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Merge branch 'master' into rf-boost-git-annex
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adswa authored Oct 13, 2023
2 parents 7a62662 + eeb7313 commit f5c085f
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22 changes: 22 additions & 0 deletions .all-contributorsrc
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Expand Up @@ -526,6 +526,28 @@
"avatar_url": [
"https://avatars.githubusercontent.com/u/1028657?v=4"
]
},
{
"login": "nobodyinperson",
"name": "Yann Büchau",
"contributions": [
"code"
],
"profile": "https://nobodyinperson.de",
"avatar_url": [
"https://avatars.githubusercontent.com/u/19148271?v=4"
]
},
{
"login": "matrss",
"name": "Matthias Riße",
"contributions": [
"code"
],
"profile": "https://github.com/matrss",
"avatar_url": [
"https://avatars.githubusercontent.com/u/9308656?v=4"
]
}
],
"contributorsPerLine": 7
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8 changes: 4 additions & 4 deletions .appveyor.yml
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Expand Up @@ -79,7 +79,7 @@ environment:
INSTALL_SYSPKGS: python3-virtualenv
CODECOV_BINARY: https://uploader.codecov.io/latest/linux/codecov
# system git-annex is way too old, use better one
INSTALL_GITANNEX: git-annex -m deb-url --url http://snapshot.debian.org/archive/debian/20210906T204127Z/pool/main/g/git-annex/git-annex_8.20210903-1_amd64.deb
INSTALL_GITANNEX: git-annex -m deb-url --url https://datasets.datalad.org/datalad/packages/neurodebian/git-annex_8.20210903-1_amd64.deb
# Windows core tests
- ID: WinP39core
# ~35 min
Expand Down Expand Up @@ -119,7 +119,7 @@ environment:
INSTALL_SYSPKGS: python3-virtualenv
CODECOV_BINARY: https://uploader.codecov.io/latest/linux/codecov
# system git-annex is way too old, use better one
INSTALL_GITANNEX: git-annex -m deb-url --url http://snapshot.debian.org/archive/debian/20210906T204127Z/pool/main/g/git-annex/git-annex_8.20210903-1_amd64.deb
INSTALL_GITANNEX: git-annex -m deb-url --url https://datasets.datalad.org/datalad/packages/neurodebian/git-annex_8.20210903-1_amd64.deb
- ID: WinP39a1
# ~40min
DTS: >
Expand Down Expand Up @@ -182,7 +182,7 @@ environment:
INSTALL_SYSPKGS: python3-virtualenv
CODECOV_BINARY: https://uploader.codecov.io/latest/linux/codecov
# system git-annex is way too old, use better one
INSTALL_GITANNEX: git-annex -m deb-url --url http://snapshot.debian.org/archive/debian/20210906T204127Z/pool/main/g/git-annex/git-annex_8.20210903-1_amd64.deb
INSTALL_GITANNEX: git-annex -m deb-url --url https://datasets.datalad.org/datalad/packages/neurodebian/git-annex_8.20210903-1_amd64.deb
- ID: Ubu20P37b
# ~25min
PY: 3.7
Expand All @@ -198,7 +198,7 @@ environment:
INSTALL_SYSPKGS: python3-virtualenv
CODECOV_BINARY: https://uploader.codecov.io/latest/linux/codecov
# system git-annex is way too old, use better one
INSTALL_GITANNEX: git-annex -m deb-url --url http://snapshot.debian.org/archive/debian/20210906T204127Z/pool/main/g/git-annex/git-annex_8.20210903-1_amd64.deb
INSTALL_GITANNEX: git-annex -m deb-url --url https://datasets.datalad.org/datalad/packages/neurodebian/git-annex_8.20210903-1_amd64.deb

matrix:
allow_failures:
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4 changes: 0 additions & 4 deletions .codespell-ignorewords

This file was deleted.

