Welcome to cadnano’s documentation!¶
cadnano is a computer-aided design tool for creating DNA nanostructures.
Quickstart¶
Installation
Install Python 3.6 , then download cadnano from pypi:
pip3 install cadnano
Usage
To launch the cadnano GUI from the command line:
python3 cadnano
To import cadnano as a Python module and work without a GUI:
import cadnano
Installation¶
Install Python 3.6¶
There are many ways to get Python on your system.
- On Mac, Homebrew is a great way to install Python.
- If you just want a clean Python install and nothing else, installers from python.org work great too.
- If you prefer the complete “batteries included” option, Anaconda Python is available for Mac, Windows or Linux.
cadnano will run on Python 3.5 and 3.6, but we only support 3.6. We do not support Python 2.X.
Install cadnano¶
Using python 3.6 pip will install cadnano and all dependencies from PyPi
$ pip3 install cadnano
or from a root of a cloned cadnano2.5 <https://github.com/cadnano/cadnano2.5> repository:
$ python setup.py install
Both of these methods will install key dependencies like:
- PyQt5>=5.8.2 <https://pypi.python.org/pypi/PyQt5/5.8>
- numpy>=1.10.0 <https://pypi.python.org/pypi/numpy/1.11.2>
- pandas>=0.18 <https://pypi.python.org/pypi/pandas/0.19.0>
- pytz>=2011k <https://pypi.python.org/pypi/pytz/2016.7>
- python-dateutil>=2 <https://pypi.python.org/pypi/python-dateutil/2.5.3>
After pip or setup.py installation you can install Windows start menu shortcuts or a MacOS Application of cadanno by running at the commandline:
$ cadnanoinstall
Allowing you to click on the application icon to launch cadnano. otherwise just run at the command line:
$ cadnano
to launch.
Advanced: Building from scratch¶
Should the above not work for you:
- Let us know
- The requirements
PyQt5andSIPare available from Riverbank Computing Limited at:
Windows¶
Instructions to come.
Mac and Linux¶
These instructions can work 10.10 Yosemite and 10.11 El Capitan under Xcode 7.0.1 and 6.5. It has also been tested on Debian 7.9 Wheezy Please provide feedback if you have problems running this in issues.
You can run the included getpyqt5.py which will grab, build and
install Qt5, SIP and PyQt5 in your python environment. It is
cleanest using virtualenv and virtualenvwrapper creating a
virtualenv with:
mkvirtualenv --always-copy <myvenv>
python pyqttools/install_pyqt_from_src.py
and then running the script, but you can definitely install in your system python if you run:
sudo python pyqttools/install_pyqt_from_src.py
This script only builds required parts of Qt5 and PyQt5.
Manual installation of PyQt5 is fine too, but you’ll need to troubleshoot on your own.
- Install
Qt5. download the online installer - Build sip and PyQt5 against this
Qt5
Of course there are many ways to accomplish this feat, but needless to
say OS X and Linux installs of PyQt5 can be painful for some people.
Tutorial¶
We have planned to create some new tutorials to add here. In the meantime, you can start by checking out the original tutorials that were released for the original version of cadnano.
|
Tutorial 1: How DNA geometry relates to building 3D shapes with a honeycomb lattice |
|
Tutorial 2: How to create a basic shape in cadnano export the DNA staple sequences |
Understanding the interface¶
The basic knowledge of DNA geometry necessary to understand the interface is covered by Tutorial 1. The new tutorial planned for this section will explain the latest version of the GUI interface in that context, and walk through what each of the tools do.
Creating a new design¶
We are also planning an updated version of Tutorial 2, which will be a step-by-step design, start to finish.
Scripting¶
Cadnano2.5 can be invoked from a Python3 script. Manipulating the cadnano
data model without invoking the GUI window can be useful for automating
certain tasks that are tedious with the mouse and keyboard. After importing the
cadnano package with import cadnano and initializing a Document, it is
straightforward to make API calls via object references to the document, part,
oligos, strands, and so on.
Note
The code block line numbers do not line up due to a bug (#415) with the readthedocs theme. It is fixed in the beta (0.2.5b2) but may not be reflected here yet.
Basic concepts¶
Here is a simple example, which can be found in misc/examples along with other scripts. It reads an input file and prints some information.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | #!/usr/bin/env python3
# bare_bones_example.py
# Shawn M Douglas, April 2017
# BSD-3 open-source license
import cadnano
from cadnano.document import Document
app = cadnano.app()
doc = app.document = Document()
doc.readFile('myfile.json')
part = doc.activePart()
oligos = part.oligos()
for oligo in oligos:
print("{0}\t{1}\t\'{2}\'\t{3}".format(oligo,
oligo.length(),
oligo.getColor(),
oligo.sequence()))
vhs = list(part.getIdNums()) # convert set to list
for vh_id in vhs[:3]: # display first 3 vhs
fwd_ss, rev_ss = part.getStrandSets(vh_id)
print('VH{0}'.format(vh_id))
print('\t', fwd_ss, '\t', [s.idxs() for s in fwd_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in fwd_ss.strands()])
print('\t', rev_ss, '\t', [s.idxs() for s in rev_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in rev_ss.strands()])
|
Let’s go line-by-line:
1 | #!/usr/bin/env python3
|
Make sure you are using the python3 interpreter, not python2.
