Fix up docs for things that have been moved

Author: dwhswenson

docs/for_core/cli.rst

@@ -81,11 +81,13 @@ the CLI:
 
 * ``contents``: list all the named objects in an OPS storage, organized by
   store (type); this is extremely useful to get the name of an object to use
-  as command-line input to one of the simulation scripts
+
+
 .. * ``strip-snapshots``: create a copy of the input storage file with the
   details (coordinates/velocities) of all snapshots removed; this allows you
   to make a much smaller copy (with results of CVs) to copy back to a local
   computer for analysis
+
 * ``append`` : add an object from once OPS storage into another one; this is
   useful for getting everything into a single file before running a
   simulation

docs/full_cli.rst

@@ -9,6 +9,6 @@ currently gives all commands alphabetically, without regard to section. In
 general, this is not yet well-organized; contributions to improve that would
 be appreciated.
 
-.. click:: paths_cli.cli:OPS_CLI
+.. click:: paths_cli.cli:main
    :prog: openpathsampling
    :show-nested:

docs/sphinx-helpers/make_param_table.py

@@ -12,6 +12,7 @@
 import click
 
 from paths_cli import parameters
+from  paths_cli import param_core
 
 TableEntry = collections.namedtuple("TableEntry",
                                     "param flags get_args help")
@@ -20,7 +21,7 @@ def is_click_decorator(thing):
     return getattr(thing, '__module__', None) == 'click.decorators'
 
 def is_parameter(thing):
-    return (isinstance(thing, parameters.AbstractLoader)
+    return (isinstance(thing, param_core.AbstractLoader)
             or is_click_decorator(thing))
 
 def rst_wrap(code):
@@ -33,18 +34,18 @@ def flags_help(click_decorator):
     return flags, help_
 
 def get_args(parameter):
-    if isinstance(parameter, parameters.StorageLoader):
+    if isinstance(parameter, param_core.StorageLoader):
         return "``name``"
-    elif isinstance(parameter, (parameters.OPSStorageLoadNames,
-                                parameters.OPSStorageLoadSingle)):
+    elif isinstance(parameter, (param_core.OPSStorageLoadNames,
+                                param_core.OPSStorageLoadSingle)):
         return "``storage``, ``name``"
     elif is_click_decorator(parameter):
         return "No ``get`` function"
     else:
         return "Unknown"
 
 def get_click_decorator(thing):
-    if isinstance(thing, parameters.AbstractLoader):
+    if isinstance(thing, param_core.AbstractLoader):
         return thing.param.clicked()
     elif is_click_decorator(thing):
         return thing

paths_cli/cli.py

@@ -146,4 +146,4 @@ def main(log):
     logger.debug("About to run command")  # TODO: maybe log invocation?
 
 if __name__ == '__main__':  # no-cov
-    cli()
+    main()