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Rc/2.16.0 #2722

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merged 95 commits into from
Nov 9, 2023
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91456bf
Add new nwb writers with metadata comparison.
morriscb Jan 19, 2023
47b14c6
Add session_type and project code parsing.
morriscb Feb 15, 2023
9ed214a
isort+black
morriscb Mar 15, 2023
c9ced58
Add stimulus_block_name column to stimulus_presentations.
morriscb Feb 28, 2023
394265b
Add trials_id creation to BehaviorSession.from_lims
morriscb Mar 22, 2023
71d98ca
isort+black
morriscb Mar 31, 2023
1ef1c85
Changes to support python 3.10
aamster Mar 31, 2023
4973c33
update setup
aamster Mar 31, 2023
6e664d7
remove upper bound on matplotlib
aamster Mar 31, 2023
627b028
Revert "allow manually running nightly"
aamster Mar 31, 2023
af046ae
set seed for df.sample
mikejhuang Mar 31, 2023
4263a89
Clean up NWB creation code.
morriscb Mar 31, 2023
4afd032
isort+black
morriscb Apr 4, 2023
61eb2b0
read session_type from db
aamster Apr 6, 2023
8cc18e1
remove logic that read session_type and daq from vbn code path
aamster Apr 6, 2023
5190992
read date of acquisition from lims
aamster Apr 6, 2023
4d07bb4
remove unused import
aamster Apr 6, 2023
b662c9c
lint
aamster Apr 6, 2023
ee98346
ignore column order in test
aamster Apr 6, 2023
80d16d8
revert left join on ophys containers
aamster Apr 6, 2023
e185833
abstracts out logic to merge columns
aamster Apr 7, 2023
640ae73
fix bug due to duplicated project_code logic
aamster Apr 7, 2023
8da875a
Update behavior metadata writer.
morriscb Apr 4, 2023
f718c57
flip input axes to _gaussian_function_2d to conform to np.array
mikejhuang Apr 21, 2023
82f6fcd
lint
mikejhuang Apr 21, 2023
7148ac8
isort+black+manual comment line length editing receptive_field_mapping
mikejhuang Apr 22, 2023
fc126ea
Updating images to use PIL Image
Ahad-Allen May 5, 2023
d9893a0
Add negative running speed check.
morriscb Mar 15, 2023
55eb2b9
Clean up for VBO update release
morriscb Apr 18, 2023
9defb58
Implement fixes to presentations table.
morriscb Jun 2, 2023
04506b3
Add new information to templates data.
morriscb Jun 14, 2023
00b4e98
Add stimulus template for movies.
morriscb Jun 20, 2023
5d7bd78
load probe lfp metadata without needing to load lfp
aamster Jul 13, 2023
005e680
Add removal of omitted stimulus to presentations.
morriscb Jul 17, 2023
e271391
Unpeg statsmodels
morriscb Jul 18, 2023
f6942c0
Check for non-zero df length.
morriscb Jul 19, 2023
6e0647b
isort+black
morriscb Jul 20, 2023
2a15fae
set structure_id to primary_injection_structure instead of first stru…
mikejhuang Jul 19, 2023
27e48f7
lint
mikejhuang Jul 24, 2023
64943f0
lint
mikejhuang Jul 24, 2023
b8e4882
Fix for namespaces issue
brendanjohnharris Aug 9, 2023
3076275
fix deprecated np.bool
mikejhuang Jul 21, 2023
745d668
fix Int64Index deprecation and explicit requirement for regex boolean…
mikejhuang Jul 21, 2023
f89538a
fix pandas reindex change
mikejhuang Jul 21, 2023
b2f540d
change check_less_precise to rtol in assert_series_equal
mikejhuang Jul 24, 2023
ad6c339
fix attempt to reindex a MultiIndex
mikejhuang Jul 24, 2023
a77531f
fix deprecated np.float and np.int
mikejhuang Jul 24, 2023
a951f09
downgrade pandas=1.53, hdmf=3.4.7, pynwb=2.3.3
mikejhuang Jul 24, 2023
d311a5e
add python 3.11 to github actions
mikejhuang Jul 24, 2023
0f714ec
add Python 3.11 in setup.py
mikejhuang Jul 24, 2023
4e65a29
remove poetry related setup config
mikejhuang Aug 10, 2023
64e334f
Updates before VBO re-release
morriscb Jul 25, 2023
7af2406
Merge branch 'ticket/PSB-171/dev' into rc/2.16.0
morriscb Aug 11, 2023
26a4665
change bool_ to bool
mikejhuang Aug 11, 2023
e768fcc
Merge pull request #2716 from AllenInstitute/psb-172/update_dependenc…
mikejhuang Aug 14, 2023
163414e
Add additional column for quality value in units.csv.
morriscb Aug 3, 2023
2c9dc0c
Fix linting on failing files updated in previous commit.
morriscb Aug 17, 2023
a3aa0cf
Merge branch 'ticket/PSB-167/addQualityToMetadataTable' into rc/2.16.0
morriscb Aug 21, 2023
b950704
Add is_sham_change column.
morriscb Aug 9, 2023
584144c
isort+black
morriscb Aug 21, 2023
420d6e2
Merge branch 'ticket/PSB-155/dev' into rc/2.16.0
morriscb Aug 21, 2023
e0aa7e3
Merge pull request #2714 from brendanjohnharris/namespace-fix
morriscb Sep 8, 2023
f952b32
unpin hdmf and pynwb
mikejhuang Sep 8, 2023
0b3d496
exclude failed version ranges from hdmf
mikejhuang Sep 8, 2023
deab76b
Merge pull request #2720 from AllenInstitute/unpin_hdmf_and_pynwb
mikejhuang Sep 8, 2023
9052d0d
Increment version.
morriscb Sep 11, 2023
2e58703
Clean up code and add info to change log/release notes.
morriscb Sep 12, 2023
22106c4
Merge branch 'ticket/PSB-200/dev' into rc/2.16.0
morriscb Sep 26, 2023
cb5c52a
Add fixes to notebooks.
morriscb Sep 27, 2023
dccacd9
Update notebooks
morriscb Sep 27, 2023
715f728
Revert to json for vbn packaging.
morriscb Sep 25, 2023
d0c44bc
Merge branch 'ticket/PSB-227/dev' into rc/2.16.0
morriscb Sep 28, 2023
50fa924
Add timezone to behavior session table daq.
morriscb Sep 28, 2023
8eb86aa
Merge branch 'ticket/PSB-235/dev' into rc/2.16.0
morriscb Oct 6, 2023
c6202e6
Add natural movie cache class.
morriscb Oct 4, 2023
ecae373
Merge branch 'ticket/PSB-207/dev' into rc/2.16.0
morriscb Oct 12, 2023
3df4687
Explicitly set xarray coordinates.
morriscb Oct 25, 2023
fe87c87
Merge branch 'ticket/PSB-257/dev' into rc/2.16.0
morriscb Oct 25, 2023
f1ae5ab
Address comments on release from Marina
morriscb Oct 17, 2023
0620446
isort+black
morriscb Nov 1, 2023
f8ea31b
Merge branch 'ticket/PSB-249/dev' into rc/2.16.0
morriscb Nov 1, 2023
03a784c
Remove skip and test lims consistency with new data.
morriscb Oct 25, 2023
fd138ea
Add section to vbo sphinx page.
morriscb Nov 3, 2023
6fe632e
isort+black
morriscb Nov 3, 2023
77737ec
Update more docs
morriscb Nov 3, 2023
5a66e26
Merge branch 'ticket/PSB-7/dev' into rc/2.16.0
morriscb Nov 3, 2023
1c51e73
Modify notebooks to use stimulus presentations.
morriscb Nov 3, 2023
18c5340
Debug notebook.
morriscb Nov 3, 2023
4b497ed
Fix type for pandas query.
morriscb Nov 6, 2023
387a0bc
Add comment.
morriscb Nov 6, 2023
9b3b52d
Update notebooks
morriscb Nov 6, 2023
5337446
Update where cache points.
morriscb Nov 8, 2023
9b17c6d
Add doc on traces.
morriscb Nov 8, 2023
b53471f
Clarify trace change log comment.
morriscb Nov 8, 2023
1454801
Update changelog and index.
morriscb Nov 9, 2023
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2 changes: 2 additions & 0 deletions .flake8
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
[flake8]
extend-ignore = E203
2 changes: 1 addition & 1 deletion .github/workflows/github-actions-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ jobs:
strategy:
matrix:
os: ["macos-latest", "windows-latest", "ubuntu-latest"]
python-version: ["3.7", "3.8", "3.9"]
python-version: ["3.8", "3.9", "3.10", "3.11"]
fail-fast: false
defaults:
run:
Expand Down
2 changes: 0 additions & 2 deletions .github/workflows/nightly.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,6 @@ name: ci/nightly
on:
schedule:
- cron: '05 6 * * *'
workflow_dispatch:



jobs:
Expand Down
7 changes: 7 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,13 @@
# Change Log
All notable changes to this project will be documented in this file.

## [2.16.0] = 2023-11-09
- Python 3.10 and 3.11 support
- Support for VBO update release.
- Uspport for new VBO release
- Various bug fixes.
- See release notes on Github

## [2.14.0] = 2022-12-12
- Support for updated vbn release containing probe, lfp and behavior only data.
- Updates to Ophys data in anticipation of a forthcoming updated data release
Expand Down
2 changes: 1 addition & 1 deletion allensdk/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
#
import logging

__version__ = '2.15.2'
__version__ = '2.16.0'


try:
Expand Down
32 changes: 31 additions & 1 deletion allensdk/api/cloud_cache/cloud_cache.py
Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,17 @@ def latest_manifest_file(self) -> str:
"""
return self._find_latest_file(self.manifest_file_names)

@property
def cache_dir(self) -> str:
"""Return the cache directory path.

Returns
-------
str
Full cache directory path
"""
return self._cache_dir

# ====================== BasicLocalCache methods ==========================

@abstractmethod
Expand Down Expand Up @@ -330,7 +341,7 @@ def data_path(self, file_id) -> dict:
RuntimeError
If the file cannot be downloaded
"""
file_attributes = self._manifest.data_file_attributes(file_id)
file_attributes = self.get_file_attributes(file_id)
exists = self._file_exists(file_attributes)
local_path = file_attributes.local_path
output = {'local_path': local_path,
Expand All @@ -339,6 +350,21 @@ def data_path(self, file_id) -> dict:

return output

def get_file_attributes(self, file_id):
"""
Retrieve file attributes for a given file_id from the meatadata.

Parameters
----------
file_id: str or int
The unique identifier of the file to be accessed

Returns
-------
CacheFileAttributes
"""
return self._manifest.data_file_attributes(file_id)


class CloudCacheBase(BasicLocalCache):
"""
Expand Down Expand Up @@ -1042,6 +1068,10 @@ def __init__(self, cache_dir, bucket_name, project_name,

_s3_client = None

@property
def bucket_name(self) -> str:
return self._bucket_name

@property
def s3_client(self):
if self._s3_client is None:
Expand Down
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