6 7 | import cadnano
from cadnano.document import Document
|
The cadnano package must be imported to make use of its functions. If the import
fails with the python3 interpreter, try calling pip3 list from the terminal
and check that cadnano and PyQt5 are both installed. If PyQt5 is installed, you
should also be able to cleanly import PyQt5 without any exception. The
submodule document contains the class Document, which we will use as well.
9 | app = cadnano.app()
|
Here we create a cadnano application object, and store a reference. See cadnano.app and cadnano.__init__.py in the source.
10 11 | doc = app.document = Document()
doc.readFile('myfile.json')
|
Create a new Document instance, assign it to the app.document
variable, as well as doc variable in the local scope. The
Document class is the root of the model. It is the parent of all
parts and maintains the undo stack.
12 | part = doc.activePart()
|
The Part class corresponds to a molecular nanostructure. NucleicAcidPart subclasses Part, and corresponds to a DNA origami design. At the lowest level, origami designs are comprised of Strand objects, which are contiguous segments of ssDNA between endpoints and/or crossovers. Parts keep track of Strands in two separate classes simultaneously: Oligo and VirtualHelix.
We can finally start doing useful maniupulations at the oligo level. Before we examine the output, let’s take a look at the input file in the GUI.
Oligos correspond to a full-length physical oligonucleotide (i.e. a “staple” or “scaffold”).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | #!/usr/bin/env python3
# bare_bones_example.py
# Shawn M Douglas, April 2017
# BSD-3 open-source license
import cadnano
from cadnano.document import Document
app = cadnano.app()
doc = app.document = Document()
doc.readFile('myfile.json')
part = doc.activePart()
oligos = part.oligos()
for oligo in oligos:
print("{0}\t{1}\t\'{2}\'\t{3}".format(oligo,
oligo.length(),
oligo.getColor(),
oligo.sequence()))
vhs = list(part.getIdNums()) # convert set to list
for vh_id in vhs[:3]: # display first 3 vhs
fwd_ss, rev_ss = part.getStrandSets(vh_id)
print('VH{0}'.format(vh_id))
print('\t', fwd_ss, '\t', [s.idxs() for s in fwd_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in fwd_ss.strands()])
print('\t', rev_ss, '\t', [s.idxs() for s in rev_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in rev_ss.strands()])
|
We can iterate over the Part’s oligos and print their repr, length, color, and sequence (which should be none since we haven’t applied anything yet.) Now let’s look at the output of lines 15–19.
<Oligo 3688>(10[53]) 24 '#f74308' None
<Oligo 1064>(7[2]) 21 '#57bb00' None
<Oligo 6560>(17[5]) 74 '#57bb00' None
<Oligo 5224>(14[57]) 18 '#57bb00' None
<Oligo 1344>(6[53]) 276 '#03b6a2' None
<Oligo 1416>(13[5]) 74 '#007200' None
<Oligo 7064>(5[21]) 42 '#0066cc' None
<Oligo 1928>(8[53]) 24 '#f7931e' None
<Oligo 1368>(11[2]) 21 '#57bb00' None
<Oligo 1544>(4[57]) 18 '#57bb00' None
<Oligo 6928>(15[5]) 74 '#57bb00' None
<Oligo 7648>(2[57]) 18 '#57bb00' None
<Oligo 8720>(5[5]) 21 '#aaaa00' None
<Oligo 3216>(0[57]) 60 '#1700de' None
<Oligo 3360>(1[5]) 21 '#57bb00' None
<Oligo 3176>(16[57]) 18 '#57bb00' None
<Oligo 5672>(0[21]) 948 '#0066cc' None
<Oligo 4304>(13[21]) 42 '#0066cc' None
<Oligo 3416>(9[2]) 21 '#b8056c' None
<Oligo 4808>(12[57]) 60 '#cc0000' None
<Oligo 9808>(3[5]) 21 '#57bb00' None
The VirtualHelix (VH) is a group of Strands that share the same double-helix axis in space. VHs each contain a “forward” and “reverse” StrandSet, which is a container class for a group of Strands along the same helix axis.
21 22 23 24 25 26 27 28 | vhs = list(part.getIdNums()) # convert set to list
for vh_id in vhs[:3]: # display first 3 vhs
fwd_ss, rev_ss = part.getStrandSets(vh_id)
print('VH{0}'.format(vh_id))
print('\t', fwd_ss, '\t', [s.idxs() for s in fwd_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in fwd_ss.strands()])
print('\t', rev_ss, '\t', [s.idxs() for s in rev_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in rev_ss.strands()])
|
Here we use Part.getStrandSets() to get references to both the fwd and rev
StrandSets, and use list concatenations to print the start and end indices via Strand.idxs(),
and color via Strand.getColor().
