Replace most of velph subcommand arguments by options

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

@@ -26,9 +26,9 @@ def cmd_el_bands():
 # velph el_bands generate
 #
 @cmd_el_bands.command("generate")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )
@@ -75,9 +75,9 @@ def cmd_plot(window: tuple[float, float], save_plot: bool):
 
 
 @cmd_el_bands.command("plot_eigenvalues")
-@click.argument(
+@click.option(
+    "--vaspout-filename",
     "vaspout_filename",
-    nargs=1,
     type=click.Path(),
     default="el_bands/dos/vaspout.h5",
 )

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

@@ -19,15 +19,14 @@
 @click.option(
     "-f",
     "toml_filename",
-    nargs=1,
     type=click.Path(exists=True),
     default="velph.toml",
     show_default=True,
     help="Specify velph.toml",
 )
 @click.option(
     "--prefix",
-    nargs=1,
+    "prefix",
     type=click.Path(),
     default="POSCAR",
     show_default=True,

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

@@ -25,11 +25,19 @@
 # velph init
 #
 @cmd_root.command("init")
-@click.argument("cell_filename", nargs=1, type=click.Path())
-@click.argument("project_folder", nargs=1, type=click.Path())
+@click.argument(
+    "cell_filename",
+    nargs=1,
+    type=click.Path(),
+)
+@click.argument(
+    "project_folder",
+    nargs=1,
+    type=click.Path(),
+)
 @click.option(
     "--amplitude",
-    nargs=1,
+    "amplitude",
     type=float,
     default=None,
     help=(
@@ -92,7 +100,6 @@
 @click.option(
     "--kspacing",
     "kspacing",
-    nargs=1,
     type=float,
     default=None,
     help=(
@@ -103,7 +110,6 @@
 @click.option(
     "--kspacing-dense",
     "kspacing_dense",
-    nargs=1,
     type=float,
     default=None,
     help=(
@@ -124,7 +130,6 @@
 @click.option(
     "--max-num-atoms",
     "max_num_atoms",
-    nargs=1,
     default=None,
     type=int,
     help=(
@@ -200,7 +205,6 @@
 @click.option(
     "--template-toml",
     "template_toml_filename",
-    nargs=1,
     type=click.Path(),
     default=None,
     help=(
@@ -211,7 +215,6 @@
 @click.option(
     "--tolerance",
     "tolerance",
-    nargs=1,
     type=float,
     default=None,
     help=(
@@ -222,7 +225,6 @@
 @click.option(
     "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default=None,
     help="File name of velph.toml type file to be created.",

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

@@ -18,9 +18,9 @@ def cmd_nac():
 
 
 @cmd_nac.command("generate")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )

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

@@ -24,9 +24,9 @@ def cmd_ph_bands():
 # velph ph_bands generate
 #
 @cmd_ph_bands.command("generate")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )

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

@@ -18,9 +18,9 @@ def cmd_ph_selfenergy():
 
 
 @cmd_ph_selfenergy.command("generate")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )
@@ -42,9 +42,9 @@ def cmd_generate(toml_filename: str, dry_run: bool):
 
 
 @cmd_ph_selfenergy.command("check-fft")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )
@@ -55,17 +55,21 @@ def cmd_check_fft(toml_filename: str):
 
 
 @cmd_ph_selfenergy.command("dump_phono3py")
-@click.argument(
+@click.option(
+    "--vaspout-filename",
     "vaspout_filename",
-    nargs=1,
     type=click.Path(),
     default="ph_selfenergy/vaspout.h5",
 )
-@click.argument(
+@click.option(
+    "--output-filename",
     "output_filename",
-    nargs=1,
     type=click.Path(),
-    default="ph_selfenergy/phono3py_elph.hdf5",
+    default="ph_selfenergy/gamma-elph{mesh}.hdf5",
+    help=(
+        'Output filename. Default is "ph_selfenergy/gamma_elph{mesh}.hdf5". '
+        '{mesh} will be replaced by the mesh size, e.g. "-m202020".'
+    ),
 )
 @click.help_option("-h", "--help")
 def cmd_dump_phono3py(vaspout_filename: str, output_filename: str):

src/phelel/velph/cli/ph_selfenergy/dump_phono3py.py

@@ -24,7 +24,10 @@ def dump_phono3py(vaspout_filename: str, output_filename: str):
         freqs_calcs, gammas_calcs, temps_calcs, indices = (
             read_freqs_and_ph_gammas_from_vaspout_h5(f)
         )
-        with h5py.File(output_filename, "w") as f_out:
+        _output_filename = output_filename.format(
+            mesh="-m" + "".join(map(str, bz_grid.D_diag))
+        )
+        with h5py.File(_output_filename, "w") as f_out:
             f_out.create_dataset("qpoint", data=ir_kpoints)
             f_out.create_dataset("weight", data=weights)
             f_out.create_dataset("mesh", data=bz_grid.D_diag)
@@ -38,8 +41,9 @@ def dump_phono3py(vaspout_filename: str, output_filename: str):
                 f_out.create_dataset(f"frequency_{i}", data=_freqs)
                 f_out.create_dataset(f"gamma_{i}", data=_gammas)
                 f_out.create_dataset(f"temperature_{i}", data=temps)
+                click.echo(f"calc-{i} temperatures: {temps}")
 
-            click.echo(f'Dumped ph_selfenergy data to "{output_filename}".')
+            click.echo(f'Dumped ph_selfenergy data to "{_output_filename}".')
 
