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Merge branch '0.11.x' into bf-wrapt-troubleshoot
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* 0.11.x: (615 commits)
  CHANGELOG.md: Update for dataladgh-3396
  DOC: log_progress: Reword cross-reference from 96b45b4
  ENH: adjust code comments
  ENH: adjust common_cfg description for datalad.ui.progressbar
  RF: use custom _naturalfloat for the best presentation of numbers
  ENH(DOC): cross reference LogProgressBar and log_progress in docstrings
  DOC: log_progress: Correct parameter name in docstring
  RF: versioned depends on sphinx within setup.py itself
  BF: do not bother estimating /sec if 0 sec passed
  RF/BF: reorder ProgressBarBase kwargs to match the one of the child
  BF(TST): making tests account for the changes
  NF: QuietConsoleLog to be used during tests (instead of SilentConsoleLog with no progress whatsoever)
  RF: AnnexRepo report to progress bar(s) that finish is partial if interrupted
  ENH+RF: LogProgressBar to log upon .finish()
  BF: report that gitrepo clone progress is about objects (not default to tqdm progress bar Bytes)
  ENH: datalad.ui.progressbar configuration
  BF: apply OP.MASK for git clone operation before considering
  CHANGELOG.md: Touch up 0.11.5 entries
  CHANGELOG.md: Second batch for 0.11.5
  RF: annexrepo: Tighten decision to commit with temporary index
  ...
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yarikoptic committed May 14, 2019
2 parents 7ddc59d + 339aa50 commit 39a6550
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1 change: 1 addition & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
Expand Up @@ -4,5 +4,6 @@ This pull request proposes

### Changes
- [ ] This change is complete
- [ ] If you would like to list yourself as a DataLad contributor and your name is not mentioned please modify .zenodo.json file.

Please have a look @datalad/developers
7 changes: 6 additions & 1 deletion .mailmap
@@ -1,9 +1,14 @@
Alejandro de la Vega <delavega@utexas.edu>
Anisha Keshavan <keshavan@berkeley.edu>
Benjamin Poldrack <benjaminpoldrack@gmail.com>
Benjamin Poldrack <bpoldrack@users.noreply.github.com>
Christian Olaf Häusler <der.haeusler@gmx.net> chris <chris@psyinfolaf.ovgu.de>
Debanjum Singh Solanky <debanjum@gmail.com> Debanjum <debanjum@gmail.com> debanjum <debanjum@gmail.com>
Jason Gors <jason.gors.work@gmail.com>
Michael Hanke <michael.hanke@gmail.com> mih <mih>
Yaroslav Halchenko <debian@onerussian.com>
Torsten Stoeter <torsten.stoeter@lin-magdeburg.de>
Yaroslav Halchenko <debian@onerussian.com>
Yaroslav Halchenko <site-github-private@onerussian.com>
Neuroimaging Community <committer@example.com>
Neuroimaging Community <test@nowhere.com>
Neuroimaging Community <test@example.com>
Empty file added .noannex
Empty file.
73 changes: 50 additions & 23 deletions .travis.yml
Expand Up @@ -17,7 +17,7 @@ env:
- DATALAD_TESTS_SSH=1
- DATALAD_LOG_CMD_ENV=GIT_SSH_COMMAND
- TESTS_TO_PERFORM=datalad
- NOSE_OPTS=-s
- NOSE_OPTS=
- NOSE_SELECTION="integration or usecase or slow"
- NOSE_SELECTION_OP="not " # so it would be "not (integration or usecase)"
# Special settings/helper for combined coverage from special remotes execution
Expand Down Expand Up @@ -112,7 +112,9 @@ matrix:
# By default no logs will be output. This one is to test with log output at INFO level
env:
- _DL_UPSTREAM_GITPYTHON=1
- _DL_UPSTREAM_GITANNEX=1
# It is not usable without setting locales env vars ATM
# see https://github.com/datalad/datalad/issues/3159
# - _DL_UPSTREAM_GITANNEX=1
# Just so we test if we did not screw up running under nose without -s as well
- NOSE_OPTS=
- _DL_CRON=1
Expand All @@ -121,6 +123,12 @@ matrix:
env:
- _DL_DEVEL_ANNEX=1
- _DL_CRON=1
# Run with latest git rather than the bundled one.
- python: 3.5
env:
- DATALAD_USE_DEFAULT_GIT=1
- _DL_UPSTREAM_GIT=1
- _DL_CRON=1
- python: 3.5
env:
# to test operation under root since also would consider FS "crippled" due to
Expand All @@ -145,14 +153,14 @@ matrix:
env:
- TMPDIR="/tmp/nfsmount"
- _DL_CRON=1
- python: 3.5
# test whether known v6 failures still fail
env:
- DATALAD_REPO_VERSION=6
- DATALAD_TESTS_KNOWNFAILURES_SKIP=no
- DATALAD_TESTS_KNOWNFAILURES_PROBE=yes
- DATALAD_TESTS_SSH=1
- _DL_CRON=1
# - python: 3.5
# # test whether known v6 failures still fail
# env:
# - DATALAD_REPO_VERSION=6
# - DATALAD_TESTS_KNOWNFAILURES_SKIP=no
# - DATALAD_TESTS_KNOWNFAILURES_PROBE=yes
# - DATALAD_TESTS_SSH=1
# - _DL_CRON=1
- python: 3.5
# test whether known direct mode failures still fail
env:
Expand All @@ -167,35 +175,53 @@ matrix:
env:
- BUILD_DATALAD_EXTENSION=datalad-crawler
- TESTS_TO_PERFORM=datalad_crawler
- NOSE_SELECTION_OP=
# Use a selector that will always be true.
- NOSE_SELECTION_OP=not
- NOSE_SELECTION=

