braindecode 0.5.1__tar.gz → 0.6__tar.gz

Braindecode-0.6/.circleci/artifact_path

@@ -0,0 +1 @@
+0/docs/_build/html/index.html

Braindecode-0.6/.circleci/config.yml

@@ -0,0 +1,56 @@
+# Tagging a commit with [circle front] will build the front page and perform test-doc.
+# Tagging a commit with [circle full] will build everything.
+version: 2.1
+parameters:
+  github-artifact-url:
+    type: string
+    default: "none"
+jobs:
+    fetch_docs_from_github:
+      docker:
+        - image: circleci/python:3.7
+      environment:
+        GITHUB_ARTIFACT_URL: << pipeline.parameters.github-artifact-url >>
+      steps:
+        - run:
+            name: Download some docs
+            command: |
+              echo "Show Github artifact url"
+              echo $GITHUB_ARTIFACT_URL
+              wget -O HTML-docs.zip $GITHUB_ARTIFACT_URL
+              ls -ahl .
+              unzip HTML-docs.zip -d downloaded_docs
+              ls -ahl .
+        # Save the outputs
+        - store_artifacts:
+           path: downloaded_docs/html/
+           destination: dev
+        - persist_to_workspace:
+           root: downloaded_docs
+           paths:
+             - html
+    dummy_job:
+      docker:
+       - image: circleci/python:3.7
+      steps:
+        - run:
+           name: Dummy echo
+           command: |
+             echo "Do nothing..."
+
+
+workflows:
+  version: 2.1
+
+  default:
+    when:
+      not:
+        equal: [ "none", << pipeline.parameters.github-artifact-url >> ]
+    jobs:
+      - fetch_docs_from_github
+
+  dummy_workflow:
+    when:
+      equal: [ "none", << pipeline.parameters.github-artifact-url >> ]
+    jobs:
+      - dummy_job

Braindecode-0.6/.github/workflows/flake8.yaml

@@ -0,0 +1,23 @@
+name: flake8-codestyle
+on: [pull_request]   
+
+jobs:
+  Flake8-Codestyle-Check:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - name: Checking Out Repository
+      uses: actions/checkout@v2
+    - name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.8"
+    - name: Install Flake8
+      run: pip install flake8
+    - name: Run Flake8
+      uses: liskin/gh-problem-matcher-wrap@v1
+      with:
+        linters: flake8
+        run: flake8 .

Braindecode-0.6/.github/workflows/link-to-doc.yaml

@@ -0,0 +1,13 @@
+on: [status]
+jobs:
+  circleci_artifacts_redirector:
+    runs-on: ubuntu-latest
+    name: Run CircleCI artifacts redirector
+    steps:
+      - name: GitHub Action step
+        uses: larsoner/circleci-artifacts-redirector-action@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          artifact-path: 0/dev/index.html
+          circleci-jobs: fetch_docs_from_github
+          job-title: Check rendered doc here!

Braindecode-0.6/.github/workflows/push-artifact-to-circleci.yml

@@ -0,0 +1,47 @@
+name: push-artifact-to-circle-ci
+
+# will be changed to on workflow_run
+on:
+  workflow_run:
+    workflows: ["tests-and-docs"]
+    branches-ignore: ["master"]
+    types:
+      - completed
+
+jobs:
+  Push-Artifact-to-CircleCI:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - name: Trigger CircleCI download and publication of HTML Doc Artifact
+      env:
+        EVENT_OBJ:  ${{ toJson(github.event) }}
+        COMMIT_SHA:  ${{ github.event.workflow_run.head_sha }}
+        REPO_NAME:  ${{ github.event.workflow_run.head_repository.full_name }}
+        CIRCLECI_TOKEN: ${{ secrets.CIRCLECI_TOKEN }}
+        RUN_ID: ${{github.event.workflow_run.id}}
+      run: |
+        echo "github.event.workflow_run.head_sha"
+        echo ${{ github.event.workflow_run.head_sha }}
+        echo "github.event.workflow_run.head_repository.html_url"
+        echo ${{ github.event.workflow_run.head_repository.html_url }}
+        # Acquire the Pull Request Number from Github API
+        echo "automated curl"
+        PR_NUMBER=$(curl -H "Accept: application/vnd.github.groot-preview+json"   https://api.github.com/repos/$REPO_NAME/commits/$COMMIT_SHA/pulls 2>/dev/null | jq '.[0].number')
+        echo $PR_NUMBER
+        
+        # Use Pull Request Number to trigger pipeline on CircleCI which will just download artifact,
+        # unzip it and make it available for browsing
+        curl --request POST \
+          --url https://circleci.com/api/v2/project/gh/braindecode/braindecode/pipeline \
+          --header "Circle-Token: $CIRCLECI_TOKEN" \
+          --header 'content-type: application/json' \
+          --header 'x-attribution-actor-id: github_actions' \
+          --header 'x-attribution-login: github_actions' \
+          --data \{\"branch\":\"pull/$PR_NUMBER/head\",\"parameters\":\{\"github-artifact-url\":\"https://nightly.link/braindecode/braindecode/actions/runs/$RUN_ID/HTML-Docs.zip\"\}\}
+        # Just for debugging
+        echo "EVENT_OBJ"
+        echo $EVENT_OBJ

