[med-svn] [Git][med-team/diann][master] 3 commits: Add missing licenses
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 18 16:17:19 GMT 2022
Andreas Tille pushed to branch master at Debian Med / diann
Commits:
571b5ece by Andreas Tille at 2022-01-18T16:35:26+01:00
Add missing licenses
- - - - -
72686f5f by Andreas Tille at 2022-01-18T17:00:36+01:00
Build and install binary
- - - - -
880b72d5 by Andreas Tille at 2022-01-18T17:03:40+01:00
complete d/copyright
- - - - -
5 changed files:
- debian/copyright
- + debian/install
- + debian/patches/series
- + debian/patches/use_debian_packaged_eigen3.patch
- debian/rules
Changes:
=====================================
debian/copyright
=====================================
@@ -12,14 +12,19 @@ Files-Excluded: mstoolkit
*.pdf
Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2014-2021 <upstream>
+License: AS-IS
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
+ OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
+ OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Files: WiffReader/*
Copyright: 2019, Vadim Demichev
-License: CC-A-4.0
- This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license,
- visit http://creativecommons.org/licenses/by/4.0/
+License: CC-BY-SA-4.0
Files: cranium/*
Copyright: 2017 Devin Soni
@@ -48,4 +53,270 @@ License: MPL-2.0
Files: debian/*
Copyright: 2021 Andreas Tille <tille at debian.org>
-License: <license>
+License: MPL-2.0
+
+License: MPL-2.0
+ On Debian systems you can find the full text of the Mozilla Public License
+ Version 2.0 at /usr/share/common-licenses.
+
+License: CC-BY-SA-4.0
+ By exercising the Licensed Rights (defined below), You accept and agree to be
+ bound by the terms and conditions of this Creative Commons
+ Attribution-ShareAlike 4.0 International Public License ("Public License"). To
+ the extent this Public License may be interpreted as a contract, You are
+ granted the Licensed Rights in consideration of Your acceptance of these terms
+ and conditions, and the Licensor grants You such rights in consideration of
+ benefits the Licensor receives from making the Licensed Material available
+ under these terms and conditions.
+ .
+ Section 1 – Definitions.
+ .
+ a. Adapted Material means material subject to Copyright and Similar Rights
+ that is derived from or based upon the Licensed Material and in which the
+ Licensed Material is translated, altered, arranged, transformed, or
+ otherwise modified in a manner requiring permission under the Copyright and
+ Similar Rights held by the Licensor. For purposes of this Public License,
+ where the Licensed Material is a musical work, performance, or sound
+ recording, Adapted Material is always produced where the Licensed Material
+ is synched in timed relation with a moving image.
+ b. Adapter's License means the license You apply to Your Copyright and Similar
+ Rights in Your contributions to Adapted Material in accordance with the
+ terms and conditions of this Public License.
+ c. BY-SA Compatible License means a license listed at creativecommons.org/
+ compatiblelicenses, approved by Creative Commons as essentially the
+ equivalent of this Public License.
+ d. Copyright and Similar Rights means copyright and/or similar rights closely
+ related to copyright including, without limitation, performance, broadcast,
+ sound recording, and Sui Generis Database Rights, without regard to how the
+ rights are labeled or categorized. For purposes of this Public License, the
+ rights specified in Section 2(b)(1)-(2) are not Copyright and Similar
+ Rights.
+ e. Effective Technological Measures means those measures that, in the absence
+ of proper authority, may not be circumvented under laws fulfilling
+ obligations under Article 11 of the WIPO Copyright Treaty adopted on
+ December 20, 1996, and/or similar international agreements.
+ f. Exceptions and Limitations means fair use, fair dealing, and/or any other
+ exception or limitation to Copyright and Similar Rights that applies to
+ Your use of the Licensed Material.
+ g. License Elements means the license attributes listed in the name of a
+ Creative Commons Public License. The License Elements of this Public
+ License are Attribution and ShareAlike.
+ h. Licensed Material means the artistic or literary work, database, or other
+ material to which the Licensor applied this Public License.
+ i. Licensed Rights means the rights granted to You subject to the terms and
+ conditions of this Public License, which are limited to all Copyright and
+ Similar Rights that apply to Your use of the Licensed Material and that the
+ Licensor has authority to license.
