[PRE REVIEW]: Taxonomy Resolver: A Python package for building and filtering taxonomy trees

[editorialbot]

Submitting author: !--author-handle-->@biomadeira<!--end-author-handle-- (Fabio Madeira) Repository: https://github.com/ebi-jdispatcher/taxonomy-resolver Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: Pending Reviewers: Pending Managing EiC: Arfon Smith

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f4753608becbcdb391b48ee95f389400"><img src="https://joss.theoj.org/papers/f4753608becbcdb391b48ee95f389400/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f4753608becbcdb391b48ee95f389400/status.svg)](https://joss.theoj.org/papers/f4753608becbcdb391b48ee95f389400)

Author instructions

Thanks for submitting your paper to JOSS @biomadeira. Currently, there isn't a JOSS editor assigned to your paper.

@biomadeira if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.1093/database/baaa062 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.5281/zenodo.13819579 is OK
- 10.1093/sysbio/syz013 is OK
- 10.1016/j.tree.2023.08.004 is OK
- 10.1016/B978-155860920-4/50005-2 is OK
- 10.1093/nar/gkae241 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Entrez Direct: E-utilities on the Unix Command Lin...
- No DOI given, and none found for title: Anytree: Python tree data library
- No DOI given, and none found for title: BigTree: Tree Implementation and Methods for Pytho...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1111/2041-210X.12628 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (760.8 files/s, 110359.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            179            199           1096
reStructuredText                 3            180            110            277
TeX                              1             11              0            158
YAML                             4              6             27             91
Markdown                         1             16              0             60
TOML                             1              4              0             37
JSON                             1              0              0             15
-------------------------------------------------------------------------------
SUM:                            17            396            336           1734
-------------------------------------------------------------------------------

Commit count by author:

   203  Fábio Madeira

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 993

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

SuchTree: Fast, thread-safe computations with phylogenetic trees Submitting author: @ryneches Handling editor: @karthik (Retired) Reviewers: @giraola Similarity score: 0.7445

Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy Submitting author: @ggonnella Handling editor: @kellyrowland (Active) Reviewers: @vinisalazar, @KonradHoeffner Similarity score: 0.7409

Ngesh: a Python library for synthetic phylogenetic data Submitting author: @tresoldi Handling editor: @majensen (Active) Reviewers: @DavidNickle, @rvosa Similarity score: 0.7097

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files Submitting author: @maxibor Handling editor: @jmschrei (Active) Reviewers: @fasnicar, @marouenbg Similarity score: 0.7026

treemaker: A Python tool for constructing a Newick formatted tree from a set of classifications. Submitting author: @SimonGreenhill Handling editor: @trallard (Retired) Reviewers: @RichardLitt, @deniederhut Similarity score: 0.6992

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[arfon]

@editorialbot query scope

@biomadeira – due to the relatively small size of this code, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. We should get back to you sometime next week.

[editorialbot]

Submission flagged for editorial review.