Braindecode-0.6/.github/workflows/tests-and-docs.yml

@@ -0,0 +1,98 @@
+name: tests-and-docs
+
+on:
+  pull_request:
+  push:
+    branches: master
+
+jobs:
+  Install-Test-Doc-Braindecode:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        skorch_version: ['main', 'stable']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+
+    ## Install Braindecode
+    - name: Checking Out Repository
+      uses: actions/checkout@v2
+    # Cache MNE Data
+    # The cache key here is fixed except for os
+    # so if you download a new mne dataset in the code, best to manually increment the key below
+    - name: Create/Restore MNE Data Cache
+      id: cache-mne_data
+      uses: actions/cache@v2
+      with:
+        path: ~/mne_data
+        key: ${{ runner.os }}-v3
+    - name: Setting Up Conda Braindecode Environment
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        environment-file: environment.yml
+        python-version: 3.7
+        activate-environment: braindecode
+        auto-activate-base: false
+    # Show Conda and Python Versions
+    - run: conda --version
+    - run: conda info --envs
+    - run: which python
+    # Install MOABB as well
+    - name: Install MOABB
+      run: pip install moabb
+    # Use skorch github master if requested, otherwise has been installed via conda in environment.yaml
+    - name: Install Skorch development version from git repo
+      if: ${{ matrix.skorch_version == 'main' }}
+      run: pip install git+https://github.com/skorch-dev/skorch.git
+    - name: Install Braindecode from Current Checkout
+      run: pip install -e .
+    # Show Braindecode Version
+    - run: python -c "import braindecode; print(braindecode.__version__)"
+
+    ## Run Tests
+    - name: Install Codecov etc.
+      run: pip install --upgrade pytest pytest-cov codecov
+    - name: Run Tests # See https://stackoverflow.com/a/59959080/1469195 for the cov-report logic
+      run: pytest --cov=braindecode test/ --cov-report term --cov-report xml:coverage.xml
+    - name: Upload Coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: true
+        file: ./coverage.xml
+        path_to_write_report: ./codecov_report.txt
+    - name: Upload Codecov Coverage report for checking
+      uses: actions/upload-artifact@v2
+      with:
+        name: codecov-report
+        path: ./codecov_report.txt
+
+    ## Create Sphinx Documentation
+    - name: Install Docs Requirements
+      run: python -m pip install --upgrade -r docs/requirements.txt
+    - name: Install newer versions scikit learn scipy to prevent error # should be removed once moabb reason is clearer
+      run: pip install --upgrade scipy scikit-learn
+    - name: Install newer version of sphinx-gallery # should be removed sphinx-gallery with v0.10
+      run: pip install -U https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master
+    - name: Create Docs
+      run: |
+        cd docs
+        make html
+    - name: Upload HTML Docs as Artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: HTML-Docs
+        path: ./docs/_build/
+
+    - name: Deploy to Github Pages if on Master
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' && matrix.skorch_version == 'stable'}}
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+        external_repository: braindecode/braindecode.github.io
+        destination_dir: master
+        publish_branch: master
+        publish_dir: ./docs/_build/html
+        cname: braindecode.org

