From b7abcee3e5f95ee2d95e8a4e77ad4d1c5f284f0c Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Wed, 14 Jul 2021 18:00:44 +0200 Subject: [PATCH] REL: v0.8 --- .circleci/config.yml | 8 +++-- .github/workflows/unit_tests.yml | 2 +- CONTRIBUTING.md | 31 +++++++++++-------- doc/_templates/docs-navbar.html | 20 ------------ doc/_templates/docs-toc.html | 13 -------- doc/_templates/navbar.html | 23 -------------- doc/_templates/version-switcher.html | 11 +++++++ doc/authors.rst | 5 ++- doc/conf.py | 6 ++-- doc/install.rst | 10 +++--- doc/whats_new.rst | 46 +++++++++++++++++++++------- doc/whats_new_previous_releases.rst | 26 ++++++++-------- examples/bidspath.py | 1 + examples/convert_ieeg_to_bids.py | 2 ++ examples/convert_mri_and_trans.py | 1 + examples/create_bids_folder.py | 1 + examples/mark_bad_channels.py | 1 + mne_bids/__init__.py | 2 +- setup.cfg | 13 ++++---- test_requirements.txt | 12 ++++---- 20 files changed, 115 insertions(+), 119 deletions(-) delete mode 100644 doc/_templates/docs-navbar.html delete mode 100644 doc/_templates/docs-toc.html delete mode 100644 doc/_templates/navbar.html create mode 100644 doc/_templates/version-switcher.html diff --git a/.circleci/config.yml b/.circleci/config.yml index d3fab9911..4a9175c67 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -55,7 +55,7 @@ jobs: docs-deploy: # will only be run on main branch docker: - - image: node:8 + - image: cimg/node:lts steps: - checkout @@ -64,8 +64,10 @@ jobs: - run: name: Install and configure dependencies + # do not update gh-pages above 3.0.0 + # see: https://github.com/tschaub/gh-pages/issues/354 command: | - npm install --global gh-pages@3.0 + npm install gh-pages@3.0.0 git config --global user.email "circle@mne.com" git config --global user.name "Circle Ci" @@ -76,7 +78,7 @@ jobs: - run: # push built docs into the `dev` directory on the `gh-pages` branch name: Deploy docs to gh-pages branch - command: gh-pages --dotfiles --message "doc updates [skip ci]" --dist doc/_build/html --dest ./dev + command: node_modules/gh-pages/bin/gh-pages.js --dotfiles --message "doc updates [skip ci]" --dist doc/_build/html --dest ./dev link-check: diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 3b1a084ef..e7065ca83 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -45,7 +45,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: [3.6, 3.7, 3.8, 3.9] + python-version: [3.7, 3.8, 3.9] steps: - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }} diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e41f4383c..8f48b13eb 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -12,12 +12,14 @@ installation as shown below. ## Running tests ### (Optional) Install development version of MNE-Python + If you want to run the tests with a development version of MNE-Python, you can install it by running $ pip install -U https://github.com/mne-tools/mne-python/archive/main.zip ### Install development version of MNE-BIDS + First, you should [fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the `mne-bids` repository. Then, clone the fork and install it in "editable" mode. @@ -26,12 +28,14 @@ First, you should [fork](https://help.github.com/en/github/getting-started-with- ### Install Python packages required to run tests -Install the following packages for testing purposes, plus all optonal MNE-BIDS -dependencies to ensure you will be able to run all tests. - $ pip install flake8 pytest pytest-cov scikit-learn nibabel nilearn pybv +You can install the testing requirements using the `test_requirements.txt` file +from the root of the mne-bids repository. + + $ pip install -r test_requirements.txt ### Install the BIDS validator + Finally, it is necessary to install the [BIDS validator](https://github.com/bids-standard/bids-validator). The outputs of MNE-BIDS are run through the BIDS validator to check if the conversion @@ -40,6 +44,7 @@ worked properly and produced datasets that conforms to the BIDS specifications. You will need the `command line version` of the validator. #### Global (system-wide) installation + - First, install [Node.js](https://nodejs.org/en/). - For installing the **stable** version of `bids-validator`, please follow the instructions as detailed in the README of the bids-validator repository. @@ -59,7 +64,7 @@ Then, retrieve the validator and install all its dependencies via `npm`. $ git clone git@github.com:bids-standard bids-validator.git $ cd bids-validator/bids-validator - $ npm i + $ npm install Test your installation by running: @@ -67,10 +72,10 @@ Test your installation by running: ### Invoke pytest + Now you can finally run the tests by running `pytest` in the `mne-bids` directory. - $ cd mne-bids $ pytest If you have installed the `bids-validator` @@ -80,18 +85,18 @@ on a per-user basis, set the environment variable `VALIDATOR_EXECUTABLE` to poin ## Building the documentation -The documentation can be built using sphinx. For that, please additionally -install the following: +The documentation can be built using sphinx. +You can install the documentation requirements using the `requirements.txt` file +in the `doc/` directory of the mne-bids repository. - $ pip install matplotlib nilearn sphinx numpydoc sphinx-gallery pydata-sphinx-theme pillow + $ pip install -r doc/requirements.txt To build the documentation locally, one can run: - $ cd doc/ - $ make html + $ make build-doc -or +or, if you don't want to run the examples to build the documentation: - $ make html-noplot + $ make -C doc/ html-noplot -if you don't want to run the examples to build the documentation. This will result in a faster build but produce no plots in the examples. +The latter command will result in a faster build but produce no plots in the examples. diff --git a/doc/_templates/docs-navbar.html b/doc/_templates/docs-navbar.html deleted file mode 100644 index 101ea6611..000000000 --- a/doc/_templates/docs-navbar.html +++ /dev/null @@ -1,20 +0,0 @@ -{%- extends "pydata_sphinx_theme/docs-navbar.html" %} - -{%- block icon_links -%} - - - -{%- include "icon-links.html" with context -%} -{%- endblock %} diff --git a/doc/_templates/docs-toc.html b/doc/_templates/docs-toc.html deleted file mode 100644 index 97dc4a69f..000000000 --- a/doc/_templates/docs-toc.html +++ /dev/null @@ -1,13 +0,0 @@ -{% set page_toc = generate_toc_html() %} - -{%- if page_toc | length >= 1 %} -
- On this page -
-{%- endif %} - - - -{% include "edit_this_page.html" %} diff --git a/doc/_templates/navbar.html b/doc/_templates/navbar.html deleted file mode 100644 index 26a9af013..000000000 --- a/doc/_templates/navbar.html +++ /dev/null @@ -1,23 +0,0 @@ -{% extends "!navbar.html" %} - -{% block navbarsearch %} -
- - -
- -{{ super() }} -{% endblock %} diff --git a/doc/_templates/version-switcher.html b/doc/_templates/version-switcher.html new file mode 100644 index 000000000..d33de0d33 --- /dev/null +++ b/doc/_templates/version-switcher.html @@ -0,0 +1,11 @@ +
+ +
+ {%- for ver, txt in versions_dropdown.items() %} + {{ txt }} + {%- endfor %} +
+
diff --git a/doc/authors.rst b/doc/authors.rst index c4a13fb95..6d5f7d230 100644 --- a/doc/authors.rst +++ b/doc/authors.rst @@ -24,4 +24,7 @@ .. _Tom Donoghue: https://github.com/TomDonoghue .. _Richard Köhler: https://github.com/richardkoehler .. _Sin Kim: https://github.com/AKSoo -.. _Jean-Rémi King: https://kingjr.github.io/ +.. _Jean-Rémi King: https://kingjr.github.io +.. _Julia Guiomar Niso Galán: https://github.com/guiomar +.. _Eric Larson: https://github.com/rob-luke +.. _Clemens Brunner: https://github.com/cbrnr diff --git a/doc/conf.py b/doc/conf.py index 133c4da2d..69412b10c 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -127,12 +127,14 @@ 'use_edit_page_button': False, 'navigation_with_keys': False, 'show_toc_level': 1, + 'navbar_end': ['version-switcher', 'navbar-icon-links'], } html_context = { 'versions_dropdown': { - 'dev': 'v0.8 (devel)', - 'stable': 'v0.7 (stable)', + 'dev': 'v0.9 (devel)', + 'stable': 'v0.8 (stable)', + 'v0.7': 'v0.7', 'v0.6': 'v0.6', 'v0.5': 'v0.5', 'v0.4': 'v0.4', diff --git a/doc/install.rst b/doc/install.rst index aae3213cf..113731d44 100644 --- a/doc/install.rst +++ b/doc/install.rst @@ -7,15 +7,15 @@ Dependencies ------------ * ``mne`` (>=0.21.2) -* ``numpy`` (>=1.15.4) -* ``scipy`` (>=1.1.0, or >=1.5.0 for certain operations with EEGLAB data) +* ``numpy`` (>=1.16.0) +* ``scipy`` (>=1.2.0, or >=1.5.0 for certain operations with EEGLAB data) * ``nibabel`` (>=2.2, optional, for processing MRI data) * ``pybv`` (>=0.5, optional, for writing BrainVision data) -* ``pandas`` (>=0.23.4, optional, for generating event statistics) -* ``matplotlib`` (optional, for using the interactive data inspector) +* ``pandas`` (>=0.24.0, optional, for generating event statistics) +* ``matplotlib`` (>=3.1.0, optional, for using the interactive data inspector) We recommend the `Anaconda `_ Python -distribution. We require that you use Python 3.6 or higher. +distribution. We require that you use Python 3.7 or higher. You may choose to install ``mne-bids`` `via pip <#Installation via pip>`_ or `via conda <#Installation via conda>`_. diff --git a/doc/whats_new.rst b/doc/whats_new.rst index 8ce6f95f6..561574815 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -10,28 +10,51 @@ What's new? .. currentmodule:: mne_bids .. _changes_0_8: -Version 0.8 (unreleased) +Version 0.8 (2021-07-15) ------------------------ -... +This release brings numerous improvements and fixes based on feedback from our +users, including those working with very large datasets. MNE-BIDS now handles +previously-overlooked edge cases, offers a much more efficient way to +store data on macOS and Linux (using symbolic links), and lays the groundwork +for supporting BIDS derivatives, i.e., storing modified data. Notable changes ~~~~~~~~~~~~~~~ -- ... +- You can now write preloaded and potentially modified data with + :func:`mne_bids.write_raw_bids` by passing ``allow_preload=True``. This is + a first step towards supporting derivative files. +- `mne_bids.BIDSPath` now has property getters and setters for all BIDS + entities. What this means is that you can now do things like + ``bids_path.subject = '01'`` instead of ``bids_path.update(subject='01')``. +- We now support Deep Brain Stimulation (DBS) data. +- The way we handle anatomical landmarks was greatly revamped to ensure we're + always using the correct coordinate systems. A new function, + `mne_bids.get_anat_landmarks`, helps with extracting fiducial points from + anatomical scans. +- When creating a BIDS dataset from FIFF files on macOS and Linux, MNE-BIDS + can now optionally generate symbolic links to the original files instead of + copies. Simply pass ``symlink=True`` to + :func:`mne_bids.write_raw_bids`. This can massively reduce the storage space + requirements. Authors ~~~~~~~ -* `Alex Rockhill`_ -* `Richard Höchenberger`_ * `Adam Li`_ +* `Alex Rockhill`_ +* `Alexandre Gramfort`_ +* `Clemens Brunner`_ * `Eduard Ort`_ -* `Richard Köhler`_ (new contributor) +* `Eric Larson`_ * `Jean-Rémi King`_ (new contributor) -* `Sin Kim`_ (new contributor) -* `Alexandre Gramfort`_ +* `Julia Guiomar Niso Galán`_ (new contributor) * `Mainak Jas`_ +* `Richard Höchenberger`_ +* `Richard Köhler`_ (new contributor) +* `Robert Luke`_ (new contributor) +* `Sin Kim`_ (new contributor) * `Stefan Appelhoff`_ Detailed list of changes @@ -40,7 +63,7 @@ Detailed list of changes Enhancements ^^^^^^^^^^^^ -- The fields "DigitizedLandmarks" and "DigitizedHeadPoints" in the json sidecar of Neuromag data are now set to True/False depending on whether any landmarks (NAS, RPA, LPA) or extra points are found in raw.info['dig'], by `Eduard Ort`_ (:gh:`772`) +- The fields "DigitizedLandmarks" and "DigitizedHeadPoints" in the json sidecar of Neuromag data are now set to ``true`` or ``false`` depending on whether any landmarks (NAS, RPA, LPA) or extra points are found in ``raw.info['dig']``, by `Eduard Ort`_ (:gh:`772`) - Updated the "Read BIDS datasets" example to use data from `OpenNeuro `_, by `Alex Rockhill`_ (:gh:`753`) - :func:`mne_bids.get_head_mri_trans` is now more lenient when looking for the fiducial points (LPA, RPA, and nasion) in the MRI JSON