Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update backend.py #105

Closed
wants to merge 13 commits into from
Closed

Update backend.py #105

Show file tree
Hide file tree
Changes from 11 commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
aa9301d
Update backend.py
mavaylon1 Jul 12, 2023
ab6bb02
Update setup.py
mavaylon1 Jul 12, 2023
fefde63
Update requirements.txt
mavaylon1 Jul 12, 2023
1bb6268
Update requirements-min.txt
mavaylon1 Jul 12, 2023
dcebd20
Update bug_report.yml
mavaylon1 Jul 12, 2023
5284ab1
Update run_all_tests.yml
mavaylon1 Jul 12, 2023
f0ff0d7
Update run_tests.yml
mavaylon1 Jul 12, 2023
ecada6a
Update setup.py
mavaylon1 Jul 12, 2023
24c371b
Update tox.ini
mavaylon1 Jul 12, 2023
a9689be
Update setup.py
mavaylon1 Jul 12, 2023
abadc1f
Merge branch 'dev' into io_er
mavaylon1 Jul 12, 2023
11ca12f
Merge branch 'dev' into io_er
mavaylon1 Jul 26, 2023
2ce146c
Merge branch 'dev' into io_er
rly Oct 1, 2023
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
1 change: 0 additions & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,6 @@ body:
attributes:
label: Python Version
options:
- "3.7"
- "3.8"
- "3.9"
- "3.10"
Expand Down
21 changes: 8 additions & 13 deletions .github/workflows/run_all_tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,24 +22,21 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- { name: linux-python3.8 , test-tox-env: py38 , build-tox-env: build-py38 , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: ubuntu-latest }
- { name: linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.11-optional , test-tox-env: py311-optional , build-tox-env: build-py311-optional , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-python3.11-prerelease , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: ubuntu-latest }
- { name: windows-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: windows-latest }
- { name: windows-python3.8 , test-tox-env: py38 , build-tox-env: build-py38 , python-ver: "3.8" , os: windows-latest }
- { name: windows-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: windows-latest }
- { name: windows-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: windows-latest }
- { name: windows-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: windows-latest }
- { name: windows-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.11-optional , test-tox-env: py311-optional , build-tox-env: build-py311-optional , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: windows-latest }
- { name: windows-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: windows-latest }
- { name: macos-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: macos-latest }
- { name: macos-python3.8 , test-tox-env: py38 , build-tox-env: build-py38 , python-ver: "3.8" , os: macos-latest }
- { name: macos-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: macos-latest }
- { name: macos-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: macos-latest }
- { name: macos-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: macos-latest }
- { name: macos-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest }
Expand Down Expand Up @@ -88,13 +85,13 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-gallery-python3.7-minimum , test-tox-env: gallery-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded , python-ver: "3.11", os: ubuntu-latest }
- { name: linux-gallery-python3.11-prerelease , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: ubuntu-latest }
- { name: windows-gallery-python3.7-minimum , test-tox-env: gallery-py37-minimum , python-ver: "3.7" , os: windows-latest }
- { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest }
- { name: windows-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded , python-ver: "3.11", os: windows-latest }
- { name: windows-gallery-python3.11-prerelease, test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: windows-latest }
- { name: macos-gallery-python3.7-minimum , test-tox-env: gallery-py37-minimum , python-ver: "3.7" , os: macos-latest }
- { name: macos-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: macos-latest }
- { name: macos-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded , python-ver: "3.11", os: macos-latest }
- { name: macos-gallery-python3.11-prerelease , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: macos-latest }
steps:
Expand Down Expand Up @@ -132,8 +129,7 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- { name: conda-linux-python3.8 , test-tox-env: py38 , build-tox-env: build-py38 , python-ver: "3.8" , os: ubuntu-latest }
- { name: conda-linux-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: conda-linux-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: ubuntu-latest }
- { name: conda-linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest }
- { name: conda-linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
Expand Down Expand Up @@ -162,8 +158,7 @@ jobs:
run: |
conda config --set always_yes yes --set changeps1 no
conda info
# the conda dependency resolution for tox under python 3.7 can install the wrong importlib_metadata
conda install -c conda-forge tox "importlib_metadata>4"
conda install -c conda-forge tox

