Hello community,
here is the log from the commit of package votca-csg for openSUSE:Factory
checked in at 2020-12-10 18:19:53
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/votca-csg (Old)
and /work/SRC/openSUSE:Factory/.votca-csg.new.2328 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "votca-csg"
Thu Dec 10 18:19:53 2020 rev:21 rq:854602 version:1.6.3
Changes:
--------
--- /work/SRC/openSUSE:Factory/votca-csg/votca-csg.changes 2020-08-25
09:37:30.160166875 +0200
+++ /work/SRC/openSUSE:Factory/.votca-csg.new.2328/votca-csg.changes
2020-12-10 18:19:55.239087300 +0100
@@ -1,0 +2,14 @@
+Wed Dec 9 20:22:15 UTC 2020 - Christoph Junghans <jungh...@votca.org>
+
+- Update to 1.6.3
+ - fix test dependencies for parallel ctest ([gh#votca/csg#585])
+ - fix trigger for gmx-2020 warning in run_gromacs.sh
+ ([gh#votca/csg#591])
+ - switch to ghcr.io for CI ([gh#votca/csg#595])
+ - format code with clang-11 ([gh#votca/csg#605])
+ - add gmx2021 builds to CI ([gh#votca/csg#607])
+ - remove set-env call from CI ([gh#votca/csg#608])
+ - use master .clang-format in format action ([gh#votca/csg#610])
+ - strip windows line endings in readers ([gh#votca/csg#614])
+
+-------------------------------------------------------------------
Old:
----
votca-csg-1.6.2.tar.gz
votca-csg-manual-1.6.2.pdf
votca-csg-tutorials-1.6.2.tar.gz
New:
----
votca-csg-1.6.3.tar.gz
votca-csg-manual-1.6.3.pdf
votca-csg-tutorials-1.6.3.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ votca-csg.spec ++++++
--- /var/tmp/diff_new_pack.3PNGRV/_old 2020-12-10 18:19:56.007089230 +0100
+++ /var/tmp/diff_new_pack.3PNGRV/_new 2020-12-10 18:19:56.011089240 +0100
@@ -18,7 +18,7 @@
Name: votca-csg
-Version: 1.6.2
+Version: 1.6.3
Release: 0
%define uversion %{version}
%define sover 6
++++++ votca-csg-1.6.2.tar.gz -> votca-csg-1.6.3.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/csg-1.6.2/.github/workflows/continuous-integration-workflow.yml
new/csg-1.6.3/.github/workflows/continuous-integration-workflow.yml
--- old/csg-1.6.2/.github/workflows/continuous-integration-workflow.yml
2020-08-22 15:31:14.000000000 +0200
+++ new/csg-1.6.3/.github/workflows/continuous-integration-workflow.yml
2020-12-09 04:54:01.000000000 +0100
@@ -7,10 +7,10 @@
jobs:
CI:
- continue-on-error: ${{ matrix.distro == 'ubuntu_devel' || matrix.distro ==
'fedora_rawhide' || matrix.continue-on-error == true }}
+ continue-on-error: ${{ matrix.distro == 'ubuntu:devel' || matrix.distro ==
'fedora:rawhide' || matrix.distro == 'opensuse:latest' ||
matrix.continue-on-error == true }}
strategy:
matrix:
- distro: [latest, fedora_rawhide, opensuse, ubuntu, ubuntu_devel,
ubuntu_rolling, ubuntu_18.04]
+ distro: ['fedora:latest', 'fedora:rawhide', 'opensuse:latest',
'ubuntu:latest', 'ubuntu:devel', 'ubuntu:rolling', 'ubuntu:18.04']
toolchain: [gnu, clang]
cmake_build_type: [Release, Debug]
minimal: [false]
@@ -18,72 +18,88 @@
module_build: [false]
coverage: [false]
include:
- - distro: fedora_nogmx
+ - distro: 'fedora:nogmx'
toolchain: gnu
cmake_build_type: Release
minimal: true
- - distro: fedora_nogmx
+ - distro: 'fedora:nogmx'
toolchain: clang
cmake_build_type: Release
minimal: true
- - distro: fedora_nogmx
+ - distro: 'fedora:nogmx'
toolchain: gnu
cmake_build_type: Release
own_gmx: true
- - distro: latest
+ - distro: 'fedora:latest'
toolchain: gnu
cmake_build_type: Release
module_build: true
- - distro: fedora_gmx2019
+ - distro: 'fedora:gmx2019'
toolchain: gnu
cmake_build_type: Release
- - distro: fedora_gmx2019
+ - distro: 'fedora:gmx2019'
toolchain: clang
cmake_build_type: Release
- - distro: fedora_gmx2019_d
+ - distro: 'fedora:gmx2019_d'
toolchain: gnu
cmake_build_type: Release
- - distro: fedora_gmx2019_d
+ - distro: 'fedora:gmx2019_d'
toolchain: clang
cmake_build_type: Release
- - distro: fedora_gmx2020
+ - distro: 'fedora:gmx2020'
toolchain: gnu
cmake_build_type: Release
no_regression_testing: true
- - distro: fedora_gmx2020