Braindecode-0.6/.gitignore

@@ -0,0 +1,63 @@
+junit-results.xml
+*.pyc
+*.pyo
+*.sh
+*.so
+*.tar.gz
+*.log
+*~
+.#*
+*.swp
+*.lprof
+*.npy
+*.zip
+*.tar.*
+*.egg*
+*.tmproj
+*.png
+*.dat
+.DS_Store
+auto_examples
+build
+coverage
+.cache/
+.pytest_cache/
+__pycache__/
+prof/
+.ipynb_checkpoints
+
+dist/
+docs/_build/
+docs/generated/
+docs/auto_examples/
+docs/auto_tutorials/
+docs/modules/generated/
+docs/sphinxext/cachedir
+docs/source
+pip-log.txt
+.coverage*
+tags
+doc/coverages
+doc/samples
+cover
+*.html
+
+*.orig
+
+# PyCharm
+.idea/**
+
+# sublime
+*-e
+
+# Visual Studio Code
+.vscode
+*.code-workspace
+
+# Emacs
+*.py#
+*.rst#
+
+.venv/
+venv/
+*.json

{Braindecode-0.5.1 → Braindecode-0.6}/Braindecode.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: Braindecode
-Version: 0.5.1
+Version: 0.6
 Summary: A deep learning toolbox to decode raw time-domain EEG.
 Home-page: https://github.com/braindecode/braindecode
 Author: Robin Tibor Schirrmeister

