pcntoolkit 0.32.0__py3-none-any.whl

pcntoolkit-0.32.0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: pcntoolkit
+Version: 0.32.0
+Summary: Predictive Clinical Neuroscience Toolkit
+License: GNU GPLv3
+Author: Andre Marquand
+Requires-Python: >=3.10,<3.13
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: bspline (>=0.1.1,<0.2.0)
+Requires-Dist: matplotlib (>=3.9.2,<4.0.0)
+Requires-Dist: nibabel (>=5.3.1,<6.0.0)
+Requires-Dist: numba (>=0.60.0,<0.61.0)
+Requires-Dist: nutpie (>=0.13.2,<0.14.0)
+Requires-Dist: pymc (>=5.18.0,<6.0.0)
+Requires-Dist: scikit-learn (>=1.5.2,<2.0.0)
+Requires-Dist: scipy (>=1.12,<2.0)
+Requires-Dist: seaborn (>=0.13.2,<0.14.0)
+Requires-Dist: six (>=1.16.0,<2.0.0)
+Requires-Dist: torch (>=2.1.1)
+Description-Content-Type: text/markdown
+
+# Predictive Clinical Neuroscience Toolkit
+[![Documentation Status](https://readthedocs.org/projects/pcntoolkit/badge/?version=latest)](https://pcntoolkit.readthedocs.io/en/latest/?badge=latest) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5207839.svg)](https://doi.org/10.5281/zenodo.5207839)
+
+[Github](https://github.com/amarquand/PCNtoolkit)
+
+
+Predictive Clinical Neuroscience software toolkit (formerly nispat). 
+
+Methods for normative modelling, spatial statistics and pattern recognition. Documentation, including tutorials can be found on [readthedocs](https://pcntoolkit.readthedocs.io/en/latest/). Click on the docs button above to visit the site. 
+
+## Basic installation (on a local machine)
+
+#### Install anaconda3 
+
+using the download here: https://www.anaconda.com/download
+
+#### Create environment 
+```
+conda create -n <env_name> python==3.12
+```
+
+#### Activate environment
+
+```
+source activate <env_name>
+```
+
+#### Install PCNtoolkit
+
+Using pip:
+```
+pip install pcntoolkit
+```
+
+Using a local clone of the repo:
+```
+python -m pip install .
+```
+
+#### Test installation  
+```
+python -c "import pcntoolkit as pk;print(pk.__file__)"
+```
+
+### Troubleshooting
+
+#### Nutpie installation failure
+On some older architectures, the installation of nutpie may fail due to a missing Rust compiler. If this is the case, you can install it manually using conda prior to installing PCNtoolkit:
+
+```
+# install nutpie
+conda install -c conda-forge nutpie
+# install PCNtoolkit
+pip install pcntoolkit
+```
+
+## Alternative installation (on a shared resource)
+
+#### Make sure conda is available on the system.
+Otherwise install it first from https://www.anaconda.com/ 
+
+```
+conda --version
+```
+
+#### Create a conda environment in a shared location
+
+```
+conda create -y python==3.12 --prefix=/shared/conda/<env_name>
+```
+
+#### Activate the conda environment 
+
+```
+conda activate /shared/conda/<env_name>
+```
+
+#### Clone the repo
+
+```
+git clone https://github.com/amarquand/PCNtoolkit.git
+```
+
+#### Install in the conda environment
+
+```
+cd PCNtoolkit/
+python -m pip install .
+```
+
+#### Test installation  
+```
+python -c "import pcntoolkit as pk;print(pk.__file__)"
+```
+
+## Quickstart usage
+
+For normative modelling, functionality is handled by the normative.py script, which can be run from the command line, e.g.
+
+```
+# python normative.py -c /path/to/training/covariates -t /path/to/test/covariates -r /path/to/test/response/variables /path/to/my/training/response/variables
+```
+
+For more information, please see the following resources:
+
+* [documentation](https://github.com/amarquand/PCNtoolkit/wiki/Home)
+* [developer documentation](https://amarquand.github.io/PCNtoolkit/doc/build/html/)
+* a tutorial and worked through example on a [real-world dataset](https://github.com/predictive-clinical-neuroscience/PCNtoolkit-demo)
+

pcntoolkit-0.32.0.dist-info/RECORD

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pcntoolkit-0.32.0.dist-info/WHEEL

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pcntoolkit-0.32.0.dist-info/entry_points.txt

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+[console_scripts]
+normative=pcntoolkit.normative:entrypoint
+normative_parallel=pcntoolkit.normative_parallel:entrypoint
+trendsurf=pcntoolkit.trendsurf:entrypoint
+