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cobib.1
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.TH COBIB 1 2024-10-30 v5.2.1
.SH NAME
coBib \- Console-based Bibliography Management
.SH SYNOPSIS
.B cobib
[\fB\-\-version\fR]
[\fB\-h\fR|\fB\-\-help\fR]
[\fB\-v\fR|\fB\-\-verbose\fR]
[\fB\-c\fR|\fB\-\-config\fR \fI<path>\fR]
\fB<subcommand>\fR [\fI<args>\fR]
.SH DESCRIPTION
coBib is a console-based bibliography manager written in Python.
It maintains a plain-text database of literature data in YAML format at
\fI$HOME/.local/share/cobib/literature.yaml\fR.
.PP
coBib provides a variety of \fBSUBCOMMANDS\fR through which you may
investigate and manage the database.
For easy of use it also comes with a textual-based \fBTUI\fR which is
automatically started when no other subcommand is found (more information is
provided in that section).
.PP
coBib also provides some "meta"-commands. These are expained in the \fBSHELL
UTILITIES\fR section.
.SH OPTIONS
.TP
.BR \-\-version
Prints the version information and exits.
.TP
.BR \-h ", " \-\-help
Prints a help message and exits.
.TP
.BR \-v ", " \-\-verbose
Increases the verbosity level of the logging. This option may be provided up to
two times (increasing the logging to \fIinfo\fR and \fIdebug\fR, respectively).
By default, the verbosity of coBib's CLI is set to \fIwarning\fR but if the TUI
is started, logging will be increased to \fIinfo\fR and redirected to
\fIconfig.logging.logfile\fR.
.TP
.BR \-p ", " \-\-porcelain
Switches the output that will be printed to the terminal to "porcelain" mode.
This is meant to be useful for parsing and testing purposes.
.TP
.BR \-c ", " \-\-config " " \fI<path>\fR
Run with an alternate configuration file at \fI<path>\fR.
.TP
.BR \-l ", " \-\-log " " \fI<path>\fR
Run with an alternate log file at \fI<path>\fR.
.SH SUBCOMMANDS
All subcommands listed below also provide the \fI\-h\fR and \fI\-\-help\fR
options which provide additional information for each subcommand.
.TP
.B cobib init \fI<args>\fR
Initializes the literature database.
The path to this file can be configured in the \fIDATABASE\fR section of the
configuration file (see also \fBCONFIGURATION\fR).
The only available argument is:
.PP
.in +8n
.BR \-g ", " \-\-git
.in +4n
Initializes coBib's integrated history tracking through git.
This command will preserve any existing database file, but it is a good idea to
make a backup before doing this, just in case.
Note, that in order to use this functionality you must also enable the
\fIDATABASE/git\fR configuration option (see also \fBCONFIGURATION\fR).
Also be sure to at least set a \fIname\fR and \fIemail\fR in the git config!
.TP
.B cobib git \fI<args>\fR ...
.in +4n
Passes through to \fIgit\fR to run operations on the underlying database.
All arguments provided after \fIgit\fR are forwarded without being changed.
.TP
.B cobib add \fI<args>\fR ...
Adds a new entry to the database.
The positional arguments may be used to provide \fItags\fR to associate with the
newly added entries.
The \fI<args>\fR may be any of the following:
.PP
.in +8n
.BR \-a ", " \-\-arxiv " " \fI<arxiv\ id>\fR
.in +4n
Adds an entry specified by the \fIarXiv\fR id.
.PP
.in +8n
.BR \-b ", " \-\-bibtex " " \fI<path>\fR
.in +4n
Adds the bibliography data from the \fIBibLaTex\fR file at the provided path.
.PP
.in +8n
.BR \-d ", " \-\-doi " " \fI<doi>\fR
.in +4n
Adds an entry specified by the \fIDOI\fR.
.PP
.in +8n
.BR \-i ", " \-\-isbn " " \fI<ISBN>\fR
.in +4n
Adds an entry specified by the \fIISBN\fR.
.PP
.in +8n
.BR \-\-url " " \fI<URL>\fR
.in +4n
Attempts to extract an entry from the \fI<URL>\fR.
.PP
.in +8n
.BR \-y ", " \-\-yaml " " \fI<path>\fR
.in +4n
Adds the bibliography data from the \fIYAML\fR file at the provided path.
The only supported YAML format is that of a coBib database file.
.PP
.in +8n
.BR \-l ", " \-\-label " " \fI<label>\fR
.in +4n
Store the newly added entry under the specified \fIlabel\fR.
.PP
.in +8n
.BR \-f ", " \-\-file " " \fI<path>\fR
.in +4n
Associate the newly added entry with the \fIfile\fR at the provided path.
As of version 2.5 you can specify multiple files, too.
.PP
.in +8n
.BR \-p ", " \-\-path " " \fI<path>\fR
.in +4n
Overwrites the location for the automatically downloaded file. If not specified,
this setting defaults to \fIconfig.utils.file_downloader.default_location\fR.
.PP
.in +8n
.BR \-\-disambiguation " " \fI<reply>\fR
.in +4n
Sets the reply for the interactive prompt if an addition needs to be
disambiguated. The possible values for \fI<reply>\fR are the following:
.in +4n
.IR keep
to keep the existing entry
.in +0n
.IR replace
to replace the existing entry
.in +0n
.IR update
to update the existing entry
.in +0n
.IR disambiguate
to disambiguate the new label from the existing one by adding a label suffix
(see also \fIconfig.database.format.label_suffix\fR)
.PP
.in +8n
.BR \-\-skip\-download
.in +4n
Skips attempting to automatically download an associated file for the entry.
This takes precedence over the \fIconfig.commands.add.skip_download\fR setting.
.PP
.in +8n
.BR \-\-force\-download
.in +4n
Forces attempting to automatically download an associated file for the entry.
This takes precedence over the \fIconfig.commands.add.skip_download\fR setting.
.TP
.B cobib delete \fI<label>\fR
Deletes the entry with the given \fIlabel\fR.
.PP
.in +8n
.BR \-\-preserve\-files
.in +4n
If specified, associated files will be preserved and \fInot\fR deleted.
This takes precedence over the \fIconfig.commands.delete.preserve_files\fR
setting.
.PP
.in +8n
.BR \-\-no\-preserve\-files
.in +4n
If specified, associated files will \fInot\fR be preserved.
This takes precedence over the \fIconfig.commands.delete.preserve_files\fR
setting.
.TP
.B cobib edit \fI<label>\fR
Opens the entry with the given \fIlabel\fR in an external editor.
The entry is copied verbatim in \fIYAML\fR format from and to the database file.
The editor respects the \fI$EDITOR\fR environment variable unless overwritten by
\fIconfig.commands.edit.editor\fR. It will fallback to \fIvim\fR if neither is
configured.
.PP
.in +8n
.BR \-a ", " \-\-add " " \fI<path>\fR
.in +4n
Allows editing a non-existing label to manually add it to the database.
.PP
.in +8n
.BR \-\-preserve\-files
.in +4n
If specified, associated files will be preserved and \fInot\fR be renamed if the
edit happens to rename the entry. This takes precedence over the
\fIconfig.commands.edit.preserve_files\fR setting.
.PP
.in +8n
.BR \-\-no\-preserve\-files
.in +4n
If specified, associated files will \fInot\fR be preserved and be renamed if the
edit happens to rename the entry. This takes precedence over the
\fIconfig.commands.edit.preserve_files\fR setting.
.TP
.B cobib modify \fI<modification>\fR \fI<args>\fR ...
Applies a modification to multiple entries at once.
The positional arguments may be used to provide \fBFILTERS\fR which the entries
must match in order to be modified \fIor\fR to provide a list of labels of the
entries which are to be modified (this requires the \fI-s\fR flag to be set).
The \fI<args>\fR may be any of the following:
.PP
.in +8n
.BR \fI<modification>\fR
.in +4n
The modification must be provided in the format \fI<field>:<value>\fR and will
set the field of all selected entries to the given value.
As of v3.2.0 the \fI<value>\fR is interpreted as an "f"-string. This means you
can even use placeholder variables and perform simple operations on them. The
available variables depend on the entry which you are modifying as they are
inferred from its stored data. For more information on "f"-strings refer to
section 2.4.3 of https://docs.python.org/3/reference/lexical_analysis.html
.PP
.in +8n
.BR \-\-dry
.in +4n
When this flag is given, the modify command runs in \fIdry\fR mode. This means,
the applied modifications are printed to stdout rather than applied directly.
This allows easy prototyping of modifications to prevent errors during large
bulk modifications.
.PP
.in +8n
.BR \-a ", " \-\-add
.in +4n
Specifying this flag will add the modification's value to the specified field of
the entry rather than overwriting it. In doing so, strings will be concatenated
with\fBOUT\fR any spaces, lists will be appended to, numbers will be added, and
anything else will be converted to a string field.
If the field did not exist previously, it will simply be initialized with the
new value.
.PP
.in +8n
.BR \-r ", " \-\-remove
.in +4n
Specifying this flag will remove the modification's value from the specified
field of the entry rather than overwriting it. In doing so, items will be
removed from lists, numbers will be subtracted, and anything else will be left
unchanged.