+ - distro: 'fedora:gmx2020'
toolchain: clang
cmake_build_type: Release
no_regression_testing: true
- - distro: fedora_gmx2020_d
+ - distro: 'fedora:gmx2020_d'
toolchain: gnu
cmake_build_type: Release
no_regression_testing: true
- - distro: fedora_gmx2020_d
+ - distro: 'fedora:gmx2020_d'
toolchain: clang
cmake_build_type: Release
no_regression_testing: true
- - distro: fedora_gmx9999
+ - distro: 'fedora:gmx2021'
+ toolchain: gnu
+ cmake_build_type: Release
+ no_regression_testing: true
+ - distro: 'fedora:gmx2021'
+ toolchain: clang
+ cmake_build_type: Release
+ no_regression_testing: true
+ - distro: 'fedora:gmx2021_d'
+ toolchain: gnu
+ cmake_build_type: Release
+ no_regression_testing: true
+ - distro: 'fedora:gmx2021_d'
+ toolchain: clang
+ cmake_build_type: Release
+ no_regression_testing: true
+ - distro: 'fedora:gmx9999'
toolchain: gnu
cmake_build_type: Release
continue-on-error: true
no_regression_testing: true
- - distro: fedora_gmx9999
+ - distro: 'fedora:gmx9999'
toolchain: clang
cmake_build_type: Release
continue-on-error: true
no_regression_testing: true
- - distro: fedora_gmx9999_d
+ - distro: 'fedora:gmx9999_d'
toolchain: gnu
cmake_build_type: Release
continue-on-error: true
no_regression_testing: true
- - distro: fedora_gmx9999_d
+ - distro: 'fedora:gmx9999_d'
toolchain: clang
cmake_build_type: Release
continue-on-error: true
no_regression_testing: true
runs-on: ubuntu-latest
- container: votca/buildenv:${{ matrix.distro }}
+ container: ghcr.io/votca/buildenv/${{ matrix.distro }}
steps:
- uses: actions/checkout@v2.2.0
with:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/.github/workflows/create-release.yml
new/csg-1.6.3/.github/workflows/create-release.yml
--- old/csg-1.6.2/.github/workflows/create-release.yml 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/.github/workflows/create-release.yml 2020-12-09
04:54:01.000000000 +0100
@@ -28,15 +28,16 @@
prerelease: ${{ contains(github.ref, 'rc') }}
body_path: 'release_changelog.md'
- name: Get version
- run: echo "::set-env name=VERSION::${GITHUB_REF#refs/tags/v}"
+ id: version
+ run: echo "::set-output name=VERSION::${GITHUB_REF#refs/tags/v}"
- name: Get manual
- run: wget https://github.com/votca/votca/releases/download/v${{
env.VERSION }}/votca-csg-manual-${{ env.VERSION }}.pdf
+ run: wget https://github.com/votca/votca/releases/download/v${{
steps.version.outputs.VERSION }}/votca-csg-manual-${{
steps.version.outputs.VERSION }}.pdf
- name: Upload manual
uses: actions/upload-release-asset@v1
env:
GITHUB_TOKEN: ${{ secrets.VOTCA_BOT_TOKEN }}
with:
upload_url: ${{ steps.create_release.outputs.upload_url }}
- asset_path: ./votca-csg-manual-${{ env.VERSION }}.pdf
- asset_name: votca-csg-manual-${{ env.VERSION }}.pdf
+ asset_path: ./votca-csg-manual-${{ steps.version.outputs.VERSION
}}.pdf
+ asset_name: votca-csg-manual-${{ steps.version.outputs.VERSION }}.pdf
asset_content_type: application/pdf
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/.github/workflows/format.yml
new/csg-1.6.3/.github/workflows/format.yml
--- old/csg-1.6.2/.github/workflows/format.yml 2020-08-22 15:31:14.000000000
+0200
+++ new/csg-1.6.3/.github/workflows/format.yml 2020-12-09 04:54:01.000000000
+0100
@@ -7,7 +7,7 @@
name: clang-format
if: ${{ github.event.comment.body == '@votca-bot format' }}
runs-on: ubuntu-latest
- container: votca/buildenv:format
+ container: ghcr.io/votca/buildenv/format:latest
steps:
- name: Check if message comes from PR
uses: octokit/request-action@v2.x
@@ -35,7 +35,9 @@
token: ${{ secrets.VOTCA_BOT_TOKEN }}
- name: Run clang-format
if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
- run: find . -type f -regex ".*\.\(c\|h\|cc\|cpp\|hpp\)" -print0 |
xargs -0 clang-format -i -style=file
+ run: |
+ curl -OL https://github.com/votca/votca/raw/master/.clang-format
+ find . -type f -regex ".*\.\(c\|h\|cc\|cpp\|hpp\)" -print0 | xargs
-0 clang-format -i -style=file
