add --directory flag to enable operation from arbitrary working directories

condainer/condainer.py

@@ -201,7 +201,7 @@ def compress_environment(cfg):
     assert(proc.returncode == 0)
 
 
-def run_cmd(args):
+def run_cmd(args, cwd):
     """Run command in a sub-process, where PATH is prepended with the 'bin' directory of the 'condainer' environment in the container.
     """
     cfg = get_cfg()
@@ -209,7 +209,7 @@ def run_cmd(args):
     bin_directory = os.path.join(env_directory, 'envs', 'condainer', 'bin')
     env = copy.deepcopy(os.environ)
     env['PATH'] = bin_directory + ':' + env['PATH']
-    proc = subprocess.Popen(args.command, env=env, shell=False)
+    proc = subprocess.Popen(args.command, cwd=cwd, env=env, shell=False)
     proc.communicate()
 
 
@@ -328,7 +328,7 @@ def umount(args):
             print("hint: condainer not mounted")
 
 
-def exec(args):
+def exec(args, cwd):
     """Run command within container, set quiet mode for minimal inference with the command output.
     """
     cfg = get_cfg()
@@ -339,7 +339,7 @@ def exec(args):
             mount_required = not is_mounted(cfg)
             if mount_required:
                 mount(args)
-            run_cmd(args)
+            run_cmd(args, cwd)
             if mount_required:
                 umount(args)
         finally:

condainer/main.py

@@ -2,6 +2,7 @@
 Argument handling and calling of the functions implemented in condainer.py
 """
 
+import os
 import sys
 import argparse
 from . import condainer
@@ -10,12 +11,13 @@ def get_args():
     """Handle command line arguments, return args.
     """
     parser = argparse.ArgumentParser(
-        formatter_class=argparse.RawDescriptionHelpFormatter,
         prog=sys.argv[0],
         description='Create and manage conda environments based on compressed squashfs images.',
-        epilog='More information at https://gitlab.mpcdf.mpg.de/khr/condainer\n\n"Do not set Anacondas free, put them into containers!"'
+        epilog='More information at https://gitlab.mpcdf.mpg.de/khr/condainer'
     )
     parser.add_argument('-q', '--quiet', action='store_true', help='be quiet, do not write to stdout unless an error occurs')
+    parser.add_argument('-d', '--directory', help='condainer project directory, the default is the current working directory')
+
     subparsers   = parser.add_subparsers(dest='subcommand', required=True)
 
     subparsers.add_parser('init', help='initialize directory with config files')
@@ -23,6 +25,7 @@ def get_args():
 
     parser_exec = subparsers.add_parser('exec', help='execute command within containerized conda environment')
     parser_exec.add_argument('command', type=str, nargs='+', help='command line of the containerized command')
+
     subparsers.add_parser('mount', help='mount containerized conda environment')
     subparsers.add_parser('umount', help='unmount ("eject") containerized conda environment')
     subparsers.add_parser('prereq', help='check if the necessary tools are installed')
@@ -37,6 +40,9 @@ def cli():
     """Entry point function to call `condainer` from the command line.
     """
     args = get_args()
+    cwd = os.getcwd()
+    if args.directory:
+        os.chdir(args.directory)
     if   args.subcommand == 'init':
         condainer.init(args)
     elif args.subcommand == 'build':
@@ -48,7 +54,7 @@ def cli():
     elif args.subcommand == 'prereq':
         condainer.prereq(args)
     elif args.subcommand == 'exec':
-        condainer.exec(args)
+        condainer.exec(args, cwd)
     elif args.subcommand == 'test':
         condainer.test(args)
     elif args.subcommand == 'status':