Merge branch 'main' of github.com:openpathsampling/openpathsampling-cli into wizard-pauses

Author: dwhswenson

paths_cli/compiling/core.py

@@ -1,13 +1,10 @@
 import json
-import yaml
-
-from collections import namedtuple
-
 import logging
 
-from .errors import InputError
 from paths_cli.utils import import_thing
 from paths_cli.plugin_management import OPSPlugin
+from paths_cli.compiling.errors import InputError
+
 
 def listify(obj):
     listified = False
@@ -16,16 +13,20 @@ def listify(obj):
         listified = True
     return obj, listified
 
+
 def unlistify(obj, listified):
     if listified:
         assert len(obj) == 1
         obj = obj[0]
     return obj
 
+
 REQUIRED_PARAMETER = object()
 
+
 class Parameter:
     SCHEMA = "http://openpathsampling.org/schemas/sim-setup/draft01.json"
+
     def __init__(self, name, loader, *, json_type=None, description=None,
                  default=REQUIRED_PARAMETER, aliases=None):
         if isinstance(json_type, str):
@@ -150,6 +151,7 @@ class InstanceCompilerPlugin(OPSPlugin):
     """
     SCHEMA = "http://openpathsampling.org/schemas/sim-setup/draft01.json"
     category = None
+
     def __init__(self, builder, parameters, name=None, aliases=None,
                  requires_ops=(1, 0), requires_cli=(0, 3)):
         super().__init__(requires_ops, requires_cli)
@@ -239,7 +241,7 @@ def __call__(self, dct):
         ops_dct = self.compile_attrs(dct)
         self.logger.debug("Building...")
         self.logger.debug(ops_dct)
-        obj =  self.builder(**ops_dct)
+        obj = self.builder(**ops_dct)
         self.logger.debug(obj)
         return obj
 
@@ -260,7 +262,7 @@ def _compile_str(self, name):
         self.logger.debug(f"Looking for '{name}'")
         try:
             return self.named_objs[name]
-        except KeyError as e:
+        except KeyError:
             raise InputError.unknown_name(self.label, name)
 
     def _compile_dict(self, dct):

paths_cli/compiling/cvs.py

@@ -1,10 +1,7 @@
-import os
-import importlib
-
-from .core import Parameter, Builder
-from .tools import custom_eval
-from .topology import build_topology
-from .errors import InputError
+from paths_cli.compiling.core import Parameter, Builder
+from paths_cli.compiling.tools import custom_eval
+from paths_cli.compiling.topology import build_topology
+from paths_cli.compiling.errors import InputError
 from paths_cli.utils import import_thing
 from paths_cli.compiling.plugins import CVCompilerPlugin, CategoryPlugin
 
@@ -21,6 +18,7 @@ def __call__(self, source):
         # on ImportError, we leave the error unchanged
         return func
 
+
 def _cv_kwargs_remapper(dct):
     kwargs = dct.pop('kwargs', {})
     dct.update(kwargs)

paths_cli/compiling/engines.py

@@ -1,9 +1,10 @@
-from .topology import build_topology
-from .core import Builder
+from paths_cli.compiling.topology import build_topology
+from paths_cli.compiling.core import Builder
 from paths_cli.compiling.core import Parameter
-from .tools import custom_eval_int_strict_pos
+from paths_cli.compiling.tools import custom_eval_int_strict_pos
 from paths_cli.compiling.plugins import EngineCompilerPlugin, CategoryPlugin
 
+
 def load_openmm_xml(filename):
     from paths_cli.compat.openmm import HAS_OPENMM, mm
     if not HAS_OPENMM:  # -no-cov-
@@ -14,6 +15,7 @@ def load_openmm_xml(filename):
 
     return obj
 
+
 def _openmm_options(dct):
     n_steps_per_frame = dct.pop('n_steps_per_frame')
     n_frames_max = dct.pop('n_frames_max')

paths_cli/compiling/errors.py

@@ -9,4 +9,3 @@ def invalid_input(cls, value, attr):
     @classmethod
     def unknown_name(cls, type_name, name):
         return cls(f"Unable to find object named {name} in {type_name}")
-

paths_cli/compiling/networks.py

@@ -10,12 +10,13 @@
     parameters=[
         Parameter('cv', compiler_for('cv'), description="the collective "
                   "variable for this interface set"),
-        Parameter('minvals', custom_eval), # TODO fill in JSON types
-        Parameter('maxvals', custom_eval), # TODO fill in JSON types
+        Parameter('minvals', custom_eval),  # TODO fill in JSON types
+        Parameter('maxvals', custom_eval),  # TODO fill in JSON types
     ],
     name='interface-set'
 )
 
+
 def mistis_trans_info(dct):
     dct = dct.copy()
     transitions = dct.pop('transitions')
@@ -31,6 +32,7 @@ def mistis_trans_info(dct):
     dct['trans_info'] = trans_info
     return dct
 
+
 def tis_trans_info(dct):
     # remap TIS into MISTIS format
     dct = dct.copy()
@@ -42,6 +44,7 @@ def tis_trans_info(dct):
                            'interfaces': interface_set}]
     return mistis_trans_info(dct)
 
+
 TPS_NETWORK_PLUGIN = NetworkCompilerPlugin(
     builder=Builder('openpathsampling.TPSNetwork'),
     parameters=[
@@ -60,6 +63,7 @@ def tis_trans_info(dct):
     name='mistis'
 )
 
+
 TIS_NETWORK_PLUGIN = NetworkCompilerPlugin(
     builder=Builder('openpathsampling.MISTISNetwork'),
     parameters=[Parameter('trans_info', tis_trans_info)],

paths_cli/compiling/plugins.py

@@ -1,12 +1,13 @@
 from paths_cli.compiling.core import InstanceCompilerPlugin
 from paths_cli.plugin_management import OPSPlugin
 
+
 class CategoryPlugin(OPSPlugin):
     """
     Category plugins only need to be made for top-level
     """
     def __init__(self, plugin_class, aliases=None, requires_ops=(1, 0),
-                 requires_cli=(0,4)):
+                 requires_cli=(0, 3)):
         super().__init__(requires_ops, requires_cli)
         self.plugin_class = plugin_class
         if aliases is None:
@@ -25,17 +26,22 @@ def __repr__(self):
 class EngineCompilerPlugin(InstanceCompilerPlugin):
     category = 'engine'
 
+
 class CVCompilerPlugin(InstanceCompilerPlugin):
     category = 'cv'
 
+
 class VolumeCompilerPlugin(InstanceCompilerPlugin):
     category = 'volume'
 
+
 class NetworkCompilerPlugin(InstanceCompilerPlugin):
     category = 'network'
 
+
 class SchemeCompilerPlugin(InstanceCompilerPlugin):
     category = 'scheme'
 
+
 class StrategyCompilerPlugin(InstanceCompilerPlugin):
     category = 'strategy'

paths_cli/compiling/root_compiler.py

@@ -6,6 +6,7 @@
 import logging
 logger = logging.getLogger(__name__)
 
+
 class CategoryCompilerRegistrationError(Exception):
     pass
 
@@ -22,6 +23,7 @@ class CategoryCompilerRegistrationError(Exception):
 
 COMPILE_ORDER = _DEFAULT_COMPILE_ORDER.copy()
 
+
 def clean_input_key(key):
     # TODO: move this to core
     """
@@ -34,12 +36,14 @@ def clean_input_key(key):
     key = key.replace("-", "_")
     return key
 
+
 ### Managing known compilers and aliases to the known compilers ############
 
 _COMPILERS = {}  # mapping: {canonical_name: CategoryCompiler}
 _ALIASES = {}  # mapping: {alias: canonical_name}
 # NOTE: _ALIASES does *not* include self-mapping of the canonical names
 
+
 def _canonical_name(alias):
     """Take an alias or a compiler name and return the compiler name
 
@@ -51,6 +55,7 @@ def _canonical_name(alias):
     alias_to_canonical.update({pname: pname for pname in _COMPILERS})
     return alias_to_canonical.get(alias, None)
 
