bsvae 0.1.2__tar.gz → 0.2.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (32) hide show
  1. bsvae-0.2.0/LICENSE +622 -0
  2. {bsvae-0.1.2 → bsvae-0.2.0}/PKG-INFO +78 -17
  3. {bsvae-0.1.2 → bsvae-0.2.0}/README.md +98 -45
  4. {bsvae-0.1.2 → bsvae-0.2.0}/pyproject.toml +23 -2
  5. bsvae-0.2.0/src/bsvae/__init__.py +12 -0
  6. bsvae-0.2.0/src/bsvae/latent/__init__.py +6 -0
  7. bsvae-0.2.0/src/bsvae/latent/latent_analysis.py +218 -0
  8. bsvae-0.2.0/src/bsvae/latent/latent_export.py +141 -0
  9. bsvae-0.2.0/src/bsvae/networks/__init__.py +13 -0
  10. bsvae-0.2.0/src/bsvae/networks/cli.py +318 -0
  11. bsvae-0.2.0/src/bsvae/networks/extract_networks.py +1229 -0
  12. bsvae-0.2.0/src/bsvae/networks/module_extraction.py +426 -0
  13. bsvae-0.2.0/src/bsvae/networks/utils.py +40 -0
  14. bsvae-0.1.2/src/bsvae/__init__.py +0 -0
  15. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/hyperparam.ini +0 -0
  16. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/main.py +0 -0
  17. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/models/__init__.py +0 -0
  18. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/models/decoder.py +0 -0
  19. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/models/encoder.py +0 -0
  20. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/models/losses.py +0 -0
  21. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/models/structured.py +0 -0
  22. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/models/vae.py +0 -0
  23. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/ppi_cli.py +0 -0
  24. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/__init__.py +0 -0
  25. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/datasets.py +0 -0
  26. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/evaluate.py +0 -0
  27. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/helpers.py +0 -0
  28. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/initialization.py +0 -0
  29. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/mapping.py +0 -0
  30. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/modelIO.py +0 -0
  31. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/ppi.py +0 -0
  32. {bsvae-0.1.2 → bsvae-0.2.0}/src/bsvae/utils/training.py +0 -0
bsvae-0.2.0/LICENSE ADDED
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+ (such as an express permission to practice a patent or covenant not to
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+ patent against the party.
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+
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+ If you convey a covered work, knowingly relying on a patent license, and
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+ the Corresponding Source of the work is not available for anyone to
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+ copy, free of charge and under the terms of this License, through a
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+ publicly available network server or other readily accessible means,
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+ then you must either (1) cause the Corresponding Source to be so
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+ available, or (2) arrange to deprive yourself of the benefit of the
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+ patent license for this particular work, or (3) arrange, in a manner
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+ consistent with the requirements of this License, to extend the patent
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+ license to downstream recipients. "Knowingly relying" means you have
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+ actual knowledge that, but for the patent license, your conveying the
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+ covered work in a country, or your recipient's use of the covered work
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+ in a country, would infringe one or more identifiable patents in that
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+ country that you have reason to believe are valid.
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+
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+ If, pursuant to or in connection with a single transaction or
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+ arrangement, you convey, or propagate by procuring conveyance of, a
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+ covered work, and grant a patent license to some of the parties
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+ receiving the covered work authorizing them to use, propagate, modify or
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+ convey a specific copy of the covered work, then the patent license you
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+ grant is automatically extended to all recipients of the covered work
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+ and works based on it.
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+
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+ A patent license is "discriminatory" if it does not include within the
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+ scope of its coverage, prohibits the exercise of, or is conditioned on
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+ the non-exercise of one or more of the rights that are specifically
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+ granted under this License. You may not convey a covered work if you are
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+ party to an arrangement with a third party that is in the business of
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+ distributing software, under which you make payment to the third party
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+ based on the extent of your activity of conveying the work, and under
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+ which the third party grants, to any of the parties who would receive
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+ the covered work from you, a discriminatory patent license (a) in
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+ connection with copies of the covered work conveyed by you (or copies
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+ made from those copies), or (b) primarily for and in connection with
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+ specific products or compilations that contain the covered work, unless
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+ you entered into that arrangement, or that patent license was granted,
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+ prior to 28 March 2007.
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+
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+ Nothing in this License shall be construed as excluding or limiting any
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+ implied license or other defenses to infringement that may otherwise be
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+ available to you under applicable patent law.
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+
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+ 12. No Surrender of Others' Freedom.
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+
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+ If conditions are imposed on you (whether by court order, agreement or
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+ otherwise) that contradict the conditions of this License, they do not
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+ excuse you from the conditions of this License. If you cannot convey a
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+ covered work so as to satisfy simultaneously your obligations under this
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+ License and any other pertinent obligations, then as a consequence you
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+ may not convey it at all. For example, if you agree to terms that
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+ obligate you to collect a royalty for further conveying from those to
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+ whom you convey the Program, the only way you could satisfy both those
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+ terms and this License would be to refrain entirely from conveying the
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+ Program.