VH0
<fwd_StrandSet(0)> [(5, 20), (21, 57)]
['#0066cc', '#0066cc']
<rev_StrandSet(0)> [(5, 20), (21, 41), (42, 57)]
['#007200', '#03b6a2', '#1700de']
VH1
<fwd_StrandSet(1)> [(5, 13), (14, 20), (21, 34), (35, 41), (42, 48), (49, 57)]
['#57bb00', '#007200', '#03b6a2', '#03b6a2', '#1700de', '#57bb00']
<rev_StrandSet(1)> [(5, 32), (33, 57)]
['#0066cc', '#0066cc']
VH2
<fwd_StrandSet(2)> [(5, 32), (33, 57)]
['#0066cc', '#0066cc']
<rev_StrandSet(2)> [(5, 20), (21, 41), (42, 48), (49, 57)]
['#57bb00', '#03b6a2', '#1700de', '#57bb00']
Apply scaffold sequence¶
TK
Modify oligo sequences by color¶
TK
Export to legacy format¶
TK
Keyboard Shortcuts¶
Document:
New ⌘N
Open ⌘O
Close ⌘W
Save ⌘S
SaveAs ⌘⇧S
Tools:
CreateTool C
InsertTool I
BreakTool B
SkipTool K
AddSequence A
Filters:
Helix H
Endpoint E
Crossover X
Scaffold S
Staple T
Fwd W
Rev R
Views:
Move ←↑↓→
Zoom to fit F
View shortcuts only work when the view has focus.
API¶
See our Scripting tutorial to get started.
Packages¶
cadnano.controllers package¶
Submodules¶
cadnano.controllers.nucleicacidpartitemcontroller module¶
cadnano.controllers.oligoitemcontroller module¶
cadnano.controllers.partitemcontroller module¶
cadnano.controllers.stranditemcontroller module¶
cadnano.controllers.viewrootcontroller module¶
cadnano.controllers.virtualhelixitemcontroller module¶
Module contents¶
cadnano.decorators package¶
Submodules¶
cadnano.decorators.insertion module¶
-
class
Insertion(index: int, length: int)¶ Bases:
object:class:`Insertion`s do affect an applied sequence and do not store a sequence themselves. They are a skip if the length is less than 0
Parameters: -
length() → int¶ This is the length of a sequence that is immutable by the strand
Returns: length of Insertion
-
setLength(length: int)¶ Setter for the length
Parameters: length –
-
updateIdx(delta: int)¶ Increment the index by delta
Parameters: delta – can be negative
-
Module contents¶
cadnano.extras package¶
Subpackages¶
cadnano.extras.fasta package¶
This convenience module is to hard-code some example FASTA files for testing and development.
cadnano.extras.genbank package¶
This convenience module is to hard-code some example GenBank files for testing and development.
cadnano.extras.math package¶
-
class
Box(min_point, max_point)¶ Bases:
objectCube box object
For doing an oct tree type thing
Parameters: - min_point (Tuple) – length 3 lower left corner
- max_point (Tuple) – length 3 diagonal opposite top corner
-
center()¶ Return the center of this Box
Returns: Vector3 – the center point of this box.
-
clone()¶ Clone this Box
Returns: Box – a copy of this box.
-
containsBox(box)¶ Does this object contain the Box box?
Parameters: Box – Returns: bool – True if box is in self otherwise False
-
containsPoint(point)¶ Is the point within this Box?
Parameters: point (Vector3) – to check for inclusion. Returns: bool – - True if the specified point lies within the boundaries
- of this box False otherwise
-
doesBoxSpan(box)¶ doe this object contain the Box box? :param Box:
Returns: bool – True if box spans self otherwise False
-
set(min_point, max_point)¶ Set the Tuples
Setter for setting the bounding points of the Box
Parameters: - min_point (Tuple) – length 3 lower left corner
- max_point (Tuple) – length 3 diagonal opposite top corner
-
size()¶ Find the dimensions of the Box
Returns: Tuple – the width, height, and depth of this box.
