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

@@ -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

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

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

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: