Merge pull request #48 from dwhswenson/new_plugins

New plugin infrastructure

Author: dwhswenson

docs/plugins.rst

@@ -8,23 +8,33 @@ There are two possible ways to distribute plugins (file plugins and
 namespace plugins), but a given plugin script could be distributed either
 way. 
 
-Writing a plugin script
------------------------
-
-An OPS plugin is simply a Python module that follows a few rules.
-
-* It must define a variable ``CLI`` that is the main CLI function is
-  assigned to.
-* It must define a variable ``SECTION`` to determine where to show it in
-  help (what kind of command it is). Valid values are ``"Simulation"``,
-  ``"Analysis"``, ``"Miscellaneous"``, or ``"Workflow"``. If ``SECTION`` is
-  defined but doesn't have one of these values, it won't show in
-  ``openpathsampling --help``, but might still be usable. If your command
-  doesn't show in the help, carefully check your spelling of the ``SECTION``
-  variable.
-* The main CLI function must be decorated as a ``click.command``.
-* (If distributed as a file plugin) It must be possible to ``exec`` it in an
-  empty namespace (mainly, this can mean no relative imports).
+Writing a command plugin
+------------------------
+
+To write an OPS command plugin, you simply need to create an instance of
+:class:`paths_cli.OPSCommandPlugin` and to install the module in a location
+where the CLI knows to look for it. The input parameters to
+``OPSCommandPlugin`` are:
+
+* ``command``: This is the main CLI function for the subcommand. It must be
+  decorated as a ``click.command``.
+* ``section``: This is a string to determine where to show it in help (what
+  kind of command it is).  Valid values are ``"Simulation"``,
+  ``"Analysis"``, ``"Miscellaneous"``, or ``"Workflow"``. If ``section``
+  doesn't have one of these values, it won't show in ``openpathsampling
+  --help``, but might still be usable. If your command doesn't show in the
+  help, carefully check your spelling of the ``section`` variable.
+* ``requires_ops`` (optional, default ``(1, 0)``): Minimum allowed version
+  of OpenPathSampling. Note that this is currently informational only, and
+  has no effect on functionality.
+* ``requires_cli`` (optional, default ``(0, 3)``): Minimum allowed version
+  of the OpenPathSampling CLI.  Note that this is currently informational
+  only, and has no effect on functionality.
+
+
+If you distribute your plugin as a file-based plugin, be aware that it must
+be possible to ``exec`` it in an empty namespace (mainly, this can mean no
+relative imports).
 
 As a suggestion, I (DWHS) tend to structure my plugins as follows:
 
@@ -41,16 +51,15 @@ As a suggestion, I (DWHS) tend to structure my plugins as follows:
         ...
         return final_status, simulation
 
-    CLI = plugin
-    SECTION = "MySection"
+    PLUGIN = OPSCommandPlugin(command=plugin, section="MySection")
 
 The basic idea is that there's a ``plugin_main`` function that is based on
 pure OPS, using only inputs that OPS can immediately understand (no need to
 process the command line). This is easy to develop/test with OPS. Then
 there's a wrapper function whose sole purpose is to convert the command line
 parameters to something OPS can understand (using the ``get`` method). This
-wrapper is the ``CLI`` variable. Give it an allowed ``SECTION``, and the
-plugin is ready!
+wrapper is the ``command`` in you ``OPSCommandPlugin``. Also provide an
+allowed ``section``, and the plugin is ready!
 
 The result is that plugins are astonishingly easy to develop, once you have
 the scientific code implemented in a library. This structure also makes it
@@ -95,4 +104,3 @@ namespace.
 .. _native namespace packages:
   https://packaging.python.org/guides/packaging-namespace-packages/#native-namespace-packages
 
-

example_plugins/one_pot_tps.py

@@ -1,4 +1,5 @@
 import click
+from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (INPUT_FILE, OUTPUT_FILE, ENGINE, STATES,
                                   N_STEPS_MC, INIT_SNAP)
 from paths_cli.commands.visit_all import visit_all_main
@@ -44,6 +45,15 @@ def one_pot_tps_main(output_storage, states, engine, engine_hot,
                                     equil_multiplier, equil_extra)
     return pathsampling_main(output_storage, scheme, equil_set, nsteps)
 
+# these lines enable this plugin to support OPS CLI < 0.3
 CLI = one_pot_tps
 SECTION = "Workflow"
 REQUIRES_OPS = (1, 2)
+
+# these lines enable this plugin to support OPS CLI >= 0.3
+PLUGIN = OPSCommandPlugin(
+    command=one_pot_tps,
+    section="Workflow",
+    requires_ops=(1, 2),
+    requires_cli=(0, 3)
+)

example_plugins/tps.py

@@ -1,4 +1,5 @@
 import click
+from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (
     INPUT_FILE, OUTPUT_FILE, ENGINE, STATES, INIT_CONDS, N_STEPS_MC
 )
@@ -40,8 +41,17 @@ def tps_main(engine, states, init_traj, output_storage, n_steps):
     return simulation.sample_set, simulation
 
 
+# these lines enable this plugin to support OPS CLI < 0.3
 CLI = tps
 SECTION = "Simulation"
 