.PP
.in +8n
.BR \-s ", " \-\-selection
.in +4n
This boolean flag enables the \fIselection\fR mode in which the positional args
are interpreted as a list of labels which are to be exported. The name for this
argument is a result of the TUI's selection interface.
.PP
.in +8n
.BR \-\-preserve\-files
.in +4n
If specified, associated files will be preserved and \fInot\fR be renamed if
the modification happens to rename the entry. This takes precedence over the
\fIconfig.commands.modify.preserve_files\fR setting.
.PP
.in +8n
.BR \-\-no\-preserve\-files
.in +4n
If specified, associated files will \fInot\fR be preserved and be renamed if
the modification happens to rename the entry. This takes precedence over the
\fIconfig.commands.modify.preserve_files\fR setting.
.TP
.B cobib note \fI<label>\fR \fI<action>\fR
Applies an action to the note of the provided entry. The available \fIactions\fR
are:
.PP
.in +8n
.BR show
.in +4n
Shows the note's contents.
.PP
.in +8n
.BR edit
.in +4n
Opens the note file in the \fIconfig.commands.edit.editor\fR for editing.
.PP
.in +8n
.BR delete
.in +4n
Deletes the note.
.TP
.B cobib review \fI<field>\fR \fI<args>\fR ...
Performs an interactive review of your database.
You can optionally review one or more specific fields of the entries by
providing the field names as arguments to the command.
The positional arguments may be used to provide \fBFILTERS\fR which the entries
must match in order to be reviewed \fIor\fR to provide a list of labels of the
entries which are to be reviewed (this requires the \fI-s\fR flag to be set).
For every entry that is being reviewed, multiple actions are possible. These
include:
.TP
.in +8n
.BR edit
.in +4n
Opens the current entry in an external editor.
.TP
.in +8n
.BR done
.in +4n
Marks the current entry as fully reviewed.
.TP
.in +8n
.BR skip
.in +4n
Skips the current entry for this review.
.TP
.in +8n
.BR context
.in +4n
Requests additional context and updates the preview to contain all the
information stored in the entry. This action is only available when no context
has been requested yet and the previewed fields are being filtered in the first
place.
.TP
.in +8n
.BR finish
.in +4n
Finishes the review early (even if some entries have not been shown yet). See
\fI\-\-resume\fR for how to resume a previously started review process.
.TP
.in +8n
.BR inline <field>
.in +4n
Edits a specific field in-line. When reviewing a single field, you can simply
type \fIinline\fR. When reviewing more than one, you need to specify which field
to edit like so \fIinline <field>\fR. This is a highly experimental feature so
please be aware of bugs and report any issues or suggestions online:
https://gitlab.com/cobib/cobib/-/issues/new
.TP
.in +8n
The \fI<args>\fR to the \fBreview\fR command may be any of the following:
.PP
.in +8n
.BR \-c ", " \-\-context
.in +4n
.PP
Enforces that context will be provided for every entry.
.in +8n
.BR \-r ", " \-\-resume " " \fI<SHA>\fR
.in +4n
If you finished a review early (see `finish` above) you can use this argument to
continue where you left. This option takes a git commit identifier as its
argument so you should either find the SHA of the auto-commit of the review that
you would like to continue (see also the \fIgit\fR command), or if you know that
it is (for example) the last thing that you did, you can simply use \fRHEAD\fR.
.PP
.in +8n
.BR \-d ", " \-\-done " " \fI<labels>\fR
.in +4n
Can supply a list of entry labels which will be considered as already reviewed
and therefore skipped. Thus, this has a higher precedence than the provided
\fBFILTERS\fR and can be used to resume a previously started review process. If
you have the \fIgit\fR integration enabled, you will likely not use this
argument manually. Instead, refer to the \fI\-\-resume\fR argument.
.PP
.in +8n
.BR \-s ", " \-\-selection
.in +4n
This boolean flag enables the \fIselection\fR mode in which the positional args
are interpreted as a list of labels which are to be exported. The name for this
argument is a result of the TUI's selection interface.
.TP
.B cobib undo \fI<args>\fR
If you enabled the git-integration of coBib (available since v2.6.0) you can
undo the changes done to your database file by commands such as add, edit and
delete. See also \fIDATABASE/git\fR in the \fBCONFIGURATION\fR section for more
information.
.PP
.in +8n
.BR \-f ", " \-\-force
.in +4n
Overwrites the check for an auto-committed change. Thus, the undo command will
now undo the last commit with a message that does not start with "Undo".