-
class
Matrix3(n11, n12, n13, n21, n22, n23, n31, n32, n33)¶ Bases:
tuplenamedtuple: 3 x 3 matrix
-
n11¶ Alias for field number 0
-
n12¶ Alias for field number 1
-
n13¶ Alias for field number 2
-
n21¶ Alias for field number 3
-
n22¶ Alias for field number 4
-
n23¶ Alias for field number 5
-
n31¶ Alias for field number 6
-
n32¶ Alias for field number 7
-
n33¶ Alias for field number 8
-
-
getNormalMatrix(m)¶ Normalize the matrix m :param m: :type m: Matrix3
Returns: Matrix3
-
class
Matrix4(n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44)¶ Bases:
tuplenamedtuple: 4 x 4 matrix
-
n11¶ Alias for field number 0
-
n12¶ Alias for field number 1
-
n13¶ Alias for field number 2
-
n14¶ Alias for field number 3
-
n21¶ Alias for field number 4
-
n22¶ Alias for field number 5
-
n23¶ Alias for field number 6
-
n24¶ Alias for field number 7
-
n31¶ Alias for field number 8
-
n32¶ Alias for field number 9
-
n33¶ Alias for field number 10
-
n34¶ Alias for field number 11
-
n41¶ Alias for field number 12
-
n42¶ Alias for field number 13
-
n43¶ Alias for field number 14
-
n44¶ Alias for field number 15
-
-
makeRotationZ(theta)¶ Create a rotation matrix of angle theta
Parameters: theta (float) – Angle in radians Returns: Matrix4 – rotation matrix about the Z axis
-
makeTranslation(x, y, z)¶ create a translation matrix given a displacement x, y, z
Parameters: - x (float) –
- y (float) –
- z (float) –
Returns: Matrix4 – translation matrix
-
class
Solid(name)¶ Bases:
object-
addFace(v1, v2, v3, normal=None)¶ List vertices using right hand rule so that unit normal will point out of the surface
vertices are given by index into vertices list
Parameters:
-
addVertex(vertex)¶ Add a vertex to the Solid :param vertex: :type vertex: Vector3
-
applyMatrix(matrix4)¶
-
computeFaceNormals()¶
-
-
class
Vector3(x, y, z)¶ Bases:
tuple-
x¶ Alias for field number 0
-
y¶ Alias for field number 1
-
z¶ Alias for field number 2
-
-
addVectors(v1, v2)¶
-
applyMatrix3(m, v)¶
-
applyMatrix4(m, v)¶
-
crossProduct(a, b)¶ return normalized cross product
-
multiplyScalar(v, s)¶ return v1*s
-
normalToPlane(v1, v2, v3)¶ Calculate unit normal to the normal to the plane defined by vertices v1, v2, and v3
-
normalizeV2(v)¶
-
normalizeV3(v)¶
-
subVectors(v1, v2)¶ return v1 - v2
-
v2AngleBetween(a, b)¶
-
v2DistanceAndAngle(a, b)¶
-
v2dot(a, b)¶
-
v3SetX(v, x)¶
-
v3SetY(v, y)¶
-
v3SetZ(v, z)¶
Submodules¶
cadnano.extras.dnasequences module¶
cadnano.extras.sequencemods module¶
cadnano.extras.wrapapi module¶
-
copyWrapAPI(cls_from, cls_to, attr_str='model')¶ Use same eval trick as decorator module on PyPi to match function signatures see also: https://emptysqua.re/blog/copying-a-python-functions-signature/
But this supports type annotations too now
maybe try to use functools.update_wrapper in the future
-
getPublicMethods(cls)¶
cadnano.gui package¶
Module contents¶
cadnano.part package¶
Submodules¶
cadnano.part.changeinstancepropertycmd module¶
cadnano.part.createvhelixcmd module¶
cadnano.part.nucleicacidpart module¶
cadnano.part.part module¶
cadnano.part.refresholigoscmd module¶
cadnano.part.refreshsegmentscmd module¶
cadnano.part.removepartcmd module¶
cadnano.part.removevhelixcmd module¶
cadnano.part.resizevirtualhelixcmd module¶
cadnano.part.translatevhelixcmd module¶
cadnano.part.virtualhelix module¶
cadnano.part.xovercmds module¶
Module contents¶
cadnano.proxies package¶
Submodules¶
cadnano.proxies.cnenum module¶
-
class
BitEnum¶ Bases:
enum.EnumAn enumeration.
-
class
EnumMask(enum, value)¶ Bases:
object
-
class
HandleEnum¶ Bases:
enum.IntEnumAn enumeration.
-
BOTTOM= 32¶
-
BOTTOM_LEFT= 64¶
-
BOTTOM_RIGHT= 16¶
-
LEFT= 128¶
-
RIGHT= 8¶
-
TOP= 2¶
-
TOP_LEFT= 1¶
-
TOP_RIGHT= 4¶
-
-
class
PointEnum¶ Bases:
enum.IntEnumFor serializing virtual helices as only pointing in the Z direction or pointing in arbitrary directions.
NOTE: This exists for legacy part importing of lattice designs when moving towards the v3 file convention
-
ARBITRARY= 1¶
-
Z_ONLY= 0¶
-
-
class
ViewReceiveEnum¶ Bases:
enum.IntEnumAn enumeration.
-
ALL= 1¶
-
GRID= 3¶
-
OUTLINER= 17¶
-
PATH= 9¶
-
PROPERTY= 33¶
-
SLICE= 5¶
-
-
class
ViewSendEnum¶ Bases:
enum.IntEnumAn enumeration.