{Braindecode-0.5.1 → Braindecode-0.6}/Braindecode.egg-info/SOURCES.txt

@@ -1,8 +1,20 @@
+.gitignore
+CONTRIBUTING.md
 LICENSE.txt
 MANIFEST.in
 README.rst
+bandit.yml
+codecov.yml
+environment.yml
+requirements.txt
 setup.cfg
 setup.py
+.circleci/artifact_path
+.circleci/config.yml
+.github/workflows/flake8.yaml
+.github/workflows/link-to-doc.yaml
+.github/workflows/push-artifact-to-circleci.yml
+.github/workflows/tests-and-docs.yml
 Braindecode.egg-info/PKG-INFO
 Braindecode.egg-info/SOURCES.txt
 Braindecode.egg-info/dependency_links.txt
@@ -14,12 +26,19 @@ braindecode/classifier.py
 braindecode/regressor.py
 braindecode/util.py
 braindecode/version.py
+braindecode/augmentation/__init__.py
+braindecode/augmentation/base.py
+braindecode/augmentation/functional.py
+braindecode/augmentation/transforms.py
 braindecode/datasets/__init__.py
 braindecode/datasets/base.py
 braindecode/datasets/bbci.py
+braindecode/datasets/bcicomp.py
+braindecode/datasets/mne.py
 braindecode/datasets/moabb.py
 braindecode/datasets/sleep_physionet.py
 braindecode/datasets/tuh.py
+braindecode/datasets/xy.py
 braindecode/datautil/__init__.py
 braindecode/datautil/mne.py
 braindecode/datautil/preprocess.py
@@ -35,9 +54,16 @@ braindecode/models/functions.py
 braindecode/models/hybrid.py
 braindecode/models/modules.py
 braindecode/models/shallow_fbcsp.py
+braindecode/models/sleep_stager_blanco_2020.py
 braindecode/models/sleep_stager_chambon_2018.py
+braindecode/models/sleep_stager_eldele_2021.py
 braindecode/models/tcn.py
+braindecode/models/tidnet.py
+braindecode/models/usleep.py
 braindecode/models/util.py
+braindecode/preprocessing/__init__.py
+braindecode/preprocessing/preprocess.py
+braindecode/preprocessing/windowers.py
 braindecode/samplers/__init__.py
 braindecode/samplers/base.py
 braindecode/samplers/ssl.py
@@ -46,12 +72,16 @@ braindecode/training/callbacks.py
 braindecode/training/losses.py
 braindecode/training/scoring.py
 braindecode/visualization/__init__.py
+braindecode/visualization/confusion_matrices.py
 braindecode/visualization/gradients.py
 docs/Makefile
 docs/api.rst
 docs/conf.py
 docs/index.rst
+docs/requirements.txt
 docs/whats_new.rst
+docs/.ipynb_checkpoints/index-checkpoint.rst
+docs/_build/html/_downloads/0b5ce52c808a6ba6c8e9d78fa3fdb68a/plot_color.ipynb
 docs/_build/html/_downloads/1224801107d6c3b138edf8ee33de0561/plot_bcic_iv_2a_moabb_cropped.ipynb
 docs/_build/html/_downloads/176a7695926ccfe061692c4af12b673d/plot_dataset_example.ipynb
 docs/_build/html/_downloads/25408d8d92a873e370d4750ba414b84a/benchmark_lazy_eager_loading.ipynb
@@ -62,8 +92,11 @@ docs/_build/html/_downloads/5bafba0488197e377d459780399abb29/plot_sleep_staging.
 docs/_build/html/_downloads/748680401b0360239d00624375dd9587/plot_bcic_iv_2a_moabb_trial.ipynb
 docs/_build/html/_downloads/8c06a965e21b52d199f98636388aaa21/tuh_eeg_corpus.ipynb
 docs/_build/html/_downloads/9c64c2c15907a661b1fe2d7dd209a434/plot_regression.ipynb
+docs/_build/html/_downloads/9d9b9ce2b20299db6129837e390cf198/plot_lukas.ipynb
 docs/_build/html/_downloads/b38e40c9ee338673865922575e84fd7f/plot_split_dataset.ipynb
 docs/_build/html/_downloads/e42b5bd97033be02521040b0d5ee21c3/plot_mne_dataset_example.ipynb
+docs/_static/cropped_explanation.png
+docs/_static/trialwise_explanation.png
 docs/_templates/autosummary/class.rst
 docs/_templates/autosummary/function.rst
 docs/auto_examples/benchmark_lazy_eager_loading.ipynb
@@ -73,12 +106,16 @@ docs/auto_examples/plot_bcic_iv_2a_moabb_cropped.ipynb
 docs/auto_examples/plot_bcic_iv_2a_moabb_cropped.rst
 docs/auto_examples/plot_bcic_iv_2a_moabb_trial.ipynb
 docs/auto_examples/plot_bcic_iv_2a_moabb_trial.rst
+docs/auto_examples/plot_color.ipynb
+docs/auto_examples/plot_color.rst
 docs/auto_examples/plot_custom_dataset_example.ipynb
 docs/auto_examples/plot_custom_dataset_example.rst
 docs/auto_examples/plot_dataset_example.ipynb
 docs/auto_examples/plot_dataset_example.rst
 docs/auto_examples/plot_load_save_datasets.ipynb
 docs/auto_examples/plot_load_save_datasets.rst
+docs/auto_examples/plot_lukas.ipynb
+docs/auto_examples/plot_lukas.rst
 docs/auto_examples/plot_mne_dataset_example.ipynb
 docs/auto_examples/plot_mne_dataset_example.rst
 docs/auto_examples/plot_regression.ipynb
@@ -100,20 +137,11 @@ docs/generated/braindecode.datasets.SleepPhysionet.rst
 docs/generated/braindecode.datasets.TUH.rst
 docs/generated/braindecode.datasets.TUHAbnormal.rst
 docs/generated/braindecode.datasets.WindowsDataset.rst
-docs/generated/braindecode.datautil.Preprocessor.rst
-docs/generated/braindecode.datautil.create_fixed_length_windows.rst
-docs/generated/braindecode.datautil.create_from_X_y.rst
-docs/generated/braindecode.datautil.create_from_mne_epochs.rst
