Some cli renames

wfl/cli/cli.py

@@ -23,6 +23,7 @@ def cli(ctx, verbose):
 @cli.group("generate")
 @click.pass_context
 def subcli_generate(ctx):
+    """Generate structures"""
     pass
 
 from wfl.cli.commands.generate import smiles, buildcell
@@ -33,31 +34,28 @@ def subcli_generate(ctx):
 @cli.group("select")
 @click.pass_context
 def subcli_select(ctx):
+    """Select structures from database"""
     pass
 
 from wfl.cli.commands.select import cur, by_lambda
 subcli_select.add_command(cur)
 subcli_select.add_command(by_lambda)
 
-
-@cli.group("eval")
+@cli.group("calc")
 @click.pass_context
-def subcli_eval(ctx):
+def subcli_calc(ctx):
+    "Calculate properties and descriptors."
     pass
 
-from wfl.cli.commands.eval import gap, ace, mace, atomization_energy 
-subcli_eval.add_command(gap)
-subcli_eval.add_command(ace)
-subcli_eval.add_command(mace)
-subcli_eval.add_command(atomization_energy)
+from wfl.cli.commands.calc import gap, ace, mace, atomization_energy, quippy
+
+subcli_calc.add_command(gap)
+subcli_calc.add_command(ace)
+subcli_calc.add_command(mace)
+subcli_calc.add_command(atomization_energy)
+subcli_calc.add_command(quippy)
 
 
-@cli.group("descriptor")
-@click.pass_context
-def subcli_descriptor(ctx):
-    pass
 
-from wfl.cli.commands.descriptor import quippy 
-subcli_descriptor.add_command(quippy)
 
 

wfl/cli/commands/eval.py → wfl/cli/commands/calc.py

@@ -6,6 +6,7 @@
 from wfl.cli import cli_options as opt
 from wfl.calculators import generic
 from wfl.utils import configs
+import wfl.descriptors.quippy
 
 
 @click.command("gap")
@@ -16,7 +17,7 @@
 @opt.prop_prefix
 @opt.num_inputs_per_python_subprocess
 def gap(ctx, inputs, outputs, param_fname, prop_prefix, num_inputs_per_python_subprocess):
-    """evaluates GAP"""
+    """evaluate GAP"""
 
     if prop_prefix is None:
         prop_prefix="gap_"
@@ -44,7 +45,7 @@ def pyjulip_ace(param_fname):
 @opt.prop_prefix
 @opt.num_inputs_per_python_subprocess
 def ace(ctx, inputs, outputs, param_fname, prop_prefix, num_inputs_per_python_subprocess):
-    """evaluates ACE"""
+    """evaluate ACE"""
 
     if prop_prefix is None:
         prop_prefix = 'ace_'
@@ -68,7 +69,7 @@ def ace(ctx, inputs, outputs, param_fname, prop_prefix, num_inputs_per_python_su
 @opt.prop_prefix
 @opt.num_inputs_per_python_subprocess
 def mace(ctx, inputs, outputs, param_fname, prop_prefix, num_inputs_per_python_subprocess, dtype):
-    """evaluates MACE"""
+    """evaluate MACE"""
 
     from mace.calculators.mace import MACECalculator 
 
@@ -93,7 +94,8 @@ def mace(ctx, inputs, outputs, param_fname, prop_prefix, num_inputs_per_python_s
     help="``atoms.info`` key on which to select isolated atoms")
 @click.option("--isolated-atom-info-value", "-v", default="default", 
     help="``atoms.info['isolated_atom_info_key']`` value for isolated atoms. Defaults to \"IsolatedAtom\" or \"isolated_atom\"")
-def atomization_energy(inputs, outputs, prop_prefix, prop, isolated_atom_info_key, isolated_atom_info_value):
+def atomization_energy(ctx, inputs, outputs, prop_prefix, prop, isolated_atom_info_key, isolated_atom_info_value):
+    """Calculte atomization energy"""
     configs.atomization_energy(
         inputs=inputs,
         outputs=outputs,
@@ -104,3 +106,22 @@ def atomization_energy(inputs, outputs, prop_prefix, prop, isolated_atom_info_ke
     )
 
 
+@click.command("quippy")
+@click.pass_context
+@click.option("--local", is_flag=True, help="calculate a local (per-atom) descriptor")
+@click.option("--force", is_flag=True, help="overwrite existing info or arrays item if present")
+@click.option("--descriptor", type=click.STRING, required=True, help="quippy.descriptors.Descriptor arg string")
+@click.option("--key", required=True, type=click.STRING, help="Atoms.info (global) or Atoms.arrays (local) for descriptor vector")
+@opt.inputs
+@opt.outputs
+def quippy(ctx, inputs, outputs, descriptor, key, local, force):
+    """Calculate quippy descriptors"""
+    wfl.descriptors.quippy.calc(
+        inputs=inputs,
+        outputs=outputs,
+        descs=descriptor,
+        key=key,
+        per_atom=local,
+        force=force
+    )
+

wfl/cli/commands/error.py

@@ -37,7 +37,7 @@ def show_error(ctx, inputs, calc_property_prefix, ref_property_prefix,
           config_properties, atom_properties, category_keys,
           weight_property, precision, fig_name, error_type, 
           cmap):
-    """Prints error summary table"""
+    """Print error summary table and plot parity plot"""
     # TODO
     # - clean up cmap
 

wfl/cli/commands/select.py

@@ -38,7 +38,7 @@ def cur(ctx, inputs, outputs, n_configs, key, keep_descriptor,
 @opt.inputs
 @opt.outputs
 def by_lambda(ctx, inputs, outputs, exec_code):
-    """selects atoms based on a lambda function"""
+    """Select atoms based on a lambda function"""
 
     at_filter_fun = eval("lambda atoms: " + exec_code)