Merge pull request #476 from joaomcteixeira/i356

Add general parameters to `haddock3-cfg` client

Author: joaomcteixeira

src/haddock/clis/cli_cfg.py

@@ -6,16 +6,19 @@
 
 Usage::
 
-    haddock3-cfg -m MODULE
+    haddock3-cfg  # prints only the general parametes
+    haddock3-cfg -g  # same as above
+    haddock3-cfg -m MODULE  # prints only the module parameters
     haddock3-cfg -m MODULE -l LEVEL
+    haddock3-cfg -m topoaa -l all
+    haddock3-cfg -m rigidbody -l all -g  # prints the module and the globals
 """
 import argparse
 import importlib
+import os
 import sys
 
 from haddock import config_expert_levels
-from haddock.gear.yaml2cfg import yaml2cfg_text
-from haddock.libs.libio import read_from_yaml
 from haddock.modules import modules_category
 
 
@@ -29,8 +32,8 @@
     "-m",
     dest="module",
     help="The module for which you want to retrieve the default configuration.",
-    required=True,
     choices=sorted(modules_category.keys()),
+    default=None,
     )
 
 ap.add_argument(
@@ -42,6 +45,14 @@
     choices=config_expert_levels + ("all",),
     )
 
+ap.add_argument(
+    '-g',
+    '--globals',
+    dest='global_params',
+    help="Add also the optional module's general parameters.",
+    action="store_true",
+    )
+
 
 def _ap():
     return ap
@@ -57,6 +68,20 @@ def load_args(ap):
 def cli(ap, main):
     """Command-line interface entry point."""
     cmd = load_args(ap)
+
+    # I didn't want to to have the `--globals` param as a negative parameter
+    # ('store_false'). However, `module` and `globals` can't both be false.
+    # In order for the commands below performing the same:
+    #
+    # haddock3-cfg
+    # haddock3-cfg -g
+    #
+    # we need this quick if statement. Which basically adjust the argparse to
+    # the default values in the main function.
+    # @joaomcteixeira
+    if cmd.global_params is False and cmd.module is None:
+        cmd.global_params = True
+
     main(**vars(cmd))
 
 
@@ -65,22 +90,69 @@ def maincli():
     cli(ap, main)
 
 
-def main(module, explevel):
-    """Extract the default configuration file for a given module."""
-    module_name = ".".join((
-        'haddock',
-        'modules',
-        modules_category[module],
-        module,
-        ))
-
-    module_lib = importlib.import_module(module_name)
-    cfg = module_lib.DEFAULT_CONFIG
-
-    ycfg = read_from_yaml(cfg)
-
-    new_config = yaml2cfg_text(ycfg, module, explevel)
-    print(new_config, file=sys.stdout, flush=True)  # noqa: T201
+def main(module=None, explevel="all", global_params=True):
+    """
+    Extract the defaults in the form of a run configuration file.
+
+    Parameters
+    ----------
+    module : str or None
+        The module name to extract the defaults from.
+        If ``None`` given, we expect ``global_params`` to be ``True``,
+        otherwise nothing will be printed.
+
+    explevel : str
+        Filter the parameters according to the expert level. Output all
+        parameters that belong to the referred level or below. Choices
+        are: all, easy, expert, and guru.
+
+    global_params : bool
+        Whether to add the module's general global parameter. If
+        ``True`` and ``module`` is ``None``, outputs only the general
+        parameters.
+    """
+    from haddock import modules_defaults_path
+    from haddock.gear.yaml2cfg import yaml2cfg_text
+    from haddock.libs.libio import read_from_yaml
+
+    new_config = ''
+
+    if global_params:
+        general_cfg = read_from_yaml(modules_defaults_path)
+        general_params_str = yaml2cfg_text(
+            general_cfg,
+            module=None,
+            explevel="all",
+            )
+        comment = os.linesep.join((
+            "# The parameters below are optional parameters. ",
+            "# They can either be used as global parameters or as part ",
+            "# of the module's parameters",
+            ))
+
+        new_config = os.linesep.join((
+            comment,
+            general_params_str,
+            ))
+
+    if module:
+
+        module_name = ".".join((
+            'haddock',
+            'modules',
+            modules_category[module],
+            module,
+            ))
+
+        module_lib = importlib.import_module(module_name)
+        cfg = module_lib.DEFAULT_CONFIG
+
+        ycfg = read_from_yaml(cfg)
+        module_config = yaml2cfg_text(ycfg, module, explevel)
+
+        new_config = os.linesep.join((new_config, module_config))
+
+    sys.stdout.write(new_config)
 
     return 0
 

src/haddock/gear/yaml2cfg.py

@@ -33,7 +33,8 @@ def yaml2cfg_text(ymlcfg, module, explevel):
         parameters will be considered.
     """
     new_config = []
-    new_config.append(f"[{module}]")
+    if module is not None:
+        new_config.append(f"[{module}]")
 
     new_config.append(_yaml2cfg_text(ymlcfg, module, explevel))
 
