From 6b41ad1d1b3357d553c1e825bbb8d72273458c27 Mon Sep 17 00:00:00 2001 From: Sylvain Chevallier Date: Sat, 31 Dec 2022 01:42:38 +0100 Subject: [PATCH] Update deps and doc cleaning (#315) * update poetry deps and start cleaning docs * update example with new seaborn version * rename page * update code link button in doc * update docs for datasets * correct error with np type, add warning for the dataset * reduce computation time for documentation * fix plot issue * update doc workflow * fix download path location * switch to pre-commit.ci * correct spelling * fix pre commit config * switch to python 3.8 and latest ubuntu * add coverage requirements * correct typo * update actions * try xml report for codecov, add coveralls * remove coveralls --- .coveragerc | 1 - .github/workflows/docs.yml | 26 +- .github/workflows/test-devel.yml | 34 +- .github/workflows/test.yml | 18 +- .pre-commit-config.yaml | 13 +- docs/source/README.md | 2 +- docs/source/conf.py | 40 +- docs/source/datasets.rst | 2 +- docs/source/index.rst | 5 - .../plot_filterbank_csp_vs_csp.py | 8 +- examples/plot_cross_session_motor_imagery.py | 10 +- examples/plot_cross_subject_ssvep.py | 2 +- examples/plot_within_session_p300.py | 2 +- examples/plot_within_session_ssvep.py | 4 +- moabb/datasets/Lee2019.py | 2 +- moabb/datasets/Weibo2014.py | 5 +- moabb/datasets/Zhou2016.py | 5 +- moabb/datasets/bbci_eeg_fnirs.py | 13 +- moabb/datasets/braininvaders.py | 82 +- moabb/datasets/neiry.py | 21 +- moabb/datasets/sosulski2019.py | 24 +- poetry.lock | 1050 ++++++----------- pyproject.toml | 49 +- requirements.txt | 518 ++------ setup.cfg | 2 +- 25 files changed, 636 insertions(+), 1302 deletions(-) diff --git a/.coveragerc b/.coveragerc index fbe79c16e..55956b374 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,7 +1,6 @@ [run] branch = True source = moabb -include = */moabb/* omit = */docs/* */pipelines/* diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 2e79b634d..297a91931 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -14,30 +14,30 @@ jobs: strategy: fail-fast: true matrix: - os: [ubuntu-18.04] + os: [ubuntu-latest] python-version: ["3.9"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Create local data folder run: | mkdir ~/mne_data - name: Setup Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Install Poetry - uses: snok/install-poetry@v1.1.6 + uses: snok/install-poetry@v1 with: virtualenvs-create: true virtualenvs-in-project: true - name: Cache datasets and docs id: cached-dataset-docs - uses: actions/cache@v2 + uses: actions/cache@v3 with: key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }} path: | @@ -68,10 +68,10 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-18.04] + os: [ubuntu-latest] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Create local data folder run: | @@ -79,7 +79,7 @@ jobs: - name: Cache datasets and docs id: cached-dataset-docs - uses: actions/cache@v2 + uses: actions/cache@v3 with: key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }} path: | @@ -87,7 +87,7 @@ jobs: docs/build - name: Checkout moabb.github.io - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: repository: "NeuroTechX/moabb.github.io" path: moabb-ghio @@ -111,10 +111,10 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-18.04] + os: [ubuntu-latest] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Create local data folder run: | @@ -122,7 +122,7 @@ jobs: - name: Cache datasets and docs id: cached-dataset-docs - uses: actions/cache@v2 + uses: actions/cache@v3 with: key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }} path: | @@ -130,7 +130,7 @@ jobs: docs/build - name: Checkout gh pages - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: ref: gh-pages path: moabb-ghpages diff --git a/.github/workflows/test-devel.yml b/.github/workflows/test-devel.yml index 2669c6542..fc7288984 100644 --- a/.github/workflows/test-devel.yml +++ b/.github/workflows/test-devel.yml @@ -13,16 +13,16 @@ jobs: strategy: fail-fast: true matrix: - os: [ubuntu-18.04, windows-latest, macOS-latest] - python-version: ["3.7"] + os: [ubuntu-latest, windows-latest, macOS-latest] + python-version: ["3.8"] defaults: run: shell: bash steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Setup Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} @@ -35,7 +35,7 @@ jobs: - name: Load cached venv if: runner.os != 'Windows' id: cached-poetry-dependencies - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: .venv key: @@ -55,6 +55,7 @@ jobs: run: | source $VENV poetry run coverage run -m unittest moabb.tests + poetry run coverage xml - name: Run pipelines run: | @@ -62,27 +63,10 @@ jobs: poetry run python -m moabb.run --pipelines=./moabb/tests/test_pipelines/ --verbose - name: Upload Coverage to Codecov - uses: codecov/codecov-action@v2 + uses: codecov/codecov-action@v3 if: success() with: verbose: true directory: /home/runner/work/moabb/moabb - files: ./.coverage - - lint: - name: lint ${{ matrix.os }}, py-${{ matrix.python-version }} - runs-on: ${{ matrix.os }} - strategy: - fail-fast: true - matrix: - os: [ubuntu-18.04] - python-version: ["3.8"] - steps: - - uses: actions/checkout@v2 - - - name: Setup Python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - - uses: pre-commit/action@v3.0.0 + files: ./.coverage,coverage.xml + env_vars: OS,PYTHON diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index fff42ab27..ea8c91981 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,16 +13,16 @@ jobs: strategy: fail-fast: true matrix: - os: [ubuntu-18.04, windows-latest, macOS-latest] - python-version: ["3.7", "3.8", "3.9"] + os: [ubuntu-latest, windows-latest, macOS-latest] + python-version: ["3.8", "3.9"] defaults: run: shell: bash steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Setup Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} @@ -35,7 +35,7 @@ jobs: - name: Load cached venv if: runner.os != 'Windows' id: cached-poetry-dependencies - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: .venv key: @@ -54,7 +54,8 @@ jobs: - name: Run tests run: | source $VENV - poetry run python -m unittest moabb.tests + poetry run coverage run -m unittest moabb.tests + poetry run coverage xml - name: Run pipelines run: | @@ -62,9 +63,10 @@ jobs: poetry run python -m moabb.run --pipelines=./moabb/tests/test_pipelines/ --verbose - name: Upload Coverage to Codecov - uses: codecov/codecov-action@v2 + uses: codecov/codecov-action@v3 if: success() with: verbose: true directory: /home/runner/work/moabb/moabb - files: ./.coverage + files: ./.coverage,coverage.xml + env_vars: OS,PYTHON diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b472500c9..0b0a59c02 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,16 @@ default_language_version: python: python3 + +ci: + autofix_commit_msg: | + [pre-commit.ci] auto fixes from pre-commit.com hooks + autofix_prs: true + autoupdate_branch: "develop" + autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate" + autoupdate_schedule: quarterly + skip: [] + submodules: false + repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v3.4.0 @@ -22,7 +33,7 @@ repos: hooks: - id: isort - - repo: https://gitlab.com/pycqa/flake8 + - repo: https://github.com/pycqa/flake8 rev: 3.8.4 hooks: - id: flake8 diff --git a/docs/source/README.md b/docs/source/README.md index 4da01fa0d..20c8a7f0a 100644 --- a/docs/source/README.md +++ b/docs/source/README.md @@ -5,7 +5,7 @@ ![banner](images/M.png)

-n Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets. + Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.

## Disclaimer diff --git a/docs/source/conf.py b/docs/source/conf.py index 97f469a5b..4b35c7754 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -36,7 +36,7 @@ # -- Project information ----------------------------------------------------- project = "moabb" -copyright = "2018-2021, Alexandre Barachant, Sylvain Chevallier" +copyright = "2018-2023 MOABB contributors" author = "Alexandre Barachant, Vinay Jayaram, Sylvain Chevallier" # The short X.Y version @@ -69,35 +69,40 @@ "sphinx.ext.napoleon", "sphinx.ext.linkcode", "sphinx.ext.mathjax", - "sphinx.ext.viewcode", + # "sphinx.ext.viewcode", "sphinx_gallery.gen_gallery", "gh_substitutions", - # "m2r2", + "m2r2", "numpydoc", ] def linkcode_resolve(domain, info): # noqa: C901 """Determine the URL corresponding to a Python object. + Parameters ---------- domain : str Only useful when 'py'. info : dict With keys "module" and "fullname". + Returns ------- url : str The code URL. + Notes ----- This has been adapted to deal with our "verbose" decorator. Adapted from SciPy (doc/source/conf.py). """ - import mne + repo = "https://github.com/NeuroTechX/moabb" if domain != "py": return None + if not info["module"]: + return None modname = info["module"] fullname = info["fullname"] @@ -112,9 +117,6 @@ def linkcode_resolve(domain, info): # noqa: C901 obj = getattr(obj, part) except Exception: return None - # deal with our decorators properly - while hasattr(obj, "__wrapped__"): - obj = obj.__wrapped__ try: fn = inspect.getsourcefile(obj) @@ -127,7 +129,7 @@ def linkcode_resolve(domain, info): # noqa: C901 fn = None if not fn: return None - fn = op.relpath(fn, start=op.dirname(mne.__file__)) + fn = op.relpath(fn, start=op.dirname(moabb.__file__)) fn = "/".join(op.normpath(fn).split(os.sep)) # in case on Windows try: @@ -140,15 +142,11 @@ def linkcode_resolve(domain, info): # noqa: C901 else: linespec = "" - if "dev" in moabb.__version__: - kind = "master" - else: - kind = "maint/%s" % (".".join(mne.__version__.split(".")[:2])) - return "http://github.com/NeuroTechX/moabb/blob/%s/moabb/%s%s" % ( # noqa - kind, - fn, - linespec, - ) + # if "dev" in moabb.__version__: + # kind = "develop" + # else: + # kind = "master" + return f"{repo}/blob/develop/moabb/{fn}{linespec}" napoleon_google_docstring = False @@ -194,7 +192,7 @@ def linkcode_resolve(domain, info): # noqa: C901 # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = "en" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -222,9 +220,9 @@ def linkcode_resolve(domain, info): # noqa: C901 # theme further. html_theme_options = { # Navigation bar title. (Default: ``project`` value) - # 'navbar_title': "Demo", + "navbar_title": "MOABB", # Tab name for entire site. (Default: "Site") - # 'navbar_site_name': "Site", + "navbar_site_name": "MOABB", # A list of tuples containing pages or urls to link to. # Valid tuples should be in the following forms: # (name, page) # a link to a page @@ -347,7 +345,7 @@ def linkcode_resolve(domain, info): # noqa: C901 "moabb Documentation", author, "moabb", - "One line description of project.", + "Mother of all BCI benchmarks.", "Miscellaneous", ), ] diff --git a/docs/source/datasets.rst b/docs/source/datasets.rst index 2545d58c1..56e6f3af7 100644 --- a/docs/source/datasets.rst +++ b/docs/source/datasets.rst @@ -40,7 +40,7 @@ ERP Datasets :toctree: generated/ :template: class.rst - bi2012a + bi2012 bi2013a bi2014a bi2014b diff --git a/docs/source/index.rst b/docs/source/index.rst index c31745043..f3dbf0264 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,8 +1,3 @@ -.. moabb documentation master file, created by - sphinx-quickstart on Sun Apr 1 17:48:47 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - .. mdinclude:: README.md What's new diff --git a/examples/advanced_examples/plot_filterbank_csp_vs_csp.py