{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2025/03/30/cdk2024-4.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/143wd-e3m51", "url": "https://chem-bla-ics.linkedchemistry.info/2025/03/30/cdk2024-4.html", "title": "cdk2024 #6: wrapping up already", "content_html": "

Tomorrow is already the last day of the NWO Open Science grant\nfor the Chemistry Development Kit. We are wrapping up, but I am happy we have a few weeks more\nto finish up the reporting. We held a user group meeting earlier this month (btw, check out the slides by Jonas),\nand I did a few more\nJUnit testing updates last week:

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Actually, you see one pull request here that I closed. I accidentally included a\ncircular dependency. Some core CDK functionality is hard to test with an implementation of the data model, but if that\nimplementation depends on the module you are testing, that won’t work (not in Maven anyway). But the good bits got included\nin the next pull request. One of the goals was to improve the code covered by the tests.

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This coverage testing has an imporant code maintenance purpose: it visualizes whih code is not checked. Sometimes\ncode is not tested that under normal conditions should have been (a bug) and sometimes it is handling a rare situation\nwhich you want tested too, to make sure that rare case does not get covered by the common code. Thus, the percentage\ncode covered by tests should be as high as is reasonable. The pull requests therefore aim to raise that percentage,\nsuch as for this pull request:

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Indeed, over the past 12 months, the coverage did improve, perhaps not as much as we liked, with 2.32 percent point\nto 64.96 percent:

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The CDK started routinely using unit testing somewhere in the zeroes, with home made continous integration\nas early as 2006,\nshared with the development community every night, thanks to Rajarshi Guha’s effort. We had our\nfirst code coverage results in the same year.\nAnd at some point we had sufficient coverage that it gave us the opportunity to routinely check\nthe impact of a patch.\nOf course, this is exactly what many open source projects do with GitHub Actions nowadays.

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Unfortunately, we also found that many of the CDK-using tools we worked on in this grant to get updated to\nuse a (more) recent CDK version do not have such solutions in place. That left us in several cases quite\nin the dark. More about that soon!

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References

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Schaub, J. (2025). Scaffolds, Functional Groups, Aglycones: Algorithmic Substructure Identification with CDK. Zenodo. https://doi.org/10.5281/ZENODO.15058009 [cito:citesAsRecommendedReading] CrossRef Scholia
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", "summary": "Tomorrow is already the last day of the NWO Open Science grant for the Chemistry Development Kit. We are wrapping up, but I am happy we have a few weeks more to finish up the reporting. We held a user group meeting earlier this month (btw, check out the slides by Jonas), and I did a few more JUnit testing updates last week:", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/cdk2024_junit.png", "date_published": "2025-03-30T00:00:00+00:00", "date_modified": "2025-04-20T00:00:00+00:00", "tags": ["cdk2024","cdk","junit"], "_references": [ { "url": "https://doi.org/10.5281/zenodo.15058009", "doi": "10.5281/zenodo.15058009" , "cito": [ "citesAsRecommendedReading" ] } ], "_funding": [{"award": { "title" : "The Chemistry Development Kit in 2024: improving cheminformatics research", "acronym" : "CDK2024", "uri" : "drc.filenumber:osf232097" }, "funder": { "name": "Dutch Research Council", "ror": "04jsz6e67" } }], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }