Dependency update

.coveragerc

@@ -0,0 +1,9 @@
+[run]
+source = navigate
+omit =
+    */config.py
+    */config-*.py
+
+[report]
+exclude_lines =
+    pragma: no cover

.github/workflows/push_checks.yaml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.operating-system }}
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.13"]
         operating-system: [windows-latest]  # [ubuntu-latest, windows-latest]
     env:
       MPLBACKEND: Agg  # https://github.com/microsoft/azure-pipelines-tasks/issues/16426
@@ -26,10 +26,16 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e '.[dev]'
+          python -m pip install uv
+
+          # sync dependencies from uv.lock
+          uv sync
+          uv sync --group dev
+
+          python -m pip install -e . --no-deps
       - name: Test with pytest
         run: |
-          python3 -m pytest
+          uv run pytest
       - name: Codecov
         uses: codecov/codecov-action@v3.1.0
         with:

README.md

@@ -14,7 +14,21 @@ navigate
 **navigate** is an open source Python package for control of light-sheet microscopes.
 It allows for easily reconfigurable hardware setups and automated acquisition routines.
 
-### Quick install
+### Quick install with UV
+
+Download and install [UV](https://uv.readthedocs.io/en/latest/installation.html).
+
+```
+cd path/to/navigate
+uv sync
+
+# Install optional dependencies for development
+uv sync --group dev --group docs
+```
+
+To test, run 'uv run navigate -sh' to launch in synthetic hardware mode.
+
+### Quick install with Miniconda
 
 Download and install [Miniconda](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links).
 

pyproject.toml

@@ -15,38 +15,40 @@ classifiers = [
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: Microsoft :: Windows",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: Implementation :: CPython",
     "Programming Language :: Python :: Implementation :: PyPy",
 ]
 
 requires-python = ">=3.9.7"
 dependencies = [
-    'matplotlib-inline==0.1.3',
-    'PyYAML==6.0',
-    'pyserial==3.5',
-    'PIPython==2.6.0.1',
-    'nidaqmx==0.5.7',
-    'tifffile==2021.11.2',
-    'scipy==1.7.3',
-    'pyusb==1.2.1',
-    'pandas==1.3.5',
-    'pandastable==0.12.2.post1',
-    'opencv-python==4.5.5.62',
-    'numpy==1.22.0; sys_platform != "darwin"',
-    'numpy==1.21.6; sys_platform == "darwin"',
-    'scikit-image==0.19.1',
-    'zarr==2.14.2',
-    'fsspec==2022.8.2; sys_platform != "darwin"',
-    'fsspec==2022.5.0; sys_platform == "darwin"',
-    'h5py==3.7.0',
-    'requests==2.28.1',
+    'matplotlib-inline',
+    "pyyaml>=6.0.2",
+    'pyserial>=3.5',
+    'PIPython>=2.6.0.1',
+    'nidaqmx>=0.5.7',
+    "tifffile>=2024.2",
+    "scipy>=1.7.3",
+    "pandas>=2.1",
+    'pandastable>=0.12.2.post1',
+    "opencv-python>=4.10",
+    "numpy>=2.0",
+    "scikit-image>=0.22",
+    'zarr<3.0.1',
+    "fsspec>=2024.3.1",
+    "h5py>=3.11",
+    "requests>=2.31",
     'psutil==6.0.0',
     ]
 
 [project.scripts]
 navigate = "navigate.main:main"
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "pytest",
     "pytest-xvfb",
@@ -66,7 +68,6 @@ docs = [
     "sphinx-copybutton",
     "sphinx-issues",
     "sphinx-design",
-    "pyyaml",
     "pydata_sphinx_theme==0.10.0rc2",
     "sphinx-toolbox",
 ]

src/navigate/config/configuration_database.py

@@ -582,7 +582,7 @@
         "Input",
         "string",
         None,
-        "Example: D:\WaveKitX64\MirrorFiles\Beads.wcs",
+        r"Example: D:\WaveKitX64\MirrorFiles\Beads.wcs",
     ],
     "n_modes": ["Number of Modes", "Input", "int", None, "Example: 32", 32],
 }

src/navigate/controller/sub_controllers/camera_map.py

@@ -127,8 +127,8 @@ def create_camera_maps(self):
         save_path_offset = Path(save_dir).joinpath(save_name_offset)
         save_path_variance = Path(save_dir).joinpath(save_name_variance)
 