-
ALL= 1¶
-
GRID= 2¶
-
OUTLINER= 16¶
-
PATH= 8¶
-
PROPERTY= 32¶
-
SLICE= 4¶
-
-
enumNames(cls)¶
cadnano.proxies.cnobject module¶
-
class
CNObject(parent)¶ Bases:
cadnano.proxies.cnproxy.ProxyObject-
undoStack()¶
-
cadnano.proxies.cnproxy module¶
-
BaseObject¶ alias of
cadnano.proxies.cnproxy.ProxyObject
-
class
ProxyObject(parent)¶ Bases:
object-
connect(sender, bsignal, method)¶
-
deleteLater()¶
-
disconnect(sender, bsignal, method)¶
-
parent()¶
-
setParent(parent)¶
-
signals()¶
-
-
ProxySignal¶ alias of
cadnano.proxies.cnproxy.DummySignal
Module contents¶
cadnano.removeinstancecmd module¶
cadnano.views package¶
Subpackages¶
cadnano.views.gridview package¶
cadnano.views.pathview package¶
cadnano.views.propertyview package¶
cadnano.views.sliceview package¶
Submodules¶
Module contents¶
Modules¶
cadnano¶
cadnano package¶
Subpackages¶
Submodules¶
This allows the model to have a Color object class without
the need for PyQt5.QtGui.QColor
When running the Qt Application, QColor will be used, otherwise an
API compatible class is used and exported as a Color object
Currently Color objects are unused in the model and colors are stored as
QColor compatible hex string in format ‘#rrggbbaa’, and therefore is not
exposed in the API documentation
-
class
Color(*args)¶ Bases:
objectOverloaded constructor using *args to be compatible with
QColorusage:
Color(r, g, b)
or:
Color('#rrggbb') for hex
-
hex() → str¶ The hex string name.
Returns: QColorcompatible hex string in format ‘#rrggbbaa’
-
name() → str¶ The hex string name. For
QColorcompatibilityReturns: QColorcompatible hex string in format ‘#rrggbbaa’
-
setAlpha(a: int)¶ Set the alpha 8 bit value
Parameters: a (int) – 0 - 255
-
setRgb(r: int, g: int, b: int, a: int = 255)¶ Set the r, g, b and alpha 8 bit values
Parameters: - r – 0 - 255
- g – 0 - 255
- b – 0 - 255
- a – 0 - 255
-
-
intToColorHex(color_number: int) → str¶ Convert an integer to a hexadecimal string compatible with
QColorParameters: color_number – integer value of a RGB color Returns: QColorcompatible hex string in format ‘#rrggbb’
-
class
SetPropertyCommand(objs: Iterable, key: str, value: Any)¶ Bases:
cadnano.undocommand.UndoCommandUndo ready command for setting an object property Can be used by any objects implementing
getProperty()and_setProperty()Parameters: - objs (list) – iterable of objects
- key (str) – property key
- value (any) – new value
-
redo()¶
-
undo()¶
-
class
SetVHPropertyCommand(part, id_nums, keys, values, safe)¶ Bases:
cadnano.undocommand.UndoCommandUndo ready command for setting an VirtualHelix for a part
Parameters: - part (NucleicAcidPart) –
- id_nums (list) – iterable of objects
- key (str) – property key
- value (any) – new value
-
redo()¶
-
undo()¶
Module contents¶
-
app()¶ The global cadnano application object.
-
getBatch()¶
-
getReopen()¶
-
initAppWithGui(app_args=None, do_exec=True)¶ Initializes CadnanoQt object with arguments argv, and then starts the application main event loop if do_exec is True. We may want to delay exec for checking user-provided args, or running automated tests.
See: https://doc.qt.io/qt-5/qapplication.html#exec
Parameters: - app_args (string) – see util.py
parse_args() - do_exec (bool) – don’t invoke exec yet
Returns: shared_app (CadnanoQt) – instance of app.
- app_args (string) – see util.py
-
setBatch(is_batch)¶
-
setReopen(is_reopen)¶
Detail¶
Cadnano source code is organized using a Model-View-Controller (MVC) design pattern.
Model¶
The model consists of data structures and algorithms for managing and manipulating information related to Cadnano designs. It is a standalone system and can be used without any graphical user interface, though it is much more useful and intuitive with a GUI.
Views¶
Views are a visual representations of the model state. Cadnano provides several views of the model, each serving a different purpose. Most user interaction is done in the Sliceview, is an orthographic 2D projection of DNA helices, and the Pathview, a schematic blueprint of the routes of individual oligos in a design. The Inspector window is a text-based widget that consists of the Outlinerview, a hierarchical listing of the components of a design, and the Propertyview which allows for editing properties of selected components. We have future plans for a 3D view and a console view.
Controllers¶
Controllers are responsible for setting up and managing the communication between the model and views.
Note
By a traditional MVC definition, Cadnano views have integrated controller functionality, i.e. they interpret user actions and send them to the model.
Signals and Slots¶
We use Qt’s Signals and Slots framework. The model is responsible for emitting relevant “signals” when modified, and the views can subscribe to those signals with local “slots” which are methods that receive model change information as argments and then decide what to do with it, for example updating a graphical element to reflect the change, or simply ignoring it.
Virtualenv¶
We develop cadnano using virtualenv and virtualenvwrapper. Virtualenvs make it harder to mess up your entire system, and easy to start over when you mess up locally. If you wish to make modifications to the cadnano source code, you can first start by replicating our setup.
What are virtual environments?¶
A virtual environment consists of a separate copy of python3 that lives in your home directory and some scripts that set up your shell environment so the local python copy is used instead of the system python. Virtualenvwrapper is a shell script that provides some convenient commands to easily manage multiple virtualenvs.
