recognize "bibentry" and "nobibliography"

adstex

Tired of copying and pasting bibtex entries? Here's a new way to manage your bibtex entries — do not manage them!

adstex automatically identifies all citation keys (e.g., identifiers, author+year) in your TeX source files and use NASA's Astrophysics Data System (ADS) to generate corresponding bibtex entries!

adstex was featured in an ADS blog post "User-Developed Tools for ADS"!

Features

Write your papers without worrying about the bibtex entries. Simply put down arXiv IDs, ADS bibcodes, DOIs, or first author & year citation keys in your \cite commands, and then use adstex to automatically generate the bibtex file for you.
adstex recognizes all variants of the \cite commands, and works with various styles of citation keys. For example, adstex would work with all the following:
```
\citet{1705.03888}
\citep[e.g.,][]{Mao:2015, White2018}
\citealt{10.1093/mnras/stx3111, 2017arXiv170909665M}
```
adstex works along with your existing bibtex files. It simply skips (or updates) those citation keys that already have corresponding bibtex entries.
adstex will also update existing bibtex entries for you! Citing an arXiv preprint which is now published in a journal? No problem, adstex will detect this and automatically update the bibtex entry. (This is amazing, yes, I know!)
adstex also detects citation keys that actually refer to the same paper (e.g., you use an author:year citation key but another collaborator uses an arxiv ID as key for the same paper), and will prompt you to fix these issues.

Installation and Setup

Install `adstex`

You can install adstex from conda-forge

conda install adstex --channel conda-forge

Or from PyPI

pip install adstex

Set up an ADS API token

adstex requires an API token to use ADS. Here's how to obtain one:

Visit NASA/ADS to sign up for an account if you don't have one.
Visit the API Token page, log in with your ADS account and you will see an API token string. Copy that token string.

Set your token string to an environment variable named ADS_API_TOKEN. You can do that by running:

# If you use bash or bash-like shells --
export ADS_API_TOKEN="your token string here"

# If you use csh or csh-like shells --
setenv ADS_API_TOKEN "your token string here"

You can put this line into your ~/.bashrc or ~/.cshrc file.

Usage

Once you finish the paper (sorry, can't help with that!), simply run adstex with the following command (Internet connection is needed for adstex to work.):

# Note: if you are using version 0.2.x, please add the -o option. See below.

adstex your_tex_source.tex

adstex will automatically build the bibtex files, and write to the bibtex source that you specified in your tex source file.

If you want to have more control on the output file (or if you are using adstex v0.2.x), use the -o option:
```
adstex your_tex_source.tex -o your_bib_source.bib
```
Once adstex is done, it will write all bibtex entries in the file that you specified with the -o option.

You can also provide multiple TeX source files at once:

adstex your_tex_source1.tex [your_tex_source2.tex [...]] -o your_bib_source.bib

For citation keys that are arXiv IDs, ADS bibcodes, or DOIs, adstex will automatically find the corresponding bibtex entries.
For first author + year citation keys, adstex will search on NASA ADS and provide you a list of candidate papers to select from. If you don't see the paper you are looking for, you can directly enter an ADS bibcode or arXiv ID when prompted.
You can also find a complete option list by running:
```
adstex --help
```
However, you may find the following FAQs more informative.

FAQs

Can adstex recognize citation keys with multiple authors or compound surnames?

Not always; adstex uses regular expression, not AI.

For citation keys with multiple authors, if you use a separator to separate the surnames, (e.g., \cite{Press:Schechter:1974}), the adstex will be able to identify the first author and year to conduct a search on the ADS.

For compound surnames, your best bets are joining the words without the spaces (e.g., \cite{deSitter:1913}), and keeping the hyphens (e.g., \cite{Boylan-Kolchin:1913}).

Note that in the event that adstex cannot find the correct paper from a first author + year citation key, it will prompt you to enter an identifier (ADS bibcode, arXiv ID, or DOI) for that key.
I have some other bibtex files, how to ask adstex to skip citation keys that already have existing entries in those files?

Use the -r option to provide additional existing bibtex files. adstex will read in these files without modifying them (only the file specified by -o will be modified). Here's an example command:
```
adstex main.tex -o main.bib -r software.bib classic.bib
```
How do I use adstex as a reference manager? Or can I use adstex with other reference managers (e.g., JabRef, Mendeley, Zotero)?

adstex is not a reference manager, and will not be one. The philosophy behind adstex is to not manage the references, because NASA's ADS is already doing that for us (and is doing an excellent job)! So adstex simply generates the bibtex file using the ADS on the fly.

If you are already using a reference manager, you may want to continue to use it to generate bibtex files. You can then use adstex to fetch just the new entries (see FAQ #2). You can also use adstex to update all existing entries with the latest version from the ADS by running:
```
adstex your_bibtex_file.bib
```
Does this work with the ADS astronomy database only?

For citation keys that are arXiv IDs, ADS bibcodes, or DOIs, adstex would work with any entry as long as it is in the ADS.

For first author + year citation keys, by default adstex would only search the astronomy database on NASA ADS. However, you can use --include-physics to include the ADS physics database.

adstex only works with the ADS, and hence the name of this program :)
adstex seems to run very slowly. Is there any way to speed it up?

By default, adstex check if existing entries have any updates (e.g., arXiv preprint becoming a journal paper), and this process may slow down the execution. You can use --no-update to turn this feature off, so that adstex will only look for new entries.

In addition, you can turn on parallel execution by adding the --parallel (-p) option. You can further specify the number of threads it uses with --threads=x (default is 8).
I have different citation keys that point to the same paper in my tex file, can adstex merge and remove the repetitions?

adstex will warn you (near the end of its execution) if it detects multiple keys that point to the same paper. It will list all those citation keys, but it will not merge them automatically. adstex never edits the tex source files; hence, you need to update the citation keys in the tex source files manually.
Is there a way to use adstex with Overleaf?

If you or your institution has an Overleaf subscription, you can use Overleaf's git or Dropbox integration to fetch the source files to your local machine, run adstex locally, and then push back to Overleaf via git (in the case of Dropbox, no pushing needed).

If you don't have access to Overleaf's premium features, you can still just download the tex source file and bib file, run adstex locally, and then upload the updated bib file back to Overleaf (tex source file will not be changed by adstex).
I got a SSLCertVerificationError! How to fix it?

This error usually happens when the ADS SSL certification has been updated, but your local SSL certification has not yet. The error should go away once the local certification is updated too.

With adstex 0.4.0+, you can use the --disable-ssl-verification option to temporarily disable the verification of SSL certification. This option can be handy if you don't have control of your local SSL certification installation. Note that with this option, your ADS API key may be vulnerable to a man-in-the-middle attack. You can generate new ADS API key on ADS website if you think your API key may have been compromise.
adstex saves me so much time. How do I acknowledge it?

First of all, thank you :)

adstex won't exist without NASA's ADS, so please do acknowledge them by adding the following to your acknowledgements section:
```
This research has made use of NASA's Astrophysics Data System.
```
(Note: adstex is not affiliated with nor endorsed by NASA's ADS.)

Then, if you would like to also acknowledge adstex, you can add the following to your acknowledgements section:
```
This research has made use of adstex (\url{https://github.com/yymao/adstex}).
```

	if (key_exists and args.update) or (
	key_exists_in_others and args.merge_other and args.update
	):
	bibcode = extract_bibcode(bib.entries_dict[key])
	bibcode_new = entry2bibcode(bib.entries_dict[key])

yymao / adstex Goto Github PK

adstex's Introduction

adstex

Features

Installation and Setup

Install adstex

Set up an ADS API token

Usage

FAQs

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