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For first RC release

  • Change topology-biopolymer-refactor to main
    • Update GH settings to make main default
    • Update PRs to topology-biopolyer-refactor to point to main
  • Change master to 0-10-x
    • Update PRs to master to point to 0-10-x
  • Make RC tag on openff-toolkit
  • Make RC tag on openff-interchange
  • Make openff-toolkit package on rc channel WITHOUT interchange
    • Update deps, but don’t add interchange
    • Remove create_openmm_system line in conda-forge builds
    • Make conda package
  • make openff-interchange package on rc channel
    • Update deps to pin to openff-toolkit 0.11.0rc1,
    • Update channel_sources to include conda-forge/label/openff-toolkit-rc
  • Make openff-toolkit package on rc channel WITH interchange
    • Add interchange to openff-toolkit-base recipe
    • Add openff-interchange to openff-toolkit deps, NOT openff-toolkit-base
    • Update channel_sources to include conda-forge/label/openff-interchange-rc
    • Re-enable create_openmm_system test
  • Update alpha notebook to use conda package (and anywhere else)
  • Make code changes
    • Make missing interchange error not imply that interchange is “Optional”
    • OE PDB → lots of stereochemistry warnings
    • OE atom indices in written PDB are all 0
    • OE bfactors are lost
    • Insertion code handling
    • Fix from_polymer_pdb docstring (metadata goes into atom.metadata)
    • RDKit PDB writing misformats things somehow (run pre alpha notebook and try to visualize)
  • Make new tag for Toolkit and interchange if needed
  • Make new conda packages
    • Don’t strict-pin the other package
  • Announce RC period

We’ve begin the 1-month release candidate period for the 0.11.0 OpenFF Toolkit release, with support for biopolymers! To try out the release candidate, run

conda create -n offtk-0-11-0-rc -c conda-forge/label/openff-toolkit_rc -c conda-forge/label/openff-interchange-rc -c conda-forge openff-toolkit

Note a few cool things:

  • Now we can load proteins - Molecule.from_polymer_pdb('path_to_pdb') - These proteins need to have explicit hydrogens and no missing atoms. More info here: (FROM POLYMER PDB docs)

  • Imports are easier - from openff.toolkit.typing.engines.smirnoff import ForceField is now just from openff.toolkit import ForceField - Same for Molecule, Topology, RDKitToolkitWrapper and others

  • Molecule and Topology objects no longer have virtual sites or particles - Those only exist AFTER parameter assignment and it made the code really complex to try and handle strange cases where molecules/topologies had vsites BEFORE parameter assignment

So in the bigger picture:

RC “release checklist”

git checkout main
git pull
git tag 0.11.0rc2
git push origin --tags
cd ../openff-toolkit-feedstock
git pull --set-upstream git@github.com:conda-forge/openff-toolkit-feedstock.git
git push --set-upstream git@github.com:j-wags/openff-toolkit-feedstock.git
# Update version, build, SHA, and sometimes deps
# SHA command: curl -sL https://github.com/openforcefield/openff-toolkit/archive/0.11.0rc2.tar.gz | openssl sha256 

(Do stuff on the feedstock repo)

conda install -c conda-forge/label/openff-toolkit-rc -c conda-forge/label/openff-interchange-rc -c conda-forge openff-toolkit

We want the following behavior

  • A way to install “everything” for vanilla users:

    • conda install openff-toolkit -c conda-forge brings in full versions of the toolkit and Interchange, along with OpenMM, RDKit, and AmberTools

  • A way for users to jump through hoops to get the Python packages available without AmberTools or RDKit showing up in their environment

    • conda install openff-toolkit-base openeye-toolkits -c conda-forge -c openeye brings in the Python packages, OpenEye Toolkits, and OpenMM, but no AmberTools or RDKit

This can be enabled by

  • openff-toolkit-base

    • Pulls in Python stuff only

  • openff-toolkit

    • Pulls in openff-toolkit-base, AmberTools, RDKit, openff-interchange-base, and (by extension) OpenMM

  • openff-interchange-base

    • Pulls in the Python stuff, depends on openff-toolkit-base, and OpenMM

  • openff-interchange

    • Pulls in openff-toolkit

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