8 changes: 8 additions & 0 deletions .codespellrc
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
[codespell]
skip = .venv,venvs,.git,build,*.egg-info,*.lock,.asv,.mypy_cache,.tox,fixtures,_version.py,*.pem,trash,dist
# commitish - vote if we want to fix (should be committish) -- used in GitRepo API
# froms - plural "from" introduced by export_archive_ora
# ned - Ned is a name
# includeds - func arg name
ignore-words-list = afile,ba,commitish,froms,ro,ned,includeds
exclude-file = .codespell-ignorelines
4 changes: 2 additions & 2 deletions .github/workflows/test_extensions.yml
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Expand Up @@ -39,10 +39,10 @@ jobs:
with:
fetch-depth: 0

- name: Set up Python 3.7
- name: Set up Python 3.8
uses: actions/setup-python@v4
with:
python-version: 3.7
python-version: 3.8

- name: Install DataLad and dependencies
run: |
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4 changes: 2 additions & 2 deletions .github/workflows/update-contributors.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ jobs:
uses: actions/checkout@v3

- name: Tributors Update
uses: con/tributors@0.0.21
uses: con/tributors@0.1.1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
Expand Down Expand Up @@ -79,7 +79,7 @@ jobs:
echo "PULL_REQUEST_BODY='Tributors update automated pull request.\n\n[skip ci]'" >> $GITHUB_ENV
- name: Open Pull Request
uses: vsoch/[email protected].23
uses: vsoch/[email protected].24
if: ${{ env.OPEN_PULL_REQUEST == '1' }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
repos:
- repo: https://github.com/PyCQA/isort
rev: 5.9.3
rev: 5.12.0
hooks:
- id: isort
7 changes: 4 additions & 3 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -87,13 +87,13 @@ matrix:
- PYTEST_SELECTION_OP=not
- DATALAD_SSH_MULTIPLEX__CONNECTIONS=0
- DATALAD_RUNTIME_PATHSPEC__FROM__FILE=always
- _DL_ANNEX_INSTALL_SCENARIO="miniconda --python-match minor --batch git-annex=10.20220525 -m conda"
- _DL_ANNEX_INSTALL_SCENARIO="miniconda=py37_23.1.0-1 --python-match minor --batch git-annex=10.20220525 -m conda"
- python: 3.7
env:
- PYTEST_SELECTION_OP=""
- DATALAD_SSH_MULTIPLEX__CONNECTIONS=0
- DATALAD_RUNTIME_PATHSPEC__FROM__FILE=always
- _DL_ANNEX_INSTALL_SCENARIO="miniconda --python-match minor --batch git-annex=8.20210310 -m conda"
- _DL_ANNEX_INSTALL_SCENARIO="miniconda=py37_23.1.0-1 --python-match minor --batch git-annex=8.20210310 -m conda"
# To test https://github.com/datalad/datalad/pull/4342 fix in case of no "not" for pytest.
# From our testing in that PR seems to have no effect, but kept around since should not hurt.
- LANG=bg_BG.UTF-8
Expand Down Expand Up @@ -158,6 +158,7 @@ matrix:
- python: 3.7
env:
- _DL_ANNEX_INSTALL_SCENARIO="miniconda --python-match minor --batch git-annex=8.20210223 -m conda"

