Flexibilize type hints, drop Python 3.10, support 3.11 to 3.15

.github/workflows/pipeline.yml

@@ -10,13 +10,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14", "3.15"]
     steps:
     - uses: actions/checkout@v7
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
+        allow-prereleases: true
     - name: Install dependencies
       run: |
         pip install -e .

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v7
       with:
-        python-version: "3.11"
+        python-version: "3.14"
     - name: Install dependencies
       run: |
         pip install -e .

.gitignore

@@ -477,3 +477,4 @@ healthchecksdb
 .vscode
 *.gwl
 *Sandbox*.ipynb
+uv.lock

.pre-commit-config.yaml

@@ -2,24 +2,24 @@
 exclude: \.(ipynb|nblink)$
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v6.0.0
   hooks:
     - id: check-merge-conflict
     - id: check-toml
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 9.0.2
   hooks:
     - id: isort
       name: isort
 - repo: https://github.com/psf/black
-  rev: 22.3.0
+  rev: 26.5.1
   hooks:
     - id: black
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.3.0
+  rev: v2.4.0
   hooks:
   -   id: mypy
       exclude: 'test_.*?\.py$'

pyproject.toml

@@ -4,27 +4,27 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "robotools"
-version = "1.15.0"
+version = "1.16.0"
 description = "Pythonic in-silico liquid handling and creation of Tecan FreedomEVO worklists."
 readme = "README.md"
-requires-python = ">=3.10"
-license = {text = "GNU Affero General Public License v3"}
+requires-python = ">=3.11"
+license = "AGPL-3.0-or-later"
 authors = [
     {name = "Michael Osthege", email = "m.osthege@fz-juelich.de"},
 ]
 classifiers = [
     "Programming Language :: Python",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-    "License :: OSI Approved :: GNU Affero General Public License v3",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",
 ]
 dependencies = [
     "numpy",
-    "typing_extensions",
 ]
 
 [project.urls]

robotools/evotools/__init__.py

@@ -2,3 +2,12 @@
 from robotools.evotools.utils import get_well_position
 from robotools.evotools.worklist import EvoWorklist
 from robotools.worklists.exceptions import InvalidOperationError
+
+__all__ = (
+    "Labwares",
+    "Tip",
+    "int_to_tip",
+    "get_well_position",
+    "EvoWorklist",
+    "InvalidOperationError",
+)

robotools/evotools/commands.py

@@ -1,10 +1,13 @@
 """This module implements functions to create advanced worklist commands."""
-from typing import Iterable, List, Optional, Sequence, Tuple, Union
+
+from typing import Iterable, Sequence
 
 import numpy as np
+import numpy.typing as npt
 
 from robotools.evotools.types import Tip, int_to_tip
 from robotools.evotools.utils import to_hex
+from robotools.typing import Bools2D, Strings2D
 from robotools.worklists.exceptions import InvalidOperationError
 
 from .. import transform
@@ -21,7 +24,7 @@
 """"Maximum dilutor volume in µL"""
 
 
-def evo_make_selection_array(rows: int, columns: int, wells: Union[Iterable[str], np.ndarray]) -> np.ndarray:
+def evo_make_selection_array(rows: int, columns: int, wells: Iterable[str] | npt.NDArray[np.str_]) -> Bools2D:
     """Translate well IDs to a numpy array with 1s (selected) and 0s (not selected).
 
     Parameters
@@ -38,17 +41,10 @@ def evo_make_selection_array(rows: int, columns: int, wells: Union[Iterable[str]
     selection_array : np.ndarray
         Numpy array in labware dimensions with selected wells as 1 and others as 0
     """
-    # create array with a shape beffiting the labware dimensions
-    selection_array = np.zeros((rows, columns))
-    # get a dictionary with the "coordinates" of well IDs (A01, B01 etc) as tuples
-    well_index_dict = transform.make_well_index_dict(rows, columns)
-    # insert 1s for all selected wells
-    for well in np.asarray(wells).flatten():
-        selection_array[well_index_dict[well]] = 1
-    return selection_array
+    return np.isin(transform.make_well_array(rows, columns), wells)
 
 
-def evo_get_selection(rows: int, cols: int, selected: np.ndarray) -> str:
+def evo_get_selection(rows: int, cols: int, selected: Bools2D) -> str:
     """Function to generate the code string for the well selection of pipetting actions in EvoWare scripts (.esc).
 