- python: 3.5
# test with extension datalad-neuroimaging
env:
- BUILD_DATALAD_EXTENSION=datalad-neuroimaging
- TESTS_TO_PERFORM=datalad_neuroimaging
- NOSE_SELECTION_OP=
# Use a selector that will always be true.
- NOSE_SELECTION_OP=not
- NOSE_SELECTION=

- python: 3.5
# test with extension datalad-container
env:
- BUILD_DATALAD_EXTENSION=datalad-container
- TESTS_TO_PERFORM=datalad_container
- NOSE_SELECTION_OP=
# Use a selector that will always be true.
- NOSE_SELECTION_OP=not
- NOSE_SELECTION=

# Requires current master (0.12.x) so cannot be tested against 0.11.x
#
# - python: 3.5
# # test with extension datalad-revolution
# env:
# - BUILD_DATALAD_EXTENSION=datalad-revolution
# - DATALAD_REPO_VERSION=6
# - TESTS_TO_PERFORM=datalad_revolution
# # Use a selector that will always be true.
# - NOSE_SELECTION_OP=not
# - NOSE_SELECTION=

allow_failures:
# Test under NFS mount (full, only in master)
- python: 3.5
env:
- TMPDIR="/tmp/nfsmount"
- _DL_CRON=1
# test whether known v6 failures still fail
- env:
- DATALAD_REPO_VERSION=6
- DATALAD_TESTS_KNOWNFAILURES_SKIP=no
- DATALAD_TESTS_KNOWNFAILURES_PROBE=yes
- DATALAD_TESTS_SSH=1
- _DL_CRON=1
# # test whether known v6 failures still fail
# - env:
# - DATALAD_REPO_VERSION=6
# - DATALAD_TESTS_KNOWNFAILURES_SKIP=no
# - DATALAD_TESTS_KNOWNFAILURES_PROBE=yes
# - DATALAD_TESTS_SSH=1
# - _DL_CRON=1
# test whether known direct mode failures still fail
- env:
- DATALAD_REPO_DIRECT=yes
Expand Down Expand Up @@ -236,18 +262,19 @@ before_install:
- if [ ! -z "${_DL_UPSTREAM_GITANNEX:-}" ]; then sudo tools/ci/install-annex-snapshot.sh; sudo ln -s `find /usr/local/lib/git-annex.linux -maxdepth 1 -type f -perm /+x` /usr/local/bin/; else sudo eatmydata apt-get install git-annex-standalone ; fi
# Install optionally -devel version of annex, and if goes wrong (we have most recent), exit right away
- if [ ! -z "${_DL_DEVEL_ANNEX:-}" ]; then tools/ci/prep-travis-devel-annex.sh || exit 0; fi
# Optionally install the latest Git. Exit code 100 indicates that bundled is same as the latest.
- if [ ! -z "${_DL_UPSTREAM_GIT:-}" ]; then sudo tools/ci/install-latest-git.sh || [ $? -eq 100 ] && exit 0; fi