b/examples/advanced_examples/plot_filterbank_csp_vs_csp.py index ac3784a9e..149b6bcc5 100644 --- a/examples/advanced_examples/plot_filterbank_csp_vs_csp.py +++ b/examples/advanced_examples/plot_filterbank_csp_vs_csp.py @@ -57,7 +57,7 @@ # The first one is a standard `LeftRightImagery` with a 8 to 35 Hz broadband # filter. # -# The second is a `FilterBankLeftRightImagery` with a bank of 6 filter, ranging +# The second is a `FilterBankLeftRightImagery` with a bank of 2 filters, ranging # from 8 to 35 Hz. # Because this is being auto-generated we only use 2 subjects @@ -75,8 +75,8 @@ ) results = evaluation.process(pipelines) -# Bank of 6 filters, by 4 Hz increment -filters = [[8, 12], [12, 16], [16, 20], [20, 24], [24, 28], [28, 35]] +# Bank of 2 filters +filters = [[8, 24], [16, 32]] paradigm = FilterBankLeftRightImagery(filters=filters) evaluation = CrossSessionEvaluation( paradigm=paradigm, datasets=datasets, suffix="examples", overwrite=overwrite @@ -111,7 +111,7 @@ zorder=1, palette="Set1", ) -sns.pointplot(data=results, y="score", x="pipeline", ax=axes[0], zorder=1, palette="Set1") +sns.pointplot(data=results, y="score", x="pipeline", ax=axes[0], palette="Set1") axes[0].set_ylabel("ROC AUC") axes[0].set_ylim(0.5, 1) diff --git a/examples/plot_cross_session_motor_imagery.py b/examples/plot_cross_session_motor_imagery.py index b1c1ce253..ede6a94ed 100644 --- a/examples/plot_cross_session_motor_imagery.py +++ b/examples/plot_cross_session_motor_imagery.py @@ -93,6 +93,9 @@ # # Here we plot the results. We first make a pointplot with the average # performance of each pipeline across session and subjects. +# The second plot is a paired scatter plot. Each point representing the score +# of a single session. An algorithm will outperform another is most of the +# points are in its quadrant. fig, axes = plt.subplots(1, 2, figsize=[8, 4], sharey=True) @@ -106,16 +109,11 @@ zorder=1, palette="Set1", ) -sns.pointplot(data=results, y="score", x="pipeline", ax=axes[0], zorder=1, palette="Set1") +sns.pointplot(data=results, y="score", x="pipeline", ax=axes[0], palette="Set1") axes[0].set_ylabel("ROC AUC") axes[0].set_ylim(0.5, 1) -############################################################################## -# The second plot is a paired scatter plot. Each point representing the score -# of a single session. An algorithm will outperform another is most of the -# points are in its quadrant. - paired = results.pivot_table( values="score", columns="pipeline", index=["subject", "session"] ) diff --git a/examples/plot_cross_subject_ssvep.py b/examples/plot_cross_subject_ssvep.py index e01488a23..5e9574da1 100644 --- a/examples/plot_cross_subject_ssvep.py +++ b/examples/plot_cross_subject_ssvep.py @@ -160,7 +160,7 @@ zorder=1, palette="Set1", ) -sns.pointplot(data=results, y="score", x="pipeline", ax=ax, zorder=1, palette="Set1") +sns.pointplot(data=results, y="score", x="pipeline", ax=ax, palette="Set1") ax.set_ylabel("Accuracy") ax.set_ylim(0.1, 0.6) plt.show() diff --git a/examples/plot_within_session_p300.py b/examples/plot_within_session_p300.py index 6b9cf815f..bff442f52 100644 --- a/examples/plot_within_session_p300.py +++ b/examples/plot_within_session_p300.py @@ -129,7 +129,7 @@ def transform(self, X): zorder=1, palette="Set1", ) -sns.pointplot(data=results, y="score", x="pipeline", ax=ax, zorder=1, palette="Set1") +sns.pointplot(data=results, y="score", x="pipeline", ax=ax, palette="Set1") ax.set_ylabel("ROC AUC") ax.set_ylim(0.5, 1) diff --git a/examples/plot_within_session_ssvep.py b/examples/plot_within_session_ssvep.py index dbc9e6188..9ee91f20a 100644 --- a/examples/plot_within_session_ssvep.py +++ b/examples/plot_within_session_ssvep.py @@ -1,7 +1,7 @@ """ -=================== +===================== Within Session SSVEP -=================== +===================== This Example show how to perform a within-session SSVEP analysis on the MAMEM dataset 3, using a CCA pipeline. diff --git a/moabb/datasets/Lee2019.py b/moabb/datasets/Lee2019.py index 1c7c4b857..99dfcfa63 100644 --- a/moabb/datasets/Lee2019.py +++ b/moabb/datasets/Lee2019.py @@ -325,7 +325,7 @@ class Lee2019_ERP(Lee2019): and gazing at the next target character. The participant was instructed to attend to the target symbol by counting the number of times each target character had been flashed. - In the training session, subjects were asked to copy-spell + In the training session, subjects were asked to copy-spell a given sentence, "NEURAL NETWORKS AND DEEP LEARNING" (33 characters including spaces) by gazing at the target character on the screen. The training session was performed in the offline diff --git a/moabb/datasets/Weibo2014.py b/moabb/datasets/Weibo2014.py index e41754ab7..54cb46d2b 100644 --- a/moabb/datasets/Weibo2014.py +++ b/moabb/datasets/Weibo2014.py @@ -9,11 +9,11 @@ import mne import numpy as np -from mne.datasets.utils import _get_path from pooch import Unzip, retrieve from scipy.io import loadmat from .base import BaseDataset +from .download import get_dataset_path log = logging.getLogger(__name__) @@ -172,8 +172,7 @@ def data_path( ): if subject not in self.subject_list: raise (ValueError("Invalid subject number")) - key = "MNE_DATASETS_WEIBO2014_PATH" - path = _get_path(path, key, "Weibo 2014") + path = get_dataset_path("WEIBO", path) basepath = os.path.join(path, "MNE-weibo-2014") if not os.path.isdir(basepath): os.makedirs(basepath) diff --git a/moabb/datasets/Zhou2016.py b/moabb/datasets/Zhou2016.py index 3b143aa51..17707544b 100644 --- a/moabb/datasets/Zhou2016.py +++ b/moabb/datasets/Zhou2016.py @@ -9,11 +9,11 @@ import numpy as np from mne.channels import make_standard_montage -from mne.datasets.utils