cli: add more flags to 'popper sh' command (#923)

Added --skip-pull, --skip-clone, --config, and --substitution flags to 'popper sh'

fixes #913

src/popper/commands/cmd_sh.py

@@ -23,24 +23,55 @@
     required=False,
     default="/bin/bash",
 )
+@click.option(
+    "--skip-pull",
+    help="Skip pulling container images (assume they exist in local cache).",
+    required=False,
+    is_flag=True,
+)
+@click.option(
+    "--skip-clone",
+    help="Skip cloning repositories (assume they have been cloned).",
+    required=False,
+    is_flag=True,
+)
+@click.option(
+    "-s",
+    "--substitution",
+    help="A key-value pair defining a substitution. " "Can be given multiple times.",
+    required=False,
+    default=list(),
+    multiple=True,
+)
+@click.option(
+    "-c", "--conf", help="Path to file with configuration options.", required=False
+)
 @pass_context
-def cli(ctx, file, step, entrypoint):
+def cli(ctx, file, step, entrypoint, skip_pull, skip_clone, substitution, conf):
     """Opens an interactive shell using all the attributes defined in the workflow file
     for the given STEP, but ignoring ``runs`` and ``args``. By default, it invokes
     /bin/bash. If you need to invoke another one, you can specify it in the --entrypoint
     flag.
 
     NOTE: this command only works for (local) host runner in Docker.
     """
-    wf = WorkflowParser.parse(file=file, step=step, immutable=False)
+    wf = WorkflowParser.parse(
+        file=file, step=step, immutable=False, substitutions=substitution
+    )
 
     # override entrypoint
     step = wf.steps[0]
     step.args = []
     step.runs = entrypoint
 
     # configure runner so containers execute in attached mode and create a tty
-    config = ConfigLoader.load(engine_name="docker", pty=True)
+    config = ConfigLoader.load(
+        engine_name="docker",
+        pty=True,
+        skip_pull=skip_pull,
+        skip_clone=skip_clone,
+        config_file=conf,
+    )
 
     with WorkflowRunner(config) as runner:
         try: