Post-acceptance TODOs for PyGMT paper

[seisman]

🎆 The good news is that the PyGMT paper is accepted in G-cubed and will be published in a few weeks. This PR tracks the remaining post-acceptance tasks and follow-up work.

Feel free to make edits and add more related tasks

Before proof

• Get the paper DOI from G-cubed 10.1029/2026GC013105

• Update CITATION.cff with final journal reference Add the citation information of the PyGMT paper to CITATION.cff and README.md #4713

• Update README citation block (preferred citation + DOI + Zenodo + journal link) Add the citation information of the PyGMT paper to CITATION.cff and README.md #4713

• Update Zenodo metadata to link to final journal version of record. [Done in the v0.18.0 record]
  

• Finalize scripts in the pygmt-paper-figure repository

• Confirm all manuscript scripts run correctly with v0.19.0 (no dev version dependencies)

• Verify all figures are fully reproducible from clean environment (fresh install test)

• Archive pygmt-paper-figure on Zenodo and obtain DOI

• For the pygmt-paper-figure archive, decide whether to cite: Zenodo concept DOI, or version-specific DOI [I think we should use the concept DOI 10.5281/zenodo.19412361, which is more stable, and allows us to do minor tweaks even after the paper is published]

• Release v0.19.0 (Release PyGMT v0.19.0 #4649)

During proof

• Fix ruff to Ruff Fix package names ruff->Ruff and ghostscript->Ghostscript #4682
• In “Availability Statement”, cite PyGMT v0.19.0 (not dev or RC version)
• In "Acknowledgments", add codespell and typos used for finding common misspellings [maybe not, because they're not the de-facto standard tool for correcting typos and we may drop one of them and even switch to other tools shortly]
• Ensure all URLs (Zenodo, GitHub, documentation) are up to date and resolvable
• If possible / allowed: Update the PyGMT logo in Figure 2 to the final version (in case there were changes since the revision)
• If possible / allowed: Update the GitHub starts data in Figure 7 (have to check how much has changed since the revision) [7 more stars for GMT, 3 for PyGMT, and 3 for GMT.jl. I don't think it's worth the time to update Fig. 7]
• Double check that affiliations, names and ORCIDs are correct and consistent; especially the one of Joaquim
• In "Acknowledgments" (or somewhere else, should check the G3 guidelines), some statement regarding (not) using AI / ML tools?

Post-publication

• Announce paper in What we need for a first PyGMT paper? #677 and close the issue
• Announce paper on the GMT Forum
• Announce paper on the GMT website Add the PyGMT paper website#165
• Add paper to ResearchGate: Already done by G-Cubed, https://www.researchgate.net/publication/409962284_PyGMT_Bridging_Python_and_the_Generic_Mapping_Tools_for_Geospatial_Visualization_and_Analysis
• Add PyGMT Ecosystem figure (Fig. 2 in the paper) to the PyGMT Ecosystem page [Check licensing/reuse policy OR regenerate a version if needed] Add the PyGMT ecosystem image to the Ecosystem page #4728

[seisman]

I've received the paper DOI 10.1029/2026GC013105 from G-Cubed. Of course, it is not resolvable yet.

I manually added the paper information to Zotero, and the exported BibTeX entry is:

@article{Tian_Froehlich_Leong_Grund_Schlitzer_Jones_Uieda_Luis_2026,
  title   = {PyGMT: Bridging Python and the Generic Mapping Tools for Geospatial Visualization and Analysis},
  journal = {Geochemistry, Geophysics, Geosystems},
  volume  = {27},
  number  = {XX},
  pages   = {e2026GC013105},
  year    = {2026},
  publisher = {American Geophysical Union},
  doi     = {10.1029/2026GC013105},
  author  = {Tian, Dongdong and Fr{\"o}hlich, Yvonne and Leong, Wei Ji and Grund, Michael and Schlitzer, William and Jones, Max and Uieda, Leonardo and Luis, Joaquim F.}
}

And the citation in AGU style is:

Tian, D., Fröhlich, Y., Leong, W. J., Grund, M., Schlitzer, W., Jones, M., et al. (2026). PyGMT: Bridging Python and the Generic Mapping Tools for Geospatial Visualization and Analysis. Geochemistry, Geophysics, Geosystems, 27(XX), e2026GC013105. https://doi.org/10.1029/2026GC013105

A few notes:

• The volume is 27 for the year 2026 (see: https://agupubs.onlinelibrary.wiley.com/loi/15252027).
• The issue number is not known yet, but it's likely 7 if published online in July. It seems the AGU citation tool often omit it even when available (e.g., visit https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2025GC012743 and click "Cite"), so we can likely drop it too.
• The manuscript number is the DOI with the prefix e, i.e., e2026GC013105.
• The AGU/Zotero citation style typically lists only the first few authors, but I think we should include all authors for completeness, i.e.,

Tian, D., Fröhlich, Y., Leong, W. J., Grund, M., Schlitzer, W., Jones, M., Uieda, L., Luis, J. F. (2026). PyGMT: Bridging Python and the Generic Mapping Tools for Geospatial Visualization and Analysis. Geochemistry, Geophysics, Geosystems, 27, e2026GC013105. https://doi.org/10.1029/2026GC013105

Since we now have the citation information, I think we can include it in the PyGMT v0.19.0 release, even though the DOI may not be resolvable at the time of the release.

