lazar-gui 1.0.2 → 1.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 73b1ebc482909563260253f205416c5c911a35fb
-  data.tar.gz: d877b6229e467eef3b6260614166eb2e3646da29
+  metadata.gz: 8471bbac9d27b47075f4cc80dab7127b2577ad27
+  data.tar.gz: 6d5c63ed374f0eb2a1b64bfc1f72fd614a3f527f
 SHA512:
-  metadata.gz: 1d3427a9798157f3aff1abfd04807575e3d995409822d0081a175cc1cbe1e72a842c1e54899c7ee7f698a526497e7a10eada83a9ebb9289c45d6af0336d1e7a7
-  data.tar.gz: 4f33655f3c099ab5b2d3c9d1d3d7b192049c9dca150432ccf780544dbcfac65074b85ebd1625695f5a2344463348ac2acd7d0c61a94aedd0c98281f293009e11
+  metadata.gz: 2352c365b7444cffa06747c119bbade66aad4288fc84807eb9adda5ad39c424cc8d74092d4de054164219119f26abbbc5a51c27a9d60cf65c2541eae934ebcd7
+  data.tar.gz: 2f3a3172f32289e3db73eca1630b95f498dd8c012d287f9818f8ef9cbac6526ea6ded6c9ae088a4825b0d41771e5c9effe593babb5531e664b9c729d15cd6fe3

data/.gitignore

@@ -1,3 +1,2 @@
 Gemfile.lock
 .sass-cache/
-tmp/*

data/FAQ.md

@@ -1,29 +1,18 @@
-Frequently Asked Questions
-==========================
-<br>
-####How does this prediction works?
->
+## lazar Frequently Asked Questions
 
-####You talk about significant fragments. Where can I find them?
-> We will show up those significant fragments in a further version.
+####The LAZAR program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence?
 
-####What is endpoint details about?
-> You get the source from where we took compounds for the endpoint. The type and the number of compounds we used.
+In the past many users had problems to interpret the confidence level,
+for this reason we provide now the probabilities that the prediction
+belongs to one of the two classes. In contrast to the confidence level,
+these numbers can be interpreted as real probabilities ranging from 0 to
+1.
 
-####What is three times independent validation about?
->
+Reliable prediction have a high probability for the predicted class and
+a low probability for the other one. Unreliable predictions have similar
+values for both classes, and are caused by a lot of contradictory
+activities of similar compounds.
 
-####Do you consider providing plots for the validation results?
-> In a further version we will show up confidence and correlation plots.
-
-####What does 'Not enough similar compounds in training dataset' mean?
-> Lazar uses neighbors from the training dataset of the endpoint to predict your compound. If there are not enough neighbors for Lazar it is not possible to make a prediction.
-
-####Is there a minimum number of necessary neighbors to make a prediction?
->  
-
-####How can I activate the 'batch prediction' option?
-> Please contact us directly via [mail](mailto:support@in-silico.ch).
-
-####Not the right answers for me. Is there a way to contact you or report problems.
-> You can always ask your questions via [mail](mailto:support@in-silico.ch). If you run into problems with the GUI please post your issue [here](https://github.com/opentox/lazar-gui/issues). If you would like to post any other issue e.g. about an expected prediction result please use this [form](https://github.com/opentox/lazar/issues).
+Probabilities are calculated from the activities and similarities of
+neighbors, please make sure to inspect the neighbors list for any
+inconsistencies that might affect the prediction.

data/Gemfile

@@ -1,7 +1,9 @@
 source "https://rubygems.org"
 gemspec
-gem "lazar"
+gem "lazar", :path => "../lazar"
 gem "gem-path"
 gem "sinatra"
+gem "sinatra-reloader"
 gem "haml"
 gem "sass"
+gem "rdiscount"

data/LICENSE.md

@@ -0,0 +1,596 @@
+GNU GENERAL PUBLIC LICENSE
+==========================
+
+Version 3, 29 June 2007
+
+Copyright &copy; 2007 Free Software Foundation, Inc. &lt;<http://fsf.org/>&gt;
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
+
+The GNU General Public License is a free, copyleft license for software and other
+kinds of works.
+
+The licenses for most software and other practical works are designed to take away
+your freedom to share and change the works. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change all versions of a
+program--to make sure it remains free software for all its users. We, the Free
+Software Foundation, use the GNU General Public License for most of our software; it
+applies also to any other work released this way by its authors. You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our General
+Public Licenses are designed to make sure that you have the freedom to distribute
+copies of free software (and charge for them if you wish), that you receive source
+code or can get it if you want it, that you can change the software or use pieces of
+it in new free programs, and that you know you can do these things.
+
+To protect your rights, we need to prevent others from denying you these rights or
+asking you to surrender the rights. Therefore, you have certain responsibilities if
+you distribute copies of the software, or if you modify it: responsibilities to
+respect the freedom of others.
+
+For example, if you distribute copies of such a program, whether gratis or for a fee,
+you must pass on to the recipients the same freedoms that you received. You must make
+sure that they, too, receive or can get the source code. And you must show them these
+terms so they know their rights.
+
+Developers that use the GNU GPL protect your rights with two steps: (1) assert
+copyright on the software, and (2) offer you this License giving you legal permission
+to copy, distribute and/or modify it.
+
+For the developers' and authors' protection, the GPL clearly explains that there is
+no warranty for this free software. For both users' and authors' sake, the GPL
+requires that modified versions be marked as changed, so that their problems will not
+be attributed erroneously to authors of previous versions.
+
+Some devices are designed to deny users access to install or run modified versions of
+the software inside them, although the manufacturer can do so. This is fundamentally
+incompatible with the aim of protecting users' freedom to change the software. The
+systematic pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we have designed
+this version of the GPL to prohibit the practice for those products. If such problems
+arise substantially in other domains, we stand ready to extend this provision to
+those domains in future versions of the GPL, as needed to protect the freedom of
+users.
+
+Finally, every program is threatened constantly by software patents. States should
+not allow patents to restrict development and use of software on general-purpose
+computers, but in those that do, we wish to avoid the special danger that patents
+applied to a free program could make it effectively proprietary. To prevent this, the
+GPL assures that patents cannot be used to render the program non-free.
+
+The precise terms and conditions for copying, distribution and modification follow.
+
+## TERMS AND CONDITIONS
+
+### 0. Definitions.
+
+&ldquo;This License&rdquo; refers to version 3 of the GNU General Public License.
+
+&ldquo;Copyright&rdquo; also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+&ldquo;The Program&rdquo; refers to any copyrightable work licensed under this
+License. Each licensee is addressed as &ldquo;you&rdquo;. &ldquo;Licensees&rdquo; and
+&ldquo;recipients&rdquo; may be individuals or organizations.
+
+To &ldquo;modify&rdquo; a work means to copy from or adapt all or part of the work in
+a fashion requiring copyright permission, other than the making of an exact copy. The
+resulting work is called a &ldquo;modified version&rdquo; of the earlier work or a
+work &ldquo;based on&rdquo; the earlier work.
+
+A &ldquo;covered work&rdquo; means either the unmodified Program or a work based on
+the Program.
+
+To &ldquo;propagate&rdquo; a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for infringement under
+applicable copyright law, except executing it on a computer or modifying a private
+copy. Propagation includes copying, distribution (with or without modification),
+making available to the public, and in some countries other activities as well.
+
+To &ldquo;convey&rdquo; a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through a computer
+network, with no transfer of a copy, is not conveying.
+
+An interactive user interface displays &ldquo;Appropriate Legal Notices&rdquo; to the
+extent that it includes a convenient and prominently visible feature that (1)
+displays an appropriate copyright notice, and (2) tells the user that there is no
+warranty for the work (except to the extent that warranties are provided), that
+licensees may convey the work under this License, and how to view a copy of this
+License. If the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+### 1. Source Code.
+
+The &ldquo;source code&rdquo; for a work means the preferred form of the work for
+making modifications to it. &ldquo;Object code&rdquo; means any non-source form of a
+work.
+
+A &ldquo;Standard Interface&rdquo; means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of interfaces
+specified for a particular programming language, one that is widely used among
+developers working in that language.
+
+The &ldquo;System Libraries&rdquo; of an executable work include anything, other than
+the work as a whole, that (a) is included in the normal form of packaging a Major
+Component, but which is not part of that Major Component, and (b) serves only to
+enable use of the work with that Major Component, or to implement a Standard
+Interface for which an implementation is available to the public in source code form.
+A &ldquo;Major Component&rdquo;, in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system (if any) on which
