diff options
| -rw-r--r-- | debian/changelog | 34 | ||||
| -rw-r--r-- | debian/control | 32 | ||||
| -rw-r--r-- | debian/copyright | 43 | ||||
| -rw-r--r-- | debian/hera-utils.install | 1 | ||||
| -rw-r--r-- | debian/libhera-dev.install | 2 | ||||
| -rw-r--r-- | debian/patches/0001-Use-system-catch2.patch | 114 | ||||
| -rw-r--r-- | debian/patches/0002-Use-system-PHAT.patch | 55 | ||||
| -rw-r--r-- | debian/patches/series | 2 | ||||
| -rwxr-xr-x | debian/rules | 30 | ||||
| -rw-r--r-- | debian/source/format | 1 | ||||
| -rw-r--r-- | debian/tests/control | 7 | ||||
| -rwxr-xr-x | debian/tests/upstream-bottleneck.sh | 19 | ||||
| -rwxr-xr-x | debian/tests/upstream-wasserstein.sh | 17 | ||||
| -rw-r--r-- | debian/upstream/metadata | 19 | ||||
| -rw-r--r-- | debian/watch | 4 |
15 files changed, 380 insertions, 0 deletions
diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..2a80dae --- /dev/null +++ b/debian/changelog @@ -0,0 +1,34 @@ +hera (0~git20210508+dfsg-1) unstable; urgency=medium + + * New upstream, based on commit + 2ed9afc052bee7956f6abb195947de1f80cb9d91. + - Refresh patch. + * Correct upstream metadata. + * Drop unneccessary version bounds. + * Actually depend on PHAT. + - Add patch to use the system PHAT version instead of DFSG-deleted + bundled copy. + * Run build-time tests from the correct directory. + + -- Gard Spreemann <gspr@nonempty.org> Sat, 14 Aug 2021 18:42:03 +0200 + +hera (0~git20200602+dfsg-3) unstable; urgency=medium + + * Add upstream metadata file with paper references. + * Move git to Salsa. + * Standards-version 4.5.1. No changes needed. + + -- Gard Spreemann <gspr@nonempty.org> Fri, 22 Jan 2021 19:11:10 +0100 + +hera (0~git20200602+dfsg-2) unstable; urgency=medium + + * Add tests. + + -- Gard Spreemann <gspr@nonempty.org> Sat, 06 Jun 2020 16:39:33 +0200 + +hera (0~git20200602+dfsg-1) unstable; urgency=medium + + * Initial commit, based on upstream commit + b73ed1face2c609958556e6f2b7704bbd8aaa263. (Closes: #961784) + + -- Gard Spreemann <gspr@nonempty.org> Tue, 02 Jun 2020 20:40:30 +0200 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..aa6d206 --- /dev/null +++ b/debian/control @@ -0,0 +1,32 @@ +Source: hera +Maintainer: Gard Spreemann <gspr@nonempty.org> +Section: math +Priority: optional +Standards-Version: 4.5.1 +Build-Depends: catch2, + cmake, + debhelper-compat (= 13), + libboost-dev, + libphat-dev +Rules-Requires-Root: no +Homepage: https://github.com/anigmetov/hera/ +Vcs-Browser: https://salsa.debian.org/gspr/hera +Vcs-Git: https://salsa.debian.org/gspr/hera.git -b debian/sid + +Package: libhera-dev +Section: libdevel +Architecture: all +Multi-Arch: foreign +Depends: libboost-dev, libphat-dev, ${misc:Depends} +Description: Library for efficient bottleneck and Wasserstein distances + A header-only C++ library for efficient computation of bottleneck and + Wasserstein distances between persistence diagrams. + +Package: hera-utils +Section: math +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends} +Description: Utilities built from the Hera library + Some simple utilities for efficient bottleneck and Wasserstein + distances between persistence diagrams built from the Hera library + (see libhera-dev). diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..e8ad71f --- /dev/null +++ b/debian/copyright @@ -0,0 +1,43 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: hera +Files-Excluded: bottleneck/include/catch matching/include/catch wasserstein/include/catch matching/include/phat +Source: https://github.com/anigmetov/hera +Comment: Deleted upstream bundling of catch and PHAT for DFSG repack. +License: BSD-3-clause + +Files: * +Copyright: 2015-2021 M. Kerber, D. Morozov, A. Nigmetov +License: BSD-3-clause + +Files: debian/* +Copyright: 2020-2021 Gard Spreemann <gspr@nonempty.org> +License: BSD-3-clause + +License: BSD-3-clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + . + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + . + 3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + . + 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.
