Improve biodynamo cli (#215)

* Create build directory when using 'biodynamo new'

* Write output of build and run stage continously to stdout

* Add short 'bdm' command which is the same as 'biodynamo'

cli/bdm.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python3
+# -----------------------------------------------------------------------------
+#
+# Copyright (C) 2021 CERN & Newcastle University for the benefit of the
+# BioDynaMo collaboration. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# See the LICENSE file distributed with this work for details.
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# -----------------------------------------------------------------------------
+
+from main import Main
+
+if __name__ == "__main__":
+    Main()

cli/biodynamo.py

@@ -13,84 +13,8 @@
 #
 # -----------------------------------------------------------------------------
 
-import argparse
-import sys
-from build_command import BuildCommand
-from demo_command import DemoCommand
-from new_command import NewCommand
-from run_command import RunCommand
-from bdm_version import Version
+from main import Main
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        prog="biodynamo",
-        description="This is the BioDynaMo command line interface. It guides "
-        "you during the whole simulation workflow. From starting a new project,"
-        "to compiling and executing your simulation.",
-        epilog="",
-    )
+    Main()
 
-    sp = parser.add_subparsers(dest="cmd")
-    parser.add_argument("-v",
-                        "--version",
-                        action="store_true",
-                        help="Display BioDynaMo version")
-    parser.add_argument("--shortversion",
-                        action="store_true",
-                        help="Display BioDynaMo short version")
-
-    build_sp = sp.add_parser("build", help="Builds the simulation binary")
-
-    clean_sp = sp.add_parser("clean", help="Removes all build files")
-
-    demo_sp = sp.add_parser("demo", help="Creates pre-built demos.")
-
-    new_sp = sp.add_parser(
-        "new",
-        help="Creates a new simulation project. Creates a template project, "
-        "renames it to the given simulation name, configures git.",
-    )
-    new_sp.add_argument("SIMULATION_NAME",
-                        type=str,
-                        help="simulation name help")
-    new_sp.add_argument("--github",
-                        action="store_true",
-                        help="Create a Github repository.")
-
-    run_sp = sp.add_parser("run", help="Executes the simulation")
-
-    args, unknown = parser.parse_known_args()
-
-    if args.cmd == "new":
-        if len(unknown) != 0:
-            new_sp.print_help()
-            sys.exit()
-        NewCommand(args.SIMULATION_NAME, args.github)
-    elif args.cmd == "build":
-        if len(unknown) != 0:
-            build_sp.print_help()
-            sys.exit()
-        BuildCommand()
-    elif args.cmd == "clean":
-        if len(unknown) != 0:
-            clean_sp.print_help()
-            sys.exit()
-        BuildCommand(clean=True, build=False)
-    elif args.cmd == "demo":
-        demo_name = None
-        destination = None
-        if len(unknown) >= 1:
-            demo_name = unknown[0]
-        if len(unknown) >= 2:
-            destination = unknown[1]
-        DemoCommand(demo_name, destination)
-    elif args.cmd == "run":
-        RunCommand(args=unknown)
-    elif args.version:
-        print(Version.string())
-        sys.exit()
-    elif args.shortversion:
-        print(Version.shortstring())
-        sys.exit()
-    else:
-        parser.print_help()

cli/build_command.py

@@ -16,60 +16,35 @@
 import subprocess as sp
 from pathlib import Path
 from print_command import Print
+from util import RunProcessAndWriteToStdOut
 
 
 # The BioDynaMo CLI command to build a simulation binary.
-def BuildCommand(clean=False, debug=False, build=True):
+def BuildCommand(clean=False, build=True):
     build_dir = "build"
-    debug_dir = "debug"
 
     Print.new_step("Build")
 
-    if clean or debug:
+    if clean:
         Print.new_step("Clean build directory")
         sp.check_output(["rm", "-rf", build_dir])
         sp.check_output(["mkdir", build_dir])
-    else:
+
+    elif build:
         if not os.path.exists(build_dir):
             sp.check_output(["mkdir", build_dir])
 