# Run with git's master branch rather the default one on the system.
- if: type = cron
python: 3.7
Expand Down Expand Up @@ -212,7 +213,7 @@ before_install:
# If we requested to run only not slow (typically <10sec) tests, fail if a test
# takes 3x more than that - it needs to get @slow or @turtle annotation
- if echo "$PYTEST_SELECTION_OP($PYTEST_SELECTION)" | grep -q "^not.*slow"; then
PYTEST_OPTS=( "${PYTEST_OPTS[@]}" --doctest-modules --durations=0 --durations-min=5 --fail-slow 30 );
PYTEST_OPTS=( "${PYTEST_OPTS[@]}" --doctest-modules --durations=0 --durations-min=5 --fail-slow 60 );
export DATALAD_TESTS_SETUP_TESTREPOS=1;
fi
# Show git describe output to ensure that we did fetch all the tags etc
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101 changes: 70 additions & 31 deletions .tributors
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Expand Up @@ -31,9 +31,11 @@
"bio": "Postdoc 🧠👨🏻‍💻 in the Gallant Lab at UC Berkeley"
},
"mih": {
"name": "mih",
"name": "Michael Hanke",
"blog": "https://github.com/mih",
"email": "[email protected]"
"email": "[email protected]",
"orcid": "0000-0001-6398-6370",
"affiliation": "Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany and Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany"
},
"yarikoptic": {
"name": "Yaroslav Halchenko",
Expand All @@ -44,87 +46,96 @@
"affiliation": "Dartmouth College"
},
"loj": {
"name": "loj",
"name": "Laura Waite",
"blog": "https://github.com/loj",
"email": "[email protected]"
},
"feilong": {
"name": "feilong",
"name": "Feilong Ma",
"blog": "https://github.com/feilong"
},
"jhpoelen": {
"name": "jhpoelen",
"blog": "https://github.com/jhpoelen"
},
"andycon": {
"name": "andycon",
"name": "Andrew Connolly",
"blog": "https://github.com/andycon"
},
"nicholsn": {
"name": "nicholsn",
"name": "Nolan Nichols",
"blog": "https://github.com/nicholsn"
},
"adelavega": {
"name": "Alejandro de la Vega",
"blog": "https://github.com/adelavega",
"email": "[email protected]",
"bio": "Research Scientist @ UT Austin. "
"bio": "Research Scientist @ UT Austin. ",
"orcid": "0000-0001-9062-3778",
"affiliation": "The University of Texas at Austin"
},
"kskyten": {
"name": "kskyten",
"blog": "https://github.com/kskyten"
},
"TheChymera": {
"name": "TheChymera",
"name": "Horea-Ioan Ioanas",
"blog": "https://github.com/TheChymera",
"email": "[email protected]",
"bio": "I bring Reproducibility, Freedom, and Open Source to Neuroscience, Academic Publishing, Software, and Life."
"bio": "I bring Reproducibility, Freedom, and Open Source to Neuroscience, Academic Publishing, Software, and Life.",
"orcid": "0000-0001-7037-2449",
"affiliation": "Dartmouth College"
},
"effigies": {
"name": "effigies",
"name": "Chris Markiewicz",
"blog": "https://github.com/effigies",
"email": "[email protected]"
},
"jgors": {
"name": "jgors",
"name": "Jasong Gors",
"blog": "https://github.com/jgors"
},
"debanjum": {
"name": "debanjum",
"blog": "https://github.com/debanjum"
"name": "Debanjum Singh Solanky",
"blog": "https://github.com/debanjum",
"orcid": "0000-0002-0774-6564",
"affiliation": "Dartmouth College, Hanover, NH, United States"
},
"nellh": {
"name": "nellh",
"blog": "https://github.com/nellh"
},
"emdupre": {
"name": "emdupre",
"name": "Elizabeth DuPre",
"blog": "https://github.com/emdupre",
"bio": "Neuroscience graduate student at McGill University"
},
"aqw": {
"name": "aqw",
"name": "Alex Waite",
"blog": "https://github.com/aqw",
"email": "[email protected]"
},
"vsoch": {
"name": "vsoch",
"name": "Vanessa Sochat",
"blog": "https://github.com/vsoch",
"bio": "I'm the Vanessasaurus!"
"bio": "I'm the Vanessasaurus!",
"orcid": "0000-0002-4387-3819"
},
"kyleam": {
"name": "kyleam",
"name": "Kyle Meyer",
"blog": "https://github.com/kyleam",
"email": "[email protected]"
},
"driusan": {
"name": "driusan",
"name": "Dave MacFarlane",
"blog": "https://github.com/driusan",
"email": "[email protected]",
