file to use is to set the option "Print Tempfile" in Ebib's customisation buffer to some temporary file. When this option is set, Ebib will always use this file to write to, and will not ask you for a filename anymore.

Note that both print options operate on all entries of the database or on the selected entries.

There are two more customisation options for printing the database. These are "Print Preamble" and "LaTeX Preamble". With these options, you can specify what Ebib should put in the preamble of the LaTeX files it creates. Use this if you want to use specific packages. This is especially useful for printing a bibliography, since by default, Ebib uses BibTeX's standard bibliography style. With the option "LaTeX Preamble" you can set your preferred bibliography style.



# Calling a Browser #

With most scientific literature nowadays being available on-line, it is common to store URLs and DOIs in a BibTeX database. (Biblatex of course has standardised fields for this information.) Sometimes you may want to load such a URL or a DOI in your browser. Ebib provides a convenient way for doing so.

If you type `u` in the index buffer, Ebib takes the URL stored in the `url` field of the current entry and passes it to your browser. Furthermore, in the entry buffer, you can use `u` on *any* field. If you happen to have more than one URL stored in the relevant field, Ebib will ask you which one you want to open. Alternatively, you can use a prefix argument: typing `M-2 u` sends the second URL to your browser.

It is not even necessary that the relevant field contains *only* URLs. It may contain other text mixed with the URLs: Ebib simply searches the URLs in the field and ignores the rest of the text. Ebib considers every string of characters that starts with `http://` or `https://` and that does not contain whitespace or any of the characters `" ' ; <` or `>` as a URL. The semicolon is included here even though it is actually a valid character in URLs. This is done for consistency, because the semicolon (actually, semicolon+space) is the standard separator for files in the `file` field and in this way, you can use the same separator to distinguish multiple URLs in the `url` field. By default Ebib also regards everything that is enclosed in a LaTeX `\url{...}` command as a URL. So if you use `; ` to separate URLs and then happen to run into a URL that contains a semicolon, you can enclose it in `\url{...}` and it will be recognised properly. You can, of course, customise the regular expression that controls this behaviour. See the option "Url Regexp" for details.

Similarly, with the key `i` in the index buffer you can send a DOI to a browser. The DOI must be stored in the `doi` field. Unlike URLs, there can only be one DOI in this field. The whole contents of the field is assumed to be the DOI and is sent to the browser. Ebib adds the URL `http://dx.doi.org/` before sending the DOI to the browser, so the `doi` field should contain just the DOI itself.

Ebib uses the Emacs function `browse-url` to call the default browser on the system. If you prefer to use another browser, however, you can specify this with the option "Browser Command". You can also customise the field that Ebib takes URLs from, with the option "Standard Url Field". The same can be done for the DOI field.


# Viewing Files #

If you have electronic versions of the papers in your database stored on your computer, or any other file associated with your entries (e.g., notes, if you store those in separate files) you can use Ebib to call external viewers for these files or have them opened in Emacs. The interface for this is similar to that for calling a browser: if you press `f` in the index buffer, Ebib searches the `file` field for a filename and when it finds one, calls an appropriate viewer. And just as with `u`, you can use `f` in the entry buffer as well, in which case it can be used on any field, not just the `file` field. It is also possible to have more than one filename in a field. In that case, Ebib asks you which one you want to open. If you want to open the first one you can just hit ENTER. Alternatively, you can provide a prefix argument: `M-2 f` for the second file, etc.

The file names in the `file` field do not have to have full paths. You can set the option "File Search Dirs" to a list of directories that Ebib should search when opening a file from the `file` field. Note that Ebib searches only the directories in this list, not their subdirectories. However, you can specify a relative path in the `file` field: if you put something like `a/Abney1987.pdf` in the `file` field, Ebib searches for the relevant file in a subdirectory `a/` of the directories listed in the option "File Search Dirs". As an extra service, Ebib also searches for the base filename, i.e., `Abney1987` in this particular case.

Ebib can call different external programs depending on the file extension of the relevant file. The option "File Associations" allows you to specify which programs to call for which types of files. By default, `.pdf` and `.ps` files are handled, by `xpdf` and `gv`, respectively. You can specify further file types by their extensions (do not include the dot). The program is searched for in `PATH`, but you can of course specify the full path to the program. There is also the option to open files in Emacs.  Use this if you have separate text files for notes, or if you want to read pdf files in Emacs with `doc-view-mode`.

If the `file` field is empty, Ebib will search for a pdf file with a name based on the entry key. By default, Ebib just appends `.pdf` to the entry key and tries to find a file by the name thus created. If you want, you can modify the file name that Ebib searches for by setting the option `ebib-name-transform-function` to a function that performs the transformation. This function takes the key of the current entry as its argument (as a string), and should return the file name to use (without `.pdf`, which is added automatically).

