From 538c0b9fb93557841024ef47a452c5fc227b50f0 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Sat, 4 Apr 2020 00:18:17 +0200 Subject: [PATCH] REL 0.4 (#385) --- .circleci/config.yml | 2 +- .travis.yml | 8 +++---- README.rst | 2 +- appveyor.yml | 4 ++-- doc/_templates/navbar.html | 1 + doc/conf.py | 2 +- doc/environment.yml | 4 ++-- doc/whats_new.rst | 39 ++++++++++++++++++++++++---------- environment.yml | 2 +- examples/convert_empty_room.py | 6 +++--- mne_bids/__init__.py | 2 +- mne_bids/config.py | 2 +- mne_bids/write.py | 8 +++---- 13 files changed, 50 insertions(+), 32 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a27a744c9..937aab18d 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -39,7 +39,7 @@ jobs: conda update --yes --quiet conda conda env create -f environment.yml --name=testenv source activate testenv - pip install -U https://api.github.com/repos/mne-tools/mne-python/zipball/master + pip install mne==0.20 python setup.py develop - run: diff --git a/.travis.yml b/.travis.yml index 4937be5fd..e5e694783 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,13 +9,13 @@ matrix: # Linux - os: linux env: CONDA_ENV="environment.yml" - MNE_VERSION="master" + MNE_VERSION="maint/0.20" name: "Linux conda full" # OSX conda - os: osx env: CONDA_ENV="environment.yml" - MNE_VERSION="master" + MNE_VERSION="maint/0.20" name: "MacOS conda full" # Minimal @@ -28,7 +28,7 @@ matrix: # Linux with timezone = Berlin, i.e. UTC+1 (CET) or UTC+2 (CEST) - os: linux env: CONDA_ENV="environment.yml" - MNE_VERSION="master" + MNE_VERSION="maint/0.20" TZ="Europe/Berlin" name: "Linux conda full, timezone Europe/Berlin" @@ -36,7 +36,7 @@ matrix: env: global: # can be "stable", or anything that can be used with git checkout - - VALIDATOR_VERSION="347117838f2b929e" + - VALIDATOR_VERSION="8887074e5f5f48a768842ffcf96fb2952dbe0e38" # can be any branch of MNE-Python (e.g., "maint/0.18", "master", ...) before_install: diff --git a/README.rst b/README.rst index f34ad2857..b25219e51 100644 --- a/README.rst +++ b/README.rst @@ -199,7 +199,7 @@ Example: Bug reports ----------- -Use the `github issue tracker `_ +Use the `GitHub issue tracker `_ to report bugs. Contributing diff --git a/appveyor.yml b/appveyor.yml index 69b9c013e..a0a68679e 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -4,9 +4,9 @@ environment: # latter case, you MUST adjust VALIDATOR_EXECUTABLE to the following value: # "C:\\projects\\mne-bids\\bids-validator\\bids-validator\\bin\\bids-validator" # ... whereas for "stable", VALIDATOR_EXECUTABLE MUST be set to "n/a" - VALIDATOR_VERSION: "347117838f2b929e" + VALIDATOR_VERSION: "8887074e5f5f48a768842ffcf96fb2952dbe0e38" # can be any branch of MNE-Python (e.g., "maint/0.18", "master", ...) - MNE_VERSION: "master" + MNE_VERSION: "maint/0.20" VALIDATOR_EXECUTABLE: "C:\\projects\\mne-bids\\bids-validator\\bids-validator\\bin\\bids-validator" NODEJS_VERSION: "10.16.1" PYTHON: "C:\\conda" diff --git a/doc/_templates/navbar.html b/doc/_templates/navbar.html index e4f68b136..18b9d2c8b 100644 --- a/doc/_templates/navbar.html +++ b/doc/_templates/navbar.html @@ -9,6 +9,7 @@
  • Development
  • Stable
    • +
  • v0.4
  • v0.3
  • v0.2
  • v0.1
