From 732e32fb14587f4c43357620ddadd90aca6ea4c9 Mon Sep 17 00:00:00 2001
From: "Martin K. Scherer" <marscher@users.noreply.github.com>
Date: Thu, 14 Jul 2016 12:13:43 +0200
Subject: [PATCH] [progressreporter] fixed a bug in force_finish, where
 numerator could raise above denominator. (#869)

* [progressreporter] fixed a bug in force_finish, where numerator could raise above denominator.

This used to happen when the progress bar gets updated beyond its previously
registered amount of work.

* [doc] added missing changelog entries...
---
 doc/source/CHANGELOG.rst            | 26 ++++++++++++++++++++------
 pyemma/_base/progress/reporter.py   |  5 ++++-
 pyemma/_base/tests/test_progress.py | 10 ++++++++++
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/doc/source/CHANGELOG.rst b/doc/source/CHANGELOG.rst
index 1e76b15dd..ef45331d6 100644
--- a/doc/source/CHANGELOG.rst
+++ b/doc/source/CHANGELOG.rst
@@ -1,15 +1,29 @@
 Changelog
 =========
 
-2.2.2 ()
---------
-
-*Fixes**:
+2.2.2 (7-14-16)
+---------------
 
-- coordinates: set chunksize correctly. #846
+**New features**:
+- coordinates: SQLite backend for trajectory info data. This enables fast access to this data
+  on parallel filesystems where multiple processes are writing to the database. This greatly
+  speeds ups reader construction and enables fast random access for formats which usually do not
+  support it. #798
 - plots: new optional parameter **arrow_label_size** for network plotting functions to use a custom
   font size for the arrow labels; the default state and arrow label sizes are now determined by the
-  matplotlib default.
+  matplotlib default. #858
+- coordinates: save_trajs takes optional parameter "image_molecules" to correct for broken
+  molecules across periodic boundary conditions. #841
+
+**Fixes**:
+
+- coordinates: set chunksize correctly. #846
+- coordinates: For angle features it was possible to use both cossin=True and deg=True, which
+  makes not sense. #857
+- coordinates: fixed a memory error in kmeans clustering which affected large data sets (>=64GB). #839
+- base: fixed a bug in ProgressReporter (_progress_force_finish in stack trace). #869
+- docs: fixed a lot of docstrings for inherited classes both in coordinates and msm package.
+
 
 2.2.1 (6-21-16)
 ---------------
diff --git a/pyemma/_base/progress/reporter.py b/pyemma/_base/progress/reporter.py
index ba8d810aa..fe6cf0d71 100644
--- a/pyemma/_base/progress/reporter.py
+++ b/pyemma/_base/progress/reporter.py
@@ -202,7 +202,10 @@ def _progress_force_finish(self, stage=0, description=None):
         pg = self._prog_rep_progressbars[stage]
         if not isinstance(pg, _ProgressBar):
             return
-        pg.numerator = pg.denominator
+
+        if pg.numerator < pg.denominator:
+            pg.numerator = pg.denominator
+
         pg._eta.eta_epoch = 0
 
         if description is not None:
diff --git a/pyemma/_base/tests/test_progress.py b/pyemma/_base/tests/test_progress.py
index 1a87b645a..bb7c77e32 100644
--- a/pyemma/_base/tests/test_progress.py
+++ b/pyemma/_base/tests/test_progress.py
@@ -91,5 +91,15 @@ def call_back(stage, progressbar, *args, **kw):
             worker._progress_update(1, stage=0)
         self.assertEqual(self.has_been_called, amount_of_work)
 
+    def test_force_finish(self):
+        import warnings
+        worker = ProgressReporter()
+        worker._progress_register(100)
+        # intentionally overshoot registered work
+        with warnings.catch_warnings(record=True) as cm:
+            worker._progress_update(101)
+        self.assertIn("more work than registered", cm[0].message[0])
+        worker._progress_force_finish()
+
 if __name__ == "__main__":
     unittest.main()