qsar-report 0.0.5 → 1.0.0

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data/.yardopts CHANGED
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  --readme README.md
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  --title 'QMRF and QPRF reporting class for OpenTox'
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  --charset utf-8
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- yardoc lib/*.rb - README.md ChangeLog VERSION LICENSE
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+ yardoc lib/*.rb - README.md ChangeLog VERSION LICENSE lib/template/LICENSE_qmrf.xsd.txt example/example.rb
data/ChangeLog CHANGED
@@ -1,6 +1,10 @@
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+ * Add Tests.
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+ * Change License text to GPL-3
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+ v0.0.5
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+ * add change_attributes method to edit QMRF 6.1-6.4 and 7.1-7.4
5
+ * fix catalog referencing code, adjust node search
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  v0.0.2
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  * add QPRF reporting
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  * rename gem qmrf-report to qsar-report
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  v0.0.1
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- * initial version
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-
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+ * initial version
data/LICENSE CHANGED
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+ d) Convey the object code by offering access from a designated
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+ e) Convey the object code using peer-to-peer transmission, provided
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+ you inform other peers where the object code and Corresponding
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+ Source of the work are being offered to the general public at no
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+ charge under subsection 6d.
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+ A separable portion of the object code, whose source code is excluded
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+ from the Corresponding Source as a System Library, need not be
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+ included in conveying the object code work.
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+ A "User Product" is either (1) a "consumer product", which means any
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+ tangible personal property which is normally used for personal, family,
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+ code is in no case prevented or interfered with solely because
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+ modification has been made.
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+ If you convey an object code work under this section in, or with, or
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+ Corresponding Source conveyed under this section must be accompanied
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+ by the Installation Information. But this requirement does not apply
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+ if neither you nor any third party retains the ability to install
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+ modified object code on the User Product (for example, the work has
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+ been installed in ROM).
328
+
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+ The requirement to provide Installation Information does not include a
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+ the User Product in which it has been modified or installed. Access to a
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+ network may be denied when the modification itself materially and
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335
+ protocols for communication across the network.
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+
337
+ Corresponding Source conveyed, and Installation Information provided,
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+ in accord with this section must be in a format that is publicly
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+ documented (and with an implementation available to the public in
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+ source code form), and must require no special password or key for
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+ unpacking, reading or copying.
342
+
343
+ 7. Additional Terms.
344
+
345
+ "Additional permissions" are terms that supplement the terms of this
346
+ License by making exceptions from one or more of its conditions.
347
+ Additional permissions that are applicable to the entire Program shall
348
+ be treated as though they were included in this License, to the extent
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+ that they are valid under applicable law. If additional permissions
350
+ apply only to part of the Program, that part may be used separately
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+ under those permissions, but the entire Program remains governed by
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+ this License without regard to the additional permissions.
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354
+ When you convey a copy of a covered work, you may at your option
355
+ remove any additional permissions from that copy, or from any part of
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+ it. (Additional permissions may be written to require their own
357
+ removal in certain cases when you modify the work.) You may place
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+ additional permissions on material, added by you to a covered work,
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+ for which you have or can give appropriate copyright permission.
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361
+ Notwithstanding any other provision of this License, for material you
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+ add to a covered work, you may (if authorized by the copyright holders of
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365
+ a) Disclaiming warranty or limiting liability differently from the
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+ terms of sections 15 and 16 of this License; or
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368
+ b) Requiring preservation of specified reasonable legal notices or
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372
+ c) Prohibiting misrepresentation of the origin of that material, or
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376
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379
+ e) Declining to grant rights under trademark law for use of some
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388
+ All other non-permissive additional terms are considered "further
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+ restrictions" within the meaning of section 10. If the Program as you
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+ received it, or any part of it, contains a notice stating that it is
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392
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403
+ Additional terms, permissive or non-permissive, may be stated in the
404
+ form of a separately written license, or stated as exceptions;
405
+ the above requirements apply either way.
406
+
407
+ 8. Termination.
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+
409
+ You may not propagate or modify a covered work except as expressly
410
+ provided under this License. Any attempt otherwise to propagate or
411
+ modify it is void, and will automatically terminate your rights under
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+ paragraph of section 11).
414
+
415
+ However, if you cease all violation of this License, then your
416
+ license from a particular copyright holder is reinstated (a)
417
+ provisionally, unless and until the copyright holder explicitly and
418
+ finally terminates your license, and (b) permanently, if the copyright
419
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420
+ prior to 60 days after the cessation.
421
+
422
+ Moreover, your license from a particular copyright holder is
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+ reinstated permanently if the copyright holder notifies you of the
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+ violation by some reasonable means, this is the first time you have
425
+ received notice of violation of this License (for any work) from that
426
+ copyright holder, and you cure the violation prior to 30 days after
427
+ your receipt of the notice.
428
+
429
+ Termination of your rights under this section does not terminate the
430
+ licenses of parties who have received copies or rights from you under
431
+ this License. If your rights have been terminated and not permanently
432
+ reinstated, you do not qualify to receive new licenses for the same
433
+ material under section 10.
434
+
435
+ 9. Acceptance Not Required for Having Copies.
436
+
437
+ You are not required to accept this License in order to receive or
438
+ run a copy of the Program. Ancillary propagation of a covered work
439
+ occurring solely as a consequence of using peer-to-peer transmission
440
+ to receive a copy likewise does not require acceptance. However,
441
+ nothing other than this License grants you permission to propagate or
442
+ modify any covered work. These actions infringe copyright if you do
443
+ not accept this License. Therefore, by modifying or propagating a
444
+ covered work, you indicate your acceptance of this License to do so.
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+
446
+ 10. Automatic Licensing of Downstream Recipients.
447
+
448
+ Each time you convey a covered work, the recipient automatically
449
+ receives a license from the original licensors, to run, modify and
450
+ propagate that work, subject to this License. You are not responsible
451
+ for enforcing compliance by third parties with this License.
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+
453
+ An "entity transaction" is a transaction transferring control of an
454
+ organization, or substantially all assets of one, or subdividing an
455
+ organization, or merging organizations. If propagation of a covered
456
+ work results from an entity transaction, each party to that
457
+ transaction who receives a copy of the work also receives whatever
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459
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461
+ the predecessor has it or can get it with reasonable efforts.
462
+
463
+ You may not impose any further restrictions on the exercise of the
464
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465
+ not impose a license fee, royalty, or other charge for exercise of
466
+ rights granted under this License, and you may not initiate litigation
467
+ (including a cross-claim or counterclaim in a lawsuit) alleging that
468
+ any patent claim is infringed by making, using, selling, offering for
469
+ sale, or importing the Program or any portion of it.
470
+
471
+ 11. Patents.
472
+
473
+ A "contributor" is a copyright holder who authorizes use under this
474
+ License of the Program or a work on which the Program is based. The
475
+ work thus licensed is called the contributor's "contributor version".
476
+
477
+ A contributor's "essential patent claims" are all patent claims
478
+ owned or controlled by the contributor, whether already acquired or
479
+ hereafter acquired, that would be infringed by some manner, permitted
480
+ by this License, of making, using, or selling its contributor version,
481
+ but do not include claims that would be infringed only as a
482
+ consequence of further modification of the contributor version. For
483
+ purposes of this definition, "control" includes the right to grant
484
+ patent sublicenses in a manner consistent with the requirements of
195
485
  this License.
196
486
 
197
- 7. If, as a consequence of a court judgment or allegation of patent
198
- infringement or for any other reason (not limited to patent issues),
199
- conditions are imposed on you (whether by court order, agreement or
487
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
488
+ patent license under the contributor's essential patent claims, to
489
+ make, use, sell, offer for sale, import and otherwise run, modify and
490
+ propagate the contents of its contributor version.
491
+
492
+ In the following three paragraphs, a "patent license" is any express
493
+ agreement or commitment, however denominated, not to enforce a patent
494
+ (such as an express permission to practice a patent or covenant not to
495
+ sue for patent infringement). To "grant" such a patent license to a
496
+ party means to make such an agreement or commitment not to enforce a
497
+ patent against the party.
498
+
499
+ If you convey a covered work, knowingly relying on a patent license,
500
+ and the Corresponding Source of the work is not available for anyone
501
+ to copy, free of charge and under the terms of this License, through a
502
+ publicly available network server or other readily accessible means,
503
+ then you must either (1) cause the Corresponding Source to be so
504
+ available, or (2) arrange to deprive yourself of the benefit of the
505
+ patent license for this particular work, or (3) arrange, in a manner
506
+ consistent with the requirements of this License, to extend the patent
507
+ license to downstream recipients. "Knowingly relying" means you have
508
+ actual knowledge that, but for the patent license, your conveying the
509
+ covered work in a country, or your recipient's use of the covered work
510
+ in a country, would infringe one or more identifiable patents in that
511
+ country that you have reason to believe are valid.
512
+
513
+ If, pursuant to or in connection with a single transaction or
514
+ arrangement, you convey, or propagate by procuring conveyance of, a
515
+ covered work, and grant a patent license to some of the parties
516
+ receiving the covered work authorizing them to use, propagate, modify
517
+ or convey a specific copy of the covered work, then the patent license
518
+ you grant is automatically extended to all recipients of the covered
519
+ work and works based on it.
520
+
521
+ A patent license is "discriminatory" if it does not include within
522
+ the scope of its coverage, prohibits the exercise of, or is
523
+ conditioned on the non-exercise of one or more of the rights that are
524
+ specifically granted under this License. You may not convey a covered
525
+ work if you are a party to an arrangement with a third party that is
526
+ in the business of distributing software, under which you make payment
527
+ to the third party based on the extent of your activity of conveying
528
+ the work, and under which the third party grants, to any of the
529
+ parties who would receive the covered work from you, a discriminatory
530
+ patent license (a) in connection with copies of the covered work
531
+ conveyed by you (or copies made from those copies), or (b) primarily
532
+ for and in connection with specific products or compilations that
533
+ contain the covered work, unless you entered into that arrangement,
534
+ or that patent license was granted, prior to 28 March 2007.
535
+
536
+ Nothing in this License shall be construed as excluding or limiting
537
+ any implied license or other defenses to infringement that may
538
+ otherwise be available to you under applicable patent law.
539
+
540
+ 12. No Surrender of Others' Freedom.
541
+
542
+ If conditions are imposed on you (whether by court order, agreement or
200
543
  otherwise) that contradict the conditions of this License, they do not
201
- excuse you from the conditions of this License. If you cannot
202
- distribute so as to satisfy simultaneously your obligations under this
203
- License and any other pertinent obligations, then as a consequence you
204
- may not distribute the Program at all. For example, if a patent
205
- license would not permit royalty-free redistribution of the Program by
206
- all those who receive copies directly or indirectly through you, then
207
- the only way you could satisfy both it and this License would be to
208
- refrain entirely from distribution of the Program.
209
-
210
- If any portion of this section is held invalid or unenforceable under
211
- any particular circumstance, the balance of the section is intended to
212
- apply and the section as a whole is intended to apply in other
213
- circumstances.
214
-
215
- It is not the purpose of this section to induce you to infringe any
216
- patents or other property right claims or to contest validity of any
217
- such claims; this section has the sole purpose of protecting the
218
- integrity of the free software distribution system, which is
219
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220
- generous contributions to the wide range of software distributed
221
- through that system in reliance on consistent application of that
222
- system; it is up to the author/donor to decide if he or she is willing
223
- to distribute software through any other system and a licensee cannot
224
- impose that choice.
225
-
226
- This section is intended to make thoroughly clear what is believed to
227
- be a consequence of the rest of this License.
228
-
229
- 8. If the distribution and/or use of the Program is restricted in
230
- certain countries either by patents or by copyrighted interfaces, the
231
- original copyright holder who places the Program under this License
232
- may add an explicit geographical distribution limitation excluding
233
- those countries, so that distribution is permitted only in or among
234
- countries not thus excluded. In such case, this License incorporates
235
- the limitation as if written in the body of this License.
236
-
237
- 9. The Free Software Foundation may publish revised and/or new versions
238
- of the General Public License from time to time. Such new versions will
544
+ excuse you from the conditions of this License. If you cannot convey a
545
+ covered work so as to satisfy simultaneously your obligations under this
546
+ License and any other pertinent obligations, then as a consequence you may
547
+ not convey it at all. For example, if you agree to terms that obligate you
548
+ to collect a royalty for further conveying from those to whom you convey
549
+ the Program, the only way you could satisfy both those terms and this
550
+ License would be to refrain entirely from conveying the Program.
551
+
552
+ 13. Use with the GNU Affero General Public License.
553
+
554
+ Notwithstanding any other provision of this License, you have
555
+ permission to link or combine any covered work with a work licensed
556
+ under version 3 of the GNU Affero General Public License into a single
557
+ combined work, and to convey the resulting work. The terms of this
558
+ License will continue to apply to the part which is the covered work,
559
+ but the special requirements of the GNU Affero General Public License,
560
+ section 13, concerning interaction through a network will apply to the
561
+ combination as such.
562
+
563
+ 14. Revised Versions of this License.
564
+
565
+ The Free Software Foundation may publish revised and/or new versions of
566
+ the GNU General Public License from time to time. Such new versions will
239
567
  be similar in spirit to the present version, but may differ in detail to
240
568
  address new problems or concerns.
241
569
 
242
- Each version is given a distinguishing version number. If the Program
243
- specifies a version number of this License which applies to it and "any
244
- later version", you have the option of following the terms and conditions
245
- either of that version or of any later version published by the Free
246
- Software Foundation. If the Program does not specify a version number of
247
- this License, you may choose any version ever published by the Free Software
248
- Foundation.
249
-
250
- 10. If you wish to incorporate parts of the Program into other free
251
- programs whose distribution conditions are different, write to the author
252
- to ask for permission. For software which is copyrighted by the Free
253
- Software Foundation, write to the Free Software Foundation; we sometimes
254
- make exceptions for this. Our decision will be guided by the two goals
255
- of preserving the free status of all derivatives of our free software and
256
- of promoting the sharing and reuse of software generally.
257
-
258
- NO WARRANTY
259
-
260
- 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
261
- FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
262
- OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
263
- PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
264
- OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
265
- MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
266
- TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
267
- PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
268
- REPAIR OR CORRECTION.
269
-
270
- 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
271
- WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
272
- REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
273
- INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
274
- OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
275
- TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
276
- YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
277
- PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
278
- POSSIBILITY OF SUCH DAMAGES.
570
+ Each version is given a distinguishing version number. If the
571
+ Program specifies that a certain numbered version of the GNU General
572
+ Public License "or any later version" applies to it, you have the
573
+ option of following the terms and conditions either of that numbered
574
+ version or of any later version published by the Free Software
575
+ Foundation. If the Program does not specify a version number of the
576
+ GNU General Public License, you may choose any version ever published
577
+ by the Free Software Foundation.
578
+
579
+ If the Program specifies that a proxy can decide which future
580
+ versions of the GNU General Public License can be used, that proxy's
581
+ public statement of acceptance of a version permanently authorizes you
582
+ to choose that version for the Program.
583
+
584
+ Later license versions may give you additional or different
585
+ permissions. However, no additional obligations are imposed on any
586
+ author or copyright holder as a result of your choosing to follow a
587
+ later version.
588
+
589
+ 15. Disclaimer of Warranty.
590
+
591
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592
+ APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
593
+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
594
+ OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
595
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
596
+ PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
597
+ IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
598
+ ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
599
+
600
+ 16. Limitation of Liability.
601
+
602
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
603
+ WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
604
+ THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
605
+ GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
606
+ USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
607
+ DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
608
+ PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609
+ EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610
+ SUCH DAMAGES.
611
+
612
+ 17. Interpretation of Sections 15 and 16.
613
+
614
+ If the disclaimer of warranty and limitation of liability provided
615
+ above cannot be given local legal effect according to their terms,
616
+ reviewing courts shall apply local law that most closely approximates
617
+ an absolute waiver of all civil liability in connection with the
618
+ Program, unless a warranty or assumption of liability accompanies a
619
+ copy of the Program in return for a fee.
279
620
 