 
 def _collect_data_from_vaspout(

src/phelel/velph/cli/ph_selfenergy/plot/cmd_plot.py

@@ -24,9 +24,9 @@ def cmd_plot():
 
 
 @cmd_plot.command("selfenergy")
-@click.argument(
+@click.option(
+    "--vaspout-filename",
     "vaspout_filename",
-    nargs=1,
     type=click.Path(),
     default="ph_selfenergy/vaspout.h5",
 )
@@ -35,7 +35,7 @@ def cmd_plot():
     "save_plot",
     is_flag=bool,
     default=False,
-    help=("Save plot to file."),
+    help="Save plot to file.",
 )
 @click.help_option("-h", "--help")
 def cmd_plot_selfenergy(vaspout_filename: str, save_plot: bool):
@@ -49,15 +49,14 @@ def cmd_plot_selfenergy(vaspout_filename: str, save_plot: bool):
 
 
 @cmd_plot.command("eigenvalues")
-@click.argument(
+@click.option(
+    "--vaspout-filename",
     "vaspout_filename",
-    nargs=1,
     type=click.Path(),
     default="ph_selfenergy/vaspout.h5",
 )
 @click.option(
     "--tid",
-    nargs=1,
     type=int,
     default=None,
     help=(
@@ -67,7 +66,6 @@ def cmd_plot_selfenergy(vaspout_filename: str, save_plot: bool):
 )
 @click.option(
     "--calcid",
-    nargs=1,
     type=int,
     default=None,
     help=(

src/phelel/velph/cli/phelel/cmd_phelel.py

@@ -28,16 +28,11 @@ def cmd_phelel():
 # velph phelel init
 #
 @cmd_phelel.command("init")
-@click.argument("toml_filename", nargs=1, type=click.Path(), default="velph.toml")
 @click.option(
-    "--dir-name",
-    "dir_name",
-    type=str,
-    default="phelel",
-    help=(
-        'Used for backward compatibility, for which set "supercell". '
-        '(dir_name: str, default="phelel")'
-    ),
+    "--toml-filename",
+    "toml_filename",
+    type=click.Path(),
+    default="velph.toml",
 )
 @click.help_option("-h", "--help")
 def cmd_init(toml_filename: str, dir_name: str):
@@ -64,16 +59,11 @@ def cmd_init(toml_filename: str, dir_name: str):
 # velph phelel generate
 #
 @cmd_phelel.command("generate")
-@click.argument("toml_filename", nargs=1, type=click.Path(), default="velph.toml")
 @click.option(
-    "--dir-name",
-    "dir_name",
-    type=str,
-    default="phelel",
-    help=(
-        'Used for backward compatibility, for which set "supercell". '
-        '(phelel_dirname: str, default="phelel")'
-    ),
+    "--toml-filename",
+    "toml_filename",
+    type=click.Path(),
+    default="velph.toml",
 )
 @click.help_option("-h", "--help")
 def cmd_generate(toml_filename: str, dir_name: str):
@@ -91,20 +81,14 @@ def cmd_generate(toml_filename: str, dir_name: str):
 # velph supercell differentiate
 #
 @cmd_phelel.command("differentiate")
-@click.argument("toml_filename", nargs=1, type=click.Path(), default="velph.toml")
 @click.option(
-    "--dir-name",
-    "dir_name",
-    type=str,
-    default="phelel",
-    help=(
-        'Used for backward compatibility, for which set "supercell". '
-        '(phelel_dirname: str, default="phelel")'
-    ),
+    "--toml-filename",
+    "toml_filename",
+    type=click.Path(),
+    default="velph.toml",
 )
 @click.option(
     "--encut",
-    nargs=1,
     type=float,
     default=None,
     help=(
@@ -182,16 +166,11 @@ def cmd_differentiate(
 # velph phelel phonopy
 #
 @cmd_phelel.command("phonopy")
-@click.argument("toml_filename", nargs=1, type=click.Path(), default="velph.toml")
 @click.option(
-    "--dir-name",
-    "dir_name",
-    type=str,
-    default="phelel",
-    help=(
-        'Used for backward compatibility, for which set "supercell". '
-        '(phelel_dirname: str, default="phelel")'
-    ),
+    "--toml-filename",
+    "toml_filename",
+    type=click.Path(),
+    default="velph.toml",
 )
 @click.help_option("-h", "--help")
 def cmd_phonopy(toml_filename: str, dir_name: str):

src/phelel/velph/cli/phono3py/cmd_phono3py.py

@@ -24,16 +24,15 @@ def cmd_phono3py():
 # velph phono3py init
 #
 @cmd_phono3py.command("init")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )
 @click.option(
     "--rd",
     "random_displacements",
-    nargs=1,
     default=None,
     type=int,
     help="Number of snapshots of supercells with random directional displacement.",
@@ -68,9 +67,9 @@ def cmd_init(
 # velph phono3py generate
 #
 @cmd_phono3py.command("generate")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )

src/phelel/velph/cli/phonopy/cmd_phonopy.py

@@ -23,9 +23,9 @@ def cmd_phonopy():
 # velph phonopy init
 #
 @cmd_phonopy.command("init")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )
@@ -53,9 +53,9 @@ def cmd_init(toml_filename: str):
 # velph phonopy generate
 #
 @cmd_phonopy.command("generate")
-@click.argument(
+@click.option(
+    "--toml-filename",
     "toml_filename",
-    nargs=1,
     type=click.Path(),
     default="velph.toml",
 )