AllenCellModeling · toloudis · Apr 14, 2023 · Nov 16, 2022 · Nov 16, 2022 · Feb 15, 2023
diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml
@@ -17,11 +17,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', 3.11]
         os: [
-          ubuntu-20.04,
+          ubuntu-latest,
           windows-latest,
-          macos-11,
+          macos-latest,
         ]
     steps:
       - uses: actions/checkout@v2
@@ -55,7 +55,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', 3.11]
         os: [
           ubuntu-20.04,
           windows-latest,
@@ -110,7 +110,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.10'
+          python-version: 3.11
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
@@ -130,7 +130,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.10'
+          python-version: 3.11
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip

diff --git a/.github/workflows/test-and-lint.yml b/.github/workflows/test-and-lint.yml
@@ -13,11 +13,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', 3.11]
         os: [
-          ubuntu-20.04,
+          ubuntu-latest,
           windows-latest,
-          macos-11,
+          macos-latest,
         ]
     steps:
       - uses: actions/checkout@v2
@@ -51,7 +51,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', 3.11]
         os: [
           ubuntu-20.04,
           windows-latest,
@@ -105,7 +105,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.10'
+          python-version: 3.11
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
@@ -123,7 +123,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.10'
+          python-version: 3.11
       - name: Install Dependencies
         run: |
           pip install --upgrade pip

diff --git a/.github/workflows/test-upstreams.yml b/.github/workflows/test-upstreams.yml
@@ -20,11 +20,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', 3.11]
         os: [
-          ubuntu-20.04,
+          ubuntu-latest,
           windows-latest,
-          macos-11,
+          macos-latest,
         ]
     steps:
       - uses: actions/checkout@v2

diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in P
     -   `TIFF`
     -   `ND2` -- (`pip install aicsimageio[nd2]`)
     -   `DV` -- (`pip install aicsimageio[dv]`)
-    -   `CZI` -- (`pip install aicspylibczi>=3.0.5 fsspec>=2022.7.1`)
+    -   `CZI` -- (`pip install aicspylibczi>=3.1.1 fsspec>=2022.8.0`)
     -   `LIF` -- (`pip install readlif>=0.6.4`)
     -   `PNG`, `GIF`, [etc.](https://github.com/imageio/imageio) -- (`pip install aicsimageio[base-imageio]`)
     -   Files supported by [Bio-Formats](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html) -- (`pip install aicsimageio bioformats_jar`) (Note: requires `java` and `maven`, see below for details.)
@@ -55,7 +55,7 @@ optionally installed using `[...]` syntax.
 -   For multiple additional supported formats: `pip install aicsimageio[base-imageio,nd2]`
 -   For all additional supported (and openly licensed) formats: `pip install aicsimageio[all]`
 -   Due to the GPL license, LIF support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio readlif>=0.6.4`
--   Due to the GPL license, CZI support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio aicspylibczi>=3.0.5 fsspec>=2022.7.1`
+-   Due to the GPL license, CZI support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio aicspylibczi>=3.1.1 fsspec>=2022.8.0`
 -   Due to the GPL license, Bio-Formats support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio bioformats_jar`. **Important!!** Bio-Formats support also requires a `java` and `mvn` executable in the environment. The simplest method is to install `bioformats_jar` from conda: `conda install -c conda-forge bioformats_jar` (which will additionally bring `openjdk` and `maven` packages).
 
 ## Documentation
@@ -340,6 +340,7 @@ If you find `aicsimageio` useful, please cite this repository as:
 > Eva Maxfield Brown, Dan Toloudis, Jamie Sherman, Madison Swain-Bowden, Talley Lambert, AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio
 