install:
# Install standalone build of git-annex for the recent enough version
- travis_retry sudo eatmydata apt-get install zip pandoc
- travis_retry sudo eatmydata apt-get install zip pandoc p7zip-full
- travis_retry sudo eatmydata apt-get install shunit2
# for metadata support
- travis_retry sudo eatmydata apt-get install exempi
- git config --global user.email "test@travis.land"
- git config --global user.name "Travis Almighty"
- cd ..; pip install -q codecov; cd -
- pip install -r requirements-devel.txt
- pip install 'sphinx>=1.7.8'
# So we could test under sudo -E with PATH pointing to installed location
- sudo sed -i -e 's/^Defaults.*secure_path.*$//' /etc/sudoers
# TMPDIRs
Expand All @@ -274,7 +301,7 @@ script:
- http_proxy=
PATH=$PWD/../tools/coverage-bin:$PATH
$NOSE_WRAPPER `which nosetests` $NOSE_OPTS
-v -A "$NOSE_SELECTION_OP($NOSE_SELECTION)"
-A "$NOSE_SELECTION_OP($NOSE_SELECTION)"
--with-doctest
--with-cov --cover-package datalad
--logging-level=INFO
Expand Down
91 changes: 91 additions & 0 deletions .zenodo.json
@@ -0,0 +1,91 @@
{
"creators": [
{
"affiliation": "Dartmouth College: Hanover, NH, United States",
"name": "Halchenko, Yaroslav O.",
"orcid": "0000-0003-3456-2493"
},
{
"affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
"name": "Hanke, Michael",
"orcid": "0000-0001-6398-6370"
},
{
"name": "Poldrack, Benjamin"
},
{
"name": "Meyer, Kyle"
},
{
"name": "Solanky, Debanjum Singh"
},
{
"name": "Alteva, Gergana"
},
{
"name": "Gors, Jason"
},
{
"name": "MacFarlane, Dave"
},
{
"name": "Olaf Häusler, Christian"
},
{
"name": "Olson, Taylor"
},
{
"name": "Waite, Alex"
},
{
"affiliation": "University of Texas at Austin",
"name": "De La Vega, Alejandro",
"orcid": "0000-0001-9062-3778"
},
{
"name": "Sochat, Vanessa"
},
{
"affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
"name": "Keshavan, Anisha",
"orcid": "0000-0003-3554-043X"
},
{
"name": "Ma, Feilong"
},
{
"name": "Christian, Horea"
},
{
"name": "Poelen, Jorrit"
},
{
"name": "Skytén, Kusti"
},
{
"affiliation": "UC Berkeley",
"name": "Visconti di Oleggio Castello, Matteo",
"orcid": "0000-0001-7931-5272"
},
{
"name": "Hardcastle, Nell"
},
{
"name": "Stoeter, Torsten"
},
{
"name": "C Lau, Vicky"
}
],
"grants": [
{"id": "10.13039/100000001::1429999"}
],
"keywords": [
"data version control",
"data distribution",
"execution provenance tracking"
],
"access_right": "open",
"license": "MIT",
"upload_type": "software"
}

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