Merge pull request #2 from Edinburgh-Genome-Foundry/dev

Biopython v1.78

.gitignore

@@ -36,7 +36,7 @@ nosetests.xml
 .pydevproject
 
 # Temp files
-
+.vscode/
 *~
 
 # Pipy codes

LICENCE.txt

@@ -1,8 +1,4 @@
-
-The MIT License (MIT)
-[OSI Approved License]
-
-The MIT License (MIT)
+MIT License
 
 Copyright (c) 2017 Edinburgh Genome Foundry
 
@@ -13,13 +9,13 @@ 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:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 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.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

@@ -10,6 +10,10 @@
    :target: https://travis-ci.org/Edinburgh-Genome-Foundry/GoldenHinges
    :alt: Travis CI build status
 
+.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/GoldenHinges/badge.svg?branch=master
+   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/GoldenHinges?branch=master
+
+
 Golden Hinges (full documentation `here <https://edinburgh-genome-foundry.github.io/GoldenHinges/>`_) is a Python library to find sets
 of overhangs (also called junctions, or protusions) for multipart DNA assembly
 such as Golden Gate assembly.
@@ -24,14 +28,14 @@ mandatory and forbidden overhangs) Golden Hinges enables to find:
   decomposition, in exterme cases where the original sequence does not allow
   for such decomposition.
 
-You can see Golden Hinges in action in this
-`web demo <http://cuba.genomefoundry.org/design-overhangs>`_:
+You can see Golden Hinges in action in this web demo:
+`Design Golden Gate Overhangs <http://cuba.genomefoundry.org/design-overhangs>`_
 
 Examples of use
-----------------
+---------------
 
-Finding maximal overhangs sets
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Finding maximal overhang sets
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Let us compute a collection of overhangs, as large as possible, where
 
@@ -91,8 +95,8 @@ attempt to find larger sets:
 Using experimental annealing data from Potapov 2018
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-`This study by Potapov *et al.* <https://www.biorxiv.org/content/early/2018/05/15/322297>`_
-provides insightful data on overhangs annealing, in particular which overhangs
+`This study by Potapov et al. <https://www.biorxiv.org/content/early/2018/05/15/322297>`_
+provides insightful data on overhang annealing, in particular which overhangs
 have weak general annealing power, and which pairs of overhangs have significant
 "cross-talk". You can use the data in this paper via the Python
 `tatapov <https://github.com/Edinburgh-Genome-Foundry/tatapov>`_ library
@@ -183,7 +187,7 @@ Note that solutions involving base changes are penalized and solutions involving
 the original solution will always be prefered, so no base change will be
 suggested unless strictly necessary.
 
-If the input record has `DnaChisel <https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_
+If the input record has `DNA Chisel <https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_
 annotations such as ``@AvoidChanges`` or ``@EnforceTranslation``, these will be
 enforced to forbid some mutations.
 
@@ -228,11 +232,11 @@ using this command:
 
 
 
-Contribute !
---------------
+Contribute!
+-----------
 
 Golden Hinges is an open-source software originally written at the
 `Edinburgh Genome Foundry <http://edinburgh-genome-foundry.github.io/home.html>`_
 by `Zulko <https://github.com/Zulko>`_ and
 `released on Github <https://github.com/Edinburgh-Genome-Foundry/GoldenHinges>`_
-under the MIT licence. Everyone is welcome to contribute !
+under the MIT licence. Everyone is welcome to contribute!