    • diff --git a/doc/conf.py b/doc/conf.py index 56c4bb418..b93016ddd 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -107,7 +107,7 @@ intersphinx_mapping = { 'python': ('https://docs.python.org/3', None), 'mne': ('https://mne.tools/dev', None), - 'numpy': ('https://www.numpy.org/devdocs', None), + 'numpy': ('https://numpy.org/devdocs', None), 'scipy': ('https://scipy.github.io/devdocs', None), 'matplotlib': ('https://matplotlib.org', None), 'nilearn': ('https://nilearn.github.io', None), diff --git a/doc/environment.yml b/doc/environment.yml index 7826c2ba2..c0df5a0cb 100644 --- a/doc/environment.yml +++ b/doc/environment.yml @@ -4,14 +4,14 @@ channels: - conda-forge dependencies: - python<3.7 -- pip=19 +- pip<=20 - mkl - numpy>=1.14 - scipy>=0.18.1 - scikit-learn - matplotlib - pip: - - mne_bids>=0.3,<0.4 + - mne_bids>=0.4,<0.5 - mne>=0.19.1 - nibabel>=2.2 - pybv diff --git a/doc/whats_new.rst b/doc/whats_new.rst index fb5dc9c2f..922cd4a1d 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -14,17 +14,17 @@ Here we list a changelog of MNE-BIDS. .. currentmodule:: mne_bids -.. _current: +.. _changes_0_4: -Current -------- +Version 0.4 +----------- Changelog ~~~~~~~~~ - Added automatic conversion of FIF to BrainVision format with warning for EEG only data and conversion to FIF for meg non-FIF data, by `Alex Rockhill`_ (`#237 `_) - Add possibility to pass raw readers parameters (e.g. `allow_maxshield`) to :func:`read_raw_bids` to allow reading BIDS-formatted data before applying maxfilter, by `Sophie Herbst`_ -- New feature in :func`mne_bids.write.write_anat` for shear deface of mri, by `Alex Rockhill`_ (`#271 `_) +- New feature in :func:`mne_bids.write.write_anat` for shear deface of mri, by `Alex Rockhill`_ (`#271 `_) - Added option to anonymize by shifting measurement date with `anonymize` parameter, in accordance with BIDS specifications, by `Alex Rockhill`_ (`#280 `_) - Added :func:`mne_bids.get_matched_empty_room` to get empty room filename matching a data file, by `Mainak Jas`_ (`#290 `_) - Add ability for :func:`mne_bids.get_head_mri_trans` to read fiducial points from fif data without applying maxfilter, by `Maximilien Chaumon`_ (`#291 `_) @@ -33,10 +33,10 @@ Changelog - Add existence check for :func:`write_raw_bids` before :func:`make_dataset_description` is called, by `Adam Li`_ (`#331 `_) - Update scans.tsv writer to adhere to MNE-Python v0.20+ where `meas_date` is stored as a `datetime` object, by `Adam Li`_ (`#344 `_) - :func:`read_raw_bids` now reads in sidecar json files to set, or estimate Power Line Frequency, by `Adam Li`_ (`#341 `_) -- Allow FIF files with multiple parts to be read using :func:`read_raw_bids`, by `Teon Brooks`_ (`#346 `) +- Allow FIF files with multiple parts to be read using :func:`read_raw_bids`, by `Teon Brooks`_ (`#346 `_) - Added handedness to participant files, by `Dominik Welke`_ (`#354 `_) -- MNE-BIDS can now handle a paths that are `pathlib.Path` objects (in addition to strings), by `Richard Höchenberger`_ (`#362 `) -- The documentation is now available for all MNE-BIDS versions via a dropdown menu, by `Stefan Appelhoff`_(`#370 `) +- MNE-BIDS can now handle a paths that are :class:`pathlib.Path` objects (in addition to strings), by `Richard Höchenberger`_ (`#362 `_) +- The documentation is now available for all MNE-BIDS versions via a dropdown menu, by `Stefan Appelhoff`_ (`#370 `_) Bug ~~~ @@ -47,11 +47,26 @@ Bug - Fix writing to scans.tsv file when anonymization is turned on, by `Adam Li`_ (`#352 `_) - Fix :func:`read_raw_bids` to properly read in sidecar json even if a similarly named copy lives inside "derivatives/" sub-folder, by `Adam Li`_ (`#350 `_) - Fix :func:`read_raw_bids` to properly