"bio": "Professional Rubber Duck"
"bio": "Professional Rubber Duck",
"orcid": "0000-0001-9258-8099",
"affiliation": "McGill University"
},
"overlake333": {
"name": "overlake333",
"name": "Taylor M. Olson",
"blog": "https://github.com/overlake333",
"email": "[email protected]"
},
Expand All @@ -133,12 +144,14 @@
"blog": "https://github.com/akeshavan"
},
"jwodder": {
"name": "jwodder",
"name": "John T. Wodder II",
"blog": "https://github.com/jwodder"
},
"bpoldrack": {
"name": "bpoldrack",
"blog": "https://github.com/bpoldrack"
"name": "Benjamin Poldrack",
"blog": "https://github.com/bpoldrack",
"orcid": "0000-0001-7628-0801",
"affiliation": "Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany"
},
"yetanothertestuser": {
"name": "yetanothertestuser",
Expand All @@ -147,7 +160,9 @@
"christian-monch": {
"name": "Christian Mönch",
"email": "[email protected]",
"blog": "https://github.com/christian-monch"
"blog": "https://github.com/christian-monch",
"orcid": "0000-0002-3092-0612",
"affiliation": "Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany"
},
"mikapfl": {
"name": "Mika Pflüger",
Expand All @@ -171,7 +186,8 @@
"kimsin98": {
"name": "Sin Kim",
"blog": "https://orcid.org/0000-0003-4652-3758",
"bio": "I like coding, data, and open science. Current interests are adolescent development and psychiatry."
"bio": "I like coding, data, and open science. Current interests are adolescent development and psychiatry.",
"orcid": "0000-0003-4652-3758"
},
"DisasterMo": {
"name": "Michael Burgardt",
Expand All @@ -189,7 +205,9 @@
"mslw": {
"name": "Michał Szczepanik",
"bio": "Neuroinformatician.\r\nPhD candidate at Laboratory of Brain Imaging, Nencki Institute; \r\nResearch Associate at Psychoinformatics Lab, INM-7, FZ Jülich",
"blog": "https://github.com/mslw"
"blog": "https://github.com/mslw",
"orcid": "0000-0002-4028-2087",
"affiliation": "Forschungszentrum Jülich"
},
"bpinsard": {
"name": "Basile",
Expand All @@ -204,13 +222,15 @@
"name": "James Kent",
"email": "[email protected]",
"bio": "Postdoc",
"orcid": "0000-0002-4892-2659",
"blog": "https://jdkent.github.io/"
},
"jsheunis": {
"name": "Stephan Heunis",
"bio": "DataLad, decentralised (research) data management, real-time fMRI analysis, data quality control, Matlab and Python bits and pieces",
"blog": "https://jsheunis.github.io/",
"orcid": "0000-0003-3503-9872"
"orcid": "0000-0003-3503-9872",
"affiliation": "Institute of Neuroscience and Medicine, Brain & Behavior (INM-7), Research Center Juelich, Germany"
},
"lamby": {
"name": "Chris Lamb",
Expand All @@ -220,7 +240,9 @@
},
"thewtex": {
"name": "Matt McCormick",
"blog": "https://www.mmmccormick.com"
"blog": "https://www.mmmccormick.com",
"orcid": "0000-0001-9475-3756",
"affiliation": "Kitware Inc"
},
"tstoeter": {
"name": "tstoeter",
Expand All @@ -229,14 +251,31 @@
"vickychenglau": {
"name": "Vicky C Lau",
"email": "[email protected]",
"blog": "https://github.com/vickychenglau"
"blog": "https://github.com/vickychenglau",
"orcid": "0000-0002-1197-1887"
},
"xgui3783": {
"name": "xgui3783",
"blog": "https://github.com/xgui3783"
},
"asmacdo": {
"name": "Austin Macdonald",
"blog": "https://github.com/asmacdo"
"blog": "https://github.com/asmacdo",
"orcid": "0000-0002-8124-807X",
"affiliation": "Dartmouth College"
},
"nobodyinperson": {
"name": "Yann Büchau",
"email": "[email protected]",
"bio": "GitLab: https://gitlab.com/nobodyinperson\r\nPhD student at the University of Tübingen.\r\nHobbies: tinkering, coding, guitar\r\n/\r\ngpg key id: 1E1F9E",
"blog": "https://nobodyinperson.de",
"orcid": "0000-0003-2472-2051",
"affiliation": "Eberhard Karls Universität Tübingen"
},
"matrss": {
"name": "Matthias Riße",
"blog": "https://github.com/matrss",
"orcid": "0009-0006-6081-9327",
"affiliation": "Institute of Energy and Climate Research - Stratosphere (IEK-7), Research Centre Jülich, Jülich, Germany"
}
}
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