1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
|
.. This (-*- rst -*-) format file contains commonly used link targets
and name substitutions. It may be included in many files,
therefore it should only contain link targets and name
substitutions. Try grepping for "^\.\. _" to find plausible
candidates for this list.
.. NOTE: reST targets are
__not_case_sensitive__, so only one target definition is needed for
nipy, NIPY, Nipy, etc...
.. mne
.. _`MNE-Python`: http://mne.tools/mne-python-intro
.. _`MNE-Python GitHub`: https://github.com/mne-tools/mne-python
.. _`mne-scripts`: https://github.com/mne-tools/mne-scripts/
.. _`MNE-C manual`: https://mne.tools/mne-c-manual/MNE-manual-2.7.3.pdf
.. _`GitHub issues page`: https://github.com/mne-tools/mne-python/issues/
.. _`MNE Forum`: https://mne.discourse.group
.. _`MNE-BIDS`: https://mne.tools/mne-bids
.. _`MNE-BIDS-Pipeline`: https://mne.tools/mne-bids-pipeline
.. _`MNE-HCP`: http://mne.tools/mne-hcp
.. _`MNE-Realtime`: https://mne.tools/mne-realtime
.. _`MNE-MATLAB git repository`: https://github.com/mne-tools/mne-matlab
.. _`MNE-Docker`: https://github.com/mne-tools/mne-docker
.. _OpenMEEG: http://openmeeg.github.io
.. _EOSS2: https://chanzuckerberg.com/eoss/proposals/improving-usability-of-core-neuroscience-analysis-tools-with-mne-python
.. _EOSS4: https://chanzuckerberg.com/eoss/proposals/building-pediatric-and-clinical-data-pipelines-for-mne-python/
.. _`code of conduct`: https://github.com/mne-tools/.github/blob/main/CODE_OF_CONDUCT.md
.. TUTORIAL LINKS
.. _errors: https://en.wikipedia.org/w/index.php?title=Type_I_and_type_II_errors#Table_of_error_types
.. _fwer: https://en.wikipedia.org/wiki/Family-wise_error_rate
.. _fdr: https://en.wikipedia.org/wiki/False_discovery_rate
.. _ft_cluster: http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test
.. _ft_cluster_effect_size: https://mailman.science.ru.nl/pipermail/fieldtrip/2017-September/024644.html
.. _ft_exch: https://mailman.science.ru.nl/pipermail/fieldtrip/2008-October/001794.html
.. TEMPLATE FOR LINKS TO OTHER PROJECTS
.. _PROJECTNAME: http://neuroimaging.scipy.org
.. _`PROJECTNAME github`: http://github.com/nipy
.. _`PROJECTNAME mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
.. numpy
.. _numpy: http://www.numpy.org
.. _`numpy github`: http://github.com/numpy/numpy
.. _`numpy mailing list`: http://mail.scipy.org/mailman/listinfo/numpy-discussion
.. scipy
.. _scipy: http://www.scipy.org
.. _`scipy github`: http://github.com/scipy/scipy
.. _`scipy mailing list`: http://mail.scipy.org/mailman/listinfo/scipy-dev
.. freesurfer
.. _freesurfer: https://surfer.nmr.mgh.harvard.edu/
.. _`freesufer github`: https://github.com/freesurfer/freesurfer
.. _`freesurfer mailing list`: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport
.. nipy
.. _nipy: http://nipy.org/nipy
.. _`nipy github`: http://github.com/nipy/nipy
.. _`nipy mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
.. ipython
.. _ipython: https://ipython.org
.. _`ipython github`: https://github.com/ipython/ipython
.. _`ipython mailing list`: https://mail.python.org/mailman/listinfo/ipython-dev
.. dipy
.. _dipy: http://nipy.org/dipy
.. _`dipy github`: http://github.com/Garyfallidis/dipy
.. _`dipy mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
.. nibabel
.. _nibabel: http://nipy.org/nibabel
.. _`nibabel github`: http://github.com/nipy/nibabel
.. _`nibabel mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
.. h5py
.. _h5py: http://www.h5py.org
.. _`h5py github`: http://github.com/h5py/h5py
