Create joss.yml

.github/workflows/joss.yml

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+name: JOSS generation
+on:
+  push:
+    paths:
+      - joss_paper/paper.md
+      - joss_paper/paper.bib
+      - .github/workflows/joss.yml
+      - joss_paper/plots/* # Trigger the paper generation workflow when the plots have changed (only works when the plots are pushed manually)
+  workflow_call:
+
+  # Apparently this only triggers the workflow if the workflow file is on the default branch
+  # (https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_run)
+  #workflow_run:
+  #  workflows: [JOSS figure generation]
+  #  types:
+  #    - completed
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+        #uses: actions/[email protected]
+      - name: Checkout latest commit
+        run: git pull && GITHUB_SHA=$(git rev-parse HEAD)
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss_paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v3
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss_paper/paper.pdf

joss_paper/paper.bib

@@ -0,0 +1,279 @@
+@article{mikheev2024art,
+  title={The Art of Brainwaves: A Survey on Event-Related Potential Visualization Practices},
+  author={Mikheev, Vladimir and Skukies, Rene and Ehinger, Benedikt V},
+  journal={Aperture Neuro},
+  doi = {10.52294/001c.116386},
+  volume={4},
+  year={2024},
+  publisher={Organization for Human Brain Mapping}
+}
+
+@article{ehinger2019unfold,
+  title={Unfold: an integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis},
+  author={Ehinger, Benedikt V and Dimigen, Olaf},
+  journal={PeerJ},
+  doi={10.5281/zenodo.5759066},
+  volume={7},
+  pages={e7838},
+  year={2019},
+  publisher={PeerJ Inc.}
+}
+@article{danisch2021makie,
+  title={Makie.jl: Flexible high-performance data visualization for Julia},
+  author={Danisch, Simon and Krumbiegel, Julius},
+  journal={Journal of Open Source Software},
+  volume={6},
+  number={65},
+  pages={3349},
+  year={2021}
+}
+
+@article{jung1998analyzing,
+  title={Analyzing and visualizing single-trial event-related potentials},
+  author={Jung, Tzyy-Ping and Makeig, Scott and Westerfield, Marissa and Townsend, Jeanne and Courchesne, Eric and Sejnowski, Terrence J},
+  journal={Advances in neural information processing systems},
+  volume={11},
+  year={1998}
+}
+
+@article{ten2006design,
+  title={Design and evaluation of tiled parallel coordinate visualization of multichannel EEG data},
+  author={Ten Caat, Michael and Maurits, Natasha M and Roerdink, Jos BTM},
+  journal={IEEE Transactions on Visualization and Computer Graphics},
+  volume={13},
+  number={1},
+  pages={70--79},
+  year={2006},
+  publisher={IEEE}
+}
+
+@article{ehinger2018eegvis,
+  title={EEGVIS toolbox},
+  author={Ehinger, Benedikt V},
+  journal={Osnabr{\"u}ck.[Google Scholar]},
+  year={2018}
+}
+
+@article{delorme2004eeglab,
+  title={EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis},
+  author={Delorme, Arnaud and Makeig, Scott},
+  journal={Journal of neuroscience methods},
+  volume={134},
+  number={1},
+  pages={9--21},
+  year={2004},
+  publisher={Elsevier}
+}
+
+@article{oostenveld2011fieldtrip,
+  title={FieldTrip: open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data},
+  author={Oostenveld, Robert and Fries, Pascal and Maris, Eric and Schoffelen, Jan-Mathijs},
+  journal={Computational intelligence and neuroscience},
+  volume={2011},
+  number={1},
+  pages={156869},
+  year={2011},
+  publisher={Wiley Online Library}
+}
+
+@article{lopez2014erplab,
+  title={ERPLAB: an open-source toolbox for the analysis of event-related potentials},
+  author={Lopez-Calderon, Javier and Luck, Steven J},
+  journal={Frontiers in human neuroscience},
+  volume={8},
+  pages={213},
+  year={2014},
+  publisher={Frontiers Media SA}
+}
+
+@article{tadel2019meg,
+  title={MEG/EEG group analysis with brainstorm},
+  author={Tadel, Fran{\c{c}}ois and Bock, Elizabeth and Niso, Guiomar and Mosher, John C and Cousineau, Martin and Pantazis, Dimitrios and Leahy, Richard M and Baillet, Sylvain},
+  journal={Frontiers in neuroscience},
+  volume={13},
+  pages={76},
+  year={2019},
+  publisher={Frontiers Media SA}
+}
+
+@software{ehigner_2018eegvis,
+  author = {Ehinger, Benedikt V},
+  doi = {10.5281/zenodo.1312813},
+  title = {{EEGVIS toolbox}},
+  url = {https://github.com/behinger/eegvis},
+  version = {0.1},
+  year = {2018}
+}
+
+@software{Wysokinski_NeuroAnalyzer,
+  author = {Wysokiński, Adam},
+  license = {BSD-2-Clause},
+  title = {{NeuroAnalyzer}},
+  version = {0.24.11},
+  year = {2024},
+  doi = {10.5281/zenodo.14010334},
+  url = {https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl}
+}
+
+@software{Pereyra_EEGToolkit,
+  author = {Pereyra, Santiago Lopez},
+  license = {MIT},
+  title = {{EEGToolkit.jl}},
+  version = {0.2},
+  year = {2024},
+  url = {https://github.com/slopezpereyra/EEGToolkit.jl}
+}
+
+@article{Gramfort_MEG_and_EEG_2013,
+  author = {Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis A. and Strohmeier, Daniel and Brodbeck, Christian and Goj, Roman and Jas, Mainak and Brooks, Teon and Parkkonen, Lauri and Hämäläinen, Matti S.},
+  doi = {10.3389/fnins.2013.00267},
+  journal = {Frontiers in Neuroscience},
+  number = {267},
+  pages = {1--13},
+  title = {{MEG and EEG Data Analysis with MNE-Python}},
+  volume = {7},
+  year = {2013}
+}
+
+@software{Luke_Neuroimaging,
+  author = {Luke, Rob},
+  license = {BSD-3-Clause},
+  title = {{Neuroimaging.jl}},
+  version = {1.1.2},
+  year = {2021},
+  url = {https://github.com/rob-luke/Neuroimaging.jl}
+}
+
+@software{Krumbiegel_AlgebraOfGraphics,
+  author = {{Krumbiegel}, Julius and {Vertechi}, Pietro},
+  license = {MIT},
+  title = {{AlgebraOfGraphics.jl}},
+  version = {0.8.13},
+  year = {2024},
+  url = {https://github.com/MakieOrg/AlgebraOfGraphics.jl}
+}
+
+@article{BenchmarkTools_jl_2016,
+  author =	 {{Chen}, Jiahao and {Revels}, Jarrett},
+  title =	 "{Robust benchmarking in noisy environments}",
+  journal =	 {arXiv e-prints},
+  keywords =	 {Computer Science - Performance, 68N30, B.8.1, D.2.5},
+  year =	 2016,
+  month =	 "Aug",
+  eid =		 {arXiv:1608.04295},
+  archivePrefix ={arXiv},
+  eprint =	 {1608.04295},
+  primaryClass = {cs.PF},
+  adsurl =	 {https://ui.adsabs.harvard.edu/abs/2016arXiv160804295C},
+  adsnote =	 {Provided by the SAO/NASA Astrophysics Data System}
+}
+@article{robbins2012eegvis,
+  title={EEGVIS: a Matlab toolbox for browsing, exploring, and viewing large datasets},
+  author={Robbins, Kay A},
+  journal={Frontiers in Neuroinformatics},
+  volume={6},
+  pages={17},
+  year={2012},
+  publisher={Frontiers Research Foundation}
+}
+
+@software{Documenter_jl,
+    year={2024},
+    author = {M. Hatherly and M. Piibeleht and F. Ekre},
+    title = {Documenter: A documentation generator for Julia},
+    version = {1.7},
+    url = {https://github.com/JuliaDocs/Documenter.jl}
+}
+
+@software{topoplots_jl,
+    year={2024},
+    author = {Ehinger, Benedikt V and {Phillip} Alday and {Singhvi}, Anshul and {Danisch} Simon},
+    title = {TopoPlots.jl: A Julia package for topoplot generation},
+    version = {0.1.9},
+    url = {https://github.com/MakieOrg/TopoPlots.jl}
+  }
+
+@software{pymne_jl,
+    year={2024},
+    author = {Phillip Alday and Alex Arslan},
+    title = {PyMNE.jl},
+    version = {0.2.2},
+    url = {https://github.com/beacon-biosignals/PyMNE.jl}
+  }
+
+
+@article{crameri2020misuse,
+  title={The misuse of colour in science communication},
+  author={Crameri, Fabio and Shephard, Grace E and Heron, Philip J},
+  journal={Nature communications},
+  volume={11},
+  number={1},
+  pages={5444},
+  year={2020},
+  publisher={Nature Publishing Group UK London}
+}
+
+@techreport{moreland2015we,
+  title={Why We Use Bad Color Maps and What You Can Do About It.},
+  author={Moreland, Kenneth D},
+  year={2015},
+  institution={Sandia National Lab.(SNL-NM), Albuquerque, NM (United States)}
+}
+
+
+@software{simon_kornblith_2023_8344531,
+author = {Simon Kornblith and
+  Galen Lynch and
+  Martin Holters and
+  João Felipe Santos and
+  Spencer Russell and
+  Jay Kickliter and
+  Jeff Bezanson and
+  Gudmundur Adalsteinsson and
+  Alex Arslan and
+  Ryuichi Yamamoto and
+  jordancluts and
+  Matti Pastell and
+  Tony Kelman and
+  Ben Arthur and
+  Tom Krauss and
+  HDictus and
+  Hamza El-Saawy and
+  Jared Kofron and
+  Eric Hanson and
+  Rob Luke and
+  Viral B. Shah and
+  Aleco Kastanos and
+  Bill and
+  Clemens and
+  Elliot Saba and
+  ibadr and
+  Jake Bolewski and
+  Jordan Smith},
+  title = {JuliaDSP/DSP.jl: v0.7.9},
+  month = sep,
+  year = 2023,
+  publisher = {Zenodo},
+  version = {v0.7.9},
+  doi = {10.5281/zenodo.8344531},
+  url = {https://doi.org/10.5281/zenodo.8344531}
+}
+
+@article{JSSv107i04,
+ title={DataFrames.jl: Flexible and Fast Tabular Data in Julia},
+ volume={107},
+ url={https://www.jstatsoft.org/index.php/jss/article/view/v107i04},
+ doi={10.18637/jss.v107.i04},
+ number={4},
+ journal={Journal of Statistical Software},
+ author={Bouchet-Valat, Milan and Kamiński, Bogumił},
+ year={2023},
+ pages={1--32}
+}
+
+@software{Schepers_UnfoldSim_jl,
+  author = {Schepers, Judith and Lips, Luis and Marathe, Maanik and Ehinger, Benedikt},
+  title = {{UnfoldSim.jl}},
+  year={2024},
+  url = {https://github.com/unfoldtoolbox/UnfoldSim.jl}
+}