Merge branch 'develop' into alert-autofix-6

Author: shaneahmed

.github/workflows/conda-env-create.yml

@@ -1,4 +1,4 @@
-# This workflow will build a conda environment to check that it resolves in a reasonable time
+# This workflow will build a conda environment to check that it resolves
 
 name: Solve Conda Environment
 
@@ -7,48 +7,70 @@ permissions:
 
 on:
   push:
-    paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
+    paths:
+      - "requirements/requirements*.txt"
+      - "requirements/generate_conda_env.py"
+      - ".github/workflows/conda-env-create.yml"
   pull_request:
-    paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
-  schedule: # Run on the 1st of every month at midnight
-    - cron: "0 0 1 * *"
+    paths:
+      - "requirements/requirements*.txt"
+      - "requirements/generate_conda_env.py"
+      - ".github/workflows/conda-env-create.yml"
 
 jobs:
   conda_solve:
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest]
-        kind: ["dev", "prod"]
-        include:
-          - os: ubuntu-latest
-            kind: prod
-            requirements: requirements/requirements.conda.yml
-          - os: ubuntu-latest
-            kind: dev
-            requirements: requirements/requirements.dev.conda.yml
-          - os: windows-latest
-            kind: prod
-            requirements: requirements/requirements.win64.conda.yml
-          - os: windows-latest
-            kind: dev
-            requirements: requirements/requirements.win64.dev.conda.yml
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 20
+    timeout-minutes: 30
+
     steps:
       - uses: actions/checkout@v4
-      - name: Copy requirements files
-        shell: bash
-        run: |
-          cp ./requirements/requirements*.txt /tmp/
-          mkdir /tmp/docs/
-          cp ./docs/requirements*.txt /tmp/docs/
+
+      # ✅ Generate environment
+      - name: Generate conda environment
+        env:
+          PYTHON_VERSION: ${{ matrix.python-version }}
+        run: python requirements/generate_conda_env.py
+
+      # ✅ Install via micromamba
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: tiatoolbox
-          environment-file: ${{ matrix.requirements }}
-      - shell: bash -l {0}
+          environment-file: requirements/requirements.conda.generated.yml
+
+      # ✅ Validate environment
+      - name: Test environment
+        shell: bash -l {0}
         run: |
-          micromamba info
           micromamba list
-          python -c "import torch, numpy; print(torch.__version__, numpy.__version__)"
+
+          python - <<EOF
+          import sys
+          print("Python:", sys.version)
+
+          import numpy, pandas
+          print("Core OK")
+
+          try:
+              import torch
+              print("Torch OK")
+          except Exception as e:
+              print("Torch issue:", e)
+
+          try:
+              import cv2
+              print("OpenCV OK")
+          except Exception as e:
+              print("OpenCV issue:", e)
+
+          try:
+              import openslide
+              print("OpenSlide OK")
+          except Exception as e:
+              print("OpenSlide issue:", e)
+          EOF

.github/workflows/docker-publish.yml

@@ -6,7 +6,7 @@ env:
   REGISTRY: ghcr.io
   IMAGE_NAME: TissueImageAnalytics/tiatoolbox
   image: ghcr.io/tissueimageanalytics/tiatoolbox
-  TOOLBOX_VER: 2.0.1
+  TOOLBOX_VER: 2.1.0
 
 jobs:
   build-and-push-image:

.github/workflows/mypy-type-check.yml

@@ -18,7 +18,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
 
@@ -47,7 +47,7 @@ jobs:
 
     - name: Perform type checking
       run: |
-        mypy --install-types --non-interactive --follow-imports=silent \
+        mypy --install-types --non-interactive --follow-imports=skip --ignore-missing-imports \
           tiatoolbox/__init__.py \
           tiatoolbox/__main__.py \
           tiatoolbox/type_hints.py \

.github/workflows/pip-install.yml

@@ -31,7 +31,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         os: [ubuntu-24.04, windows-latest, macos-latest]
 
     # Force UTF-8 everywhere (Windows is the one that really needs it)

.github/workflows/python-package.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4

AUTHORS.md

@@ -22,6 +22,7 @@
 - Abishekraj Vinayagar Gnanasambandam \<@AbishekRajVG>
 - Wenqi Lu \<@wenqi006>
 - Saad Bashir \<@rajasaad>
+- Aakash Madhav Rao \<@mraoaakash>
 - Behnaz Elhaminia \<@behnazelhaminia>
 
