[REVIEW]: DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval

[editorialbot]

Submitting author: @Ayuei (Vincent Nguyen)
Repository: https://github.com/Ayuei/DeBEIR
Branch with paper.md (empty if default branch): paper
Version: v0.0.1
Editor: @arfon
Reviewers: @KonradHoeffner, @amitkumarj441
Archive: 10.5281/zenodo.8103783

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @KonradHoeffner

📝 Checklist for @amitkumarj441

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (730.7 files/s, 203354.8 lines/s)
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Language                     files          blank        comment           code
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HTML                            58           4385              0          29946
TeX                              1              0            154           6701
Python                          64           1443           1073           3931
JSON                             5              0              0           1629
Jupyter Notebook                 6              0           1049            268
TOML                            36             18              2            232
Markdown                         2             63              0            160
XML                              8              0              0             79
JavaScript                       1              3              3             40
Bourne Shell                     2              6              0             15
Dockerfile                       1              2              1              5
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SUM:                           184           5920           2282          43006
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1261

[arfon]

@KonradHoeffner – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

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As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[arfon]

@amitkumarj441 @JacksonMaxfield @shruti-singh – would any of you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

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- 10.18653/v1/w19-5006 may be a valid DOI for title: Transfer learning in biomedical natural language processing: An evaluation of BERT and ELMo on ten benchmarking datasets
- 10.1145/3331184.3331289 may be a valid DOI for title: An Analysis of Query Reformulation Techniques for Precision Medicine
- 10.1145/2970398.2970418 may be a valid DOI for title: Optimization Method for Weighting Explicit and Latent Concepts in Clinical Decision Support Queries
- 10.1145/3331184.3331303 may be a valid DOI for title: Deeper Text Understanding for IR with Contextual Neural Language Modeling
- 10.18653/v1/d19-1352 may be a valid DOI for title: Cross-domain modeling of sentence-level evidence for document retrieval
- 10.1186/1472-6947-12-47 may be a valid DOI for title: Computational challenges and human factors influencing the design and use of clinical research participant eligibility pre-screening tools
- 10.1016/j.jbi.2020.103406 may be a valid DOI for title: Matching patients to clinical trials using semantically enriched document representation
- 10.1200/jop.2012.000646 may be a valid DOI for title: Effort required in eligibility screening for clinical trials
- 10.1016/j.ipm.2011.02.009 may be a valid DOI for title: Quantifying the impact of concept recognition on biomedical information retrieval
- 10.1007/978-3-540-31865-1_37 may be a valid DOI for title: Terrier Information Retrieval Platform
- 10.1093/jamia/ocaa091 may be a valid DOI for title: TREC-COVID: Rationale and Structure of an Information Retrieval Shared Task for COVID-19
- 10.18653/v1/d19-1352 may be a valid DOI for title: Cross-Domain Modeling of Sentence-Level Evidence for Document Retrieval
- 10.2146/ajhp060661 may be a valid DOI for title: Role of sunitinib and sorafenib in the treatment of metastatic renal cell carcinoma
- 10.1016/j.jbi.2019.103224 may be a valid DOI for title: ARtPM: article retrieval for precision medicine
- 10.1038/d41586-020-00694-1 may be a valid DOI for title: Keep up with the latest coronavirus research
- 10.1093/jamia/ocaa271 may be a valid DOI for title: An Evaluation of Two Commercial Deep Learning-Based Information Retrieval Systems for COVID-19 Literature
- 10.18653/v1/2020.sdp-1.5 may be a valid DOI for title: Covidex: Neural Ranking Models and Keyword Search Infrastructure for the COVID-19 Open Research Dataset
- 10.1098/rsos.201199 may be a valid DOI for title: Susceptibility to misinformation about COVID-19 around the world
- 10.1016/j.conctc.2018.08.001 may be a valid DOI for title: Factors associated with clinical trials that fail and opportunities for improving the likelihood of success: a review
- 10.2196/24008 may be a valid DOI for title: Family History Extraction From Synthetic Clinical Narratives Using Natural Language Processing: Overview and Evaluation of a Challenge Data Set and Solutions for the 2019 National NLP Clinical Challenges (n2c2)/Open Health Natural Language Processing (OHNLP) Competition
- 10.7551/mitpress/7432.003.0006 may be a valid DOI for title: An introduction to conditional random fields for relational learning
- 10.18653/v1/2020.acl-main.740 may be a valid DOI for title: Don’t Stop Pretraining: Adapt Language Models to Domains and Tasks
- Errored finding suggestions for "Cost-effective Selection of Pretraining Data: A Ca...", please try later
- 10.1016/j.jbi.2013.12.006 may be a valid DOI for title: NCBI disease corpus: a resource for disease name recognition and concept normalization
