[REVIEW]: PyTASER: Simulating transient absorption spectroscopy (TAS) for crystals from first principles

[editorialbot]

Submitting author: @savya10 (Savyasanchi Aggarwal)
Repository: https://github.com/WMD-group/PyTASER
Branch with paper.md (empty if default branch): paper
Version: 2.3.0
Editor: @jgostick
Reviewers: @obaica, @JosePizarro3
Archive: 10.5281/zenodo.10634762

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/dd7ab3c3c5f05568e19adc234fd5f931/status.svg)](https://joss.theoj.org/papers/dd7ab3c3c5f05568e19adc234fd5f931)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@obaica & @JosePizarro3, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jgostick know.

✨ 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 @JosePizarro3

📝 Checklist for @obaica

[editorialbot]

Hello humans, 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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=4.71 s (12.7 files/s, 88579.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             12              0              0         411553
Python                          10            393            422           2150
Jupyter Notebook                 3              0           1237            478
TeX                              1             17              0            241
YAML                             7             44             34            218
reStructuredText                 8            119            108            206
Markdown                         2             64              0            174
DOS Batch                        1              8              1             26
SVG                              1              0              1             16
JSON                            13              0              0             13
make                             1              4              7              9
TOML                             1              2              1              8
-------------------------------------------------------------------------------
SUM:                            60            651           1811         415092
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1720

[editorialbot]

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

OK DOIs

- 10.1021/cr900271s is OK
- 10.1016/j.cpc.2014.02.013 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1063/1.4812323 is OK
- 10.1098/rspa.1950.0018 is OK
- 10.1007/s11120-009-9454-y is OK
- 10.1021/acs.jpcc.5b01858 is OK
- 10.1021/acs.jpca.5b11567 is OK

MISSING DOIs

- 10.1038/s41578-022-00433-0 may be a valid DOI for title: Electronic defects in metal oxide photocatalysts
- 10.1021/acsenergylett.1c00380.s001 may be a valid DOI for title: Rapid recombination by cadmium vacancies in CdTe

INVALID DOIs

- None

[jgostick]

Hi All, the review process is now started. Please see the instructions in the top comment made by "edtitorialbot" for info. Basically you create your own checklist, then start going through the items. Have fun!

[editorialbot]

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

[JosePizarro3]

Review checklist for @JosePizarro3

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/WMD-group/PyTASER?
• 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 (@savya10) 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)?
• 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)?
• 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?

[obaica]

Review checklist for @obaica

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/WMD-group/PyTASER?
• 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 (@savya10) 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)?
• 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)?
• 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?

[obaica]

Hi @jgostick , I've finished my review. PyTASER is a well-designed and versatile tool that represents a significant advancement in the field of materials science, particularly in the study of transient (TAS) and differential (DAS) absorption spectroscopies. This software is capable of not only processing outputs from density functional theory (DFT) calculations but also utilizing data from the (legacy) Materials Project database. It can generate predictive TAS under various conditions, such as changes in temperature and carrier concentration. I highly recommend its publication in JOSS, as it will undoubtedly be a valuable asset to the scientific community.

For the authors @savya10 et al., some comments are listed below.

• Issue with conc Parameter in TAS Generation: When altering the conc parameter in tas = tg.generate_tas(energy_min=0, energy_max=7, temp=300, conc=1e21, cshift=1e-3) to values below 1e15, I noticed that the title in the plots generated by from pytaser.plotter import TASPlotter does not display conc in scientific notation. I recommend modifying the following section to format the output of conc more effectively:

        plt.title(
                    abs_label
                    + " spectrum of "
                    + formatted_material_name
                    + " at T = "
                    + str(self.temp)
                    + " K, n = "
                    + str(self.conc)
                    + " $cm^{-3}$",
                    fontsize=25,
                )

