ReScience challenge: resurrecting a 30-year-old Turbo Pascal program for generating Maucha ionic diagrams

[MikeSilberbauer]

Original article: Silberbauer, M.J. and King, J.M., 1991. Geographical Trends in the Water Chemistry of Wetlands in the South-Western Cape Province, South Africa. Southern African Journal of Aquatic Sciences, 17 (1/2), 82–88. PDF URL: Silberbauer-2020.pdf Metadata URL: http://www.riv.co.za/wv/data/Silberbauer-2020.yaml Code URL: https://archive.softwareheritage.org/browse/origin/https://github.com/MikeSilberbauer/maucha-ionic-diagram.git/ Scientific domain: Aquatic Science Programming language: Turbo Pascal Suggested editor:

[rougier]

@MikeSilberbauer Thansk for your submission! Before we can proceed with the actual review, would it be possible to use the ReScience template for your submission? Also, After a quick read of your submission, it does not seem to have any figure showing actual results (both old and new) but only a link to some (really nice) vintage screenshots. I think you should add them to your submission (we have no limit page) since the provided link may dissappear in the future.

@karthik @ThomasA Could you edit this submission for the Ten Years Reproducibility Challenge (only 1 reviewer needed) ?

[MikeSilberbauer]

Sorry about the delay in reacting. I have not used github much and I did not notice that in the settings my primary email for notifications was my old work address, which was blocked when I retired at the end of January. Thank you for the positive response - I will try to work out how to use the template.

[MikeSilberbauer]

@rougier ReScience_C_Silberbauer_2020_5d.pdf With much assistance from Overleaf, I have converted the draft to LaTex and then PDF. I have not yet mastered the citation functions, but the document should now be in a state where it is reviewable.

[rougier]

@khinsen @pdebuyl Can you handle this submission for the Ten Years Reproducibility Challenge (only 1 reviewer needed)?

[rougier]

@ReScience/associate-editors (kind of urgent) Can any of you handle this submission for the Ten Years Reproducibility Challenge (only 1 reviewer needed)?

[oliviaguest]

I can try, yes, but it's far out of my area. Maybe if somebody can suggest reviewers?

[rougier]

Thanks. And in fact, I can probably review it. I've started reading the paper and it is quite fun!

[oliviaguest]

Fantastic! 💯

[rougier]

Here is my review:

The paper is both fun and instructive to read. I like the author's sense of humor. I think it needs only a few minor modifications that I list here in no particular order:

• Please use section* instead of subsection for top levels section (* is for removing the section / subsection number)
• Since the source is not very long, you should include the source of the program in the article and give as well the link to software heritage inside the article.
• I would be curious to know a bit more about where the source were located on your hard-drive because they are almost 30 years old. I'm probably a bit younger but I'm sure I've already lost most of the files I've created only 20 years ago.
• You could comment a bit on the source. Do you still understand what you were coding at that time ? For example, what are these "magic numbers" on lines 77-82 ?
• In your repository, you should add the CHEMDATA.DAT file, else people won't be able to run it.
• How did you find the original price of the turbo pascal compiler ?
• I would be nice to have a conclusion with your overall feeling about this successful reproduction
• Metadata will need some modification
• In the README of https://github.com/MikeSilberbauer/maucha-ionic-diagram, you could probably add a few more explanation and a link to this review and to the article once published.
• Note that I did not try to run the code.

This submission of the oldest reproduction for the Ten Years Reproducibility Challenge (almost 30 years) and it seems that the author did not encounter any problem for running the code. That's funny because some of the more recent submissions had some problems.

[MikeSilberbauer]

ReScience_C_Silberbauer_2020 (7).pdf

Thank you for your constructive comments. I have tried to deal with them in the updated PDF document. I have not yet edited the metadata, as I am not sure about the Software Heritage link.