- 10.1016/j.ypmed.2011.06.008 may be a valid DOI for title: Association between a healthy lifestyle and general obesity and abdominal obesity in an elderly population at high cardiovascular risk
- 10.3115/v1/p14-1090 may be a valid DOI for title: Information extraction over structured data: Question answering with freebase
- 10.3115/v1/p14-2105 may be a valid DOI for title: Semantic Parsing for Single-Relation Question Answering
- 10.31826/9781463230210-001 may be a valid DOI for title: The fountain of youth
- 10.1137/0402015 may be a valid DOI for title: Vertex Types in Book-Embeddings
- 10.1016/j.mejo.2010.02.002 may be a valid DOI for title: A library-based synthesis methodology for reversible logic
- 10.1007/978-3-642-59412-0_21 may be a valid DOI for title: Go to statement considered harmful
- 10.1016/0950-5849(92)90115-6 may be a valid DOI for title: Simplified Structured COBOL with Microsoft/MicroFocus COBOL
- 10.1007/978-3-540-49938-1 may be a valid DOI for title: The analysis of linear partial differential operators. III
- 10.1109/broadnets.2004.8 may be a valid DOI for title: A multi-radio unification protocol for IEEE 802.11 wireless networks
- 10.21236/ada461607 may be a valid DOI for title: Channel-Hopping Multiple Access
- 10.1145/357233.357234 may be a valid DOI for title: User recovery and reversal in interactive systems
- 10.1145/2363.2708 may be a valid DOI for title: Generalizing specifications for uniformly implemented loops
- 10.1145/3318.3321 may be a valid DOI for title: Towards monolingual programming environments
- 10.1145/579.585 may be a valid DOI for title: Distributed algorithms for finding centers and medians in networks
- 10.7146/dpb.v10i140.7415 may be a valid DOI for title: Program transformations in a denotational setting
- 10.1145/567446.567449 may be a valid DOI for title: A high-level approach to computer document formatting
- 10.1016/j.scr.2012.12.003 may be a valid DOI for title: Stemformatics: Visualisation and sharing of stem cell gene expression
- 10.1093/nar/gky1064 may be a valid DOI for title: Stemformatics: visualize and download curated stem cell data
- 10.1145/2882782 may be a valid DOI for title: Examining Additivity and Weak Baselines
- 10.1145/3077136.3084136 may be a valid DOI for title: A Task-oriented Search Engine for Evidence-based Medicine
- 10.1093/database/baq036 may be a valid DOI for title: PubMed and beyond: a survey of web tools for searching biomedical literature
- 10.1006/jbin.2001.1029 may be a valid DOI for title: A Simple Algorithm for Identifying Negated Findings and Diseases in Discharge Summaries
- 10.18653/v1/p17-4002 may be a valid DOI for title: Automating Biomedical Evidence Synthesis: RobotReviewer
- 10.1186/1472-6947-10-56 may be a valid DOI for title: ExaCT: automatic extraction of clinical trial characteristics from journal publications
- 10.1007/978-3-319-76941-7_6 may be a valid DOI for title: Choices in Knowledge-Base Retrieval for Consumer Health Search
- 10.1007/s10791-009-9123-y may be a valid DOI for title: LETOR: A Benchmark Collection for Research on Learning to Rank for Information Retrieval
- 10.1093/jamia/ocv041 may be a valid DOI for title: Assessing information system readiness for mitigating malpractice risk through simulation: results of a multi-site study
- 10.1093/jamia/ocw103 may be a valid DOI for title: Biomedical informatics advancing the national health agenda: The AMIA 2015 year-in-review in clinical and consumer informatics
- 10.1038/438897a may be a valid DOI for title: Pokemon blocks gene name
- 10.1186/1472-6947-7-16 may be a valid DOI for title: Utilization of the PICO framework to improve searching PubMed for clinical questions
- 10.1111/j.1469-8137.1912.tb05611.x may be a valid DOI for title: THE DISTRIBUTION OF THE FLORA IN THE ALPINE ZONE.1
- 10.1145/3209978.3210167 may be a valid DOI for title: An Information Retrieval Experiment Framework for Domain Specific Applications
- 10.1093/jamia/ocw177 may be a valid DOI for title: MetaMap Lite: an evaluation of a new Java implementation of MetaMap
- 10.1145/3458754 may be a valid DOI for title: Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing
- 10.1063/1.1419217 may be a valid DOI for title: Littrow Configuration Tunable External Cavity Diode Laser with Fixed Direction Output Beam
- 10.1145/3404835.3463254 may be a valid DOI for title: Simplified Data Wrangling with ir_datasets
- 10.1145/3404835.3463238 may be a valid DOI for title: Pyserini: A Python Toolkit for Reproducible Information Retrieval Research with Sparse and Dense Representations
- 10.1186/s12859-020-03894-8 may be a valid DOI for title: A2A: A platform for research in biomedical literature search
- 10.1201/9781439814680-7 may be a valid DOI for title: Heat Transfer Mechanisms
- 10.1007/978-3-030-43887-6_56 may be a valid DOI for title: Classification Betters Regression in Query-Based Multi-document Summarisation Techniques for Question Answering
- 10.1007/978-1-4615-3618-5_2 may be a valid DOI for title: Simple statistical gradient-following algorithms for connectionist reinforcement learning
- 10.18653/v1/2020.acl-main.703 may be a valid DOI for title: BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension
- 10.18653/v1/2020.acl-main.30 may be a valid DOI for title: Contextualized Weak Supervision for Text Classification
- 10.1080/10511970.2014.895459 may be a valid DOI for title: Teaching Writing and Communication in a Mathematical Modeling Course
- 10.1007/978-3-030-72113-8_36 may be a valid DOI for title: A Deep Analysis of an Explainable Retrieval Model for Precision Medicine Literature Search