• Compatibility with New pymatgen Versions: In the PyTASER Materials Project Workflow example, it seems that with newer versions of pymatgen, from pymatgen.ext.matproj import TaskType should be replaced with from pymatgen.ext.matproj_legacy import TaskType for proper functionality.
• Enhanced Documentation on Band Contributions: I suggest the manual should include more comprehensive descriptions regarding the individual band-to-band transitions observed in the examples. Specifically, elucidating the meaning of labels for band pairs in the spectrum, such as the notation “(-1,2)、(0,1)”, would be highly beneficial for a non-specialist audience.
• Additional Examples for Customizable Plotting: Incorporating more examples on customizable plotting in the manual, such as settings for image size and output format, would undoubtedly enhance the practicality of the software.
• Inclusion of Experimental Data Comparison: Given that the goal of this library is to simulate spectra for comparison with and interpretation of experiments, adding examples and explanations that compare with experimental data would significantly increase the software's power, especially for a non-specialist audience.

Thank you for your patience as I took the time to thoroughly prepare this review.

[savya10]

Thank you @obaica for the insightful comments and suggestions, they are much appreciated! We will incorporate these into a new branch and pull it all together once @JosePizarro3 is also done with his review.

[jgostick]

Hi @JosePizarro3 how are things progressing with your review? I see you created your checklist already, so hopefully you've been playing with the package?

[JosePizarro3]

Hi @savya10 @jgostick

I chained conferences with vacations, everything before Christmas. You can see the gap in my Github contributions timeline 😄

Sadly, I didn't have time to play with the package. I also predicted this in my initial emails, and communicated that by (~mid) January you will have my review. Sorry I cannot give you a more satisfactory answer as of now, but I hope you understand 🙂

[JosePizarro3]

Hi @jgostick @savya10,

Thank you very much for the patience.

I finished my review, and I have to say that this software is very interesting. I pretty much agree with @obaica's comments. I would like to stress a bit more how cool is that PyTASER can recognize first principles outputs (so far VASP and MP, but who knows, maybe in the future some more electronic structure codes and other databases?) and generate TAS and DAS 🙂 I am a big fan of scientific softwares that are interoperable with different existing codes. Furthermore, it is very nice we can indeed pass different parameters as inputs, and even fix the DFT reported band gap to calculate these spectras.

I have some comments, feedback, and questions for the authors:

1. I think adding setuptools in the requirements.txt is an unsafe practice, as it might enter in conflict with other packages, most importantly, with pip. Maybe you want to check the installation.
2. Furthermore, I was not able to install the package using setup.py. I had some troubles with spglib if pip is not upgraded prior to the installation, but then later with ruamel.yaml. This last error I was not able to fix it easily. Maybe it is a problem of the machine I used for installing the package, but I am also puzzled on why installing with pip worked, while the setup.py didn't.
3. I think you can improve a bit on the documentation (specially on the introduction and where to give installation instructions), while also leaving out some larger changes for a future version. I felt some information was repeated in the welcoming and under the Information menu.
4. I think you could directly add the nice statement of need from the paper into the documentation.
5. Can you please add "dark" and "light" labels in Figure 1 of the paper? I think you could also add this figure also in the documentation page, as an introduction of the "dark" and "light" concepts and what an user can expect when outputting spectras.
6. pytaser/__init__.py contains a different __version__ than the package one. I would simply delete this, as it forces you to keep track of the version tag there, but like you prefer.
7. There are a couple of imports not being used in pytaser/plotter.py (gettext and collections). I am surprised neither black nor flake8 caught this. Did you consider to maybe use some linting checks on the github pipeline? If so, I would suggest ruff.
8. I like the testing, but on first sight it seems you are testing generator.py, tas.py and plotter.py. Maybe you can add some other tests for the other modules in a future version. I would also suggest you add some docstrings to the testing, so it is clear which methods is covering each one of them.
9. I think the order of the x axis in the plots is a bit confusing. This is because sometimes it is inverted and sometimes not, even thought the x axis might be using Energies or Wavelengths (see e.g., cells [5] and [10] on the DFT example). I would suggest to add the gca().invert_xaxis() as an input flag of get_plot(). If this is not specified, then the method should be able to handle the fact that Energies go from smaller to larger values, while Wavelengths from larger to smaller values.
10. Finally, I think you should leave more interactivity on the plotting of the spectra. I would say that cell [23] of the DFT example is a good case for this. Maybe it is a good idea to leverage how many contributions and how many lines you want to show for a given spectra. The colors and the lines should be also checked on this (see again the cell [23]).