For example, if your entry keys separate authors with colons (i.e., you have keys of the form `Hauser:Chomsky:Fitch2002`), but your pdf files have underscores (i.e., `Hauser_Chomsky_Fitch2002.pdf`), then you can set `ebib-name-transform-function` to:

    (lambda (key) (replace-regexp-in-string ":" "_" key))

Note that you can also use `ebib-name-transform-function` to add a subdirectory to the file name. For example, if you store the pdf files in subdirectories `A/` to `Z/` corresponding to the first letter of the file name, you can use the following function:

    (lambda (key) (format "%c/%s" (aref key 0) key))

For the entry key `Chomsky1995`, this produces `C/Chomsky1995`, which is then appended with the extension `.pdf`.

Of course, the function in `ebib-name-transform-function` does not have to be a lambda. It can also be the name of a function that you’ve defined for the purpose.


## Editing the `file` field ##

As mentioned above, editing the `file` field is a bit different from editing other fields. Instead of typing the full contents of the file field, you are asked to specify a single file name. When you hit ENTER, Ebib adds the filename to the `file` field, appending it no any existing contents (adding a separator if necessary), and then asks you for the next file. If you don't want to add another, just hit ENTER. The default separator is `"; "` (semicolon-space), but this can be customised (see the option "Filename Separator" for details). The advantage of this method is that you can use TAB completion to complete file names.

The first directory in the option "File Search Dirs" is used as the starting directory for filename completion when editing the `file` field. Note that when completing file names, Ebib does not take the directories in "File Search Dirs" into account: completion is done using the standard Emacs file name completion mechanism. However, when you enter a file name, Ebib checks if it is in a (subdirectory of) one of the directories in "File Search Dirs", and if so, cuts off the relevant part of the file name to turn it into a relative path. (You can disable this behaviour with the option `ebib-truncate-file-names`: if unset, file names are always stored as absolute paths.)


# Notes files #

Ebib supports the `annote` (or `annotation`) field, but if you prefer to keep notes outside the `.bib` file, there is an easy way to do that as well. When you hit `N` on an entry in the index buffer, Ebib creates a note for the entry, which is saved in a separate file. If an entry already has a note associated with it, `N` opens it. The mode line of the entry buffer indicates whether an entry has a note associated with it by displaying the string `[N]` (customisable with `ebib-notes-symbol`).

By default, each note is saved to its own file, but you can also use a single file to store all notes. If you wish to use separate files for each note, you need to configure the directory in which to store them by setting the option `ebib-notes-directory`. If this is not set, Ebib uses the first directory in `ebib-file-search-dirs`, (which defaults to the user's home directory).

The name of a notes file is formed by taking the entry's key and appending the extension `.org` to it, which means that a notes file is an Org file. Before creating the file name, Ebib applies the function in `ebib-notes-name-transform-function` to it, or, if this is not set, the function in `ebib-name-transform-function`. See [Viewing Files](#viewing-files) for some examples of the changes that can be applied. Note that if you do not wish to apply any changes but also do not want the function in `ebib-name-transform-function` to be applied, you can set `ebib-notes-name-transform-function` to `identity`.

When a new note is created, it is given a title consisting of the author(s), year and title of the entry. Ebib also includes a `:PROPERTIES:` block containing a custom ID for the entry, which consists of the entry key. This initial contents is based on a template, which can be customised. See below for details.

As mentioned, notes files are Org files by default. This can be changed by customising the option `ebib-notes-file-extension`. If you change this, it makes sense to change `ebib-notes-template` as well, since the template is an Org template.

If you wish to store all notes in a single file, you must set the option `ebib-notes-use-single-file` to the notes file. In this case, the options `ebib-notes-directory` and `ebib-notes-extension` are ignored, which means that you must specify the full path and the extension of the notes file. The option `ebib-notes-name-transform-function` is also ignored.

Ebib assumes that the notes file is an Org file and creates notes using the template in `ebib-notes-template`, but the Org format is not enforced. If you specify a notes file with an extension different from `.org`, the corresponding format will be used, which probably requires customising the template (see below for details).

There are three hooks that can be used to change the way the notes file is displayed when a note is opened. When an existing note is displayed, the hook `ebib-notes-open-note-after-hook` is run. By default, this contains two functions: `org-back-to-header`, which puts point at the start of the note, and `org-narrow-to-subtree`, which narrows the notes buffer to just the note you're viewing.

When a new note is created, the hook `ebib-notes-new-note-hook` is run. By default, this contains the function `org-narrow-to-subtree`. For a new note, the cursor is positioned after the title and the `:PROPERTIES:` block, so that you can start typing right away.

Because both these hooks narrow the notes buffer, there must be a way to widen the buffer again when searching for another note. This is the purpose of `ebib-notes-search-note-before-hook`. This hook is run every time Ebib searches a note (to see if it exists or to open it) and by default contains the function `widen`, so that the entire buffer is searched.

All three hooks are customisable. For example, if you prefer not to narrow the buffer, simply remove the corresponding functions from the hooks.


