micromamba support for chem_data

[jonathanking-absci]

To install the chem_data, it is suggested to do conda install <chem_data package>. This command doesn't work with micromamba. I see that chem_data is generated from other repos like https://gitlab.com/phenix_project/chem_data. Do you have any advice on how I might install chem_data for the latest version of this repo using micromamba? Thank you.

micromamba install ./chem_data-2025.4-pyh66f2a00_0.conda
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
file:///home/test/linux-64 (check z.. Checked  0.0s
file:///home/test/noarch (check zst)  Checked  0.0s
file:///home/test/linux-64             ??.?MB @  ??.?MB/s 0 failed  0.0s
critical libmamba Multiple errors occured:
    Download error (37) Couldn't read a file:// file [file:///home/test/noarch/repodata.json]
    Couldn't open file /home/test/noarch/repodata.json
    Subdir file:///home/test/noarch not loaded!

[dwpaley]

I can't seem to reproduce your issue after following these steps (note copied from history after some false starts, so I hope I didn't miss anything.):

wget https://github.com/mamba-org/micromamba-releases/releases/download/2.1.1-0/micromamba-linux-64
chmod +x micromamba-linux-64
mkdir micromamba
mv micromamba-linux-64 micromamba/micromamba
eval "$(micromamba/micromamba shell hook --shell bash)"
micromamba create -p $PWD/cctbx -c conda-forge cctbx-base
wget https://github.com/cctbx/cctbx_project/releases/download/v2025.4/chem_data-2025.4-pyh66f2a00_0.conda
micromamba install ./chem_data/chem_data-2025.4-pyh66f2a00_0.conda

The chem-data installation is taking at least ~15 min to extract, but definitely no repodata.json error. If these steps don't help, could you share a more detailed reproducer?

Edit: if I insert export MAMBA_ROOT_PREFIX=$PWD/micromamba before the final step, (where $PWD is inside /dev/shm,) then the installation runs quickly and appears to work fine.

[bkpoon]

Also try downloading the chem_data package again. If there is an issue with the downloaded file, it will not work. For the next release, I can try putting SHA256 checksums for the files.

[bkpoon]

I updated the 2025.4 release page with the checksums

513fae67333f89794f0875d31a64b6394e9e456b954dff2baedde931c22a46a4  chem_data-2025.4-pyh66f2a00_0.conda
bf6e27315f6860e42574aaa46d99438b6a831b6a85668de628279e169148bac4  cctbx-2025.4.tar.gz