⬆️ Upgrade Supported Python Versions (#958)

- Drops `Python 3.9` support and adds `Python 3.13` support
- Updates NumPy from `<2.0.0` to `>=2.0.0`
- Modernizes code for new Python versions with `strict` parameters and type hint improvements
- Adds tests for type hints

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jiaqi Lv <[email protected]>

Author: 3 people

.github/workflows/docker-publish.yml

@@ -15,10 +15,6 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - dockerfile: ./docker/3.9/Debian/Dockerfile
-            mtag: py3.9-debian
-          - dockerfile: ./docker/3.9/Ubuntu/Dockerfile
-            mtag: py3.9-ubuntu
           - dockerfile: ./docker/3.10/Debian/Dockerfile
             mtag: py3.10-debian
           - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
@@ -31,7 +27,11 @@ jobs:
             mtag: py3.12-debian
           - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
             mtag: py3.12-ubuntu
-          - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
+          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
+            mtag: py3.13-debian
+          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
+            mtag: py3.13-ubuntu
+          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
             mtag: latest
     permissions:
       contents: read

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

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
 

.github/workflows/pip-install.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         os: [ubuntu-24.04, windows-latest, macos-latest]
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v3

CONTRIBUTING.rst

@@ -98,7 +98,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the pull request description.
-3. The pull request should work for Python 3.9, 3.10, 3.11, and 3.12, and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.10, 3.11, 3.12 and 3.13, and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----

README.md

@@ -106,7 +106,7 @@ Prepare a computer as a convenient platform for further development of the Pytho
 5. Create virtual environment for TIAToolbox using
 
 ```sh
-    $ conda create -n tiatoolbox-dev python=3.9 # select version of your choice
+    $ conda create -n tiatoolbox-dev python=3.10 # select version of your choice
     $ conda activate tiatoolbox-dev
     $ pip install -r requirements/requirements_dev.txt
 ```

benchmarks/annotation_store.ipynb

@@ -355,7 +355,7 @@
     "        capsize=capsize,\n",
     "        **kwargs,\n",
     "    )\n",
-    "    for i, (runs, c) in enumerate(zip(experiments, color)):\n",
+    "    for i, (runs, c) in enumerate(zip(experiments, color, strict=False)):\n",
     "        plt.text(\n",
     "            i,\n",
     "            min(runs),\n",
@@ -2418,7 +2418,7 @@
     "    )\n",
     "    total = np.sum(counts)\n",
     "    frequencies = dict.fromkeys(range(256), 0)\n",
-    "    for v, x in zip(values, counts):\n",
+    "    for v, x in zip(values, counts, strict=False):\n",
     "        frequencies[v] = x / total\n",
     "    frequency_array = np.array(list(frequencies.values()))\n",
     "    epsilon = 1e-16\n",

docs/installation.rst

@@ -55,7 +55,7 @@ MacPorts
 Installing Stable Release
 =========================
 
-Please note that TIAToolbox is tested for Python versions 3.9, 3.10, 3.11, and 3.12.
+Please note that TIAToolbox is tested for Python versions 3.10, 3.11, 3.12 and 3.13.
 
 Recommended
 -----------

examples/full-pipelines/slide-graph.ipynb

@@ -133,7 +133,7 @@
     "import warnings\n",
     "from collections import OrderedDict\n",
     "from pathlib import Path\n",
-    "from typing import TYPE_CHECKING, Callable\n",
+    "from typing import TYPE_CHECKING\n",
     "\n",
     "# Third party imports\n",
     "import joblib\n",
@@ -192,7 +192,7 @@
     ")\n",
     "\n",
     "if TYPE_CHECKING:  # pragma: no cover\n",
-    "    from collections.abc import Iterator\n",
+    "    from collections.abc import Callable, Iterator\n",
     "\n",
     "warnings.filterwarnings(\"ignore\")\n",
     "mpl.rcParams[\"figure.dpi\"] = 300  # for high resolution figure in notebook"
@@ -394,7 +394,7 @@
     "patient_uids = patient_uids[sel]\n",
     "patient_labels = patient_labels_[sel]\n",
     "assert len(patient_uids) == len(patient_labels)  # noqa: S101\n",
-    "clinical_info = OrderedDict(list(zip(patient_uids, patient_labels)))\n",
+    "clinical_info = OrderedDict(list(zip(patient_uids, patient_labels, strict=False)))\n",
     "\n",
     "# Retrieve patient code of each WSI, this is based on TCGA barcodes:\n",
     "# https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/\n",
@@ -412,7 +412,7 @@
     "wsi_names = np.array(wsi_names)[sel]\n",
     "wsi_labels = np.array(wsi_labels)[sel]\n",
     "\n",
-    "label_df = list(zip(wsi_names, wsi_labels))\n",
+    "label_df = list(zip(wsi_names, wsi_labels, strict=False))\n",
     "label_df = pd.DataFrame(label_df, columns=[\"WSI-CODE\", \"LABEL\"])"
    ]
   },
@@ -529,9 +529,9 @@
     "\n",
     "        splits.append(\n",
     "            {\n",
-    "                \"train\": list(zip(train_x, train_y)),\n",
-    "                \"valid\": list(zip(valid_x, valid_y)),\n",
-    "                \"test\": list(zip(test_x, test_y)),\n",
+    "                \"train\": list(zip(train_x, train_y, strict=False)),\n",
+    "                \"valid\": list(zip(valid_x, valid_y, strict=False)),\n",
+    "                \"test\": list(zip(test_x, test_y, strict=False)),\n",
     "            },\n",
     "        )\n",
     "    return splits"
@@ -2025,7 +2025,7 @@
     "                    output = [np.split(v, batch_size, axis=0) for v in output]\n",
     "                    # pairing such that it will be\n",
     "                    # N batch size x H head list\n",
-    "                    output = list(zip(*output))\n",
+    "                    output = list(zip(*output, strict=False))\n",
     "                    step_output.extend(output)\n",
     "                pbar.update()\n",
     "            pbar.close()\n",
@@ -2042,7 +2042,7 @@
     "            ):\n",
     "                # Expand the list of N dataset size x H heads\n",
     "                # back to a list of H Head each with N samples.\n",
-    "                output = list(zip(*step_output))\n",
+    "                output = list(zip(*step_output, strict=False))\n",
     "                logit, true = output\n",
     "                logit = np.squeeze(np.array(logit))\n",
     "                true = np.squeeze(np.array(true))\n",

examples/inference-pipelines/slide-graph.ipynb

@@ -219,7 +219,7 @@
     "import shutil\n",
     "import warnings\n",
     "from pathlib import Path\n",
-    "from typing import TYPE_CHECKING, Callable\n",
+    "from typing import TYPE_CHECKING\n",
     "\n",
     "# Third party imports\n",
     "import joblib\n",
@@ -260,6 +260,8 @@
     "from tiatoolbox.wsicore.wsireader import WSIReader\n",
     "\n",
     "if TYPE_CHECKING:\n",
+    "    from collections.abc import Callable\n",
+    "\n",
     "    from tiatoolbox.wsicore.wsimeta import Resolution, Units\n",
     "\n",
     "warnings.filterwarnings(\"ignore\")\n",