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+
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+ 13. Use with the GNU Affero General Public License.
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+
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+ Notwithstanding any other provision of this License, you have
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+ permission to link or combine any covered work with a work licensed
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+ under version 3 of the GNU Affero General Public License into a single
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+ combined work, and to convey the resulting work. The terms of this
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+ License will continue to apply to the part which is the covered work,
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+ but the special requirements of the GNU Affero General Public License,
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+ section 13, concerning interaction through a network will apply to the
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+ combination as such.
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+
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+ 14. Revised Versions of this License.
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+
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+ The Free Software Foundation may publish revised and/or new versions of
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+ the GNU General Public License from time to time. Such new versions will
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+ be similar in spirit to the present version, but may differ in detail to
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+ address new problems or concerns.
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+
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+ Each version is given a distinguishing version number. If the Program
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+ specifies that a certain numbered version of the GNU General Public
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+ License "or any later version" applies to it, you have the option of
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+ following the terms and conditions either of that numbered version or of
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+ any later version published by the Free Software Foundation. If the
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+ Program does not specify a version number of the GNU General Public
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+ License, you may choose any version ever published by the Free Software
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+ Foundation.
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+
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+ If the Program specifies that a proxy can decide which future versions
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+ of the GNU General Public License can be used, that proxy's public
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+ statement of acceptance of a version permanently authorizes you to
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+ choose that version for the Program.
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+
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+ Later license versions may give you additional or different permissions.
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+ However, no additional obligations are imposed on any author or
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+ copyright holder as a result of your choosing to follow a later version.
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+
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+ 15. Disclaimer of Warranty.
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+
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+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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+ APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
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+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
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+ OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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+ PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
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+ PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE
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+ COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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+
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+ 16. Limitation of Liability.
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+
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+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+ WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
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+ CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
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+ INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
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+ ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
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+ NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES
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+ SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
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+ WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN
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+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
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+
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+ 17. Interpretation of Sections 15 and 16.
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+
560
+ If the disclaimer of warranty and limitation of liability provided
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+ above cannot be given local legal effect according to their terms,
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+ reviewing courts shall apply local law that most closely approximates
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+ an absolute waiver of all civil liability in connection with the
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+ Program, unless a warranty or assumption of liability accompanies a
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+ copy of the Program in return for a fee.
566
+
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+ END OF TERMS AND CONDITIONS
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+
569
+ How to Apply These Terms to Your New Programs
570
+
571
+ If you develop a new program, and you want it to be of the greatest
572
+ possible use to the public, the best way to achieve this is to make it
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+ free software which everyone can redistribute and change under these
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+ terms.
575
+
576
+ To do so, attach the following notices to the program. It is safest to
577
+ attach them to the start of each source file to most effectively state
578
+ the exclusion of warranty; and each file should have at least the
579
+ "copyright" line and a pointer to where the full notice is found.
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+
581
+ <one line to give the program's name and a brief idea of what it does.>
582
+ Copyright (C) <year> <name of author>
583
+
584
+ This program is free software: you can redistribute it and/or modify
585
+ it under the terms of the GNU General Public License as published by
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+ the Free Software Foundation, either version 3 of the License, or
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+ (at your option) any later version.
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+
589
+ This program is distributed in the hope that it will be useful,
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+ but WITHOUT ANY WARRANTY; without even the implied warranty of
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+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+ GNU General Public License for more details.
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+
594
+ You should have received a copy of the GNU General Public License
595
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
596
+
597
+ Also add information on how to contact you by electronic and paper mail.
598
+
599
+ If the program does terminal interaction, make it output a short notice
600
+ like this when it starts in an interactive mode:
601
+
602
+ <program> Copyright (C) <year> <name of author>
603
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
604
+ This is free software, and you are welcome to redistribute it
605
+ under certain conditions; type `show c' for details.
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+
607
+ The hypothetical commands `show w' and `show c' should show the
608
+ appropriate parts of the General Public License. Of course, your
609
+ program's commands might be different; for a GUI interface, you would
610
+ use an "about box".
611
+
612
+ You should also get your employer (if you work as a programmer) or
613
+ school, if any, to sign a "copyright disclaimer" for the program, if
614
+ necessary. For more information on this, and how to apply and follow the
615
+ GNU GPL, see <https://www.gnu.org/licenses/>.
616
+
617
+ The GNU General Public License does not permit incorporating your
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+ program into proprietary programs. If your program is a subroutine
619
+ library, you may consider it more useful to permit linking proprietary
620
+ applications with the library. If this is what you want to do, use the
621
+ GNU Lesser General Public License instead of this License. But first,
622
+ please read <https://www.gnu.org/licenses/why-not-lgpl.html>.