REL 0.4 (#385)

.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:

.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
@@ -28,15 +28,15 @@ 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"
 
 # Specify version of BIDS-validator to be used, 'master', or 'stable'
 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:

README.rst

@@ -199,7 +199,7 @@ Example:
 Bug reports
 -----------
 
-Use the `github issue tracker <https://github.com/mne-tools/mne-bids/issues>`_
+Use the `GitHub issue tracker <https://github.com/mne-tools/mne-bids/issues>`_
 to report bugs.
 
 Contributing

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"

doc/_templates/navbar.html

@@ -9,6 +9,7 @@
   <ul class="dropdown-menu" aria-labelledby="dropdownMenu1">
     <li><a href="https://mne.tools/mne-bids/dev/index.html">Development</a></li>
     <li><a href="https://mne.tools/mne-bids/stable/index.html">Stable</a></li>
+    <li><a href="https://mne.tools/mne-bids/v0.4/index.html">v0.4</a></li>
     <li><a href="https://mne.tools/mne-bids/v0.3/index.html">v0.3</a></li>
     <li><a href="https://mne.tools/mne-bids/v0.2/index.html">v0.2</a></li>
     <li><a href="https://mne.tools/mne-bids/v0.1/index.html">v0.1</a></li>

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),

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

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 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/271>`_)
+- New feature in :func:`mne_bids.write.write_anat` for shear deface of mri, by `Alex Rockhill`_ (`#271 <https://github.com/mne-tools/mne-bids/pull/271>`_)
 - Added option to anonymize by shifting measurement date with `anonymize` parameter, in accordance with BIDS specifications, by `Alex Rockhill`_ (`#280 <https://github.com/mne-tools/mne-bids/pull/280>`_)
 - Added :func:`mne_bids.get_matched_empty_room` to get empty room filename matching a data file, by `Mainak Jas`_ (`#290 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/344>`_)
 - :func:`read_raw_bids` now reads in sidecar json files to set, or estimate Power Line Frequency, by `Adam Li`_ (`#341 <https://github.com/mne-tools/mne-bids/pull/341>`_)
-- Allow FIF files with multiple parts to be read using :func:`read_raw_bids`, by `Teon Brooks`_ (`#346 <https://github.com/mne-tools/mne-bids/pull/346>`)
+- Allow FIF files with multiple parts to be read using :func:`read_raw_bids`, by `Teon Brooks`_ (`#346 <https://github.com/mne-tools/mne-bids/pull/346>`_)
 - Added handedness to participant files, by `Dominik Welke`_ (`#354 <https://github.com/mne-tools/mne-bids/pull/354>`_)
-- MNE-BIDS can now handle a paths that are `pathlib.Path` objects (in addition to strings), by `Richard Höchenberger`_ (`#362 <https://github.com/mne-tools/mne-bids/pull/362>`)
-- The documentation is now available for all MNE-BIDS versions via a dropdown menu, by `Stefan Appelhoff`_(`#370 <https://github.com/mne-tools/mne-bids/pull/370>`)
+- MNE-BIDS can now handle a paths that are :class:`pathlib.Path` objects (in addition to strings), by `Richard Höchenberger`_ (`#362 <https://github.com/mne-tools/mne-bids/pull/362>`_)
+- The documentation is now available for all MNE-BIDS versions via a dropdown menu, by `Stefan Appelhoff`_ (`#370 <https://github.com/mne-tools/mne-bids/pull/370>`_)
 
 Bug
 ~~~
@@ -47,11 +47,26 @@ Bug
 - Fix writing to scans.tsv file when anonymization is turned on, by `Adam Li`_ (`#352 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/355>`_)
-- Avoid cases in which NumPy would raise a `FutureWarning` when populating TSV files, by `Richard Höchenberger`_ (`#372 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/375>`)
+- Avoid cases in which NumPy would raise a `FutureWarning` when populating TSV files, by `Richard Höchenberger`_ (`#372 <https://github.com/mne-tools/mne-bids/pull/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 <https://github.com/mne-tools/mne-bids/pull/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

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

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.

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

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']
 

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)