royerlab · JoOkuma · Apr 21, 2026 · Feb 12, 2026 · Feb 13, 2026 · Apr 20, 2026
diff --git a/.github/workflows/test_pull_request.yml b/.github/workflows/test_pull_request.yml
@@ -11,63 +11,64 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.platform }} ${{ matrix.python }} ${{ matrix.toxenv || matrix.backend }}
+    name: ${{ matrix.platform }} py${{ matrix.python }} ${{ matrix.backend }}
     if: github.event.pull_request.draft == false
     runs-on: ${{ matrix.platform }}
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest]
-        python: ["3.10", "3.12"]
-        backend: [pyqt5]
         include:
-          # - python: 3.11
-          #   platform: windows-latest
-          #   backend: pyqt5
-          # - python: 3.11
-          #   platform: macos-13  # latest not-arm version
-          #   backend: pyside2
-          - python: 3.11 # only this run execute coverage
-            platform: ubuntu-latest
+          - platform: ubuntu-latest
+            python: "3.11"
             backend: pyside6
             coverage: true
+          - platform: ubuntu-latest
+            python: "3.12"
+            backend: pyqt5
+          - platform: ubuntu-latest
+            python: "3.13"
+            backend: pyqt5
+          - platform: macos-latest
+            python: "3.13"
+            backend: pyqt5
+              # - platform: windows-latest
+              #   python: "3.13"
+              #   backend: pyside6
 
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.13.1
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
 
       # see https://github.com/actions/runner-images/issues/709#issuecomment-612569242
       - name: Workaround to free up space on github runner
         if: runner.os == 'Linux'
         run: sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-      - uses: prefix-dev/setup-pixi@v0.9.5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          pixi-version: v0.62.2
-          cache: true
+          python-version: ${{ matrix.python }}
+          enable-cache: true
 
-      - name: Setup headless screenL
+      - name: Setup headless display
+        if: runner.os == 'Linux'
         uses: pyvista/setup-headless-display-action@5bc8de3bc71fcda7a96439571287a554901541a0 # v4.3
         with:
           qt: true
           wm: herbstluftwm
 
-      - name: Install dependencies with pixi
-        run: pixi install -e test
-
       - name: Run pre-commit
-        run: pixi run -e test pre-commit run --all-files
+        run: uvx pre-commit run --all-files
 
       - name: Testing
-        run: pixi run -e test test --cov-report=xml
+        run: uv run --extra test --extra ml --with "${{ matrix.backend }}" pytest -v --color=yes --cov=ultrack --cov-report=xml --durations=15 .
         env:
           PLATFORM: ${{ matrix.platform }}
           BACKEND: ${{ matrix.backend }}
-          TOXENV: ${{ matrix.toxenv }}
 
       - name: Coverage
         if: ${{ matrix.coverage }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
       - id: absolufy-imports
 # sorting imports
   - repo: https://github.com/pycqa/isort
-    rev: 7.0.0
+    rev: 8.0.1
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
@@ -29,7 +29,7 @@ repos:
         args: ["--py38-plus", "--keep-runtime-typing"]
 # syntax linting and formatting
   - repo: https://github.com/myint/autoflake
-    rev: v2.3.1
+    rev: v2.3.3
     hooks:
       - id: autoflake
         args: [--in-place, --remove-all-unused-imports,
@@ -45,7 +45,7 @@ repos:
                --min-python-version, '3.9']
         additional_dependencies: [flake8-typing-imports==1.12.0]
   - repo: https://github.com/psf/black
-    rev: 25.11.0
+    rev: 26.3.1
     hooks:
       - id: black
 

diff --git a/README.md b/README.md
@@ -42,30 +42,17 @@ Zebrafish imaged using [DaXi](https://www.nature.com/articles/s41592-022-01417-2
 
 ## Installation
 
-Install or update [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html).
-
-To avoid conflicts between different packages, we recommend using conda to create an isolated environment:
-
 ```bash
-conda create -n ultrack python=3.11 higra gurobi pytorch pyqt -c pytorch -c gurobi -c conda-forge
-conda activate ultrack
 pip install ultrack
 ```
 
-The installation should take a few minutes, depending on your internet speed and conda.
-
-NOTE: `gurobi` and `-c gurobi` are optional but recommended; they can be installed later, as shown below.
+We recommend installing into a virtual environment to avoid package conflicts.
+`gurobi` is optional but recommended for best performance; see the [installation guide](https://ultrack.readthedocs.io/en/latest/install.html) for details on Gurobi setup and GPU acceleration.
 
 Optionally, we provide multiple Docker images. For instructions, see the [docker folder](https://github.com/royerlab/ultrack/tree/main/docker).
 