     Adapted from the C++ function detailed in the EvoWare manual to Python by Martin Beyß (except the test at the end).
@@ -73,7 +69,7 @@ def evo_get_selection(rows: int, cols: int, selected: np.ndarray) -> str:
     bit_mask = 0
     for x in range(cols):
         for y in range(rows):
-            if selected[y, x] == 1:
+            if selected[y, x]:
                 bit_mask |= 1 << bit_counter
             bit_counter += 1
             if bit_counter > 6:
@@ -87,15 +83,15 @@ def evo_get_selection(rows: int, cols: int, selected: np.ndarray) -> str:
 
 
 def prepare_evo_aspirate_dispense_parameters(
-    wells: Union[str, Sequence[str], np.ndarray],
+    wells: str | Sequence[str] | Strings2D,
     *,
-    labware_position: Tuple[int, int],
-    volume: Union[float, Sequence[float], int],
+    labware_position: tuple[int, int],
+    volume: float | Sequence[float] | int,
     liquid_class: str,
-    tips: Union[Sequence[Tip], Sequence[int]],
+    tips: Sequence[Tip] | Sequence[int],
     arm: int,
-    max_volume: Optional[Union[int, float]] = None,
-) -> Tuple[List[str], Tuple[int, int], List[float], str, List[Tip]]:
+    max_volume: int | float | None = None,
+) -> tuple[list[str], tuple[int, int], list[float], str, list[Tip]]:
     # wells, labware_position, volume, liquid_class, tecan_tips
     """Validates and prepares aspirate/dispense parameters.
 
@@ -175,7 +171,7 @@ def prepare_evo_aspirate_dispense_parameters(
         raise ValueError(f"Invalid volume: {volume}")
 
     # apply rounding and corrections for the right string formatting
-    volume_list: List[float] = np.round(volume, decimals=2).tolist()
+    volume_list: list[float] = np.round(volume, decimals=2).tolist()
 
     if liquid_class is None:
         raise ValueError(f"Missing required parameter: liquid_class")
@@ -202,9 +198,9 @@ def prepare_evo_aspirate_dispense_parameters(
     return wells_list, labware_position, volume_list, liquid_class, tecan_tips
 
 
-def require_single_column_selection(selection: np.ndarray):
+def require_single_column_selection(selection: Bools2D):
     """Raises an error if wells from more than one column are selected."""
-    ncols = np.any(selection > 0, axis=0).sum()
+    ncols = np.any(selection, axis=0).sum()
     if ncols >= 2:
         raise ValueError(
             "Wells from more than one column are selected.\nSelect only wells from one column per pipetting action."
@@ -216,13 +212,13 @@ def evo_aspirate(
     *,
     n_rows: int,
     n_columns: int,
-    wells: Union[str, Sequence[str]],
-    labware_position: Tuple[int, int],
-    volume: Union[float, Sequence[float], int],
+    wells: str | Sequence[str],
+    labware_position: tuple[int, int],
+    volume: float | Sequence[float] | int,
     liquid_class: str,
-    tips: Union[Sequence[Tip], Sequence[int]],
+    tips: Sequence[Tip] | Sequence[int],
     arm: int = 0,
-    max_volume: Optional[Union[int, float]] = np.nan,
+    max_volume: int | float | None = np.nan,
 ) -> str:
     """Command for aspirating with the EvoWARE aspirate command WITHOUT digital volume tracking.
 
