Merge pull request #143 from pachterlab/devel

merge devel into master

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ jobs:
       - name: Setup python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.7'
+          python-version: '3.8'
           architecture: x64
       - name: Install dependencies
         run: pip install -r dev-requirements.txt
@@ -22,8 +22,8 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python: [ '3.6', '3.7', '3.8' ]
-        os: ['ubuntu-18.04']
+        python: [3.6, 3.7, 3.8, 3.9 ]
+        os: [ubuntu-20.04]
     name: Test on Python ${{ matrix.python }}
     steps:
       - name: Checkout branch

docs/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'kb-python'
-copyright = '2019, Kyung Hoi (Joseph) Min'
+copyright = '2021, Kyung Hoi (Joseph) Min'
 author = 'Kyung Hoi (Joseph) Min'
 
 # The full version, including alpha/beta/rc tags
@@ -33,6 +33,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.napoleon',
     'autoapi.extension',
 ]
 autoapi_type = 'python'

kb_python/bins/darwin/kallisto/license.txt

@@ -1,23 +1,25 @@
-Copyright ©2015. The Regents of the University of California (Regents). All
-Rights Reserved. Permission to use, copy, modify, and distribute this software
-and its documentation for educational and research not-for-profit purposes,
-without fee and without a signed licensing agreement, is hereby granted,
-provided that the above copyright notice, this paragraph and the following two
-paragraphs appear in all copies, modifications, and distributions. Contact The
-Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 510,
-Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing
-opportunities.
+BSD 2-Clause License
 
-Created by Nicolas Bray, Harold Pimentel, Pall Melsted and Lior Pachter,
-University of California, Berkeley
+Copyright (c) 2017, Nicolas Bray, Harold Pimentel, Páll Melsted and Lior Pachter
+All rights reserved.
 
-IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL,
-INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF
-THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS
-PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

kb_python/bins/linux/kallisto/license.txt

@@ -1,23 +1,25 @@
-Copyright ©2015. The Regents of the University of California (Regents). All
-Rights Reserved. Permission to use, copy, modify, and distribute this software
-and its documentation for educational and research not-for-profit purposes,
-without fee and without a signed licensing agreement, is hereby granted,
-provided that the above copyright notice, this paragraph and the following two
-paragraphs appear in all copies, modifications, and distributions. Contact The
-Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 510,
-Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing
-opportunities.
+BSD 2-Clause License
 
-Created by Nicolas Bray, Harold Pimentel, Pall Melsted and Lior Pachter,
-University of California, Berkeley
+Copyright (c) 2017, Nicolas Bray, Harold Pimentel, Páll Melsted and Lior Pachter
+All rights reserved.
 
-IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL,
-INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF
-THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS
-PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

kb_python/bins/windows/kallisto/license.txt

@@ -1,23 +1,25 @@
-Copyright ©2015. The Regents of the University of California (Regents). All
-Rights Reserved. Permission to use, copy, modify, and distribute this software
-and its documentation for educational and research not-for-profit purposes,
-without fee and without a signed licensing agreement, is hereby granted,
-provided that the above copyright notice, this paragraph and the following two
-paragraphs appear in all copies, modifications, and distributions. Contact The
-Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 510,
-Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing
-opportunities.
+BSD 2-Clause License
 
-Created by Nicolas Bray, Harold Pimentel, Pall Melsted and Lior Pachter,
-University of California, Berkeley
+Copyright (c) 2017, Nicolas Bray, Harold Pimentel, Páll Melsted and Lior Pachter
+All rights reserved.
 
-IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL,
-INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF
-THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS
-PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.