import _get_path from mne.io import read_raw_cnt from pooch import retrieve from .base import BaseDataset +from .download import get_dataset_path DATA_PATH = "https://ndownloader.figshare.com/files/3662952" @@ -114,8 +114,7 @@ def data_path( ): if subject not in self.subject_list: raise (ValueError("Invalid subject number")) - key = "MNE_DATASETS_ZHOU2016_PATH" - path = _get_path(path, key, "Zhou 2016") + path = get_dataset_path("ZHOU", path) basepath = os.path.join(path, "MNE-zhou-2016") if not os.path.isdir(basepath): os.makedirs(basepath) diff --git a/moabb/datasets/bbci_eeg_fnirs.py b/moabb/datasets/bbci_eeg_fnirs.py index ac31b6d3e..717068021 100644 --- a/moabb/datasets/bbci_eeg_fnirs.py +++ b/moabb/datasets/bbci_eeg_fnirs.py @@ -187,8 +187,10 @@ class Shin2017A(Shin2017): Dataset from [1]_. - You should accept the licence term [2]_ to download this dataset, using:: - Shin2017A(accept=True) + + .. caution:: + You should accept the licence term [2]_ to download this dataset, using: + ``Shin2017A(accept=True)`` **Data Acquisition** @@ -279,6 +281,7 @@ class Shin2017A(Shin2017): Hwang, H.J. and Müller, K.R., 2017. Open access dataset for EEG+NIRS single-trial classification. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 25(10), pp.1735-1745. + .. [2] GNU General Public License, Version 3 ``_ """ @@ -295,8 +298,9 @@ class Shin2017B(Shin2017): Dataset from [1]_. - You should accept the licence term [2]_ to download this dataset, using:: - Shin2017A(accept=True) + .. caution:: + You should accept the licence term [2]_ to download this dataset, using: + ``Shin2017B(accept=True)`` **Data Acquisition** @@ -381,6 +385,7 @@ class Shin2017B(Shin2017): Hwang, H.J. and Müller, K.R., 2017. Open access dataset for EEG+NIRS single-trial classification. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 25(10), pp.1735-1745. + .. [2] GNU General Public License, Version 3 ``_ """ diff --git a/moabb/datasets/braininvaders.py b/moabb/datasets/braininvaders.py index 8ea72f9b0..247606cb1 100644 --- a/moabb/datasets/braininvaders.py +++ b/moabb/datasets/braininvaders.py @@ -339,8 +339,6 @@ class bi2012(BaseDataset): Dataset following the setup from [1]_ carried-out at University of Grenoble Alpes. - **Dataset Description** - This dataset contains electroencephalographic (EEG) recordings of 25 subjects testing the Brain Invaders, a visual P300 Brain-Computer Interface inspired by the famous vintage video game Space Invaders (Taito, Tokyo, Japan). The visual P300 is an event-related @@ -348,18 +346,18 @@ class bi2012(BaseDataset): data were recorded by 16 electrodes in an experiment that took place in the GIPSA-lab, Grenoble, France, in 2012). A full description of the experiment is available in [1]_. - **Authors** + :Principal Investigator: B.Sc. Gijsbrecht Franciscus Petrus Van Veen + + :Technical Supervisors: Ph.D. Alexandre Barachant, Eng. Anton Andreev, Eng. Grégoire Cattan, + Eng. Pedro. L. C. Rodrigues - Principal Investigator: B.Sc. Gijsbrecht Franciscus Petrus Van Veen - Technical Supervisors: Ph.D. Alexandre Barachant, Eng. Anton Andreev, Eng. Grégoire Cattan, - Eng. Pedro. L. C. Rodrigues - Scientific Supervisor: Ph.D. Marco Congedo + :Scientific Supervisor: Ph.D. Marco Congedo - **ID of the dataset** - BI.EEG.2012-GIPSA + :ID of the dataset: BI.EEG.2012-GIPSA Notes ----- + .. versionadded:: 0.4.6 References @@ -400,8 +398,6 @@ class bi2013a(BaseDataset): Dataset following the setup from [1]_ carried-out at University of Grenoble Alpes. - **Dataset Description** - This dataset concerns an experiment carried out at GIPSA-lab (University of Grenoble Alpes, CNRS, Grenoble-INP) in 2013. The recordings concerned 24 subjects in total. Subjects 1 to 7 participated @@ -441,11 +437,9 @@ class bi2013a(BaseDataset): * Reference: left ear-lobe. * Ground: N/A. - **Authors** - - Principal Investigators: Erwan Vaineau, Dr. Alexandre Barachant - Scientific Supervisor : Dr. Marco Congedo - Technical Supervisor : Anton Andreev + :Principal Investigators: Erwan Vaineau, Dr. Alexandre Barachant + :Scientific Supervisor: Dr. Marco Congedo + :Technical Supervisor: Anton Andreev References ---------- @@ -454,10 +448,12 @@ class bi2013a(BaseDataset): Cattan, G. & Congedo, M. (2019). Brain invaders adaptive versus non-adaptive P300 brain-computer interface dataset. arXiv preprint arXiv:1904.09111. + .. [2] Barachant A, Congedo M (2014) A Plug & Play P300 BCI using Information Geometry. arXiv:1409.0107. - .. [7] Congedo M, Goyat M, Tarrin N, Ionescu G, Rivet B,Varnet L, Rivet B, + + .. [3] Congedo M, Goyat M, Tarrin N, Ionescu G, Rivet B,Varnet L, Rivet B, Phlypo R, Jrad N, Acquadro M, Jutten C (2011) “Brain Invaders”: a prototype of an open-source P300-based video game working with the OpenViBE platform. Proc. IBCI Conf., Graz, Austria, 280-283. @@ -492,8 +488,6 @@ def data_path( class bi2014a(BaseDataset): """P300 dataset bi2014a from a "Brain Invaders" experiment - **Dataset Description** - This dataset contains electroencephalographic (EEG) recordings of 71 subjects playing to a visual P300 Brain-Computer Interface (BCI) videogame named Brain Invaders. The interface uses the oddball paradigm on a grid of 36 symbols (1 Target, 35 Non-Target) @@ -502,15 +496,14 @@ class bi2014a(BaseDataset): at GIPSA-lab, Grenoble, France, in 2014. A full description of the experiment is available at [1]_. The ID of this dataset is bi2014a. - **Authors** - - Investigators: Eng. Louis Korczowski, B. Sc. Ekaterina Ostaschenko - Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, - M. Sc. Violette Gautheret - Scientific Supervisor: Ph.D. Marco Congedo + :Investigators: Eng. Louis Korczowski, B. Sc. Ekaterina