@@ -68,7 +69,10 @@ def _yaml2cfg_text(ycfg, module, explevel):
         if isinstance(param, Mapping) and "default" not in param:
 
             params.append("")  # give extra space
-            curr_module = f"{module}.{param_name}"
+            if module is not None:
+                curr_module = f"{module}.{param_name}"
+            else:
+                curr_module = param_name
             params.append(f"[{curr_module}]")
             _ = _yaml2cfg_text(param, module=curr_module, explevel=explevel)
             params.append(_)

tests/__init__.py

@@ -11,6 +11,8 @@
 emptycfg = Path(configs_data, 'empty.cfg')
 haddock3_yaml_cfg_examples = Path(configs_data, 'yml_example.yml')
 haddock3_yaml_converted = Path(configs_data, 'yaml2cfg_converted.cfg')
+haddock3_yaml_converted_no_header = \
+    Path(configs_data, 'yaml2cfg_converted_no_header.cfg')
 clean_steps_folder = Path(tests_path, 'clean_output_data')
 
 # defines which modules are already working

tests/configs/yaml2cfg_converted_no_header.cfg

@@ -0,0 +1,32 @@
+autohis = True  # $title Automatic HIS protonation state / $group molecule
+delenph = True  # $title Keep or remove non-polar hydrogen atoms / $group molecule
+log_level = 'verbose'  # $minchars 0 / $maxchars 100 / $title Log level verbosity for CNS / $group module
+iniseed = 917  # $min 0 / $max 9999999999999999 / $precision 3 / $title Random seed / $group molecule
+ligand_param_fname = ''  # $title No title yet
+ligand_top_fname = ''  # $title No title yet
+limit = True  # $title No title yet
+tolerance = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+
+[mol1]
+prot_segid = 'A'  # $minchars 0 / $maxchars 100 / $title No title yet
+fix_origin = False  # $title No title yet
+dna = False  # $title No title yet
+shape = False  # $title No title yet
+cg = False  # $title No title yet
+cyclicpept = False  # $title No title yet
+nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+
+[mol2]
+prot_segid = 'B'  # $minchars 0 / $maxchars 100 / $title No title yet
+fix_origin = False  # $title No title yet
+dna = False  # $title No title yet
+shape = False  # $title No title yet
+cg = False  # $title No title yet
+cyclicpept = False  # $title No title yet
+nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet

tests/test_cli_cfg.py

@@ -12,10 +12,17 @@ def config_level(request):
     return request.param
 
 
-@pytest.mark.parametrize(
-    "module",
-    list(modules_category.keys()),
-    )
-def test_export_cfgs(module, config_level):
-    """Test export all configs work."""
-    cli_cfg.main(module, config_level)
+@pytest.fixture(params=(True, False))
+def global_params(request):
+    """Haddock3 config levels."""
+    return request.param
+
+
+@pytest.fixture(params=list(modules_category.keys()) + [None])
+def module(request):
+    return request.param
+
+
+def test_export_cfgs_add_global(module, config_level, global_params):
+    """Test export all configs work with `add_global` parameter."""
+    cli_cfg.main(module, explevel=config_level, global_params=global_params)

tests/test_yaml2cfg.py renamed to tests/test_gear_yaml2cfg.py

@@ -5,7 +5,11 @@
 from haddock.gear.yaml2cfg import flat_yaml_cfg, yaml2cfg_text
 from haddock.libs.libio import read_from_yaml
 
-from . import haddock3_yaml_cfg_examples, haddock3_yaml_converted
+from . import (
+    haddock3_yaml_cfg_examples,
+    haddock3_yaml_converted,
+    haddock3_yaml_converted_no_header,
+    )
 
 
 complex_cfg = {
@@ -76,3 +80,20 @@ def test_yaml2cfg_test():
 
     assert filecmp.cmp(p, haddock3_yaml_converted, shallow=False)
     p.unlink()
+
+
+def test_yaml2cfg_test_no_header():
+    """Test yaml dict to cfg."""
+    ycfg = read_from_yaml(haddock3_yaml_cfg_examples)
+    result = yaml2cfg_text(ycfg, None, "all")
+    assert isinstance(result, str)
+
+    p = Path('dummy_test.cfg')
+    p.write_text(result)
+
+    assert filecmp.cmp(
+        p,
+        haddock3_yaml_converted_no_header,
+        shallow=False,
+        )
+    p.unlink()