[seisman]

Here is my planned timeline based on the current estimated publication schedule.

• July 4 (Saturday): Merge PRs Implement Figure.pygmtlogo for the PyGMT logo #4616, DOC: Add PyGMT logo to README & docs #3845, Reformat the CITATION.cff file using cffinit #4712, and Add the citation information of the PyGMT paper to CITATION.cff and README.md #4713, and finalize PR Changelog entry for v0.19.0 #4709 so that PyGMT v0.19.0 is release-ready and can be published within a few minutes.
• July 5 (Sunday): Verify that all scripts in the pygmt-paper-figures repository run successfully with the pygmt main branch (the upcoming v0.19.0).
• Before receiving the proofs (estimated July 5–12): The proofs may arrive within the next one to two weeks. During this waiting period, we can continue improving the documentation and, if needed, tweak the logo design or other non-essential changes.
• When the proofs arrive (July 7): We will likely have only 2–3 working days to return the corrected proofs. At that point we should:
  • Release PyGMT v0.19.0 (<1 hour)
  • Perform one final verification of pygmt-paper-figures (~30 minutes)
  • Archive pygmt-paper-figures on Zenodo and update the manuscript with the final DOI (~30 minutes)
  • Complete the proof review and submit the corrections
• After submitting the corrected proofs (July 9): Complete the remaining post-release tasks.
• When the paper is published online (estimated July 20): Announce PyGMT v0.19.0 together with the paper.

[seisman]

Hi @GenericMappingTools/pygmt-maintainers, I have received the proofreading and ideally will return it within 48 hours. Plan to do the release in 24 hours.

[yvonnefroehlich]

Hi @GenericMappingTools/pygmt-maintainers, I have received the proofreading and ideally will return it within 48 hours. Plan to do the release in 24 hours.

I will have a look at the proofs this evening / night.

[yvonnefroehlich]

Verify all figures are fully reproducible from clean environment (fresh install test)

Looks good to me.

---

Only one aspect (not sure if this is an issue on my side or I missed something): In Figure 1, the transparency for the text seems only to work for PDF but not for PNG. For Figure 4, this issue does not occur. I created a new enviroment based on the provided ymal. file. I tested ghostscript versions 10.07.1 and 10.06.0.

PDF: PyGMT_map.pdf
PNG:

In the example below the transparency for fill works for PNG and PDF, but the transparency for font is only included in the PDF.

fig = pygmt.Figure()
fig.basemap(region=[-1, 1, -1, 1], projection="X5c/2c", frame="+gp8")
fig.text(x=0, y=0, text="Text Text Text", font="30p,1,red@50", fill="cyan@30")
fig.show()
fig.savefig("text_transparency.png")  # transparency for font not included in saved PNG
fig.savefig("text_transparency.pdf") 

PDF: text_transparency.pdf
PNG:

[seisman]

I can't reproduce the issue, but I'm using macOS.

[yvonnefroehlich]

I can't reproduce the issue, but I'm using macOS.

Good to know. It seems OS-dependent as I do not have this issue when creating the figure using Linux via the Windows Subsystem for Linux (WSL).

[seisman]

@GenericMappingTools/pygmt-maintainers The paper is published.

[yvonnefroehlich]

@GenericMappingTools/pygmt-maintainers The paper is published.

Great news 🥳! A big thanks to the whole team, especially Dongdong for pushing this forwardt. Really cool to see the paper finally being published. I have to finish an application until to night. But then I should have more time for helping with the release notes and posting announcements etc.

[seisman]

ChatGPT helped me draft the v0.19.0 release announcement at https://hackmd.io/xgfUvmc4TMW-fOGMoi_IbQ.

After looking it over, I realized the announcement is already quite long, so it might be better to announce the PyGMT paper in a separate thread, similar to https://forum.generic-mapping-tools.org/t/the-generic-mapping-tools-and-animations-for-the-masses-by-wessel-esteban-delaviel-anger/4747.

I'm assigning the task to @yvonnefroehlich, but let me know if you don't have time.

[yvonnefroehlich]

After looking it over, I realized the announcement is already quite long, so it might be better to announce the PyGMT paper in a separate thread, similar to https://forum.generic-mapping-tools.org/t/the-generic-mapping-tools-and-animations-for-the-masses-by-wessel-esteban-delaviel-anger/4747.

Besides this, I think it's fair to announce the paper separately to increase the visibility 🙂.

I'm assigning the task to @yvonnefroehlich, but let me know if you don't have time.

Yes, I can do this.
Edit: Done at https://forum.generic-mapping-tools.org/t/pygmt-paper-pygmt-bridging-python-and-the-generic-mapping-tools-for-geospatial-visualization-and-analysis-published-in-g-cubed/6460

As the paper is already uploaded on ResearchGate by G-Cubed (please see https://www.researchgate.net/publication/409962284_PyGMT_Bridging_Python_and_the_Generic_Mapping_Tools_for_Geospatial_Visualization_and_Analysis) I would start with the paper announcement on the forum, then do the announcement of v0.19.0 and upload it to ResearchGate. But should not wait too long as v0.19.0 is needed to run the JNs provided along with the paper.

Maybe we can wait a few days for any bugs reported by users and then decide if we do a patch or minor release regarding the fix of the BibTex entry for the PyGMT paper (see PR #4727).