@@ -257,7 +253,13 @@ def evo_aspirate(
         max_volume = MAX_DILUTOR_VOLUME
 
     # perform consistency checks
-    (wells, labware_position, volume, liquid_class, tips,) = prepare_evo_aspirate_dispense_parameters(
+    (
+        wells,
+        labware_position,
+        volume,
+        liquid_class,
+        tips,
+    ) = prepare_evo_aspirate_dispense_parameters(
         wells=wells,
         labware_position=labware_position,
         volume=volume,
@@ -293,13 +295,13 @@ def evo_dispense(
     *,
     n_rows: int,
     n_columns: int,
-    wells: Union[str, Sequence[str]],
-    labware_position: Tuple[int, int],
-    volume: Union[float, Sequence[float], int],
+    wells: str | Sequence[str],
+    labware_position: tuple[int, int],
+    volume: float | Sequence[float] | int,
     liquid_class: str,
-    tips: Union[Sequence[Tip], Sequence[int]],
+    tips: Sequence[Tip] | Sequence[int],
     arm: int = 0,
-    max_volume: Optional[Union[int, float]] = np.nan,
+    max_volume: int | float | None = np.nan,
 ) -> str:
     """Command for dispensing using the EvoWARE dispense command WITHOUT digital volume tracking.
 
@@ -334,7 +336,13 @@ def evo_dispense(
         max_volume = MAX_DILUTOR_VOLUME
 
     # perform consistency checks
-    (wells, labware_position, volume, liquid_class, tips,) = prepare_evo_aspirate_dispense_parameters(
+    (
+        wells,
+        labware_position,
+        volume,
+        liquid_class,
+        tips,
+    ) = prepare_evo_aspirate_dispense_parameters(
         wells=wells,
         labware_position=labware_position,
         volume=volume,
@@ -368,9 +376,9 @@ def evo_dispense(
 
 def prepare_evo_wash_parameters(
     *,
-    tips: Union[List[Tip], List[int]],
-    waste_location: Tuple[int, int],
-    cleaner_location: Tuple[int, int],
+    tips: Sequence[Tip] | Sequence[int],
+    waste_location: tuple[int, int],
+    cleaner_location: tuple[int, int],
     arm: int = 0,
     waste_vol: float = 3.0,
     waste_delay: int = 500,
@@ -381,7 +389,7 @@ def prepare_evo_wash_parameters(
     retract_speed: int = 30,
     fastwash: int = 1,
     low_volume: int = 0,
-) -> Tuple[List[Tip], Tuple[int, int], Tuple[int, int], int, float, int, float, int, int, int, int, int, int]:
+) -> tuple[list[Tip], tuple[int, int], tuple[int, int], int, float, int, float, int, int, int, int, int, int]:
     """Validates and prepares aspirate/dispense parameters.
 
     Parameters
@@ -445,7 +453,7 @@ def prepare_evo_wash_parameters(
     if tips is None:
         raise ValueError("Missing required parameter: tips")
 
-    tecan_tips: List[Tip] = []
+    tecan_tips: list[Tip] = []
     for tip in tips:
         if isinstance(tip, int) and not isinstance(tip, Tip):
             # User-specified integers from 1-8 need to be converted to Tecan logic
@@ -547,9 +555,9 @@ def prepare_evo_wash_parameters(
 
 def evo_wash(
     *,
-    tips: Union[List[Tip], List[int]],
-    waste_location: Tuple[int, int],
-    cleaner_location: Tuple[int, int],
+    tips: Sequence[Tip] | Sequence[int],
+    waste_location: tuple[int, int],
+    cleaner_location: tuple[int, int],
     arm: int = 0,
     waste_vol: float = 3.0,
     waste_delay: int = 500,
@@ -561,7 +569,9 @@ def evo_wash(
     fastwash: int = 1,
     low_volume: int = 0,
 ) -> str:
-    """Command for aspirating with the EvoWARE aspirate command. As many wells in one column may be selected as your liquid handling arm has pipettes.
+    """Command for aspirating with the EvoWARE aspirate command.
+
+    As many wells in one column may be selected as your liquid handling arm has pipettes.
     This method generates the full command (as can be observed when opening a .esc file with an editor) and calls upon other functions to create the code string
     specifying the target wells.
 

robotools/evotools/types.py

@@ -1,4 +1,5 @@
 """Enums and classes, and related helper functions."""
+
 import enum
 
 __all__ = (

robotools/evotools/utils.py

@@ -1,11 +1,13 @@
 """Generic utility functions."""
+
 import re
 
 from robotools.liquidhandling import Labware
 
 
 def to_hex(dec: int):
     """Method from stackoverflow to convert decimal to hex.
+
     Link: https://stackoverflow.com/questions/5796238/python-convert-decimal-to-hex
     Solution posted by user "Chunghee Kim" on 21.11.2020.
     """