Merge pull request #89 from dwhswenson/cv-mode

Author: dwhswenson

paths_cli/commands/pathsampling.py

@@ -3,7 +3,8 @@
 
 from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (
-    INPUT_FILE, OUTPUT_FILE, INIT_CONDS, SCHEME, N_STEPS_MC
+    INPUT_FILE, OUTPUT_FILE, INIT_CONDS, SCHEME, N_STEPS_MC,
+    SIMULATION_CV_MODE,
 )
 
 
@@ -16,9 +17,12 @@
 @SCHEME.clicked(required=False)
 @INIT_CONDS.clicked(required=False)
 @N_STEPS_MC
-def pathsampling(input_file, output_file, scheme, init_conds, nsteps):
+@SIMULATION_CV_MODE.clicked()
+def pathsampling(input_file, output_file, scheme, init_conds, nsteps,
+                 cv_mode):
     """General path sampling, using setup in INPUT_FILE"""
     storage = INPUT_FILE.get(input_file)
+    SIMULATION_CV_MODE(storage, cv_mode)
     pathsampling_main(output_storage=OUTPUT_FILE.get(output_file),
                       scheme=SCHEME.get(storage, scheme),
                       init_conds=INIT_CONDS.get(storage, init_conds),

paths_cli/parameters.py

@@ -1,4 +1,5 @@
 import click
+import warnings
 from paths_cli.param_core import (
     Option, Argument, OPSStorageLoadSingle, OPSStorageLoadMultiple,
     OPSStorageLoadNames, StorageLoader, GetByName, GetByNumber, GetOnly,
@@ -133,3 +134,41 @@ def get(self, storage, names):
                           help="number of Monte Carlo trials to run")
 
 MULTI_CV = CVS
+
+
+class CVMode:
+    """Class for generating CVMode parameters.
+    """
+    def __init__(self, options, default):
+        allowed = {"production", "analysis", "no-caching"}
+        if extras := set(options) - allowed:
+            raise ValueError(f"Invalid options: {extras}")
+        if default not in options:
+            raise ValueError(f"Default '{default}' not in options {options}")
+
+        self.default = default
+        self.param = Option(
+            "--cv-mode",
+            type=click.Choice(options),
+            help=(
+                "Mode for CVs (only used for SimStore DB files). Default "
+                f"'{default}'."
+            ),
+            default=default,
+        )
+
+    def clicked(self):
+        return self.param.clicked()
+
+    def __call__(self, storage, cv_mode):
+        from openpathsampling.experimental.storage import Storage
+        if cv_mode != self.default and not isinstance(storage, Storage):
+            warnings.warn("Not a SimStore file: cv-mode argument unused")
+            return
+
+        for cv in storage.cvs:
+            # TODO: add logger
+            # _logger.info(f"Setting '{cv.name}' to mode '{cv_mode}'.")
+            cv.mode = cv_mode
+
+SIMULATION_CV_MODE = CVMode(["production", "no-caching"], "production")

paths_cli/tests/test_parameters.py

@@ -511,3 +511,49 @@ def test_APPEND_FILE(ext):
     os.remove(filename)
     os.rmdir(tempdir)
     undo_monkey_patch(stored_functions)
+
+
+class TestCVMode:
+    def test_bad_option(self):
+        with pytest.raises(ValueError, match="Invalid options"):
+            CVMode(["production", "foo"], "production")
+
+    def test_bad_default(self):
+        with pytest.raises(ValueError, match="not in options"):
+            CVMode(["production", "no-caching"], "analysis")
+
+    def test_call(self, tmp_path):
+        cv_mode = CVMode(["production", "no-caching"], "no-caching")
+        from openpathsampling.experimental.storage.collective_variables \
+            import CollectiveVariable
+        from openpathsampling.experimental.storage import (
+            Storage,  monkey_patch_all
+        )
+        cv = CollectiveVariable(lambda s: s.xyz[0][0]).named('x')
+        filename = str(tmp_path / "foo.db")
+        stored_functions = pre_monkey_patch()
+        monkey_patch_all(paths)
+        st = Storage(filename, mode='w')
+        assert cv.mode == "analysis"
+        st.save(cv)
+        st.close()
+        del cv
+
+        storage = Storage(filename, mode='r')
+        cv = storage.cvs['x']
+        assert cv.mode == "analysis"
+        cv_mode(storage, "no-caching")
+        assert cv.mode == "no-caching"
+        undo_monkey_patch(stored_functions)
+
+    def test_call_non_simstore(self, tmp_path):
+        cv_mode = CVMode(["production", "no-caching"], "no-caching")
+        filename = str(tmp_path / "foo.nc")
+        cv = paths.FunctionCV("x", lambda x: x.xyz[0][0])
+        st = paths.Storage(filename, mode='w')
+        st.save(cv)
+        st.close()
+
+        storage = paths.Storage(filename, mode='r')
+        with pytest.warns(UserWarning, match="Not a SimStore"):
+            cv_mode(storage, "production")