read in events.tsv sidecar if the 'trial_type' description has a "#" character in it by `Adam Li`_ (`#355 `_) -- Avoid cases in which NumPy would raise a `FutureWarning` when populating TSV files, by `Richard Höchenberger`_ (`#372 `) -- Remove events with an unknown onset, and assume unknown event durations to be zero, when reading BIDS data via :func:`read_raw_bids`, by `Richard Höchenberger`_ (`#375 `) +- Avoid cases in which NumPy would raise a `FutureWarning` when populating TSV files, by `Richard Höchenberger`_ (`#372 `_) +- Remove events with an unknown onset, and assume unknown event durations to be zero, when reading BIDS data via :func:`read_raw_bids`, by `Richard Höchenberger`_ (`#375 `_) -API -~~~ +Authors +~~~~~~~ + +People who contributed to this release (in alphabetical order): + +* Adam Li +* Alex Rockhill +* Alexandre Gramfort +* Ariel Rokem +* Dominik Welke +* Fu-Te Wong +* Mainak Jas +* Maximilien Chaumon +* Richard Höchenberger +* Sophie Herbst +* Stefan Appelhoff +* Teon Brooks .. _changes_0_3: @@ -214,3 +229,5 @@ People who contributed to this release (in alphabetical order): .. _Adam Li: https://github.com/adam2392 .. _Fu-Te Wong: https://github.com/zuxfoucault .. _Richard Höchenberger: https://github.com/hoechenberger +.. _Alexandre Gramfort: http://alexandre.gramfort.net +.. _Ariel Rokem: https://github.com/arokem diff --git a/environment.yml b/environment.yml index 6b7a7fa02..5e789f7ee 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python<3.7 -- pip=19 +- pip<=20 - mkl - numpy>=1.14 - scipy>=0.18.1 diff --git a/examples/convert_empty_room.py b/examples/convert_empty_room.py index 48cd6d807..99b5f5c24 100644 --- a/examples/convert_empty_room.py +++ b/examples/convert_empty_room.py @@ -1,9 +1,9 @@ """ .. _ex-convert-empty-room: -====================================== -Storing empty room data in BIDS format -====================================== +========================================== +09. Storing empty room data in BIDS format +========================================== This example demonstrates how to store empty room data in BIDS format and how to retrieve them. diff --git a/mne_bids/__init__.py b/mne_bids/__init__.py index 586e2cdfd..d0b0f7bbe 100644 --- a/mne_bids/__init__.py +++ b/mne_bids/__init__.py @@ -1,6 +1,6 @@ """MNE software for easily interacting with BIDS compatible datasets.""" -__version__ = '0.4.dev0' +__version__ = '0.4' from mne_bids.write import (write_raw_bids, make_bids_basename, # noqa: E501 F401 diff --git a/mne_bids/config.py b/mne_bids/config.py index 92a84ad83..a8a11285f 100644 --- a/mne_bids/config.py +++ b/mne_bids/config.py @@ -1,6 +1,6 @@ """Configuration values for MNE-BIDS.""" -BIDS_VERSION = "1.2.0" +BIDS_VERSION = "1.2.2" ALLOWED_KINDS = ['meg', 'eeg', 'ieeg'] diff --git a/mne_bids/write.py b/mne_bids/write.py index 50b997877..7dfb01918 100644 --- a/mne_bids/write.py +++ b/mne_bids/write.py @@ -751,10 +751,10 @@ def _write_raw_brainvision(raw, bids_fname, events): meas_date = raw.info['meas_date'] if meas_date is not None: meas_date = _stamp_to_dt(meas_date) - write_brainvision(raw.get_data(), raw.info['sfreq'], - raw.ch_names, - op.splitext(op.basename(bids_fname))[0], - op.dirname(bids_fname), + write_brainvision(data=raw.get_data(), sfreq=raw.info['sfreq'], + ch_names=raw.ch_names, + fname_base=op.splitext(op.basename(bids_fname))[0], + folder_out=op.dirname(bids_fname), events=events, resolution=1e-9, meas_date=meas_date)