 bibtex:
+
 ```bibtex
 @misc{aicsimageio,
   author    = {Brown, Eva Maxfield and Toloudis, Dan and Sherman, Jamie and Swain-Bowden, Madison and Lambert, Talley and {AICSImageIO Contributors}},

diff --git a/aicsimageio/formats.py b/aicsimageio/formats.py
@@ -481,7 +481,7 @@
     "aicsimageio.readers.bioformats_reader.BioformatsReader": "bioformats_jar",
     "aicsimageio.readers.default_reader.DefaultReader": "aicsimageio[base-imageio]",
     "aicsimageio.readers.lif_reader.LifReader": "readlif>=0.6.4",
-    "aicsimageio.readers.czi_reader.CziReader": "aicspylibczi>=3.0.5",
+    "aicsimageio.readers.czi_reader.CziReader": "aicspylibczi>=3.1.1",
     "aicsimageio.readers.dv_reader.DVReader": "aicsimageio[dv]",
     "aicsimageio.readers.nd2_reader.ND2Reader": "aicsimageio[nd2]",
 }
diff --git a/aicsimageio/readers/czi_reader.py b/aicsimageio/readers/czi_reader.py
@@ -28,7 +28,7 @@
 except ImportError:
     raise ImportError(
         "aicspylibczi is required for this reader. "
-        "Install with `pip install 'aicspylibczi>=3.0.5' 'fsspec>=2022.7.1'`"
+        "Install with `pip install 'aicspylibczi>=3.1.1' 'fsspec>=2022.7.1'`"
     )
 
 ###############################################################################
@@ -82,7 +82,7 @@ class CziReader(Reader):
 
     Notes
     -----
-    To use this reader, install with: `pip install aicspylibczi>=3.0.5`.
+    To use this reader, install with: `pip install aicspylibczi>=3.1.1`.
     """
 
     @staticmethod
@@ -369,7 +369,7 @@ def _get_image_data(
 
                 # If the dim was provided in the read dims
                 # we know a single plane for that dimension was requested so remove it
-                if dim in read_dims or dim is CZI_BLOCK_DIM_CHAR:
+                if dim in read_dims or dim == CZI_BLOCK_DIM_CHAR:
                     ops.append(0)
 
                 # Otherwise just read the full slice

diff --git a/setup.py b/setup.py
@@ -32,14 +32,14 @@ def run(self):
 format_libs: Dict[str, List[str]] = {
     "base-imageio": [
         "imageio[ffmpeg]>=2.11.0",
-        "Pillow>=8.2.0,!=8.3.0,<9",
+        "Pillow>=9.3",
     ],
     "nd2": ["nd2[legacy]>=0.2.0"],
     "dv": ["mrc>=0.2.0"],
     "bfio": ["bfio>=2.3.0", "tifffile<2022.4.22"],
     # "czi": [  # excluded for licensing reasons
-    #     "fsspec>=2022.7.1",
-    #     "aicspylibczi>=3.0.5",
+    #     "fsspec>=2022.8.0",
+    #     "aicspylibczi>=3.1.1",
     # ],
     # "bioformats": ["bioformats_jar"],  # excluded for licensing reasons
     # "lif": ["readlif>=0.6.4"],  # excluded for licensing reasons
@@ -55,7 +55,6 @@ def run(self):
 ]
 
 test_requirements = [
-    "codecov>=2.1.4",
     "dask[array,distributed]>=2021.4.1,!=2022.5.1",
     "docutils>=0.10,<0.16",
     "psutil>=5.7.0",
@@ -91,7 +90,7 @@ def run(self):
     "bioformats_jar",  # to test bioformats
     "bfio>=2.3.0",
     "readlif>=0.6.4",  # to test lif
-    "aicspylibczi>=3.0.5",  # to test czi
+    "aicspylibczi>=3.1.1",  # to test czi
 ]
 
 benchmark_requirements = [
@@ -138,6 +137,7 @@ def run(self):
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
     ],
     description=(
         "Image Reading, Metadata Conversion, and Image Writing for Microscopy Images "

diff --git a/tox.ini b/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py38, py39, py310, bioformats, czi, base-imageio, dv, lif, nd2, bfio, upstreams, lint
+envlist = py38, py39, py310, py311, bioformats, czi, base-imageio, dv, lif, nd2, bfio, upstreams, lint
 skip_missing_interpreters = true
 toxworkdir={env:TOX_WORK_DIR:.tox}
 
@@ -32,8 +32,8 @@ setenv =
 extras =
     test
 deps = 
-    aicspylibczi>=3.0.5
-    fsspec>=2022.7.1
+    aicspylibczi>=3.1.1
+    fsspec>=2022.8.0
 commands =
     pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_czi_reader.py {posargs}