Refactoring of velph's directory structure

pyproject.toml

@@ -25,7 +25,7 @@ license = {file = "LICENSE"}
 [project.scripts]
 phelel = "phelel.scripts.phelel:run"
 phelel-load = "phelel.scripts.phelel_load:run"
-velph = "phelel.velph.cli:cmd_root"
+velph = "phelel.velph.cli.cmd_root:cmd_root"
 
 [tool.setuptools.dynamic]
 version = { attr = "phelel.version.__version__" }

src/phelel/velph/cli/cmd_root.py

@@ -0,0 +1,28 @@
+"""velph command line tool module."""
+
+import click
+
+
+@click.group()
+@click.help_option("-h", "--help")
+def cmd_root():
+    """Command-line utility to help VASP el-ph calculation."""
+    pass
+
+
+from phelel.velph.cli.el_bands.cmd_el_bands import cmd_el_bands  # noqa: E402, F401
+from phelel.velph.cli.generate.cmd_generate import cmd_generate  # noqa: E402, F401
+from phelel.velph.cli.init.cmd_init import cmd_init  # noqa: E402, F401
+from phelel.velph.cli.nac.cmd_nac import cmd_nac  # noqa: E402, F401
+from phelel.velph.cli.ph_bands.cmd_ph_bands import cmd_ph_bands  # noqa: E402, F401
+from phelel.velph.cli.ph_selfenergy.cmd_ph_selfenergy import (  # noqa: E402, F401
+    cmd_ph_selfenergy,
+)
+from phelel.velph.cli.phelel.cmd_phelel import cmd_phelel  # noqa: E402, F401
+from phelel.velph.cli.phono3py.cmd_phono3py import cmd_phono3py  # noqa: E402, F401
+from phelel.velph.cli.phonopy.cmd_phonopy import cmd_phonopy  # noqa: E402, F401
+from phelel.velph.cli.relax.cmd_relax import cmd_relax  # noqa: E402, F401
+from phelel.velph.cli.selfenergy.cmd_selfenergy import (  # noqa: E402, F401
+    cmd_selfenergy,
+)
+from phelel.velph.cli.transport.cmd_transport import cmd_transport  # noqa: E402, F401

src/phelel/velph/cli/el_bands/__init__.py → src/phelel/velph/cli/el_bands/cmd_el_bands.py

@@ -6,7 +6,7 @@
 
 import click
 
-from phelel.velph.cli import cmd_root
+from phelel.velph.cli.cmd_root import cmd_root
 from phelel.velph.cli.el_bands.generate import write_input_files
 from phelel.velph.cli.el_bands.plot import plot_el_bandstructures
 from phelel.velph.utils.plot_eigenvalues import (
@@ -95,12 +95,6 @@ def cmd_plot_transport_eigenvalues(
         cutoff_occupancy,
         mu,
         None,
+        None,
         calc_type="el_bands",
     )
-
-
-def plot(window: tuple[float, float], save_plot: bool = False):
-    """Plot electronic band structure."""
-    with click.Context(cmd_plot) as ctx:
-        ctx.params = {"window": window, "save_plot": save_plot}
-        cmd_plot.invoke(ctx)

src/phelel/velph/cli/generate/__init__.py → src/phelel/velph/cli/generate/cmd_generate.py

@@ -1,13 +1,15 @@
 """velph command line tool / velph-generate."""
 
+from __future__ import annotations
+
 import pathlib
 
 import click
 import tomli
 from phonopy.interface.calculator import write_crystal_structure
 from phonopy.structure.atoms import parse_cell_dict
 
-from phelel.velph.cli import cmd_root
+from phelel.velph.cli.cmd_root import cmd_root
 
 
 #
@@ -53,9 +55,16 @@ def _run_generate(toml_filename: str, prefix: str) -> None:
         _write_cell(filename, toml_dict["primitive_cell"])
 
 
-def _write_cell(filename, toml_cell_dict):
+def _write_cell(filename: str, toml_cell_dict: dict):
     if pathlib.Path(filename).exists():
         click.echo(f'"{filename}" was not overwritten because it exists.', err=True)
     else:
-        write_crystal_structure(filename, parse_cell_dict(toml_cell_dict))
-        click.echo(f'"{filename}" was generated.', err=True)
+        cell = parse_cell_dict(toml_cell_dict)
+        if cell is None:
+            click.echo(
+                f'"{filename}" was not generated because of invalid cell data.',
+                err=True,
+            )
+            return
+        write_crystal_structure(filename, cell)
+        click.echo(f'"{filename}" was generated.')

src/phelel/velph/cli/init/__init__.py → src/phelel/velph/cli/init/cmd_init.py

@@ -8,7 +8,7 @@
 
 import click
 
-from phelel.velph.cli import cmd_root
+from phelel.velph.cli.cmd_root import cmd_root
 from phelel.velph.cli.init.init import run_init
 from phelel.velph.cli.utils import (
     DefaultCellChoices,

src/phelel/velph/cli/nac/__init__.py → src/phelel/velph/cli/nac/cmd_nac.py

@@ -1,10 +1,12 @@
 """velph command line tool / velph-nac."""
 
+from __future__ import annotations
+
 import pathlib
 
 import click
 
-from phelel.velph.cli import cmd_root
+from phelel.velph.cli.cmd_root import cmd_root
 from phelel.velph.cli.nac.generate import write_input_files
 
 

src/phelel/velph/cli/ph_bands/__init__.py → src/phelel/velph/cli/ph_bands/cmd_ph_bands.py

@@ -1,10 +1,12 @@
 """velph command line tool / velph-ph_bands."""
 
+from __future__ import annotations
+
 import pathlib
 
 import click
 
-from phelel.velph.cli import cmd_root
+from phelel.velph.cli.cmd_root import cmd_root
 from phelel.velph.cli.ph_bands.generate import (
     write_input_files as write_input_files_ph_bandstructures,
 )
@@ -64,10 +66,3 @@ def cmd_plot(use_ordinary_frequency: bool, save_plot: bool):
     plot_ph_bandstructures(
         vaspout_filename, use_ordinary_frequency, save_plot=save_plot
     )
-
-
-def plot(save_plot: bool = False):
-    """Plot phonon band structure."""
-    with click.Context(cmd_plot) as ctx:
-        ctx.params = {"save_plot": save_plot}
-        cmd_plot.invoke(ctx)

src/phelel/velph/cli/ph_selfenergy/cmd_ph_selfenergy.py

@@ -3,8 +3,9 @@
 import pathlib
 
 import click
+import h5py
 
-from phelel.velph.cli import cmd_root
+from phelel.velph.cli.cmd_root import cmd_root
 from phelel.velph.cli.selfenergy.generate import write_selfenergy_input_files
 from phelel.velph.cli.utils import check_fft
 
@@ -51,3 +52,26 @@ def cmd_generate(toml_filename: str, dry_run: bool):
 def cmd_check_fft(toml_filename: str):
     """Show [NGX, NGY, NGZ] in vasprun.xml."""
     check_fft(toml_filename, "ph_selfenergy")
+
+
+@cmd_ph_selfenergy.command("dump")
+@click.argument(
+    "vaspout_filename",
+    nargs=1,
+    type=click.Path(),
+    default="ph_selfenergy/vaspout.h5",
+)
+@click.argument(
+    "output_filename",
+    nargs=1,
+    type=click.Path(),
+    default="ph_selfenergy/ph_selfenergy.hdf5",
+)
+@click.help_option("-h", "--help")
+def cmd_dump(vaspout_filename: str, output_filename: str):
+    """Dump ph_selfenergy data to HDF5 file."""
+    with h5py.File(vaspout_filename, "r") as f:
+        list(f)
+
+
+from phelel.velph.cli.ph_selfenergy.plot.cmd_plot import cmd_plot  # noqa: E402, F401