Depend on backwards-compatible focus finder (#223)

* depend on backwards compatible focus finder

* bump 3.10 to 3.11

* Fix tests

* upgrade to 3.11-compatible black

* black formatting

* roll back "black==22.3.0"

* set "black==26.1.0"

---------

Co-authored-by: Ivan Ivanov <[email protected]>

Author: talonchandler

.github/workflows/pull-request-ci.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
     - name: Checkout repo
@@ -26,7 +26,7 @@ jobs:
       run: pip install -e ".[dev]"
 
     - name: Check code style with Black
-      run: black --check -t py310 .
+      run: black --check -t py311 .
 
     - name: Check code with Flake8
       run: flake8 .
@@ -38,7 +38,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
     - name: Checkout repo

Makefile

@@ -10,12 +10,12 @@ uninstall:
 
 .PHONY: check-format
 check-format:
-	black --check -S -t py310 .
+	black --check -S -t py311 .
 	isort --check .
 
 .PHONY: format
 format:
-	black -S -t py310 .
+	black -S -t py311 .
 	isort .
 
 .PHONY: lint

README.md

@@ -11,10 +11,10 @@ This version of the code still uses the legacy name `mantis`, which overlaps wit
 
 ## Installation
 
-We recommend using a virtual conda environment with Python 3.10:
+We recommend using a virtual conda environment with Python 3.11:
 
 ```sh
-conda create -y --name mantis python=3.10
+conda create -y --name mantis python=3.11
 conda activate mantis
 
 git clone https://github.com/czbiohub-sf/shrimPy.git
@@ -24,7 +24,7 @@ pip install ./mantis
 Optionally, you can also install the [biahub](https://github.com/czbiohub-sf/biahub) image analysis library in the same environment. `biahub` is currently used when characterizing the microscope point spread function, and will be used for real-time image processing in the future. You can install both libraries in a single step with:
 
 ```sh
-conda create -y --name mantis python=3.10
+conda create -y --name mantis python=3.11
 conda activate mantis
 
 git clone https://github.com/czbiohub-sf/shrimPy.git

mantis/acquisition/AcquisitionSettings.py

@@ -57,12 +57,12 @@ def __post_init__(self):
 
 @dataclass(config=config)
 class ChannelSettings:
-    default_exposure_times_ms: Union[
-        NonNegativeFloat, List[NonNegativeFloat], None
-    ] = None  # in ms
-    default_laser_powers: Union[
-        NonNegativeFloat, List[NonNegativeFloat], List[None], None
-    ] = None
+    default_exposure_times_ms: Union[NonNegativeFloat, List[NonNegativeFloat], None] = (
+        None  # in ms
+    )
+    default_laser_powers: Union[NonNegativeFloat, List[NonNegativeFloat], List[None], None] = (
+        None
+    )
     channel_group: Optional[str] = None
     channels: List[str] = field(default_factory=list)
     use_sequencing: bool = False

mantis/acquisition/acq_engine.py

@@ -722,19 +722,19 @@ def setup_autoexposure(self):
                 )
                 if ts2_ttl_state == 32:
                     # State 32 corresponds to illumination with 488 laser
-                    self.ls_acq.channel_settings.light_sources[
-                        channel_idx
-                    ] = microscope_operations.setup_vortran_laser(VORTRAN_488_COM_PORT)
+                    self.ls_acq.channel_settings.light_sources[channel_idx] = (
+                        microscope_operations.setup_vortran_laser(VORTRAN_488_COM_PORT)
+                    )
                 elif ts2_ttl_state == 64:
                     # State 64 corresponds to illumination with 561 laser
-                    self.ls_acq.channel_settings.light_sources[
-                        channel_idx
-                    ] = microscope_operations.setup_vortran_laser(VORTRAN_561_COM_PORT)
+                    self.ls_acq.channel_settings.light_sources[channel_idx] = (
+                        microscope_operations.setup_vortran_laser(VORTRAN_561_COM_PORT)
+                    )
                 elif ts2_ttl_state == 128:
                     # State 128 corresponds to illumination with 639 laser
-                    self.ls_acq.channel_settings.light_sources[
-                        channel_idx
-                    ] = microscope_operations.setup_vortran_laser(VORTRAN_639_COM_PORT)
+                    self.ls_acq.channel_settings.light_sources[channel_idx] = (
+                        microscope_operations.setup_vortran_laser(VORTRAN_639_COM_PORT)
+                    )
                 else:
                     logger.error(
                         'Unknown TTL state {} for channel {} in config group {}'.format(
@@ -1050,6 +1050,7 @@ def refocus_ls_path(
                 pixel_size=LS_PIXEL_SIZE,
                 threshold_FWHM=threshold_FWHM,
                 plot_path=self._logs_dir / f'ls_refocus_plot_{timestamp}_Pos{stack_idx}.png',
+                return_statistics=True,
             )
             focus_indices.append(idx)
             peak_indices.append(stats['peak_index'])
@@ -1350,11 +1351,11 @@ def acquire(self):
                         channel_index = self.ls_acq.channel_settings.channels.index(
                             _event['axes']['channel']
                         )
-                        _event[
-                            'exposure'
-                        ] = self.ls_acq.channel_settings.exposure_times_per_well[well_id][
-                            channel_index
-                        ]
+                        _event['exposure'] = (
+                            self.ls_acq.channel_settings.exposure_times_per_well[well_id][
+                                channel_index
+                            ]
+                        )
 
                 globals.lf_last_img_idx = lf_events[-1]['axes']
                 globals.ls_last_img_idx = ls_events[-1]['axes']

mantis/acquisition/microscope_operations.py

@@ -374,7 +374,8 @@ def acquire_defocus_stack(
     else:
         raise RuntimeError(f'Unknown z stage: {z_stage}')
 
-    move_z(z_range[0]); time.sleep(0.3)
+    move_z(z_range[0])
+    time.sleep(0.3)
     for z_ind, rel_z in enumerate(z_range):
         # set z position
         move_z(rel_z)

mantis/tests/test_cli.py

@@ -5,7 +5,7 @@
 
 def test_main():
     runner = CliRunner()
-    result = runner.invoke(cli)
+    result = runner.invoke(cli, ['--help'])
 
     assert result.exit_code == 0
     assert "tools for mantis" in result.output

pyproject.toml

@@ -6,7 +6,7 @@ name = "mantis"
 description = "Acquisition engine for collecting data on the mantis microscope"
 readme = "README.md"
 license = { file = "LICENSE" }
-requires-python = ">=3.10, <4.0"
+requires-python = ">=3.11, <4.0"
 
 # the dynamically determined project metadata attributes
 dynamic = ["version"]
@@ -15,7 +15,7 @@ classifiers = [
   "Development Status :: 3 - Alpha",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
 ]
 
 # list package dependencies here
@@ -28,14 +28,14 @@ dependencies = [
   "pydantic>=2.0.0",
   "pylablib==1.4.1",
   "tifffile",
-  "waveorder @ git+https://github.com/mehta-lab/waveorder@return_peak_stats",
+  "waveorder @ git+https://github.com/mehta-lab/waveorder@focus-statistics-api",
 ]
 
 
 [project.optional-dependencies]
 # note that dev dependencies are only pinned to major versions
 dev = [
-  "black==22.3.0",
+  "black==26.1.0",
   "flake8~=5.0",
   "isort~=5.12",
   "pre-commit~=2.19",
@@ -60,7 +60,7 @@ version = { attr = "mantis.__version__" }
 
 [tool.black]
 line-length = 95
-target-version = ['py310']
+target-version = ['py311']
 include = '\.pyi?$'
 skip-string-normalization = true
 exclude = '''