\ No newline at end of file diff --git a/debian/hera-utils.install b/debian/hera-utils.install new file mode 100644 index 0000000..1e881ed --- /dev/null +++ b/debian/hera-utils.install @@ -0,0 +1 @@ +usr/bin
\ No newline at end of file diff --git a/debian/libhera-dev.install b/debian/libhera-dev.install new file mode 100644 index 0000000..a0ad680 --- /dev/null +++ b/debian/libhera-dev.install @@ -0,0 +1,2 @@ +bottleneck/include/* /usr/include/hera/bottleneck/ +wasserstein/include/* /usr/include/hera/wasserstein/ diff --git a/debian/patches/0001-Use-system-catch2.patch b/debian/patches/0001-Use-system-catch2.patch new file mode 100644 index 0000000..536b23c --- /dev/null +++ b/debian/patches/0001-Use-system-catch2.patch @@ -0,0 +1,114 @@ +From: Gard Spreemann <gspr@nonempty.org> +Date: Wed, 3 Jun 2020 09:32:19 +0200 +Subject: Use system catch2. + +--- + bottleneck/tests/test_hera_bottleneck.cpp | 2 +- + bottleneck/tests/tests_main.cpp | 2 +- + matching/tests/test_bifiltration.cpp | 2 +- + matching/tests/test_common.cpp | 2 +- + matching/tests/test_matching_distance.cpp | 2 +- + matching/tests/test_module.cpp | 2 +- + matching/tests/tests_main.cpp | 2 +- + wasserstein/tests/test_hera_wasserstein.cpp | 2 +- + wasserstein/tests/test_hera_wasserstein_pure_geom.cpp | 2 +- + wasserstein/tests/tests_main.cpp | 2 +- + 10 files changed, 10 insertions(+), 10 deletions(-) + +diff --git a/bottleneck/tests/test_hera_bottleneck.cpp b/bottleneck/tests/test_hera_bottleneck.cpp +index c74e800..b97fe6f 100644 +--- a/bottleneck/tests/test_hera_bottleneck.cpp ++++ b/bottleneck/tests/test_hera_bottleneck.cpp +@@ -1,4 +1,4 @@ +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/bottleneck/tests/tests_main.cpp b/bottleneck/tests/tests_main.cpp +index d24407e..1f558c8 100644 +--- a/bottleneck/tests/tests_main.cpp ++++ b/bottleneck/tests/tests_main.cpp +@@ -1,3 +1,3 @@ + #define LOG_AUCTION + #define CATCH_CONFIG_MAIN +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> +diff --git a/matching/tests/test_bifiltration.cpp b/matching/tests/test_bifiltration.cpp +index 742dab8..f63e231 100644 +--- a/matching/tests/test_bifiltration.cpp ++++ b/matching/tests/test_bifiltration.cpp +@@ -1,4 +1,4 @@ +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/matching/tests/test_common.cpp b/matching/tests/test_common.cpp +index 9079a56..d390585 100644 +--- a/matching/tests/test_common.cpp ++++ b/matching/tests/test_common.cpp +@@ -1,4 +1,4 @@ +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/matching/tests/test_matching_distance.cpp b/matching/tests/test_matching_distance.cpp +index 115c8d9..08c59c0 100644 +--- a/matching/tests/test_matching_distance.cpp ++++ b/matching/tests/test_matching_distance.cpp +@@ -1,4 +1,4 @@ +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/matching/tests/test_module.cpp b/matching/tests/test_module.cpp +index bae1f78..3dbe5b1 100644 +--- a/matching/tests/test_module.cpp ++++ b/matching/tests/test_module.cpp +@@ -1,4 +1,4 @@ +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/matching/tests/tests_main.cpp b/matching/tests/tests_main.cpp +index 1c77b13..4ed06df 100644 +--- a/matching/tests/tests_main.cpp ++++ b/matching/tests/tests_main.cpp +@@ -1,2 +1,2 @@ + #define CATCH_CONFIG_MAIN +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> +diff --git a/wasserstein/tests/test_hera_wasserstein.cpp b/wasserstein/tests/test_hera_wasserstein.cpp +index 6f5de3b..83a781a 