[med-svn] [Git][med-team/dssp][master] 2 commits: New upstream version 4.5.7
Maarten L. Hekkelman (@mhekkel-guest)
gitlab at salsa.debian.org
Wed Nov 26 10:01:29 GMT 2025
Maarten L. Hekkelman pushed to branch master at Debian Med / dssp
Commits:
126cab52 by Maarten L. Hekkelman at 2025-11-26T10:56:27+01:00
New upstream version 4.5.7
- - - - -
bc33a493 by Maarten L. Hekkelman at 2025-11-26T10:57:21+01:00
Update upstream source from tag 'upstream/4.5.7'
Update to upstream version '4.5.7'
with Debian dir 1cfa6a94fde8d5239cafec64ee9aafe06f6a9618
- - - - -
8 changed files:
- CMakeLists.txt
- Dockerfile
- changelog
- debian/changelog
- libdssp/CMakeLists.txt
- + libdssp/VERSION
- libdssp/src/dssp-io.cpp
- test/1cbs-dssp.cif
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -24,8 +24,10 @@
cmake_minimum_required(VERSION 3.23)
-# set the project name
-project(mkdssp VERSION 4.5.5 LANGUAGES CXX)
+file(READ libdssp/VERSION VER_FILE_CONTENT)
+string(STRIP ${VER_FILE_CONTENT} VER_FILE_CONTENT)
+
+project(mkdssp VERSION ${VER_FILE_CONTENT} LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
=====================================
Dockerfile
=====================================
@@ -5,7 +5,7 @@ RUN apt-get update && \
apt-get install -yq tzdata && \
ln -fs /usr/share/zoneinfo/Europe/Amsterdam /etc/localtime && \
dpkg-reconfigure -f noninteractive tzdata && \
- apt install -y build-essential cmake zlib1g-dev git libeigen3-dev
+ apt install -y build-essential cmake zlib1g-dev git libeigen3-dev libpcre2-dev
WORKDIR /build
@@ -21,4 +21,4 @@ RUN cd /src && \
rm -rf /src /build
WORKDIR /data
-ENTRYPOINT ["mkdssp"]
\ No newline at end of file
+ENTRYPOINT ["mkdssp"]
=====================================
changelog
=====================================
@@ -1,3 +1,6 @@
+Version 4.5.7
+- Fix for unit-test in Debian repository
+
Version 4.5.6
- Using libcifpp version 9.0.0
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+dssp (4.5.7-1) unstable; urgency=medium
+
+ * New upstream version 4.5.7
+ * Closes: #1121383
+
+ -- Maarten L. Hekkelman <maarten at hekkelman.com> Wed, 26 Nov 2025 10:56:41 +0100
+
dssp (4.5.6-1) unstable; urgency=medium
* Update debian/salsa-ci.yml file
=====================================
libdssp/CMakeLists.txt
=====================================
@@ -1,9 +1,33 @@
-# Use the version of the parent list file, if any. May need a fix someday.
-if(NOT CMAKE_PARENT_LIST_FILE)
- set(PROJECT_VERSION 4.5.2)
-endif()
-
-project(libdssp VERSION ${PROJECT_VERSION})
+# SPDX-License-Identifier: BSD-2-Clause
+#
+# Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
+#
+# 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.
+#
+# 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 OWNER 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.
+
+cmake_minimum_required(VERSION 3.23)
+
+file(READ VERSION VER_FILE_CONTENT)
+string(STRIP ${VER_FILE_CONTENT} VER_FILE_CONTENT)
+
+project(libdssp VERSION ${VER_FILE_CONTENT} LANGUAGES CXX)
include(CMakePackageConfigHelpers)
=====================================
libdssp/VERSION
=====================================
@@ -0,0 +1 @@
+4.5.7
\ No newline at end of file
=====================================
libdssp/src/dssp-io.cpp
=====================================
@@ -524,7 +524,7 @@ void writeStatistics(cif::datablock &db, const dssp &dssp)
{ "nr_of_ss_bridges_total", stats.count.SS_bridges },
{ "nr_of_ss_bridges_intra_chain", stats.count.intra_chain_SS_bridges },
{ "nr_of_ss_bridges_inter_chain", stats.count.SS_bridges - stats.count.intra_chain_SS_bridges },
- { "accessible_surface_of_protein", surface_accessibility } });
+ { "accessible_surface_of_protein", surface_accessibility, 2 } });
auto &dssp_struct_hbonds = db["dssp_statistics_hbond"];
=====================================
test/1cbs-dssp.cif
=====================================
@@ -7,7 +7,7 @@ _audit_conform.dict_name
_audit_conform.dict_version
_audit_conform.dict_location
mmcif_pdbx.dic 5.279 http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
-dssp-extension.dic 1.1 https://pdb-redo.eu/dssp/dssp-extension.dic
+dssp-extension.dic 1.1.1 https://pdb-redo.eu/dssp/dssp-extension.dic
#
_struct_biol.id 1
#
View it on GitLab: https://salsa.debian.org/med-team/dssp/-/compare/0296fa033c7d3acec199177cf9a6a01c5464aa10...bc33a493ab3e521ada18b91c5f6cdc84a42af197
--
View it on GitLab: https://salsa.debian.org/med-team/dssp/-/compare/0296fa033c7d3acec199177cf9a6a01c5464aa10...bc33a493ab3e521ada18b91c5f6cdc84a42af197
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