INVALID DOIs

- https://doi.org/10.1006/jbin.2001.1004 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jclinepi.2019.02.004 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.ijmedinf.2017.11.006 is INVALID because of 'https://doi.org/' prefix
- 10.1136/jAmericanMedicalInformaticsAssociation.2009.002733 is INVALID
- 10.1007/978-0-387-39940-9\_488 URL is INVALID
- 10.1007/978-0-387-39940-9\_3032 URL is INVALID
- https://doi.org/10.1016/j.jksuci.2018.08.005 is INVALID because of 'https://doi.org/' prefix
- 10.1162/tacl\_a\_00097 URL is INVALID
- 10.1007/11736790\_21 URL is INVALID
- https://doi.org/10.1016/j.jbi.2011.08.008 is INVALID because of 'https://doi.org/' prefix
- 10.1007/3-540-65193-4\_29 URL is INVALID
- 99.9999/woot07-S422 is INVALID
- http://doi.acm.org/10.1145/351827.384253 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1016/j.inffus.2009.01.002 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1109/ICWS.2004.64 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1137/080734467 is INVALID because of 'https://doi.org/' prefix
- http://doi.acm.org/10.1145/800025.1198348 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jbi.2013.07.011 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0079-7421(08)60536-8 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jbi.2022.104005 is INVALID because of 'https://doi.org/' prefix

[KonradHoeffner]

Review checklist for @KonradHoeffner

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Ayuei/DeBEIR?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Ayuei) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

• API documentation exists but is not complete, see API Documentation incomplete Ayuei/DeBEIR#9

• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  *Writing quality and structure is OK but, there needs to be a correction pass for language. For example, there are spaces in front of full stops: "DeBeIR .", "issues .". "github" *-> "GitHub". Hugggingface -> Huggingface.
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[KonradHoeffner]

@Ayuei: The paper has three authors but you are the only contributor of the repository. Can you clarify the contribution of your coauthors?