+ j. Licensor means the individual(s) or entity(ies) granting rights under this
+ Public License.
+ k. Share means to provide material to the public by any means or process that
+ requires permission under the Licensed Rights, such as reproduction, public
+ display, public performance, distribution, dissemination, communication, or
+ importation, and to make material available to the public including in ways
+ that members of the public may access the material from a place and at a
+ time individually chosen by them.
+ l. Sui Generis Database Rights means rights other than copyright resulting
+ from Directive 96/9/EC of the European Parliament and of the Council of 11
+ March 1996 on the legal protection of databases, as amended and/or
+ succeeded, as well as other essentially equivalent rights anywhere in the
+ world.
+ m. You means the individual or entity exercising the Licensed Rights under
+ this Public License. Your has a corresponding meaning.
+ .
+ Section 2 – Scope.
+ .
+ a. License grant.
+ 1. Subject to the terms and conditions of this Public License, the
+ Licensor hereby grants You a worldwide, royalty-free,
+ non-sublicensable, non-exclusive, irrevocable license to exercise the
+ Licensed Rights in the Licensed Material to:
+ A. reproduce and Share the Licensed Material, in whole or in part; and
+ B. produce, reproduce, and Share Adapted Material.
+ 2. Exceptions and Limitations. For the avoidance of doubt, where
+ Exceptions and Limitations apply to Your use, this Public License does
+ not apply, and You do not need to comply with its terms and conditions.
+ 3. Term. The term of this Public License is specified in Section 6(a).
+ 4. Media and formats; technical modifications allowed. The Licensor
+ authorizes You to exercise the Licensed Rights in all media and formats
+ whether now known or hereafter created, and to make technical
+ modifications necessary to do so. The Licensor waives and/or agrees not
+ to assert any right or authority to forbid You from making technical
+ modifications necessary to exercise the Licensed Rights, including
+ technical modifications necessary to circumvent Effective Technological
+ Measures. For purposes of this Public License, simply making
+ modifications authorized by this Section 2(a)(4) never produces Adapted
+ Material.
+ 5. Downstream recipients.
+ A. Offer from the Licensor – Licensed Material. Every recipient of the
+ Licensed Material automatically receives an offer from the Licensor
+ to exercise the Licensed Rights under the terms and conditions of
+ this Public License.
+ B. Additional offer from the Licensor – Adapted Material. Every
+ recipient of Adapted Material from You automatically receives an
+ offer from the Licensor to exercise the Licensed Rights in the
+ Adapted Material under the conditions of the Adapter’s License You
+ apply.
+ C. No downstream restrictions. You may not offer or impose any
+ additional or different terms or conditions on, or apply any
+ Effective Technological Measures to, the Licensed Material if doing
+ so restricts exercise of the Licensed Rights by any recipient of
+ the Licensed Material.
+ 6. No endorsement. Nothing in this Public License constitutes or may be
+ construed as permission to assert or imply that You are, or that Your
+ use of the Licensed Material is, connected with, or sponsored,
+ endorsed, or granted official status by, the Licensor or others
+ designated to receive attribution as provided in Section 3(a)(1)(A)(i).
+ b. Other rights.
+ .
+ 1. Moral rights, such as the right of integrity, are not licensed under
+ this Public License, nor are publicity, privacy, and/or other similar
+ personality rights; however, to the extent possible, the Licensor
+ waives and/or agrees not to assert any such rights held by the Licensor
+ to the limited extent necessary to allow You to exercise the Licensed
+ Rights, but not otherwise.
+ 2. Patent and trademark rights are not licensed under this Public License.
+ 3. To the extent possible, the Licensor waives any right to collect
+ royalties from You for the exercise of the Licensed Rights, whether
+ directly or through a collecting society under any voluntary or
+ waivable statutory or compulsory licensing scheme. In all other cases
+ the Licensor expressly reserves any right to collect such royalties.
+ .
+ Section 3 – License Conditions.
+ .
+ Your exercise of the Licensed Rights is expressly made subject to the following
+ conditions.
+ .
+ a. Attribution.
+ .