280
621
  END OF TERMS AND CONDITIONS
281
622
 
@@ -287,15 +628,15 @@ free software which everyone can redistribute and change under these terms.
287
628
 
288
629
  To do so, attach the following notices to the program. It is safest
289
630
  to attach them to the start of each source file to most effectively
290
- convey the exclusion of warranty; and each file should have at least
631
+ state the exclusion of warranty; and each file should have at least
291
632
  the "copyright" line and a pointer to where the full notice is found.
292
633
 
293
- {description}
294
- Copyright (C) {year} {fullname}
634
+ <one line to give the program's name and a brief idea of what it does.>
635
+ Copyright (C) <year> <name of author>
295
636
 
296
- This program is free software; you can redistribute it and/or modify
637
+ This program is free software: you can redistribute it and/or modify
297
638
  it under the terms of the GNU General Public License as published by
298
- the Free Software Foundation; either version 2 of the License, or
639
+ the Free Software Foundation, either version 3 of the License, or
299
640
  (at your option) any later version.
300
641
 
301
642
  This program is distributed in the hope that it will be useful,
@@ -303,38 +644,31 @@ the "copyright" line and a pointer to where the full notice is found.
303
644
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
304
645
  GNU General Public License for more details.
305
646
 
306
- You should have received a copy of the GNU General Public License along
307
- with this program; if not, write to the Free Software Foundation, Inc.,
308
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
647
+ You should have received a copy of the GNU General Public License
648
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
309
649
 
310
650
  Also add information on how to contact you by electronic and paper mail.
311
651
 
312
- If the program is interactive, make it output a short notice like this
313
- when it starts in an interactive mode:
652
+ If the program does terminal interaction, make it output a short
653
+ notice like this when it starts in an interactive mode:
314
654
 
315
- Gnomovision version 69, Copyright (C) year name of author
316
- Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
655
+ <program> Copyright (C) <year> <name of author>
656
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
317
657
  This is free software, and you are welcome to redistribute it
318
658
  under certain conditions; type `show c' for details.
319
659
 
320
660
  The hypothetical commands `show w' and `show c' should show the appropriate
321
- parts of the General Public License. Of course, the commands you use may
322
- be called something other than `show w' and `show c'; they could even be
323
- mouse-clicks or menu items--whatever suits your program.
324
-
325
- You should also get your employer (if you work as a programmer) or your
326
- school, if any, to sign a "copyright disclaimer" for the program, if
327
- necessary. Here is a sample; alter the names:
328
-
329
- Yoyodyne, Inc., hereby disclaims all copyright interest in the program
330
- `Gnomovision' (which makes passes at compilers) written by James Hacker.
331
-
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- {signature of Ty Coon}, 1 April 1989
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- Ty Coon, President of Vice
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-
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- This General Public License does not permit incorporating your program into
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- proprietary programs. If your program is a subroutine library, you may
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- consider it more useful to permit linking proprietary applications with the
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- library. If this is what you want to do, use the GNU Lesser General
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- Public License instead of this License.
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-
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+ parts of the General Public License. Of course, your program's commands
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+ might be different; for a GUI interface, you would use an "about box".
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+
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+ You should also get your employer (if you work as a programmer) or school,
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+ if any, to sign a "copyright disclaimer" for the program, if necessary.
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+ For more information on this, and how to apply and follow the GNU GPL, see
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+ <http://www.gnu.org/licenses/>.
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+
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+ The GNU General Public License does not permit incorporating your program
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+ into proprietary programs. If your program is a subroutine library, you
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+ may consider it more useful to permit linking proprietary applications with
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+ the library. If this is what you want to do, use the GNU Lesser General
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+ Public License instead of this License. But first, please read
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+ <http://www.gnu.org/philosophy/why-not-lgpl.html>.