.TP
.B cobib redo
If you enabled the git-integration of coBib (available since v2.6.0) you can
reapply the last undone changes (see above). See also \fIDATABASE/git\fR in the
\fBCONFIGURATION\fR section for more information.
.TP
.B cobib open \fI<label>\fR
Opens any associated \fIfile\fR of the entry with the given \fIlabel\fR.
If multiple files are associated with the entry, the user can choose which
file(s) to open through an interactive menu.
.PP
.in +8n
.BR \-f ", " \-\-field " " \fI<choice>\fR
.in +4n
Specifies the field type to open. This bypasses the interactive prompt if
multiple actionable fields are found. The choice can be either \fIall\fR or any
of the values configured in \fIconfig.commands.open.fields\fR.
.TP
.B cobib show \fI<label>\fR
Prints the entry with the given \fIlabel\fR in \fIBibLaTex\fR format to stdout.
.TP
.B cobib list \fI<args>\fR
Lists all entries of the database in a basic table format to stdout which match
the specified \fBFILTERS\fR (more information is provided in that section).
Additionally, the following \fI<args>\fR are also allowed:
.PP
.in +8n
.BR \-s ", " \-\-sort " " \fI<field>\fI
.in +4n
Specify the entry field to use as the \fIsorting column\fR of the table.
.PP
.in +8n
.BR \-r ", " \-\-reverse
.in +4n
Reverses the sorting order.
.PP
.in +8n
.BR \-l ", " \-\-limit " " \fI<int>\fI
.in +4n
Limits the number of displayed results to the specified number.
.PP
.in +8n
.BR \-i ", " \-\-ignore\-case
.in +4n
Makes the entry matching case-insensitive.
This takes precedence over the \fIconfig.commands.list_.ignore_case\fR setting.
.PP
.in +8n
.BR \-I ", " \-\-no\-ignore\-case
.in +4n
Makes the entry matching case-sensitive.
This takes precedence over the \fIconfig.commands.list_.ignore_case\fR setting.
.PP
.in +8n
.BR \-\-decode\-latex
.in +4n
Makes the entry matching decode all LaTeX sequences.
This takes precedence over the \fIconfig.commands.list_.decode_latex\fR setting.
.PP
.in +8n
.BR \-\-no\-decode\-latex
.in +4n
Makes the entry matching preserve all LaTeX sequences.
This takes precedence over the \fIconfig.commands.list_.decode_latex\fR setting.
.PP
.in +8n
.BR \-\-decode\-unicode
.in +4n
Makes the entry matching decode all Unicode characters.
This takes precedence over the \fIconfig.commands.list_.decode_unicode\fR
setting.
.PP
.in +8n
.BR \-\-no\-decode\-unicode
.in +4n
Makes the entry matching preserve all Unicode characters.
This takes precedence over the \fIconfig.commands.list_.decode_unicode\fR
setting.
.PP
.in +8n
.BR \-z ", " \-\-fuzziness " " \fI<int>\fI
.in +4n
Specifies how many fuzzy errors to allow during entry matching.
The default value is 0 but can be configured via
\fIconfig.commands.list_.fuzziness\fR.
.PP
.in +8n
.BR \-x ", " \-\-or
.in +4n
Concatenate the filters using logical \fIOR\fR rather than the default
\fIAND\fR.
.TP
.B cobib search \fI<query>\fR \fI<args>\fR ...
Searches the database recursively (i.e. including any associated files) for the
specified queries (if multiple are given, these will be searched independently).
The positional arguments may be used to provide \fBFILTERS\fR which the entries
must match in order to be included in the export.
Additionally, the following \fI<args>\fR are also allowed:
.PP
.in +8n
.BR \-c ", " \-\-context " " \fI<int>\fI
.in +4n
Specify the number of context lines to provide for each match.
The default value is 1 but can be configured via
\fIconfig.commands.search.context\fR.
.PP
.in +8n
.BR \-i ", " \-\-ignore\-case
.in +4n
Makes the search case-insensitive.
This takes precedence over the \fIconfig.commands.search.ignore_case\fR setting.
.PP
.in +8n
.BR \-I ", " \-\-no\-ignore\-case
.in +4n
Makes the search case-insensitive.
This takes precedence over the \fIconfig.commands.search.ignore_case\fR setting.
.PP
.in +8n
.BR \-l ", " \-\-decode\-latex
.in +4n
Makes the search decode all LaTeX sequences.
This takes precedence over the \fIconfig.commands.search.decode_latex\fR
setting.
