Release candidate for v1.0.0 (#502)

sylvchev · Sylvain Chevallier · PierreGtch · web-flow · commit 0f8b864c3d85 · 2023-10-19T17:54:51.000+02:00
* enh: update to RC

* fix: add versionadded

* fix: update poetry dependencies

* enh: update deployment tools

* enh: update dependencies

* fix: correct error in doc building

* fix: error with tensorflow 3.13

* fix: add classes_ to SSVEP_CCA to comply with new sklearn version

* fix: precommit CI

* fix: SSVEP_CCA classes_ and onehot vector

* Try fix subject int instead of str

* update requirements.txt

* fix: remove requirement, pip compatible with pyproject.toml

* fix: avoid downloading dataset in CI

* fix: do not build VR examples to avoid zenodo timeout

* fix: revert to urllib3 &lt;= 2 to fix timeout in CI

* revert: put back VR-PC example

* fix: revert to h5py 3.8

* fix: do not build examples with error after dependency update

* Improve msg

* Improve msg

* fixing crop

---------

Co-authored-by: Sylvain Chevallier &lt;sylain.chevallier@universite-paris-saclay.fr&gt;
Co-authored-by: PierreGtch &lt;25532709+PierreGtch@users.noreply.github.com&gt;
Co-authored-by: qbarthelemy &lt;q.barthelemy@gmail.com&gt;
Co-authored-by: bruAristimunha &lt;a.bruno@aluno.ufabc.edu.br&gt;
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,7 +16,7 @@ jobs:
         python-version: ["3.9"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create local data folder
         run: |
@@ -44,10 +44,10 @@ jobs:
 
       - name: Install dependencies
         if: steps.cached-dataset-docs.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root --with docs,deeplearning
+        run: poetry install --no-interaction --no-root --with docs --extras deeplearning
 
       - name: Install library
-        run: poetry install --no-interaction --with docs,deeplearning
+        run: poetry install --no-interaction --with docs --extras deeplearning
 
       - name: Build docs
         run: |
@@ -69,7 +69,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create local data folder
         run: |
@@ -85,7 +85,7 @@ jobs:
             docs/build
 
       - name: Checkout moabb.github.io
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: "NeuroTechX/moabb.github.io"
           path: moabb-ghio
@@ -101,7 +101,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create local data folder
         run: |
@@ -117,7 +117,7 @@ jobs:
             docs/build
 
       - name: Checkout gh pages
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
           path: moabb-ghpages
diff --git a/.github/workflows/test-devel.yml b/.github/workflows/test-devel.yml
@@ -19,7 +19,7 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -46,11 +46,11 @@ jobs:
         if: |
           (runner.os != 'Windows') &&
           (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
-        run: poetry install --no-interaction --no-root --with deeplearning
+        run: poetry install --no-interaction --no-root --extras deeplearning
 
       - name: Install library (Linux/OSX)
         if: ${{ runner.os != 'Windows' }}
-        run: poetry install --no-interaction --with deeplearning
+        run: poetry install --no-interaction --extras deeplearning
 
       - name: Install library (Windows)
         if: ${{ runner.os == 'Windows' }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -19,7 +19,7 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -46,11 +46,11 @@ jobs:
         if: |
           (runner.os != 'Windows') &&
           (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
-        run: poetry install --no-interaction --no-root --with deeplearning
+        run: poetry install --no-interaction --no-root --extras deeplearning
 
       - name: Install library (Linux/OSX)
         if: ${{ runner.os != 'Windows' }}
-        run: poetry install --no-interaction --with deeplearning
+        run: poetry install --no-interaction --extras deeplearning
 