 ## Usage
 
-**ATTENTION**: every time you need to run this software, you'll have to activate this environment
-
-```bash
-conda activate ultrack
-```
-
 Here is a basic example to get you started:
 
 ```python

diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -1,27 +1,38 @@
 Installation
 ============
 
-The recommended way to install the package is to use the conda (or mamba) package manager.
+The simplest way to install ``ultrack`` is with pip:
 
-We also provide a `pixi <https://pixi-docs.com/>`_ configuration for the package, which allows you to setup an environment with all the dependencies in a single command. See the section :ref:`pixi_install` for more details.
+.. code-block:: bash
 
-If you do not have conda installed, we recommend to install mamba first, which is a faster alternative to conda.
-You can find mamba installation instructions `here <https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html>`_.
+    pip install ultrack
 
-Once you have conda (mamba) installed, you should create an environment for ``ultrack`` as follows:
+We recommend installing into a virtual environment to avoid package conflicts.
+With Python's built-in ``venv`` on Linux / macOS:
 
 .. code-block:: bash
 
-    conda create -n ultrack python=3.11 higra gurobi pytorch pyqt -c pytorch -c gurobi -c conda-forge
+    python -m venv ultrack-env
+    source ultrack-env/bin/activate
+    pip install ultrack
+
+On Windows:
+
+.. code-block:: bat
+
+    python -m venv ultrack-env
+    ultrack-env\Scripts\activate
+    pip install ultrack
 
-Then, you can activate the environment and install ``ultrack``:
+Or with `conda <https://docs.conda.io/projects/conda/en/latest/>`_:
 
 .. code-block:: bash
 
+    conda create -n ultrack python=3.11
     conda activate ultrack
     pip install ultrack
 
-You can check if the installation was successful by running:
+You can verify the installation by running:
 
 .. code-block:: bash
 
@@ -31,54 +42,43 @@ You can check if the installation was successful by running:
 GPU acceleration
 ----------------
 
-Ultrack makes use of GPU for image processing operations.
-You can install the additional packages required for GPU acceleration by running (Linux and Windows only):
+Ultrack uses the GPU for image processing operations.
+Install the additional packages for GPU acceleration (Linux and Windows only):
 
 .. code-block:: bash
 
-    conda install pytorch-cuda -c pytorch -c nvidia
-    conda install cupy -c conda-forge
-    # linux only
-    conda install cucim -c rapidsai
-    # for windows, you can install cucim using pip
-    pip install "git+https://github.com/rapidsai/cucim.git@v22.04.00#egg=cucim&subdirectory=python/cucim"
+    # Install PyTorch with CUDA — pick the right version at https://pytorch.org/get-started/locally/
+    pip install torch --index-url https://download.pytorch.org/whl/cu124
+    pip install cupy-cuda12x
+    # Linux only
+    pip install cucim-cu12
 
-See the `PyTorch website <https://pytorch.org/get-started/locally/>`_ for more information on how to install PyTorch with GPU support.
+See the `PyTorch website <https://pytorch.org/get-started/locally/>`_ for the full list of CUDA builds.
 
 .. _gurobi_install:
 
 Gurobi setup
 ------------
 
-Gurobi is a commercial optimization solver that is used in the tracking module of ``ultrack``.
-While it is not a requirement, it is recommended to install it for the best performance.
-
-To use it, you need to obtain a license (free for academics) and activate it.
-
-Install gurobi using conda
-``````````````````````````
-
-You can skip this step if you have already installed Gurobi.
-
-In your existing Conda environment, install Gurobi with the following command:
-
-.. code-block:: bash
+Gurobi is a commercial optimization solver used in the tracking module of ``ultrack``.
+While not required, it is recommended for best performance.
 
-    conda install -c gurobi gurobi
+``gurobipy`` is installed automatically with ``ultrack`` — no extra install step is needed.
+To use the solver, you must obtain and activate a license (free for academics).
 
 Obtain and activate an academic license
 ```````````````````````````````````````
 
 **Obtaining a license:** register for an account using your academic email at `Gurobi's website <https://portal.gurobi.com/iam/login>`_.
 Navigate to the Gurobi's `named academic license page <https://www.gurobi.com/features/academic-named-user-license/>`_, and follow the instructions to get your academic license key.
 
-**Activating license:** In your Conda environment, run:
+**Activating license:** run:
 
 .. code-block:: bash
 
     grbgetkey YOUR_LICENSE_KEY
 
-Replace YOUR_LICENSE_KEY with the key you received. Follow the prompts to complete activation.
+Replace ``YOUR_LICENSE_KEY`` with the key you received. Follow the prompts to complete activation.
 
 Test the installation
 `````````````````````
@@ -92,26 +92,28 @@ Verify Gurobi's installation by running:
 Troubleshooting
 ```````````````
 
-Depending on the operating system, the gurobi library might be missing and you need to install it from `here <https://www.gurobi.com/downloads/gurobi-software>`_.
+Depending on the operating system, the Gurobi library might be missing.
+Download it from `Gurobi's website <https://www.gurobi.com/downloads/gurobi-software>`_.
 
