Drop Python 3.9 support (#377)

* Drop Python 3.9

* Apply ruff safe fixes

* Apply ruff unsafe fixes

* Apply manual ruff fixes

* Update docs

* Drop upper Python limit

* Use strict for all zips

* Add missing future annotations

* Revert "Implement temporary fix for CI (#376)"

This reverts commit fe6e6d9.

* Drop Python 3.9 from Mac CI

* Apply new ruff fixes

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ['3.9','3.10','3.11','3.12']
+        python-version: ["3.10","3.11","3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -27,9 +27,7 @@ jobs:
         env:
           # show timings of tests
           PYTEST_ADDOPTS: "--durations=0"
-        run: |
-          unset CI
-          uv run pytest --run-extra-mlips --cov janus_core --cov-append .
+        run: uv run pytest --run-extra-mlips --cov janus_core --cov-append .
 
       - name: Report coverage to Coveralls
         uses: coverallsapp/github-action@v2

.github/workflows/mac.yml

@@ -10,7 +10,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ['3.9','3.10','3.11','3.12']
+        python-version: ["3.10","3.11","3.12"]
 
     steps:
       - uses: actions/checkout@v4

README.md

@@ -18,7 +18,7 @@ Tools for machine learnt interatomic potentials
 
 `janus-core` dependencies currently include:
 
-- Python >= 3.9
+- Python >= 3.10
 - ASE >= 3.23
 - mace-torch = 0.3.8
 - chgnet = 0.3.8 (optional)

docs/source/getting_started/getting_started.rst

@@ -7,7 +7,7 @@ Dependencies
 
 ``janus-core`` dependencies currently include:
 
-- Python >= 3.9
+- Python >= 3.10
 - ASE >= 3.23
 - mace-torch = 0.3.8
 - chgnet = 0.3.8 (optional)

janus_core/calculations/eos.py

@@ -322,7 +322,9 @@ def run(self) -> EoSResults:
         if self.write_results:
             with open(f"{self.file_prefix}-eos-raw.dat", "w", encoding="utf8") as out:
                 print("#Lattice Scalar | Energy [eV] | Volume [Å^3] ", file=out)
-                for eos_data in zip(self.lattice_scalars, self.energies, self.volumes):
+                for eos_data in zip(
+                    self.lattice_scalars, self.energies, self.volumes, strict=True
+                ):
                     print(*eos_data, file=out)
 
         eos = EquationOfState(self.volumes, self.energies, self.eos_type)

janus_core/calculations/geom_opt.py

@@ -2,7 +2,8 @@
 
 from __future__ import annotations
 
-from typing import Any, Callable
+from collections.abc import Callable
+from typing import Any
 import warnings
 
 from ase import Atoms, filters, units

janus_core/cli/descriptors.py

@@ -1,12 +1,9 @@
-# ruff: noqa: I002, FA100
 """Set up MLIP descriptors commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -49,7 +46,7 @@ def descriptors(
     device: Device = "cpu",
     model_path: ModelPath = None,
     out: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 "Path to save structure with calculated descriptors. Default is "

janus_core/cli/eos.py

@@ -1,12 +1,9 @@
-# ruff: noqa: I002, FA100
 """Set up eos commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Annotated, Optional, get_args
+from typing import Annotated, get_args
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -66,7 +63,7 @@ def eos(
     read_kwargs: ReadKwargsLast = None,
     calc_kwargs: CalcKwargs = None,
     file_prefix: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 """

janus_core/cli/geomopt.py

@@ -1,12 +1,9 @@
-# ruff: noqa: I002, FA100
 """Set up geomopt commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Annotated, Any, Optional
+from typing import Annotated, Any
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -30,7 +27,7 @@
 
 def _set_minimize_kwargs(
     minimize_kwargs: dict[str, Any],
-    traj: Optional[str],
+    traj: str | None,
     opt_cell_lengths: bool,
     pressure: float,
 ) -> None:
@@ -91,7 +88,7 @@ def geomopt(
     ctx: Context,
     struct: StructPath,
     optimizer: Annotated[
-        Optional[str],
+        str | None,
         Option(help="Name of ASE optimizer function to use."),
     ] = "LBFGS",
     fmax: Annotated[
@@ -112,7 +109,7 @@ def geomopt(
         ),
     ] = False,
     filter_func: Annotated[
-        Optional[str],
+        str | None,
         Option(
             help=(
                 "Name of ASE filter/constraint function to use. If using "
@@ -134,7 +131,7 @@ def geomopt(
         ),
     ] = 0.001,
     out: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 "Path to save optimized structure. Default is inferred from name "

janus_core/cli/janus.py

@@ -1,9 +1,6 @@
-# ruff: noqa: I002, FA100
 """Set up commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from typing import Annotated
 