- name: Commit and push
if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
run: |
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/CHANGELOG.md new/csg-1.6.3/CHANGELOG.md
--- old/csg-1.6.2/CHANGELOG.md 2020-08-22 15:31:14.000000000 +0200
+++ new/csg-1.6.3/CHANGELOG.md 2020-12-09 04:54:01.000000000 +0100
@@ -1,7 +1,17 @@
For more detailed information about the changes see the history of the
[repository](https://github.com/votca/csg/commits/master).
-## Version 1.6.2 (released 22.08.20)
+## Version 1.6.3 (released 09.12.20)
+* fix test dependencies for parallel ctest (#585)
+* fix trigger for gmx-2020 warning in run_gromacs.sh (#591)
+* switch to ghcr.io for CI (#595)
+* format code with clang-11 (#605)
+* add gmx2021 builds to CI (#607)
+* remove set-env call from CI (#608)
+* use master .clang-format in format action (#610)
+* strip windows line endings in readers (#614)
+
+## Version 1.6.2 _SuperGitta_ (released 22.08.20)
* move CI to GitHub Actions (#563, #567, #569)
* add max scaling parameter to pressure correction (#565)
* fix test dependencies for parallel ctest (#573)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/CMakeLists.txt new/csg-1.6.3/CMakeLists.txt
--- old/csg-1.6.2/CMakeLists.txt 2020-08-22 15:31:14.000000000 +0200
+++ new/csg-1.6.3/CMakeLists.txt 2020-12-09 04:54:01.000000000 +0100
@@ -2,7 +2,7 @@
project(votca-csg)
-set(PROJECT_VERSION "1.6.2")
+set(PROJECT_VERSION "1.6.3")
set(PROJECT_CONTACT "b...@votca.org")
string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION
"${PROJECT_VERSION}")
if (NOT ${SOVERSION} MATCHES "[1-9]+")
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/CMakeModules/CheckFunctionExists.cpp
new/csg-1.6.3/CMakeModules/CheckFunctionExists.cpp
--- old/csg-1.6.2/CMakeModules/CheckFunctionExists.cpp 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/CMakeModules/CheckFunctionExists.cpp 2020-12-09
04:54:01.000000000 +0100
@@ -2,22 +2,21 @@
char CHECK_FUNCTION_EXISTS();
#ifdef __CLASSIC_C__
-int main(){
+int main() {
int ac;
- char*av[];
+ char* av[];
#else
-int main(int ac, char*av[]){
+int main(int ac, char* av[]) {
#endif
CHECK_FUNCTION_EXISTS();
- if(ac > 1000)
- {
+ if (ac > 1000) {
return *av[0];
- }
+ }
return 0;
}
-#else /* CHECK_FUNCTION_EXISTS */
+#else /* CHECK_FUNCTION_EXISTS */
-# error "CHECK_FUNCTION_EXISTS has to specify the function"
+#error "CHECK_FUNCTION_EXISTS has to specify the function"
#endif /* CHECK_FUNCTION_EXISTS */
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/include/votca/csg/interaction.h
new/csg-1.6.3/include/votca/csg/interaction.h
--- old/csg-1.6.2/include/votca/csg/interaction.h 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/include/votca/csg/interaction.h 2020-12-09
04:54:01.000000000 +0100
@@ -99,9 +99,7 @@
inline void Interaction::RebuildName() {
std::stringstream s;
if (_mol != -1) {
- {
- s << "molecule " << _mol;
- }
+ { s << "molecule " << _mol; }
}
if (!_group.empty()) {
s << ":" << _group;
@@ -110,9 +108,7 @@
}
}
if (_index != -1) {
- {
- s << ":index " << _index;
- }
+ { s << ":index " << _index; }
}
_name = s.str();
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/include/votca/csg/molecule.h
new/csg-1.6.3/include/votca/csg/molecule.h
--- old/csg-1.6.2/include/votca/csg/molecule.h 2020-08-22 15:31:14.000000000
+0200
+++ new/csg-1.6.3/include/votca/csg/molecule.h 2020-12-09 04:54:01.000000000
+0100
@@ -107,9 +107,7 @@
inline Index Molecule::getBeadIdByName(const std::string &name) {
Index i = getBeadByName(name);
if (i < 0) {
- {
- return i;
- }
+ { return i; }
}
return _beads[i]->getId();
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/include/votca/csg/xyzreader.h
new/csg-1.6.3/include/votca/csg/xyzreader.h
--- old/csg-1.6.2/include/votca/csg/xyzreader.h 2020-08-22 15:31:14.000000000
+0200
+++ new/csg-1.6.3/include/votca/csg/xyzreader.h 2020-12-09 04:54:01.000000000
+0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -24,6 +24,7 @@