[KonradHoeffner]

@Ayuei: Is it “DeBIR” or “DeBEIR”? The paper is titled DeBIR but the repository title and README contains “DeBEIR”. The code in the paper uses both. Please use a consistent name. Or are they actually two different things?

[KonradHoeffner]

Success in information retrieval was limited until 2021

@Ayuei: A paper from 2019 is cited next, which talks about how the breakthrough came in 2018 or 2019. Please confirm that 2021 is indeed the correct year.

[KonradHoeffner]

Additional hackability

@Ayuei: I didn’t know the word “hackability” in this context but I’m not a native speaker and had to look it up to find out that it has two different meanings. If possible I would use a less ambiguous term to not confuse other non-native speakers.

[KonradHoeffner]

Please describe author affiliation in more detail. I had to Google “CSIRO’s Data61” to understand what it is. “Australian National University” is also very general. Which department and research group? You could move part of that from the acknowledgements.

[KonradHoeffner]

A brief summary of the pipeline stages are

Summary is singular so it should be “is”, not “are”. Also please refer to figure 1 here, which illustrates the stages.

• “Figure” is repeated several times as “Figure Figure”

Similar libraries that exist include sentence-transformers, openNIR

Add “such as”, cite publication

but have less of a focus on all stages of the dense retrieval pipeline

Please explain in more detail which stages of the pipeline are not covered enough by all existing libraries and what the benefits of DeBIR over those existing libraries are. This is important to clarify, how exactly it "either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler)." as part of the "substantial scholarly effort" criterion and for the statement of need criterion.

[arfon]

@Ayuei – please shorten your BibTeX file to include only those entries cited by this paper.

[Ayuei]

@arfon Hi, I've shortened the BibTex and recompiled the paper.

@KonradHoeffner Thank you for taking time to review the work and for the detailed comments, I'm still working on addressing concerns and issues.

[arfon]

👋 @kuutsav would you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

[kuutsav]

👋 @kuutsav would you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

@arfon Thanks for reaching out. I have a very busy schedule this month. If you are still looking for a reviewer at the end of the month, please reach out to me again. All the best!

[amitkumarj441]

I am back to reviewing the codebase and was able to run the Python tests without a hitch, given this library has support enabled for both ES and Solr which works in a standalone manner. However, the automated tests pipeline via Docker runs on MacOs which is not platform-agnostic, though, you may add a bit about instructions on how to run this dockerized image for indexing on Linux. The main pros of this library for reproducing a similar case in IR is the support of an extended list of metrics (NDCG@k, p@k, r@k, etc.). Apart from this, the documentation should clarify on the timeout for ES such as L16.

[Ayuei]

I am back to reviewing the codebase and was able to run the Python tests without a hitch, given this library has support enabled for both ES and Solr which works in a standalone manner. However, the automated tests pipeline via Docker runs on MacOs which is not platform-agnostic, though, you may add a bit about instructions on how to run this dockerized image for indexing on Linux. The main pros of this library for reproducing a similar case in IR is the support of an extended list of metrics (NDCG@k, p@k, r@k, etc.). Apart from this, the documentation should clarify on the timeout for ES such as L16.

Thank you for your review @amitkumarj441,

I added more documentation about the ES config in commit b25dd9

I think the testing should be platform agnostic on the main branch (https://github.com/Ayuei/DeBEIR/blob/main/tests/build_test_env.sh), which has seen major refactoring since the paper submission.

[amitkumarj441]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/CVPR.2015.7298594 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/D19-1387 is OK
- 10.1093/bioinformatics/btz682 is OK
- 10.18653/v1/D19-1410 is OK
- 10.1145/3336191.3371864 is OK

MISSING DOIs

- 10.1145/3065386 may be a valid DOI for title: ImageNet Classification with Deep Convolutional Neural Networks
- 10.1162/coli_r_00468 may be a valid DOI for title: Pretrained transformers for text ranking: Bert and beyond

INVALID DOIs

- https://doi.org/10.1016/j.jbi.2022.104005 is INVALID because of 'https://doi.org/' prefix

[amitkumarj441]

@Ayuei That's helpful to run tests, however, under the main branch in the central instructions file (README.md), you should fix the typo of the shell script file as below

cd tests/
./build_test.env.sh -> ./build_test_env.sh
pytest .