+
 def _get_compiler(category):
     """
     _get_compiler must only be used after the CategoryCompilers have been
@@ -69,6 +74,7 @@ def _get_compiler(category):
         _COMPILERS[category] = CategoryCompiler(None, category)
     return _COMPILERS[canonical_name]
 
+
 def _register_compiler_plugin(plugin):
     DUPLICATE_ERROR = CategoryCompilerRegistrationError(
         f"The category '{plugin.name}' has been reserved by another plugin"
@@ -87,7 +93,7 @@ def _register_compiler_plugin(plugin):
 
 
 ### Handling delayed loading of compilers ##################################
-#
+
 # Many objects need to use compilers to create their input parameters. In
 # order for them to be able to access dynamically-loaded plugins, we delay
 # the loading of the compiler by using a proxy object.
@@ -111,6 +117,7 @@ def named_objs(self):
     def __call__(self, dct):
         return self._proxy(dct)
 
+
 def compiler_for(category):
     """Delayed compiler calling.
 
@@ -142,11 +149,13 @@ def _get_registration_names(plugin):
             found_names.add(name)
     return ordered_names
 
+
 def _register_builder_plugin(plugin):
     compiler = _get_compiler(plugin.category)
     for name in _get_registration_names(plugin):
         compiler.register_builder(plugin, name)
 
+
 def register_plugins(plugins):
     builders = []
     compilers = []
@@ -162,6 +171,7 @@ def register_plugins(plugins):
     for plugin in builders:
         _register_builder_plugin(plugin)
 
+
 ### Performing the compiling of user input #################################
 
 def _sort_user_categories(user_categories):
@@ -179,6 +189,7 @@ def _sort_user_categories(user_categories):
     )
     return sorted_keys
 
+
 def do_compile(dct):
     """Main function for compiling user input to objects.
     """

paths_cli/compiling/schemes.py

@@ -26,6 +26,7 @@
     name='spring-shooting',
 )
 
+
 class BuildSchemeStrategy:
     def __init__(self, scheme_class, default_global_strategy):
         self.scheme_class = scheme_class

paths_cli/compiling/shooting.py

@@ -4,18 +4,21 @@
 from paths_cli.compiling.root_compiler import compiler_for
 from paths_cli.compiling.tools import custom_eval
 
+
 build_uniform_selector = InstanceCompilerPlugin(
     builder=Builder('openpathsampling.UniformSelector'),
     parameters=[],
     name='uniform',
 )
 
+
 def _remapping_gaussian_stddev(dct):
     dct['alpha'] = 0.5 / dct.pop('stddev')**2
     dct['collectivevariable'] = dct.pop('cv')
     dct['l_0'] = dct.pop('mean')
     return dct
 
+
 build_gaussian_selector = InstanceCompilerPlugin(
     builder=Builder('openpathsampling.GaussianBiasSelector',
                     remapper=_remapping_gaussian_stddev),
@@ -27,6 +30,7 @@ def _remapping_gaussian_stddev(dct):
     name='gaussian',
 )
 
+
 shooting_selector_compiler = CategoryCompiler(
     type_dispatch={
         'uniform': build_uniform_selector,

paths_cli/compiling/strategies.py

@@ -5,17 +5,19 @@
 )
 from paths_cli.compiling.root_compiler import compiler_for
 
+
 def _strategy_name(class_name):
     return f"openpathsampling.strategies.{class_name}"
 
+
 def _group_parameter(group_name):
     return Parameter('group', str, default=group_name,
                      description="the group name for these movers")
 
+
 # TODO: maybe this moves into shooting once we have the metadata?
 SP_SELECTOR_PARAMETER = Parameter('selector', shooting_selector_compiler,
                                   default=None)
-
 ENGINE_PARAMETER = Parameter('engine', compiler_for('engine'),
                              description="the engine for moves of this "
                              "type")
@@ -39,6 +41,7 @@ def _group_parameter(group_name):
     name='one-way-shooting',
 )
 build_one_way_shooting_strategy = ONE_WAY_SHOOTING_STRATEGY_PLUGIN
+
 # build_two_way_shooting_strategy = StrategyCompilerPlugin(
 #     builder=Builder(_strategy_name("TwoWayShootingStrategy")),
 #     parameters = [