#include <votca/csg/topologyreader.h>
#include <votca/csg/trajectoryreader.h>
#include <votca/tools/constants.h>
+#include <votca/tools/getline.h>
#include <type_traits>
namespace votca {
@@ -104,7 +105,7 @@
template <bool topology, class T>
inline bool XYZReader::ReadFrame(T &container) {
std::string line;
- std::getline(_fl, line);
+ tools::getline(_fl, line);
++_line;
if (!_fl.eof()) {
// read the number of atoms
@@ -121,11 +122,11 @@
"number of beads in topology and trajectory differ");
}
// the title line
- getline(_fl, line);
+ tools::getline(_fl, line);
++_line;
// read atoms
for (Index i = 0; i < natoms; ++i) {
- getline(_fl, line);
+ tools::getline(_fl, line);
++_line;
if (_fl.eof()) {
throw std::runtime_error("unexpected end of file in xyz file");
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/share/scripts/inverse/run_gromacs.sh
new/csg-1.6.3/share/scripts/inverse/run_gromacs.sh
--- old/csg-1.6.2/share/scripts/inverse/run_gromacs.sh 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/share/scripts/inverse/run_gromacs.sh 2020-12-09
04:54:01.000000000 +0100
@@ -62,7 +62,7 @@
[[ -n "$(type -p ${grompp[0]})" ]] || die "${0##*/}: grompp binary
'${grompp[0]}' not found"
gmx_ver="$(critical ${grompp[@]} -h 2>&1)"
-[[ ${gmx_ver} = *"VERSION 2020"* ]] && die "GROMACS 2020 doesn't support
tabulated interactions, that are needed for coarse-graining (see and comment on
https://redmine.gromacs.org/issues/1347). Please use GROMACS 2019 for now."
+[[ ${gmx_ver} = *"version 2020"* ]] && die "GROMACS 2020 doesn't support
tabulated interactions, that are needed for coarse-graining (see and comment on
https://redmine.gromacs.org/issues/1347). Please use GROMACS 2019 for now."
traj=$(csg_get_property cg.inverse.gromacs.traj)
# in main simulation we usually do care about traj and temperature
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/csg_boltzmann/main.cc
new/csg-1.6.3/src/csg_boltzmann/main.cc
--- old/csg-1.6.2/src/csg_boltzmann/main.cc 2020-08-22 15:31:14.000000000
+0200
+++ new/csg-1.6.3/src/csg_boltzmann/main.cc 2020-12-09 04:54:01.000000000
+0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -29,6 +29,7 @@
#include <math.h>
#include <string>
#include <votca/csg/csgapplication.h>
+#include <votca/tools/getline.h>
#include <votca/tools/rangeparser.h>
#include <votca/tools/tokenizer.h>
@@ -181,7 +182,7 @@
while (1) {
string line;
cout << "> ";
- getline(cin, line);
+ votca::tools::getline(cin, line);
boost::trim(line);
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/libcsg/imcio.cc
new/csg-1.6.3/src/libcsg/imcio.cc
--- old/csg-1.6.2/src/libcsg/imcio.cc 2020-08-22 15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/imcio.cc 2020-12-09 04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -115,7 +115,7 @@
std::vector<double> result;
Index numrows = 0;
size_t numcols = 0;
- while (getline(intt, line)) {
+ while (tools::getline(intt, line)) {
if (line[0] == '#') {
continue;
}
@@ -148,7 +148,7 @@
std::vector<std::pair<std::string, tools::RangeParser> > indeces;
string line;
// read till the first data line
- while (getline(in, line)) {
+ while (tools::getline(in, line)) {
// remove comments and xmgrace stuff
line = line.substr(0, line.find("#"));
line = line.substr(0, line.find("@"));
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/csg-1.6.2/src/libcsg/modules/io/dlpolytopologyreader.cc
new/csg-1.6.3/src/libcsg/modules/io/dlpolytopologyreader.cc
--- old/csg-1.6.2/src/libcsg/modules/io/dlpolytopologyreader.cc 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/modules/io/dlpolytopologyreader.cc 2020-12-09
04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -47,7 +47,7 @@
size_t i_nws = 0;
do {
- getline(fs, line);
+ tools::getline(fs, line);
if (fs.eof()) {
throw std::runtime_error("Error: unexpected end of dlpoly file '" +
@@ -374,7 +374,7 @@
}
#ifdef DEBUG
- getline(fl, line); // is "close" found?
