osl-ephys 2.0.0__tar.gz

osl_ephys-2.0.0/LICENSE

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+Copyright 2021-2024 University of Oxford, Oxford, UK.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+
+
+This software includes code from MNE-Python, which is licensed under the BSD-3-Clause license:
+https://github.com/mne-tools/mne-python/blob/main/LICENSE.txt
+
+This software includes code from FSL-Python, which is licensed under the Apache License:
+https://git.fmrib.ox.ac.uk/fsl/fslpy/-/blob/main/LICENSE
+
+For the full text of these licenses, please see the LICENSE file in the root directory of these projects.

osl_ephys-2.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: osl-ephys
+Version: 2.0.0
+Summary: OHBA Software Library for the analysis of electrophysiological data
+Author: OHBA Analysis Group
+License: MIT
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: mne~=1.3.1
+Requires-Dist: scikit-learn
+Requires-Dist: fslpy
+Requires-Dist: sails
+Requires-Dist: tabulate
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: neurokit2
+Requires-Dist: jinja2==3.0.3
+Requires-Dist: glmtools
+Requires-Dist: numba
+Requires-Dist: nilearn
+Requires-Dist: dask
+Requires-Dist: distributed
+Requires-Dist: parse
+Requires-Dist: opencv-python
+Requires-Dist: panel
+Requires-Dist: h5io
+Provides-Extra: dev
+Requires-Dist: setuptools>=41.0.1; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx==5.3.0; extra == "doc"
+Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: sphinx_gallery; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Provides-Extra: full
+Requires-Dist: setuptools>=41.0.1; extra == "full"
+Requires-Dist: pytest; extra == "full"
+Requires-Dist: pytest-cov; extra == "full"
+Requires-Dist: coverage; extra == "full"
+Requires-Dist: flake8; extra == "full"
+Requires-Dist: sphinx==5.3.0; extra == "full"
+Requires-Dist: numpydoc; extra == "full"
+Requires-Dist: sphinx_gallery; extra == "full"
+Requires-Dist: pydata-sphinx-theme; extra == "full"
+
+# The OHBA Software Library for the analysis of electrophysiological data (osl-ephys)
+
+Tools for MEG/EEG analysis.
+
+Documentation: https://osl-ephys.readthedocs.io/en/latest/.
+
+## Installation
+
+See the [official documentation](https://osl-ephys.readthedocs.io/en/latest/install.html) for recommended installation instructions.
+
+Alternatively, osl-ephys can be installed from source code within a [Miniconda](https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html) (or [Anaconda](https://docs.anaconda.com/free/anaconda/install/index.html)) environment using the following.
+
+### Linux
+
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/linux.yml
+conda activate osle
+pip install -e .
+```
+
+### Mac
+
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/mac.yml
+conda activate osle
+pip install -e .
+```
+
+### Oxford-specific computers
+
+If you are installing on an OHBA workstation computer (HBAWS) use:
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/hbaws.yml
+conda activate osle
+pip install -e .
+pip install spyder==5.1.5
+```
+
+Or on the BMRC cluster:
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/bmrc.yml
+conda activate osle
+pip install -e .
+```
+
+## Removing OSL
+
+Simply removing the conda environment and delete the repository:
+```
+conda env remove -n osle
+rm -rf osl-ephys
+```
+
+## For Developers
+
+Run tests:
+```
+cd osl_ephys
+pytest tests
+```
+or to run a specific test:
+```
+cd osl_ephys/tests
+pytest test_file_handling.py
+```
+
+Build documentation (if `build_sphinx` is not recognised, first try `pip install sphinx==5.3.0`):
+```
+python setup.py build_sphinx
+```
+Compiled docs can be found in `doc/build/html/index.html`.

osl_ephys-2.0.0/README.md

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+# The OHBA Software Library for the analysis of electrophysiological data (osl-ephys)
+
+Tools for MEG/EEG analysis.
+
+Documentation: https://osl-ephys.readthedocs.io/en/latest/.
+
+## Installation
+
+See the [official documentation](https://osl-ephys.readthedocs.io/en/latest/install.html) for recommended installation instructions.
+
+Alternatively, osl-ephys can be installed from source code within a [Miniconda](https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html) (or [Anaconda](https://docs.anaconda.com/free/anaconda/install/index.html)) environment using the following.
+
+### Linux
+
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/linux.yml
+conda activate osle
+pip install -e .
+```
+
+### Mac
+
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/mac.yml
+conda activate osle
+pip install -e .
+```
+
+### Oxford-specific computers
+
+If you are installing on an OHBA workstation computer (HBAWS) use:
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/hbaws.yml
+conda activate osle
+pip install -e .
+pip install spyder==5.1.5
+```
+
+Or on the BMRC cluster:
+```
+git clone https://github.com/OHBA-analysis/osl-ephys.git
+cd osl-ephys
+conda env create -f envs/bmrc.yml
+conda activate osle
+pip install -e .
+```
+
+## Removing OSL
+
+Simply removing the conda environment and delete the repository:
+```
+conda env remove -n osle
+rm -rf osl-ephys
+```
+
+## For Developers
+
+Run tests:
+```
+cd osl_ephys
+pytest tests
+```
+or to run a specific test:
+```
+cd osl_ephys/tests
+pytest test_file_handling.py
+```
+
+Build documentation (if `build_sphinx` is not recognised, first try `pip install sphinx==5.3.0`):
+```
+python setup.py build_sphinx
+```
+Compiled docs can be found in `doc/build/html/index.html`.

osl_ephys-2.0.0/osl_ephys/__init__.py

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+#!/usr/bin/python
+
+# --------------------------------------------------------
+# If user hasn't configured NumExpr environment the an irritating low-level log
+# is generated. We supress it by setting a default value of 8 if not already
+# set.
+#
+# https://numexpr.readthedocs.io/projects/NumExpr3/en/latest/user_guide.html#threadpool-configuration
+# https://github.com/pydata/numexpr/blob/7c2ef387d81cd450e8220fe4174cf46ec559994c/numexpr/utils.py#L118
+
+import os
+if 'NUMEXPR_MAX_THREADS' not in os.environ:
+    os.environ['NUMEXPR_MAX_THREADS'] = '8'
+
+# Some modules are chatty by default when a logger is on - set log-levels to
+# WARNING on setup
+import logging
+logging.getLogger("asyncio").setLevel(logging.WARNING)
+logging.getLogger("matplotlib").setLevel(logging.WARNING)
+logging.getLogger("PIL").setLevel(logging.WARNING)
+
+# Feels like there should be a better solution for this. How do we setup a
+# logger which only produces OSL outputs?!
+
+# --------------------------------------------------------
+# Main importing - set module structure here
+
+from . import utils  # noqa: F401, F403
+from . import preprocessing  # noqa: F401, F403
+from . import maxfilter  # noqa: F401, F403
+from . import report  # noqa: F401, F403
+from . import source_recon  # noqa: F401, F403
+from . import glm  # noqa: F401, F403
+
+# --------------------------------------------------------
+osl_logger = logging.getLogger(__name__)
+osl_logger.debug('osl-ephys main init complete')
+
+# --------------------------------------------------------
+__version__ = '2.0.0'

osl_ephys-2.0.0/osl_ephys/glm/README.md

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+# GLM
+
+osl-ephys's GLM (generalized linear model) module, with modality specific functions based on https://pypi.org/project/glmtools/

osl_ephys-2.0.0/osl_ephys/glm/__init__.py

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+
+from .glm_spectrum import *
+from .glm_epochs import *
+
+with open(os.path.join(os.path.dirname(__file__), "README.md"), 'r') as f:
+    __doc__ = f.read()