align-toolbox 0.5.1__tar.gz

align_toolbox-0.5.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, Sacha Psalmon, Towbin Lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

align_toolbox-0.5.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: align_toolbox
+Version: 0.5.1
+Summary: This package implements most of the functions used in the ALIGN pipeline, a modular image analysis workflow adapted for longitudinal, high-troughput microscopy. Developed by the Towbin Lab of the University of Bern.
+Author-email: Sacha Psalmon <sacha.psalmon@unibe.ch>, Boris Gusev <boris.gusev@unibe.ch>
+Maintainer-email: Sacha Psalmon <sacha.psalmon@unibe.ch>
+Project-URL: Repository, https://github.com/spsalmon/align_toolbox
+Project-URL: Documentation, https://align-toolbox.readthedocs.io
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: pytorch-lightning
+Requires-Dist: torchmetrics
+Requires-Dist: pytorch-toolbelt
+Requires-Dist: segmentation-models-pytorch
+Requires-Dist: timm
+Requires-Dist: monai
+Requires-Dist: csbdeep
+Requires-Dist: scikit-learn
+Requires-Dist: xgboost
+Requires-Dist: joblib
+Requires-Dist: opencv-contrib-python
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: polars
+Requires-Dist: pyarrow
+Requires-Dist: scipy
+Requires-Dist: ome-types
+Requires-Dist: pyyaml
+Requires-Dist: whittaker-eilers
+Requires-Dist: bottleneck
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: microfilm
+Requires-Dist: statsmodels
+Requires-Dist: statannotations
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Dynamic: license-file
+
+# ALIGN toolbox!
+
+This package implements most of the functions used in the ALIGN pipeline, a modular image analysis workflow adapted for longitudinal, high-troughput microscopy. Developed by the Towbin Lab of the University of Bern.
+
+This package goes hand in hand with our modular pipelining tool : <https://github.com/spsalmon/align_pipeline>
+
+Documentation : <https://align-toolbox.readthedocs.io/en/latest/index.html>
+## Install the package using pip
+
+Simply run the following command:
+
+```bash
+pip3 install align_toolbox
+```
+
+## Build the package and install it
+
+1. First, make sure build is installed:
+
+   ```bash
+   pip3 install build
+
+   ```
+
+2. Go to the package directory, eg:
+
+   ```bash
+   cd ~/align_toolbox
+
+   ```
+
+3. Build the package:
+
+   ```bash
+   python3 -m build
+
+   ```
+
+4. Install the package you just built:
+
+   ```bash
+   pip3 install dist/*.whl
+   ```

align_toolbox-0.5.1/README.md

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+# ALIGN toolbox!
+
+This package implements most of the functions used in the ALIGN pipeline, a modular image analysis workflow adapted for longitudinal, high-troughput microscopy. Developed by the Towbin Lab of the University of Bern.
+
+This package goes hand in hand with our modular pipelining tool : <https://github.com/spsalmon/align_pipeline>
+
+Documentation : <https://align-toolbox.readthedocs.io/en/latest/index.html>
+## Install the package using pip
+
+Simply run the following command:
+
+```bash
+pip3 install align_toolbox
+```
+
+## Build the package and install it
+
+1. First, make sure build is installed:
+
+   ```bash
+   pip3 install build
+
+   ```
+
+2. Go to the package directory, eg:
+
+   ```bash
+   cd ~/align_toolbox
+
+   ```
+
+3. Build the package:
+
+   ```bash
+   python3 -m build
+
+   ```
+
+4. Install the package you just built:
+
+   ```bash
+   pip3 install dist/*.whl
+   ```

align_toolbox-0.5.1/align_toolbox/__init__.py

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+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("align_toolbox")
+except PackageNotFoundError:
+    __version__ = "unknown"

align_toolbox-0.5.1/align_toolbox/classification/__init__.py

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+from .qc_tools import compute_qc_features
+
+__all__ = [
+    "compute_qc_features",
+]