Ostaschenko + :Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, + M. Sc. Violette Gautheret + :Scientific Supervisor: Ph.D. Marco Congedo Notes ----- + .. versionadded:: 0.4.6 References @@ -546,8 +539,6 @@ def data_path( class bi2014b(BaseDataset): """P300 dataset bi2014b from a "Brain Invaders" experiment - **Dataset Description** - This dataset contains electroencephalographic (EEG) recordings of 38 subjects playing in pair (19 pairs) to the multi-user version of a visual P300-based Brain-Computer Interface (BCI) named Brain Invaders. The interface uses the oddball paradigm on a grid of 36 symbols (1 Target, @@ -557,15 +548,14 @@ class bi2014b(BaseDataset): (Solo1, Solo2, Collaboration). The experiment took place at GIPSA-lab, Grenoble, France, in 2014. A full description of the experiment is available at [1]_. The ID of this dataset is bi2014b. - **Authors** - - Investigators: Eng. Louis Korczowski, B. Sc. Ekaterina Ostaschenko - Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, - M. Sc. Violette Gautheret - Scientific Supervisor: Ph.D. Marco Congedo + :Investigators: Eng. Louis Korczowski, B. Sc. Ekaterina Ostaschenko + :Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, + M. Sc. Violette Gautheret + :Scientific Supervisor: Ph.D. Marco Congedo Notes ----- + .. versionadded:: 0.4.6 References @@ -601,8 +591,6 @@ def data_path( class bi2015a(BaseDataset): """P300 dataset bi2015a from a "Brain Invaders" experiment - **Dataset Description** - This dataset contains electroencephalographic (EEG) recordings of 43 subjects playing to a visual P300 Brain-Computer Interface (BCI) videogame named Brain Invaders. The interface uses the oddball paradigm @@ -613,15 +601,14 @@ class bi2015a(BaseDataset): A full description of the experiment is available at [1]_. The ID of this dataset is bi2015a. - **Authors** - - Investigators: Eng. Louis Korczowski, B. Sc. Martine Cederhout - Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, - M. Sc. Violette Gautheret - Scientific Supervisor: Ph.D. Marco Congedo + :Investigators: Eng. Louis Korczowski, B. Sc. Martine Cederhout + :Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, + M. Sc. Violette Gautheret + :Scientific Supervisor: Ph.D. Marco Congedo Notes ----- + .. versionadded:: 0.4.6 References @@ -657,8 +644,6 @@ def data_path( class bi2015b(BaseDataset): """P300 dataset bi2015b from a "Brain Invaders" experiment - **Dataset Description** - This dataset contains electroencephalographic (EEG) recordings of 44 subjects playing in pair to the multi-user version of a visual P300 Brain-Computer Interface (BCI) named Brain Invaders. The interface @@ -672,15 +657,14 @@ class bi2015b(BaseDataset): A full description of the experiment is available at [1]_. The ID of this dataset is bi2015a. - **Authors** - - Investigators: Eng. Louis Korczowski, B. Sc. Martine Cederhout - Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, - M. Sc. Violette Gautheret - Scientific Supervisor: Ph.D. Marco Congedo + :Investigators: Eng. Louis Korczowski, B. Sc. Martine Cederhout + :Technical Support: Eng. Anton Andreev, Eng. Grégoire Cattan, Eng. Pedro. L. C. Rodrigues, + M. Sc. Violette Gautheret + :Scientific Supervisor: Ph.D. Marco Congedo Notes ----- + .. versionadded:: 0.4.6 References diff --git a/moabb/datasets/neiry.py b/moabb/datasets/neiry.py index af9d4d4b3..f3141fb61 100644 --- a/moabb/datasets/neiry.py +++ b/moabb/datasets/neiry.py @@ -14,6 +14,11 @@ class DemonsP300(BaseDataset): """Visual P300 dataset recorded in Virtual Reality (VR) game Raccoons versus Demons. + .. danger:: + + This dataset contains major unresolved issues and could removed in the near futur. Use it in a benchmark + at your own risk. See https://github.com/NeuroTechX/moabb/issues/216 + **Dataset Description** We publish dataset of visual P300 BCI performed in Virtual Reality (VR) game Raccoons versus @@ -75,18 +80,18 @@ class DemonsP300(BaseDataset): _act_dtype = np.dtype( [ - ("id", np.int), - ("target", np.int), - ("is_train", np.bool), - ("prediction", np.int), - ("sessions", np.object), # list of `_session_dtype` + ("id", int), + ("target", int), + ("is_train", bool), + ("prediction", int), + ("sessions", object), # list of `_session_dtype` ] ) _session_dtype = np.dtype( [ - ("eeg", np.object), - ("starts", np.object), - ("stimuli", np.object), + ("eeg", object), + ("starts", object), + ("stimuli", object), ] ) diff --git a/moabb/datasets/sosulski2019.py b/moabb/datasets/sosulski2019.py index 1e41ad9c6..d6c0f540e 100644 --- a/moabb/datasets/sosulski2019.py +++ b/moabb/datasets/sosulski2019.py @@ -17,7 +17,7 @@ class Sosulski2019(BaseDataset): """P300 dataset from initial spot study. - Dataset [1], study on spatial transfer between SOAs [2], actual paradigm / online optimization [3]. + Dataset [1]_, study on spatial transfer between SOAs [2]_, actual paradigm / online optimization [3]_. **Dataset Description** @@ -49,20 +49,30 @@ class Sosulski2019(BaseDataset): only scalp EEG and the EOG channel is available in all subjects. The markers in the marker file indicate the onset of target tones (21) and non-target tones (1). - WARNING: Note that this wrapper currently only loads the second part of the experiment and uses pseudo-sessions - to achieve the functionality to handle different conditions in MOABB. As a result, the statistical testing - features of MOABB cannot be used for this dataset. + .. caution:: + + Note that this wrapper currently only loads the second part of the experiment and uses pseudo-sessions + to achieve the functionality to handle different conditions in MOABB. As a result, the statistical testing + features of MOABB cannot be used for this dataset. References ---------- .. [1] Sosulski, J., Tangermann, M.: Electroencephalogram signals recorded from 13 healthy subjects during an - auditory oddball paradigm under different stimulus onset asynchrony conditions. Dataset. DOI: 10.6094/UNIFR/154576 + auditory oddball paradigm under different stimulus onset asynchrony conditions. + Dataset. DOI: 10.6094/UNIFR/154576 + .. [2] Sosulski, J., Tangermann, M.: Spatial filters for auditory evoked potentials transfer between different - experimental conditions. Graz BCI Conference. 