Show external usage on RSD

[jvdzwaan]

To show impact of the template, it would be nice if we could link to external software for which the template was used. Maybe we can stimulate external users to report usage and/or have an automated process that does this.

[jspaaks]

You can already do this by adding external software as a Web Page. Set the title to something that is useful for the RSD frontend, like I have done here: https://www.zotero.org/groups/1689348/netherlands_escience_center/items/itemKey/XYUL4J3A

Regarding the second part of the issue, i.e. stimulating external users for reporting: I'm not holding my breath for that one, since we can't even manage to do this within our own organization; see your experience with asking through email. At the same time it can't hurt so why the heck shouldn't we ask users to report their usage of le template. You've found one through googling the credit line, didn't you?

Other places that may be helpful:

1. GitHub forks
2. dependents page (https://github.com/NLeSC/python-template/network/dependents). I once found a copy of cffconvert there that had been cloned and pushed as opposed to forked, https://github.com/citation-file-format/cff-converter-python/network/dependents

Finally, maybe you could get a more complete impression of who is using the software by ending the cookiecutter question with something like:

Would you allow cookiecutter to ping the developers?
Doing so helps justify our continued involvement in maintaining the template. Y/n

[jspaaks]

BTW I found a bunch more users through github search: https://github.com/search?p=2&q=nlesc+cookiecutter&type=Code

Might be worth considering adding a random string to, say, the setup.cfg file and then search for that string, so the search results are not as cluttered with unrelated stuff.

[jvdzwaan]

Thanks for the suggestions, Jurriaan!

I had a look at the github search results, and most of them are demo projects or not very active projects. This raises the question when projects should be added/how active projects should be. I guess having a release on PyPI is a good start.

I like having a random string in e.g. setup.cfg better than asking users whether we can ping them... Although the search string puts the burden on us, and a ping pro-actively informs us.

BTW, what do you mean with ping, send an email using a gmail address, or did you have something else in mind?

[jspaaks]

Not sure if it is feasible, but I was thinking of having cookiecutter "call home" so to speak during install && with permission of whoever is installing. Note that requires us to set up some kind of server for it to connect to, but maybe we can piggyback on some other service we have running.

[jvdzwaan]

Yes, that's why I was suggesting gmail, we wouldn't have to set up that ourselves. There is the matter of the password, of course...

I was also thinking of raising this issue with the cookiecutter people. I'm sure other people would be interested in getting usage statistics. Surprisingly, I was unable to find an issue about it...

[fdiblen]

on RSD

• [x] Add relation between the tools GT created and this template https://www.research-software.nl/software/nlesc-python-template
• [x] send email to NLeSC engineers to relate their python packages with this template

[jspaaks]

https://github.com/citation-file-format/pycff

[eriktks]

Lists of repositories using this Python template on 13 April 2021 based on searching Github: https://github.com/search?p=2&q=nlesc+cookiecutter&type=Code (the search finds several other irrelevant pages). Lists expanded on 4 May 2021 with ten more repositories from among others https://github.com/search?p=6&q=%22Relevant+section+in+the+guide%22&type=Code

External (unknown project or owner)

1. https://github.com/arredondo23/workshop_pypkg
2. https://github.com/bstienen/particlefilter
3. https://github.com/cory-imel/veracode-results-parser
4. https://github.com/davislf2/Spark101
5. https://github.com/FAIR-data-for-CAPACITY/CAPACITY-mapping
6. https://github.com/GO-Eratosthenes/start-code
7. https://github.com/JesseKerkvliet/workshop_reproducibility_local
8. https://github.com/quanpan302/template/tree/master/Python/NLeSC
9. https://github.com/rajkumar-d83/nse_project
10. https://github.com/sunxb05/aichem
11. https://github.com/thehyve/python_transmart_loader

Internal (eScience project or owner)

