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Merge pull request #829 from Remi-Gau/v2.3.0
[REL] v2.3.0
2 parents 8e1490b + 5841aa7 commit bbfa79c

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‎CITATION.cff

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title: "bidspm"
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version: 2.2.0
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version: 2.3.0
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abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12.
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‎Dockerfile

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ENV LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8"
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LABEL version="2.2.0"
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LABEL version="2.3.0"
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LABEL maintainer="Rémi Gau <[email protected]>"
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RUN mkdir code input output
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# COPY . /home/neuro/bidspm # this is for local development
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RUN git clone --branch v2.2.0 --depth 1 --recursive https://github.com/cpp-lln-lab/bidspm.git
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RUN git clone --branch v2.3.0 --depth 1 --recursive https://github.com/cpp-lln-lab/bidspm.git
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RUN cd bidspm && pip3 install .
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RUN echo '\n'

‎README.md

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license = {GPL-3.0},
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title = {bidspm},
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url = {https://github.com/cpp-lln-lab/bidspm},
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version = {2.2.0}
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version = {2.3.0}
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doi = {10.5281/zenodo.3554331},
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publisher = {Zenodo},
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journal = {Software}

‎docs/bidspm-manual.pdf

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‎docs/source/dev_doc.rst

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.. autofunction:: src.bids_model.getInclusiveMask
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.. _cli:
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cli
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===
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.. _getOptionsFromCliArgument:
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.. autofunction:: src.cli.getOptionsFromCliArgument
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.. _defaults:
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defaults

‎docs/source/examples/bidspm.bib

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@software{bidspm,
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author = {Gau, Rémi and Barilari, Marco and Battal, Ceren and Rezk, Mohamed and Collignon, Olivier and Gurtubay, Ane and Falagiarda, Federica and MacLean, Michèle and Cerpelloni, Filippo and Shahzad, Iqra and Nunes, Márcia and Caron-Guyon, Jeanne and Chouinard-Leclaire, Christine and Yang, Ying and Mattioni, Stefania},
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license = {GPL-3.0},
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title = {bidspm},
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url = {https://github.com/cpp-lln-lab/bidspm},
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version = {2.3.0}
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doi = {10.5281/zenodo.3554331},
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publisher = {Zenodo},
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journal = {Software}
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}
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@article{Corbin2018,
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author = {Corbin, Nadège and Todd, Nick and Friston, Karl J. and Callaghan, Martina F.},
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title = {Accurate modeling of temporal correlations in rapidly sampled fMRI time series},
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journal = {Human Brain Mapping},
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volume = {39},
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number = {10},
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pages = {3884-3897},
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doi = {10.1002/hbm.24218},
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year = {2018}
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}

‎docs/source/examples/preprocess_citation.md

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## Pre processing
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The (f)MRI data were pre-processed with bidspm (v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm])
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using statistical parametric mapping
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(SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK;
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https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037)
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using MATLAB 9.4.0.813654 (R2018a)
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on a unix computer (Linux version 5.15.0-53-generic (build@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
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)
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.
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The preprocessing of the functional images was performed in the following order:
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- removing of dummy scans
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- slice timing correction
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- realignment and unwarping
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- segmentation and skullstripping
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- normalization MNI space
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- smoothing
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{{nb}} dummy scans were removed to allow for signal stabilization.
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Slice timing correction was performed
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taking the ^th slice as a reference
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(interpolation: sinc interpolation).
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Functional scans from each participant were realigned and unwarped using the mean image as a reference
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(SPM single pass; number of degrees of freedom: 6 ;
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cost function: least square) (Friston et al, 1995).
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The anatomical image was bias field corrected.
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The bias field corrected image was segmented and normalized to
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MNI space
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(target space: IXI549Space;
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target resolution: 1 mm;
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interpolation: 4th degree b-spline)
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using a unified segmentation.
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The tissue propability maps generated by the segmentation
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were used to skullstripp the bias corrected image removing any voxel with
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p(gray matter) + p(white matter) + p(CSF) > 0.75.
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The mean functional image obtained from realignement was co-registered to the
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bias corrected anatomical image
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(number of degrees of freedom: 6 ;
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cost function: normalized mutual information)
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(Friston et al, 1995).
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The transformation matrix from this coregistration was applied to all the functional images.
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The deformation field obtained from the segmentation was applied to all the functional images
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(target space: IXI549Space;
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target resolution: equal to that used at acquisition;
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interpolation: 4th degree b-spline).
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Preprocessed functional images were spatially smoothed using a 3D
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gaussian kernel (FWHM = 6 mm).
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## References
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This method section was automatically generated using bidspm
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(v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331)
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and octache (https://github.com/Remi-Gau/Octache).

‎docs/source/examples/stats_model-resampling_citation.md

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## fMRI statistical analysis
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The fMRI data were analysed with bidspm (v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm])
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using statistical parametric mapping
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(SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK;
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https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037)
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using MATLAB 9.4.0.813654 (R2018a)
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on a unix computer (Linux version 5.15.0-53-generic (build@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
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)
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The input data were the preprocessed BOLD images in IXI549Space space for the task " facerepetition ".
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### Run / subject level analysis
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At the subject level, we performed a mass univariate analysis with a linear
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regression at each voxel of the brain, using generalized least squares with a
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global AR(1) model to account for temporal auto-correlation
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and a drift fit with discrete cosine transform basis ( 128 seconds cut-off).
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Image intensity scaling was done run-wide before statistical modeling such that
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the mean image would have a mean intracerebral intensity of 100.
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We modeled the fMRI experiment in a event design with regressors
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entered into the run-specific design matrix. The onsets
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were convolved with SPM canonical hemodynamic response function (HRF)
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and its temporal and dispersion derivatives for the conditions:
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- `famous_1`,
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- `famous_2`,
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- `unfamiliar_1`,
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- `unfamiliar_2`,
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.
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Nuisance covariates included:
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- `trans_?`,
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- `rot_?`,
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to account for residual motion artefacts,
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.
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## References
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This method section was automatically generated using bidspm
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(v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331)
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and octache (https://github.com/Remi-Gau/Octache).

‎setup.cfg

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%(demo)s
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%(doc)s
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%(style)s
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cffconvert
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ruamel.yaml
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doc =
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myst-parser
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sphinxcontrib-mermaid
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style =
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black
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codespell
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flake8
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flake8-docstrings
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miss-hit
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[flake8]
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max-line-length = 99
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max-complexity = 10
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ignore = F841
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ignore = F841, D100, D101, D103, D104
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exclude =
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*build
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.git
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__pycache__
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tests/*

‎src/parsers.py

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def bidspm_log(name: str = "bidspm") -> logging.Logger:
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"""Create log."""
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FORMAT = "bidspm - %(asctime)s - %(levelname)s - %(message)s"
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if not name:

‎src/reports/bidspm.bib

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license = {GPL-3.0},
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title = {bidspm},
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version = {2.2.0}
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version = {2.3.0}
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doi = {10.5281/zenodo.3554331},
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journal = {Software}

‎tools/bump_version.sh

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cd tools || exit
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echo "Version updated to $VERSION"

‎version.txt

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v2.2.0
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v2.3.0

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