Switch farg_flags to farg.flags to fix bug in batch mode

.gitignore

@@ -14,3 +14,4 @@ seqsee.main
 *~
 build
 *.egg-info
+.vscode/

data/pyseqsee_app_template/batch_ui.py_tmpl

@@ -13,7 +13,7 @@ order to automatically answer questions such as the one above.).
 from farg.core.ui.batch_ui import BatchUI
 
 # If you need access to flags, you need:
-# import farg_flags
+# import farg.flags as farg_flags
 # # The flag --foo is available at farg_flags.FargFlags.foo
 
 class {application_class}BatchUI(BatchUI):

data/pyseqsee_app_template/controller.py_tmpl

@@ -4,7 +4,7 @@ from farg.core.ltm.manager import LTMManager
 import sys
 
 # If you need access to flags, you need:
-# import farg_flags
+# import farg.flags as farg_flags
 # # The flag --foo is available at farg_flags.FargFlags.foo
 
 kLTMName = '{application_name}.main'

data/pyseqsee_app_template/run_{application_name}.py_tmpl

@@ -7,7 +7,7 @@ from farg.apps.{application_name}.read_input_spec import {application_class}Read
 from farg.apps.{application_name}.stopping_conditions import {application_class}StoppingConditions
 from farg.core.main import Main
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 {application_name}_parser = argparse.ArgumentParser(parents=[farg_flags.core_parser])
 # Flags for specifying the input and, for use in testing, expected output.

docs/howto/flags.rst

@@ -11,7 +11,7 @@ Where the flags are defined
 Core flags are defined in 'farg_flags.py', which defines the flags parser called 'core_parser'. The
 entry point for each app extends this. Currently, in Seqsee (run_seqsee.py), we see::
 
-  import farg_flags
+  import farg.flags as farg_flags
   seqsee_parser = argparse.ArgumentParser(parents=[farg_flags.core_parser])
   seqsee_parser.add_argument('--sequence', type=int, nargs='*')
 
@@ -39,7 +39,7 @@ The entry point of apps
 To summerize, here are the relevant bits of the Seqsee app's entry point::
 
   import argparse
-  import farg_flags
+  import farg.flags as farg_flags
   from farg.core.main import Main
   
   seqsee_parser = argparse.ArgumentParser(parents=[farg_flags.core_parser])
@@ -64,7 +64,7 @@ Where the flags get stored
 Flags, after processing, end up both in Main.flags and farg_flags.FargFlags. Other modules will use
 this latter route for accessing. A module may say::
 
-  import farg_flags
+  import farg.flags as farg_flags
   if farg_flags.FargFlags.use_stored_ltm:
     Do something
 

docs/new_app/add_input_flags.rst

@@ -46,7 +46,7 @@ Accessing flags from other files
 These flags will be needed in other parts of the app. In any file needing them, add the following
 lines::
 
-  import farg_flags
+  import farg.flags as farg_flags
 
   # later...
   farg_flags.FargFlags.left

docs/new_app/update_workspace.rst

@@ -51,7 +51,7 @@ This is how the BongardController class currently looks::
       
 We will make a couple of changes for now. First, we will make the flags accessible from this file::
 
-  import farg_flags
+  import farg.flags as farg_flags
   
 And we will update the workspace with the relevant inputs::
 

farg/apps/bongard/batch_ui.py

@@ -13,7 +13,7 @@
 from farg.core.ui.batch_ui import BatchUI
 
 # If you need access to flags, you need:
-# import farg_flags
+# import farg.flags as farg_flags
 # # The flag --foo is available at farg_flags.FargFlags.foo
 
 class BongardBatchUI(BatchUI):

farg/apps/bongard/controller.py

@@ -5,7 +5,7 @@
 from farg.core.ltm.manager import LTMManager
 import sys
 
-import farg_flags
+import farg.flags as farg_flags
 
 kLTMName = 'bongard.main'
 

farg/apps/bongard/run_bongard.py

@@ -7,7 +7,7 @@
 from farg.apps.bongard.stopping_conditions import BongardStoppingConditions
 from farg.core.main import Main
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 bongard_parser = argparse.ArgumentParser(parents=[farg_flags.core_parser])
 # Flags for specifying the input and, for use in testing, expected output.

farg/apps/seqsee/batch_ui.py

@@ -15,7 +15,7 @@
 from farg.core.exceptions import SuccessfulCompletion
 from farg.core.ui.batch_ui import BatchUI
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 def HasAsPrefix(longer_list, shorter_list):
   return longer_list[:len(shorter_list)] == shorter_list

farg/apps/seqsee/controller.py

@@ -20,7 +20,7 @@
 import logging
 import sys
 
-import farg_flags
+import farg.flags as farg_flags
 
 kLTMName = 'seqsee.main'
 

farg/apps/seqsee/relation.py

@@ -15,7 +15,7 @@
 from farg.core.util import SelectWeightedByActivation
 from farg.core.codelet import Codelet
 from farg.core.focusable_mixin import FocusableMixin
-import farg_flags
+import farg.flags as farg_flags
 from farg.core.history import History, ObjectType
 