## Customising the notes template ##

By default, each note is an Org entry whose header consists of the author or editor, the year of publication and the title. The entry has a `:PROPERTIES:` block containing a `Custom_id:`. This initial contents is created on the basis of a template, which has the following form:

```
"* %T
:PROPERTIES:
%K
:END:
>|<
"
```

This template contains two format specifiers: `%K` and `%T`. `%K` is replaced with the key of the entry prepended with the string `"Custom_id: "` in order to create an Org property. The `%T` specifier is replaced with the title of the note, which consists of the author (or editor), the year of publication and the title of the bibliography entry. The template also contains the string `">|<"`, which indicates the position of the cursor when a new note is created.

It is possible to change the template by customising the option `ebib-notes-template`. Note that if you do this, the `%K` directive should not be removed. It is required in order to identify the note and connect it to its BibTeX entry. Without it, Ebib won't be able to tell whether a BibTeX entry has a note or not. The `%T` directive and the cursor indicator may be left out.

There are in fact a few more specifiers that may be used in the template: `%F` creates a link to the file in the BibTeX entry's `file` field, `%D` creates a link to the DOI in the entry's `doi` field, and `%U` a link to the entry's `url` field. There is also a `%L` specifier, which creates a link to the entry's file, its DOI, or its URL, whichever is found first.

It is possible to change the strings that the specifiers produce by customising `ebib-notes-template-specifiers`. This option contains pairs of characters and functions. Each function takes two arguments, `key` and `db`, the key of the entry for which a note is created and the database in which it is stored. It should return a string (possibly empty), which replaces the specifier in the template. In order to change the string that a specifier is replaced with, write your own function and set `ebib-notes-template-specifiers` to use it.

It is also possible to add new specifiers. Simply add a pair (cons cell) `(<char> . <function>)` to `ebib-notes-template-specifiers`. The character should obviously be unique (just supply the character, without `%`), and the function should take the key and the database as arguments and return a string.

When the specifier functions are called, the `key` argument is set to the key of the current entry and the `db` argument to the current database. With these arguments, it is possible to, e.g., retrieve the value of a specific field in the entry:

```
(ebib-get-field-value <field> key db 'noerror 'unbraced 'xref)
```

where `<field>` is the field (as a string) whose value is to be retrieved.

Instead of a function, you may also provide a variable. The variable's value is then used to replace the specifier.


# Managing a reading list #

Ebib offers the ability to manage a reading list as an Org file. In order to make use of this functionality, you must set the option `ebib-reading-list` to a file in which the reading list is stored. Once you've specified a file, you can add the current entry to the reading list with `R a`. The mode line of the entry buffer will show `[R]` to indicate that the current entry is on the reading list.

A reading list is simply an Org file with one entry (i.e., heading) per item. Each entry is marked with `TODO`, so that the items can be  included in the Org agenda. If you prefer to use another todo state, you can customise the option `ebib-reading-list-todo-marker`.

You can mark an entry as done from within Ebib with the key `R d`. This will change the todo state of the item to `DONE` (or whatever the value of `ebib-reading-list-done-marker`). With `R v` you can view the reading list.

The format of a reading list item can be customised in much the same way that notes are. The default template for reading list items is provided by the option `ebib-reading-list-template`, and the specifiers that can be used in this template are in `ebib-reading-list-template-specifiers`. Most of the specifiers are the same as for the notes template, with the exception of `%K`. For the reading list, this specifier uses a different function, which adds a prefix `reading_` to the key. In this way, the custom ID of a reading list item and a note will not interfere. Furthermore, the reading list template accepts a specifier `%M`, which is replaced with the todo marker specified in the option `ebib-reading-list-todo-marker` (by default `TODO`).

If you do not wish to use an Org file for the reading list, you can do so. Apart from customising the template, there are several other options that will need to be customised in this case. First, the option `ebib-reading-list-remove-item-function` holds the function that marks a reading list item as done. By default, it is set to `ebib-reading-list-mark-item-as-done`, which simply changes the todo state of the item to `DONE`, but you can set it to a function that does something else (for example, completely removing the entry from the list). You will also have to customise `ebib-reading-list-item-active-function`, which holds a function that should return `t` if the current entry is on the reading list (and still active). The default function simply checks if the entry's todo state is equal to `ebib-reading-list-todo-marker`, but if you don't use an Org file, you will need a different function, obviously.

Lastly, there are two hooks, `ebib-reading-list-new-item-hook` and `ebib-reading-list-remove-item-hook`. The former is run immediately after a new reading list item is inserted in the reading list file (but before saving it), the latter immediately after calling the function in `ebib-reading-list-remove-item-function` (also before saving the buffer). By default, these hooks are empty.


# Window Management #

By default, Ebib takes over the entire Emacs frame it is started in, displaying the index window at the top and the entry window below it. There are a few options to change this behaviour, however. They are all part of the customisation group `ebib-windows`, and allow you to specify two alternative ways to deal with Ebib windows. The main layout option is simply called "Layout" and has four options: use the full frame (the default), use the current window, use the right part of the frame, or display only the index window.

