Add a config file option for multiple options

README.md

@@ -82,21 +82,59 @@ Similarly, the `test/leapfrog` directory contains a set of example Leapfrog rese
 ```
 for example.
 
+## Configuration files
+
+Once a workflow uses more than a handful of options, putting them in a config file is easier than re-typing the same command line. `em2ex` accepts a YAML config via `--config`:
+
+```bash
+./em2ex.py --config my_workflow.yaml model.grdecl
+```
+
+The config is a YAML mapping. Each key is **the CLI flag name with the leading `--` stripped and hyphens converted to underscores** — exactly what you'd type after `--` in the shell, normalised for YAML. So `--refine-xy` becomes `refine_xy` (or, if you prefer, `refine-xy` — both work). Values follow the option's natural type: a single string or number for single-value flags, a YAML list for multi-value flags, a boolean for switches:
+
+```yaml
+# Geometry transforms
+extract_i: [10, 50]
+extract_j: [10, 50]
+refine_xy: [2, 2]
+
+# Property handling
+extra_keywords:
+  - PVTNUM
+  - EQLNUM
+
+# Output controls
+output: model.e             # corresponds to --output
+force: true                 # corresponds to --force
+fault_sidesets: true
+convert_to_m: true
+
+# Mesh quality
+strict_jacobians: true
+```
+
+The `filename` can be specified in the config too (`filename: path/to/model.grdecl`), in which case the positional argument can be omitted on the CLI.
+
+**Precedence**: command-line flags always win over config values, and config values win over the parser's own defaults. So a config that defaults `force: false` can still be overridden by passing `-f` at the prompt.
+
+**Unknown keys are rejected** with a list of valid keys, so typos like `refine_xz` (when you meant `refine_xy`) surface immediately rather than being silently ignored.
+
 ## Commandline options
 
 A number of optional commandline options are available, and can be seen by passing the `--help` flag:
 ```bash
 $ ./em2ex.py --help
 
-usage: em2ex.py [-h] [-o OUTPUT_FILE] [--filetype {eclipse,leapfrog}]
-                [--no-nodesets] [--no-sidesets] [-f] [-u] [--flip]
+usage: em2ex.py [-h] [--config FILE] [-o OUTPUT_FILE]
+                [--filetype {eclipse,leapfrog}] [--no-nodesets]
+                [--no-sidesets] [-f] [-u] [--flip]
                 [--translate TRANSLATE TRANSLATE] [--mapaxes] [--pinch]
                 [--pinch-tol PINCH_TOL] [--refine-xy RX RY]
                 [--extract-i I_LO I_HI] [--extract-j J_LO J_HI]
                 [--extract-k K_LO K_HI] [--extra-keywords KEY [KEY ...]]
                 [--fault-sidesets] [--convert-to-m]
                 [--no-check-jacobians] [--strict-jacobians]
-                filename
+                [filename]
 
 Converts earth model to Exodus II format
 
@@ -105,6 +143,11 @@ positional arguments:
 
 options:
   -h, --help            show this help message and exit
+  --config FILE         YAML config file specifying default values for any of
+                        this script's options. Values from the config are
+                        overridden by command-line flags. Use the option's
+                        `dest` name as the key (e.g. refine_xy, extract_i,
+                        extra_keywords).
   -o OUTPUT_FILE, --output OUTPUT_FILE
                         File name for output
   --filetype {eclipse,leapfrog}

em2ex.py

@@ -7,6 +7,75 @@
 from exodus_model import ExodusModel
 import argparse
 import os
+import sys
+
+def _load_config(path):
+    ''' Load a YAML config file. The file must contain a mapping from option
+    `dest` names (e.g. `refine_xy`, `extract_i`, `extra_keywords`) to values.
+    Lists are written as YAML sequences; booleans as `true` / `false`.
+    Returns the loaded dict. '''
+    import yaml
+    if not os.path.exists(path):
+        sys.exit("Config file not found: {}".format(path))
+    with open(path) as f:
+        cfg = yaml.safe_load(f) or {}
+    if not isinstance(cfg, dict):
+        sys.exit("Config file must contain a YAML mapping (got {})".format(type(cfg).__name__))
+    return cfg
+
+def _build_config_key_mapping(parser):
+    ''' Build a mapping from acceptable config-file key names to canonical
+    argparse `dest` names. The user can write any of:
+
+      - the CLI flag name with leading dashes stripped (e.g. `refine-xy`)
+      - the CLI flag name with hyphens converted to underscores (`refine_xy`)
+      - the argparse `dest` itself (also `refine_xy` here, but for options like
+        `--flip` -> `flip_z` or `--force` -> `force_overwrite` the dest is
+        different from the flag and both forms are accepted)
+
+    Short options (e.g. `-f`) are deliberately excluded to keep the config
+    keys descriptive. Returns (mapping, valid_canonical_keys).
+    '''
+    mapping = {}
+    canonical = []
+    for action in parser._actions:
+        if action.dest == 'help':
+            continue
+        canonical.append(action.dest)
+        # The dest itself is always accepted.
+        mapping[action.dest] = action.dest
+        # Each long-option flag is also accepted (after stripping `--` and
+        # normalising hyphens to underscores).
+        for opt in action.option_strings:
+            stripped = opt.lstrip('-')
+            if len(stripped) < 2:
+                continue   # skip short flags like -f / -o / -u
+            mapping[stripped.replace('-', '_')] = action.dest
+    return mapping, sorted(canonical)
+
+
+def _validate_and_normalize_config(cfg, parser):
+    ''' Resolve every config key to its canonical `dest` name. Accepts the
+    flexible forms documented in _build_config_key_mapping; rejects anything
+    that doesn't match any option, listing the valid keys.
+
+    Returns a new dict keyed by canonical `dest` names. '''
+    mapping, canonical = _build_config_key_mapping(parser)
+    normalized = {}
+    unknown = []
+    for key, value in cfg.items():
+        candidate = key.lstrip('-').replace('-', '_')
+        if candidate in mapping:
+            normalized[mapping[candidate]] = value
+        else:
+            unknown.append(key)
+    if unknown:
+        sys.exit(
+            "Unknown keys in config file: {}\n"
+            "Valid keys (or any long CLI flag name with leading dashes\n"
+            "stripped and hyphens converted to underscores): {}".format(
+                ', '.join(unknown), ', '.join(canonical)))
+    return normalized
 
