daler · daler · Jan 24, 2022 · Jan 24, 2022 · Jan 24, 2022 · Jan 24, 2022
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -5,7 +5,7 @@ jobs:
   build-and-test:
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2

diff --git a/.travis.yml b/.travis.yml
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,19 +1,22 @@
-Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working
-with BED, BAM, GFF, and VCF files
+Wrapper -- and more -- for BEDtools
 
-Copyright (c) 2010-2015 Ryan Dale
+Copyright (c) 2010-2022 Ryan Dale
 All rights reserved.
 
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
 
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
-You should have received a copy of the GNU General Public License along
-with this program; if not, write to the Free Software Foundation, Inc., 51
-Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/condatest.sh b/condatest.sh
diff --git a/docs/source/changes.rst b/docs/source/changes.rst
@@ -3,6 +3,35 @@
 Changelog
 =========
 
+Changes in v0.9
+---------------
+
+2022-01-23
+
+The biggest change is that pybedtools is now under the MIT license, following
+the lead of BEDTools itself.
+
+Bugfixes:
+
+* Bugfix: `Interval` objects representing VCF lines now have their `start`
+  attribute correctly zero-based, as indicated in the docs and consistent with
+  other 1-based formats. See `#355 <https://github.com/daler/pybedtools/issues/355>`_.
+* Bugfix: Manually creating `Interval` objects using the `otherfields` argument
+  now correctly converts to C++ strings. See `#348
+  <https://github.com/daler/pybedtools/issues/348>`_.
+* Bugfix: Workaround for `BedTool.intersect` which in some versions of BEDTools
+  requires a specific order of arguments. Fixes `#345
+  <https://github.com/daler/pybedtools/issues/345>`_ and also is a better way
+  of addressing `#81 <https://github.com/daler/pybedtools/issues/81>`_.
+
+Code cleanup:
+
+* Removed some remnants of Python 2.7 support (thanks @DavidCain)
+* Updates to setup.py classifiers to better reflect state of code (thanks @DavidCain)
+* Sorted filenames in setup.py to improve reproducibility of build (thanks @lamby)
+* Tests converted to run on GitHub Actions (see `#339
+  <https://github.com/daler/pybedtools/pull/339>`_).
+
 Changes in v0.8.2
 -----------------
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -12,8 +12,9 @@
 
 
 
-`pybedtools` is released under the GPLv2 license; see LICENSE.txt for more
-info.
+As of 2022, `pybedtools` is released under the MIT license; see LICENSE.txt for
+more info.
+
 
 .. note::
 

diff --git a/pybedtools/include/bedFile.cpp b/pybedtools/include/bedFile.cpp
@@ -7,7 +7,7 @@ Department of Biochemistry and Molecular Genetics
 University of Virginia
 [email protected]
 
-Licensed under the GNU General Public License 2.0 license.
+Licensed under the MIT license (as of Jan 2022)
 ******************************************************************************/
 #include "bedFile.h"
 

diff --git a/pybedtools/include/bedFile.h b/pybedtools/include/bedFile.h
@@ -7,7 +7,7 @@
   University of Virginia
   [email protected]
 
-  Licensed under the GNU General Public License 2.0 license.
+  Licensed under the MIT license (as of Jan 2022)
 ******************************************************************************/
 #ifndef BEDFILE_H
 #define BEDFILE_H

diff --git a/pybedtools/include/fileType.cpp b/pybedtools/include/fileType.cpp
@@ -7,7 +7,7 @@
   University of Virginia
   [email protected]
 
-  Licensed under the GNU General Public License 2.0 license.
+  Licensed under the MIT license (as of Jan 2022)
 ******************************************************************************/
 
 #include "fileType.h"

diff --git a/pybedtools/include/fileType.h b/pybedtools/include/fileType.h
@@ -7,7 +7,7 @@
   University of Virginia
   [email protected]
 
-  Licensed under the GNU General Public License 2.0 license.
+  Licensed under the MIT license (as of Jan 2022)
 ******************************************************************************/
 #ifndef FILETYPE_H
 #define FILETYPE_H

diff --git a/setup.py b/setup.py
@@ -76,8 +76,8 @@
 
 
 MAJ = 0
-MIN = 8
-REV = 2
+MIN = 9
+REV = 0
 VERSION = '%d.%d.%d' % (MAJ, MIN, REV)
-Original file line number
+Diff line change
@@ Expand Up / @@ -76,8 +76,8 @@ @@
     MAJ = 0
-    MIN = 8
-    REV = 2
+    MIN = 9
+    REV = 0
     VERSION = '%d.%d.%d' % (MAJ, MIN, REV)
@@ Expand Down @@