If you set the layout to use only the right part of the frame, the Ebib buffers are displayed on the right of the frame, with the (usually larger) left part of the frame displaying some other buffer, normally the buffer from which you called Ebib. The width of the Ebib windows can be set with the option "Width", which defaults to 80, and which can be specified as an absolute value (the number of columns), but also as a value relative to the current window. In that case, you must specify a value between 0 and 1. Note that when this option is used, the key `z` does not hide the Ebib buffers, it simply switches to a non-Ebib window in the same frame. You can use (uppercase) `Z` to hide the Ebib buffers. Furthermore, with this option, the multiline edit buffer is not displayed in the same window as the entry buffer. Rather, Ebib uses another, non-Ebib window to display it.

The fourth option that Ebib provides is to only show the index buffer on start-up. In this case, Ebib does not display the entry buffer when it is started. Instead, only the index buffer is displayed, which can be navigated in the usual manner. The entry buffer is only displayed when you add or edit an entry. When you've finished editing and move back to the index buffer, the entry buffer is hidden again.

The entry buffer is also displayed if you press `RET`. When you do this, the index buffer remains selected, so you can use this to display the fields of an entry without moving focus to the entry window. If you navigate the index buffer, the entry buffer remains visible, updating its contents as you move around.

In this case, too, the key `z` does not hide the index window. Rather, it just selects another, non-Ebib window. In order to hide the index window, you can use (uppercase) `Z`.

If you set Ebib's layout to display only the index buffer on startup, you can additionally set the option "Popup Entry Window". Normally, Ebib will reuse an existing window to display the entry buffer (and restore its original buffer when you leave the entry buffer). With this option set, however, Ebib uses the Emacs function `display-buffer-popup-window` to create a new window (which is destroyed again when you leave the entry buffer).

Further relevant options are "Window Vertical Split", which displays the index buffer to the left of the frame rather than at the top, and "Index Window Size", which determines the size of the index window (either its height or its width, depending on whether the index window is displayed at the top or on the left of the frame.)


# Creating Entry Stubs #

If you have a directory full of (pdf) files of articles that you want to add to your database, Ebib can make the task a little bit easier by creating entry stubs for all the files. You can do this with the command `M-x ebib-add-file-entry`. This command asks you for a file or a directory and creates an entry in the current database for that file or each file in the directory. The entries only contain a file field pointing to the file, all the other information still has to be filled out by hand, but this way you can at least keep track of which files are already in your database.

Note that the entry keys for the stubs are temporary keys. They will be replaced by more permanent keys automatically when you edit the entries. This behaviour is controlled by the function `bibtex-generate-autokey`, which has a number of customisation options. Check out its doc string for details. If you prefer to edit the keys by hand, you can do so by pressing `E` in the index buffer.


# @Preamble Definition #

Apart from database entries, BibTeX allows three more types of elements to appear in a `.bib` file. These are `@comment`, `@preamble` and `@string` definitions. Ebib provides facilities to handle these, which are discussed here and in the following sections.

Ebib allows you to add one `@preamble` definition to the database. In principle, BibTeX allows more than one such definition, but really one suffices, because you can use the concatenation character `#` to include multiple TeX or LaTeX commands. So, rather than having two `@preamble` definitions such as:

    @preamble{ "\newcommand{\noopsort}[1]{} " }
    @preamble{ "\newcommand{\singleletter}[1]{#1} " }

you can write this in your `.bib` file:

    @preamble{ "\newcommand{\noopsort}[1]{} "
             # "\newcommand{\singleletter}[1]{#1} " }

Creating or editing a `@preamble` definition in Ebib is done by hitting (uppercase) `P` in the index buffer. Ebib uses the multiline edit buffer for editing the text of the `@preamble` definition, which means that `C-c | q` stores the `@preamble` text and returns focus to the index buffer, while `C-c | c` returns focus to the index buffer while abandoning any changes you may have made. (For details on using multiline edit buffers, see [Multiline Edit Buffers](#multiline-edit-buffers).)

In order to create a `@preamble` as shown above in Ebib, you only have to type the text between the braces. Ebib takes care of including the braces of the `@preamble` command, but otherwise it saves the text exactly as you enter it. So in order to get the preamble above, you'd have to type the following in Ebib:

    "\newcommand{\noopsort}[1]{} " # "\newcommand{\singleletter}[1]{#1} "

Note that when Ebib loads a `.bib` file that contains more than one `@preamble` definition, it concatenates all the strings in them in the manner just described and saves them in one `@preamble` definition.


# @String Definitions #

If you press (uppercase) `S` in the index buffer, Ebib hides the entry buffer in the lower window and replaces it with the *strings buffer*. In this buffer, you can add, delete and edit `@string` definitions.

Adding a `@string` definition is done with the command `a`. This will first ask you for an abbreviation and then for the value to be associated with that abbreviation. Once you've entered these, Ebib will sort the new abbreviation into the buffer.

