From 88caad213c40c5f4643b3dfb76cb50d5fcf1d0c9 Mon Sep 17 00:00:00 2001
From: Matthew D <matthew.dangerfield@yandex.com>
Date: Thu, 9 Feb 2017 17:27:50 -0600
Subject: [PATCH] Switch farg_flags to farg.flags to fix bug in batch mode

---
 .gitignore                                                | 1 +
 data/pyseqsee_app_template/batch_ui.py_tmpl               | 2 +-
 data/pyseqsee_app_template/controller.py_tmpl             | 2 +-
 data/pyseqsee_app_template/run_{application_name}.py_tmpl | 2 +-
 docs/howto/flags.rst                                      | 6 +++---
 docs/new_app/add_input_flags.rst                          | 2 +-
 docs/new_app/update_workspace.rst                         | 2 +-
 farg/apps/bongard/batch_ui.py                             | 2 +-
 farg/apps/bongard/controller.py                           | 2 +-
 farg/apps/bongard/run_bongard.py                          | 2 +-
 farg/apps/seqsee/batch_ui.py                              | 2 +-
 farg/apps/seqsee/controller.py                            | 2 +-
 farg/apps/seqsee/relation.py                              | 2 +-
 farg/apps/seqsee/run_seqsee.py                            | 2 +-
 farg/apps/seqsee/subspaces/are_we_done.py                 | 2 +-
 farg/apps/seqsee/subspaces/get_mapping.py                 | 2 +-
 farg/core/controller.py                                   | 2 +-
 farg/core/ltm/manager.py                                  | 6 ++----
 farg/core/main.py                                         | 2 +-
 farg/core/run_mode/batch.py                               | 2 +-
 farg/core/run_mode/non_interactive.py                     | 2 +-
 farg/core/run_mode/single.py                              | 2 +-
 farg/core/run_mode/sxs.py                                 | 2 +-
 farg/core/ui/batch_ui.py                                  | 2 +-
 farg/core/ui/gui/__init__.py                              | 2 +-
 farg/core/ui/gui/central_pane.py                          | 2 +-
 farg_flags.py => farg/flags.py                            | 0
 27 files changed, 29 insertions(+), 30 deletions(-)
 rename farg_flags.py => farg/flags.py (100%)

diff --git a/.gitignore b/.gitignore
index 8e7eb04..7283deb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,3 +14,4 @@ seqsee.main
 *~
 build
 *.egg-info
+.vscode/
diff --git a/data/pyseqsee_app_template/batch_ui.py_tmpl b/data/pyseqsee_app_template/batch_ui.py_tmpl
index 2011341..cca0a29 100644
--- a/data/pyseqsee_app_template/batch_ui.py_tmpl
+++ b/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):
diff --git a/data/pyseqsee_app_template/controller.py_tmpl b/data/pyseqsee_app_template/controller.py_tmpl
index 9309df8..3c7d440 100644
--- a/data/pyseqsee_app_template/controller.py_tmpl
+++ b/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'
diff --git a/data/pyseqsee_app_template/run_{application_name}.py_tmpl b/data/pyseqsee_app_template/run_{application_name}.py_tmpl
index 7c21431..e131923 100644
--- a/data/pyseqsee_app_template/run_{application_name}.py_tmpl
+++ b/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.
diff --git a/docs/howto/flags.rst b/docs/howto/flags.rst
index dde8aac..a82d290 100644
--- a/docs/howto/flags.rst
+++ b/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
 
diff --git a/docs/new_app/add_input_flags.rst b/docs/new_app/add_input_flags.rst
index 0b3a771..e5b214a 100644
--- a/docs/new_app/add_input_flags.rst
+++ b/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
\ No newline at end of file
diff --git a/docs/new_app/update_workspace.rst b/docs/new_app/update_workspace.rst
index c8547ea..5c0e7de 100644
--- a/docs/new_app/update_workspace.rst
+++ b/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::
 