- name: Conda reporting
run: |
Expand Down
12 changes: 6 additions & 6 deletions .github/workflows/run_tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,13 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- { name: linux-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest }
# NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
- { name: linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest , upload-wheels: true }
- { name: windows-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: windows-latest }
- { name: windows-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: windows-latest }
- { name: windows-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: windows-latest }
- { name: macos-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: macos-latest }
- { name: macos-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: macos-latest }
- { name: macos-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: macos-latest }
steps:
- name: Cancel non-latest runs
Expand Down Expand Up @@ -76,9 +76,9 @@ jobs:
fail-fast: false
matrix:
include:
- { name: linux-gallery-python3.7-minimum , test-tox-env: gallery-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: linux-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: ubuntu-latest }
- { name: windows-gallery-python3.7-minimum , test-tox-env: gallery-py37-minimum , python-ver: "3.7" , os: windows-latest }
- { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py37-minimum , python-ver: "3.8" , os: windows-latest }
- { name: windows-gallery-python3.11-upgraded, test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: windows-latest }
steps:
- name: Cancel non-latest runs
Expand Down Expand Up @@ -114,7 +114,7 @@ jobs:
fail-fast: false
matrix:
include:
- { name: conda-linux-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- { name: conda-linux-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: ubuntu-latest }
- { name: conda-linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest }
steps:
- name: Cancel non-latest runs
Expand Down
2 changes: 1 addition & 1 deletion requirements-min.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
hdmf==3.5.4
hdmf==3.7.0
zarr==2.11.0
numcodecs==0.9.1
pynwb==2.3.2
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# pinned dependencies to reproduce an entire development environment to use HDMF-ZARR
hdmf==3.5.4
hdmf==3.7.0
rly marked this conversation as resolved.
Show resolved Hide resolved
zarr==2.11.0
pynwb==2.3.2
numpy==1.23.5
Expand Down
7 changes: 3 additions & 4 deletions setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@


reqs = [
'hdmf==3.5.4', # temporary
'hdmf>=3.7.0',
'zarr>=2.11.0',
'numpy>=1.22, <1.24; python_version>"3.7"',
'numpy>=1.22',
'numcodecs>=0.9.1',
'pynwb>=2.3.2',
'setuptools',
Expand All @@ -42,10 +42,9 @@
'packages': pkgs,
'package_dir': {'': 'src'},
'package_data': {},
'python_requires': '>=3.7',
'python_requires': '>=3.8',
'classifiers': [
"Programming Language :: Python",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
Expand Down
10 changes: 6 additions & 4 deletions src/hdmf_zarr/backend.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,11 +95,13 @@ def can_read(path):
{'name': 'object_codec_class', 'type': None,
'doc': 'Set the numcodec object codec class to be used to encode objects.'
'Use numcodecs.pickles.Pickle by default.',
'default': None})
'default': None},
{'name': 'external_resources_path', 'type': str, 'doc': 'The path to the ExternalResources',
'default': None},)
def __init__(self, **kwargs):
self.logger = logging.getLogger('%s.%s' % (self.__class__.__module__, self.__class__.__qualname__))
path, manager, mode, synchronizer, object_codec_class = popargs(
'path', 'manager', 'mode', 'synchronizer', 'object_codec_class', kwargs)
path, manager, mode, synchronizer, object_codec_class, external_resources_path = popargs(
'path', 'manager', 'mode', 'synchronizer', 'object_codec_class', 'external_resources_path', kwargs)
if manager is None:
manager = BuildManager(TypeMap(NamespaceCatalog()))
if isinstance(synchronizer, bool):
Expand All @@ -121,7 +123,7 @@ def __init__(self, **kwargs):
source_path = self.__path
if isinstance(self.__path, SUPPORTED_ZARR_STORES):
source_path = self.__path.path
super().__init__(manager, source=source_path)
super().__init__(manager, source=source_path, external_resources_path=external_resources_path)

@property
def file(self):
Expand Down
22 changes: 9 additions & 13 deletions tox.ini
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
# and then run "tox" from this directory.

[tox]
envlist = py37, py38, py39, py310, py311
envlist = py38, py39, py310, py311
requires = pip >= 22.0

[testenv]
Expand Down Expand Up @@ -61,9 +61,9 @@ deps =
# -rrequirements-opt.txt
commands = {[testenv]commands}

# Test with python 3.7; pinned dev reqs; minimum run reqs
[testenv:py37-minimum]
basepython = python3.7
# Test with python 3.8; pinned dev reqs; minimum run reqs
[testenv:py38-minimum]
basepython = python3.8
deps =
-rrequirements-dev.txt
-rrequirements-min.txt
Expand All @@ -75,10 +75,6 @@ commands =
python -m pip install --upgrade build
python -m build

[testenv:build-py37]
basepython = python3.7
commands = {[testenv:build]commands}

[testenv:build-py38]
basepython = python3.8
commands = {[testenv:build]commands}
Expand Down Expand Up @@ -120,8 +116,8 @@ deps =
# -rrequirements-opt.txt
commands = {[testenv:build]commands}

[testenv:build-py37-minimum]
basepython = python3.7
[testenv:build-py38-minimum]
basepython = python3.8
deps =
-rrequirements-dev.txt
-rrequirements-min.txt
Expand Down Expand Up @@ -187,9 +183,9 @@ deps =
# -rrequirements-opt.txt
commands = {[testenv:gallery]commands}

# Test with python 3.7; pinned dev and doc reqs; minimum run reqs
[testenv:gallery-py37-minimum]
basepython = python3.7
# Test with python 3.8; pinned dev and doc reqs; minimum run reqs
[testenv:gallery-py38-minimum]
basepython = python3.8
deps =
-rrequirements-dev.txt
-rrequirements-min.txt
Expand Down