+# these lines enable this plugin to support OPS CLI >= 0.3
+PLUGIN = OPSCommandPlugin(
+    command=tps,
+    section="Simulation"
+)
+
+
+# this allows you to use this as a script, independently of the OPS CLI
 if __name__ == "__main__":
     tps()

paths_cli/__init__.py

@@ -1,3 +1,6 @@
+from .plugin_management import (
+    OPSCommandPlugin,
+)
 from .cli import OpenPathSamplingCLI
 from . import commands
 from . import version

paths_cli/cli.py

@@ -13,7 +13,8 @@
 # import click_completion
 # click_completion.init()
 
-from .plugin_management import FilePluginLoader, NamespacePluginLoader
+from .plugin_management import (FilePluginLoader, NamespacePluginLoader,
+                                OPSCommandPlugin)
 
 CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
 
@@ -31,10 +32,10 @@ def app_dir_plugins(posix):
             ).resolve() / 'cli-plugins')
 
         self.plugin_loaders = [
-            FilePluginLoader(commands),
-            FilePluginLoader(app_dir_plugins(posix=False)),
-            FilePluginLoader(app_dir_plugins(posix=True)),
-            NamespacePluginLoader('paths_cli_plugins')
+            FilePluginLoader(commands, OPSCommandPlugin),
+            FilePluginLoader(app_dir_plugins(posix=False), OPSCommandPlugin),
+            FilePluginLoader(app_dir_plugins(posix=True), OPSCommandPlugin),
+            NamespacePluginLoader('paths_cli_plugins', OPSCommandPlugin)
         ]
 
         plugins = sum([loader() for loader in self.plugin_loaders], [])

paths_cli/commands/append.py

@@ -1,4 +1,5 @@
 import click
+from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (
     INPUT_FILE, APPEND_FILE, MULTI_CV, MULTI_ENGINE, MULTI_VOLUME,
     MULTI_NETWORK, MULTI_SCHEME, MULTI_TAG
@@ -55,6 +56,9 @@ def append(input_file, append_file, engine, cv, volume, network, scheme,
     storage.close()
 
 
-CLI = append
-SECTION = "Miscellaneous"
-REQUIRES_OPS = (1, 0)
+PLUGIN = OPSCommandPlugin(
+    command=append,
+    section="Miscellaneous",
+    requires_ops=(1, 0),
+    requires_cli=(0, 3)
+)

paths_cli/commands/contents.py

@@ -1,5 +1,6 @@
 import click
 from paths_cli.parameters import INPUT_FILE
+from paths_cli import OPSCommandPlugin
 
 UNNAMED_SECTIONS = ['steps', 'movechanges', 'samplesets', 'trajectories',
                     'snapshots']
@@ -112,6 +113,10 @@ def get_section_string_nameable(section, store, get_named):
                     + _item_or_items(n_unnamed))
     return out_str
 
-CLI = contents
-SECTION = "Miscellaneous"
-REQUIRES_OPS = (1, 0)
+
+PLUGIN = OPSCommandPlugin(
+    command=contents,
+    section="Miscellaneous",
+    requires_ops=(1, 0),
+    requires_cli=(0, 3)
+)

paths_cli/commands/equilibrate.py

@@ -1,6 +1,7 @@
 import click
 # import openpathsampling as paths
 
+from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (
     INPUT_FILE, OUTPUT_FILE, INIT_CONDS, SCHEME
 )
@@ -58,6 +59,10 @@ def equilibrate_main(output_storage, scheme, init_conds, multiplier,
     return simulation.sample_set, simulation
 
 
-CLI = equilibrate
-SECTION = "Simulation"
-REQUIRES_OPS = (1, 2)
+PLUGIN = OPSCommandPlugin(
+    command=equilibrate,
+    section="Simulation",
+    requires_ops=(1, 2),
+    requires_cli=(0, 3)
+)
+

paths_cli/commands/md.py

@@ -1,6 +1,7 @@
 import click
 
 import paths_cli.utils
+from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (INPUT_FILE, OUTPUT_FILE, ENGINE,
                                   MULTI_ENSEMBLE, INIT_SNAP)
 
@@ -197,7 +198,10 @@ def md_main(output_storage, engine, ensembles, nsteps, initial_frame):
                                      'final_conditions')
     return trajectory, None
 
-CLI = md
-SECTION = "Simulation"
-REQUIRES_OPS = (1, 0)
 
+PLUGIN = OPSCommandPlugin(
+    command=md,
+    section="Simulation",
+    requires_ops=(1, 0),
+    requires_cli=(0, 3)
+)

paths_cli/commands/pathsampling.py

@@ -1,6 +1,7 @@
 import click
 # import openpathsampling as paths
 
+from paths_cli import OPSCommandPlugin
 from paths_cli.parameters import (
     INPUT_FILE, OUTPUT_FILE, INIT_CONDS, SCHEME, N_STEPS_MC
 )
@@ -37,6 +38,9 @@ def pathsampling_main(output_storage, scheme, init_conds, n_steps):
     return simulation.sample_set, simulation
 
 
-CLI = pathsampling
-SECTION = "Simulation"
-REQUIRES_OPS = (1, 0)
+PLUGIN = OPSCommandPlugin(
+    command=pathsampling,
+    section="Simulation",
+    requires_ops=(1, 0),
+    requires_cli=(0, 3)
+)