2019. - .. [3] Sosulski, J., Hübner, D., Klein, A., Tangermann, M.: Online Optimization of Stimulation Speed in an Auditory Brain-Computer Interface under Time Constraints. arXiv preprint. 2021. + experimental conditions. Graz BCI Conference. 2019. + + .. [3] Sosulski, J., Hübner, D., Klein, A., Tangermann, M.: Online Optimization of Stimulation Speed in + an Auditory Brain-Computer Interface under Time Constraints. arXiv preprint. 2021. + + Notes + ----- .. versionadded:: 0.4.5 + """ def __init__( diff --git a/poetry.lock b/poetry.lock index eb90e59e7..8267ccf07 100644 --- a/poetry.lock +++ b/poetry.lock @@ -16,30 +16,22 @@ python-versions = "*" [[package]] name = "babel" -version = "2.9.1" +version = "2.11.0" description = "Internationalization utilities" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] pytz = ">=2015.7" -[[package]] -name = "cached-property" -version = "1.5.2" -description = "A decorator for caching properties in classes." -category = "main" -optional = false -python-versions = "*" - [[package]] name = "certifi" -version = "2021.10.8" +version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "cfgv" @@ -51,33 +43,51 @@ python-versions = ">=3.6.1" [[package]] name = "charset-normalizer" -version = "2.0.12" +version = "2.1.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = ">=3.5.0" +python-versions = ">=3.6.0" [package.extras] unicode_backport = ["unicodedata2"] [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.6" description = "Cross-platform colored terminal text." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" + +[[package]] +name = "contourpy" +version = "1.0.6" +description = "Python library for calculating contours of 2D quadrilateral grids" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = ">=1.16" + +[package.extras] +bokeh = ["bokeh", "selenium"] +docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"] +test = ["pytest", "matplotlib", "pillow", "flake8", "isort"] +test-minimal = ["pytest"] +test-no-codebase = ["pytest", "matplotlib", "pillow"] [[package]] name = "coverage" -version = "5.5" +version = "7.0.1" description = "Code coverage measurement for Python" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" +python-versions = ">=3.7" [package.extras] -toml = ["toml"] +toml = ["tomli"] [[package]] name = "cycler" @@ -87,9 +97,17 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +category = "main" +optional = false +python-versions = ">=3.5" + [[package]] name = "distlib" -version = "0.3.4" +version = "0.3.6" description = "Distribution utilities" category = "dev" optional = false @@ -97,39 +115,40 @@ python-versions = "*" [[package]] name = "docutils" -version = "0.16" +version = "0.19" description = "Docutils -- Python Documentation Utilities" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.7" [[package]] name = "filelock" -version = "3.6.0" +version = "3.9.0" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] -testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] +docs = ["furo (>=2022.12.7)", "sphinx-autodoc-typehints (>=1.19.5)", "sphinx (>=5.3)"] +testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)", "pytest (>=7.2)"] [[package]] name = "fonttools" -version = "4.29.1" +version = "4.38.0" description = "Tools to manipulate font files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] graphite = ["lz4 (>=1.7.4.2)"] interpolatable = ["scipy", "munkres"] lxml = ["lxml (>=4.0,<5)"] pathops = ["skia-pathops (>=0.5.0)"] plot = ["matplotlib"] +repacker = ["uharfbuzz (>=0.23.0)"] symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] @@ -138,19 +157,18 @@ woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] [[package]] name = "h5py" -version = "3.6.0" +version = "3.7.0" description = "Read and write HDF5 files from Python" category = "main" optional = false python-versions = ">=3.7" [package.dependencies] -cached-property = {version = "*", markers = "python_version < \"3.8\""} numpy = ">=1.14.5" [[package]] name = "identify" -version = "2.4.10" +version = "2.5.11" description = "File identification library for Python" category = "dev" optional = false @@ -161,7 +179,7 @@ license = ["ukkonen"] [[package]] name = "idna" -version = "3.3" +version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false @@ -169,7 +187,7 @@ python-versions = ">=3.5" [[package]] name = "imagesize" -version = "1.3.0" +version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" category = "dev" optional = false @@ -177,28 +195,27 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.11.1" +version = "5.2.0" description = "Read metadata from Python packages" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} zipp = ">=0.5" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8", "importlib-resources (>=1.3)"] [[package]] name = "jinja2" -version = "3.0.3" +version = "3.1.2" description = "A very fast and expressive template engine." -category = "dev" +category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] MarkupSafe = ">=2.0" @@ -208,15 +225,15 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "joblib" -version = "1.1.0" +version = "1.2.0" description = "Lightweight