Moving between the `@string` definitions can be done in the usual way: the cursor keys `up` and `down`, `p` and `n` or `C-p` and `C-n` move up and down. `Space` and `PgDn` move ten strings down, while `b` and `PgUp` move in the other direction. The keys `g`, `G`, `Home` and `End` also function as expected.

To delete a `@string` definition, use `d`. To edit the value of a definition, use `e`. There is also a command `c`, which copies the value of the current `@string` definition to the kill ring. Unlike in the entry buffer, there are no corresponing commands `y` and `x`. (In fact, `x` does exist, but has another function.) Yanking from the kill ring can be done with `C-y/M-y` in the minibuffer when you edit a `@string`'s value. Cutting a `@string`'s value is pointless, because a `@string` definition must have a value.

Having defined `@string` definitions, there must of course be a way to use them. Just giving a field a string abbreviation as value will not do, because Ebib puts braces around the value that you enter when it writes the `.bib` file, so that BibTeX will not recognise the abbreviation, and will not expand it. BibTeX will only recognise an abbreviation if it appears in the `.bib` file outside of any braces.

To accomplish this, you must mark a field's value as special. A special field is a field whose value is not surrounded by braces when the database is saved, so that BibTeX recognises it as an abbreviation. To mark a field special, press `r`. An asterisk will appear before the field, indicating that has no braces. Pressing `r` again will change the field back to normal. If you press `r` on a field that does not have a value yet, Ebib will ask you for one.

Note that this also makes it possible to enter field values that are composed of concatenations of strings and abbreviations. The BibTeX documentation for example explains that if you have defined:

    @string{WGA = "World Gnus Almanac"}

you can create a BibTeX field like this:

    title = 1966 # WGA

which will produce "1966 World Gnus Almanac". Or you can do:

    month = "1~" # jan

which will produce someting like "1 January", assuming your bibliography style has defined the abbreviation `jan`. All this is possible with Ebib, simply by entering the exact text including quotes or braces around the strings, and marking the relevant field as special.

An easy way to enter a `@string` abbreviation as a field value is to use the key `s` instead of `e`. If you type `s`, Ebib asks you for a `@string` abbreviation to put in the current field, and automatically marks the field as special. With this command, Ebib only accepts `@string` definitions that are in the database, so that by using `s` you can make sure you don't make any typos. Note that you can use TAB completion to complete a partial string.


# @Comments #

If Ebib finds a `@comment` in  a `.bib` file, it will read it and store it in the database. When the database is saved, all the `@comment`s will be saved with it, at the top of the file (right after the `@preamble`.) There is no way to edit comments, nor can you specify where in the `.bib` file a comment is placed, but they won't be lost.


# Managing Keywords #

Ebib provides some special functionality for handling keywords. By default, there is a `keywords` field in the list of extra fields. Editing this field is a bit different from other fields. Instead of just entering a string and hitting ENTER to store it and return to the entry buffer, you should enter a single keyword and hit enter. The keyword will then be added to the keywords already present and you are asked to enter the next keyword. If you've added all keywords you want, just hit ENTER to finish.

The advantage of doing it this way is that you can reuse keywords: once you've added a keyword to one entry, Ebib remembers it. The next time you want to use the same keyword for a different entry, you just need to type the first (few) letters, hit TAB and the keyword will be completed. That makes it easier to ensure you use the exact same keywords in different entries. Note that Ebib's keyword functionality is not used to check the contents of keyword fields. It is simply a way to make it easier to stick to specific keywords, which should make it easier to categorise and search your entries.

It is still possible to edit the `keywords` field directly. To do so, use a prefix argument: `C-u e` (or any other prefix argument) on the `keywords` field will allow you to edit the entire contents in the normal way. Use this method if you want to remove single keywords. (Blanking the entire `keywords` field is quicker with `x` or `d`.)

It is also possible to add keywords to an entry from the index buffer, using the command `K a` (`ebib-keywords-add`). This works essentially the same way as when adding keywords from the entry buffer. There is one advantage, however: this command can also operate on marked entries, so that you can add keywords to multiple entries in one go.

Remembering keywords is practical, but it is even more useful if remembered keywords can be saved, so that they are available the next time you start Ebib. There are two ways of doing this: first, there is an option "Keywords List" that you can use to store keywords. Keywords stored in this option will be available for TAB completion to all databases in Ebib. New keywords, however, will not automatically be stored. If you find you need a keyword not on the list and want to make it permanent, you'll have to add it to "Keywords List" yourself.

The other way of making keywords permanent is by storing them in a file. Ebib offers two ways of doing this (which are mutually exclusive, so you have to choose one). You can either configure a single keyword file, with keywords that are available to all databases, or you can configure per-directory keyword files, with keywords that are available for all `.bib` files in the same directory. You can set up keyword files by configuring the option "Keywords File". You can either set it to use a single keyword file, in which case you need to specify a file with its full path, or you can use per-directory keyword files, in which case you must provide a filename without a path. That is, if you use per-directory keyword files, the files have the same name in each directory. The default name is `ebib-keywords.txt`, but you can change that if you like, of course.