-docs/generated/braindecode.datautil.create_from_mne_raw.rst
-docs/generated/braindecode.datautil.create_windows_from_events.rst
-docs/generated/braindecode.datautil.exponential_moving_demean.rst
-docs/generated/braindecode.datautil.exponential_moving_standardize.rst
-docs/generated/braindecode.datautil.filterbank.rst
+docs/generated/braindecode.datasets.create_from_X_y.rst
+docs/generated/braindecode.datasets.create_from_mne_epochs.rst
+docs/generated/braindecode.datasets.create_from_mne_raw.rst
 docs/generated/braindecode.datautil.load_concat_dataset.rst
-docs/generated/braindecode.datautil.preprocess.rst
 docs/generated/braindecode.datautil.save_concat_dataset.rst
-docs/generated/braindecode.datautil.scale.rst
-docs/generated/braindecode.datautil.zscore.rst
 docs/generated/braindecode.models.Deep4Net.rst
 docs/generated/braindecode.models.EEGNetv1.rst
 docs/generated/braindecode.models.EEGNetv4.rst
@@ -122,7 +150,17 @@ docs/generated/braindecode.models.HybridNet.rst
 docs/generated/braindecode.models.ShallowFBCSPNet.rst
 docs/generated/braindecode.models.SleepStagerChambon2018.rst
 docs/generated/braindecode.models.TCN.rst
+docs/generated/braindecode.models.TIDNet.rst
 docs/generated/braindecode.models.get_output_shape.rst
+docs/generated/braindecode.preprocessing.Preprocessor.rst
+docs/generated/braindecode.preprocessing.create_fixed_length_windows.rst
+docs/generated/braindecode.preprocessing.create_windows_from_events.rst
+docs/generated/braindecode.preprocessing.exponential_moving_demean.rst
+docs/generated/braindecode.preprocessing.exponential_moving_standardize.rst
+docs/generated/braindecode.preprocessing.filterbank.rst
+docs/generated/braindecode.preprocessing.preprocess.rst
+docs/generated/braindecode.preprocessing.scale.rst
+docs/generated/braindecode.preprocessing.zscore.rst
 docs/generated/braindecode.regressor.EEGRegressor.rst
 docs/generated/braindecode.samplers.RecordingSampler.rst
 docs/generated/braindecode.samplers.RelativePositioningSampler.rst
@@ -132,29 +170,59 @@ docs/generated/braindecode.training.PostEpochTrainScoring.rst
 docs/generated/braindecode.training.trial_preds_from_window_preds.rst
 docs/generated/braindecode.util.set_random_seeds.rst
 docs/generated/braindecode.visualization.compute_amplitude_gradients.rst
+docs/sphinxext/gh_substitutions.py
+examples/README.rst
+examples/benchmark_lazy_eager_loading.py
+examples/plot_bcic_iv_2a_moabb_cropped.py
+examples/plot_bcic_iv_2a_moabb_trial.py
+examples/plot_bcic_iv_4_ecog_cropped.py
+examples/plot_bcic_iv_4_ecog_trial.py
+examples/plot_benchmark_preprocessing.py
+examples/plot_custom_dataset_example.py
+examples/plot_data_augmentation.py
+examples/plot_dataset_example.py
+examples/plot_load_save_datasets.py
+examples/plot_mne_dataset_example.py
+examples/plot_regression.py
+examples/plot_relative_positioning.py
+examples/plot_sleep_staging_usleep.py
+examples/plot_split_dataset.py
+examples/plot_tuh_discrete_multitarget.py
+examples/plot_tuh_eeg_corpus.py
 test/__init__.py
 test/acceptance_tests/__init__.py
 test/acceptance_tests/test_cropped_decoding.py
 test/acceptance_tests/test_eeg_classifier.py
 test/acceptance_tests/test_model_architectures.py
 test/acceptance_tests/test_trialwise_decoding.py
+test/acceptance_tests/test_variable_length_trials_decoding.py
 test/unit_tests/__init__.py
 test/unit_tests/test_eeg_classifier.py
 test/unit_tests/test_eeg_regressor.py
-test/unit_tests/test_scoring.py
 test/unit_tests/test_util.py
+test/unit_tests/augmentation/__init__.py
+test/unit_tests/augmentation/conftest.py
+test/unit_tests/augmentation/test_base.py
+test/unit_tests/augmentation/test_transforms.py
 test/unit_tests/datasets/__init__.py
+test/unit_tests/datasets/test_bcicomp.py
 test/unit_tests/datasets/test_dataset.py
 test/unit_tests/datasets/test_mne.py
 test/unit_tests/datasets/test_sleep_physionet.py
 test/unit_tests/datasets/test_tuh.py
 test/unit_tests/datasets/test_xy.py
 test/unit_tests/datautil/__init__.py
-test/unit_tests/datautil/test_preprocess.py
 test/unit_tests/datautil/test_serialization.py
-test/unit_tests/datautil/test_windowers.py
 test/unit_tests/models/__init__.py
 test/unit_tests/models/test_models.py
+test/unit_tests/models/test_modules.py
 test/unit_tests/models/test_util.py
+test/unit_tests/preprocessing/__init__.py
+test/unit_tests/preprocessing/test_preprocess.py
+test/unit_tests/preprocessing/test_windowers.py
+test/unit_tests/samplers/test_samplers.py
+test/unit_tests/training/__init__.py
+test/unit_tests/training/test_losses.py
+test/unit_tests/training/test_scoring.py
 test/unit_tests/visualization/__init__.py
 test/unit_tests/visualization/test_gradients.py