+ tools::getline(fl, line); // is "close" found?
if (line == "close") {
cout << "Read from dlpoly file '" << _fname << "' : '" << line
<< "' - done with topology" << endl;
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/csg-1.6.2/src/libcsg/modules/io/dlpolytrajectoryreader.cc
new/csg-1.6.3/src/libcsg/modules/io/dlpolytrajectoryreader.cc
--- old/csg-1.6.2/src/libcsg/modules/io/dlpolytrajectoryreader.cc
2020-08-22 15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/modules/io/dlpolytrajectoryreader.cc
2020-12-09 04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -102,14 +102,14 @@
if (_first_frame) {
- getline(_fl, line); // title
+ tools::getline(_fl, line); // title
#ifdef DEBUG
cout << "Read from dlpoly file '" << _fname << "' : '" << line
<< "' - header" << endl;
#endif
- getline(_fl, line); // 2nd header line
+ tools::getline(_fl, line); // 2nd header line
#ifdef DEBUG
cout << "Read from dlpoly file '" << _fname << "' : '" << line
@@ -179,8 +179,8 @@
// read normal frame
if (!_isConfig) {
- getline(_fl, line); // timestep line - only present in HISTORY, and not in
- // CONFIG
+ tools::getline(_fl, line); // timestep line - only present in HISTORY, and
+ // not in CONFIG
#ifdef DEBUG
cout << "Read from dlpoly file '" << _fname << "' : '" << line << "'"
<< endl;
@@ -283,7 +283,7 @@
Eigen::Matrix3d box = Eigen::Matrix3d::Zero();
for (Index i = 0; i < 3; i++) { // read 3 box/cell lines
- getline(_fl, line);
+ tools::getline(_fl, line);
#ifdef DEBUG
cout << "Read from dlpoly file '" << _fname << "' : '" << line
@@ -308,7 +308,7 @@
for (Index i = 0; i < natoms; i++) {
{
- getline(_fl, line); // atom header line
+ tools::getline(_fl, line); // atom header line
#ifdef DEBUG
cout << "Read from dlpoly file '" << _fname << "' : '" << line << "'"
@@ -336,7 +336,7 @@
Eigen::Matrix3d atom_vecs = Eigen::Matrix3d::Zero();
for (Index j = 0; j < std::min(navecs, Index(2)) + 1; j++) {
- getline(_fl, line); // read atom positions
+ tools::getline(_fl, line); // read atom positions
#ifdef DEBUG
cout << "Read from dlpoly file '" << _fname << "' : '" << line << "'"
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/libcsg/modules/io/groreader.cc
new/csg-1.6.3/src/libcsg/modules/io/groreader.cc
--- old/csg-1.6.2/src/libcsg/modules/io/groreader.cc 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/modules/io/groreader.cc 2020-12-09
04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -61,11 +61,11 @@
bool GROReader::NextFrame(Topology &top) {
string tmp;
- getline(_fl, tmp); // title
+ tools::getline(_fl, tmp); // title
if (_fl.eof()) {
return !_fl.eof();
}
- getline(_fl, tmp); // number atoms
+ tools::getline(_fl, tmp); // number atoms
Index natoms = std::stoi(tmp);
if (!_topology && natoms != top.BeadCount()) {
throw std::runtime_error(
@@ -74,7 +74,7 @@
for (Index i = 0; i < natoms; i++) {
string line;
- getline(_fl, line);
+ tools::getline(_fl, line);
string resNum, resName, atName, x, y, z;
try {
resNum = string(line, 0, 5); // %5i
@@ -142,7 +142,7 @@
}
}
- getline(_fl, tmp); // read box line
+ tools::getline(_fl, tmp); // read box line
if (_fl.eof()) {
throw std::runtime_error(
"unexpected end of file in poly file, when boxline");
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/libcsg/modules/io/lammpsdatareader.cc
new/csg-1.6.3/src/libcsg/modules/io/lammpsdatareader.cc
--- old/csg-1.6.2/src/libcsg/modules/io/lammpsdatareader.cc 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/modules/io/lammpsdatareader.cc 2020-12-09