sidecar file, and accepts a larger variety of landmark names (upper- and lowercase letters; ``'nasion'`` instead of only ``'NAS'``), by `Richard Höchenberger`_ (:gh:`769`) - :func:`mne_bids.get_head_mri_trans` gained a new keyword argument ``t1_bids_path``, allowing for the MR scan to be stored in a different session or even in a different BIDS dataset than the electrophysiological recording, by `Richard Höchenberger`_ (:gh:`771`) @@ -51,7 +74,7 @@ Enhancements - :func:`mne_bids.write_raw_bids` gained a new parameter ``empty_room`` that allows to specify an associated empty-room recording when writing an MEG data file. This information will be stored in the ``AssociatedEmptyRoom`` field of the MEG JSON sidecar file, by `Richard Höchenberger`_ (:gh:`795`) - Added support for the new channel type ``'dbs'`` (Deep Brain Stimulation), which was introduced in MNE-Python 0.23, by `Richard Köhler`_ (:gh:`800`) - :func:`mne_bids.read_raw_bids` now warns in many situations when it encounters a mismatch between the channels in ``*_channels.tsv`` and the raw data, by `Richard Höchenberger`_ (:gh:`823`) -- MNE BIDS now accepts ".mrk" head digitization files used in the KIT/Yokogawa/Ricoh MEG system, by `Jean-Rémi King`_ and `Stefan Appelhoff`_ (:gh:`842`) +- MNE BIDS now accepts ``.mrk`` head digitization files used in the KIT/Yokogawa/Ricoh MEG system, by `Jean-Rémi King`_ and `Stefan Appelhoff`_ (:gh:`842`) API and behavior changes ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -71,6 +94,7 @@ Requirements - For downloading `OpenNeuro `_ datasets, ``openneuro-py`` is now required to run the examples and build the documentation, by `Alex Rockhill`_ (:gh:`753`) - MNE-BIDS now depends on `setuptools `_. This package is normally installed by your Python distribution automatically, so we don't expect any users to be affected by this change, by `Richard Höchenberger`_ (:gh:`794`) +- MNE-BIDS now requires Python 3.7 or higher, because Python 3.6 is soon reaching its end of life. Bug fixes ^^^^^^^^^ @@ -84,7 +108,7 @@ Bug fixes - :func:`mne_bids.read_raw_bids` crashed when the (optional) ``acq_time`` column was missing in ``*_scans.tsv``, by `Alexandre Gramfort`_ (:gh:`814`) - :func:`mne_bids.write_raw_bids` doesn't crash anymore if the designated output directory contains the string ``"tsv"``, by `Richard Höchenberger`_ (:gh:`833`) - :func:`mne_bids.get_head_mri_trans` gave incorrect results when the T1 image was not in LIA format, now all formats function properly, by `Alex Rockhill`_ and `Alexandre Gramfort`_ (:gh:`827`) -- :func:`mne_bids.get_head_mri_trans` and :func:`mne_bids.write_anat` used a T1w image but depended specifically on the freesurfer T1w image. Now the freesurfer subject directory is used, by `Alex Rockhill`_ and `Alexandre Gramfort`_ (:gh:`827`) +- :func:`mne_bids.get_head_mri_trans` and :func:`mne_bids.write_anat` used a T1w image but depended specifically on the freesurfer T1w image. Now the FreeSurfer subjects directory is used, by `Alex Rockhill`_ and `Alexandre Gramfort`_ (:gh:`827`) :doc:`Find out what was new in previous releases ` diff --git a/doc/whats_new_previous_releases.rst b/doc/whats_new_previous_releases.rst index 91ae29769..0f2b69624 100644 --- a/doc/whats_new_previous_releases.rst +++ b/doc/whats_new_previous_releases.rst @@ -10,8 +10,8 @@ What was new in previous releases? .. currentmodule:: mne_bids .. _changes_0_7: -Version 0.7 ------------ +Version 0.7 (2021-03-22) +------------------------ This release brings numerous enhancements and bug fixes that enhance reading and writing BIDS data, and improve compatibility with the latest BIDS @@ -93,8 +93,8 @@ Bug fixes .. _changes_0_6: -Version 0.6 🎄 --------------- +Version 0.6 🎄 (2020-12-16) +--------------------------- These are challenging days for many of us, and to make your lives ever so slightly easier, we've been working hard to deliver this early @@ -135,7 +135,7 @@ Authors * `Alexandre Gramfort`_ * `Austin Hurst`_ * `Ethan Knights`_ (new contributor) -* `Mainak Jas`_ +* `Mainak Jas`_ * `Richard