(Although, I’m not sure how acceptable this would be for larger changes.) I wish I’d asked for this immediately! But ultimately in this case, the maintainer did fix the upstream source after not too much of a delay. It turns out it’s possible to ask to be added to a conda-forge feedstock, and if after a week the author hasn’t responded you can then make a patch to update the source. Open source contributors can hardly be expected to be on hand to patch these breaking changes as soon as they happen, but it did (for me) expose some vulnerabilities in this package architecture. However, there was about a six week author absence where the versions on conda and PyPI remained unpatched (breaking progressively more downstream pacakges). The author of HDBSCAN pretty quickly put a patch out, which was great. But I just managed to install it with Mamba thanks to your mamba command which is surpirsing as it rbase latest version seems to be 3. An incredible increase, and a reminder to use mamba for everything in the future! Fixing HDBSCAN Thanks a lot mate I had tried it with conda install it state such package does not exist as r-base maxed out at version r-base 3.6.1, shown above. Resolving, downloading and installing the environment now takes all of about two minutes, and is even cached so that subsequent pushes work in about 30s. This was in fact far simpler than the conda version I had previously (thanks mostly to better documentation of the shell option). uses: - name: Set up Python $ run: | python -m pip install -no-deps -ignore-installed. But times seemed to be getting longer again (especially on the CI, not sure why), and I think mamba actually remains fundamentally different to the conda solver.Īnyway, replacing conda with mamba in github actions turned out to be trivial: It worked really well and was much faster, but I’d since read that some of its techniques were being merged into conda, and in general I stopped having hugely long times while solving the environment. Even without the pin, environment resolution increased from about an hour to 3-4hrs, so the CI would only sometimes run.Ībout 4/5 years ago I’d tried using mamba as a replacement for conda.Solving a conda environment pinning joblib to 1.1 takes about 12 hours (□) to solve (longer than the 4 hour github limit). joblib v1.2 introduced a breaking security change which meant that hdbscan errored.However, in the past month two things happened: It’s been working pretty well and wasn’t too bad to set up, and integrates nicely into the pull requests. We moved from Azure to github actions to run the continuous integration tests in PopPUNK about a year ago.
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