Merge pull request #1692 from dib-lab/fix/pre_v21rc1

Update author lists

.mailmap

@@ -1,6 +1,7 @@
+Daniel Standage <[email protected]> <[email protected]>
 Shannon EK Joslin <[email protected]>
-Ali <[email protected]>
-Russell <[email protected]>
+Ali Aliyari <[email protected]>
+Russell Neches <[email protected]>
 Ryan Shean <[email protected]>
 Nicole Kingsley <[email protected]>
 Lisa Cohen <[email protected]>

CHANGELOG.md

@@ -6,7 +6,7 @@ The khmer project's command line scripts adhere to
 [Semantic Versioning](http://semver.org/). The Python and C++ APIs are not yet
 under semantic versioning, but will be in future versions of khmer.
 
-## [Unreleased]
+## [2.1] - 2017-05-XX
 ### Added
 - New `--no-reformat` option for `interleave-reads.py` script disables default
   read name correction behavior.

Makefile

@@ -355,29 +355,14 @@ convert-release-notes:
 		pandoc --from=markdown --to=rst $${file} > $${file%%.md}.rst; \
 		done
 
-list-authors:
-	@echo '\author[1]{Michael R. Crusoe}'
-	@git log --format='\author[]{%aN}' | sort -uk2 | \
-		grep -v 'root\|crusoe\|titus'
-	@echo '\author[]{C. Titus Brown}'
-	@echo '\affil[1]{[email protected]}'
-	@git log --format='\author[]{%aN} \affil[]{%aE}' | sort -uk2 | \
-		awk -F\\ '{print "\\"$$3}' | grep -v \
-		'root\|crusoe\|titus\|waffle\|boyce\|pickett.rodney'
-	# R. Boyce requested to be removed 2015/05/21
-	# via pers correspondence to MRC
-	# P Rodney requested to be removed 2015/06/22 via pers correspondence
-	# to MRC
-	@echo '\affil[]{[email protected]}'
-
 list-author-emails:
-	@echo 'name, E-Mail Address'
-	@git log --format='%aN,%aE' | sort -u | grep -v 'root\|waffle\|boyce'
+	@echo 'name,E-Mail Address'
+	@echo 'Daniel Standage,[email protected]'
+	@git log --format='%aN,%aE' | sort -u | grep -v -F -f author-skips.txt
+	@echo 'C. Titus Brown,[email protected]'
 
 list-citation:
-	git log --format='%aN,%aE' | sort -u | grep -v \
-		'root\|crusoe\|titus\|waffleio\|Hello\|boyce\|rodney' \
-		> authors.csv
+	git log --format='%aN,%aE' | sort -u | grep -v -F -f author-skips.txt > authors.csv
 	python sort-authors-list.py
 
 ## cpp-demos   : run programs demonstrating access to the (unstable) C++ API

author-skips.txt

@@ -0,0 +1,11 @@
+root
+[email protected]
+[email protected]
+standage
+titus
+waffleio
+Hello
+# R. Boyce requested to be removed 2015/05/21 via pers correspondence to MRC
+boyce
+# P. Rodney requested to be removed 2015/06/22 via pers correspondence to MRC
+rodney

authors.csv

@@ -0,0 +1,69 @@
+Adam Caldwell,[email protected]
+Adina Howe,[email protected]
+Aditi Gupta,[email protected]
+Alex Hyer,[email protected]
+Alexander Johan Nederbragt,[email protected]
+Ali Aliyari,[email protected]
+Amanda Charbonneau,[email protected]
+Andreas Härpfer,[email protected]
+Bede Constantinides,[email protected]
+Benjamin Taylor,[email protected]
+Brian Wyss,[email protected]
+Cait Sydney,[email protected]
+Camille Scott,[email protected]
+Charles Pepe-Ranney,[email protected]
+Connor T. Skennerton,[email protected]
+David Lin,[email protected]
+Elmar Bucher,[email protected]
+Eric McDonald,[email protected]
+Erich Schwarz,[email protected]
+Greg Edvenson,[email protected]
+Heather L. Wiencko,[email protected]
+Humberto Ortiz-Zuazaga,[email protected]
+Hussien F. Alameldin,[email protected]
+Iván González,[email protected]
+Jacob Fenton,[email protected]
+James A. Stapleton,[email protected]
+James Spencer,[email protected]
+Jared Simpson,[email protected]
+Jason Pell,[email protected]
+Jeramia Ory,[email protected]
+Jessica Mizzi,[email protected]
+Jiarong Guo,[email protected]
+Joe Stein,[email protected]
+Jonathan Gluck,[email protected]
+Jordan Fish,[email protected]
+Joshua R. Herr,[email protected]
+Joshua R. Nahum,[email protected]
+Josiah Seaman,[email protected]
+Justin Lippi,[email protected]
+Kaben Nanlohy,[email protected]
+Kevin D. Murray,[email protected]
+Leonor Garcia-Gutierrez,[email protected]
+Lisa Cohen,[email protected]
+Luiz Irber,[email protected]
+Michael R. Crusoe,[email protected]
+Michael Wright,[email protected]
+Nicole Kingsley,[email protected]
+Pamela McA'Nulty,[email protected]
+Phillip Garland,[email protected]
+Qingpeng Zhang,[email protected]
+Ramakrishnan Srinivasan,[email protected]
+Reed Cartwright,[email protected]
+Rhys Kidd,[email protected]
+Russell Neches,[email protected]
+Ryan Shean,[email protected]
+Sarah Guermond,[email protected]
+Sascha Steinbiss,[email protected]
+Scott Fay,[email protected]
+Scott Sievert,[email protected]
+Shannon EK Joslin,[email protected]
+Sherine Awad,[email protected]
+Susan R Steinman,[email protected]
+Sydney Pickens,[email protected]
+Tamer Mansour,[email protected]
+Thomas Fenzl,[email protected]
+Tim Head,[email protected]
+Will Trimble,[email protected]
+Zachary N Russ,[email protected]
+en zyme,[email protected]

doc/index.rst

@@ -76,22 +76,25 @@ started on khmer development <dev/getting-started>`.
 Details
 =======
 
-:Authors: Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar
-        Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede
-        Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl,
-        Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck,
-        Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R.
-        Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd,
-        David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric
-        McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben
-        Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia
-        Ory, Jason Pell, Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz,
-        Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T.
-        Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage,
-        James A. Stapleton, Joe Stein, Susan R Steinman, Benjamin Taylor, Will
+:Authors: Daniel Standage, Hussien F. Alameldin, Ali Aliyari, Sherine
+        Awad, Elmar Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau,
+        Lisa Cohen, Bede Constantinides, Michael R. Crusoe, Greg Edvenson,
+        Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-
+        Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah
+        Guermond, Jiarong Guo, Aditi Gupta, Tim Head, Joshua R. Herr, Adina
+        Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Shannon EK Joslin, Rhys
+        Kidd, Nicole Kingsley, David Lin, Justin Lippi, Tamer Mansour, Pamela
+        McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R.
+        Nahum, Kaben Nanlohy, Russell Neches, Alexander Johan Nederbragt,
+        Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney,
+        Sydney Pickens, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah
+        Seaman, Ryan Shean, Scott Sievert, Jared Simpson, Connor T. Skennerton,
+        James Spencer, Ramakrishnan Srinivasan, James A. Stapleton, Joe Stein,
+        Sascha Steinbiss, Susan R Steinman, Cait Sydney, Benjamin Taylor, Will
         Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng
         Zhang, en zyme, C. Titus Brown
 
+
 :Contact: [email protected]
 :GitHub: https://github.com/dib-lab/khmer
 :License: BSD

setup.py

@@ -45,6 +45,7 @@
 import shutil
 import subprocess
 import tempfile
+import csv
 
 from setuptools import setup
 from setuptools import Extension
@@ -192,35 +193,28 @@ def check_for_openmp():
 else:
     CLASSIFIERS.append("Development Status :: 5 - Production/Stable")
 
+
+# This sorts the author list by first name rather than last name. Not worth
+#     fixing for PyPI in my opinion. The sort-authors-list.py handles it
+#     correctly for the citation information, but this requires a non-standard
+#     library that we don't want to add as a dependency for `setup.py`.
+#     -- Daniel Standage, 2017-05-21
+with open('authors.csv', 'r') as csvin:
+    authors = csv.reader(csvin)
+    authorstr = ', '.join([row[0] for row in authors])
+    authorstr = 'Daniel Standage, ' + authorstr + ', C. Titus Brown'
+
+
 SETUP_METADATA = \
     {
         "name": "khmer",
         "version": versioneer.get_version(),
         "description": 'khmer k-mer counting library',
         "long_description": open("README.rst").read(),
-        "author": "Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, "
-                  "Elmar Bucher, Adam Caldwell, Reed Cartwright, "
-                  "Amanda Charbonneau, Bede Constantinides, Greg Edvenson, "
-                  "Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, "
-                  "Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, "
-                  "Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, "
-                  "Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, "
-                  "Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, "
-                  "Tamer Mansour, Pamela McA'Nulty, Eric McDonald, "
-                  "Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, "
-                  "Kaben Nanlohy, Alexander Johan Nederbragt, "
-                  "Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, "
-                  "Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, "
-                  "Camille Scott, Josiah Seaman, Scott Sievert, "
-                  "Jared Simpson, Connor T. Skennerton, James Spencer, "
-                  "Ramakrishnan Srinivasan, Daniel Standage, "
-                  "James A. Stapleton, Joe Stein, Susan R Steinman, "
-                  "Benjamin Taylor, Will Trimble, Heather L. Wiencko, "
-                  "Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme, "
-                  "C. Titus Brown",
+        "author": authorstr,
         "author_email": '[email protected]',
-        # "maintainer": 'Michael R. Crusoe', # this overrides the author field
-        # "maintainer_email": '[email protected]', # so don't include it
+        # "maintainer": 'Daniel Standage', # this overrides the author field
+        # "maintainer_email": '[email protected]', # so don't include
         # http://docs.python.org/2/distutils/setupscript.html
         # additional-meta-data note #3
         "url": 'https://khmer.readthedocs.io/',

sort-authors-list.py

@@ -46,7 +46,7 @@
         authors.append((HumanName(name), address))
 
 authors = sorted(authors, key=lambda author: author[0].last)
-authors.insert(0, (HumanName("Michael R. Crusoe"), "[email protected]"))
+authors.insert(0, (HumanName("Daniel Standage"), "[email protected]"))
 authors.append((HumanName("C. Titus Brown"), "[email protected]"))
 
 # print(authors)