Update typer and Optional parameters (stfc#296)

janus_core/cli/descriptors.py

@@ -1,7 +1,7 @@
 """Set up MLIP descriptors commandline interface."""
 
 from pathlib import Path
-from typing import Annotated
+from typing import Annotated, Optional
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -53,7 +53,7 @@ def descriptors(
     device: Device = "cpu",
     model_path: ModelPath = None,
     out: Annotated[
-        Path,
+        Optional[Path],
         Option(
             help=(
                 "Path to save structure with calculated descriptors. Default is "
@@ -101,10 +101,10 @@ def descriptors(
         Keyword arguments to pass to ase.io.write when saving results. Default is {}.
     log : Optional[Path]
         Path to write logs to. Default is inferred from the name of the structure file.
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is inferred from the name of the structure file.
-    config : Path
+    config : Optional[Path]
         Path to yaml configuration file to define the above options. Default is None.
     """
     # Check options from configuration file are all valid

janus_core/cli/eos.py

@@ -129,10 +129,10 @@ def eos(
         chemical formula.
     log : Optional[Path]
         Path to write logs to. Default is inferred from the name of the structure file.
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is inferred from the name of the structure file.
-    config : Path
+    config : Optional[Path]
         Path to yaml configuration file to define the above options. Default is None.
     """
     # Check options from configuration file are all valid

janus_core/cli/geomopt.py

@@ -96,7 +96,7 @@ def geomopt(
     ctx: Context,
     struct: StructPath,
     optimizer: Annotated[
-        str,
+        Optional[str],
         Option(help="Name of ASE optimizer function to use."),
     ] = "LBFGS",
     fmax: Annotated[
@@ -117,7 +117,7 @@ def geomopt(
         ),
     ] = False,
     filter_func: Annotated[
-        str,
+        Optional[str],
         Option(
             help=(
                 "Name of ASE filter/constraint function to use. If using "
@@ -130,7 +130,7 @@ def geomopt(
         float, Option(help="Scalar pressure when optimizing cell geometry, in GPa.")
     ] = 0.0,
     out: Annotated[
-        Path,
+        Optional[Path],
         Option(
             help=(
                 "Path to save optimized structure. Default is inferred from name "
@@ -140,7 +140,7 @@ def geomopt(
     ] = None,
     traj: Annotated[
         str,
-        Option(help="Path if saving optimization frames.  [default: None]"),
+        Option(help="Path if saving optimization frames."),
     ] = None,
     read_kwargs: ReadKwargsLast = None,
     calc_kwargs: CalcKwargs = None,
@@ -202,10 +202,10 @@ def geomopt(
         Default is {}.
     log : Optional[Path]
         Path to write logs to. Default is inferred from the name of the structure file.
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is inferred from the name of the structure file.
-    config : Path
+    config : Optional[Path]
         Path to yaml configuration file to define the above options. Default is None.
     """
     # Check options from configuration file are all valid

janus_core/cli/md.py

@@ -129,7 +129,7 @@ def md(
         int, Option(help="Restart files to keep if rotating.")
     ] = 4,
     final_file: Annotated[
-        Path,
+        Optional[Path],
         Option(
             help=(
                 """
@@ -140,7 +140,7 @@ def md(
         ),
     ] = None,
     stats_file: Annotated[
-        Path,
+        Optional[Path],
         Option(
             help=(
                 """
@@ -152,7 +152,7 @@ def md(
     ] = None,
     stats_every: Annotated[int, Option(help="Frequency to output statistics.")] = 100,
     traj_file: Annotated[
-        Path,
+        Optional[Path],
         Option(help="File to save trajectory. Default inferred from `file_prefix`."),
     ] = None,
     traj_append: Annotated[bool, Option(help="Whether to append trajectory.")] = False,
@@ -162,17 +162,17 @@ def md(
     ] = 100,
     temp_start: Annotated[
         Optional[float],
-        Option(help="Temperature to start heating, in K.  [default: None]"),
+        Option(help="Temperature to start heating, in K."),
     ] = None,
     temp_end: Annotated[
         Optional[float],
-        Option(help="Maximum temperature for heating, in K.  [default: None]"),
+        Option(help="Maximum temperature for heating, in K."),
     ] = None,
     temp_step: Annotated[
-        float, Option(help="Size of temperature steps when heating, in K.")
+        Optional[float], Option(help="Size of temperature steps when heating, in K.")
     ] = None,
     temp_time: Annotated[
-        float, Option(help="Time between heating steps, in fs.")
+        Optional[float], Option(help="Time between heating steps, in fs.")
     ] = None,
     write_kwargs: WriteKwargs = None,
     post_process_kwargs: PostProcessKwargs = None,
@@ -292,10 +292,10 @@ def md(
         Default is None.
     log : Optional[Path]
         Path to write logs to. Default is inferred from the name of the structure file.
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is inferred from the name of the structure file.
-    config : Path
+    config : Optional[Path]
         Path to yaml configuration file to define the above options. Default is None.
     """
     # Check options from configuration file are all valid

janus_core/cli/phonons.py

@@ -188,10 +188,10 @@ def phonons(
         chemical formula.
     log : Optional[Path]
         Path to write logs to. Default is inferred from the name of the structure file.
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is inferred from the name of the structure file.
-    config : Path
+    config : Optional[Path]
         Path to yaml configuration file to define the above options. Default is None.
     """
     # Check options from configuration file are all valid

janus_core/cli/singlepoint.py

@@ -1,7 +1,7 @@
 """Set up singlepoint commandline interface."""
 