When a virtualenv is activated in the terminal (using the workon command), everything feels basically the same, but there are a few important differences.
shawn ~/Desktop/projects/cadnano2.5 $ which python
/usr/bin/python
shawn ~/Desktop/projects/cadnano2.5 $ workon c25
(c25) shawn ~/Desktop/projects/cadnano2.5 $ which python
/Users/shawn/.virtualenvs/c25/bin/python
You’ll notice the active virtualenv prefixes your path with its name (“c25” in my case). Behind the scenes, your paths are set up such that the local copy of python3 will run instead of whatever is in your default path, as well the python package manager pip3. Thus, any libraries or packages that you install with the virtualenv active will go into the virtualenv subfolder as well.
Setting up virtualenv and virtualenvwrapper¶
These instructions assume you’ve already set up python3 on your system. (Personally, I use Homebrew to do this.)
Note
If you only wish to run cadnano, none of this necessary. Just perform the basic installation.
Getting started
Run this command from the terminal:
pip3 install virtualenv virtualenvwrapper
Updating your .bash_profile
We want to invoke virtualenvwrapper whenever we open a terminal window. To do this, we edit .bash_profile.
Here are the virtualenv-related lines of my .bash_profile, per the virtualenvwrapper docs:
export WORKON_HOME=$HOME/.virtualenvs
export PROJECT_HOME=$HOME/Devel
export VIRTUALENVWRAPPER_PYTHON=/usr/local/bin/python3
source /Library/Frameworks/Python.framework/Versions/3.6/bin/virtualenvwrapper.sh
Once you add these lines, open a new terminal window to verify they are working. If you get an error, you may need to confirm your python3 is correctly installed, and possibly modify the path to virtualenvwrapper.sh if you aren’t using homebew and your copy of python3 lives somewhere else.
Creating a virtualenv
Use the virtualenvwrapper command mkvirtualenv to create a new virtualenv. For this example, we’ll call our virtualenv “cndev”:
shawn ~ $ mkvirtualenv cndev
Using base prefix '/Library/Frameworks/Python.framework/Versions/3.6'
New python executable in /Users/shawn/.virtualenvs/cndev/bin/python3.6
Also creating executable in /Users/shawn/.virtualenvs/cndev/bin/python
Installing setuptools, pip, wheel...done.
virtualenvwrapper.user_scripts creating /Users/shawn/.virtualenvs/cndev/bin/predeactivate
virtualenvwrapper.user_scripts creating /Users/shawn/.virtualenvs/cndev/bin/postdeactivate
virtualenvwrapper.user_scripts creating /Users/shawn/.virtualenvs/cndev/bin/preactivate
virtualenvwrapper.user_scripts creating /Users/shawn/.virtualenvs/cndev/bin/postactivate
virtualenvwrapper.user_scripts creating /Users/shawn/.virtualenvs/cndev/bin/get_env_details
If everything worked, you should see an output resembling the above.
Running cadnano from a virtualenv¶
Now that we have a virtualenv working, let’s get all the cadnano dependencies, and download the git repository.
(cndev) shawn ~ $ pip3 install PyQt5 PyQt3D pandas termcolor
Collecting PyQt5
Using cached PyQt5-5.9.2-5.9.3-cp35.cp36.cp37-abi3-macosx_10_6_intel.whl
Collecting PyQt3D
Using cached PyQt3D-5.9.2-5.9.3-cp35.cp36.cp37-abi3-macosx_10_6_intel.whl
Collecting pandas
Using cached pandas-0.22.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting termcolor
Collecting sip<4.20,>=4.19.4 (from PyQt5)
Using cached sip-4.19.6-cp36-cp36m-macosx_10_6_intel.whl
Collecting numpy>=1.9.0 (from pandas)
Using cached numpy-1.14.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pytz>=2011k (from pandas)
Using cached pytz-2017.3-py2.py3-none-any.whl
Collecting python-dateutil>=2 (from pandas)
Using cached python_dateutil-2.6.1-py2.py3-none-any.whl
Collecting six>=1.5 (from python-dateutil>=2->pandas)
Using cached six-1.11.0-py2.py3-none-any.whl
Installing collected packages: sip, PyQt5, PyQt3D, numpy, pytz, six, python-dateutil, pandas, termcolor
Successfully installed PyQt3D-5.9.2 PyQt5-5.9.2 numpy-1.14.0 pandas-0.22.0 python-dateutil-2.6.1 pytz-2017.3 sip-4.19.6 six-1.11.0 termcolor-1.1.0
(cndev) shawn ~/Desktop $ git clone https://github.com/cadnano/cadnano2.5.git
Cloning into 'cadnano2.5'...
remote: Counting objects: 15865, done.
remote: Compressing objects: 100% (219/219), done.
remote: Total 15865 (delta 288), reused 288 (delta 198), pack-reused 15448
Receiving objects: 100% (15865/15865), 12.38 MiB | 846.00 KiB/s, done.
Resolving deltas: 100% (12982/12982), done.
(cndev) shawn ~/Desktop $ cd cadnano2.5/
(cndev) shawn ~/Desktop/cadnano2.5 $ python cadnano/bin/main.py
If everything works, the cadnano window should open.