[rougier]

For the software heritage link, it's mostly a matter of visiting https://archive.softwareheritage.org/save/ and you have to enter the address of your github repository and you're done. You should then obtain your swid

[MikeSilberbauer]

Original article: Silberbauer, M.J. and King, J.M., 1991. Geographical Trends in the Water Chemistry of Wetlands in the South-Western Cape Province, South Africa. Southern African Journal of Aquatic Sciences, 17 (1/2), 82–88. PDF URL: Silberbauer-2020.pdf Metadata URL: http://www.riv.co.za/wv/data/Silberbauer-2020.yaml Code URL: https://github.com/MikeSilberbauer/maucha-ionic-diagram Scientific domain: Aquatic Science Programming language: Turbo Pascal Suggested editor: Nicolas P. Rougier

[rougier]

@MikeSilberbauer Not sure about the meaning of your post actually.

[MikeSilberbauer]

Sorry, I gave too much information - I wanted to inform you that the Metadata file at http://www.riv.co.za/wv/data/Silberbauer-2020.yaml now contains the Software Heritage ID for the Pascal program. The file at https://github.com/ReScience/submissions/files/4832693/ReScience_C_Silberbauer_2020.7.pdf contains the edits that I made in response to your review. I am not sure what the next step in the process is.

[rougier]

Now I get it! I'm satistified with the correction and figure 5 is just fantastic ! @oliviaguest I'm satisfied with the correction and recommend acceptation.

Minor typo at the top abot the title, it should read "Reproduction in Zoology" (Zoology?)

[MikeSilberbauer]

ReScience_C_Silberbauer_2020 (9).pdf

Thank you!

I have fixed a problem with the last pages in the Appendix, which had lost subsubheading floating around.

I am probably being a bit dim, but I have not been able to work out what part of the submission you are referring to regarding the "minor typo at the top" about the title. If this helps: the subject area is "Aquatic science" or "Limnology" or even "Water chemistry". So "Reproduction in Limnology". (?)

[rougier]

I meant the text just above the title that is generated automatically from the metadata. The type of work is "Reproduction" and for the domain you indicated "Aquatic Science" such that the heading should red "Reproduction in Aquatic Science"

[MikeSilberbauer]

ReScience_C_Silberbauer_2020 (10).pdf OK, thank you for the explanation, now I understand. I had not entered all the required information into metadata.tex before compiling in Overleaf.

[rougier]

@oliviaguest I think we're good for publication!

[oliviaguest]

Fantastic!

[oliviaguest]

@rougier naive question I should know the answer to but are references like [1] meant to be clickable and then scroll to 1 in the reference list in the PDF?

[MikeSilberbauer]

The references probably are meant to work like that, but I couldn't find out how to get the bibliography to work automatically in the Overleaf editor, so I must confess that I hard-coded it. I can try to figure it out or manually insert cross-references if necessary.

[oliviaguest]

@rougier do you know how to address this? I think maybe giving a clear way to do it for overleaf might be a bit too much but surely a way to do it step-by-step is somewhere already, right? In the README? Have you tried that @MikeSilberbauer?

[MikeSilberbauer]

I will read the Overleaf instructions again and try to find out what I am missing.

[MikeSilberbauer]

It was as simple as putting this in the right place: \addbibresource{bibliography.bib}

ReScience_C_Silberbauer_2020 (11).pdf

[oliviaguest]

@MikeSilberbauer in order to run:

./process.py --sandbox --metadata metadata.yaml --pdf article.pdf

I need your metadata and the ability to compile the PDF — can you link me to the repo for your article, please? Alternatively, you can do all the steps yourself if you prefer and just involve me at the very end, I think? Is that right, @rougier? See: https://github.com/ReScience/articles/blob/master/README.md

[MikeSilberbauer]

@oliviaguest All the files for compiling the PDF are on Overleaf at this link: https://www.overleaf.com/5771591391kxmhgdrygdzw I hope that helps?

[oliviaguest]

Fab — thank you. I might push some minor changes and recompile, if that's OK. ☺️

[MikeSilberbauer]

Yes, please do: I am very much a beginner with LaTeX and Github.

