Merge branch 'master' of gits-15.sys.kth.se:maaskola/spatial-transcriptome-deconvolution

Author: maaskola

.gitignore

@@ -1,4 +1,5 @@
-build
+build/release
+build/debug
 *.swp
 *.swo
 *~

CMakeLists.txt

@@ -22,7 +22,9 @@ SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/")
 # Change build configuration
 #
 # SET(CMAKE_BUILD_TYPE Debug)
-SET(CMAKE_BUILD_TYPE Release)
+# SET(CMAKE_BUILD_TYPE Release)
+
+SET(CMAKE_DEBUG_POSTFIX -dbg)
 
 # Set installation destination and prefix path to find libraries installed on
 # this sytem. If this is not specified, /usr/local/ will be used.

build/Makefile

@@ -0,0 +1,20 @@
+SUBDIRS := $(wildcard */.)  # e.g. "foo/. bar/."
+TARGETS := all install clean  # whatever else, but must not contain '/'
+
+# foo/.all bar/.all foo/.clean bar/.clean
+SUBDIRS_TARGETS := \
+	$(foreach t,$(TARGETS),$(addsuffix $t,$(SUBDIRS)))
+
+.PHONY : $(TARGETS) $(SUBDIRS_TARGETS)
+
+# static pattern rule, expands into:
+# all clean : % : foo/.% bar/.%
+$(TARGETS) : % : $(addsuffix %,$(SUBDIRS))
+	@echo 'Done "$*" target'
+
+# here, for foo/.all:
+#   $(@D) is foo
+#   $(@F) is .all, with leading period
+#   $(@F:.%=%) is just all
+$(SUBDIRS_TARGETS) :
+	$(MAKE) -C $(@D) $(@F:.%=%)

build/gen_build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+mkdir -p release && cd release && cmake ../.. -DCMAKE_BUILD_TYPE=Release $@ && cd ..
+mkdir -p debug && cd debug && cmake ../.. -DCMAKE_BUILD_TYPE=Debug $@ && cd ..

src/CMakeLists.txt

@@ -47,6 +47,7 @@ IF(GOOGLEPERFTOOLS_FOUND)
 ENDIF()
 
 CONFIGURE_FILE(git_config.hpp.in git_config.hpp)
+SET_TARGET_PROPERTIES(std PROPERTIES DEBUG_POSTFIX ${CMAKE_DEBUG_POSTFIX})
 
 # INSTALL(TARGETS enrich DESTINATION bin)
 INSTALL(TARGETS std DESTINATION bin)

src/cli.cpp

@@ -58,10 +58,11 @@ int process_cli_options(
     const std::string &usage_string,
     boost::program_options::options_description &cli_options,
     bool use_positional_options,
-    boost::program_options::positional_options_description &positional_options) {
+    boost::program_options::positional_options_description
+        &positional_options) {
   namespace po = boost::program_options;
-  exec_info
-      = ExecutionInformation(argv[0], GIT_DESCRIPTION, GIT_BRANCH, argc, argv);
+  exec_info = ExecutionInformation(argv[0], GIT_DESCRIPTION, GIT_BRANCH,
+                                   BUILD_TYPE, argc, argv);
 
   const size_t MIN_COLS = 60;
   const size_t MAX_COLS = 80;

src/executioninformation.cpp

@@ -1,11 +1,11 @@
 
+#include "executioninformation.hpp"
+#include <boost/date_time/posix_time/posix_time.hpp>
+#include <boost/filesystem.hpp>
 #include <cstdio>
 #include <ctime>
 #include <random>
-#include <boost/filesystem.hpp>
-#include <boost/date_time/posix_time/posix_time.hpp>
 #include "entropy.hpp"
-#include "executioninformation.hpp"
 
 using namespace std;
 
@@ -17,22 +17,25 @@ string reconstitute_cmdline(int argc, const char **argv) {
 }
 
 ExecutionInformation::ExecutionInformation()
-    : ExecutionInformation("program_name", "unknown", "unknown", "") {}
+    : ExecutionInformation("program_name", "unknown", "unknown", "unknown", "") {}
 
 ExecutionInformation::ExecutionInformation(const string &name,
                                            const string &version,
-                                           const string &branch, int argc,
+                                           const string &branch,
+                                           const string &build, int argc,
                                            const char **argv)
-    : ExecutionInformation(name, version, branch,
+    : ExecutionInformation(name, version, branch, build,
                            reconstitute_cmdline(argc, argv)) {}
 
 ExecutionInformation::ExecutionInformation(const string &name,
                                            const string &version,
                                            const string &branch,
+                                           const string &build,
                                            const string &cmd)
     : program_name(boost::filesystem::path(name).filename().string()),
       program_version(version),
       git_branch(branch),
+      build_type(build),
       cmdline(cmd),
       datetime(),
       directory(boost::filesystem::initial_path().string()) {
@@ -43,7 +46,7 @@ ExecutionInformation::ExecutionInformation(const string &name,
 }
 
 string ExecutionInformation::name_and_version() const {
-  return program_name + " " + program_version + " [" + git_branch + " branch]";
+  return program_name + " " + program_version + " [" + git_branch + " branch] - " + build_type + " build";
 }
 
 string generate_random_label(const string &prefix, size_t n_rnd_char) {

src/executioninformation.hpp

@@ -35,15 +35,16 @@
 
 struct ExecutionInformation {
   ExecutionInformation();
-  ExecutionInformation(const std::string &name, const std::string &hmm_version,
-                       const std::string &git_branch, int argc,
-                       const char **argv);
-  ExecutionInformation(const std::string &name, const std::string &hmm_version,
-                       const std::string &git_branch,
+  ExecutionInformation(const std::string &name, const std::string &version,
+                       const std::string &git_branch, const std::string &build,
+                       int argc, const char **argv);
+  ExecutionInformation(const std::string &name, const std::string &version,
+                       const std::string &git_branch, const std::string &build,
                        const std::string &cmdline);
   std::string program_name;
   std::string program_version;
   std::string git_branch;
+  std::string build_type;
   std::string cmdline;
   std::string datetime;
   std::string directory;

src/git_config.hpp.in

@@ -4,5 +4,6 @@
 #define GIT_SHA1 "@GIT_SHA1@"
 #define GIT_DESCRIPTION "@GIT_DESCRIPTION@"
 #define GIT_BRANCH "@GIT_BRANCH@"
+#define BUILD_TYPE "@CMAKE_BUILD_TYPE@"
 
 #endif