+ 1. If You Share the Licensed Material (including in modified form), You
+ must:
+ .
+ A. retain the following if it is supplied by the Licensor with the
+ Licensed Material:
+ i. identification of the creator(s) of the Licensed Material and
+ any others designated to receive attribution, in any reasonable
+ manner requested by the Licensor (including by pseudonym if
+ designated);
+ ii. a copyright notice;
+ iii. a notice that refers to this Public License;
+ iv. a notice that refers to the disclaimer of warranties;
+ v. a URI or hyperlink to the Licensed Material to the extent
+ reasonably practicable;
+ B. indicate if You modified the Licensed Material and retain an
+ indication of any previous modifications; and
+ C. indicate the Licensed Material is licensed under this Public
+ License, and include the text of, or the URI or hyperlink to, this
+ Public License.
+ 2. You may satisfy the conditions in Section 3(a)(1) in any reasonable
+ manner based on the medium, means, and context in which You Share the
+ Licensed Material. For example, it may be reasonable to satisfy the
+ conditions by providing a URI or hyperlink to a resource that includes
+ the required information.
+ 3. If requested by the Licensor, You must remove any of the information
+ required by Section 3(a)(1)(A) to the extent reasonably practicable.
+ b. ShareAlike.
+ .
+ In addition to the conditions in Section 3(a), if You Share Adapted
+ Material You produce, the following conditions also apply.
+ .
+ 1. The Adapter’s License You apply must be a Creative Commons license with
+ the same License Elements, this version or later, or a BY-SA Compatible
+ License.
+ 2. You must include the text of, or the URI or hyperlink to, the Adapter's
+ License You apply. You may satisfy this condition in any reasonable
+ manner based on the medium, means, and context in which You Share
+ Adapted Material.
+ 3. You may not offer or impose any additional or different terms or
+ conditions on, or apply any Effective Technological Measures to,
+ Adapted Material that restrict exercise of the rights granted under the
+ Adapter's License You apply.
+ .
+ Section 4 – Sui Generis Database Rights.
+ .
+ Where the Licensed Rights include Sui Generis Database Rights that apply to
+ Your use of the Licensed Material:
+ .
+ a. for the avoidance of doubt, Section 2(a)(1) grants You the right to
+ extract, reuse, reproduce, and Share all or a substantial portion of the
+ contents of the database;
+ b. if You include all or a substantial portion of the database contents in a
+ database in which You have Sui Generis Database Rights, then the database
+ in which You have Sui Generis Database Rights (but not its individual
+ contents) is Adapted Material, including for purposes of Section 3(b); and
+ c. You must comply with the conditions in Section 3(a) if You Share all or a
+ substantial portion of the contents of the database.
+ .
+ For the avoidance of doubt, this Section 4 supplements and does not replace
+ Your obligations under this Public License where the Licensed Rights include
+ other Copyright and Similar Rights.
+ .
+ Section 5 – Disclaimer of Warranties and Limitation of Liability.
+ .
+ a. Unless otherwise separately undertaken by the Licensor, to the extent
+ possible, the Licensor offers the Licensed Material as-is and as-available,
+ and makes no representations or warranties of any kind concerning the
+ Licensed Material, whether express, implied, statutory, or other. This
+ includes, without limitation, warranties of title, merchantability, fitness
+ for a particular purpose, non-infringement, absence of latent or other
+ defects, accuracy, or the presence or absence of errors, whether or not
+ known or discoverable. Where disclaimers of warranties are not allowed in
+ full or in part, this disclaimer may not apply to You.
+ b. To the extent possible, in no event will the Licensor be liable to You on
+ any legal theory (including, without limitation, negligence) or otherwise
+ for any direct, special, indirect, incidental, consequential, punitive,
+ exemplary, or other losses, costs, expenses, or damages arising out of this
+ Public License or use of the Licensed Material, even if the Licensor has
+ been advised of the possibility of such losses, costs, expenses, or
+ damages. Where a limitation of liability is not allowed in full or in part,
+ this limitation may not apply to You.
+ .
+ c. The disclaimer of warranties and limitation of liability provided above
+ shall be interpreted in a manner that, to the extent possible, most closely
+ approximates an absolute disclaimer and waiver of all liability.