04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -106,9 +106,9 @@
bool LAMMPSDataReader::NextFrame(Topology &top) {
string header;
- getline(fl_, header);
+ tools::getline(fl_, header);
string line;
- getline(fl_, line);
+ tools::getline(fl_, line);
while (!fl_.eof()) {
tools::Tokenizer tok(line, " ");
@@ -128,7 +128,7 @@
string err = "Unrecognized line in lammps .data file:\n" + line;
throw runtime_error(err);
}
- getline(fl_, line);
+ tools::getline(fl_, line);
}
return !fl_.eof();
}
@@ -272,7 +272,7 @@
for (Index i = 1; i < 3; ++i) {
string line;
- getline(fl_, line);
+ tools::getline(fl_, line);
tools::Tokenizer tok(line, " ");
tok.ConvertToVector(fields);
if (fields.size() != 4) {
@@ -286,8 +286,8 @@
void LAMMPSDataReader::SortIntoDataGroup_(string tag) {
string line;
- getline(fl_, line);
- getline(fl_, line);
+ tools::getline(fl_, line);
+ tools::getline(fl_, line);
vector<vector<string>> group;
string data_elem;
@@ -295,7 +295,7 @@
tools::Tokenizer tok(line, " ");
vector<string> fields = tok.ToVector();
group.push_back(fields);
- getline(fl_, line);
+ tools::getline(fl_, line);
}
data_[tag] = group;
@@ -358,8 +358,8 @@
}
string line;
- getline(fl_, line);
- getline(fl_, line);
+ tools::getline(fl_, line);
+ tools::getline(fl_, line);
lammps_format format = determineDataFileFormat_(line);
bool chargeRead = false;
@@ -381,7 +381,7 @@
issfirst >> startingIndexMolecule;
}
sorted_file[startingIndex] = line;
- getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
Index atomId = 0;
@@ -393,7 +393,7 @@
iss >> moleculeId;
}
sorted_file[atomId] = line;
- getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
if (atomId < startingIndex) {
startingIndex = atomId;
@@ -503,8 +503,8 @@
void LAMMPSDataReader::ReadBonds_(Topology &top) {
string line;
- getline(fl_, line);
- getline(fl_, line);
+ tools::getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
Index bondId;
@@ -540,7 +540,7 @@
}
++bond_count;
- getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
}
@@ -557,8 +557,8 @@
void LAMMPSDataReader::ReadAngles_(Topology &top) {
string line;
- getline(fl_, line);
- getline(fl_, line);
+ tools::getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
Index angleId;
@@ -599,7 +599,7 @@
++angle_count;
- getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
}
@@ -616,17 +616,17 @@
void LAMMPSDataReader::SkipImpropers_() {
string line;
- getline(fl_, line);
- getline(fl_, line);
+ tools::getline(fl_, line);
+ tools::getline(fl_, line);
while (!line.empty()) {
- getline(fl_, line);
+ tools::getline(fl_, line);
}
}
void LAMMPSDataReader::ReadDihedrals_(Topology &top) {
string line;
- getline(fl_, line);
- getline(fl_, line);
+ tools::getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
Index dihedralId;
@@ -668,7 +668,7 @@
mi->AddInteraction(ic);
}
++dihedral_count;
- getline(fl_, line);
+ tools::getline(fl_, line);
boost::trim(line);
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/libcsg/modules/io/lammpsdumpreader.cc
new/csg-1.6.3/src/libcsg/modules/io/lammpsdumpreader.cc
--- old/csg-1.6.2/src/libcsg/modules/io/lammpsdumpreader.cc 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/modules/io/lammpsdumpreader.cc 2020-12-09
04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -64,7 +64,7 @@
bool LAMMPSDumpReader::NextFrame(Topology &top) {
string line;
- getline(_fl, line);
+ tools::getline(_fl, line);
boost::algorithm::trim(line);
while (!_fl.eof()) {
if (line.substr(0, 5) != "ITEM:") {
@@ -85,7 +85,7 @@
throw std::ios_base::failure("unknown item lammps file : " +