-        tifffile.imsave(save_path_offset, self.off)
-        tifffile.imsave(save_path_variance, self.var)
+        tifffile.imwrite(save_path_offset, self.off)
+        tifffile.imwrite(save_path_variance, self.var)
 
     def display_plot(self):
         """Display the offset and variance maps."""

src/navigate/controller/sub_controllers/keystrokes.py

@@ -127,7 +127,7 @@ def __init__(self, main_view: MainApp, parent_controller: Any) -> None:
         self.multi_table = main_view.settings.multiposition_tab.multipoint_list.pt
 
         #: MultiPositionTable: Multiposition Table
-        self.multi_table.rowheader.bind(
+        self.multi_table.row_header.bind(
             "<Double-Button-1>", self.multi_controller.handle_double_click
         )
 

src/navigate/controller/sub_controllers/multiposition.py

@@ -318,7 +318,9 @@ def move_to_position(self) -> None:
 
     def insert_row_func(self) -> None:
         """Insert a row in the Multi-Position Acquisition Interface."""
-        self.table.model.addRow(self.table.currentrow)
+        insert_at = max(self.table.currentrow, 0)
+        self.table.model.insertRow(insert_at)
+        self.table.currentrow = insert_at
         self.table.update_rowcolors()
         self.table.redraw()
         self.table.tableChanged()
@@ -356,8 +358,9 @@ def append_position(self, position: dict) -> None:
         self.table.model.df = self.table.model.df.reindex(columns=headers)
 
         # temp = list(map(lambda k: position[k], position))
-        self.table.model.df = self.table.model.df.append(
-            pd.DataFrame([temp], columns=headers), ignore_index=True
+        new_row = pd.DataFrame([temp], columns=headers)
+        self.table.model.df = pd.concat(
+            [self.table.model.df, new_row], ignore_index=True
         )
         self.table.currentrow = self.table.model.df.shape[0] - 1
         self.table.update_rowcolors()

src/navigate/model/data_sources/tiff_data_source.py

@@ -226,7 +226,7 @@ def write(self, data: npt.ArrayLike, **kw) -> None:
         data : npt.ArrayLike
             Data to write to file.
         kw : dict
-            Keyword arguments to pass to tifffile.imsave.
+            Keyword arguments to pass to tifffile.imwrite.
         """
         self.mode = "w"
 

src/navigate/model/devices/APIs/thorlabs/kcube_inertial.py

@@ -5,15 +5,14 @@
 Tested on Thorlabs KIM001.
 """
 
-
 import ctypes
 import ctypes.wintypes
 from enum import IntEnum
 
 CODING = "ascii"
 
 __dll = ctypes.WinDLL(
-    "C:\Program Files\Thorlabs\Kinesis\Thorlabs.MotionControl.KCube.InertialMotor.dll"
+    r"C:\Program Files\Thorlabs\Kinesis\Thorlabs.MotionControl.KCube.InertialMotor.dll"
 )
 
 

src/navigate/model/devices/APIs/thorlabs/kcube_steppermotor.py

@@ -13,6 +13,7 @@
 import ctypes
 import ctypes.wintypes
 from enum import IntEnum
+
 # from System import Decimal  # necessary for real world units
 
 """
@@ -29,7 +30,7 @@
 CODING = "ascii"
 
 __dll = ctypes.WinDLL(
-    "C:\Program Files\Thorlabs\Kinesis\Thorlabs.MotionControl.KCube.StepperMotor.dll"
+    r"C:\Program Files\Thorlabs\Kinesis\Thorlabs.MotionControl.KCube.StepperMotor.dll"
 )
 
 
@@ -418,6 +419,7 @@ def KST_StartPolling(serial_no, milliseconds):
 __dll.SCC_StopPolling.argtypes = [ctypes.c_char_p]
 __dll.SCC_StopPolling.restype = ctypes.c_short
 
+
 def KST_StopPolling(serial_no):
     """
     Stops the internal polling loop.
@@ -470,17 +472,16 @@ def KST_RequestPosition(serial_no):
 
 
 def KST_MoveToPosition(serial_no, position):
-    """Move to position
-    """
+    """Move to position"""
     return __dll.SCC_MoveToPosition(serial_no.encode(CODING), int(position))
-    
-    
+
+
 __dll.SCC_GetPosition.argtypes = [ctypes.c_char_p]
 __dll.SCC_GetPosition.restype = ctypes.c_int
 
 
 def KST_GetCurrentPosition(serial_no):
-    """Get the current position      
+    """Get the current position
 
     Parmeters
     ---------
@@ -492,18 +493,18 @@ def KST_GetCurrentPosition(serial_no):
     int
         Current position.
     """
-     # check if polling is active, if not RequestPosition
-    if __dll.SCC_PollingDuration(serial_no.encode(CODING))==0:
+    # check if polling is active, if not RequestPosition
+    if __dll.SCC_PollingDuration(serial_no.encode(CODING)) == 0:
         KST_RequestPosition(serial_no)
-    
+
     return __dll.SCC_GetPosition(serial_no.encode(CODING))
 
 
 __dll.SCC_MoveAbsolute.argtypes = [ctypes.c_char_p]
 __dll.SCC_MoveAbsolute.restype = ctypes.c_short
 __dll.SCC_MoveAbsolute.errcheck = errcheck
-                        
-                                                
+
+
 def KST_MoveAbsolute(serial_no):
     """
     Move absolute to set position.
@@ -520,7 +521,7 @@ def KST_MoveAbsolute(serial_no):
     int
         The error code or 0 if successful.
     """
-    
+
     return __dll.SCC_MoveAbsolute(serial_no.encode(CODING))
 
 
@@ -545,7 +546,7 @@ def KST_SetAbsolutePosition(serial_no, position):
     int
         The error code or 0 if successful.
     """
-    
+
     return __dll.SCC_SetMoveAbsolutePosition(serial_no.encode(CODING), int(position))
 
 
@@ -578,13 +579,16 @@ def KST_MoveJog(serial_no, jog_direction):
         The error code or 0 if successful.
     """
 
-    return __dll.SCC_MoveJog(serial_no.encode(CODING), MOT_TravelDirection(jog_direction))
+    return __dll.SCC_MoveJog(
+        serial_no.encode(CODING), MOT_TravelDirection(jog_direction)
+    )
 
 
 __dll.SCC_StopProfiled.argtypes = [ctypes.c_char_p]
 __dll.SCC_StopProfiled.restype = ctypes.c_short
 __dll.SCC_StopProfiled.errcheck = errcheck
 
+
 def KST_MoveStop(serial_no):
     """
     Halt motion
@@ -605,7 +609,7 @@ def KST_MoveStop(serial_no):
     # SCC_StopImmediate(char const * serialNo)
     # NOTE: for stopping using the current velocity params use:
     # return __dll.SCC_StopProfiled(serial_no.encode(CODING))
-    
+
     return __dll.SCC_StopProfiled(serial_no.encode(CODING))
 
 
@@ -615,15 +619,14 @@ def KST_MoveStop(serial_no):
 
 
 def KST_HomeDevice(serial_no):
-    """Home Device
-    """
+    """Home Device"""
     return __dll.SCC_Home(serial_no.encode(CODING))
 
+
 def KST_SetVelocityParams(serial_no, velocity):
-    """Set velocity profile required for move
-    """
+    """Set velocity profile required for move"""
     current_velocity = 0
     current_accel = 0
-    
+
     __dll.SCC_GetVelParams(serial_no.encode(CODING), current_velocity, current_accel)
-    __dll.SCC_SetVelParams(serial_no.encode(CODING), current_accel, velocity)
+    __dll.SCC_SetVelParams(serial_no.encode(CODING), current_accel, velocity)

src/navigate/model/features/image_writer.py

@@ -41,7 +41,7 @@
 
 # Third Party Imports
 import numpy as np
-from tifffile import imsave
+from tifffile import imwrite
 
 # Local imports
 import navigate
@@ -257,7 +257,7 @@ def save_image(self, frame_ids):
                             + str(t_idx).zfill(6)
                             + ".tif"
                         )
-                        imsave(
+                        imwrite(
                             os.path.join(self.mip_directory, mip_name),
                             self.mip[c_save_idx, :, :],
                         )

src/navigate/model/features/volume_search.py

@@ -459,7 +459,7 @@ def end_data_func(self):
             if self.debug:
                 import tifffile
 
-                tifffile.imsave(
+                tifffile.imwrite(
                     "volume_search_2d_debug_result.tif", self.volumes_selected
                 )
         return self.end_flag