 """A relation is a specific instance of a mapping."""

farg/apps/seqsee/run_seqsee.py

@@ -19,7 +19,7 @@
 from farg.apps.seqsee.read_input_spec import SeqseeReadInputSpec
 from farg.apps.seqsee.stopping_conditions import SeqseeStoppingConditions
 from farg.core.main import Main
-import farg_flags
+import farg.flags as farg_flags
 import sys
 
 seqsee_parser = argparse.ArgumentParser(parents=[farg_flags.core_parser])

farg/apps/seqsee/subspaces/are_we_done.py

@@ -11,7 +11,7 @@
 # You should have received a copy of the GNU General Public License along with this
 # program.  If not, see <http://www.gnu.org/licenses/>
 from farg.core.subspace import Subspace, QuickReconnResults
-import farg_flags
+import farg.flags as farg_flags
 
 class SubspaceAreWeDone(Subspace):
   """Checks if we should stop because we have found or explained the answer.

farg/apps/seqsee/subspaces/get_mapping.py

@@ -23,7 +23,7 @@
 
 from farg.apps.seqsee.sobject import SGroup
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 # TODO(#53 --- Dec 29, 2011): Needs big fat documentation.
 

farg/core/controller.py

@@ -23,7 +23,7 @@
 from farg.core.stream import Stream
 from farg.core.util import Toss
 
-import farg_flags
+import farg.flags as farg_flags
 
 class Controller:
   """Purely mechanical (read "dumb") loop to control entire app or individual subspaces.

farg/core/ltm/manager.py

@@ -14,12 +14,10 @@
 """Manages the set of LTMs."""
 
 import logging
-
-from farg.core.ltm.graph import LTMGraph
 import os.path
-import sys
 
-import farg_flags
+from farg.core.ltm.graph import LTMGraph
+import farg.flags as farg_flags
 
 kLogger = logging.getLogger("LTM")
 

farg/core/main.py

@@ -23,7 +23,7 @@
 import logging.config
 import os.path
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 class Main:
   """The Base class for the Main class of an application.

farg/core/run_mode/batch.py

@@ -12,7 +12,7 @@
 # program.  If not, see <http://www.gnu.org/licenses/>
 
 from collections import defaultdict
-import farg_flags
+import farg.flags as farg_flags
 from farg.core.run_mode.non_interactive import RunModeNonInteractive, RunMultipleTimes, MultipleRunGUI
 from farg.core.run_stats import RunStats
 import os.path

farg/core/run_mode/non_interactive.py

@@ -28,7 +28,7 @@
 import subprocess
 import sys
 import threading
-import farg_flags
+import farg.flags as farg_flags
 
 class RunMultipleTimes(threading.Thread, metaclass=ABCMeta):
   """Class to run the application several times on a set of inputs.

farg/core/run_mode/single.py

@@ -15,7 +15,7 @@
 from farg.core.run_mode.non_interactive import RunModeNonInteractive
 from io import StringIO
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 
 class RunModeSingle(RunModeNonInteractive):

farg/core/run_mode/sxs.py

@@ -14,7 +14,7 @@
 from farg.core.run_mode.non_interactive import (RunModeNonInteractive, RunMultipleTimes,
                                                 MultipleRunGUI)
 import sys
-import farg_flags
+import farg.flags as farg_flags
 
 class SxSRunMultipleTimes(RunMultipleTimes):
   """Multiple-runner specialized for SxS."""

farg/core/ui/batch_ui.py

@@ -12,7 +12,7 @@
 # program.  If not, see <http://www.gnu.org/licenses/>
 
 from farg.core.ltm.manager import LTMManager
-import farg_flags
+import farg.flags as farg_flags
 
 class BatchUI:
   def __init__(self, *, controller_class, stopping_condition_fn=None):

farg/core/ui/gui/__init__.py

@@ -22,7 +22,7 @@
 from tkinter.messagebox import askyesno, showinfo
 import logging
 import threading
-import farg_flags
+import farg.flags as farg_flags
 
 class RunForNSteps(threading.Thread):
   """Runs controller for up to n steps.

farg/core/ui/gui/central_pane.py

@@ -17,7 +17,7 @@
 
 Each view is an instance of a subclass of :py:class:`~farg.core.ui.gui.views.viewport.ViewPort`.
 """
-import farg_flags
+import farg.flags as farg_flags
 import sys
 from tkinter import ALL, Canvas, Menu