.PP
.in +8n
.BR \-L ", " \-\-no\-decode\-latex
.in +4n
Makes the search preserve all LaTeX sequences.
This takes precedence over the \fIconfig.commands.search.decode_latex\fR
setting.
.PP
.in +8n
.BR \-u ", " \-\-decode\-unicode
.in +4n
Makes the search decode all Unicode characters.
This takes precedence over the \fIconfig.commands.search.decode_unicode\fR
setting.
.PP
.in +8n
.BR \-U ", " \-\-no\-decode\-unicode
.in +4n
Makes the search preserve all Unicode characters.
This takes precedence over the \fIconfig.commands.search.decode_unicode\fR
setting.
.PP
.in +8n
.BR \-z ", " \-\-fuzziness " " \fI<int>\fI
.in +4n
Specifies how many fuzzy errors to allow during search.
The default value is 0 but can be configured via
\fIconfig.commands.search.fuzziness\fR.
.PP
.in +8n
.BR \-\-skip\-files
.in +4n
Skips searching the associated files.
This takes precedence over the \fIconfig.commands.search.skip_files\fR setting.
.PP
.in +8n
.BR \-\-include\-files
.in +4n
Enables searching the associated files.
This takes precedence over the \fIconfig.commands.search.skip_files\fR setting.
.PP
.in +8n
.BR \-\-skip\-notes
.in +4n
Skips searching the associated notes.
This takes precedence over the \fIconfig.commands.search.skip_notes\fR setting.
.PP
.in +8n
.BR \-\-include\-notes
.in +4n
Enables searching the associated notes.
This takes precedence over the \fIconfig.commands.search.skip_notes\fR setting.
.TP
.B cobib export \fI<args>\fR ...
Exports the database.
The positional arguments may be used to provide \fBFILTERS\fR which the entries
must match in order to be included in the export \fIor\fR to provide a list of
labels of the entries which are to be exported (this requires the \fI-s\fR flag
to be set).
The \fI<args>\fR may be any of the following:
.PP
.in +8n
.BR \-b ", " \-\-bibtex " " \fI<path>\fR
.in +4n
Export the entries to a \fIBibLaTex\fR file at the specified path.
.PP
.in +8n
.BR \-z ", " \-\-zip " " \fI<path>\fR
.in +4n
Export a \fIBibLaTex\fR file of the entries and all of the associated files into
a single \fIZIP\fR file at the specified path.
.PP
.in +8n
.BR \-s ", " \-\-selection
.in +4n
This boolean flag enables the \fIselection\fR mode in which the positional args
are interpreted as a list of labels which are to be exported. The name for this
argument is a result of the TUI's selection interface.
.PP
.in +8n
.BR \-a ", " \-\-abbreviate
.in +4n
Causes all Journal names to be abbreviated. For this option to take effect, a
list of abbreviations must be configured via
\fIconfig.utils.journal_abbreviations\fR.
.PP
.in +8n
.BR \-\-dotless
.in +4n
Works in conjunction with the \fIabbreviate\fR argument in order to remove
punctuation from the journal abbreviations.
.TP
.B cobib import \fI<args>\fR ...
Imports entries from another bibliography manager. You usually only need to run
this command once.
The \fI<args>\fR may be any of the following:
.PP
.in +8n
.BR \-\-skip\-download
.in +4n
Skips downloading of attachments encountered during the library import.
This takes precedence over the \fIconfig.commands.import_.skip_download\fR
setting.
.PP
.in +8n
.BR \-\-force\-download
.in +4n
Forces downloading of attachments encountered during the library import.
This takes precedence over the \fIconfig.commands.import_.skip_download\fR
setting.
.PP
.in +8n
Furthermore you can specify one of the following sources from which to import
your library. Each of those sources can optionally take further arguments via
positional arguments following a \fI--\fR separator.
.PP
.in +8n
.BR \-\-zotero " -- " \fI<args>\fR
.in +4n
The \fI<args>\fR may be any of the following:
.PP
.in +12n
.BR \-\-no-cache
.in +8n
Disabling loading or storing of cached OAuth authentication tokens.
.PP
.in +12n
.BR \-\-user-id " " \fI<user\ ID>\fR
.in +8n
Provide a custom Zotero user ID. If this is a publicly accessible library, no
API key is required. Otherwise you must also use the following argument.
.PP
.in +12n
.BR \-\-api-key " "\fI<API\ key>\fR
.in +8n
Provide a custom Zotero API key.
.TP
.B cobib lint
Lints the database file for potential points of formatting improvements.
.PP
.in +8n
.BR \-f ", " \-\-format
.in +4n
If you provide this option, coBib will automatically format your database to
resolve all found lint messages.