Besides these, I think the code is very clean and nicely written, congratulations! 😄

[savya10]

Hi @JosePizarro3, thanks very much for the comprehensive review and nice feedback! We'll implement the helpful changes that both you and @obaica mentioned and will release an updated version soon.
Regarding leaving some more of the background/theory in the documentation, we will shortly be releasing a separate paper going into more detail about this, but will certainly add some more into the current docs if you believe it will help.

Thanks again, and happy new year to all! 😁

[jgostick]

Hi All, I see that the reviewers have checked all their boxes! So we can proceed with the review. Please accept my apologies for not moving this along sooner...I mis-interpreted the above comment to mean that @savya10 was going to implement some changes, but I see now that they were just peripheral items and not core to the review.

[jgostick]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[jgostick]

Hi @savya10, as you can see there are several more tasks for you to do. Could you please address those, and I will begin working on my part.

[jgostick]

@editorialbot generate pdf

[editorialbot]

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

[jgostick]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1021/cr900271s is OK
- 10.1016/j.cpc.2014.02.013 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1063/1.4812323 is OK
- 10.1098/rspa.1950.0018 is OK
- 10.1007/s11120-009-9454-y is OK
- 10.1021/acs.jpcc.5b01858 is OK
- 10.1021/acs.jpca.5b11567 is OK

MISSING DOIs

- 10.1038/s41578-022-00433-0 may be a valid DOI for title: Electronic defects in metal oxide photocatalysts
- 10.1021/acsenergylett.1c00380.s001 may be a valid DOI for title: Rapid recombination by cadmium vacancies in CdTe

INVALID DOIs

- None

[jgostick]

Hi @savya10, the editorialbot has suggested some DOIs for the citations that are missing some. Though it missed "Perovskite-147 inspired materials for photovoltaics and beyond—from design to devices". Please update the paper.md file.

[jgostick]

My checklist also suggests that I look for inconsistencies in the bibliography. Most things seem ok, but here are few suggestions:

• The reference to "On the quantization of the monoatomic ideal gas" is actually a translation of a Fermi paper correct? Would it be more correct to actually cite the original?
• The reference to "Dresselhaus, M. S. (2001)" is to lecture notes...is there a more generally available source for this material, or are these lecture notes considered "part of the literature" in the field?
• The capitalization of the article titles is not consistent. Most are in normal sentence case, but a few have each word capitalized.

[savya10]

Hi @jgostick thanks for this. Currently adding the updates according to the comments from both the reviewers, will let you know when done!

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[jgostick]

@editorialbot check references

[jgostick]

@editorialbot set 2.3.0 as version

[editorialbot]

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

OK DOIs

- 10.1021/cr900271s is OK
- 10.1016/j.cpc.2014.02.013 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1063/1.4812323 is OK
- 10.1098/rspa.1950.0018 is OK
- 10.1007/s11120-009-9454-y is OK
- 10.1021/acs.jpcc.5b01858 is OK
- 10.1021/acs.jpca.5b11567 is OK
- 10.1142/p276 is OK
- 10.1098/rspa.1926.0133 is OK
- 10.1088/1361-6528/abcf6d is OK
- 10.1038/s41578-022-00433-0 is OK
- 10.1021/acsenergylett.1c00380 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jgostick]

@editorialbot generate pdf

[savya10]

Hi @savya10 The author list on the zenodo archive and the one is the paper kinda match, but there are a lot of variations like "Youngwon" on the zenodo site and "Young Won" on the paper. Can update one or the other of these? Probably easier to update the paper?