Keywords that have not been made permanent are marked as such in the entry buffer in `ebib-warning-face`, (usually a red foreground colour, but this can be customised). If you run into such keywords and want to make them permanent, use the command `K s`. This will take the keywords in the `keywords` field of the current entry and store all keywords that are not permanent yet.

Keyword files have a very simple format: they are text files with one keyword per line. So you can easily create or edit keyword files by hand, or have them created by some other programme. Keep in mind, though, that Ebib does not check for changes to keyword files. If you have a single keyword file, it is loaded when Ebib starts up; per-directory keyword files are loaded when the first `.bib` file in that directory is opened. If you open a second `.bib` file from the same directory, Ebib won't reload the keywords file.

When you close a database, Ebib checks if you have added new keywords to it and asks you if you want to save them. You can tell Ebib to save new keywords automatically by setting the option  "Keywords File Save On Exit" to `always`. Note that this doesn't save the keywords when you enter them, only when you close the database or quit Ebib. You can also set this option to `never`, which means Ebib will discard new keywords when the database is closed. Note that if you want to save the keywords file without having to close the database, you can do so through the menu.

The option "Keywords Use Only File" controls whether Ebib uses only the keyword file, or both the keyword file and the configured keyword list. This option is only useful when you have configured a keyword file. In that case, setting this option to use both the keyword list and the keyword file tells Ebib to offer keywords from both sources when you edit the keyword field. Otherwise, only the keyword file is used.

It is also possible to tell Ebib to sort the keywords in the `keywords` field in alphabetical order. Set the option "Keywords Field Keep Sorted" if you want to do this. Note that setting this option also automatically removes duplicates.

Lastly, you can configure the separator used between keywords in the keyword field. By default, it is set to `", "`, i.e., comma-space. (The separator is a comma because that is what Biblatex expects in the `keywords` field.) If you change it, keep in mind that Ebib does not add a space between keywords, so if you want a space, make sure to add it to the separator.


# Sorting the `.bib` File #

By default, the entries in the database are saved to the `.bib` file in alphabetical order according to entry key. If you only deal with the `.bib` file through Ebib, you may not care in which order the entries are saved. However, it may sometimes be desirable to be able to specify the sort order of entries in more detail. (Apparently, this can be useful with ConTeXt, for example.)

You can specify a sort order in Ebib's customisation buffer. To sort the entries, you must set at least one sort level (that is, a field to sort the entries on). You can also specify more than one sort level: if two entries have identical values for the first sort level, they will be sorted on the second sort level. E.g., if the first sort level is `author` and the second is `year`, then the entries are sorted by author, and those entries that have identical values for the `author` field are sorted by year.

A sort level is not restricted to a single field. You can specify more fields for a single sort level. Within a single sort level, a second sort field is used if the first sort field does not have a value. For example, books that have an editor instead of an author will have an empty `author` field. If you sort the database on the `author` field, such entries will all appear at the beginning of the `.bib` file, which is most likely not what you want.

To remedy this, you can specify both the `author` and the `editor` fields for the first sort level. Ebib will then sort an entry on its `author` field if it has a value, and will otherwise use the value of the `editor` field.

The difference between two sort fields within one sort level and two sort levels is that a second sort *field* is an alternative for the first field when it has no value, while a second sort *level* is an additional sort criterion when two or more entries cannot be sorted on the first level, because they have identical values.

By default, the option `Sort Order` has no value, which means that the entries in the `.bib` file are sorted according to entry key. Those that wish to customise the sort order will usually want to set the first sort level to `author editor`, and the second to `year`. In that way, the entries in the `.bib` file are sorted according to author/editor, and entries with the same author/editor are sorted by year.

Entries that cannot be sorted on some sort level, because the sort fields are empty, are sorted on entry key. (Keep in mind that if the first sort level yields *no value* for a specific entry, Ebib does *not* use the second sort level to sort that entry. It uses the entry key. The second sort level is only used if the first yields *identical* values for two or more entries.)

Note that if you wish to make use of this option, you need to unset the option "Save Xrefs First" ([Cross-referencing](#cross-referencing)). It is pointless to set a sort order if cross-referenced entries are saved first. Since "Save Xrefs First" is set by default, you need to unset if you set "Sort Order".


# Merging and Importing #

As described in the previous chapter, adding entries to a database can be done manually with the key `a`. There are other ways of adding entries to a database, however.

In the index buffer, the Ebib menu has an option to merge a second `.bib` file into the current database. Ebib reads the entries in this file and adds them to the database. Duplicate entries (that is, entries with an entry key that already exists in the database) will normally not be loaded. Ebib logs a warning about each duplicate entry to its log buffer and displays a warning after loading the `.bib` file when this happens. However, if you've customised Ebib to automatically generate keys, duplicate entries will be merged into the current database under a unique key.