pipelining with Python functions" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "kiwisolver" -version = "1.3.2" +version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false @@ -224,86 +241,93 @@ python-versions = ">=3.7" [[package]] name = "m2r2" -version = "0.2.8" +version = "0.3.3" description = "Markdown and reStructuredText in a single file." category = "dev" optional = false python-versions = "*" [package.dependencies] -docutils = "*" -mistune = "*" +docutils = ">=0.19" +mistune = "0.8.4" [[package]] name = "markupsafe" -version = "2.1.0" +version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.5.1" +version = "3.6.2" description = "Python plotting package" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] +contourpy = ">=1.0.1" cycler = ">=0.10" fonttools = ">=4.22.0" kiwisolver = ">=1.0.1" -numpy = ">=1.17" +numpy = ">=1.19" packaging = ">=20.0" pillow = ">=6.2.0" pyparsing = ">=2.2.1" python-dateutil = ">=2.7" -setuptools_scm = ">=4" +setuptools_scm = ">=7" [[package]] name = "mistune" -version = "2.0.3" -description = "A sane Markdown parser with useful plugins and renderers" +version = "0.8.4" +description = "The fastest markdown parser in pure Python" category = "dev" optional = false python-versions = "*" [[package]] name = "mne" -version = "0.24.1" +version = "1.3.0" description = "MNE-Python project for MEG and EEG data analysis." category = "main" optional = false python-versions = ">=3.7" [package.dependencies] +decorator = "*" +jinja2 = "*" +matplotlib = "*" numpy = ">=1.15.4" +packaging = "*" +pooch = ">=1.5" scipy = ">=1.1.0" +tqdm = "*" [package.extras] -data = ["tqdm", "pooch (>=1.5)"] -test = ["pytest (!=4.6.0)", "pytest-cov", "pytest-timeout", "pytest-harvest", "flake8", "flake8-array-spacing", "numpydoc", "codespell", "pydocstyle", "check-manifest", "twine", "wheel", "pooch", "nitime", "nbclient", "sphinx-gallery", "eeglabio", "edflib-python", "imageio-ffmpeg"] +hdf5 = ["h5io", "pymatreader"] +test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-harvest", "flake8", "flake8-array-spacing", "numpydoc", "codespell", "pydocstyle", "check-manifest", "twine", "wheel", "nitime", "nbclient", "sphinx-gallery", "eeglabio", "edflib-python", "pybv", "imageio-ffmpeg"] [[package]] name = "nodeenv" -version = "1.6.0" +version = "1.7.0" description = "Node.js virtual environment builder" category = "dev" optional = false -python-versions = "*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" [[package]] name = "numpy" -version = "1.21.1" -description = "NumPy is the fundamental package for array computing with Python." +version = "1.24.1" +description = "Fundamental package for array computing in Python" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [[package]] name = "numpydoc" -version = "1.2" +version = "1.5.0" description = "Sphinx extension to support docstrings in Numpy format" category = "dev" optional = false @@ -311,57 +335,62 @@ python-versions = ">=3.7" [package.dependencies] Jinja2 = ">=2.10" -sphinx = ">=1.8" +sphinx = ">=4.2" [package.extras] -testing = ["matplotlib", "pytest-cov", "pytest"] +testing = ["pytest", "pytest-cov", "matplotlib"] [[package]] name = "packaging" -version = "21.3" +version = "22.0" description = "Core utilities for Python packages" category = "main" optional = false -python-versions = ">=3.6" - -[package.dependencies] -pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" +python-versions = ">=3.7" [[package]] name = "pandas" -version = "1.1.5" +version = "1.5.2" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" [package.dependencies] -numpy = ">=1.15.4" -python-dateutil = ">=2.7.3" -pytz = ">=2017.2" +numpy = [ + {version = ">=1.20.3", markers = "python_version < \"3.10\""}, + {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, + {version = ">=1.23.2", markers = "python_version >= \"3.11\""}, +] +python-dateutil = ">=2.8.1" +pytz = ">=2020.1" [package.extras] -test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"] +test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] name = "pillow" -version = "9.0.1" +version = "9.3.0" description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.7" +[package.extras] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] + [[package]] name = "platformdirs" -version = "2.5.1" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +version = "2.6.2" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] -test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.19.5)", "sphinx (>=5.3)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2)"] [[package]] name = "pooch" @@ -377,53 +406,54 @@ packaging = ">=20.0" requests = ">=2.19.0" [package.extras] -xxhash = ["xxhash (>=1.4.3)"] -sftp = ["paramiko (>=2.7.0)"] progress = ["tqdm (>=4.41.0,<5.0.0)"] +sftp = ["paramiko (>=2.7.0)"] +xxhash = ["xxhash (>=1.4.3)"] [[package]] name = "pre-commit" -version = "2.17.0" +version = "2.21.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.dependencies] cfgv = ">=2.0.0" identify = ">=1.0.0" -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} nodeenv = ">=0.11.1" pyyaml = ">=5.1" -toml = "*" -virtualenv = ">=20.0.8" +virtualenv = ">=20.10.0" [[package]] name = "pygments" -version = "2.11.2" +version = "2.13.