Useful virtualenvwrapper commands¶
workon: activate the virtualenv, e.g. workon cndev
deactivate: drop out of the virtualenv, back into the normal terminal
lssitepackages: list the active virtualenv’s installed packages
rmvirtualenv: remove the virtualenv, e.g. rmvirtualenv cndev
Building¶
Building Qt, PyQt5, SIP, and PyQt3D from source¶
Warning
Not recommended for novice users. But a great way to learn :)
If the packages available on pypi are lagging behind some bleeding-edge feature in Qt, sometimes it’s necessary to build everything from source. In the cadnano directory there’s a script called getpyqt5.py. Before using it, make sure your virtualenv was created with the –always-copy flag.
mkvirtualenv --always-copy <myenv>
The source urls are typically out of date as soon as the script is more than about 1 month old, so you’ll need to update it manually.
Testing¶
Cadnano has a handful of automated tests that get run automatically by TravisCI on every commit pushed to Github. The tests help ensure the integrity of the our data model, or at least notify us quickly when we’ve broken something. We also test the GUI by recording and playing back user interactions with QTest.
If you’d like to modify cadnano, we recommend setting up automated testing in your local development environment. You’ll first want to install pytest.
pip install pytest
Running Tests¶
To run non-GUI tests:
pytest cadnano/tests
To run GUI tests:
pytest -c cadnano/tests/pytestgui.ini cadnano/tests/
Currently, we do not automate GUI tests on TravisCI, so they must be run locally.
Automating Tests with a Pre-Commit Hook¶
Pre-commit hooks are a great way to make sure that the test suite is run before committing. Doing this ensures that code that is committed will always pass the test suite.
A script to accomplish this when committing via the git command line is
included in this repository. To activate it, run
ln -s "$(git rev-parse --show-toplevel)/misc/git-hooks/pre-commit" $(git rev-parse --show-toplevel)/.git/hooks/
anywhere in the cadnano repository. This will symlink the pre-commit hook to
your .git/hooks directory. Now, whenever you commit, the test suite will be
run before you commit:
❱ git commit
Running tests in $HOME/cadnano2.5/cadnano/tests...
============================== test session starts ==============================
platform darwin -- Python 3.6.3, pytest-3.3.1, py-1.5.2, pluggy-0.6.0
PyQt5 5.9.2 -- Qt runtime 5.9.3 -- Qt compiled 5.9.3
rootdir: $HOME/cadnano2.5/cadnano/tests, inifile: pytest.ini
plugins: qt-2.3.0
collected 12 items
cadnano/tests/functionaltest.py ....... [ 58%]
cadnano/tests/nucleicacidparttest.py .... [ 91%]
cadnano/tests/strandsettest.py . [100%]
=========================== 12 passed in 1.47 seconds ===========================
and if any of the tests fail, committing will be blocked:
Running tests in $HOME/cadnano2.5/cadnano/tests...
============================== test session starts ==============================
platform darwin -- Python 3.6.3, pytest-3.3.1, py-1.5.2, pluggy-0.6.0
PyQt5 5.9.2 -- Qt runtime 5.9.3 -- Qt compiled 5.9.3
rootdir: $HOME/cadnano2.5/cadnano/tests, inifile: pytest.ini
plugins: qt-2.3.0
collected 5 items / 1 errors
==================================== ERRORS =====================================
______________________ ERROR collecting functionaltest.py _______________________
cadnano-virtualenv/lib/python3.6/site-packages/_pytest/python.py:403: in _importtestmodule
mod = self.fspath.pyimport(ensuresyspath=importmode)
cadnano-virtualenv/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport
__import__(modname)
E File "$HOME/cadnano2.5/cadnano/tests/functionaltest.py", line 14
E def
E ^
E SyntaxError: invalid syntax
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!
============================ 1 error in 0.68 seconds ============================
Tests failed; commit aborted
To commit without this hook running, pass the --no-verify argument
As the last line says, if you want to ignore the fact that tests are failing and
commit anyway, pass the --no-verify argument to git commit.
Docs¶
Cadnano2.5 documentation is built with sphinx and hosted at readthedocs.io.
Building the docs¶
Summary
pip3 install sphinx sphinx_rtd_theme==0.2.5b2 recommonmark sphinx-autobuild
cd cadnano/docs
make clean
make api
make html
make livehtml
Getting started
Try setting up your own separate test sphinx project using sphinx-quickstart. Once you understand how sphinx works, read through the cadnano/docs Makefile and conf.py to understand our configuration.
Install dependencies
From the terminal, use pip to install sphinx and cadnano docs dependencies.
pip3 install sphinx sphinx_rtd_theme==0.2.5b2 recommonmark sphinx-autobuild
Building
First, make sure you are in the docs directory. Clear out the old documentation, if any.
cd cadnano/docs
make clean
Build the API. This generates sphinx .rst sources in docs/api using sphinx-autodoc.
make api
Build the html. This converts the .rst and .md sources into HTML files. If successful, HTML pages should be placed in _build/html. You can open the index.html to inspect your edits.
make html
If you want to do everything together in a single command:
make clean; make api; make html
Autobuild
It can get tedious to rebuild the docs during heavy editing sessions. Instead, you can use sphinx-autobuild to rebuild the documentation whenever a change is detected. Autobuild conveniently spawns a local server (at 127.0.0.1:8000 unless you specify otherwise with -p) that will refresh as needed.
make livehtml
reStructuredText vs Markdown¶
Like docutils, Sphinx uses reStructuredText, whose filenames have an .rst extension. ReStructuredText is tailored for technical documentation, and predates Markdown by about 2 years.