       - name: Install library (Windows)
         if: ${{ runner.os == 'Windows' }}
diff --git a/bash/meta_requirements.txt b/bash/meta_requirements.txt
@@ -1,5 +1,5 @@
 mne
-#if you want used a specific branch instead of branch devolop
+#if you want used a specific branch instead of branch develop
 #changing the branch name git+REPOSITORY_LINK@BRANCH#egg=MOABB
 git+https://github.com/NeuroTechX/moabb#egg=moabb
 gdown
diff --git a/docs/source/whats_new.rst b/docs/source/whats_new.rst
@@ -18,6 +18,24 @@ Develop branch
 Enhancements
 ~~~~~~~~~~~~
 
+- None
+
+Bugs
+~~~~
+
+- None
+
+API changes
+~~~~~~~~~~~
+
+- None
+
+
+Version - 1.0.0  (Stable - PyPi)
+---------------------------------
+
+Enhancements
+~~~~~~~~~~~~
 
 - Adding extra thank you section in the documentation (:gh:`390` by `Bruno Aristimunha`_)
 - Adding new script to get the meta information of the datasets (:gh:`389` by `Bruno Aristimunha`_)
@@ -59,7 +77,7 @@ Bugs
 
 - Restore 3 subject from Cho2017 (:gh:`392` by `Igor Carrara`_ and `Sylvain Chevallier`_)
 - Correct downloading with VirtualReality BrainInvaders dataset (:gh:`393` by `Gregoire Cattan`_)
-- Rename event `substraction` to `subtraction` in :func:`moabb.datasets.Shin2017B` (:gh:`397` by `Pierre Guetschel`_)
+- Rename event `subtraction` in :func:`moabb.datasets.Shin2017B` (:gh:`397` by `Pierre Guetschel`_)
 - Save parameters of :func:`moabb.datasets.PhysionetMI` (:gh:`403` by `Pierre Guetschel`_)
 - Fixing issue with parallel evaluation (:gh:`401` by `Bruno Aristimunha`_ and `Igor Carrara`_)
 - Fixing SSLError from BCI competition IV (:gh:`404` by `Bruno Aristimunha`_)
@@ -81,15 +99,16 @@ Bugs
 - Removing joblib Parallel (:gh:`488` by `Igor Carrara`_)
 - Fix case when events specified via ``raw.annotations`` but no events (:gh:`491` by `Pierre Guetschel`_)
 - Fix bug in downloading Shin2017A dataset (:gh:`493` by `Igor Carrara`_)
+- Fix the cropped option in the dataset preprocessing (:gh:`502` by `Bruno Aristimunha`_)
 
 API changes
 ~~~~~~~~~~~
 
 - None
 
 
-Version - 0.5.0  (Stable - PyPi)
----------------------------------
+Version - 0.5.0
+---------------
 