[oliviaguest]

Yeah, don't worry I'm struggling just as much with the new way of doing things! 🤣

[oliviaguest]

@rougier I am trying to compile the PDF, but get:

(base) MBpro:5e9eb999ec43100001b5cbca olivia$ make
./yaml-to-latex.py -i metadata.yaml -o metadata.tex
make: ./yaml-to-latex.py: Permission denied
make: *** [metadata.tex] Error 1

What am I doing wrong?

[rougier]

chmod 755 yaml-to-latex.py maybe?

[oliviaguest]

Oh, ha! Thanks, @rougier. What do we put for the 2nd reviewer? Leave it blank, right?

[rougier]

Yes. If blank, it should not appear in the PDF.

[oliviaguest]

Is this OK, @rougier?

[oliviaguest]

Also hmm... the references are not looking correct either, right? 🤔

[rougier]

References are wrong yes. And why do I get a n°2. Is my name listed as first or second reviewer in the metadata ?

[MikeSilberbauer]

If I understood what I was doing, the files that I edited in Overleaf have just been updated in https://github.com/MikeSilberbauer/Silberbauer-2020, in case that helps.

[oliviaguest]

@rougier @MikeSilberbauer Thank you both for the feedback/comments. Lemme try again...!

[oliviaguest]

@MikeSilberbauer can you make the repo you linked to public, please? The link 404s, so I assume it's private?

[MikeSilberbauer]

@oliviaguest - it should be accessible to you now, if I have read the manual correctly...

[oliviaguest]

@MikeSilberbauer can you add @rougier too, please? I have pushed these two files and I want to make sure they look right as the reviewer issue is not resolved @rougier. Do these files look right?

https://github.com/MikeSilberbauer/Silberbauer-2020/blob/master/article.pdf

https://github.com/MikeSilberbauer/Silberbauer-2020/blob/master/metadata.yaml

[MikeSilberbauer]

OK, @rougier is added

[oliviaguest]

@MikeSilberbauer please don't feel this is your fault BTW — I suck at this! 🤣

[MikeSilberbauer]

Not at all - I appreciate all the assistance. I used to wonder what Github was all about, so having to jump in at the deep end is one way of learning.

[rougier]

• In the metadata, type should be Reproduction (not Replication, the commented list is actually missing "* Reproduction")
• Title should be "[Rp] Geographical Trends in the Water Chemistry of Wetlands in the South-Western Cape Province, South Africa." (not "Re ReScience challenge: resurrecting a 30-year-old Turbo Pascal program for generating Maucha ionic diagrams")
• For the reviewer 2, something wrong. Maybe @MikeSilberbauer needs to use the latest ReScience template. Have a look at at this entry for what it is supposed to look like

[MikeSilberbauer]

@rougier Your article is most fascinating, and I was impressed that your program could be loaded onto the online Apple emulator. The scanned pages from the original computer magazine remind me of the publication style of the day - I laboriously typed a couple of Fortran 7 program listings from journals onto the old corporate mainframe computer to see what they could do. There was an Apple ][ that acted as a process controller for a scintillation counter, but we junior staff were not allowed near it.

Regarding the version of the template that I used, could you please remind me of the correct link so that I can make sure?

[rougier]

Thanks :) Here is the link, hopefully, the "Reviewer 2" will disappear. Else, I'll need to investigate here the "2" comes from.

[MikeSilberbauer]

@oliviaguest - I have modified metadata.yaml and manually edited metadata.txt on https://github.com/MikeSilberbauer/Silberbauer-2020/: https://github.com/MikeSilberbauer/Silberbauer-2020/blob/master/metadata.tex In Overleaf, the notes in the left margin of the PDF file look better - I have placed a copy of the output from Overleaf here: https://github.com/MikeSilberbauer/Silberbauer-2020/blob/master/ReScience_C_Silberbauer_2020.pdf

[rougier]

Looks good to me no. @oliviaguest will give you issue number and DOI.