Initial release (v0.1)

README.md

@@ -1,2 +1,93 @@
 # bibextract
-Extract bibliography entries from LaTeX sources
+Extract bibliography entries from a reference BibTeX file using citations from
+LaTeX sources, to create project-specific BibTeX files.
+
+> For now, in order to work properly, both `bibx` and `ext.sh` **NEED** to be
+> in the same directory. This is expected to change in a future release.
+
+## Dependencies
+* Python >= 3.5
+* [`python-bibtexparser`](https://github.com/sciunto-org/python-bibtexparser)
+    * [Install](https://bibtexparser.readthedocs.io/en/master/install.html#how-to-install)
+
+## Installation
+Once you have installed the dependencies, clone this repository
+```sh
+git clone https://github.com/CodePurble/bibextract.git
+```
+
+Run `install.sh`. The files will be installed to `/usr/local/bin`. This can be
+changed by modifying the `PREFIX` variable in `install.sh`.
+```sh
+./install.sh
+```
+
+> **NOTE**: To uninstall, use the provided `uninstall.sh` script. If you edited
+> `PREFIX` while installing, make sure to update `uninstall.sh` also with the
+> same value before running.
+
+### Updating an existing install
+First, navigate to where you initially cloned this repo and pull down the latest changes:
+```sh
+cd path/to/repo
+git pull origin master
+```
+
+Then, rerun `install.sh`
+```sh
+./install.sh
+```
+
+## Usage
+Check the help-text:
+```sh
+bibx -h
+```
+
+Also read the manpage:
+```sh
+man bibx
+```
+
+### Example
+Assume that there are two LaTeX files: `a.tex` and `b.tex`, the reference
+BibTeX file is `g.bib` and we want the output file to be `refs.bib`. The
+command to achieve this would be:
+```sh
+bibx -b g.bib -o refs.bib a.tex b.tex
+
+# A variation
+bibx -b g.bib -o refs.bib *.tex
+```
+
+## Bugs
+If you find a bug or are facing some problem, please [open an
+issue](https://github.com/CodePurble/bibextract/issues/new/choose).
+
+## Contributing
+Contributions are welcome: features, documentation, whatever! Fork this repo
+and create a new branch for your changes, please do not commit directly to the
+master branch. Then create a pull-request.
+
+Take a look at the [TODO](./TOOD.md) or
+[issues](https://github.com/CodePurble/bibextract/issues) for some inspiration!
+
+If you are updating the manpage, you will need
+[`pandoc`](https://pandoc.org/index.html) to generate it from
+[`bibx.1.md`](./bibx.1.md). Use the following command to generate the manpage:
+```sh
+pandoc --standalone --to man bibx.1.md -o bibx.1
+```
+
+### Tests
+If contributing to the code, please run the following test after your edits:
+```
+./bibx -b test/global.bib -o test/ext.bib test/*.tex
+diff test/ext.bib test/ext-golden.bib
+```
+The `diff` command must return **NOTHING**. This means that the output is as
+expected for the given inputs.
+
+## License
+Free use of this software is granted under the terms of the [GPLv3
+License](https://github.com/CodePurble/bibextract/blob/master/LICENSE).

TOOD.md

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+- [ ] Remove dependency on `ext.sh`
+- [ ] Support multiple reference BibTeX files
+- [ ] Support a directory of reference BibTeX files

bibx

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+#!/usr/bin/env python3
+
+import argparse
+import bibtexparser
+import subprocess
+import shlex
+from bibtexparser.bparser import BibTexParser, BibDatabase
+from bibtexparser.bwriter import BibTexWriter
+
+def main():
+    parser = argparse.ArgumentParser(
+            description="""Extract bibliography entries from LaTeX sources
+            using a reference BibTeX file""",
+            epilog="""For reporting bugs, giving suggestions and contributing
+            to this project, visit https://github.com/CodePurble/bibextract"""
+            )
+    parser.add_argument("-b",
+                        "--bib",
+                        required=True,
+                        help="BibTeX file to look for entries in"
+                        )
+    parser.add_argument("-o",
+                        "--output",
+                        default="ext.bib",
+                        help="""File to which the extracted entries are output
+                        to. Default is './ext.bib'""",
+                        )
+    parser.add_argument("-e",
+                        "--entries",
+                        help="""Text file containing entries to extract from
+                        the BibTeX file, each line in the file must have ONE
+                        BibTeX label"""
+                        )
+    parser.add_argument("-q",
+                        "--quiet",
+                        default=False,
+                        help="Suppress output to stdout",
+                        action="store_true"
+                        )
+    parser.add_argument("files",
+                        help="""LaTeX files to scan for citations whose BibTeX
+                        entries need to be extract""",
+                        action="extend",
+                        nargs="+"
+                        )
+    parser.add_argument("-i",
+                        "--indent",
+                        help="""Indentation to be used in the generated BibTeX
+                        file. Default is four spaces""",
+                        default="    ",
+                        )
+
+    args = parser.parse_args()
+
+    # Scan LaTeX files for citations and generate set containing BibTeX entry
+    # labels
+    e_set = set()
+    for file in args.files:
+        output = subprocess.run(['./ext.sh', shlex.quote(file)],
+                                capture_output=True
+                                )
+        if(output.returncode == 0):
+            e_set = e_set.union(set(output.stdout.decode().rstrip().split('\n')))
+
+    # Merge custom BibTeX entry labels into main set if any
+    if(args.entries is not None):
+        with open(args.entries, 'r') as en:
+            while(entry := en.readline()):
+                e_set = e_set.union(entry)
+
+    parser = BibTexParser()
+    parser.ignore_nonstandard_types = False
+    with open(args.bib) as bibtex_file:
+        bib_database = bibtexparser.load(bibtex_file, parser)
+
+    e_dict = bib_database.entries_dict
+    out_db = BibDatabase()
+
+    entrycount = 0
+    found = 0
+    for entry in e_set:
+        entrycount += 1
+        if entry in e_dict.keys():
+            if not args.quiet:
+                print(f"Found: {entry}")
+            found += 1
+            out_db.entries.append(e_dict[entry])
+        else:
+            if not args.quiet:
+                print(f"Not found: {entry}")
+
+
+    writer = BibTexWriter()
+    writer.indent = args.indent
+    writer.add_trailing_comma = True
+    with open(args.output, 'w') as outfile:
+        bibtexparser.dump(out_db, outfile, writer)
+
+    if not args.quiet:
+        print(f"\nFound {found}/{entrycount} entries")
+
+if __name__ == "__main__":
+    main()

bibx.1

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+.\" Automatically generated by Pandoc 2.19.2
+.\"
+.\" Define V font for inline verbatim, using C font in formats
+.\" that render this, and otherwise B font.
+.ie "\f[CB]x\f[]"x" \{\
+. ftr V B
+. ftr VI BI
+. ftr VB B
+. ftr VBI BI
+.\}
+.el \{\
+. ftr V CR
+. ftr VI CI
+. ftr VB CB
+. ftr VBI CBI
+.\}
+.TH "BIBX" "1" "" "Version 1.0" "bibx Command Documentation"
+.hy
+.SH NAME
+.PP
+bibx \[em] Extract bibliography entries from a reference BibTeX file
+using citations from LaTeX sources, to create project-specific BibTeX
+files.
+.SH SYNOPSIS
+.PP
+bibx [-h] -b BIB [-o OUTPUT] [-e ENTRIES] [-q] [-i INDENT] files [files
+\&...]
+.SH DESCRIPTION
+.PP
+This program extracts citations made in LaTeX source files and generates
+a BibTeX file with entries that are found.
+In order to generate the BibTeX file, a single \[lq]global\[rq] BibTeX
+file that acts as a database to look for matching entries.
+Output is written to `ext.bib' by default.
+Requires at least one LaTeX source.
+.PP
+If extra entries other than those found from the LaTeX sources are to be
+added to the output file, it can be done by using the -e option.
+The file must contain a single BibTeX label on each line.
+.PP
+For example:
+.IP
+.nf
+\f[C]
+label1
+label2
+label3
+\f[R]
+.fi
+.SH OPTIONS
+.PP
+-h, \[en]help
+.IP
+.nf
+\f[C]
+Show help and exit
+\f[R]
+.fi
+.PP
+-b BIB, \[en]bib BIB
+.IP
+.nf
+\f[C]
+Specify global BibTeX file to look for entries in
+\f[R]
+.fi
+.PP
+-o OUTPUT, \[en]output OUTPUT
+.IP
+.nf
+\f[C]
+Specify file to write the BibTeX output to. Defaults to \[aq]./ext.bib\[aq].
+\f[R]
+.fi
+.PP
+-e ENTRIES, \[en]entries ENTRIES
+.IP
+.nf
+\f[C]
+Specify file containing extra entries names to be searched and included in
+the final output.
+\f[R]
+.fi
+.PP
+-i INDENT, \[en]indent INDENT
+.IP
+.nf
+\f[C]
+Specify the character(s) to be used to indent the BibTeX entries in the
+final output. Defaults to four spaces. Example: -i \[dq]  \[dq] (use two spaces).
+\f[R]
+.fi
+.PP
+-q, \[en]quiet
+.IP
+.nf
+\f[C]
+Suppress output to stdout
+\f[R]
+.fi
+.SH EXAMPLE
+.PP
+Assume that there are two LaTeX files: \f[V]a.tex\f[R] and
+\f[V]b.tex\f[R], the reference BibTeX file is \f[V]g.bib\f[R] and we
+want the output file to be \f[V]refs.bib\f[R].
+.PP
+The command to achieve this would be:
+.IP
+.nf
+\f[C]
+bibx -b g.bib -o refs.bib a.tex b.tex
+\f[R]
+.fi
+.SH BUGS
+.PP
+See GitHub issues: https://github.com/CodePurble/bibextract/issues
+.SH AUTHOR
+.PP
+Ramprakash C (https://github.com/CodePurble)
+.SH COPYRIGHT
+.PP
+Free use of this software is granted under the terms of the GPLv3
+License.
+.PP
+See: https://github.com/CodePurble/bibextract/blob/master/LICENSE
+.SH SEE ALSO
+.PP
+bibtex(1), latex(1)