.TP
.B cobib unify_labels
Updates all entry labels in your database to follow the default naming pattern.
.PP
.in +8n
.BR \-a ", " \-\-apply
.in +4n
If you provide this option, coBib will actually apply the updates rather than
preview them in dry-mode.
.SH FILTERS
In order to limit the output of the \fIlist\fR, \fImodify\fR, \fIsearch\fR, and
\fIexport\fR commands you can apply additional filters via keyword arguments.
Their availability depends on your database since they are added to the argument
parser at runtime.
However, you can find a full list for your specific case with \fIcobib list
\-\-help\fR.
.PP
The general syntax for filtering is the following
.in +8n
[\fB++\fR|\fB\-\-\fR]\fB<field>\fR \fI<value>\fR
.in
which is to be understood as the following:
When the keyword argument is started with \fB++\fR the entry must positively
\fImatch\fR this filter; if started with \fB\-\-\fR it must \fINOT\fR match.
The \fB<field>\fR may be any available field in your database.
It should be noted, that this string is matched exactly which means no plurals
are allowed.
The \fI<value>\fR finally specifies what is matched against. As of version
v3.2.0 this value gets interpreted as a regex pattern, enabling powerful filter
matching.
.PP
In general, multiple filters provided to the \fIlist\fR and \fIexport\fR
commands are combined with logical \fIAND\fR.
This may be overwritten by adding the \fI\-x\fR or \fI\-\-or\fR arguments as
described in the arguments section of the \fIlist\fR command.
More generally, you may also provide any of the other arguments of the
\fIlist\fR command allowing you to sort and limit the number of entries which
you want to further act on.
.SH EXAMPLES
This section provides a few examples of \fBFILTERS\fR as described above.
.TP
.B cobib list ++year 2020
Lists only entries which were published in 2020.
.TP
.B cobib list --tags chemistry
Lists only entries without the `chemistry` tag.
.TP
.B cobib list ++year 2019 ++tags quantum
Lists only entries with the `quantum` tag from the year 2019.
.TP
.B cobib list -x ++year 2019 ++year 2020
Lists only entries published in 2019 or 2020.
.SH TUI
The textual-based TUI is started automatically when no other subcommand is
supplied, i.e. by simply running \fBcobib\fR.
By default, it lists all entries of the database in a scrollable view and
displays the bibtex-representation of the entry under the cursor in a side
panel. You can scroll using vim-like keybindings \fIh,j,k,l\fR or the arrow
keys.
The following key bindings are available:
.TP
.BR q " " quit
Quits the TUI.
.TP
.BR ? " " help
Opens a small window providing help for the key bindings.
.TP
.BR _ " " layout
Toggles between a horizontally and vertically split layout.
.TP
.BR SPACE " " folds
When displaying search results, toggles the visibility of any tree node.
.TP
.BR : " " prompt
Opens a command prompt allowing the user to execute an arbitrary coBib CLI
command.
.TP
.BR v " " select
Adds the current label to the \fIselection\fR.
.TP
.BR / " " search
Opens a search prompt and views the results in an interactive tree structure.
.TP
.BR digit " " preset
Immediately seledcts the preset filter given by that digit (0 = reset).
.TP
.BR a " " add
Opens a command prompt which allows running the \fBadd\fR command as if outside
of the TUI.
.TP
.BR d " " delete
Deletes the current (or \fIselected\fR) label(s).
.TP
.BR e " " edit
Opens the current label in an external editor.
.TP
.BR f " " filter
Allows adding filters to the list of displayed entries.
.TP
.BR i " " import
Opens a command prompt which allows running the \fBimport\fR command as if
outside of the TUI.
.TP
.BR m " " modify
Opens a command prompt which allows running the \fBmodify\fR command as if
outside of the TUI. If a \fIselection\fR is present, the \fI-s\fR argument will
be set automatically.
.TP
.BR o " " open
Opens the current (or \fIselected\fR) label(s).
.TP
.BR p " " preset
Allows selecting a preset filter (see \fIconfig.tui.preset_filters\fR).
.TP
.BR r " " redo
Reapplies the last undone change.
This requires the git-integration (since v2.6.0) to be enabled!
.TP
.BR s " " sort
Allows sorting the list view.
.TP
.BR u " " undo
Undoes the last auto-committed change to the database file.
This requires the git-integration (since v2.6.0) to be enabled!
.TP
.BR x " " export
Opens a command prompt which allows running the \fBexport\fR command as if
outside of the TUI. If a \fIselection\fR is present, the \fI-s\fR argument will
be set automatically.