 from pathlib import Path
-from typing import Annotated
+from typing import Annotated, Optional
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -41,7 +41,7 @@ def singlepoint(
     device: Device = "cpu",
     model_path: ModelPath = None,
     properties: Annotated[
-        list[str],
+        Optional[list[str]],
         Option(
             help=(
                 "Properties to calculate. If not specified, 'energy', 'forces' "
@@ -50,7 +50,7 @@ def singlepoint(
         ),
     ] = None,
     out: Annotated[
-        Path,
+        Optional[Path],
         Option(
             help=(
                 "Path to save structure with calculated results. Default is inferred "
@@ -94,10 +94,10 @@ def singlepoint(
         Keyword arguments to pass to ase.io.write when saving results. Default is {}.
     log : Optional[Path]
         Path to write logs to. Default is inferred from the name of the structure file.
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is inferred from the name of the structure file.
-    config : Path
+    config : Optional[Path]
         Path to yaml configuration file to define the above options. Default is None.
     """
     # Check options from configuration file are all valid

janus_core/cli/train.py

@@ -41,7 +41,7 @@ def train(
         Whether to fine-tune a foundational model. Default is False.
     log : Optional[Path]
         Path to write logs to. Default is Path("train-log.yml").
-    summary : Path
+    summary : Optional[Path]
         Path to save summary of inputs, start/end time, and carbon emissions. Default
         is Path("train-summary.yml").
     """

janus_core/cli/types.py

@@ -2,7 +2,7 @@
 
 import ast
 from pathlib import Path
-from typing import Annotated, Union
+from typing import Annotated, Optional, Union
 
 from typer import Option
 
@@ -63,40 +63,44 @@ def __str__(self):
 
 StructPath = Annotated[Path, Option(help="Path of structure to simulate.")]
 
-Architecture = Annotated[str, Option(help="MLIP architecture to use for calculations.")]
-Device = Annotated[str, Option(help="Device to run calculations on.")]
-ModelPath = Annotated[str, Option(help="Path to MLIP model.  [default: None]")]
+Architecture = Annotated[
+    Optional[str], Option(help="MLIP architecture to use for calculations.")
+]
+Device = Annotated[Optional[str], Option(help="Device to run calculations on.")]
+ModelPath = Annotated[Optional[str], Option(help="Path to MLIP model.")]
 
 ReadKwargsAll = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
             """
             Keyword arguments to pass to ase.io.read. Must be passed as a dictionary
-            wrapped in quotes, e.g. "{'key' : value}".  [default: "{'index': ':'}"]
+            wrapped in quotes, e.g. "{'key' : value}". By default,
+            read_kwargs['index'] = ':', so all structures are read.
             """
         ),
         metavar="DICT",
     ),
 ]
 
 ReadKwargsLast = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
             """
             Keyword arguments to pass to ase.io.read. Must be passed as a dictionary
-            wrapped in quotes, e.g. "{'key' : value}".  [default: "{'index': -1}"]
+            wrapped in quotes, e.g. "{'key' : value}". By default,
+            read_kwargs['index'] = -1, so only the last structure is read.
             """
         ),
         metavar="DICT",
     ),
 ]
 
 CalcKwargs = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
@@ -111,36 +115,35 @@ def __str__(self):
 ]
 
 WriteKwargs = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
             """
             Keyword arguments to pass to ase.io.write when saving results. Must be
             passed as a dictionary wrapped in quotes, e.g. "{'key' : value}".
-             [default: "{}"]
             """
         ),
         metavar="DICT",
     ),
 ]
 
 OptKwargs = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
             """
             Keyword arguments to pass to optimizer. Must be passed as a dictionary
-            wrapped in quotes, e.g. "{'key' : value}".  [default: "{}"]
+            wrapped in quotes, e.g. "{'key' : value}".
             """
         ),
         metavar="DICT",
     ),
 ]
 
 MinimizeKwargs = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
@@ -154,7 +157,7 @@ def __str__(self):
 ]
 
 EnsembleKwargs = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
@@ -168,7 +171,7 @@ def __str__(self):
 ]
 
 PostProcessKwargs = Annotated[
-    TyperDict,
+    Optional[TyperDict],
     Option(
         parser=parse_dict_class,
         help=(
@@ -182,7 +185,7 @@ def __str__(self):
 ]
 
 LogPath = Annotated[
-    Path,
+    Optional[Path],
     Option(
         help=(
             "Path to save logs to. Default is inferred from the name of the structure "
@@ -192,7 +195,7 @@ def __str__(self):
 ]
 
 Summary = Annotated[
-    Path,
+    Optional[Path],
     Option(
         help=(
             "Path to save summary of inputs, start/end time, and carbon emissions. "

pyproject.toml

@@ -37,7 +37,7 @@ seekpath = "^1.9.7"
 spglib = "^2.3.0"
 torch = ">= 2.1, <= 2.2" # Range required for dgl
 torch-dftd = "0.4.0"
-typer = "^0.9.0"
+typer = "^0.12.5"
 typer-config = "^1.4.0"
 
 alignn = { version = "2024.5.27", optional = true }