[med-svn] [Git][med-team/scrm][upstream] New upstream version 1.7.4
Andreas Tille
gitlab at salsa.debian.org
Thu Mar 12 21:34:02 GMT 2020
Andreas Tille pushed to branch upstream at Debian Med / scrm
Commits:
cc548284 by Andreas Tille at 2020-03-12T22:03:40+01:00
New upstream version 1.7.4
- - - - -
11 changed files:
- + .devcontainer/Dockerfile
- + .devcontainer/devcontainer.json
- .gitignore
- .travis.yml
- NEWS.md
- README.md
- configure.ac
- src/forest.cc
- src/param.cc
- tests/test_binaries.sh
- + tests/tree.newick
Changes:
=====================================
.devcontainer/Dockerfile
=====================================
@@ -0,0 +1,18 @@
+FROM debian:buster-slim
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends \
+ autoconf \
+ autoconf-archive \
+ automake \
+ build-essential \
+ git \
+ libcppunit-dev \
+ valgrind && \
+ apt-get clean && \
+ rm -rf /var/lib/apt/lists/ && \
+ rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+RUN adduser developer
+
+USER developer
=====================================
.devcontainer/devcontainer.json
=====================================
@@ -0,0 +1,34 @@
+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.101.1/containers/docker-existing-dockerfile
+{
+ "name": "scrm:develop",
+
+ // Sets the run context to one level up instead of the .devcontainer folder.
+ "context": ".",
+
+ // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+ "dockerFile": "Dockerfile",
+
+ // Set *default* container specific settings.json values on container create.
+ "settings": {
+ "terminal.integrated.shell.linux": null
+ },
+
+ // Add the IDs of extensions you want installed when the container is created.
+ "extensions": ["ms-vscode.cpptools"],
+
+ // Use 'forwardPorts' to make a list of ports inside the container available locally.
+ // "forwardPorts": [],
+
+ // Uncomment the next line to run commands after the container is created - for example installing git.
+ // "postCreateCommand": "apt-get update && apt-get install -y git",
+
+ // Uncomment when using a ptrace-based debugger like C++, Go, and Rust
+ // "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],
+
+ // Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-in-docker.
+ // "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+
+ // Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
+ "remoteUser": "developer"
+}
=====================================
.gitignore
=====================================
@@ -36,6 +36,7 @@ tests/*working*
scrm
scrm_dbg
scrm_prof
+scrm_asan
# automake
Makefile
=====================================
.travis.yml
=====================================
@@ -13,7 +13,7 @@ matrix:
- os: osx
env: CXXFLAGS="-m32 -Werror"
sudo: required
-dist: xenial
+dist: bionic
before_install: .travis/setup.sh "$TRAVIS_OS_NAME" "$CXX" "$CXXFLAGS"
before_script:
- ./bootstrap
=====================================
NEWS.md
=====================================
@@ -1,6 +1,17 @@
scrm Version History
========================
+scrm 1.7.4
+------------------------
+Released: 2020-03-07
+
+### Bug Fixes
++ Fixes the initialization with an inital tree in Newick format (`-init`).
+ Big thanks to @nspope for reporting and locating this bug along with
+ suggesting a fix!
+
+
+
scrm 1.7.3
------------------------
Released: 2018-11-18
=====================================
README.md
=====================================
@@ -1,4 +1,4 @@
-[](http://www.repostatus.org/#active)
+[](https://www.repostatus.org/#inactive)
[](https://travis-ci.org/scrm/scrm)
scrm
@@ -45,8 +45,7 @@ Details are available [in the wiki][2].
## Troubleshooting
If you encounter problems while using _scrm_, please
-[file a bug report](https://github.com/scrm/scrm/wiki/Reporting-Bugs) or mail to
-`develop (at) paulstaab.de`.
+[file a bug report](https://github.com/scrm/scrm/wiki/Reporting-Bugs).
## Citation
=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT([scrm], [1.7.3],[https://github.com/paulstaab/scrm/issues])
+AC_INIT([scrm], [1.7.4],[https://github.com/paulstaab/scrm/issues])
AM_INIT_AUTOMAKE([subdir-objects -Wall -Werror foreign])
# Use -O3 as default optimization level
@@ -52,6 +52,7 @@ AX_CHECK_COMPILE_FLAG([-Wcast-align], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wcast-align"
AX_CHECK_COMPILE_FLAG([-Wunused], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wunused"], [], [-Werror])
AX_CHECK_COMPILE_FLAG([-Woverloaded-virtual], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Woverloaded-virtual"], [], [-Werror])
AX_CHECK_COMPILE_FLAG([-pedantic], [OPT_CXXFLAGS="$OPT_CXXFLAGS -pedantic"], [], [-Werror])
+AX_CHECK_COMPILE_FLAG([-Wcatch-value], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wcatch-value"], [], [-Werror])
AC_CONFIG_FILES([Makefile])
AC_OUTPUT
=====================================
src/forest.cc
=====================================
@@ -1324,7 +1324,8 @@ Node* Forest::readNewickNode( std::string &in_str, std::string::iterator &it, si
void Forest::readNewick( std::string &in_str ){
- this->current_rec_ = 1;
+ this->set_next_base(0.0);
+ ++current_rec_;
std::string::iterator it = in_str.begin();
(void)this->readNewickNode( in_str, it );
this->set_local_root( this->nodes()->last() );
=====================================
src/param.cc
=====================================
@@ -132,7 +132,7 @@ Model Param::parse() {
// there might or might not follow a symmetric migration rate
try {
model.addSymmetricMigration(0.0, readNextInput<double>()/(model.population_number()-1), true, true);
- } catch (std::invalid_argument e) {
+ } catch (std::invalid_argument& e) {
--argv_i;
}
}
@@ -382,7 +382,7 @@ Model Param::parse() {
try {
// Maybe read in up to 3 seeds (ms compatibility)
for (size_t i = 1; i < 3; ++i) seeds.at(i) = readNextInt();
- } catch (std::invalid_argument e) {
+ } catch (std::invalid_argument& e) {
--argv_i;
}
=====================================
tests/test_binaries.sh
=====================================
@@ -13,6 +13,7 @@ make scrm_asan 2> /dev/null
supports_sanitizers=$?
if [ "$supports_sanitizers" == "0" ]; then
echo "Using address sanitizers"
+ export ASAN_OPTIONS=detect_leaks=0
fi
function test_scrm {
@@ -60,6 +61,7 @@ echo "Testing Initial Tree"
test_scrm 25 1 -T || exit 1
test_scrm 10 5 -I 1 5 -eI 1.0 5 -L || exit 1
test_scrm 10 5 -I 2 2 2 0.5 -eI 1.0 3 3 -L || exit 1
+ test_scrm 3 1 -init tests/tree.newick -t 5 || exit 1
echo ""
echo "Testing Recombinations"
@@ -67,6 +69,7 @@ echo "Testing Recombinations"
test_scrm 6 10 -r 1 100 -t 5 -L -T -transpose-segsites -l -1 || exit 1
test_scrm 8 10 -r 1 100 -t 5 -oSFS -O -l -1 || exit 1
test_scrm 10 5 -r 5 100 -I 2 2 2 0.5 -eI 1.0 3 3 -L -l -1 || exit 1
+ test_scrm 3 10 -r 5 100 -init tests/tree.newick -t 5 || exit 1
echo ""
echo "Testing Pruning"
=====================================
tests/tree.newick
=====================================
@@ -0,0 +1 @@
+((1:1.0,2:1.0):1.0,3:1.0);
View it on GitLab: https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e
--
View it on GitLab: https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e
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