100644 +--- a/wasserstein/tests/test_hera_wasserstein.cpp ++++ b/wasserstein/tests/test_hera_wasserstein.cpp +@@ -1,5 +1,5 @@ + #define LOG_AUCTION +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/wasserstein/tests/test_hera_wasserstein_pure_geom.cpp b/wasserstein/tests/test_hera_wasserstein_pure_geom.cpp +index 9603ceb..3110c4c 100644 +--- a/wasserstein/tests/test_hera_wasserstein_pure_geom.cpp ++++ b/wasserstein/tests/test_hera_wasserstein_pure_geom.cpp +@@ -1,4 +1,4 @@ +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> + + #include <sstream> + #include <iostream> +diff --git a/wasserstein/tests/tests_main.cpp b/wasserstein/tests/tests_main.cpp +index d24407e..1f558c8 100644 +--- a/wasserstein/tests/tests_main.cpp ++++ b/wasserstein/tests/tests_main.cpp +@@ -1,3 +1,3 @@ + #define LOG_AUCTION + #define CATCH_CONFIG_MAIN +-#include "catch/catch.hpp" ++#include <catch2/catch.hpp> diff --git a/debian/patches/0002-Use-system-PHAT.patch b/debian/patches/0002-Use-system-PHAT.patch new file mode 100644 index 0000000..b99adc6 --- /dev/null +++ b/debian/patches/0002-Use-system-PHAT.patch @@ -0,0 +1,55 @@ +From: Gard Spreemann <gspr@nonempty.org> +Date: Sat, 14 Aug 2021 19:05:48 +0200 +Subject: Use system PHAT + +--- + matching/include/bifiltration.h | 4 ++-- + matching/include/common_util.h | 2 +- + matching/include/persistence_module.h | 6 +++--- + 3 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/matching/include/bifiltration.h b/matching/include/bifiltration.h +index 5b188d4..25b3bff 100644 +--- a/matching/include/bifiltration.h ++++ b/matching/include/bifiltration.h +@@ -12,8 +12,8 @@ + #include "box.h" + #include "simplex.h" + #include "dual_point.h" +-#include "phat/boundary_matrix.h" +-#include "phat/compute_persistence_pairs.h" ++#include <phat/boundary_matrix.h> ++#include <phat/compute_persistence_pairs.h> + + #include "common_util.h" + +diff --git a/matching/include/common_util.h b/matching/include/common_util.h +index 20a151a..61476a5 100644 +--- a/matching/include/common_util.h ++++ b/matching/include/common_util.h +@@ -12,7 +12,7 @@ + #include <functional> + + #include "common_defs.h" +-#include "phat/helpers/misc.h" ++#include <phat/helpers/misc.h> + + namespace md { + +diff --git a/matching/include/persistence_module.h b/matching/include/persistence_module.h +index 4df2148..80ff3c1 100644 +--- a/matching/include/persistence_module.h ++++ b/matching/include/persistence_module.h +@@ -9,9 +9,9 @@ + #include <algorithm> + #include <unordered_set> + +-#include "phat/boundary_matrix.h" +-#include "phat/compute_persistence_pairs.h" +-#include "phat/algorithms/standard_reduction.h" ++#include <phat/boundary_matrix.h> ++#include <phat/compute_persistence_pairs.h> ++#include <phat/algorithms/standard_reduction.h> + + #include "common_util.h" + #include "dual_point.h" diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..78f2fb4 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,2 @@ +0001-Use-system-catch2.patch +0002-Use-system-PHAT.patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..30c7235 --- /dev/null +++ b/debian/rules @@ -0,0 +1,30 @@ +#!