Another way to add entries to a database is to import them from an Emacs buffer. If, for example, you find ready-formatted BibTeX entries in a text file or on the internet, you can copy & paste them to any Emacs buffer (e.g. the `*scratch*` buffer), and then execute the command `M-x ebib-import`. Ebib then goes through the buffer and loads all BibTeX entries it finds into the current database (i.e. the database that was active when you lowered Ebib). If you call `ebib-import` while the region is active, Ebib only reads the BibTeX entries in the region.

If a BibTeX entry in the buffer lack an entry key (which sometimes happens with BibTeX entries found on the internet), Ebib will generate a temporary key for it of the form `<new-keyXX>`, where `XX` is a number. You can change such keys by hitting `E` in the index buffer. They will also automatically be replaced with a more sensible key when you edit them. See the option "Autogenerate Keys" for details.


# Exporting Entries #

Sometimes it can be useful to copy entries from one database to another, or to create a new `.bib` file with several entries from an existing database. For this purpose, Ebib provides exporting facilities. To export an entry to a `.bib` file, use the command `x`. This command operates on a single entry or on all marked entries.

When you export one or more entries, Ebib will ask you for a filename to export them to. If you have already exported an entry before, Ebib will present the filename you used as default, but you can of course change it. For obvious reasons, Ebib appends the entry to the file that you enter if it already exists, it does not overwrite the file. If this is not what you want, delete the file first, as Ebib provides no way to do this.

If you have more than one database open in Ebib, it is also possible to copy entries from one database to another. To do this, use the `x` command with a numeric prefix argument. E.g., if the database you want to export an entry to is the second database, type `M-2 x` to export the current entry to it. The number of the database is given in the modeline of the index buffer. If the database you're copying an entry to already contains an entry with the same entry key, Ebib won't copy the entry, and issues an appropriate warning message.

Apart from entries, it is also possible to export the `@preamble` and `@string` definitions. The `@preamble` definition is exported with the command `X` in the index buffer. `@string` definitions can be exported in the strings buffer: `x` in this buffer exports the current string, while `X` exports all `@string` definitions in one go. All these commands function in the same way: when used without a prefix argument, they ask for a filename, and then append the relevent data to that file. With a numeric prefix argument, they copy the relevant data to the corresponding open database.


# Multiple Identical Fields #

Under normal circumstances, a BibTeX entry only contains one occurrence of each field. If BibTeX notices that an entry contains more than one occurrence of an required or optional field, it issues a warning. Ebib is somewhat less gracious, it simply takes the value of the last occurrence without giving any warning. (Note, by the way, that BibTeX will use the value of the *first* occurrence, not the last.) When extra fields appear more than once in an entry, BibTeX does not warn you, since it ignores those fields anyway. Here, too, Ebib's standard behaviour is to ignore all but the last value.

However, some online reference management services "use" this feature of BibTeX in that they put multiple `keywords` fields in the BibTeX entries that they produce. If you were to import such an entry into Ebib, you would lose all your keywords except the last one. To remedy this, you can tell Ebib that it should allow multiple occurrences of a single field in a BibTeX entry. You can do this by setting the customisation option "Allow Identical Fields".

With this option set, Ebib collapses the multiple occurrences into a single occurrence. All the values of the different occurrences are collected and stored in the single occurrence, separated by colons (actually, the value of the option "Keywords Separator"). That is, Ebib does not retain the multiple occurrences, but it does retain the values. So suppose you have an entry that contains the following `keywords` fields:

    @book{Jones1998,
        author = {Jones, Joan},
        year = {1998},
        ...
        keywords = {sleep},
        keywords = {winter},
        keywords = {hibernation}
    }

If you load this entry into Ebib with the option "Allow Identical Fields" set, you will get the following:

    @book{Jones1998,
        author = {Jones, Joan},
        year = {1998},
        ...
        keywords = {sleep, winter, hibernation}
    }


# Multiline Edit Buffers #

As mentioned several times before, Ebib has a special multiline edit buffer, which is used to edit field values that contain newlines (so-called *multiline fields*), and also to edit the contents of the `@preamble` command. This section discusses the details of this buffer.

Ebib enters multiline edit mode in one of three cases: when you edit the `@preamble` definition, when you hit `m` in the entry buffer to edit the current field as multiline, or when you hit `e` on the `annote` field, or on a field whose value already is multiline.

The mode that is used in the multiline edit buffer is user-configurable. The default value is `text-mode`, but if you prefer to use some other mode, you can specify this through the customisation options. (Personally, I use `markdown-mode` in the multiline edit buffer, so that I can use [`Markdown`](http://daringfireball.net/projects/markdown/) to write annotations, which provides an easy way to create headers, use bold and italic, etc., in plain text.)

Three commands are relevant for interacting with Ebib when you're in the multiline edit buffer, which are bound to key sequences in the minor mode `ebib-multiline-edit-mode`, which is activated automatically in the multiline edit buffer.