diff --git a/farg/apps/bongard/batch_ui.py b/farg/apps/bongard/batch_ui.py
index 922027a..7999550 100644
--- a/farg/apps/bongard/batch_ui.py
+++ b/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):
diff --git a/farg/apps/bongard/controller.py b/farg/apps/bongard/controller.py
index 9b03dd6..ad0116d 100644
--- a/farg/apps/bongard/controller.py
+++ b/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'
 
diff --git a/farg/apps/bongard/run_bongard.py b/farg/apps/bongard/run_bongard.py
index de90a7e..2bf18cf 100644
--- a/farg/apps/bongard/run_bongard.py
+++ b/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.
diff --git a/farg/apps/seqsee/batch_ui.py b/farg/apps/seqsee/batch_ui.py
index ac1199a..1ae747b 100644
--- a/farg/apps/seqsee/batch_ui.py
+++ b/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
diff --git a/farg/apps/seqsee/controller.py b/farg/apps/seqsee/controller.py
index 70cc882..6e25e1c 100644
--- a/farg/apps/seqsee/controller.py
+++ b/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'
 
diff --git a/farg/apps/seqsee/relation.py b/farg/apps/seqsee/relation.py
index 87b6a4b..b234b56 100644
--- a/farg/apps/seqsee/relation.py
+++ b/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."""
diff --git a/farg/apps/seqsee/run_seqsee.py b/farg/apps/seqsee/run_seqsee.py
index 1ed2a35..ecabad6 100755
--- a/farg/apps/seqsee/run_seqsee.py
+++ b/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])
diff --git a/farg/apps/seqsee/subspaces/are_we_done.py b/farg/apps/seqsee/subspaces/are_we_done.py
index 30050bc..44ba477 100644
--- a/farg/apps/seqsee/subspaces/are_we_done.py
+++ b/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.
diff --git a/farg/apps/seqsee/subspaces/get_mapping.py b/farg/apps/seqsee/subspaces/get_mapping.py
index 0325910..9bd953c 100644
--- a/farg/apps/seqsee/subspaces/get_mapping.py
+++ b/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.
 
diff --git a/farg/core/controller.py b/farg/core/controller.py
index 7303d17..2089a52 100644
--- a/farg/core/controller.py
+++ b/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.
diff --git a/farg/core/ltm/manager.py b/farg/core/ltm/manager.py
index e9f2fc8..42b17dc 100644
--- a/farg/core/ltm/manager.py
+++ b/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")
 
diff --git a/farg/core/main.py b/farg/core/main.py
index bb7aac5..0d7e896 100644
--- a/farg/core/main.py
+++ b/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.
diff --git a/farg/core/run_mode/batch.py b/farg/core/run_mode/batch.py
index f95f9fb..b78646d 100644
--- a/farg/core/run_mode/batch.py
+++ b/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
diff --git a/farg/core/run_mode/non_interactive.py b/farg/core/run_mode/non_interactive.py
index eacff21..74d1a58 100644
--- a/farg/core/run_mode/non_interactive.py
+++ b/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.
diff --git a/farg/core/run_mode/single.py b/farg/core/run_mode/single.py
index a725d26..c7e8b21 100644
--- a/farg/core/run_mode/single.py
+++ b/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):
diff --git a/farg/core/run_mode/sxs.py b/farg/core/run_mode/sxs.py
index aed07b5..17b2897 100644
--- a/farg/core/run_mode/sxs.py
+++ b/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."""
diff --git a/farg/core/ui/batch_ui.py b/farg/core/ui/batch_ui.py
index 9d3a512..a1fbbe7 100644
--- a/farg/core/ui/batch_ui.py
+++ b/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):
diff --git a/farg/core/ui/gui/__init__.py b/farg/core/ui/gui/__init__.py
index ddefe14..e96d2f2 100644
--- a/farg/core/ui/gui/__init__.py
+++ b/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.
diff --git a/farg/core/ui/gui/central_pane.py b/farg/core/ui/gui/central_pane.py
index c84bb9b..347e49b 100644
--- a/farg/core/ui/gui/central_pane.py
+++ b/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
 
diff --git a/farg_flags.py b/farg/flags.py
similarity index 100%
rename from farg_flags.py
rename to farg/flags.py