.. _`h5py mailing list`: https://groups.google.com/forum/#!forum/h5py
.. Pytest
.. _pytest: https://docs.pytest.org/
.. Flake8
.. _Flake8: http://flake8.pycqa.org/
.. pymatreader
.. _pymatreader: https://gitlab.com/obob/pymatreader
.. h5io
.. _h5io: https://github.com/h5io/h5io
.. CuPy
.. _CuPy: https://cupy.chainer.org/
.. Dask
.. _Dask: https://dask.org/
.. git stuff
.. _git: https://git-scm.com/
.. _github: https://github.com
.. _GitHub Help: https://help.github.com
.. _GitHub learning lab: https://lab.github.com/
.. _pro git book: https://git-scm.com/book/
.. _git bash: https://gitforwindows.org/
.. _git for Windows: https://gitforwindows.org/
.. _git clone: http://schacon.github.com/git/git-clone.html
.. _git checkout: https://schacon.github.io/git/git-checkout.html
.. _git commit: https://schacon.github.io/git/git-commit.html
.. _git push: https://schacon.github.io/git/git-push.html
.. _git pull: https://schacon.github.io/git/git-pull.html
.. _git add: https://schacon.github.io/git/git-add.html
.. _git status: https://schacon.github.io/git/git-status.html
.. _git diff: https://schacon.github.io/git/git-diff.html
.. _git log: https://schacon.github.io/git/git-log.html
.. _git branch: https://schacon.github.io/git/git-branch.html
.. _git remote: https://schacon.github.io/git/git-remote.html
.. _git rebase: https://schacon.github.io/git/git-rebase.html
.. _git config: https://schacon.github.io/git/git-config.html
.. other stuff
.. _python: http://www.python.org
.. _Brain Imaging Data Structure: https://bids.neuroimaging.io/
.. python packages
.. _pep8: https://pypi.org/project/pep8/
.. _pyflakes: https://pypi.org/project/pyflakes
.. _coverage: https://pypi.python.org/pypi/coverage
.. _mayavi: https://docs.enthought.com/mayavi/mayavi/
.. _nitime: http://nipy.org/nitime/
.. _joblib: https://pypi.python.org/pypi/joblib
.. _scikit-learn: https://scikit-learn.org/stable/
.. _pyDICOM: https://pypi.python.org/pypi/pydicom/
.. _matplotlib: https://matplotlib.org/
.. _sphinx: https://www.sphinx-doc.org/
.. _pandas: https://pandas.pydata.org/
.. _PIL: https://pypi.python.org/pypi/PIL
.. _tqdm: https://tqdm.github.io/
.. _pooch: https://www.fatiando.org/pooch/latest/
.. python editors
.. _Spyder: https://www.spyder-ide.org/
.. _`integrated development environment`: https://en.wikipedia.org/wiki/Integrated_development_environment
.. _`spyder`: https://www.spyder-ide.org/
.. _`visual studio code`: https://code.visualstudio.com/
.. _`pycharm`: https://www.jetbrains.com/pycharm/
.. _anaconda: https://www.anaconda.com/products/individual
.. _miniconda: https://conda.io/en/latest/miniconda.html
.. _miniforge: https://github.com/conda-forge/miniforge
.. _installation instructions for Anaconda: http://docs.continuum.io/anaconda/install
.. _installation instructions for Miniconda: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
.. _Anaconda troubleshooting guide: http://conda.pydata.org/docs/troubleshooting.html
.. installation links
.. _requirements file: https://raw.githubusercontent.com/mne-tools/mne-python/main/requirements.txt
.. _NVIDIA CUDA GPU processing: https://developer.nvidia.com/cuda-zone
.. _NVIDIA proprietary drivers: https://www.geforce.com/drivers
.. _Sphinx documentation: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
.. _sphinx-gallery: https://sphinx-gallery.github.io
.. _NumPy docstring style guidelines: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard
.. _Stack Overflow: https://stackoverflow.com/
.. vim: ft=rst
|