@@ -39,7 +36,7 @@ def print_version(
     version: Annotated[
         bool, Option("--version", help="Print janus version and exit.")
     ] = None,
-) -> False:
+) -> None:
     """
     Print current janus-core version and exit.
 

janus_core/cli/md.py

@@ -1,12 +1,9 @@
-# ruff: noqa: I002, FA100
 """Set up md commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Annotated, Optional, get_args
+from typing import Annotated, get_args
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -101,7 +98,7 @@ def md(
         int, Option(help="Frequency to rescale velocities during equilibration.")
     ] = 10,
     file_prefix: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 """
@@ -116,7 +113,7 @@ def md(
         bool, Option(help="Whether to infer restart file if restarting dynamics.")
     ] = True,
     restart_stem: Annotated[
-        Optional[Path],
+        Path | None,
         Option(help="Stem for restart file name. Default inferred from `file_prefix`."),
     ] = None,
     restart_every: Annotated[
@@ -129,7 +126,7 @@ def md(
         int, Option(help="Restart files to keep if rotating.")
     ] = 4,
     final_file: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 """
@@ -140,7 +137,7 @@ def md(
         ),
     ] = None,
     stats_file: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 """
@@ -152,7 +149,7 @@ def md(
     ] = None,
     stats_every: Annotated[int, Option(help="Frequency to output statistics.")] = 100,
     traj_file: Annotated[
-        Optional[Path],
+        Path | None,
         Option(help="File to save trajectory. Default inferred from `file_prefix`."),
     ] = None,
     traj_append: Annotated[bool, Option(help="Whether to append trajectory.")] = False,
@@ -161,23 +158,23 @@ def md(
         int, Option(help="Frequency of steps to save trajectory.")
     ] = 100,
     temp_start: Annotated[
-        Optional[float],
+        float | None,
         Option(help="Temperature to start heating, in K."),
     ] = None,
     temp_end: Annotated[
-        Optional[float],
+        float | None,
         Option(help="Maximum temperature for heating, in K."),
     ] = None,
     temp_step: Annotated[
-        Optional[float], Option(help="Size of temperature steps when heating, in K.")
+        float | None, Option(help="Size of temperature steps when heating, in K.")
     ] = None,
     temp_time: Annotated[
-        Optional[float], Option(help="Time between heating steps, in fs.")
+        float | None, Option(help="Time between heating steps, in fs.")
     ] = None,
     write_kwargs: WriteKwargs = None,
     post_process_kwargs: PostProcessKwargs = None,
     seed: Annotated[
-        Optional[int],
+        int | None,
         Option(help="Random seed for numpy.random and random functions."),
     ] = None,
     log: LogPath = None,

janus_core/cli/phonons.py

@@ -1,12 +1,9 @@
-# ruff: noqa: I002, FA100
 """Set up phonons commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -67,7 +64,7 @@ def phonons(
         ),
     ] = 51,
     qpoint_file: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 "Path to yaml file with info to generate a path of q-points for band "
@@ -125,7 +122,7 @@ def phonons(
     read_kwargs: ReadKwargsLast = None,
     calc_kwargs: CalcKwargs = None,
     file_prefix: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 """

janus_core/cli/preprocess.py

@@ -1,9 +1,6 @@
-# noqa: I002, FA102
 """Set up MLIP preprocessing commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
 from typing import Annotated

janus_core/cli/singlepoint.py

@@ -1,12 +1,9 @@
-# ruff: noqa: I002, FA100
 """Set up singlepoint commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 from typer import Context, Option, Typer
 from typer_config import use_config
@@ -37,7 +34,7 @@ def singlepoint(
     device: Device = "cpu",
     model_path: ModelPath = None,
     properties: Annotated[
-        Optional[list[str]],
+        list[str] | None,
         Option(
             help=(
                 "Properties to calculate. If not specified, 'energy', 'forces' "
@@ -46,7 +43,7 @@ def singlepoint(
         ),
     ] = None,
     out: Annotated[
-        Optional[Path],
+        Path | None,
         Option(
             help=(
                 "Path to save structure with calculated results. Default is inferred "

janus_core/cli/train.py

@@ -1,9 +1,6 @@
-# noqa: I002, FA102
 """Set up MLIP training commandline interface."""
 
-# Issues with future annotations and typer
-# c.f. https://github.com/maxb2/typer-config/issues/295
-# from __future__ import annotations
+from __future__ import annotations
 
 from pathlib import Path
 from typing import Annotated