Opens a small window providing help for the key bindings.
.SH CONFIGURATION
Since version 3.0, coBib can be configured directly via \fIPython\fR. To do so,
you must place the configuration file at \fI$HOME/.config/cobib/config.py\fR.
If you don't have a configuration file yet, you can get started by copying the
well-documented example configuration to the right location via:
.in +4n
\fIcobib example_config > ~/.config/cobib/config.py\fR
.in -4n
If you do have an old configuration file (prior to v3.0) and would like some
guidance on how to migrate it, please read this short blog post of mine:
https://mrossinek.gitlab.io/programming/cobibs-new-configuration/
.PP
Since v3.5, coBib also respects the \fICOBIB_CONFIG\fR environment variable.
With this you can either specify a custom path to your configuration file or
disable the loading of a configuration file entirely by setting it to one of the
following values: \fI"", 0, "f", "false", "nil", "none"\fR.
.PP
The following section summarizes the syntax and all possibly settings, for
completeness.
.TP
.BR Configuration " " Syntax
Internally, coBib's configuration is nothing but a (nested) Python dataclass.
Thus, after importing the config with
.in +4n
\fIfrom cobib.config import config\fR
.in -4n
it is very straight forward to change any setting by simply changing the value
of an attribute. For example:
.in +4n
\fIconfig.database.git = True\fR
.in -4n
.PP
.BR LOGGING
.TP
.IR config.logging.cache = '~/.cache/cobib/cache'
This settings sets the path to the default cache file.
.TP
.IR config.logging.logfile = '~/.cache/cobib/cobib.log'
This setting sets the path to the default logfile. This setting can be
overwritten at runtime using the \fI--logfile\fR command-line argument.
.TP
.IR config.logging.version = '~/.cache/cobib/version'
In this file, the last run version of coBib gets cached. After an update, coBib
automatically prints the newest section of the Changelog. To disable this
functionality entirely, set this option to \fINone\fR.
.PP
.BR COMMANDS
.TP
.IR config.commands.add.skip_download = False
Specifies whether to skip the attempt of downloading PDF files of added entries.
.TP
.IR config.commands.delete.confirm = True
Specifies whether or not to prompt for confirmation before deleting an entry.
.TP
.IR config.commands.delete.preserve_files = False
Specifies whether associates files should be preserved during deletion.
.TP
.IR config.commands.edit.default_entry_type = 'article'
This setting indicates the default entry type which will be used for manually
entered entries.
.TP
.IR config.commands.edit.editor = $EDITOR " if available else " 'vim'
This setting can be used to overwrite the external editor used for manual
editing of database entries. It defaults to the environment variable
\fI$EDITOR\fR and falls back to \fIvim\fR if that is not set either.
.TP
.IR config.commands.edit.preserve_files = False
Specifies whether associates files should be preserved during renaming.
.TP
.IR config.commands.import_.skip_download = False
Specifies whether to skip downloading of attachments encountered during the
library import.
.TP
.IR config.commands.list_.default_columns = ['label',\ 'title']
Specifies the default columns displayed during the \fIlist\fR command.
.TP
.IR config.commands.list_.ignore_case = False
Specifies whether filter matching should be performed case-insensitive.
.TP
.IR config.commands.list_.decode_unicode = False
Specifies whether filter matching should decode all Unicode characters.
.TP
.IR config.commands.list_.decode_latex = False
Specifies whether filter matching should decode all LaTeX sequences.
.TP
.IR config.commands.list_.fuzziness = 0
Specifies the amount of fuzzy errors to allow for filter matching. Using this
feature requires the optional \fIregex\fR dependency to be installed.
.TP
.IR config.commands.modify.preserve_files = False
Specifies whether associates files should be preserved during renaming.
.TP
.IR config.commands.note.default_filetype = 'txt'
Specifies the default filetype to use for associated notes.
.TP
.IR config.commands.open.command = 'xdg-open' " (on Linux); " 'open' " (on Mac OS)"
Specifies the program used to open associated files.
.TP
.IR config.commands.open.fields = ['file',\ 'url']
Specifies the names of the data fields which are to be checked for openable
URLs.
.TP
.IR config.commands.search.context = 1
Specifies the default number of context lines to provide for each search query
match.
.TP
.IR config.commands.search.grep = 'grep'
Specifies the program used to search in associated files.
.TP
.IR config.commands.search.grep_args = []
Allows the specification of additional arguments for the \fIgrep\fR command.
.TP
.IR config.commands.search.ignore_case = False
This boolean setting indicates whether search defaults to be case-insensitive.
.TP
.IR config.commands.search.decode_unicode = False
Specifies whether searches should decode all Unicode characters.
