Add APPEND_FILE parameter

Author: dwhswenson

paths_cli/parameters.py

@@ -1,4 +1,5 @@
 import click
+import os
 # import openpathsampling as paths
 
 class AbstractParameter(object):
@@ -40,8 +41,17 @@ def __init__(self, param, mode):
         super(StorageLoader, self).__init__(param)
         self.mode = mode
 
+    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
+        if self.mode == 'a' and not os.path.exists(name):
+            st = paths.Storage(name, mode='w')
+            st.close()
+
     def get(self, name):
         import openpathsampling as paths
+        self.workaround(name)
         return paths.Storage(name, mode=self.mode)
 
 
@@ -194,5 +204,12 @@ def init_snap_fallback(parameter, storage, name):
     mode='w'
 )
 
+APPEND_FILE = StorageLoader(
+    param=Option('-a', '--append-file',
+                 type=click.Path(writable=True, readable=True),
+                 help="file to append to"),
+    mode='a'
+)
+
 N_STEPS_MC = click.option('-n', '--nsteps', type=int,
                           help="number of Monte Carlo trials to run")

paths_cli/tests/test_parameters.py

@@ -319,3 +319,23 @@ def test_OUTPUT_FILE():
     os.remove(filename)
     os.rmdir(tempdir)
 
+def test_APPEND_FILE():
+    tempdir = tempfile.mkdtemp()
+    filename = os.path.join(tempdir, "test_append_file.nc")
+    assert not os.path.exists(filename)
+    storage = APPEND_FILE.get(filename)
+    print(storage)
+    assert os.path.exists(filename)
+    traj = make_1d_traj([0.0, 1.0])
+    storage.tags['first_save'] = traj[0]
+    storage.close()
+    storage = APPEND_FILE.get(filename)
+    assert storage.tags['first_save'] == traj[0]
+    storage.tags['second_save'] = traj[1]
+    storage.close()
+    storage = APPEND_FILE.get(filename)
+    assert len(storage.tags) == 2
+    storage.close()
+    os.remove(filename)
+    os.rmdir(tempdir)
+