mainly, adding the append command

Author: dwhswenson

paths_cli/cli.py

@@ -7,6 +7,8 @@
 import os
 
 import click
+# import click_completion
+# click_completion.init()
 
 CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
 

paths_cli/commands/append.py

@@ -0,0 +1,40 @@
+import click
+from paths_cli.parameters import (
+    INPUT_FILE, APPEND_FILE, MULTI_CV, MULTI_ENGINE, MULTI_VOLUME,
+    MULTI_NETWORK, MULTI_SCHEME, MULTI_TAG
+)
+
+@click.command(
+    'append',
+    short_help="add objects from INPUT_FILE  to another file"
+)
+@INPUT_FILE.clicked(required=True)
+@APPEND_FILE.clicked(required=True)
+@MULTI_ENGINE.clicked(required=False)
+@MULTI_CV.clicked(required=False)
+@MULTI_VOLUME.clicked(required=False)
+@MULTI_NETWORK.clicked(required=False)
+@MULTI_SCHEME.clicked(required=False)
+@MULTI_TAG.clicked(required=False)
+def append(input_file, append_file, engine, cv, volume, network, scheme,
+           tag):
+    """Append objects from INPUT_FILE to another file.
+    """
+    storage = INPUT_FILE.get(input_file)
+    output_storage = APPEND_FILE.get(append_file)
+    params = [MULTI_ENGINE, MULTI_CV, MULTI_VOLUME, MULTI_NETWORK,
+              MULTI_SCHEME, MULTI_TAG]
+    args = [engine, cv, volume, network, scheme, tag]
+    to_save = []
+    for arg, param in zip(args, params):
+        to_save.extend(param.get(storage, arg))
+
+    for obj in to_save:
+        output_storage.save(obj)
+
+    output_storage.close()
+
+
+CLI = append
+SECTION = "Miscellaneous"
+REQUIRES_OPS = (1, 0)

paths_cli/parameters.py

@@ -43,7 +43,7 @@ def __init__(self, param, mode):
         super(StorageLoader, self).__init__(param)
         self.mode = mode
 
-    def workaround(self, name):
+    def _workaround(self, name):
         # this is messed up... for some reason, storage doesn't create a new
         # file in append mode. That may be a bug
         import openpathsampling as paths
@@ -53,7 +53,7 @@ def workaround(self, name):
 
     def get(self, name):
         import openpathsampling as paths
-        self.workaround(name)
+        self._workaround(name)
         return paths.Storage(name, mode=self.mode)
 
 
@@ -257,3 +257,5 @@ def init_snap_fallback(parameter, storage, name):
 
 N_STEPS_MC = click.option('-n', '--nsteps', type=int,
                           help="number of Monte Carlo trials to run")
+
+MULTI_CV = CVS

paths_cli/tests/test_parameters.py

@@ -338,4 +338,3 @@ def test_APPEND_FILE():
     storage.close()
     os.remove(filename)
     os.rmdir(tempdir)
-