diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 283e8b8e..87273f86 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,11 +1,11 @@ repos: - repo: https://github.com/astral-sh/uv-pre-commit - rev: 0.12.23 + rev: 0.13.0 hooks: - id: uv-lock - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.16.10 + rev: v0.17.0 hooks: - id: ruff name: ruff linter @@ -20,11 +20,10 @@ repos: additional_dependencies: [tomli] - repo: https://github.com/mscheltienne/bibclean - rev: 0.8.0 + rev: 1.0.0 hooks: - id: bibclean-fix files: doc/references.bib - args: [--exit-non-zero-on-fix] - repo: https://github.com/pappasam/toml-sort rev: v0.25.0 diff --git a/doc/references.bib b/doc/references.bib index 53db0d08..b3169da6 100644 --- a/doc/references.bib +++ b/doc/references.bib @@ -1,127 +1,127 @@ @article{bids-eeg_2019, - author = {Pernet, Cyril R. and Appelhoff, Stefan and Gorgolewski, Krzysztof J. and Flandin, Guillaume and Phillips, Christophe and Delorme, Arnaud and Oostenveld, Robert}, - doi = {10.1038/s41597-019-0104-8}, - journal = {Scientific Data}, - month = {December}, - number = {1}, - pages = {103}, - title = {{EEG}-{BIDS}, an extension to the brain imaging data structure for electroencephalography}, - volume = {6}, - year = {2019} + author = {Pernet, Cyril R. and Appelhoff, Stefan and Gorgolewski, Krzysztof J. and Flandin, Guillaume and Phillips, Christophe and Delorme, Arnaud and Oostenveld, Robert}, + doi = {10.1038/s41597-019-0104-8}, + journal = {Scientific Data}, + month = dec, + number = {1}, + pages = {103}, + title = {{EEG}-{BIDS}, an extension to the brain imaging data structure for electroencephalography}, + volume = {6}, + year = {2019} } @article{bids-ieeg_2019, - author = {Holdgraf, Christopher and Appelhoff, Stefan and Bickel, Stephan and Bouchard, Kristofer and D’Ambrosio, Sasha and David, Olivier and Devinsky, Orrin and Dichter, Benjamin and Flinker, Adeen and Foster, Brett L. and Gorgolewski, Krzysztof J. and Groen, Iris and Groppe, David and Gunduz, Aysegul and Hamilton, Liberty and Honey, Christopher J. and Jas, Mainak and Knight, Robert and Lachaux, Jean-Philippe and Lau, Jonathan C. and Lee-Messer, Christopher and Lundstrom, Brian N. and Miller, Kai J. and Ojemann, Jeffrey G. and Oostenveld, Robert and Petridou, Natalia and Piantoni, Gio and Pigorini, Andrea and Pouratian, Nader and Ramsey, Nick F. and Stolk, Arjen and Swann, Nicole C. and Tadel, François and Voytek, Bradley and Wandell, Brian A. and Winawer, Jonathan and Whitaker, Kirstie and Zehl, Lyuba and Hermes, Dora}, - doi = {10.1038/s41597-019-0105-7}, - journal = {Scientific Data}, - month = {December}, - number = {1}, - pages = {102}, - title = {{iEEG}-{BIDS}, extending the {Brain} {Imaging} {Data} {Structure} specification to human intracranial electrophysiology}, - volume = {6}, - year = {2019} + author = {Holdgraf, Christopher and Appelhoff, Stefan and Bickel, Stephan and Bouchard, Kristofer and D’Ambrosio, Sasha and David, Olivier and Devinsky, Orrin and Dichter, Benjamin and Flinker, Adeen and Foster, Brett L. and Gorgolewski, Krzysztof J. and Groen, Iris and Groppe, David and Gunduz, Aysegul and Hamilton, Liberty and Honey, Christopher J. and Jas, Mainak and Knight, Robert and Lachaux, Jean-Philippe and Lau, Jonathan C. and Lee-Messer, Christopher and Lundstrom, Brian N. and Miller, Kai J. and Ojemann, Jeffrey G. and Oostenveld, Robert and Petridou, Natalia and Piantoni, Gio and Pigorini, Andrea and Pouratian, Nader and Ramsey, Nick F. and Stolk, Arjen and Swann, Nicole C. and Tadel, François and Voytek, Bradley and Wandell, Brian A. and Winawer, Jonathan and Whitaker, Kirstie and Zehl, Lyuba and Hermes, Dora}, + doi = {10.1038/s41597-019-0105-7}, + journal = {Scientific Data}, + month = dec, + number = {1}, + pages = {102}, + title = {{iEEG}-{BIDS}, extending the {Brain} {Imaging} {Data} {Structure} specification to human intracranial electrophysiology}, + volume = {6}, + year = {2019} } @article{bids-meg_2018, - author = {Niso, Guiomar and Gorgolewski, Krzysztof J. and Bock, Elizabeth and Brooks, Teon L. and Flandin, Guillaume and Gramfort, Alexandre and Henson, Richard N. and Jas, Mainak and Litvak, Vladimir and T. Moreau, Jeremy and Oostenveld, Robert and Schoffelen, Jan-Mathijs and Tadel, Francois and Wexler, Joseph and Baillet, Sylvain}, - doi = {10.1038/sdata.2018.110}, - journal = {Scientific Data}, - month = {December}, - number = {1}, - pages = {180110}, - title = {{MEG}-{BIDS}, the brain imaging data structure extended to magnetoencephalography}, - volume = {5}, - year = {2018} + author = {Niso, Guiomar and Gorgolewski, Krzysztof J. and Bock, Elizabeth and Brooks, Teon L. and Flandin, Guillaume and Gramfort, Alexandre and Henson, Richard N. and Jas, Mainak and Litvak, Vladimir and T. Moreau, Jeremy and Oostenveld, Robert and Schoffelen, Jan-Mathijs and Tadel, Francois and Wexler, Joseph and Baillet, Sylvain}, + doi = {10.1038/sdata.2018.110}, + journal = {Scientific Data}, + month = dec, + number = {1}, + pages = {180110}, + title = {{MEG}-{BIDS}, the brain imaging data structure extended to magnetoencephalography}, + volume = {5}, + year = {2018} } @article{mne-bids_2019, - author = {Appelhoff, Stefan and Sanderson, Matthew and Brooks, Teon and van Vliet, Marijn and Quentin, Romain and Holdgraf, Chris and Chaumon, Maximilien and Mikulan, Ezequiel and Tavabi, Kambiz and Höchenberger, Richard and Welke, Dominik and Brunner, Clemens and Rockhill, Alexander and Larson, Eric and Gramfort, Alexandre and Jas, Mainak}, - doi = {10.21105/joss.01896}, - journal = {Journal of Open Source Software}, - month = {December}, - number = {44}, - pages = {1896}, - title = {{MNE}-{BIDS}: {Organizing} electrophysiological data into the {BIDS} format and facilitating their analysis}, - volume = {4}, - year = {2019} + author = {Appelhoff, Stefan and Sanderson, Matthew and Brooks, Teon and van Vliet, Marijn and Quentin, Romain and Holdgraf, Chris and Chaumon, Maximilien and Mikulan, Ezequiel and Tavabi, Kambiz and Höchenberger, Richard and Welke, Dominik and Brunner, Clemens and Rockhill, Alexander and Larson, Eric and Gramfort, Alexandre and Jas, Mainak}, + doi = {10.21105/joss.01896}, + journal = {Journal of Open Source Software}, + month = dec, + number = {44}, + pages = {1896}, + title = {{MNE}-{BIDS}: {Organizing} electrophysiological data into the {BIDS} format and facilitating their analysis}, + volume = {4}, + year = {2019} } @article{mne-icalabel_2022, - author = {Li, Adam and Feitelberg, Jacob and Saini, Anand Prakash and Höchenberger, Richard and Scheltienne, Mathieu}, - doi = {10.21105/joss.04484}, - journal = {Journal of Open Source Software}, - month = {August}, - number = {76}, - pages = {4484}, - title = {{MNE}-{ICALabel}: {Automatically} annotating {ICA} componentswith {ICLabel} in {Python}}, - volume = {7}, - year = {2022} + author = {Li, Adam and Feitelberg, Jacob and Saini, Anand Prakash and Höchenberger, Richard and Scheltienne, Mathieu}, + doi = {10.21105/joss.04484}, + journal = {Journal of Open Source Software}, + month = aug, + number = {76}, + pages = {4484}, + title = {{MNE}-{ICALabel}: {Automatically} annotating {ICA} componentswith {ICLabel} in {Python}}, + volume = {7}, + year = {2022} } @article{mne-python_2013, - author = {Gramfort, Alexandre}, - doi = {10.3389/fnins.2013.00267}, - journal = {Frontiers in Neuroscience}, - title = {{MEG} and {EEG} data analysis with {MNE}-{Python}}, - volume = {7}, - year = {2013} + author = {Gramfort, Alexandre}, + doi = {10.3389/fnins.2013.00267}, + journal = {Frontiers in Neuroscience}, + title = {{MEG} and {EEG} data analysis with {MNE}-{Python}}, + volume = {7}, + year = {2013} } @article{mne_2014, - author = {Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis A. and Strohmeier, Daniel and Brodbeck, Christian and Parkkonen, Lauri and Hämäläinen, Matti S.}, - doi = {10.1016/j.neuroimage.2013.10.027}, - journal = {NeuroImage}, - month = {February}, - pages = {446--460}, - title = {{MNE} software for processing {MEG} and {EEG} data}, - volume = {86}, - year = {2014} + author = {Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis A. and Strohmeier, Daniel and Brodbeck, Christian and Parkkonen, Lauri and Hämäläinen, Matti S.}, + doi = {10.1016/j.neuroimage.2013.10.027}, + journal = {NeuroImage}, + month = feb, + pages = {446--460}, + title = {{MNE} software for processing {MEG} and {EEG} data}, + volume = {86}, + year = {2014} } @article{numpy_2020, - author = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.}, - doi = {10.1038/s41586-020-2649-2}, - journal = {Nature}, - month = {September}, - number = {7825}, - pages = {357--362}, - title = {Array programming with {NumPy}}, - volume = {585}, - year = {2020} + author = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.}, + doi = {10.1038/s41586-020-2649-2}, + journal = {Nature}, + month = sep, + number = {7825}, + pages = {357--362}, + title = {Array programming with {NumPy}}, + volume = {585}, + year = {2020} } @article{picard_2018, - author = {Ablin, Pierre and Cardoso, Jean-François and Gramfort, Alexandre}, - doi = {10.1109/TSP.2018.2844203}, - journal = {IEEE Transactions on Signal Processing}, - month = {August}, - number = {15}, - pages = {4040--4049}, - title = {Faster independent component analysis by preconditioning with {Hessian} approximations}, - volume = {66}, - year = {2018} + author = {Ablin, Pierre and Cardoso, Jean-François and Gramfort, Alexandre}, + doi = {10.1109/TSP.2018.2844203}, + journal = {IEEE Transactions on Signal Processing}, + month = aug, + number = {15}, + pages = {4040--4049}, + title = {Faster independent component analysis by preconditioning with {Hessian} approximations}, + volume = {66}, + year = {2018} } @article{psychopy2_2019, - author = {Peirce, Jonathan and Gray, Jeremy R. and Simpson, Sol and MacAskill, Michael and Höchenberger, Richard and Sogo, Hiroyuki and Kastman, Erik and Lindeløv, Jonas Kristoffer}, - doi = {10.3758/s13428-018-01193-y}, - journal = {Behavior Research Methods}, - month = {February}, - number = {1}, - pages = {195--203}, - title = {{PsychoPy2}: {Experiments} in behavior made easy}, - volume = {51}, - year = {2019} + author = {Peirce, Jonathan and Gray, Jeremy R. and Simpson, Sol and MacAskill, Michael and Höchenberger, Richard and Sogo, Hiroyuki and Kastman, Erik and Lindeløv, Jonas Kristoffer}, + doi = {10.3758/s13428-018-01193-y}, + journal = {Behavior Research Methods}, + month = feb, + number = {1}, + pages = {195--203}, + title = {{PsychoPy2}: {Experiments} in behavior made easy}, + volume = {51}, + year = {2019} } @article{scipy_2020, - author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, İlhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Antônio H. and Pedregosa, Fabian and van Mulbregt, Paul and {SciPy 1.0 Contributors} and Vijaykumar, Aditya and Bardelli, Alessandro Pietro and Rothberg, Alex and Hilboll, Andreas and Kloeckner, Andreas and Scopatz, Anthony and Lee, Antony and Rokem, Ariel and Woods, C. Nathan and Fulton, Chad and Masson, Charles and Häggström, Christian and Fitzgerald, Clark and Nicholson, David A. and Hagen, David R. and Pasechnik, Dmitrii V. and Olivetti, Emanuele and Martin, Eric and Wieser, Eric