Command-line tools
GBibClean
Clean a BibTeX database:
Stripping it from unnecessary fields.
Unifying the formatting of authors.
Ensuring the proper special characters and math mode settings.
Removing duplicates.
Finding/unifying arxivid and doi.
This script preserves order to help tracking changes.
usage: GBibClean [-h] [-o OUTPUT] [--in-place] [-j JOURNAL_TYPE]
[--journals JOURNALS] [--arxiv ARXIV]
[--rename-field RENAME_FIELD RENAME_FIELD]
[--add-field ADD_FIELD] [--remove-field REMOVE_FIELD]
[--no-title] [--author-sep AUTHOR_SEP]
[--journal-sep JOURNAL_SEP] [--raw-author RAW_AUTHOR]
[--ignore-case] [--ignore-math] [--ignore-unicode]
[--rename RENAME RENAME] [--merge MERGE MERGE]
[--sort-entries] [--unique UNIQUE] [--diff DIFF]
[--diff-context] [--diff-numlines DIFF_NUMLINES]
[--diff-type DIFF_TYPE] [--diff-keys DIFF_KEYS] [-f] [-v]
[files ...]
Positional Arguments
- files
Input files. If using
--in-place
files are treated separately. Otherwise they are merged to single output file.
Named Arguments
- -o, --output
Output file (required unless
--in-place
is used).- --in-place
If specified, each input file is separately treated and formatted in-place.
Default: False
- -j, --journal-type
Unify journal titles (if recognised). If “acronym” is selected, “abbreviation” is used for journals without an “acronym”.
Default: “abbreviation”
- --journals
Database(s) with official journal names, abbreviations, and acronyms. To make no modifications to journals use
--journal=""
.Default: “pnas,physics,mechanics”
- --arxiv
Format arXiv preprints using a specific formatter. Use “{}” in the formatter to include the arxivid, e.g.: “arXiv preprint {}”.
- --rename-field
Rename field (e.g. “arxivid” to “eprint”).
- --add-field
Add field. For all types
"field"
, only for one typetypename:field
.- --remove-field
Remove field. For all types
"field"
, only for one typetypename:field
.- --no-title
Remove title from BibTeX file.
Default: False
- --author-sep
Character to separate authors’ initials.
Default: “”
- --journal-sep
Character to separate journal abbreviations.
Default: “”
- --raw-author
List entries for which names are not abbreviated.
- --ignore-case
Do apply case protection of title.
Default: False
- --ignore-math
Do not apply math-mode fix.
Default: False
- --ignore-unicode
Do not apply unicode fix.
Default: False
- --rename
Rename citation keys (applied after merging).
- --merge
Force merging of items.
- --sort-entries
Sort output by entries.
Default: False
- --unique
Merge identical entries with different keys. Argument: output YAML file.
- --diff
Write diff to HTML file which shows the old and the reformatted file side-by-side. See
difflib.HtmlDiff.make_file
.- --diff-context
Show contextual differences. See
difflib.HtmlDiff.make_file
.Default: False
- --diff-numlines
Controls the number of context lines which surround the difference highlights.
Default: 5
- --diff-type
Show difference between
<output>
and compared to<input>
that is: * raw: not parsed at all (can lead to a mess because of sorting). * plain: parsed as little as possible. * select: parsed as little as possible, but with only selected output fields.Default: “select”
- --diff-keys
Limit diff to certain keys separated by spaces (e.g. “author,journal,doi”).
- -f, --force
Force overwrite of existing output file.
Default: False
- -v, --version
show program’s version number and exit
GbibDiscover
Check online databases (can be slow!).
usage: GbibDiscover [-h] -o OUTPUT [--arxiv] [-f] [-s] [-v] [files ...]
Positional Arguments
- files
Bib-file(s) considered concatenated if more files are specified.
Named Arguments
- -o, --output
Output file (yaml).
- --arxiv
Check arXiv as follows:
If the item is an arXiv preprint: check if a journal doi was registered at arXiv.
If the item is a journal article: try to find the arxivid based on the journal doi.
Default: False
- -f, --force
Force overwrite output file.
Default: False
- -s, --silent
Run without status bars.
Default: False
- -v, --version
show program’s version number and exit