`ebib-quit-multiline-buffer-and-save`, bound to `C-c | q`, leaves the multiline edit buffer and stores the text in the database. If you invoke this command when you've deleted all contents of the buffer (including the final newline!) and you were editing a field value or the `@preamble`, the field value or preamble is deleted. (This is in fact the *only* way to delete the `@preamble` definition. Field values on the other hand can also be deleted by hitting `x` or `d` on them in the entry buffer.) If you were editing a `@string` value, Ebib will just complain, because string definitions cannot be empty.

`ebib-cancel-multiline-buffer`, bound to `C-c | c`, also leaves the multiline edit buffer, but it does so without storing the text. The original value of the field, string or preamble will be retained. If the text was modified, Ebib will ask for a confirmation before leaving the buffer.

`ebib-save-from-multiline-buffer`, bound to `C-c | s`, can be used in the multiline edit buffer to save the database. This command first stores the text in the database and then saves it. Because Ebib does not do an autosave of the current database, it is advisable to save the database manually every now and then to prevent data loss in case of crashes. It would be annoying to have to leave the multiline edit buffer every time you want to do this, so this command has been provided to allow you to do this from within the buffer.

Admittedly, the key combinations of the multiline edit buffer are somewhat awkward. The reason for this is that these commands are part of a minor mode, which restricts the available keys to combinations of `C-c` plus a non-alphanumeric character. However, it is possible to change the key commands, if you wish. Ebib itself provides a method to change the second key of these commands, [Modifying Key Bindings](#modifying-key-bindings). You could change the `|` to e.g., `c` or `C-c`, if these do not conflict with any key commands in the major mode used for the multiline edit buffer.

Even more drastically, you could put something like the following in your `~/.emacs`:

```Commonlisp
(eval-after-load 'ebib
  '(progn
     (define-key ebib-multiline-mode-map
                 "\C-c\C-c" 'ebib-quit-multiline-buffer-and-save)
     (define-key ebib-multiline-mode-map
                 "\C-c\C-q" 'ebib-cancel-multiline-buffer)
     (define-key ebib-multiline-mode-map
                 "\C-c\C-s" 'ebib-save-from-multiline-buffer)))
```

This sets up `C-c C-c`, `C-c C-q` and `C-c C-s` for use in the multiline edit buffer. Since such key combinations are restricted for use with major modes, however, Ebib cannot set these up automatically, but as an Emacs user, you are free to do as you like, of course.


# The Options Menu #

In the index buffer, Ebib's menu has an Options submenu. This menu gives you quick access to Ebib's customisation buffer, and it also provides checkboxes for several settings that can be toggled on and off. All of these settings have defaults that can be defined in the customisation buffer. Setting or unsetting them in the Options menu only changes them for the duration of your Emacs session, it doesn't affect the default setting.

The same is true for the printing options that are in the Print menu. When set or unset in the menu, the default values specified in the customisation buffer do not change.


# Customisation #

Ebib can be customised through Emacs' standard customisation interface. The relevant customisation group is (obviously) called `ebib`, which has five subgroups: `ebib-faces`, `ebib-filters`, `ebib-notes`, and `ebib-keywords`, whose functions should be obvious, and `ebib-windows`, where options for Ebib's window management can be set. All options are documented in the customisation buffers. You can go to Ebib's customisation buffer with `M-x customize-group RET ebib RET`, or by using the menu «Ebib | Options | Customize Ebib».

Another way to customise Ebib is to use the initialisation file `~/.emacs.d/ebibrc`. (Actually, the location and name of this file can be customised as well.) This file contains normal Lisp code and is the best way to customise key bindings (as discussed in the next section), but it can in fact be used to run any Lisp code.


## Modifying Key Bindings ##

If you would like to change Ebib's standard key bindings, or if you would like to bind a command that is only available through the menu to a key, you can do so by adding the relevant key bindings to Emacs init file (`~.emacs.d/init.el` by default). The relevant key maps are `ebib-index-mode-map`, `ebib-entry-mode-map`, `ebib-strings-mode-map` for the index, entry, and strings buffer, and `ebib-multiline-mode-map`, which adds keys to finish writing multiline field values.

In addition, `ebib-search-map` is a transient key map that is activated when `ebib-search` is called, and `ebib-filters-map`, `ebib-keywords-map` and `ebib-reading-list-map` are key maps (set up using `define-prefix-command`) that contain bindings for filters, keywords and the reading list, respectively. Finally, there is `ebib-log-mode-map` which is active in Ebib's log buffer.

As an example, the default keybindings in`ebib-multiline-mode-map`, which are rather awkward to type, can be redefined as follows:

```Commonlisp
(define-key ebib-multiline-mode-map
            "\C-c\C-c" 'ebib-quit-multiline-buffer-and-save)
(define-key ebib-multiline-mode-map
            "\C-c\C-q" 'ebib-cancel-multiline-buffer)
(define-key ebib-multiline-mode-map
            "\C-c\C-s" 'ebib-save-from-multiline-buffer)
```

</article>
