From ef15992fd8af7bd91277e2c5bffaf4fe9280681b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Iv=C3=A1n=20Pulido?= <2949729+ijpulidos@users.noreply.github.com> Date: Tue, 22 Aug 2023 19:00:46 -0400 Subject: [PATCH] Realtime analysis interval to default to checkpoint interval (#1227) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * Changing offline freq default to checkpoint interval * Fixing input yaml for example * commenting offline-freq param --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> --- .github/workflows/CI.yaml | 3 +-- devtools/conda-envs/test_env.yaml | 2 +- examples/protein-ligand-repex/cli/protein-ligand.yaml | 2 +- perses/app/setup_relative_calculation.py | 8 ++++---- 4 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 1ef61cfd7..dd072768d 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -72,7 +72,6 @@ jobs: extra-specs: | python==${{ matrix.python-version }} openmm==${{ matrix.openmm }} - openmmtools==0.23.0 - name: Install package shell: bash -l {0} @@ -108,4 +107,4 @@ jobs: uses: codecov/codecov-action@v1 with: file: ./coverage.xml - fail_ci_if_error: true + fail_ci_if_error: false diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index a482b0ccd..c6162b7ae 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -28,7 +28,7 @@ dependencies: - openff-units >=0.1.8 - openmm >=7.7 - openmmforcefields >=0.9.0 - - openmmtools # may need to sort out ambermini/ambertools/parmed dependencies + - openmmtools >=0.23 # may need to sort out ambermini/ambertools/parmed dependencies - openmoltools # may need to sort out ambermini/ambertools/parmed dependencies (we don't want ambertools) - parmed - pdbfixer diff --git a/examples/protein-ligand-repex/cli/protein-ligand.yaml b/examples/protein-ligand-repex/cli/protein-ligand.yaml index cf7bc7852..b053662e6 100644 --- a/examples/protein-ligand-repex/cli/protein-ligand.yaml +++ b/examples/protein-ligand-repex/cli/protein-ligand.yaml @@ -50,7 +50,7 @@ bond_expession: # One of ['repex', 'nonequilibrium', 'sams'] fe_type: repex checkpoint_interval: 100 # number of iterations -offline-freq: 100 # Real time FE estimate analysis -- multiple of checkpoint interval +#offline-freq: 100 # Real time FE estimate analysis -- multiple of checkpoint interval (optional) # Number of iterations to run n_cycles: 5000 diff --git a/perses/app/setup_relative_calculation.py b/perses/app/setup_relative_calculation.py index d30655831..c43ff6054 100644 --- a/perses/app/setup_relative_calculation.py +++ b/perses/app/setup_relative_calculation.py @@ -149,8 +149,8 @@ def getSetupOptions(filename, override_string=None): setup_options['flatness-criteria'] = 'minimum-visits' _logger.info(f"\t\t\tflatness-criteria not specified: default to minimum-visits.") if 'offline-freq' not in setup_options: - setup_options['offline-freq'] = 10 - _logger.info(f"\t\t\toffline-freq not specified: default to 10.") + setup_options['offline-freq'] = setup_options["checkpoint_interval"] + _logger.info(f"\t\t\toffline-freq not specified: default to checkpoint interval.") if 'gamma0' not in setup_options: setup_options['gamma0'] = 1. _logger.info(f"\t\t\tgamma0 not specified: default to 1.0.") @@ -162,8 +162,8 @@ def getSetupOptions(filename, override_string=None): elif setup_options['fe_type'] == 'repex': _logger.info(f"\t\tfe_type: repex") if 'offline-freq' not in setup_options: - setup_options['offline-freq'] = 10 - _logger.info(f"\t\t\toffline-freq not specified: default to 10.") + setup_options['offline-freq'] = setup_options["checkpoint_interval"] + _logger.info(f"\t\t\toffline-freq not specified: default to checkpoint interval.") elif setup_options['fe_type'] == 'neq': #there are some neq attributes that are not used with the equilibrium samplers... _logger.info(f"\t\tfe_type: neq") if 'n_equilibrium_steps_per_iteration' not in setup_options: