Bump Python, iohub, and waveorder (#478)

* update iohub dependency

* bump waveorder

* update workflow and format yaml

* bump python

* bump tox env

* update workflow

* remove unused arguments

* prepare to unpin pydantic

---------

Co-authored-by: Aaron Alvarez <aaron.alvarez@czbiohub.org>

.github/workflows/pytests.yml

@@ -7,38 +7,37 @@ on: [push]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-    - name: Checkout repo
-      uses: actions/checkout@v2
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install ".[acq,dev]"
-
-#    - name: Lint with flake8
-#      run: |
-#        pip install flake8
-#        # stop the build if there are Python syntax errors or undefined names
-#        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-#        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-#        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    - name: Test with pytest
-      run: |
-        pytest -v
-        pytest --cov=./ --cov-report=xml
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[acq,dev]"
+
+      #    - name: Lint with flake8
+      #      run: |
+      #        pip install flake8
+      #        # stop the build if there are Python syntax errors or undefined names
+      #        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+      #        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+      #        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Test with pytest
+        run: |
+          pytest -v
+          pytest --cov=./ --cov-report=xml
 
 #    - name: Upload coverage to Codecov
 #      uses: codecov/codecov-action@v1

.github/workflows/test_and_deploy.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v3
@@ -85,4 +85,4 @@ jobs:
 #        run: |
 #          git tag
 #          python -m build .
-#          twine upload --repository testpypi dist/* # Commented until API key is on github
+#          twine upload --repository testpypi dist/* # Commented until API key is on github

recOrder/cli/apply_inverse_models.py

@@ -1,6 +1,7 @@
 """
 This module converts recOrder's reconstructions into waveorder calls
 """
+
 import numpy as np
 import torch
 from waveorder.models import (
@@ -99,8 +100,6 @@ def phase(
             real_potential_transfer_function,
             imaginary_potential_transfer_function,
             z_padding=settings_phase.transfer_function.z_padding,
-            z_pixel_size=settings_phase.transfer_function.z_pixel_size,
-            wavelength_illumination=settings_phase.transfer_function.wavelength_illumination,
             **settings_phase.apply_inverse.dict(),
         )
 
@@ -213,8 +212,6 @@ def birefringence_and_phase(
             real_potential_transfer_function,
             imaginary_potential_transfer_function,
             z_padding=settings_phase.transfer_function.z_padding,
-            z_pixel_size=settings_phase.transfer_function.z_pixel_size,
-            wavelength_illumination=settings_phase.transfer_function.wavelength_illumination,
             **settings_phase.apply_inverse.dict(),
         )
 

recOrder/cli/settings.py

@@ -1,7 +1,7 @@
 import os
 from typing import List, Literal, Optional, Union
 
-from pydantic import (
+from pydantic.v1 import (
     BaseModel,
     Extra,
     NonNegativeFloat,

recOrder/tests/cli_tests/test_settings.py

@@ -1,7 +1,7 @@
 import pytest
 from recOrder.cli import settings
 from recOrder.io import utils
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 
 def test_reconstruction_settings():

setup.cfg

@@ -11,9 +11,9 @@ classifiers =
 	License :: OSI Approved :: BSD License
 	Programming Language :: Python
 	Programming Language :: Python :: 3 :: Only
-	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
 	Topic :: Scientific/Engineering
 	Topic :: Scientific/Engineering :: Visualization
 	Topic :: Scientific/Engineering :: Information Analysis
@@ -33,17 +33,18 @@ project_urls =
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.9
+python_requires = >=3.10
 setup_requires = setuptools_scm
 install_requires =
-	waveorder==2.0.0rc3
+	waveorder==2.2.0rc0
 	click>=8.0.1
 	natsort>=7.1.1
 	colorspacious>=1.1.2
 	importlib-metadata
-	iohub==0.1.0.dev5
+	iohub==0.1.0
 	wget>=3.2
 	psutil
+	pydantic>=1.10.17
 
 [options.extras_require]
 dev =

tox.ini

@@ -1,14 +1,14 @@
 # Modified from from cookiecutter-napari-plugin
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{39,310,311}-{linux,macos,windows}
+envlist = py{310,311,312}-{linux,macos,windows}
 isolated_build=true
 
 [gh-actions]
 python =
-    3.9: py39
     3.10: py310
     3.11: py311
+    3.12: py312
 
 [gh-actions:env]
 PLATFORM =