/usr/bin/make -f + +export DEB_BUILD_MAINT_OPTIONS = hardening=+all + +%: + dh $@ + +override_dh_clean: +# dh_clean nukes an upstream file. + dh_clean -X.bak + +override_dh_auto_clean: + dh_auto_clean --builddirectory=build-bottleneck --sourcedirectory=bottleneck + dh_auto_clean --builddirectory=build-wasserstein --sourcedirectory=wasserstein + +override_dh_auto_configure: + dh_auto_configure --builddirectory=build-bottleneck --sourcedirectory=bottleneck + dh_auto_configure --builddirectory=build-wasserstein --sourcedirectory=wasserstein + +override_dh_auto_build: + dh_auto_build --builddirectory=build-bottleneck --sourcedirectory=bottleneck + dh_auto_build --builddirectory=build-wasserstein --sourcedirectory=wasserstein + +execute_before_dh_install: + install -D build-bottleneck/bottleneck_dist debian/tmp/usr/bin/hera-bottleneck + install -D build-wasserstein/wasserstein_dist debian/tmp/usr/bin/hera-wasserstein + install -D build-wasserstein/wasserstein_dist_dipha debian/tmp/usr/bin/hera-wasserstein-dipha + +override_dh_auto_test: + cd wasserstein/tests/data && ../../../build-wasserstein/wasserstein_test diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 0000000..159f48c --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,7 @@ +Tests: upstream-bottleneck.sh +Depends: build-essential, catch2, libhera-dev +Restrictions: allow-stderr + +Tests: upstream-wasserstein.sh +Depends: build-essential, catch2, libhera-dev +Restrictions: allow-stderr
\ No newline at end of file diff --git a/debian/tests/upstream-bottleneck.sh b/debian/tests/upstream-bottleneck.sh new file mode 100755 index 0000000..a11a13b --- /dev/null +++ b/debian/tests/upstream-bottleneck.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +set -e +set -u + +tmpdir=$AUTOPKGTEST_TMP/bottleneck + +mkdir -p $tmpdir +cp -R $PWD/bottleneck/tests/* $tmpdir + +cd $tmpdir +ln -s /usr/include/catch2 catch + +set -x +g++ -O2 -I/usr/include/hera/bottleneck -o test tests_main.cpp test_hera_bottleneck.cpp +./test +cd data +../test + diff --git a/debian/tests/upstream-wasserstein.sh b/debian/tests/upstream-wasserstein.sh new file mode 100755 index 0000000..070e5c6 --- /dev/null +++ b/debian/tests/upstream-wasserstein.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +set -e +set -u + +tmpdir=$AUTOPKGTEST_TMP/wasserstein + +mkdir -p $tmpdir +cp -R $PWD/wasserstein/tests/* $tmpdir + +cd $tmpdir +ln -s /usr/include/catch2 catch + +set -x +g++ -O2 -I/usr/include/hera/wasserstein -o test tests_main.cpp test_hera_wasserstein.cpp test_hera_wasserstein_pure_geom.cpp +cd data +../test diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..76b11d6 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,19 @@ +Cite-As: > + Michael Kerber, Dmitriy Morozov, and Arnur Nigmetov, + "Geometry Helps to Compare Persistence Diagrams.", + Journal of Experimental Algorithmics, vol. 22, 2017, pp. 1--20. +Reference: + Title: "Geometry helps to compare persistence diagrams" + Author: Kerber, Michael and Morozov, Dmitriy and Nigmetov, Arnur + Journal: Journal of Experimental Algorithmics (JEA) + Volume: 22 + Pages: 1--20 + Year: 2017 + Publisher: ACM New York, NY, USA +Reference: + Title: "Efficient Approximation of the Matching Distance for 2-parameter persistence" + Author: Kerber, Michael and Nigmetov, Arnur + Year: 2020 + Type: inproceedings + Journal: SoCG 2020 + diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..61c78cb --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +version=4 +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*@ARCHIVE_EXT@)%@PACKAGE@-$1%, repacksuffix=+dfsg, dversionmangle=auto" \ + https://github.com/anigmetov/hera/tags \ + (?:.*?/)?v?@ANY_VERSION@@ARCHIVE_EXT@
\ No newline at end of file |