Skip to content
This repository has been archived by the owner on Nov 19, 2024. It is now read-only.

[Do not merge] PR for diff of DANDI vs. LINC #63

Closed
wants to merge 170 commits into from
Closed
Show file tree
Hide file tree
Changes from 161 commits
Commits
Show all changes
170 commits
Select commit Hold shift + click to select a range
eca9e2d
bump more values
Nov 20, 2023
68e3a66
more progress
Nov 20, 2023
57ab95e
Merge pull request #1 from lincbrain/ak-linc
aaronkanzer Nov 20, 2023
c2a440a
trivial change
Nov 20, 2023
e4822be
try versioning correctly
Nov 20, 2023
85dfd00
bump
Nov 20, 2023
80114bc
Draft: comment out problematic versioneer code
Nov 22, 2023
062cbc5
Revise dandi-cli to conform for linc-cli
Nov 27, 2023
7eb75fe
remove unnecessary files
Nov 27, 2023
61ea2b0
minor naming changes
Jan 10, 2024
3e3af7a
more auditing of dandi to lincbrain renaming
Jan 10, 2024
a1b5be9
Push temp progress from ak-comment branch
Jan 29, 2024
9d7c211
api change prior to branching
Jan 29, 2024
8bada31
include dist temp to go back in time
Jan 29, 2024
c54fc2a
New branch to resolve publishing
Jan 29, 2024
b80fcdc
whooops
Jan 29, 2024
d6ef525
uncomment out versioneer
Jan 29, 2024
76fb6a6
use dandi-cli setup
Jan 29, 2024
c03ab6f
bump autorc file
Jan 29, 2024
93b4b73
resolve linting
Jan 29, 2024
6a2e0b3
trivial change
Jan 29, 2024
7c2e6c9
Merge pull request #7 from lincbrain/ak-new-publish
aaronkanzer Jan 29, 2024
89415ee
remove typo in autorc
Jan 29, 2024
f811b9d
Merge pull request #8 from lincbrain/ak-autorc
aaronkanzer Jan 29, 2024
d5deb81
trivial change
Jan 29, 2024
3887fce
Merge pull request #9 from lincbrain/ak-temp
aaronkanzer Jan 29, 2024
b155b07
trivial change x2
Jan 29, 2024
0171c36
Merge pull request #10 from lincbrain/ak-release
aaronkanzer Jan 29, 2024
6bda865
Include permissions for actions bot
Jan 30, 2024
8bc9e42
Merge pull request #11 from lincbrain/ak-perms
aaronkanzer Jan 30, 2024
2033480
Trivial change -- forgot labels
Jan 30, 2024
57ee5af
Merge pull request #12 from lincbrain/ak-forgot
aaronkanzer Jan 30, 2024
c36e344
Include PR from main branch for GHA test
Jan 30, 2024
7bbc177
Merge pull request #13 from lincbrain/ak-pr-1
aaronkanzer Jan 30, 2024
7b6924a
Clean changelog for tagging
Jan 30, 2024
9318a81
Merge pull request #14 from lincbrain/ak-changelog
aaronkanzer Jan 30, 2024
2543444
trivial change for one more git tag
Jan 30, 2024
3c742e5
Trivial change with remote tags cleaned up
Jan 30, 2024
c95f939
Merge pull request #15 from lincbrain/ak-tag
aaronkanzer Jan 30, 2024
3d53b92
Update main branch for tagging
Jan 30, 2024
118d43e
Merge pull request #16 from lincbrain/ak-one
aaronkanzer Jan 30, 2024
01b7bee
Update CHANGELOG.md [skip ci]
Jan 30, 2024
838dd51
Add naming suffix to circumvent PyPI historical sem var history
Jan 30, 2024
9e97f9d
Merge pull request #17 from lincbrain/ak-name
aaronkanzer Jan 30, 2024
f442a3c
Update CHANGELOG.md [skip ci]
Jan 30, 2024
5f05ae6
Conform to PEP versioning standards
Jan 30, 2024
f9a7ec9
Merge pull request #18 from lincbrain/ak-post
aaronkanzer Jan 30, 2024
eae9d64
Update CHANGELOG.md [skip ci]
Jan 30, 2024
6feea1e
use custom script to pep name files to upload
Jan 30, 2024
2582555
merge master
Jan 30, 2024
fa32e44
Merge pull request #19 from lincbrain/ak-dist
aaronkanzer Jan 30, 2024
a8e220f
Update CHANGELOG.md [skip ci]
Jan 30, 2024
0847577
revise versioning
Jan 30, 2024
a727363
Merge pull request #20 from lincbrain/ak-1
aaronkanzer Jan 30, 2024
afc639c
Update CHANGELOG.md [skip ci]
Jan 30, 2024
2e01797
Fix autorc
Jan 30, 2024
9a2a483
Merge pull request #21 from lincbrain/ak-rc
aaronkanzer Jan 30, 2024
32b4bdc
Update CHANGELOG.md [skip ci]
Jan 30, 2024
5100cc4
Include proper PEP naming
Jan 30, 2024
05ba285
Merge pull request #22 from lincbrain/ak-p1