line.substr(6));
}
- getline(_fl, line);
+ tools::getline(_fl, line);
boost::algorithm::trim(line);
}
if (_topology) {
@@ -98,7 +98,7 @@
void LAMMPSDumpReader::ReadTimestep(Topology &top) {
string s;
- getline(_fl, s);
+ tools::getline(_fl, s);
boost::algorithm::trim(s);
top.setStep(boost::lexical_cast<Index>(s));
cout << "Reading frame, timestep " << top.getStep() << endl;
@@ -110,7 +110,7 @@
Eigen::Matrix3d m = Eigen::Matrix3d::Zero();
for (Index i = 0; i < 3; ++i) {
- getline(_fl, s);
+ tools::getline(_fl, s);
boost::algorithm::trim(s);
tools::Tokenizer tok(s, " ");
@@ -126,7 +126,7 @@
void LAMMPSDumpReader::ReadNumAtoms(Topology &top) {
string s;
- getline(_fl, s);
+ tools::getline(_fl, s);
boost::algorithm::trim(s);
_natoms = boost::lexical_cast<Index>(s);
if (!_topology && _natoms != top.BeadCount()) {
@@ -179,7 +179,7 @@
for (Index i = 0; i < _natoms; ++i) {
string s;
- getline(_fl, s);
+ tools::getline(_fl, s);
boost::algorithm::trim(s);
if (_fl.eof()) {
throw std::runtime_error("Error: unexpected end of lammps file '" +
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/libcsg/modules/io/pdbreader.cc
new/csg-1.6.3/src/libcsg/modules/io/pdbreader.cc
--- old/csg-1.6.2/src/libcsg/modules/io/pdbreader.cc 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/libcsg/modules/io/pdbreader.cc 2020-12-09
04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -96,7 +96,7 @@
// Read in information from .pdb file
////////////////////////////////////////////////////////////////////////////////
Index bead_count = 0;
- while (std::getline(_fl, line)) {
+ while (tools::getline(_fl, line)) {
if (tools::wildcmp("CRYST1*", line)) {
string a, b, c, alpha, beta, gamma;
try {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/tests/test_tabulatedpotential.cc
new/csg-1.6.3/src/tests/test_tabulatedpotential.cc
--- old/csg-1.6.2/src/tests/test_tabulatedpotential.cc 2020-08-22
15:31:14.000000000 +0200
+++ new/csg-1.6.3/src/tests/test_tabulatedpotential.cc 2020-12-09
04:54:01.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -26,6 +26,8 @@
#include <string>
#include <vector>
+#include <votca/tools/getline.h>
+
using namespace std;
using namespace votca::csg;
using namespace votca::tools;
@@ -36,7 +38,7 @@
file.open(file_name);
string line;
if (file.is_open()) {
- while (getline(file, line)) {
+ while (votca::tools::getline(file, line)) {
string word;
istringstream ss(line);
for (votca::Index i = 0; i < column; ++i) {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-1.6.2/src/tools/CMakeLists.txt
new/csg-1.6.3/src/tools/CMakeLists.txt
--- old/csg-1.6.2/src/tools/CMakeLists.txt 2020-08-22 15:31:14.000000000
+0200
+++ new/csg-1.6.3/src/tools/CMakeLists.txt 2020-12-09 04:54:01.000000000
+0100
@@ -210,15 +210,14 @@
--options ${REFPATH}/settings_imc.xml
WORKING_DIRECTORY ${RUNPATH})
set_tests_properties(integration_Run_csg_stat_imc_multi PROPERTIES LABELS
"csg;tools;votca;integration")
- set_tests_properties(integration_Run_csg_stat_imc_multi PROPERTIES DEPENDS
integration_Run_gmx_mdrun_multi)
add_test(NAME integration_Compare_csg_stat-imc_multi_output COMMAND
$<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1
all.imc -f2 ${REFPATH}/all.imc WORKING_DIRECTORY ${RUNPATH})
- set_tests_properties(integration_Compare_csg_stat-imc_multi_output
PROPERTIES DEPENDS integration_Run_csg_stat-imc)
+ set_tests_properties(integration_Compare_csg_stat-imc_multi_output
PROPERTIES DEPENDS integration_Run_csg_stat_imc_multi)
set_tests_properties(integration_Compare_csg_stat-imc_multi_output
