Add TOML configuration file

mdbenchmark/cli/commands.py

@@ -29,6 +29,8 @@
     validate_number_of_nodes,
 )
 
+from mdbenchmark.config import _add_single_context, _import_config_into_context
+
 
 @click.group(cls=AliasedGroup)
 @click.version_option()
@@ -86,6 +88,13 @@ def analyze(directory, plot, ncores, save_csv):
 
 
 @cli.command()
+@click.option(
+    "--config",
+    "config_file",
+    help="Parse settings from config file instead of command-line. Ignores all other options.",
+    callback=_import_config_into_context,
+    type=click.Path(exists=True),
+)
 @click.option(
     "-n",
     "--name",
@@ -99,13 +108,15 @@ def analyze(directory, plot, ncores, save_csv):
     help="Use CPUs for benchmark.",
     default=True,
     show_default=True,
+    callback=_add_single_context,
 )
 @click.option(
     "-g/-ng",
     "--gpu/--no-gpu",
     is_flag=True,
     help="Use GPUs for benchmark.",
     show_default=True,
+    callback=_add_single_context,
 )
 @click.option(
     "-m",
@@ -128,20 +139,23 @@ def analyze(directory, plot, ncores, save_csv):
     help="Minimal number of nodes to request.",
     default=1,
     show_default=True,
+    callback=_add_single_context,
     type=int,
 )
 @click.option(
     "--max-nodes",
     help="Maximal number of nodes to request.",
     default=5,
     show_default=True,
+    callback=_add_single_context,
     type=int,
 )
 @click.option(
     "--time",
     help="Run time for benchmark in minutes.",
     default=15,
     show_default=True,
+    callback=_add_single_context,
     type=click.IntRange(1, 1440),
 )
 @click.option(
@@ -156,15 +170,22 @@ def analyze(directory, plot, ncores, save_csv):
     "--skip-validation",
     help="Skip the validation of module names.",
     default=False,
+    callback=_add_single_context,
     is_flag=True,
 )
 @click.option(
     "--job-name", help="Give an optional to the generated benchmarks.", default=None
 )
 @click.option(
-    "-y", "--yes", help="Answer all prompts with yes.", default=False, is_flag=True
+    "-y",
+    "--yes",
+    help="Answer all prompts with yes.",
+    default=False,
+    callback=_add_single_context,
+    is_flag=True,
 )
 def generate(
+    config_file,
     name,
     cpu,
     gpu,

mdbenchmark/cli/validators.py

@@ -5,6 +5,9 @@
 
 def validate_name(ctx, param, name=None):
     """Validate that we are given a name argument."""
+    # Fetch name from context read in config file
+    name = ctx.params.get("name", name)
+
     if name is None:
         raise click.BadParameter(
             "Please specify the base name of your input files.",
@@ -16,6 +19,9 @@ def validate_name(ctx, param, name=None):
 
 def validate_module(ctx, param, module=None):
     """Validate that we are given a module argument."""
+    # Fetch module from context read in config file
+    module = ctx.params.get("module", module)
+
     if module is None or not module:
         raise click.BadParameter(
             "Please specify which MD engine module to use for the benchmarks.",
@@ -63,6 +69,9 @@ def validate_hosts(ctx, param, host=None):
     templates. If the hostname matches the template name, we continue by
     returning the hostname.
     """
+    # Fetch host from context read in config file
+    host = ctx.params.get("host", host)
+
     if host is None:
         host = utils.guess_host()
         if host is None:

mdbenchmark/config.py

@@ -0,0 +1,71 @@
+from tomlkit import parse
+from tomlkit.exceptions import ParseError
+
+from mdbenchmark import console
+
+CONFIG_KEY_TO_CTX = {"skip_prompts": "yes", "input": "name", "modules": "module"}
+ALLOWED_CONFIG_KEYS = [
+    "input",
+    "job_name",
+    "modules",
+    "skip_validation",
+    "min_nodes",
+    "max_nodes",
+    "time",
+    "host",
+    "cpu",
+    "gpu",
+    "skip_prompts",
+]
+
+
+def parse_config(toml_file):
+    """
+    Open config file and parse its content.
+    """
+    with open(toml_file, "r") as f:
+        content = "".join(f.readlines())
+
+    try:
+        parsed = parse(content)
+    except ParseError as e:
+        console.error(
+            "{filename}: {error}".format(filename=toml_file, error=e.__str__())
+        )
+
+    return parsed
+
+
+def _add_single_context(ctx, param, value):
+    """
+    Get a value from the context, otherwise set value defined by user.
+    """
+    return ctx.params.get(param.name, value)
+
+
+def _import_config_into_context(ctx, param, config_file):
+    """
+    Parse config file and put settings into click.Context.
+    """
+    console.info(
+        'Using settings from config file "{config_file}".'.format(
+            config_file=config_file
+        )
+    )
+
+    parsed_config = parse_config(config_file)
+
+    for key in parsed_config.keys():
+        # Ignore invalid keys from config file
+        if key not in ALLOWED_CONFIG_KEYS:
+            console.info('Ignoring setting for unknown key "{key}".'.format(key=key))
+            continue
+
+        try:
+            ctx_key = CONFIG_KEY_TO_CTX[key]
+        except KeyError:
+            ctx_key = key
+
+        ctx.params[ctx_key] = parsed_config[key]
+
+    return config_file