Höchenberger`_ Detailed list of changes @@ -316,8 +316,8 @@ Further API changes: .. _changes_0_4: -Version 0.4 ------------ +Version 0.4 (2020-04-04) +------------------------ Changelog ~~~~~~~~~ @@ -370,8 +370,8 @@ People who contributed to this release (in alphabetical order): .. _changes_0_3: -Version 0.3 ------------ +Version 0.3 (2019-12-17) +------------------------ Changelog ~~~~~~~~~ @@ -415,8 +415,8 @@ People who contributed to this release (in alphabetical order): .. _changes_0_2: -Version 0.2 ------------ +Version 0.2 (2019-04-26) +------------------------ Changelog ~~~~~~~~~ @@ -472,8 +472,8 @@ People who contributed to this release (in alphabetical order): .. _changes_0_1: -Version 0.1 ------------ +Version 0.1 (2018-11-05) +------------------------ Changelog ~~~~~~~~~ diff --git a/examples/bidspath.py b/examples/bidspath.py index 86ad98d6b..02ac1e73b 100644 --- a/examples/bidspath.py +++ b/examples/bidspath.py @@ -9,6 +9,7 @@ operations. Learn here how to use it. """ # Author: Richard Höchenberger +# # License: BSD (3-clause) # %% diff --git a/examples/convert_ieeg_to_bids.py b/examples/convert_ieeg_to_bids.py index 30b3cf3a0..6832e1f6d 100644 --- a/examples/convert_ieeg_to_bids.py +++ b/examples/convert_ieeg_to_bids.py @@ -46,6 +46,8 @@ # # License: BSD (3-clause) +# %% + import os.path as op import shutil from pprint import pprint diff --git a/examples/convert_mri_and_trans.py b/examples/convert_mri_and_trans.py index b49e9ffbf..659cf2f80 100644 --- a/examples/convert_mri_and_trans.py +++ b/examples/convert_mri_and_trans.py @@ -31,6 +31,7 @@ # Authors: Stefan Appelhoff # Alex Rockhill # Alex Gramfort +# # License: BSD (3-clause) # %% diff --git a/examples/create_bids_folder.py b/examples/create_bids_folder.py index f83cf9718..c17170660 100644 --- a/examples/create_bids_folder.py +++ b/examples/create_bids_folder.py @@ -14,6 +14,7 @@ """ # Authors: Chris Holdgraf +# # License: BSD (3-clause) # %% diff --git a/examples/mark_bad_channels.py b/examples/mark_bad_channels.py index 15241b875..9b676bd3c 100644 --- a/examples/mark_bad_channels.py +++ b/examples/mark_bad_channels.py @@ -16,6 +16,7 @@ """ # noqa:E501 # Authors: Richard Höchenberger +# # License: BSD (3-clause) # %% diff --git a/mne_bids/__init__.py b/mne_bids/__init__.py index 38519fe90..7772946b4 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__ = '0.8.dev0' +__version__ = '0.8' from mne_bids import commands from mne_bids.report import make_report from mne_bids.path import (BIDSPath, get_datatypes, get_entity_vals, diff --git a/setup.cfg b/setup.cfg index f1efd4f1f..60144463b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -24,7 +24,6 @@ classifiers = Operating System :: Unix Operating System :: MacOS Programming Language :: Python - Programming Language :: Python :: 3.6 Programming Language :: Python :: 3.7 Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 @@ -34,11 +33,11 @@ project_urls = Source = https://github.com/mne-tools/mne-bids [options] -python_requires = ~= 3.6 +python_requires = ~= 3.7 install_requires = mne >= 0.21.2 - numpy>=1.15.4 - scipy>=1.1.0 + numpy >= 1.16.0 + scipy >= 1.2.0 setuptools packages = find: include_package_data = True @@ -47,8 +46,8 @@ include_package_data = True full = nibabel >= 2.2 pybv >= 0.5 - matplotlib - pandas >= 0.23.4 + matplotlib >= 3.1.0 + pandas >= 0.24.0 openneuro-py [options.entry_points] @@ -91,7 +90,7 @@ convention = pep257 match_dir = ^(?!\.|doc|examples).*$ add-ignore = D100,D104,D107,D413 add-select = D214,D215,D404,D405,D406,D407,D408,D409,D410,D411 -ignore-decorators = property +ignore-decorators = property [coverage:run] omit = diff --git a/test_requirements.txt b/test_requirements.txt index 5a8279c24..14033c894 100644 --- a/test_requirements.txt +++ b/test_requirements.txt @@ -1,14 +1,14 @@ -numpy>=1.14 +numpy>=1.16.0 scipy>=1.5.0 mne>=0.21.2 -nibabel>=2.2 -pybv>=0.4 +matplotlib<3.4 +pandas>=0.24.0 +nibabel>=2.5 +pybv>=0.5 +openneuro-py pytest pytest-cov pytest-sugar check-manifest pydocstyle flake8 -matplotlib<3.4 -pandas>=0.23.4 -openneuro-py