Implement support for version from last git commit and bugfix for PR #390 (#392)

* Implement support for version from last git commit
  - coreneuron version was printed as "version id unimplemented"
  - add cmake module GitRevision.cmake to find git commit information
  - this commit adds support to print project version along with
    git commit and it's date. e.g.
      Version : 0.21.0 bd747a8 (14-09-2020 16:03)
* Added --version CLI flag
  - Use git show instead of git show to be compatible with older git (e.g. on BB5)
* Avoid nrn_abort when --help is called
* Bug fix for merged pull request #390 : tid and ith args were mixed
* For BB5 Jenkins, exclude problematic agent bb5-07 (has strange PGI compiler issue)

Co-authored-by: Michael Hines <[email protected]>

Author: pramodk

CMake/GitRevision.cmake

@@ -0,0 +1,22 @@
+# For now use simple approach to get version information as git is
+# often avaialble on the machine where we are building from source
+
+find_package(Git)
+
+if(GIT_FOUND)
+  # get last commit sha1
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} log -1 --format=%h
+    WORKING_DIRECTORY ${CORENEURON_PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE GIT_REVISION_SHA1
+    ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+  # get last commit date
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} show -s --format=%ci
+    WORKING_DIRECTORY ${CORENEURON_PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE GIT_REVISION_DATE
+    ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+  set(CN_GIT_REVISION "${GIT_REVISION_SHA1} (${GIT_REVISION_DATE})")
+else()
+  set(CN_GIT_REVISION "unknown")
+endif()

CMakeLists.txt

@@ -63,6 +63,7 @@ include(SetRpath)
 include(CTest)
 include(AddRandom123Submodule)
 include(AddCLI11Submodule)
+include(GitRevision)
 
 add_subdirectory(${CORENEURON_PROJECT_SOURCE_DIR}/external/CLI11)
 
@@ -104,6 +105,15 @@ if(CORENEURON_AS_SUBPROJECT)
   set(CORENRN_ENABLE_UNIT_TESTS OFF)
 endif()
 
+# =============================================================================
+# Project version from git and project directories
+# =============================================================================
+set(CN_PROJECT_VERSION ${PROJECT_VERSION})
+
+# generate file with version number from git and nrnunits.lib file path
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/coreneuron/config/config.cpp.in
+               ${PROJECT_BINARY_DIR}/coreneuron/config/config.cpp @ONLY)
+
 # =============================================================================
 # Include cmake modules after cmake options
 # =============================================================================

coreneuron/CMakeLists.txt

@@ -35,6 +35,7 @@ file(GLOB_RECURSE CORENEURON_CUDA_FILES "*.cu")
 file(GLOB SCOPMATH_CODE_FILES "sim/scopmath/*.cpp")
 file(COPY ${CORENEURON_PROJECT_SOURCE_DIR}/external/Random123/include/Random123
      DESTINATION ${CMAKE_BINARY_DIR}/include)
+list(APPEND CORENEURON_CODE_FILES ${PROJECT_BINARY_DIR}/coreneuron/config/config.cpp)
 
 set(DIMPLIC_CODE_FILE "mechanism/mech/dimplic.cpp")
 set(ENGINEMECH_CODE_FILE "mechanism/mech/enginemech.cpp")

coreneuron/apps/corenrn_parameters.cpp

@@ -28,7 +28,11 @@ THE POSSIBILITY OF SUCH DAMAGE.
 
 #include "coreneuron/apps/corenrn_parameters.hpp"
 
+
 namespace coreneuron {
+
+extern std::string cnrn_version();
+
 corenrn_parameters::corenrn_parameters(){
 
     app.set_config("--read-config", "", "Read parameters from ini file", false)
@@ -100,6 +104,8 @@ corenrn_parameters::corenrn_parameters(){
     sub_output -> add_option("-o, --outpath", this->outpath, "Path to place output data files.", true);
     sub_output -> add_option("--checkpoint", this->checkpointpath, "Enable checkpoint and specify directory to store related files.");
 
+    app.add_flag("-v, --version", this->show_version, "Show version information and quit.");
+
     CLI::retire_option(app, "--show");
 };
 
@@ -111,13 +117,21 @@ void corenrn_parameters::parse (int argc, char** argv) {
             nrn_nobanner_ = 1;
         }
     } catch (const CLI::ExtrasError &e) {
-        std::cerr << "Single-dash arguments such as -mpi are deleted, please check ./coreneuron_exec --help for more information. \n" << std::endl;
+        // in case of parsing errors, show message with exception
+        std::cerr << "CLI parsing error, see nrniv-core --help for more information. \n" << std::endl;
         app.exit(e);
         throw e;
 
     } catch (const CLI::ParseError &e) {
+        // use --help is also ParseError; in this case exit by showing all options
         app.exit(e);
-        throw e;
+        exit(0);
+    }
+
+    // is user has asked for version info, print it and exit
+    if (show_version) {
+        std::cout << "CoreNEURON Version : " << cnrn_version() << std::endl;
+        exit(0);
     }
 };
 

coreneuron/apps/corenrn_parameters.hpp

@@ -85,6 +85,8 @@ struct corenrn_parameters {
     bool gpu=false;                /// Enable GPU computation.
     bool binqueue=false;           /// Use bin queue.
 
+    bool show_version=false;       /// Print version and exit.
+
     verbose_level verbose{verbose_level::DEFAULT}; /// Verbosity-level
 
     double tstop=100;              /// Stop time of simulation in msec

coreneuron/apps/main1.cpp

@@ -37,6 +37,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <memory>
 #include <vector>
 
+#include "coreneuron/config/config.h"
 #include "coreneuron/engine.h"
 #include "coreneuron/utils/randoms/nrnran123.h"
 #include "coreneuron/nrnconf.h"
@@ -339,12 +340,12 @@ void handle_forward_skip(double forwardskip, int prcellgid) {
     t = savet;
     dt2thread(-1.);
 
-    // clear spikes generated during forward skip (with negative time) 
+    // clear spikes generated during forward skip (with negative time)
     clear_spike_vectors();
 }
 
-const char* nrn_version(int) {
-    return "version id unimplemented";
+std::string cnrn_version() {
+    return coreneuron::version::to_string();
 }
 
 // bsize = 0 then per step transfer
@@ -428,12 +429,7 @@ using namespace coreneuron;
 
 extern "C" void mk_mech_init(int argc, char** argv) {
     // read command line parameters and parameter config files
-    try {
-        corenrn_param.parse(argc, argv);
-    }
-    catch (...) {
-        nrn_abort(1);
-    }
+    corenrn_param.parse(argc, argv);
 
 #if NRNMPI
     if (corenrn_param.mpi_enable) {

coreneuron/config/config.cpp.in

@@ -0,0 +1,7 @@
+#include "coreneuron/config/config.h"
+
+/// Git version of the project
+const std::string coreneuron::version::GIT_REVISION = "@CN_GIT_REVISION@";
+
+/// CoreNEURON version
+const std::string coreneuron::version::CORENEURON_VERSION = "@CN_PROJECT_VERSION@";

coreneuron/config/config.h

@@ -0,0 +1,31 @@
+#pragma once
+
+/**
+ * \dir
+ * \brief Global project configurations
+ *
+ * \file
+ * \brief Version information
+ */
+
+#include <string>
+
+namespace coreneuron {
+
+/**
+ * \brief Project version information
+ */
+struct version {
+    /// git revision id
+    static const std::string GIT_REVISION;
+
+    /// project tagged version in the cmake
+    static const std::string CORENEURON_VERSION;
+
+    /// return version string (version + git id) as a string
+    static std::string to_string() {
+        return CORENEURON_VERSION + " " + GIT_REVISION;
+    }
+};
+
+}  // namespace coreneuron

coreneuron/io/mk_mech.cpp

@@ -49,7 +49,7 @@ namespace coreneuron {
 extern int nrn_nobanner_;
 
 // NB: this should go away
-extern const char* nrn_version(int);
+extern std::string cnrn_version();
 std::map<std::string, int> mech2type;
 
 extern "C" {
@@ -140,7 +140,7 @@ static void mk_mech(std::istream& s) {
     if (nrnmpi_myid < 1 && nrn_nobanner_ == 0) {
         fprintf(stderr, " \n");
         fprintf(stderr, " %s\n", banner);
-        fprintf(stderr, " %s\n", nrn_version(1));
+        fprintf(stderr, " Version : %s\n", cnrn_version().c_str());
         fprintf(stderr, " \n");
         fflush(stderr);
     }

coreneuron/network/netpar.cpp

@@ -654,7 +654,7 @@ double set_mindelay(double maxdelay) {
             }  
             PreSyn* ps;
             InputPreSyn* psi;
-            netpar_tid_gid2ps(ith, gid, &ps, &psi);
+            netpar_tid_gid2ps(tid, gid, &ps, &psi);
             if (psi) {
                 chk = true;
             } else if (all) {