.TP
.IR config.commands.search.decode_latex = False
Specifies whether searches should decode all LaTeX sequences.
.TP
.IR config.commands.search.fuzziness = 0
Specifies the amount of fuzzy errors to allow for searches. Using this feature
requires the optional \fIregex\fR dependency to be installed.
.TP
.IR config.commands.search.skip_files = False
Specifies whether searches should skip looking through associated files.
.TP
.IR config.commands.search.skip_notes = False
Specifies whether searches should skip looking through associated notes.
.TP
.IR config.commands.show.encode_latex = True
This boolean setting indicates whether non-ASCII characters should be encoded
using LaTeX sequences during rendering via the \fIshow\fR command.
.PP
.BR DATABASE
.TP
.IR config.database.file = '~/.local/share/cobib/literature.yaml'
This setting sets the path to the database file. You can use \fI~\fR to
represent your \fI$HOME\fR directory.
.TP
.IR config.database.cache = '~/.cache/cobib/databases/'
This settings sets the path to the folder in which already parsed databases
should be stored. Set this to \fINone\fR if you want to disable caching
entirely.
.TP
.IR config.database.git = False
This boolean field indicates whether the database file should automatically be
tracked in a git repository.
Note, that you must initialize the git-tracking with \fIcobib init --git\fR. If
you already have an existing database file, it will be preserved. Nonetheless,
it is a good idea to make a backup before doing so, just in case.
Also be sure to at least set a \fIname\fR and \fIemail\fR in the git config!
.TP
.IR config.database.format.author_format = AuthorFormat.YAML
This field specifies in which format to store the \fIauthor\fR information of
each entries. See the detailed online documentation of the \fiAuthorFormat\fR
enum for all possible values. As of version 4.3.0 this defaults to a YAML format
in which each author information is stored in detailed form by splitting out the
first and last names as well as name pre- and suffixes.
.TP
.IR config.database.format.label_default = '{unidecode(label)}'
This field specifies the default label format in an f-string modification style
as interpreted by the \fImodify\fR command. The default configuration value
passes the originally provided label through \fItext-unidecode\fR which replaces
all Unicode symbols with pure ASCII ones. A more useful example is
\fI'{unidecode(author[0].last)}{year}'\fR which takes the surname of the first
author, replaces the Unicode characters and then immediately appends the
publication year.
.TP
.IR config.database.format.label_suffix = ('_',\ LabelSuffix.ALPHA)
This field specifies the default label disambiguator. The option takes a tuple
of length 2, where the first entry is the string separating the proposed label
from the disambiguator and the second one is one of the enumerators provided by
\ficonfig.LabelSuffix\fR.
.TP
.IR config.database.format.suppress_latex_warnings = True
This boolean field indicates whether latex warnings will be ignored during the
escaping of special characters.
.TP
.IR config.database.format.verbatim_fields = ['file',\ 'url']
Specifies the names of the data fields which are kept verbatim and, thus remain
unaffected from any special character conversions (e.g. LaTeX encoding).
.TP
Some fields are internally stored as lists. Upon conversion to the BibTeX
format, these need to be converted to a basic string. In this process the
entries of the list will be joined using the separators configured by the
following settings.
.TP
.IR config.database.stringify.list_separator.file = ',\ '
.TP
.IR config.database.stringify.list_separator.tags = ',\ '
.TP
.IR config.database.stringify.list_separator.url = ',\ '
.PP
.BR PARSERS
.TP
.IR config.parsers.bibtex.ignore_non_standard_types = False
This boolean setting indicates whether non-standard BibLaTex entry types should
be ignored or not.
.TP
.IR config.parsers.yaml.use_c_lib_yaml = True
This boolean setting indicates whether to use the C-based implementation of the
YAML parser. For this to work, additional packages may need to be installed.
Read https://yaml.readthedocs.io/en/latest/install.html#optional-requirements
for more details.
.PP
.BR THEME
.TP
.IR config.theme.dark = True
Specifies whether a dark or light color scheme is used.
.TP
.IR config.theme.design = DEFAULT_COLORS
This setting allows you to specify the \fIColorSystem\fR of the entire TUI.
Since this is tightly coupled to textual's documentation, the explanation of
this setting is best viewed online:
https://cobib.gitlab.io/cobib/cobib/config/config.html#ThemeConfig.design
.TP
.IR config.theme.search.label = 'blue'
Specifies the color used to highlight the entry labels when displaying search
rsults.
.TP
.IR config.theme.search.label = 'red'
Specifies the color used to highlight the query matches when displaying search
results.