1. https://github.com/CARRIER-project/vantage6-algorithms
2. https://github.com/ci-for-research/zenodo
3. https://github.com/citation-file-format/pycff
4. https://github.com/DeepRank/deeprank
5. https://github.com/DeepRank/pdb2sql
6. https://github.com/egpbos/egp
7. https://github.com/eWaterCycle/ewatercycle
8. https://github.com/fair-data/fairdatapoint
9. https://github.com/fair-data/fairdatapoint-client
10. https://github.com/fair-software/fairtally
11. https://github.com/fair-software/howfairis
12. https://github.com/fair-workflows/DemoFlask
13. https://github.com/fdiblen/simit
14. https://github.com/FEDMix/fedmix-backend
15. https://github.com/FEDMix/fedmix-viewer
16. https://github.com/Filter-Bubble/stance_finder
17. https://github.com/Filter-Bubble/stanza_wrapper
18. https://github.com/geek-yang/META
19. https://github.com/GO-Eratosthenes/image_retrieval
20. https://github.com/hpgem/nanomesh
21. https://github.com/iomega/spec2vec
22. https://github.com/jspaaks/test
23. https://github.com/matchms/matchms
24. https://github.com/NLeSC/dask-cassandra-loader
25. https://github.com/NLeSC-GO-common-infrastructure/dcachefs
26. https://github.com/NLeSC-GO-common-infrastructure/stac2dcache
27. https://github.com/NLESC-JCER/pyspectra
28. https://github.com/NLESC-JCER/pyZacros
29. https://github.com/NLESC-JCER/refac
30. https://github.com/nlesc-nano/ceiba
31. https://github.com/nlesc-nano/ceiba-cli
32. https://github.com/nlesc-nano/flamingo
33. https://github.com/nlesc-nano/insilico-database
34. https://github.com/nlesc-nano/Tutorials
35. https://github.com/online-behaviour/machine-learning
36. https://github.com/parallelwindfarms/byteparsing
37. https://github.com/phenology/cgc
38. https://github.com/puregome/notebooks
39. https://github.com/sequgen/sequgen
40. https://github.com/sundial-pointcloud-geometry/ectopylasm
41. https://github.com/sverhoeven/justatest
42. https://github.com/TICCLAT/ticclat
43. https://github.com/twinl/location
44. https://github.com/votca/PyVOTCA

[fdiblen]

Some extra repos from @CunliangGeng :

https://github.com/DeepRank/deeprank https://github.com/DeepRank/pdb2sql https://github.com/fair-data/fairdatapoint https://github.com/fair-data/fairdatapoint-client

[fdiblen]

BTW I found a bunch more users through github search: https://github.com/search?p=2&q=nlesc+cookiecutter&type=Code

Might be worth considering adding a random string to, say, the setup.cfg file and then search for that string, so the search results are not as cluttered with unrelated stuff.

I think this is a very good idea to see how many packages are using the template.

[eriktks]

Note: the strings that I searched for to compile a list of repositories that used the Python template (cookiecutter and NLeSC) were added to the template on 3 Sep 2018. There are probably several older uses of the template that do not contain these strings.

[egpbos]

Unfortunately it's not possible to filter code by date yet on GitHub, which makes the process of updating this list quite cumbersome. I found a few new (and old) ones nevertheless with @eriktks's search term (https://github.com/search?p=6&q=%22Relevant+section+in+the+guide%22&type=Code):

External

1. https://github.com/OpenDA-Association/pyopenda

Internal

1. https://github.com/eriktks/find-journalists
2. https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing
3. https://github.com/AI4S2S/s2spy
4. https://github.com/dianna-ai/dianna
5. https://github.com/dianna-ai/distance_explainer
6. https://github.com/EDG-Acoustics/edg-acoustics
7. https://github.com/Filter-Bubble/e2e_wrapper
8. https://github.com/AI4S2S/lilio
9. https://github.com/NPLinker/nplinker
10. https://github.com/LAHTeR/htr-quality-classifier
11. https://github.com/point-cloud-radar/bird-cloud-gnn
12. https://github.com/eWaterCycle/pywflow
13. https://github.com/aiproteomics/aiproteomics
14. https://github.com/SDCCA/quafing
15. https://github.com/FAIR-data-for-CAPACITY/ZIB-uploader
16. https://github.com/mapping-gait-ai/gait-mapper
17. https://github.com/NLESC-JCER/roquefort

[LourensVeen]

Also (albeit a long time ago)

• https://github.com/multiscale/ymmsl-python
• https://github.com/md-studio/cerulean
• https://github.com/yatiml/yatiml

Cerise seems to predate the template, and I think MUSCLE3 took some stuff from my other template-based repos but wasn't instantiated from the template directly. It's a mixed Python/C++/Fortran project anyway.

[bvreede]

Another internal package: https://github.com/elpaco-escience/scikit-talk