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A builder for classical md workflows #1010

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Closed

A builder for classical md workflows #1010

wants to merge 134 commits into from

Commits on Mar 30, 2024

  1. Add test files.

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    orionarcher committed Mar 30, 2024
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Commits on Mar 31, 2024

  1. Add in tests systems for classical_md builders and README files for d… 

    …ata generation.
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  2. Missed dcd in previous commit

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  3. Remove unused test files.

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Commits on Apr 1, 2024

  1. Add basic fixtures and new folders for utilities.

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  2. Add functionality for labeling universe and skeleton tests.

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Commits on Apr 10, 2024

  1. Move classical md schema to tasks.py in classical_md directory. Add i… 

    …mport to __init__.py to keep imports the same.
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  2. Move openmm schema to openmm/tasks.py in classical_md directory.

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  3. Add utility functions and testing.

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  4. Add core task doc and solvation builder.

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  5. Remove import from atomate2

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  6. Create HexBytes type for serializing blobs and make interchange and t… 

    …raj_blob HexBytes.
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  7. Check that dcd exists before loading.

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  8. Merge branch 'refs/heads/main' into schema_updates

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  9. Merge branch 'refs/heads/md_builders' into schema_updates

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  10. Small linting fix.

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Commits on Apr 11, 2024

  1. Merge branch 'refs/heads/only_schemas' into md_builders

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    orionarcher committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. Fix file name being set even if it doesn't exist.

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Commits on Apr 14, 2024

  1. Add nearly complete draft of OpenMMBuilder.

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  2. Add basic end to end test for openmm builder

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  3. Add json documents serializing stores for builder tests.

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  4. Remove atomate2 import

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  5. Add init files to create package.

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  6. Recreate and move stores

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  7. Finish process_items and rename builder to ElectrolyteBuilder

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  8. Add Na+ and Br- to test system.

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  9. Add identify_solute and identify_networking_solvents functions and up… 

    …date label_charges logic.
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  10. Finish process_items logic and add update_targets.

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  11. Overwrite source keys without warning in ElectrolyteBuilder

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  12. Merge remote-tracking branch 'refs/remotes/origin/main' into md_builders

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Commits on Apr 16, 2024

  1. Expect different state files from each job in calc output from_directory

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  2. Small refactor and add instantiate)solute method + testing

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    orionarcher committed Apr 16, 2024
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  3. Fix loading of pd.Dataframes in SolvationDoc with custom DataFrame type.

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  4. Fix error in identify_networking_solvents

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Commits on Apr 19, 2024

  1. Automatically create directory when instantiating universe.

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    orionarcher committed Apr 19, 2024
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Commits on May 8, 2024

  1. Allow instantiate universe to avoid downloading files.

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  2. Different implementation of default kernel kwargs

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  3. Add new EC/EMC test system.

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Commits on May 13, 2024

  1. Exclude solute from Solute.solvents by default.

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Commits on May 28, 2024

  1. Remove unused calculations file.

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  2. Add ability to select analysis_classes to create_solute.

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  3. Add CalculationsDoc for tracking workflow history.

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  4. Add high level import slot.

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  5. Merge branch 'refs/heads/main' into md_builders

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  6. Linting.

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Commits on Jun 2, 2024

  1. delete unused system.

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  2. Update ElectrolyteBuilder to accept no input for solute and calculati… 

    …ons Stores.
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  3. Update SolvationDoc to not require all analysis classes.

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  4. By default, do not calculate residence times when creating solute

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  5. Add tests and link to correct test files.

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  6. Add improved documentation.

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  7. Merge branch 'refs/heads/main' into md_builders

    @orionarcher
    orionarcher committed Jun 2, 2024
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  8. Update requirements

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  9. Add new requirements file to CI.

    @orionarcher
    orionarcher committed Jun 2, 2024
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  10. Fix typo in testing.yml

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Commits on Jun 3, 2024

  1. Move pip installable requirements to emmet-core setup.py.

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  2. Move conda requirements out of their own file.

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  3. mdanalysis -> MDAnalysis

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  4. Fix test and mypy issue.

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  5. Fix mypy issue.

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Commits on Jun 4, 2024

  1. Fix some dependencies

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    orionarcher committed Jun 4, 2024
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  2. Update deployment.txt

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  3. Merge branch 'refs/heads/main' into md_builders 

    # Conflicts:
#	emmet-core/requirements/ubuntu-latest_py3.10_extras.txt
#	emmet-core/requirements/ubuntu-latest_py3.11_extras.txt
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  4. Update python 3.9 extras

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Commits on Jun 6, 2024

  1. Merge branch 'main' into md_builders

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  2. Update testing.yml

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Commits on Jun 7, 2024

  1. Merge remote-tracking branch 'personal/md_builders' into md_builders

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Commits on Jun 8, 2024

  1. Merge branch 'refs/heads/main' into md_builders

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  2. Update union types to use explicit type expressions for 3.9 compatabi… 

    …lity.
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  3. Fix another type issue.

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  4. Fix another type issue.

    @orionarcher
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  5. Fix another type issue.

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  6. Rerun tests, transitory error.

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  7. Try another type fix.

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Commits on Jun 16, 2024

  1. Remove redundant dependencies from emmet-builders.

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  2. Merge remote-tracking branch 'origin/main' into md_builders 

    # Conflicts:
#	emmet-core/requirements/ubuntu-latest_py3.10_extras.txt
#	emmet-core/requirements/ubuntu-latest_py3.11_extras.txt
#	emmet-core/requirements/ubuntu-latest_py3.9_extras.txt
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Commits on Jul 20, 2024

  1. Add transport analysis requirement.

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  2. Remove residence times from solute analysis class defaults.