 Enhancements
 ~~~~~~~~~~~~
@@ -316,7 +335,7 @@ Bugs
 - Use stim_channels or check annotation when loading files in Paradigm  (:gh:`72` by `Jan Sosulski`_)
 - Correct MNE issues (:gh:`76` by `Sylvain Chevallier`_)
 - Fix capitalization in channel names of cho dataset  (:gh:`90` by `Jan Sosulski`_)
-- Correct failling CI tests (:gh:`100` by `Sylvain Chevallier`_)
+- Correct failing CI tests (:gh:`100` by `Sylvain Chevallier`_)
 - Fix EPFL dataset flat signal sections and wrong scaling (:gh:`104` and :gh:`96` by  `Jan Sosulski`_)
 - Fix schirrmeister dataset for Python3.8 (:gh:`105` by `Robin Schirrmeister`_)
 - Correct event detection problem and duplicate event error (:gh:`106` by `Sylvain Chevallier`_)
diff --git a/examples/noplot_bids_conversion.py b/examples/noplot_bids_conversion.py
diff --git a/examples/noplot_phmd_ml_spectrum.py b/examples/noplot_phmd_ml_spectrum.py
diff --git a/examples/noplot_vr_pc_p300_different_epoch_size.py b/examples/noplot_vr_pc_p300_different_epoch_size.py
diff --git a/moabb/__init__.py b/moabb/__init__.py
@@ -1,5 +1,5 @@
 # flake8: noqa
-__version__ = "0.5.0"
+__version__ = "1.0.0"
 
 from .benchmark import benchmark
-from .utils import set_download_dir, set_log_level, setup_seed
+from .utils import make_process_pipelines, set_download_dir, set_log_level, setup_seed
diff --git a/moabb/analysis/results.py b/moabb/analysis/results.py
@@ -120,9 +120,9 @@ def add(self, results, pipelines, process_pipeline):  # noqa: C901
         """Add results."""
 
         def to_list(res):
-            if type(res) is dict:
+            if isinstance(res, dict):
                 return [res]
-            elif type(res) is not list:
+            elif not isinstance(res, list):
                 raise ValueError(
                     "Results are given as neither dict nor"
                     "list but {}".format(type(res).__name__)
diff --git a/moabb/datasets/base.py b/moabb/datasets/base.py
@@ -44,6 +44,12 @@ class CacheConfig:
         will be automatically downloaded to the specified folder.
     verbose:
         Verbosity level. See mne.verbose.
+
+    Notes
+    -----
+
+    .. versionadded:: 1.0.0
+
     """
 
     save_raw: bool = False
@@ -272,7 +278,7 @@ def get_data(
         process_pipeline=None,
     ):
         """
-        Return the data correspoonding to a list of subjects.
+        Return the data corresponding to a list of subjects.
 
         The returned data is a dictionary with the following structure::
 
diff --git a/moabb/datasets/bids_interface.py b/moabb/datasets/bids_interface.py
@@ -75,6 +75,12 @@ class BIDSInterfaceBase(abc.ABC):
         The processing pipeline used to convert the data.
     verbose : str
         The verbosity level.
+
+    Notes
+    -----
+
+    .. versionadded:: 1.0.0
+
     """
 
     dataset: "BaseDataset"
@@ -300,7 +306,7 @@ def _write_file(self, bids_path, raw):
         if raw.info.get("subject_info", None) is None:
             # specify subject info as required by BIDS
             raw.info["subject_info"] = {
-                "his_id": self.subject,
+                "his_id": subject_moabb_to_bids(self.subject),
             }
         if raw.info.get("device_info", None) is None:
             # specify device info as required by BIDS
diff --git a/moabb/datasets/bnci.py b/moabb/datasets/bnci.py
@@ -1229,7 +1229,7 @@ class BNCI2015_004(MNEBNCI):
     ground were placed at the left and right mastoid, respectively.  The g.tec
     GAMMAsys system with g.LADYbird active electrodes and two g.USBamp
     biosignal
-    amplifiers (Guger Technolgies, Graz, Austria) was used for recording.  EEG
+    amplifiers (Guger Technologies, Graz, Austria) was used for recording.  EEG
     was band pass filtered 0.5-100 Hz (notch filter at 50 Hz) and sampled at a
     rate of 256 Hz.
 
diff --git a/moabb/datasets/phmd_ml.py b/moabb/datasets/phmd_ml.py
@@ -52,7 +52,7 @@ class Cattan2019_PHMD(BaseDataset):
     Notes
     -----
 
-    .. versionadded:: 0.6.0
+    .. versionadded:: 1.0.0
 
     References
     ----------
diff --git a/moabb/datasets/preprocessing.py b/moabb/datasets/preprocessing.py
@@ -125,8 +125,8 @@ def transform(self, raw, y=None):
         if (
             "Target" in event_id