aaronkanzer Jan 30, 2024
0998490
Update CHANGELOG.md [skip ci]
Jan 30, 2024
3119ad1
use lincbrain release
Jan 30, 2024
ca53025
Merge pull request #23 from lincbrain/ak-53
aaronkanzer Jan 30, 2024
c484c73
Update CHANGELOG.md [skip ci]
Jan 30, 2024
67ea68a
more more trivial change
Jan 30, 2024
8eac876
Merge pull request #24 from lincbrain/ak-54
aaronkanzer Jan 30, 2024
ff1258c
Update CHANGELOG.md [skip ci]
Jan 30, 2024
b5571b6
Route to lincbrain-cli for installation
Jan 30, 2024
e8e2382
include changelog
Jan 30, 2024
2f0f629
bump
Jan 30, 2024
d5f414b
Merge pull request #25 from lincbrain/ak-55
aaronkanzer Jan 30, 2024
1e5b569
Update CHANGELOG.md [skip ci]
Jan 30, 2024
a1fd232
naming convention in setup.py
Jan 30, 2024
7704eec
Merge pull request #26 from lincbrain/ak-cli
aaronkanzer Jan 30, 2024
5a7bcd2
Update CHANGELOG.md [skip ci]
Jan 30, 2024
9c0a018
remove changelog
Jan 30, 2024
9d5ba39
Merge pull request #27 from lincbrain/ak-change
aaronkanzer Jan 30, 2024
7de4d8c
Update CHANGELOG.md [skip ci]
Jan 30, 2024
c05b37b
Update readme for instructions, correct links
Jan 30, 2024
bd598c5
Merge pull request #28 from lincbrain/ak-readme-u
aaronkanzer Jan 30, 2024
2fa1e79
Look into CLI test failures via GHA
Jan 31, 2024
b766ee8
update rules
Jan 31, 2024
6665d2c
Alter imports for linc-archive tests
Jan 31, 2024
5121624
Merge pull request #29 from lincbrain/ak-ci
aaronkanzer Jan 31, 2024
edbd89c
Update CHANGELOG.md [skip ci]
Jan 31, 2024
a0134c3
Resolve one other test import
Jan 31, 2024
41e5b83
Merge pull request #30 from lincbrain/ak-mark
aaronkanzer Jan 31, 2024
9a19be7
Update CHANGELOG.md [skip ci]
Jan 31, 2024
0a7bd4c
resolve build process with correct files
Jan 31, 2024
5ba2618
Merge pull request #31 from lincbrain/ak-mani
aaronkanzer Jan 31, 2024
392c528
Update CHANGELOG.md [skip ci]
Jan 31, 2024
a27c02e
More test fixes for patching in test suite
Jan 31, 2024
1d5db72
Update DANDI_API_KEY to LINCBRAIN_API_KEY
Feb 12, 2024
09efec3
Merge pull request #33 from lincbrain/ak-cli-name
aaronkanzer Feb 12, 2024
08767db
Update CHANGELOG.md [skip ci]
Feb 12, 2024
aab1f4f
resolve CLI reference to staging
Feb 12, 2024
f28ed89
Merge pull request #34 from lincbrain/ak-stag
aaronkanzer Feb 12, 2024
94d0470
Update CHANGELOG.md [skip ci]
Feb 12, 2024
99c5e61
Update messaging and root directory for lincbrain logs
Feb 14, 2024
85ca628
Merge pull request #35 from lincbrain/ak-word
aaronkanzer Feb 14, 2024
38c1b06
Update CHANGELOG.md [skip ci]
Feb 14, 2024
37a5e04
Merge 0.59.1 of dandi-cli into linc-cli
Feb 14, 2024
7531f80
Trivial change to update LINC release from dandi-0.59-1
Feb 14, 2024
3186b3d
Merge pull request #36 from lincbrain/ak-0-6
aaronkanzer Feb 14, 2024
9c7df71
Update CHANGELOG.md [skip ci]
Feb 14, 2024
b532967
Change naming conventions in CLI tool to match LINC
Feb 14, 2024
25f85db
Merge pull request #37 from lincbrain/ak-naming
aaronkanzer Feb 14, 2024
2a49b7f
Update CHANGELOG.md [skip ci]
Feb 14, 2024
82294f0
Merge upstream changes from dandi-cli for pydantic 2.0
Mar 13, 2024
4158f34
Trivial change to bump linc-cli to include pydantic 2 updates
Mar 13, 2024
86934b9
Merge pull request #38 from lincbrain/ak-pydantic
aaronkanzer Mar 13, 2024
90e0754
Update CHANGELOG.md [skip ci]
Mar 13, 2024
5e8189b
Refresh permissions on pypi
Mar 13, 2024
923ffb7
Merge pull request #39 from lincbrain/ak-2
aaronkanzer Mar 13, 2024
9789c48
Update CHANGELOG.md [skip ci]
Mar 13, 2024
98169ed
Include new token for PyPI push
Mar 13, 2024
a986f89
Merge pull request #40 from lincbrain/ak-new
aaronkanzer Mar 13, 2024
9ad0699
Update CHANGELOG.md [skip ci]
Mar 13, 2024
f1d5e1b
Include explicit auth call on move cmd
Apr 9, 2024
8b8fbf9
Include logic to properly authenticate a user upon the move command