+the executable work runs, or a compiler used to produce the work, or an object code
+interpreter used to run it.
+
+The &ldquo;Corresponding Source&rdquo; for a work in object code form means all the
+source code needed to generate, install, and (for an executable work) run the object
+code and to modify the work, including scripts to control those activities. However,
+it does not include the work's System Libraries, or general-purpose tools or
+generally available free programs which are used unmodified in performing those
+activities but which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for the work, and
+the source code for shared libraries and dynamically linked subprograms that the work
+is specifically designed to require, such as by intimate data communication or
+control flow between those subprograms and other parts of the work.
+
+The Corresponding Source need not include anything that users can regenerate
+automatically from other parts of the Corresponding Source.
+
+The Corresponding Source for a work in source code form is that same work.
+
+### 2. Basic Permissions.
+
+All rights granted under this License are granted for the term of copyright on the
+Program, and are irrevocable provided the stated conditions are met. This License
+explicitly affirms your unlimited permission to run the unmodified Program. The
+output from running a covered work is covered by this License only if the output,
+given its content, constitutes a covered work. This License acknowledges your rights
+of fair use or other equivalent, as provided by copyright law.
+
+You may make, run and propagate covered works that you do not convey, without
+conditions so long as your license otherwise remains in force. You may convey covered
+works to others for the sole purpose of having them make modifications exclusively
+for you, or provide you with facilities for running those works, provided that you
+comply with the terms of this License in conveying all material for which you do not
+control copyright. Those thus making or running the covered works for you must do so
+exclusively on your behalf, under your direction and control, on terms that prohibit
+them from making any copies of your copyrighted material outside their relationship
+with you.
+
+Conveying under any other circumstances is permitted solely under the conditions
+stated below. Sublicensing is not allowed; section 10 makes it unnecessary.
+
+### 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+No covered work shall be deemed part of an effective technological measure under any
+applicable law fulfilling obligations under article 11 of the WIPO copyright treaty
+adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention
+of such measures.
+
+When you convey a covered work, you waive any legal power to forbid circumvention of
+technological measures to the extent such circumvention is effected by exercising
+rights under this License with respect to the covered work, and you disclaim any
+intention to limit operation or modification of the work as a means of enforcing,
+against the work's users, your or third parties' legal rights to forbid circumvention
+of technological measures.
+
+### 4. Conveying Verbatim Copies.
+
+You may convey verbatim copies of the Program's source code as you receive it, in any
+medium, provided that you conspicuously and appropriately publish on each copy an
+appropriate copyright notice; keep intact all notices stating that this License and
+any non-permissive terms added in accord with section 7 apply to the code; keep
+intact all notices of the absence of any warranty; and give all recipients a copy of
+this License along with the Program.
+
+You may charge any price or no price for each copy that you convey, and you may offer
+support or warranty protection for a fee.
+
+### 5. Conveying Modified Source Versions.
+
+You may convey a work based on the Program, or the modifications to produce it from
+the Program, in the form of source code under the terms of section 4, provided that
+you also meet all of these conditions:
+
+* **a)** The work must carry prominent notices stating that you modified it, and giving a
+relevant date.
+* **b)** The work must carry prominent notices stating that it is released under this
+License and any conditions added under section 7. This requirement modifies the
+requirement in section 4 to &ldquo;keep intact all notices&rdquo;.
+* **c)** You must license the entire work, as a whole, under this License to anyone who
+comes into possession of a copy. This License will therefore apply, along with any
+applicable section 7 additional terms, to the whole of the work, and all its parts,
+regardless of how they are packaged. This License gives no permission to license the
+work in any other way, but it does not invalidate such permission if you have
+separately received it.
+* **d)** If the work has interactive user interfaces, each must display Appropriate Legal
+Notices; however, if the Program has interactive interfaces that do not display
+Appropriate Legal Notices, your work need not make them do so.
+
+A compilation of a covered work with other separate and independent works, which are
+not by their nature extensions of the covered work, and which are not combined with
+it such as to form a larger program, in or on a volume of a storage or distribution
+medium, is called an &ldquo;aggregate&rdquo; if the compilation and its resulting
+copyright are not used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work in an aggregate
+does not cause this License to apply to the other parts of the aggregate.
+
+### 6. Conveying Non-Source Forms.
+
+You may convey a covered work in object code form under the terms of sections 4 and
+5, provided that you also convey the machine-readable Corresponding Source under the
+terms of this License, in one of these ways:
+
+* **a)** Convey the object code in, or embodied in, a physical product (including a
+physical distribution medium), accompanied by the Corresponding Source fixed on a
+durable physical medium customarily used for software interchange.
+* **b)** Convey the object code in, or embodied in, a physical product (including a
+physical distribution medium), accompanied by a written offer, valid for at least
+three years and valid for as long as you offer spare parts or customer support for
+that product model, to give anyone who possesses the object code either (1) a copy of
+the Corresponding Source for all the software in the product that is covered by this
+License, on a durable physical medium customarily used for software interchange, for
+a price no more than your reasonable cost of physically performing this conveying of
+source, or (2) access to copy the Corresponding Source from a network server at no
+charge.
+* **c)** Convey individual copies of the object code with a copy of the written offer to
+provide the Corresponding Source. This alternative is allowed only occasionally and
+noncommercially, and only if you received the object code with such an offer, in
+accord with subsection 6b.
+* **d)** Convey the object code by offering access from a designated place (gratis or for
+a charge), and offer equivalent access to the Corresponding Source in the same way
+through the same place at no further charge. You need not require recipients to copy
+the Corresponding Source along with the object code. If the place to copy the object
+code is a network server, the Corresponding Source may be on a different server
+(operated by you or a third party) that supports equivalent copying facilities,
+provided you maintain clear directions next to the object code saying where to find
+the Corresponding Source. Regardless of what server hosts the Corresponding Source,
+you remain obligated to ensure that it is available for as long as needed to satisfy
+these requirements.
+* **e)** Convey the object code using peer-to-peer transmission, provided you inform
+other peers where the object code and Corresponding Source of the work are being
+offered to the general public at no charge under subsection 6d.
+
+A separable portion of the object code, whose source code is excluded from the
+Corresponding Source as a System Library, need not be included in conveying the
+object code work.
+
+A &ldquo;User Product&rdquo; is either (1) a &ldquo;consumer product&rdquo;, which
+means any tangible personal property which is normally used for personal, family, or
+household purposes, or (2) anything designed or sold for incorporation into a
+dwelling. In determining whether a product is a consumer product, doubtful cases
+shall be resolved in favor of coverage. For a particular product received by a
+particular user, &ldquo;normally used&rdquo; refers to a typical or common use of
+that class of product, regardless of the status of the particular user or of the way
+in which the particular user actually uses, or expects or is expected to use, the
+product. A product is a consumer product regardless of whether the product has
+substantial commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+
+&ldquo;Installation Information&rdquo; for a User Product means any methods,
+procedures, authorization keys, or other information required to install and execute
+modified versions of a covered work in that User Product from a modified version of
+its Corresponding Source. The information must suffice to ensure that the continued
+functioning of the modified object code is in no case prevented or interfered with
+solely because modification has been made.
+
+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.
+
+### 7. Additional Terms.
+
+&ldquo;Additional permissions&rdquo; 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:
+
+* **a)** Disclaiming warranty or limiting liability differently from the terms of
+sections 15 and 16 of this License; or
+* **b)** 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
+* **c)** 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
+* **d)** Limiting the use for publicity purposes of names of licensors or authors of the
+material; or
+* **e)** 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 &ldquo;further
+restrictions&rdquo; 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.
+
+### 8. 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.
+
+### 9. 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.
+
+### 10. 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 &ldquo;entity transaction&rdquo; 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.
+
+### 11. Patents.
+
+A &ldquo;contributor&rdquo; 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 &ldquo;contributor version&rdquo;.
+
+A contributor's &ldquo;essential patent claims&rdquo; 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, &ldquo;control&rdquo; 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 &ldquo;patent license&rdquo; 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 &ldquo;grant&rdquo; 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. &ldquo;Knowingly relying&rdquo; 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 &ldquo;discriminatory&rdquo; 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.
+
+### 12. 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.
+
+### 13. 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.
+
+### 14. 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 &ldquo;or any later
+version&rdquo; 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.
+
+### 15. 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 &ldquo;AS IS&rdquo; 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.
+
+### 16. 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.
+
+### 17. 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 &ldquo;copyright&rdquo; 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 <http://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:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type 'show c' for details.
+
+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 &ldquo;about box&rdquo;.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a &ldquo;copyright disclaimer&rdquo; for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+&lt;<http://www.gnu.org/licenses/>&gt;.
+
+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
+&lt;<http://www.gnu.org/philosophy/why-not-lgpl.html>&gt;.