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" + +[package.extras] +plugins = ["importlib-metadata"] [[package]] name = "pyparsing" -version = "3.0.7" -description = "Python parsing module" +version = "3.0.9" +description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.6.8" [package.extras] -diagrams = ["jinja2", "railroad-diagrams"] +diagrams = ["railroad-diagrams", "jinja2"] [[package]] name = "pyriemann" -version = "0.2.7" +version = "0.3" description = "Riemannian Geometry for python" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" [package.dependencies] joblib = "*" @@ -432,6 +462,10 @@ pandas = "*" scikit-learn = "*" scipy = "*" +[package.extras] +docs = ["sphinx-gallery", "sphinx-bootstrap-theme", "numpydoc", "mne", "seaborn"] +tests = ["pytest", "seaborn", 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name = "moabb" version = "0.4.6" description = "Mother of All BCI Benchmarks" authors = ["Alexandre Barachant", "Vinay Jayaram"] -maintainers = ["Sylvain Chevallier "] +maintainers = ["Sylvain Chevallier "] readme = "README.md" repository = "https://github.com/NeuroTechX/moabb" -documentation = "http://moabb.neurotechx.com/docs/index.html" +documentation = "https://neurotechx.github.io/moabb" keywords = ["eeg", "datasets", "reproducibility", "bci", "benchmark"] license = "BSD-3-Clause" [tool.poetry.dependencies] -python = "^3.7" -numpy = "^1.19.0" -scipy = "^1.5" -mne = ">=0.19" -pandas = "^1.0" -h5py = "^3.0" -scikit-learn = "^1.0" -pyriemann = ">=0.2.6" -matplotlib = "^3.0" -seaborn = ">=0.9" -PyYAML = "^5.0" -pooch = "^1.6" -requests = "^2.15.1" -coverage = "^5.5" -tqdm = "^4.62" +python = "^3.8" +numpy = "^1.24.1" +scipy = "^1.9.3" +mne = "^1.3.0" +pandas = "^1.5.2" +h5py = "^3.7.0" +scikit-learn = "^1.2.0" +matplotlib = "^3.6.2" +seaborn = "^0.12.1" +pyriemann = "^0.3" +PyYAML = "^6.0" +pooch = "^1.6.0" +requests = "^2.28.1" +tqdm = "^4.64.1" +coverage = "^7.0.1" [tool.poetry.dev-dependencies] -Sphinx = "^3.3" -sphinx-gallery = "^0.8.2" -sphinx-bootstrap-theme = "^0.8" -numpydoc = "^1.1.0" -m2r2 = "^0.2.7" -mistune = "<3" -pre-commit = "^2.11.1" +Sphinx = "^6.0.0" +sphinx-gallery = "^0.11.1" +sphinx-bootstrap-theme = "^0.8.1" +numpydoc = "^1.5.0" +pre-commit = "^2.21.0" +m2r2 = "^0.3.3" tdlda = {git = "https://github.com/jsosulski/tdlda.git", rev = "0.1.0"} [build-system] @@ -43,7 +42,7 @@ build-backend = "poetry.core.masonry.api" [tool.black] line-length = 90 -target-version = ["py36"] +target-version = ["py38"] [tool.isort] src_paths = ["moabb"] diff --git a/requirements.txt b/requirements.txt index 9551f57f3..dc37f13cb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,421 +1,127 @@ -appdirs==1.4.4; python_version >= "3.6" \ +appdirs==1.4.4; python_version >= "3.7" \ --hash=sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128 \ 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python_full_version >= "3.5.0" and platform_system == "Windows" \ - --hash=sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2 \ - --hash=sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b -coverage==5.5; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") \ - --hash=sha256:b6d534e4b2ab35c9f93f46229363e17f63c53ad01330df9f2d6bd1187e5eaacf \ - --hash=sha256:b7895207b4c843c76a25ab8c1e866261bcfe27bfaa20c192de5190121770672b \ - --hash=sha256:c2723d347ab06e7ddad1a58b2a821218239249a9e4365eaff6649d31180c1669 \ - --hash=sha256:900fbf7759501bc7807fd6638c947d7a831fc9fdf742dc10f02956ff7220fa90 \ - --hash=sha256:004d1880bed2d97151facef49f08e255a20ceb6f9432df75f4eef018fdd5a78c \ - --hash=sha256:06191eb60f8d8a5bc046f3799f8a07a2d7aefb9504b0209aff0b47298333302a \ - --hash=sha256:7501140f755b725495941b43347ba8a2777407fc7f250d4f5a7d2a1050ba8e82 \ - 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--hash=sha256:d67d839ede4ed1b28a4e8909735fc992a923cdb84e618544973d7dfc71540803 \ + --hash=sha256:cba8c411ef271aa037d7357a2bc8f9ee8b58b9965831d9e51baf703280dc73d3 \ + --hash=sha256:40527857252b61eacd1d9af500c3337ba8deb8fc298940291486c465c8b46ec0 \ + --hash=sha256:b5b9eccad747aabaaffbc6064800670f0c297e52c12754eb1d976c57e4f74dcb \ + --hash=sha256:b3d267842bf12586ba6c734f89d1f5b871df0273157918b0ccefa29deb05c21c \ + --hash=sha256:68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2 +requests==2.28.1; python_version >= "3.7" and python_version < "4" +scikit-learn==1.2.0; python_version >= "3.8" +scipy==1.9.3; python_version >= "3.8" +seaborn==0.12.2; python_version >= "3.7" +setuptools-scm==7.1.0; python_version >= "3.8" +six==1.16.0; python_version >= "3.8" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.8" \ --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254 \ --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 -threadpoolctl==3.1.0; python_version >= "3.7" \ +threadpoolctl==3.1.0; python_version >= "3.8" \ --hash=sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b \ --hash=sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380 -tomli==2.0.1; python_version >= "3.7" \ +tomli==2.0.1; python_version < "3.11" and python_version >= "3.8" \ --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \ --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f -tqdm==4.62.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") \ - --hash=sha256:8dd278a422499cd6b727e6ae4061c40b48fce8b76d1ccbf5d34fca9b7f925b0c \ - --hash=sha256:d359de7217506c9851b7869f3708d8ee53ed70a1b8edbba4dbcb47442592920d -urllib3==1.26.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6" \ - --hash=sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed \ - --hash=sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c +tqdm==4.64.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") +typing-extensions==4.4.0; python_version >= "3.8" +urllib3==1.26.13; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.7" and python_version < "4" and python_full_version >= "3.6.0" diff --git a/setup.cfg b/setup.cfg index 624bcb93f..18b66d8ca 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [flake8] -ignore = E203, E501, W503, B950 +ignore = E203, E501, W503, B905, B950 max-line-length = 90 max-complexity = 12 select = B, C, E, F, W, B9