             and "NonTarget" in event_id
-            and type(event_id["Target"]) is list
-            and type(event_id["NonTarget"]) is list
+            and isinstance(event_id["Target"], list)
+            and isinstance(event_id["NonTarget"], list)
         ):
             event_id_new = dict(Target=1, NonTarget=0)
             events = mne.merge_events(events, event_id["Target"], 1)
@@ -254,7 +254,7 @@ def get_filter_pipeline(fmin, fmax):
 
 def get_crop_pipeline(tmin, tmax):
     return FunctionTransformer(
-        methodcaller("crop", tmin=tmax, tmax=tmin, verbose=False),
+        methodcaller("crop", tmin=tmin, tmax=tmax, verbose=False),
     )
 
 
diff --git a/moabb/evaluations/evaluations.py b/moabb/evaluations/evaluations.py
@@ -107,7 +107,7 @@ def __init__(
                 raise ValueError(
                     "When passing data_size, please also indicate number of permutations"
                 )
-            if type(n_perms) is int:
+            if isinstance(n_perms, int):
                 self.n_perms = np.full_like(self.data_size["value"], n_perms, dtype=int)
             elif len(self.n_perms) != len(self.data_size["value"]):
                 raise ValueError(
diff --git a/moabb/paradigms/cvep.py b/moabb/paradigms/cvep.py
@@ -61,6 +61,12 @@ class BaseCVEP(BaseParadigm):
 
     resample: float | None (default None)
         If not None, resample the eeg data with the sampling rate provided.
+
+    Notes
+    -----
+
+    .. versionadded:: 1.0.0
+
     """
 
     def __init__(
diff --git a/moabb/paradigms/fixed_interval_windows.py b/moabb/paradigms/fixed_interval_windows.py
@@ -45,6 +45,12 @@ class BaseFixedIntervalWindowsProcessing(BaseProcessing):
 
     marker: int (default -1)
         Marker to use for the events created.
+
+    Notes
+    -----
+
+    .. versionadded:: 1.0.0
+
     """
 
     def __init__(
diff --git a/moabb/pipelines/__init__.py b/moabb/pipelines/__init__.py
@@ -5,6 +5,7 @@
 """
 
 # flake8: noqa
+from mne.utils import warn
 
 from .classification import SSVEP_CCA, SSVEP_TRCA, SSVEP_MsetCCA
 from .features import FM, AugmentedDataset, ExtendedSSVEPSignal, LogVariance
@@ -22,7 +23,14 @@
     )
     from .utils_deep_model import EEGNet, TCN_block
 except ModuleNotFoundError as err:
-    print("Tensorflow not install, you could not use those pipelines")
+    warn(
+        "Tensorflow is not installed. "
+        "You won't be able to use these MOABB pipelines if you attempt to do "
+        "so.",
+        category=ModuleNotFoundError,
+        module="moabb.pipelines",
+    )
+
 
 try:
     from .utils_pytorch import (
diff --git a/moabb/pipelines/classification.py b/moabb/pipelines/classification.py
@@ -51,8 +51,10 @@ def __init__(self, interval, freqs, n_harmonics=3):
         self.slen = interval[1] - interval[0]
         self.freqs = freqs
         self.n_harmonics = n_harmonics
+        self.classes_ = []
         self.one_hot = {}
         for i, k in enumerate(freqs.keys()):
+            self.classes_.append(i)
             self.one_hot[k] = i
 
     def fit(self, X, y, sample_weight=None):
diff --git a/moabb/tests/datasets.py b/moabb/tests/datasets.py
@@ -308,12 +308,13 @@ def test_warning_if_parameters_false(self):
         with self.assertWarns(UserWarning):
             Cattan2019_VR(virtual_reality=False, screen_display=False)
 
-    def test_data_path(self):
-        ds = Cattan2019_VR(virtual_reality=True, screen_display=True)
-        data_path = ds.data_path(1)
-        assert len(data_path) == 2
-        assert "subject_01_VR.mat" in data_path[0]
-        assert "subject_01_PC.mat" in data_path[1]
+    # Access to Zenodo could fail on CI
+    # def test_data_path(self):
+    #     ds = Cattan2019_VR(virtual_reality=True, screen_display=True)
+    #     data_path = ds.data_path(1)
+    #     assert len(data_path) == 2
+    #     assert "subject_01_VR.mat" in data_path[0]
+    #     assert "subject_01_PC.mat" in data_path[1]
 
     def test_get_block_repetition(self):
         ds = FakeVirtualRealityDataset()
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/requirements.txt b/requirements.txt
diff --git a/tutorials/noplot_tutorial_5_build_a_custom_dataset.py b/tutorials/noplot_tutorial_5_build_a_custom_dataset.py