-If you're still having trouble, with the installation we recommend reaching out to us or using the docker image, see  :doc:`Docker instructions <docker/README>`.
+If you're still having trouble, reach out to us or use the Docker image — see :doc:`Docker instructions <docker/README>`.
 
 .. _pixi_install:
 
 Ultrack environment with pixi
 -----------------------------
 
-This is an alternative to the conda installation for environment management, using the `pixi <https://pixi-docs.com/>`_ package manager.
+For contributors and advanced users, we provide a `pixi <https://pixi.sh/>`_ configuration
+that sets up a full development environment in a single command.
 
-First, install ``pixi`` following the instructions for your operating system:
+Install ``pixi`` following the instructions for your operating system:
 
-For Linux and OSX:
+For Linux and macOS:
 
 .. code-block:: bash
 
     curl -fsSL https://pixi.sh/install.sh | bash
 
-For Windows, using PowerShell:
+For Windows (PowerShell):
 
 .. code-block:: powershell
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -8,7 +8,7 @@ dynamic = ["version"]
 description = "Large-scale multi-hypotheses cell tracking"
 readme = "README.md"
 license = "BSD-3-Clause"
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.11,<3.14"
 authors = [
     { name = "Jordao Bragantini", email = "jordao.bragantini@czbiohub.org" },
 ]
@@ -17,10 +17,9 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: BSD License",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering",
   "Topic :: Scientific/Engineering :: Image Processing",
   "Topic :: Scientific/Engineering :: Artificial Intelligence",
@@ -82,10 +81,10 @@ test = [
     "asv >=0.5.1",
     "pre-commit >=3.2.2",
     "pytest >=7.3.1",
+    "pytest-cov >=6.0.0",
     "pytest-qt >=4.2.0",
     "pytrackmate >=1.3.4",
     "napari[testing] >0.4.18",
-    "pyqt5 >=5.15.4",
 ]
 ml = [
     "catboost >=1.2.7",

diff --git a/ultrack/__init__.py b/ultrack/__init__.py
@@ -10,7 +10,7 @@
 # ignoring small float32/64 zero flush warning
 warnings.filterwarnings("ignore", message="The value of the smallest subnormal for")
 
-__version__ = "0.7.2"
+__version__ = "0.7.3"
 
 from ultrack.config.config import MainConfig, load_config
 from ultrack.core.export.ctc import to_ctc

diff --git a/ultrack/core/export/_test/test_ctc.py b/ultrack/core/export/_test/test_ctc.py
@@ -49,10 +49,10 @@ def dataframe_forest() -> pd.DataFrame:
 def dataframe_forest_with_time(dataframe_forest: pd.DataFrame) -> pd.DataFrame:
     df = dataframe_forest.copy()
     df["t"] = -1
-    df["t"].values[:10] = np.arange(10)
-    df["t"].values[10:20] = np.arange(10, 20)
-    df["t"].values[20:30] = np.arange(10, 20)
-    df["t"].values[30:40] = np.arange(5, 15)
+    df.iloc[:10, df.columns.get_loc("t")] = np.arange(10)
+    df.iloc[10:20, df.columns.get_loc("t")] = np.arange(10, 20)
+    df.iloc[20:30, df.columns.get_loc("t")] = np.arange(10, 20)
+    df.iloc[30:40, df.columns.get_loc("t")] = np.arange(5, 15)
     return df
 
 

diff --git a/ultrack/core/export/ctc.py b/ultrack/core/export/ctc.py
@@ -32,6 +32,7 @@
     tracks_df_forest,
 )
 from ultrack.tracks.stats import estimate_drift
+from ultrack.utils.array import make_array_writeable
 from ultrack.utils.constants import NO_PARENT
 from ultrack.utils.data import validate_and_overwrite_path
 
@@ -370,9 +371,13 @@ def condition(node: Node) -> bool:
             stitch_tracks=stitch_tracks,
         )
 
-    df["track_id"], fw, _ = relabel_sequential(df["track_id"].values)
+    df["track_id"], fw, _ = relabel_sequential(
+        make_array_writeable(df["track_id"].values)
+    )
     mask = df["parent_track_id"] != NO_PARENT
-    df.loc[mask, "parent_track_id"] = fw[df.loc[mask, "parent_track_id"].values]
+    df.loc[mask, "parent_track_id"] = fw[
+        make_array_writeable(df.loc[mask, "parent_track_id"].values)
+    ]
 
     # convert to CTC format and write output
     tracks_df = ctc_compress_forest(df)

diff --git a/ultrack/core/segmentation/hierarchy.py b/ultrack/core/segmentation/hierarchy.py
@@ -68,7 +68,7 @@ def create_hierarchies(
         #  This is mainly for lonely cells.
         morphology.remove_small_objects(
             labels,
-            min_size=int(kwargs["min_area"] / kwargs.get("min_area_factor", 4.0)),
+            max_size=int(kwargs["min_area"] / kwargs.get("min_area_factor", 4.0)) - 1,
             out=labels,
         )