 ## Contributors

CITATION.cff

@@ -44,7 +44,7 @@ authors:
   given-names: "Shan E Ahmed"
   orcid: "https://orcid.org/0000-0002-1097-1738"
 title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
-version: 2.0.1  # TIAToolbox version
+version: 2.1.0  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"

HISTORY.md

@@ -1,5 +1,37 @@
 # History
 
+## TIAToolbox v2.1.0 (2026-05-19)
+
+### ✨ Major Updates and Feature Improvements
+
+- Python ≥3.11 required
+  - Supports up to 3.14 (#1035)
+  - Drops support for 3.10 (#1034)
+- Zarr v3 Support (#904)
+  - New storage APIs (zarr.Array, LocalStore, FsspecStore)
+  - Removal of object arrays → rectangular storage via pad_contours
+  - Update `FsspecJsonWSIReader` to support Zarr v3 (#1049), thanks to @aacic
+
+### ⚠️ API Changes
+
+- Python requirement updated → >=3.11, \<3.15
+
+### 🐞 Bug Fixes and Other Changes
+
+- Fixed
+  - Contour serialization and padding issues (Zarr compatibility) (#904)
+  - Invalid Geometry in JSON Outputs (#1057)
+- Fix typographical errors in `pre-trained` documentation (#1043, #1062)
+
+### 🛠️ Development-Related Changes
+
+- Use `uv` to set up CI environments, reduces installation time
+  - Update instructions for `uv` install
+- Use `max_image` for `remove_small_objects` in `scikit-image` usage (#1048)
+- Improve `mypy` workflow and typing errors (#1045)
+
+______________________________________________________________________
+
 ## TIAToolbox v2.0.1 (2026-03-16)
 
 ### Bug Fixes and Other Changes

docs/installation.rst

@@ -59,7 +59,7 @@ MacPorts
 Installing Stable Release
 =========================
 
-Please note that TIAToolbox is currently tested with Python versions 3.11, 3.12, and 3.13. For the full range of supported Python versions, please refer to the package metadata (for example, the ``python_requires`` setting in ``setup.py`` or ``pyproject.toml``)
+Please note that TIAToolbox is tested for Python versions 3.11, 3.12, 3.13 and 3.14. For the full range of supported Python versions, please refer to the package metadata (for example, the ``python_requires`` setting in ``setup.py`` or ``pyproject.toml``)
 
 Recommended
 -----------

docs/pretrained.rst

@@ -163,8 +163,8 @@ The input output configuration is as follows:
 
    .. code-block:: python
 
-        from tiatoolbox.models import IOSegmentorConfig
-        ioconfig = IOSegmentorConfig(
+        from tiatoolbox.models import IOInstanceSegmentorConfig
+        ioconfig = IOInstanceSegmentorConfig(
             input_resolutions=[
                 {'units': 'mpp', 'resolution': 0.25}
             ],
@@ -205,8 +205,8 @@ The input output configuration is as follows:
 
    .. code-block:: python
 
-        from tiatoolbox.models import IOSegmentorConfig
-        ioconfig = IOSegmentorConfig(
+        from tiatoolbox.models import IOInstanceSegmentorConfig
+        ioconfig = IOInstanceSegmentorConfig(
             input_resolutions=[
                 {'units': 'mpp', 'resolution': 0.25}
             ],
@@ -246,8 +246,8 @@ The input output configuration is as follows:
 
    .. code-block:: python
 
-        from tiatoolbox.models import IOSegmentorConfig
-        ioconfig = IOSegmentorConfig(
+        from tiatoolbox.models import IOInstanceSegmentorConfig
+        ioconfig = IOInstanceSegmentorConfig(
             input_resolutions=[
                 {'units': 'mpp', 'resolution': 0.25}
             ],
@@ -281,8 +281,8 @@ The input output configuration is as follows:
 
    .. code-block:: python
 
-        from tiatoolbox.models import IOSegmentorConfig
-        ioconfig = IOSegmentorConfig(
+        from tiatoolbox.models import IOInstanceSegmentorConfig
+        ioconfig = IOInstanceSegmentorConfig(
             input_resolutions=[
                 {'units': 'mpp', 'resolution': 0.25}
             ],
@@ -313,8 +313,8 @@ The input output configuration is as follows:
 
    .. code-block:: python
 
-        from tiatoolbox.models import IOSegmentorConfig
-        ioconfig = IOSegmentorConfig(
+        from tiatoolbox.models import IOInstanceSegmentorConfig
+        ioconfig = IOInstanceSegmentorConfig(
             input_resolutions=[
                 {'units': 'mpp', 'resolution': 0.25}
             ],