PROPERTIES LABELS "csg;tools;votca;integration")
add_test(NAME integration_Compare_csg_stat-imc_multi_output_2 COMMAND
$<TARGET_FILE:VOTCA::votca_compare> --etol ${REGRESSIONTEST_TOLERANCE} -f1
all.gmc -f2 ${REFPATH}/all.gmc WORKING_DIRECTORY ${RUNPATH})
- set_tests_properties(integration_Compare_csg_stat-imc_multi_output_2
PROPERTIES DEPENDS integration_Run_csg_stat-imc)
+ set_tests_properties(integration_Compare_csg_stat-imc_multi_output_2
PROPERTIES DEPENDS integration_Run_csg_stat_imc_multi)
set_tests_properties(integration_Compare_csg_stat-imc_multi_output_2
PROPERTIES LABELS "csg;tools;votca;integration")
add_test(NAME integration_Compare_csg_stat-imc_multi_output_3 COMMAND
${CMAKE_COMMAND} -E compare_files all.idx ${REFPATH}/all.idx WORKING_DIRECTORY
${RUNPATH})
- set_tests_properties(integration_Compare_csg_stat-imc_multi_output_3
PROPERTIES DEPENDS integration_Run_csg_stat-imc)
+ set_tests_properties(integration_Compare_csg_stat-imc_multi_output_3
PROPERTIES DEPENDS integration_Run_csg_stat_imc_multi)
set_tests_properties(integration_Compare_csg_stat-imc_multi_output_3
PROPERTIES LABELS "csg;tools;votca;integration")
set(RUNPATH ${CMAKE_CURRENT_BINARY_DIR}/Run_csg_resample)
++++++ votca-csg-manual-1.6.2.pdf -> votca-csg-manual-1.6.3.pdf ++++++
(binary differes)
++++++ votca-csg-tutorials-1.6.2.tar.gz -> votca-csg-tutorials-1.6.3.tar.gz
++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/csg-tutorials-1.6.2/.github/workflows/continuous-integration-workflow.yml
new/csg-tutorials-1.6.3/.github/workflows/continuous-integration-workflow.yml
---
old/csg-tutorials-1.6.2/.github/workflows/continuous-integration-workflow.yml
2020-08-22 15:31:16.000000000 +0200
+++
new/csg-tutorials-1.6.3/.github/workflows/continuous-integration-workflow.yml
2020-12-09 04:54:03.000000000 +0100
@@ -7,10 +7,10 @@
jobs:
CI:
- continue-on-error: ${{ matrix.distro == 'ubuntu_devel' || matrix.distro ==
'fedora_rawhide' || matrix.continue-on-error == true }}
+ continue-on-error: ${{ matrix.distro == 'ubuntu:devel' || matrix.distro ==
'opensuse:latest' || matrix.distro == 'fedora:rawhide' ||
matrix.continue-on-error == true }}
strategy:
matrix:
- distro: [latest, fedora_rawhide, opensuse, ubuntu_18.04]
+ distro: ['fedora:latest', 'fedora:rawhide', 'opensuse:latest',
'ubuntu:18.04']
toolchain: [gnu]
cmake_build_type: [Release]
minimal: [false]
@@ -18,22 +18,22 @@
module_build: [false]
coverage: [false]
include:
- - distro: fedora_nogmx
+ - distro: 'fedora:nogmx'
toolchain: gnu
cmake_build_type: Release
own_gmx: true
- - distro: latest
+ - distro: 'fedora:latest'
toolchain: gnu
cmake_build_type: Release
module_build: true
- - distro: fedora_gmx2019
+ - distro: 'fedora:gmx2019'
toolchain: gnu
cmake_build_type: Release
- - distro: fedora_gmx2019_d
+ - distro: 'fedora:gmx2019_d'
toolchain: gnu
cmake_build_type: Release
runs-on: ubuntu-latest
- container: votca/buildenv:${{ matrix.distro }}
+ container: ghcr.io/votca/buildenv/${{ matrix.distro }}
steps:
- uses: actions/checkout@v2.2.0
with:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-tutorials-1.6.2/CMakeLists.txt
new/csg-tutorials-1.6.3/CMakeLists.txt
--- old/csg-tutorials-1.6.2/CMakeLists.txt 2020-08-22 15:31:16.000000000
+0200
+++ new/csg-tutorials-1.6.3/CMakeLists.txt 2020-12-09 04:54:03.000000000
+0100
@@ -2,7 +2,7 @@
project(csg-tutorials)
-set(PROJECT_VERSION "1.6.2")
+set(PROJECT_VERSION "1.6.3")
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
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