For the sake of consistency and leveraging core sphinx features, we initially just learned the basics of rST and used it for most doc sources, including the API. However, it is possible to create documentation in markdown format using recommonmark. This source files for this page (cadnano/docs/docs.md). New top-level documentation files that do not require rsT features should be created in markdown with the .md extension.
Known Issues¶
toctree Warnings
When building the docs, you may see warnings like:
WARNING: toctree contains reference to nonexisting document 'api/cadnano.controllers.documentcontroller'
WARNING: toctree contains reference to nonexisting document 'api/cadnano.gui.mainwindow.ui_mainwindow'
WARNING: toctree contains reference to nonexisting document 'api/cadnano.views.cnmainwindow'
WARNING: toctree contains reference to nonexisting document 'api/cadnano.views.outlinerview.outlinertreewidget'
These modules import the PyQt5 classes in a way that doesn’t play nicely with sphinx, so they are specifically excluded in docs/conf.py. Consequently, the documentation for these modules will be missing until someone tracks down the root cause of this issue and figures out a workaround. Possible starting point: stackoverflow.com/questions/25960309/
segfaults
You may see segfaults when trying to run make html or make livehtml that
look like this:
...
reading sources... [ 70%] api/cadnano.views.pathview.strand.stranditem
reading sources... [ 71%] api/cadnano.views.pathview.strand.xoveritem
reading sources... [ 71%] api/cadnano.views.pathview.tools
reading sources... [ 72%] api/cadnano.views.pathview.tools.abstractpathtool
reading sources... [ 72%] api/cadnano.views.pathview.tools.addseqtool
make: *** [html] Segmentation fault: 11
If you encounter this, you may need to exclude the offending source from the
build. Add the last source read before the segfault to the exclude_patterns
list in conf.py. Ensure that you include the trailing .rst in the string.
Changelog¶
v2.5.2¶
- Code: Reorganized to flatten module structure
- Code: Bugfixes for issues #107, #108, #112
- GUI: Legacy-style Sliceview for lattice designs
- Installer: Update to PyQt 5.9.3
v2.5.1¶
- API: Oligo.isLoop() → isCircular()
- Code: flake8 linting (ignoring E226,E266,E731,E501)
- Code: Bugfixes for issues #94, #95, #105
- Docs: Scripting examples
- Docs: How to build sphinx docs
- GUI: Updated styles to better match cadnano2
- GUI: Improvements to sliceview grid
- Installer: Update to PyQt 5.8.2
- Installer: Windows shortcut icon
- I/O: v3 oligo property “is_loop” → “is_circular”
v2.5¶
Major changes and new features since cadnano 2:
- Installer: Distribution as a Python package
- Design/GUI: Helices no longer constrained to lattices
- Design/GUI: Added support for “abstract” sequences
- Design/GUI: Added support for parallel crossovers
- Code: Updated from Python 2 → 3
- Code: Updated from PyQt4 → PyQt5
- Code: Rewrote underlying data model
- Code: Better stability
- GUI: Improved hinting across views
- GUI/Installer: Removed Maya plugin code
- I/O: New file format
- I/O: Easier scripting via command-line mode
- I/O: Export to STL (experimental)
Unreleased¶
- GUI: 3D view
- I/O: Export to PDB (experimental)
Authors¶
Development Leads¶
- Nick Conway <nick.conway@wyss.harvard.edu>
- Shawn Douglas <shawn.douglas@ucsf.edu>
Patches and Suggestions¶
- Rasmus Schøler Sørensen <rasmusscholer@gmail.com>
- Hadrien Mary <hadrien.mary@mcgill.ca>
- Christopher Maffeo <cmaffeo2@illinois.edu>
- Nick Fong <https://github.com/nickfong>
- Heinrich Grabmayr <https://github.com/Heerpa>
License¶
Copyright (c) 2018, Wyss Institute at Harvard University and University of California San Francisco
The BSD 3-Clause License¶
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).
The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.
- Additional Terms.
“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
- Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
- Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
- Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
- Limiting the use for publicity purposes of names of licensors or authors of the material; or
- Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
- Termination.
You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
- Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
- Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party’s predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
- Patents.
A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor’s “contributor version”.
A contributor’s “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient’s use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
- No Surrender of Others’ Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
- Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
- Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
- Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
- Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
- Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
<one line to give the program’s name and a brief idea of what it does.> Copyright (C) <year> <name of author>
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 3 of the License, or (at your option) any later version.
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.
You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
The hypothetical commands `show w’ and `show c’ should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <https://www.gnu.org/licenses/why-not-lgpl.html>.