Apr 9, 2024
40a8c76
cleanup
Apr 9, 2024
5995675
Merge pull request #42 from lincbrain/ak-auth-move
aaronkanzer Apr 10, 2024
7c8c734
Update badges on readme
kabilar Jun 6, 2024
ad0c7f1
Update readme links from dandi
kabilar Jun 6, 2024
60d96bf
Fix spelling
kabilar Jun 6, 2024
b0aa55d
Temp: local updates
Jul 18, 2024
78edc36
temp bump on local version
Jul 18, 2024
81639be
revert docstring
Jul 18, 2024
06492d3
Revert "revert docstring"
Jul 18, 2024
db46def
revert correctly
Jul 18, 2024
884858c
Merge pull request #49 from lincbrain/ak-auth-move
aaronkanzer Jul 18, 2024
ccfc2ce
Merge pull request #46 from kabilar/readme2
aaronkanzer Jul 18, 2024
b97f59e
Removed conda installation instructions
kabilar Jul 18, 2024
2c056b6
Rename `LINC Brain archive` to `LINC Data Platform`
kabilar Jul 18, 2024
9837555
bump
Jul 19, 2024
9f75e3a
bump again
Jul 19, 2024
33b1aba
remove unnecessary venv
Jul 19, 2024
93f0bb9
Merge pull request #51 from lincbrain/ak-versioneer
aaronkanzer Jul 19, 2024
de8c37a
Merge pull request #50 from kabilar/readme2
aaronkanzer Jul 19, 2024
c5f0ccb
Update CHANGELOG.md [skip ci]
Jul 19, 2024
192a976
Replace netlify staging url with staging.lincbrain.org url in CLI
Jul 22, 2024
84b7c50
Merge pull request #53 from lincbrain/ak-link
aaronkanzer Jul 22, 2024
3b07071
Clean up for readthedocs generation
Jul 24, 2024
5efee0b
more progress for docs including ci
Jul 24, 2024
cd3d173
cleanup
Jul 24, 2024
655105e
Merge updates for zarr completion upstream in dandi cli
Aug 2, 2024
e010988
exclude specific changes
Aug 2, 2024
a59d808
revise per Kabi's comments
Aug 2, 2024
8433acf
Merge pull request #54 from lincbrain/ak-link
aaronkanzer Aug 2, 2024
45f8d9a
Merge branch 'ak-link' into ak-zarr-fix
Aug 2, 2024
a106fb3
Merge pull request #55 from lincbrain/ak-zarr-fix
aaronkanzer Aug 2, 2024
bf5e8ca
trivial change to invoke deployment of 0.11.0
Aug 2, 2024
387751e
Merge pull request #56 from lincbrain/ak-trivial
aaronkanzer Aug 2, 2024
d7fce11
Update CHANGELOG.md [skip ci]
Aug 2, 2024
e668a53
Update etelemetry reference for lincbrain
Aug 6, 2024
e6fb46f
Merge remote-tracking branch 'upstream/master' into ak-preserve-tree
Aug 6, 2024
16d7648
Merge pull request #60 from lincbrain/ak-preserve-tree
kabilar Aug 7, 2024
d682859
Update CHANGELOG.md [skip ci]
Aug 7, 2024
fa887fa
Include reference to appropriate docker test container
Aug 26, 2024
39d75d5
Merge pull request #62 from lincbrain/ak-docker
aaronkanzer Aug 26, 2024
623bca6
Update CHANGELOG.md [skip ci]
Aug 26, 2024
ed22409
Bump dandischema to 0.10.4
Nov 15, 2024
e901013
Merge pull request #64 from lincbrain/ak-10-4
aaronkanzer Nov 15, 2024
3b1c72b
Trivial change to release new version
Nov 15, 2024
425665f
Merge pull request #65 from lincbrain/ak-t
aaronkanzer Nov 15, 2024
f6b4bff
Update CHANGELOG.md [skip ci]
Nov 15, 2024
7fd338b
Update README to redirect to DANDI CLI
Nov 19, 2024
e1fb45a
Update README.md
aaronkanzer Nov 19, 2024
1aad588
Merge pull request #67 from lincbrain/ak-dandi
aaronkanzer Nov 19, 2024
ce44305
Update CHANGELOG.md [skip ci]
Nov 19, 2024
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .autorc
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"onlyPublishWithReleaseLabel": true,
"baseBranch": "master",
"author": "DANDI Bot <team@dandiarchive.org>",
"author": "LINC Bot <team@lincbrain.org>",
"noVersionPrefix": true,
"plugins": [
"git-tag",
Expand Down
2 changes: 1 addition & 1 deletion .gitattributes
Original file line number Diff line number Diff line change
@@ -1 +1 @@
dandi/_version.py export-subst
lincbrain/_version.py export-subst
10 changes: 5 additions & 5 deletions .github/workflows/docs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ name: Build Docs
on:
push:
branches:
- master
- ak-link
pull_request:

jobs:
Expand All @@ -13,10 +13,10 @@ jobs:
fail-fast: false
matrix:
python:
- 3.8
#- 3.9
#- 3.10
#- 3.11
- '3.8'
- '3.9'
- '3.10'
- '3.11'
steps:
- name: Check out repository
uses: actions/checkout@v4
Expand Down
9 changes: 7 additions & 2 deletions .github/workflows/release.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
name: Auto-release on PR merge

permissions:
contents: write
packages: write


on:
# ATM, this is the closest trigger to a PR merging
push:
Expand Down Expand Up @@ -34,7 +39,7 @@ jobs:
run: ~/auto shipit -vv
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
TWINE_USERNAME: linc-
TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN_NEW }}

# vim:set sts=2:
31 changes: 16 additions & 15 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
@@ -1,12 +1,17 @@
name: Tests

#on:
# push:
# branches:
# - master
# pull_request:
# schedule:
# - cron: '0 6 * * *'


on:
push:
branches:
- master
pull_request:
schedule:
- cron: '0 6 * * *'
- push
- pull_request

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.ref_name }}
Expand Down Expand Up @@ -89,10 +94,6 @@ jobs:
echo HOME=/tmp/nfsmount/home >> "$GITHUB_ENV"
echo DANDI_DEVEL_INSTRUMENT_REQUESTS_SUPERLEN=1 >> "$GITHUB_ENV"

- name: Use scheduled test configuration
if: github.event_name == 'schedule'
run: echo PYTEST_ADDOPTS=--scheduled >> "$GITHUB_ENV"

- name: Run all tests
if: matrix.mode != 'dandi-api'
run: |
Expand All @@ -110,20 +111,20 @@ jobs:
- name: Run Dandi API tests only
if: matrix.mode == 'dandi-api'
run: |
python -m pytest -s -v --cov=dandi --cov-report=xml --dandi-api dandi
python -m pytest -s -v --cov=dandi --cov-report=xml --dandi-api lincbrain

- name: Dump Docker Compose logs
if: failure() && startsWith(matrix.os, 'ubuntu')
run: |
docker compose \
-f dandi/tests/data/dandiarchive-docker/docker-compose.yml \
docker-compose \
-f lincbrain/tests/data/dandiarchive-docker/docker-compose.yml \
logs --timestamps

- name: Shut down Docker Compose
if: startsWith(matrix.os, 'ubuntu')
run: |
docker compose \
-f dandi/tests/data/dandiarchive-docker/docker-compose.yml \
docker-compose \
-f lincbrain/tests/data/dandiarchive-docker/docker-compose.yml \
down -v

- name: Upload coverage to Codecov
Expand Down
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -15,4 +15,5 @@ pip-wheel-metadata/
sandbox/
venv/
venvs/
.pypirc
.DS_Store
Loading