 def _positive_int(s):
     ''' argparse type for strictly positive integers (refinement factors and
@@ -34,7 +103,10 @@ def get_parser():
     ''' Read commandline options and filename '''
 
     parser = argparse.ArgumentParser(description='Converts earth model to Exodus II format')
-    parser.add_argument('filename')
+    parser.add_argument('filename', nargs='?', default=None,
+        help='Input reservoir model file. Optional only when provided via --config.')
+    parser.add_argument('--config', dest='config_file', default=None, metavar='FILE',
+        help='YAML config file specifying default values for any of this script\'s options. Values from the config are overridden by command-line flags. Use the option\'s `dest` name as the key (e.g. refine_xy, extract_i, extra_keywords).')
     parser.add_argument('-o', '--output', default = None, dest = 'output_file', help = 'File name for output')
     parser.add_argument('--filetype', default = None, dest = 'filetype',
         choices = ['eclipse', 'leapfrog'], help = 'Explicitly state the filetype for unknown extensions')
@@ -75,10 +147,22 @@ def get_parser():
 def main():
     ''' Parse the Earth model and write out an Exodus II file '''
 
-    # Parse commandline options
+    # Parse commandline options. If --config is given, load the YAML file and
+    # apply its values as parser defaults; command-line flags then override
+    # those defaults in the usual way (precedence: CLI > config > parser default).
     parser = get_parser()
+    pre_parser = argparse.ArgumentParser(add_help=False)
+    pre_parser.add_argument('--config', dest='config_file', default=None)
+    pre_args, _ = pre_parser.parse_known_args()
+    if pre_args.config_file:
+        config = _load_config(pre_args.config_file)
+        config = _validate_and_normalize_config(config, parser)
+        parser.set_defaults(**config)
     args = parser.parse_args()
 
+    if not args.filename:
+        parser.error('filename is required (provide as a positional argument or as `filename: ...` in --config)')
+
     # If --use-official-api is passed, then import exodus from exodus.py. Note:
     # this requires that exodus.py is in the $PYTHONPATH environment variable
     if args.use_official_api:

test/eclipse/config_bad_key.yaml

@@ -0,0 +1,4 @@
+# Deliberately-bad config: `refine_xz` is not a real option (refine_xy was meant).
+# Used by the yaml exception test to verify the config loader rejects typos.
+
+refine_xz: [2, 2]

test/eclipse/config_extract_refine.yaml

@@ -0,0 +1,12 @@
+# Example em2ex config file. Drives the same conversion as the yaml entry
+# `simple_cube_extract_refine` (extract a sub-region and then refine it).
+#
+# Keys are CLI flag names with the leading `--` stripped (and hyphens may be
+# converted to underscores for YAML cleanliness). Sequences map to multi-value
+# flags, booleans to store_true/store_false flags. CLI flags override these
+# values when both are given.
+
+extract_i: [2, 3]
+extract_j: [1, 2]
+extract_k: [1, 1]
+refine_xy: [2, 2]

test/eclipse/tests

@@ -150,6 +150,23 @@ strict_jacobians_inverted:
   cli_args: --strict-jacobians
   expected_error: exiting due to invalid Jacobians
 
+# Driven entirely by a YAML config file (extract + refine settings). The
+# output must match the same gold as the CLI-driven simple_cube_extract_refine
+# test, proving the config loader applies values correctly.
+config_extract_refine:
+  filename: simple_cube_extract.grdecl
+  type: exodiff
+  cli_args: --config test/eclipse/config_extract_refine.yaml
+  gold: simple_cube_extract_refine.e
+
+# Typo in config key name -- the loader should reject it up front with a
+# helpful "Unknown keys" message rather than silently ignore it.
+config_bad_key:
+  filename: simple_cube.grdecl
+  type: exception
+  cli_args: --config test/eclipse/config_bad_key.yaml
+  expected_error: "Unknown keys in config file: refine_xz"
+
 missing_specgrid:
   filename: missing_specgrid.grdecl
   type: exception