-    if debug:
-        if not os.path.exists(debug_dir):
-            sp.check_output(["mkdir", debug_dir])
-
-        with open(debug_dir + "/cmake_output.log", "w") as file:
-            try:
-                sp.check_call(["cmake", "-B./" + build_dir, "-H."],
-                              stdout=file,
-                              stderr=file)
-            except sp.CalledProcessError as err:
-                Print.error(
-                    "Failed to run CMake. Generating debug/cmake_output.log..."
-                )
-                return
-
-        with open(debug_dir + "/make_output.log", "w") as file:
-            try:
-                sp.check_call(["make", "-C", build_dir],
-                              stdout=file,
-                              stderr=file)
-            except sp.CalledProcessError as err:
-                Print.error(
-                    "Compilation failed. Generating debug/make_output.log...")
-                return
-
-    elif build:
         # if CMakeCache.txt does not exist, run cmake
         if not Path(build_dir + "/CMakeCache.txt").is_file():
             try:
-                sp.check_output(["cmake", "-B./" + build_dir, "-H."])
+                RunProcessAndWriteToStdOut(["cmake", "-B./" + build_dir, "-H."])
             except sp.CalledProcessError as err:
                 Print.error(
                     "Failed to run CMake. Check the debug output above.")
                 sys.exit(1)
 
         try:
-            sp.check_output(["make", "-j4", "-C", build_dir])
+            RunProcessAndWriteToStdOut(["make", "-j4", "-C", build_dir])
         except:
             Print.error("Compilation failed. Check the debug output above.")
             sys.exit(1)

cli/main.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python3
+# -----------------------------------------------------------------------------
+#
+# Copyright (C) 2021 CERN & Newcastle University for the benefit of the
+# BioDynaMo collaboration. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# See the LICENSE file distributed with this work for details.
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# -----------------------------------------------------------------------------
+
+import argparse
+import sys
+from build_command import BuildCommand
+from demo_command import DemoCommand
+from new_command import NewCommand
+from run_command import RunCommand
+from bdm_version import Version
+
+def Main():
+    parser = argparse.ArgumentParser(
+        prog="biodynamo",
+        description="This is the BioDynaMo command line interface. It guides "
+        "you during the whole simulation workflow. From starting a new project,"
+        "to compiling and executing your simulation.",
+        epilog="",
+    )
+
+    sp = parser.add_subparsers(dest="cmd")
+    parser.add_argument("-v",
+                        "--version",
+                        action="store_true",
+                        help="Display BioDynaMo version")
+    parser.add_argument("--shortversion",
+                        action="store_true",
+                        help="Display BioDynaMo short version")
+
+    build_sp = sp.add_parser("build", help="Builds the simulation binary")
+
+    clean_sp = sp.add_parser("clean", help="Removes all build files")
+
+    demo_sp = sp.add_parser("demo", help="Creates pre-built demos.")
+
+    new_sp = sp.add_parser(
+        "new",
+        help="Creates a new simulation project. Creates a template project, "
+        "renames it to the given simulation name, configures git.",
+    )
+    new_sp.add_argument("SIMULATION_NAME",
+                        type=str,
+                        help="simulation name help")
+    new_sp.add_argument("--github",
+                        action="store_true",
+                        help="Create a Github repository.")
+
+    run_sp = sp.add_parser("run", help="Executes the simulation")
+
+    args, unknown = parser.parse_known_args()
+
+    if args.cmd == "new":
+        if len(unknown) != 0:
+            new_sp.print_help()
+            sys.exit()
+        NewCommand(args.SIMULATION_NAME, args.github)
+    elif args.cmd == "build":
+        if len(unknown) != 0:
+            build_sp.print_help()
+            sys.exit()
+        BuildCommand()
+    elif args.cmd == "clean":
+        if len(unknown) != 0:
+            clean_sp.print_help()
+            sys.exit()
+        BuildCommand(clean=True, build=False)
+    elif args.cmd == "demo":
+        demo_name = None
+        destination = None
+        if len(unknown) >= 1:
+            demo_name = unknown[0]
+        if len(unknown) >= 2:
+            destination = unknown[1]
+        DemoCommand(demo_name, destination)
+    elif args.cmd == "run":
+        RunCommand(args=unknown)
+    elif args.version:
+        print(Version.string())
+        sys.exit()
+    elif args.shortversion:
+        print(Version.shortstring())
+        sys.exit()
+    else:
+        parser.print_help()
+

cli/new_command.py

@@ -102,6 +102,8 @@ def CustomizeFiles(sim_name):
         Print.error("Error: File customizations failed")
         CleanupOnError(sim_name)
 