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  3. Create a SolventBenchmarkingDoc with density, viscosity, and dielectr… 

    …ic calculations.
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  4. Update blobs and docs stores in test files

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  5. Update blobs and docs stores in test files

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  6. Delete duplicate props entry

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  7. Split insert_blobs and instantiate_universe out of ElectrolyteBuilder… 

    … and into a utils file for easier reuse in other builders.
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  8. Add a SolventBenchmarkingBuilder and corresponding testing.

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Commits on Jul 24, 2024

  1. Add a FauxInterchange object

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    orionarcher committed Jul 24, 2024
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  2. Merge branch 'refs/heads/main' into md_builders 

    # Conflicts:
#	emmet-core/requirements/deployment.txt
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Commits on Jul 29, 2024

  1. bug warning, unfixed

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  2. replace online simulation data with locally generated data

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  3. Add test for elyte builder

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  4. Add READMEs for autogenerated test data

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  5. Update stores

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  6. Delete conftest

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  7. Change FauxInterchange to OpenMMInterchange

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  8. Add more detailed viscosity data to BM builder

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  9. Remove classical_md directory and rename it openmm and openff, as app… 

    …ropriate.
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  10. Remove classical_md directory and rename it openmm and openff, as app… 

    …ropriate.
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Commits on Jul 30, 2024

  1. Add job_uuids to classical md task doc

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  2. Add option to rebase traj path in builder if jobs have been moved.

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  3. Delete commented out code.

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  4. Refactor testing and regenerate test data to use OpenMMFlowMaker and … 

    …new atomate2 wf
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  5. Merge branch 'refs/heads/main' into md_builders

    @orionarcher
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  6. Add xml files with opls params

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  7. Refactor data generating fixture

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  8. Add multiple interchange parsing in solvation builder

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  9. OPLS data generating fixture

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    orionarcher committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Refactor SolventBuilder and BenchmarkingBuilder to reuse code from so… 

    …me utility funcitons
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  2. Modify create universe to accept interchange or openmminterchange

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    orionarcher committed Jul 31, 2024
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  3. PDBxFile to PDBFile

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    orionarcher committed Jul 31, 2024
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  4. Finish OPLS test with benchmarking builder

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    orionarcher committed Jul 31, 2024
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  5. Adjsut prev_task to prev_dir and regenerate input files

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    orionarcher committed Jul 31, 2024
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Commits on Aug 11, 2024

  1. Update stores data

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    orionarcher committed Aug 11, 2024
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  2. Merge branch 'refs/heads/main' into md_builders

    Orion Cohen authored and Orion Cohen committed Aug 11, 2024
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  3. Merge remote-tracking branch 'refs/remotes/personal/md_builders' into… 

    … md_builders
    Orion Cohen authored and Orion Cohen committed Aug 11, 2024
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  4. Move openmm_md testing out of classical_md directory.

    @orionarcher
    orionarcher committed Aug 11, 2024
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  5. Update benchmarking doc

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    orionarcher committed Aug 11, 2024
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  6. allow benchmarking builder to work with local files.

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    orionarcher committed Aug 11, 2024
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Commits on Aug 18, 2024

  1. Finish SolventBenchmarkingDoc and add more robust testing.

    @orionarcher
    orionarcher committed Aug 18, 2024
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  2. Raise meaningful error and add comment

    @orionarcher
    orionarcher committed Aug 18, 2024
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  3. Merge branch 'refs/heads/main' into md_builders

    @orionarcher
    orionarcher committed Aug 18, 2024
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  4. Lint files

    @orionarcher
    orionarcher committed Aug 18, 2024
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  5. Rerun tests

    @orionarcher
    orionarcher committed Aug 18, 2024
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  6. Test update targets in benchmark builder

    @orionarcher
    orionarcher committed Aug 18, 2024
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  7. Add tags and run kwargs to benchmarking builder

    @orionarcher
    orionarcher committed Aug 18, 2024
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  8. Manually update transport analysis version.

    @orionarcher
    orionarcher committed Aug 18, 2024
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  9. Make sure tags are put in BM doc

    @orionarcher
    orionarcher committed Aug 18, 2024
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  10. Make sure sure kwargs are put in BM doc

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    orionarcher committed Aug 18, 2024
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  11. Fix mypy linting error

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    orionarcher committed Aug 18, 2024
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Commits on Aug 30, 2024

  1. Split out MDTaskDoc from ClassicalMDTaskDoc and migrate name of MDTas… 

    …kDoc.molecule_specs -> MDTaskDoc.interchange_meta
    @orionarcher
    orionarcher committed Aug 30, 2024
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  2. Update __init__

    @orionarcher
    orionarcher committed Aug 30, 2024
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  3. Run pre-commit

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    orionarcher committed Aug 30, 2024
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Commits on Sep 4, 2024

  1. Merge branch 'main' into md_builders

    @tschaume
    tschaume committed Sep 4, 2024
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  2. Merge branch 'main' into md_builders

    @tschaume
    tschaume committed Sep 4, 2024
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  3. Run pre-commit

    @orionarcher
    orionarcher committed Sep 4, 2024
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Commits on Sep 5, 2024

  1. Merge branch 'materialsproject:main' into md_builders

    @orionarcher
    orionarcher committed Sep 5, 2024
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