Sure - will update the zenodo as I just remembered that Young Won is the correct way

[editorialbot]

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

[savya10]

Hi @savya10 The author list on the zenodo archive and the one is the paper kinda match, but there are a lot of variations like "Youngwon" on the zenodo site and "Young Won" on the paper. Can update one or the other of these? Probably easier to update the paper?

Sure - will update the zenodo as I just remembered that Young Won is the correct way

done!

[jgostick]

Some of the affiliations are different between the two, but this is because zenodo only reports the university, while the paper adds an extra layer of granularity and includes the faculty/department. I am just noting this for reference.

[jgostick]

@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

- 10.1021/cr900271s is OK
- 10.1016/j.cpc.2014.02.013 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1063/1.4812323 is OK
- 10.1098/rspa.1950.0018 is OK
- 10.1007/s11120-009-9454-y is OK
- 10.1021/acs.jpcc.5b01858 is OK
- 10.1021/acs.jpca.5b11567 is OK
- 10.1142/p276 is OK
- 10.1098/rspa.1926.0133 is OK
- 10.1088/1361-6528/abcf6d is OK
- 10.1038/s41578-022-00433-0 is OK
- 10.1021/acsenergylett.1c00380 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-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#4994, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot set 2.3.0 as version

[editorialbot]

Done! version is now 2.3.0

[Kevin-Mattheus-Moerman]

@savya10 as AEiC I will now assist in the final steps to process paper acceptance. I have checked the paper, the archive link, this review, and your repository. Most seems in order, I only have the below minor points which requires your attention (no new version/archive is needed):

Typos:

• Check spelling for receieved which should read received

[savya10]

Hi @Kevin-Mattheus-Moerman, this has been fixed now!

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@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: Aggarwal
  given-names: Savyasanchi
  orcid: "https://orcid.org/0009-0007-7128-3465"
- family-names: Kavanagh
  given-names: Seán R.
  orcid: "https://orcid.org/0000-0003-4577-9647"
- family-names: Woo
  given-names: Young Won
- family-names: Verga
  given-names: Lucas G.
  orcid: "https://orcid.org/0000-0002-7453-238X"
- family-names: Ganose
  given-names: Alex M.
  orcid: "https://orcid.org/0000-0002-4486-3321"
- family-names: Walsh
  given-names: Aron
  orcid: "https://orcid.org/0000-0001-5460-7033"
contact:
- family-names: Walsh
  given-names: Aron
  orcid: "https://orcid.org/0000-0001-5460-7033"
doi: 10.5281/zenodo.10634762
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Aggarwal
    given-names: Savyasanchi
    orcid: "https://orcid.org/0009-0007-7128-3465"
  - family-names: Kavanagh
    given-names: Seán R.
    orcid: "https://orcid.org/0000-0003-4577-9647"
  - family-names: Woo
    given-names: Young Won
  - family-names: Verga
    given-names: Lucas G.
    orcid: "https://orcid.org/0000-0002-7453-238X"
  - family-names: Ganose
    given-names: Alex M.
    orcid: "https://orcid.org/0000-0002-4486-3321"
  - family-names: Walsh
    given-names: Aron
    orcid: "https://orcid.org/0000-0001-5460-7033"
  date-published: 2024-02-14
  doi: 10.21105/joss.05999
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5999
  title: "PyTASER: Simulating transient absorption spectroscopy (TAS)
    for crystals from first principles"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05999"
  volume: 9
title: "PyTASER: Simulating transient absorption spectroscopy (TAS) for
  crystals from first principles"

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.05999 joss-papers#5011
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05999
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...

[Kevin-Mattheus-Moerman]

@savya10 congratulations on this JOSS publication!

Thanks for editing @jgostick!

And a special thank you to the reviewers: @obaica, @JosePizarro3 !!

[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.05999/status.svg)](https://doi.org/10.21105/joss.05999)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05999">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05999/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05999/status.svg
   :target: https://doi.org/10.21105/joss.05999

This is how it will look in your documentation:

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