+ .
+ Section 6 – Term and Termination.
+ .
+ a. This Public License applies for the term of the Copyright and Similar
+ Rights licensed here. However, if You fail to comply with this Public
+ License, then Your rights under this Public License terminate
+ automatically.
+ b. Where Your right to use the Licensed Material has terminated under Section
+ 6(a), it reinstates:
+ .
+ 1. automatically as of the date the violation is cured, provided it is
+ cured within 30 days of Your discovery of the violation; or
+ 2. upon express reinstatement by the Licensor.
+ For the avoidance of doubt, this Section 6(b) does not affect any right the
+ Licensor may have to seek remedies for Your violations of this Public
+ License.
+ c. For the avoidance of doubt, the Licensor may also offer the Licensed
+ Material under separate terms or conditions or stop distributing the
+ Licensed Material at any time; however, doing so will not terminate this
+ Public License.
+ d. Sections 1, 5, 6, 7, and 8 survive termination of this Public License.
+ .
+ Section 7 – Other Terms and Conditions.
+ .
+ a. The Licensor shall not be bound by any additional or different terms or
+ conditions communicated by You unless expressly agreed.
+ b. Any arrangements, understandings, or agreements regarding the Licensed
+ Material not stated herein are separate from and independent of the terms
+ and conditions of this Public License.
+ .
+ Section 8 – Interpretation.
+ .
+ a. For the avoidance of doubt, this Public License does not, and shall not be
+ interpreted to, reduce, limit, restrict, or impose conditions on any use of
+ the Licensed Material that could lawfully be made without permission under
+ this Public License.
+ b. To the extent possible, if any provision of this Public License is deemed
+ unenforceable, it shall be automatically reformed to the minimum extent
+ necessary to make it enforceable. If the provision cannot be reformed, it
+ shall be severed from this Public License without affecting the
+ enforceability of the remaining terms and conditions.
+ c. No term or condition of this Public License will be waived and no failure
+ to comply consented to unless expressly agreed to by the Licensor.
+ d. Nothing in this Public License constitutes or may be interpreted as a
+ limitation upon, or waiver of, any privileges and immunities that apply to
+ the Licensor or You, including from the legal processes of any jurisdiction
+ or authority.
=====================================
debian/install
=====================================
@@ -0,0 +1 @@
+diann usr/bin
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+use_debian_packaged_eigen3.patch
=====================================
debian/patches/use_debian_packaged_eigen3.patch
=====================================
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>s
+Last-Update: Tue, 18 Jan 2022 14:59:21 +0100
+Description: Use Debian packaged eigen3 library
+
+--- a/src/diann.cpp
++++ b/src/diann.cpp
+@@ -49,8 +49,8 @@ Uncomment "#define _NO_THERMORAW" in RAW
+
+ #include "cpu_info.h"
+ #include "../cranium/src/cranium.h"
+-#include "../eigen/Eigen/Dense"
+-#include "../eigen/Eigen/Sparse"
++#include <Eigen/Dense>
++#include <Eigen/Sparse>
+ #ifdef CPP17
+ #include <experimental/filesystem> // requires C++17
+ #endif
=====================================
debian/rules
=====================================
@@ -4,28 +4,18 @@
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
-#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-# do_stuff_for_testing
-#endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-# . debian/get-orig-source
+# Options removed from ../linux-build-gcc-7: -static -msse2 -march=core2
+override_dh_auto_build:
+ $(CPP) $(CFLAGS) -o diann \
+ src/diann.cpp \
+ -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++17 -lstdc++fs -fpermissive -O3 -mfpmath=sse -w \
+ -I/usr/include/libmstoolkit -lmstoolkitlite \
+ -I/usr/include/eigen3 \
+ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
View it on GitLab: https://salsa.debian.org/med-team/diann/-/compare/cac28a0493a69be3f2751514d00c0df701ffea96...880b72d511329a9ccb15db545c65959b476a9f4c
--
View it on GitLab: https://salsa.debian.org/med-team/diann/-/compare/cac28a0493a69be3f2751514d00c0df701ffea96...880b72d511329a9ccb15db545c65959b476a9f4c
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