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HTF migration #24

Merged
merged 27 commits into from
Mar 8, 2024
Merged

HTF migration #24

merged 27 commits into from
Mar 8, 2024

Commits on Jan 22, 2024

  1. WIP -- Starting HTF migration

    @ijpulidos
    ijpulidos committed Jan 22, 2024
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Commits on Feb 27, 2024

  1. remove flatten torsions option

    @richardjgowers
    richardjgowers committed Feb 27, 2024
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  2. reinclude fix from openfe #675 (perses #1230)

    @richardjgowers
    richardjgowers committed Feb 27, 2024
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  3. HTF: simplify _add_nonbonded_force_terms

    @richardjgowers
    richardjgowers committed Feb 27, 2024
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  4. Merge pull request #26 from choderalab/htf-migration_openfe_patches 

    Htf migration openfe patches
    @ijpulidos
    ijpulidos authored Feb 27, 2024
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  5. port openfe version of LambdaProtocol into feflow 

    perses version hasn't been touched since April '22
    @richardjgowers
    richardjgowers committed Feb 27, 2024
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  6. fixup attempt to be clever...

    @richardjgowers
    richardjgowers committed Feb 27, 2024
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  7. port tests from perses to feflow 

    and modernise to pytest
    @richardjgowers
    richardjgowers committed Feb 27, 2024
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  8. Merge pull request #28 from choderalab/include_LambdaProtocol 

    port openfe version of LambdaProtocol into feflow
    @richardjgowers
    richardjgowers authored Feb 27, 2024
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  9. Upgraded badges and acknowledgements

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  10. Removing non-relevant tests (protein mut., REST, etc.). Style formatt… 

    …ing.
    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  11. using gufe tests path fixture

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  12. Comments on why lists objs are needed

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  13. Start of organized module for HTF testing -- WIP

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  14. Renaming to lambda_protocol.py

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  15. Ingesting tests/utils from perses

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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  16. Need openeye for testing

    @ijpulidos
    ijpulidos committed Feb 27, 2024
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Commits on Feb 29, 2024

  1. old positions with old system. Fix callable.

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  2. Utility function to extract HTF data from perses top proposal

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  3. Adapt HTF signature. Skipping difficult ones.

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  4. Need to pin minimum openfe version for CI

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  5. Testing convergence difficult overlap

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  6. Modular testing. Software vs science test modules.

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  7. Skip hard to converge test.

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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  8. Fix proposal from perses obj

    @ijpulidos
    ijpulidos committed Feb 29, 2024
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Commits on Mar 5, 2024

  1. fixup lambdaprotocol tests

    @richardjgowers
    richardjgowers committed Mar 5, 2024
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Commits on Mar 8, 2024

  1. Migrate tests for "new" HTF features (#32) 

    * Vsites tests

* temporarily try to get CI working

* Add lambda schedule tests

* add basic tests for mdt and omm topology attributes

* try to fix scope issues

* more scope limiting

* fix lambda_schedule check

* missing self entry

* make gufe_data_dir session scoped

* fix to_openmm calls

* Add gitignore and fix tests

* Update ci.yaml
    @IAlibay
    IAlibay authored Mar 8, 2024
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