Also, fix the missing and erroneous references as listed above.
I am happy to recommend the paper for publication at this stage provided that the above suggestions are taken into consideration.

[Ayuei]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/3065386 is OK
- 10.1109/CVPR.2015.7298594 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/D19-1387 is OK
- 10.1093/bioinformatics/btz682 is OK
- 10.1145/3331184.3331340 is OK
- 10.18653/v1/D19-1410 is OK
- 10.1016/j.jbi.2022.104005 is OK
- 10.1145/3336191.3371864 is OK
- 10.1162/coli_r_00468 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Ayuei]

@Ayuei That's helpful to run tests, however, under the main branch in the central instructions file (README.md), you should fix the typo of the shell script file as below

cd tests/
./build_test.env.sh -> ./build_test_env.sh
pytest .

Also, fix the missing and erroneous references as listed above. I am happy to recommend the paper for publication at this stage provided that the above suggestions are taken into consideration.

@amitkumarj441 Thanks for catching this!

I just fixed this in the main and paper branches. I also fixed the missing and erroneous DOIs (Commit Ayuei/DeBEIR@8a9714a).

[amitkumarj441]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/3065386 is OK
- 10.1109/CVPR.2015.7298594 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/D19-1387 is OK
- 10.1093/bioinformatics/btz682 is OK
- 10.1145/3331184.3331340 is OK
- 10.18653/v1/D19-1410 is OK
- 10.1016/j.jbi.2022.104005 is OK
- 10.1145/3336191.3371864 is OK
- 10.1162/coli_r_00468 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[amitkumarj441]

@arfon I think it's much improved, and I'm happy to sign-off the full review.

[arfon]

@Ayuei – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• Finally, please make sure you give the paper a final proof read yourself before I do.

I can then move forward with accepting the submission.

[Ayuei]

@Ayuei – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• Finally, please make sure you give the paper a final proof read yourself before I do.

I can then move forward with accepting the submission.

Hi @arfon,

Thank you for the detailed instructions

• I published the new release here with all the changes from the reviews: Latest Release
• I made the archive here with Zenodo here: 10.5281/zenodo.8103783
• Finally, I also did proof read and uploaded the changes the paper branch: paper branch

If there is anything else I need to do, please let me know.

[arfon]

@editorialbot set 10.5281/zenodo.8103783 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8103783

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/3065386 is OK
- 10.1109/CVPR.2015.7298594 is OK
- 10.18653/v1/N19-1423 is OK
- 10.18653/v1/D19-1387 is OK
- 10.1093/bioinformatics/btz682 is OK
- 10.1145/3331184.3331340 is OK
- 10.18653/v1/D19-1410 is OK
- 10.1016/j.jbi.2022.104005 is OK
- 10.1145/3336191.3371864 is OK
- 10.1162/coli_r_00468 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4374, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Nguyen
  given-names: Vincent
  orcid: "https://orcid.org/0000-0003-1787-8090"
- family-names: Karimi
  given-names: Sarvnaz
  orcid: "https://orcid.org/0000-0002-4927-3937"
- family-names: Xing
  given-names: Zhenchang
  orcid: "https://orcid.org/0000-0001-7663-1421"
doi: 10.5281/zenodo.8103783
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Nguyen
    given-names: Vincent
    orcid: "https://orcid.org/0000-0003-1787-8090"
  - family-names: Karimi
    given-names: Sarvnaz
    orcid: "https://orcid.org/0000-0002-4927-3937"
  - family-names: Xing
    given-names: Zhenchang
    orcid: "https://orcid.org/0000-0001-7663-1421"
  date-published: 2023-07-05
  doi: 10.21105/joss.05017
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5017
  title: "DeBEIR: A Python Package for Dense Bi-Encoder Information
    Retrieval"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05017"
  volume: 8
title: "DeBEIR: A Python Package for Dense Bi-Encoder Information
  Retrieval"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05017 joss-papers#4379
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05017
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@KonradHoeffner, @amitkumarj441 – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@Ayuei – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05017/status.svg)](https://doi.org/10.21105/joss.05017)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05017">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05017/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05017/status.svg
   :target: https://doi.org/10.21105/joss.05017

This is how it will look in your documentation:

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