+def CreateBuildDir(build_dir):
+    sp.check_output(["mkdir", build_dir])
 
 def NewCommand(sim_name, github):
     if github:
@@ -114,6 +116,7 @@ def NewCommand(sim_name, github):
     CopySupportFiles(sim_name)
     CustomizeFiles(sim_name)
     InitializeNewGitRepo(sim_name)
+    CreateBuildDir("{}/build".format(sim_name))
     if github:
         CreateNewGithubRepository(sim_name)
 

cli/run_command.py

@@ -17,33 +17,27 @@
 from print_command import Print
 from build_command import BuildCommand
 from util import GetBinaryName
+from util import RunProcessAndWriteToStdOut
 
 
 ## The BioDynaMo CLI command to run a simulation
 ##
 ## @param      sim_name  The simulation name
 ##
-def RunCommand(args, debug=False):
+def RunCommand(args):
     sim_name = GetBinaryName()
     args_str = " ".join(args)
     cmd = "./build/" + sim_name
-    if platform.system() == "Darwin":
-        launcher = os.environ["BDMSYS"] + "/bin/launcher.sh"
-    else:
-        launcher = ""
 
     try:
         BuildCommand()
         Print.new_step("Run " + sim_name + " " + args_str)
-        if debug:
-            sp.check_output(
-                [launcher + " " + cmd, "&>", "debug/runtime_output.log"])
+        if platform.system() == "Darwin":
+            launcher = os.environ["BDMSYS"] + "/bin/launcher.sh"
+            RunProcessAndWriteToStdOut([launcher, cmd, args_str])
         else:
-            print(
-                sp.check_output([launcher + " " + cmd, args_str],
-                                stderr=sp.STDOUT,
-                                shell=True).decode("utf-8"))
-            Print.success("Finished successfully")
+            RunProcessAndWriteToStdOut([cmd, args_str])
+        Print.success("Finished successfully")
     except sp.CalledProcessError as err:
         print(err.output.decode("utf-8"))
         Print.error("Error during execution of {0}".format(cmd))

cli/util.py

@@ -17,9 +17,23 @@
 import re
 import subprocess as sp
 import sys
+import select
 
 
 def GetBinaryName():
     with open("CMakeLists.txt") as f:
         content = f.read()
         return re.search("project\((.*)\)", content).group(1)
+
+def RunProcessAndWriteToStdOut(cmd_args):
+    p = sp.Popen(cmd_args, stdout=sp.PIPE, stderr=sp.PIPE)
+
+    poll = select.poll()
+    poll.register(p.stdout)
+    poll.register(p.stderr)
+
+    while p.poll() is None:
+        rlist = poll.poll()
+        for fd, event in rlist:
+            sys.stdout.write(os.read(fd, 1024).decode('utf-8'))
+

cmake/utils.cmake

@@ -196,6 +196,13 @@ function(install_inside_build)
             DEPENDS ${CMAKE_SOURCE_DIR}/cli/biodynamo.py
     )
     list(APPEND artifact_files_builddir ${CMAKE_INSTALL_BINDIR}/biodynamo)
+    # Copy bdm.py and make it executable.
+    add_custom_command(
+            OUTPUT ${CMAKE_INSTALL_BINDIR}/bdm
+            COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/cli/bdm.py ${CMAKE_INSTALL_BINDIR}/bdm
+            DEPENDS ${CMAKE_SOURCE_DIR}/cli/bdm.py
+    )
+    list(APPEND artifact_files_builddir ${CMAKE_INSTALL_BINDIR}/bdm)
 
     # Copy header files
     add_copy_directory(copy_files_bdm