and Silva, Fabrice and Lenders, Felix and Wilhelm, Florian and Young, G. and Price, Gavin A. and Ingold, Gert-Ludwig and Allen, Gregory E. and Lee, Gregory R. and Audren, Hervé and Probst, Irvin and Dietrich, Jörg P. and Silterra, Jacob and Webber, James T and Slavič, Janko and Nothman, Joel and Buchner, Johannes and Kulick, Johannes and Schönberger, Johannes L. and de Miranda Cardoso, José Vinícius and Reimer, Joscha and Harrington, Joseph and Rodríguez, Juan Luis Cano and Nunez-Iglesias, Juan and Kuczynski, Justin and Tritz, Kevin and Thoma, Martin and Newville, Matthew and Kümmerer, Matthias and Bolingbroke, Maximilian and Tartre, Michael and Pak, Mikhail and Smith, Nathaniel J. and Nowaczyk, Nikolai and Shebanov, Nikolay and Pavlyk, Oleksandr and Brodtkorb, Per A. and Lee, Perry and McGibbon, Robert T. and Feldbauer, Roman and Lewis, Sam and Tygier, Sam and Sievert, Scott and Vigna, Sebastiano and Peterson, Stefan and More, Surhud and Pudlik, Tadeusz and Oshima, Takuya and Pingel, Thomas J. and Robitaille, Thomas P. and Spura, Thomas and Jones, Thouis R. and Cera, Tim and Leslie, Tim and Zito, Tiziano and Krauss, Tom and Upadhyay, Utkarsh and Halchenko, Yaroslav O. and Vázquez-Baeza, Yoshiki}, - doi = {10.1038/s41592-019-0686-2}, - journal = {Nature Methods}, - month = {March}, - number = {3}, - pages = {261--272}, - title = {{SciPy} 1.0: fundamental algorithms for scientific computing in {Python}}, - volume = {17}, - year = {2020} + author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, İlhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Antônio H. and Pedregosa, Fabian and van Mulbregt, Paul and {SciPy 1.0 Contributors} and Vijaykumar, Aditya and Bardelli, Alessandro Pietro and Rothberg, Alex and Hilboll, Andreas and Kloeckner, Andreas and Scopatz, Anthony and Lee, Antony and Rokem, Ariel and Woods, C. Nathan and Fulton, Chad and Masson, Charles and Häggström, Christian and Fitzgerald, Clark and Nicholson, David A. and Hagen, David R. and Pasechnik, Dmitrii V. and Olivetti, Emanuele and Martin, Eric and Wieser, Eric and Silva, Fabrice and Lenders, Felix and Wilhelm, Florian and Young, G. and Price, Gavin A. and Ingold, Gert-Ludwig and Allen, Gregory E. and Lee, Gregory R. and Audren, Hervé and Probst, Irvin and Dietrich, Jörg P. and Silterra, Jacob and Webber, James T and Slavič, Janko and Nothman, Joel and Buchner, Johannes and Kulick, Johannes and Schönberger, Johannes L. and de Miranda Cardoso, José Vinícius and Reimer, Joscha and Harrington, Joseph and Rodríguez, Juan Luis Cano and Nunez-Iglesias, Juan and Kuczynski, Justin and Tritz, Kevin and Thoma, Martin and Newville, Matthew and Kümmerer, Matthias and Bolingbroke, Maximilian and Tartre, Michael and Pak, Mikhail and Smith, Nathaniel J. and Nowaczyk, Nikolai and Shebanov, Nikolay and Pavlyk, Oleksandr and Brodtkorb, Per A. and Lee, Perry and McGibbon, Robert T. and Feldbauer, Roman and Lewis, Sam and Tygier, Sam and Sievert, Scott and Vigna, Sebastiano and Peterson, Stefan and More, Surhud and Pudlik, Tadeusz and Oshima, Takuya and Pingel, Thomas J. and Robitaille, Thomas P. and Spura, Thomas and Jones, Thouis R. and Cera, Tim and Leslie, Tim and Zito, Tiziano and Krauss, Tom and Upadhyay, Utkarsh and Halchenko, Yaroslav O. and Vázquez-Baeza, Yoshiki}, + doi = {10.1038/s41592-019-0686-2}, + journal = {Nature Methods}, + month = mar, + number = {3}, + pages = {261--272}, + title = {{SciPy} 1.0: fundamental algorithms for scientific computing in {Python}}, + volume = {17}, + year = {2020} } diff --git a/pyproject.toml b/pyproject.toml index 0c80242a..a385483e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ ide = [ 'ipython', ] style = [ - 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