Merge pull request #442 from cogent3/release

merged release branch 2019.12.6a

.hgtags

@@ -9,3 +9,4 @@ beaba5e226bc1f3a9673caf1a1ce6c8dd19c0434 2019.10.17a
 aa75049787af4c6bcdf1c9d2c322e179031a27e9 2019.11.15a
 aa75049787af4c6bcdf1c9d2c322e179031a27e9 2019.11.15a
 7a82cae4574720a68aa05fe14fff8bc409d41612 2019.11.15a
+be3ef6a5a2538ab5cc50d8bb26d25c22babe47e7 2019.12.6a

README.md

@@ -29,7 +29,7 @@ $ pip install cogent3
 ### Installing the development version
 
 ```bash
-$ pip install git+https://github.com/cogent3/cogent3.git@master#egg=cogent3
+$ pip install git+https://github.com/cogent3/cogent3.git@develop#egg=cogent3
 ```
 
 ## Project Information

doc/conf.py

@@ -41,7 +41,7 @@
 
 version = ""
 
-release = "2019.11.15.a"
+release = "2019.12.6a"
 
 # exclude_trees = ["_build"]
 

setup.py

@@ -19,7 +19,7 @@
     "Daniel McDonald",
 ]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/__init__.py

@@ -69,7 +69,7 @@
     "Daniel McDonald",
 ]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Gavin Huttley"
 __email__ = "gavin.huttley@anu.edu.au"
 __status__ = "Production"

src/cogent3/align/__init__.py

@@ -25,7 +25,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Jeremy Widmann", "Gavin Huttley", "Rob Knight"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Gavin Huttley"
 __email__ = "gavin.huttley@anu.edu.au"
 __status__ = "Production"

src/cogent3/align/_compare.pyx

@@ -2,7 +2,7 @@
 """
 
 version_info = (1, 3)
-__version__ = "('2019', '11', '15', 'a')"
+__version__ = "('2019', '12', '6a')"
 
 cdef int cmax(int a, int b):
     if a > b:

src/cogent3/align/_pairwise_pogs.pyx

@@ -12,7 +12,7 @@ cdef extern from "math.h":
     double log (double x)
 
 version_info = (3, 2)
-__version__ = "('2019', '11', '15', 'a')"
+__version__ = "('2019', '12', '6a')"
 
 cdef double SCALE_STEP, MIN_FLOAT_VALUE
 SCALE_STEP = 2.0**50

src/cogent3/align/_pairwise_seqs.pyx

@@ -14,7 +14,7 @@ cdef extern from "math.h":
     double log (double x)
 
 version_info = (3, 2)
-__version__ = "('2019', '11', '15', 'a')"
+__version__ = "('2019', '12', '6a')"
 
 cdef double SCALE_STEP, MIN_FLOAT_VALUE
 SCALE_STEP = 2.0**50

src/cogent3/align/align.py

@@ -13,7 +13,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/align/dp_calculation.py

@@ -18,7 +18,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Gavin Huttleuy"
 __email__ = "gavin.huttley@anu.edu.au"
 __status__ = "Production"

src/cogent3/align/indel_model.py

@@ -10,7 +10,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/align/indel_positions.py

@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/align/pairwise.py

@@ -60,7 +60,7 @@ def _importedPyrexAligningModule(name):
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/align/progressive.py

@@ -12,7 +12,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/align/pycompare.py

@@ -11,7 +11,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Gavin Huttley"
 __email__ = "gavin.huttley@anu.edu.au"
 __status__ = "Production"

src/cogent3/align/traceback.py

@@ -10,7 +10,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Rob Knight", "Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"

src/cogent3/app/__init__.py

@@ -8,7 +8,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Gavin Huttley"]
 __license__ = "BSD-3"
-__version__ = "2019.11.15.a"
+__version__ = "2019.12.6a"
 __maintainer__ = "Gavin Huttley"
 __email__ = "Gavin.Huttley@anu.edu.au"
 __status__ = "Alpha"