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Migrate to py310 #14

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Merged
merged 14 commits into from
Aug 27, 2025
Merged

Migrate to py310 #14

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c7c696c
extend tests to py3.10
sjanssen2 Aug 26, 2025
e1551dc
try to import current module OR (for older py versions) from deprecat…
sjanssen2 Aug 26, 2025
92fdf87
use pytest instead of nose
sjanssen2 Aug 26, 2025
08a1c99
change flag
sjanssen2 Aug 26, 2025
39e5d77
add classifiers for py3.9 and py3.10
sjanssen2 Aug 26, 2025
51bb51a
trigger tests for even more recent py versions
sjanssen2 Aug 26, 2025
e05217a
Merge pull request #2 from jlab/test_py311-py312
sjanssen2 Aug 26, 2025
3a172f0
add classifiers
sjanssen2 Aug 26, 2025
bfc36a7
Merge branch 'test_py311-py312' of github.com:jlab/qiita-files into m…
sjanssen2 Aug 26, 2025
af6a435
Merge branch 'migrate_py310' of github.com:jlab/qiita-files into migr…
sjanssen2 Aug 26, 2025
46964c5
also test old py versions
sjanssen2 Aug 26, 2025
0ef315b
Update qiita-plugin-ci.yml
sjanssen2 Aug 26, 2025
d80ba79
Update qiita-plugin-ci.yml
sjanssen2 Aug 26, 2025
194f6a8
Update qiita-plugin-ci.yml
sjanssen2 Aug 26, 2025
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12 changes: 7 additions & 5 deletions .github/workflows/qiita-plugin-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,9 @@ jobs:
# derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml
main:
runs-on: ubuntu-latest

strategy:
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
steps:
# Downloads a copy of the code in your repository before running CI tests
- name: Check out repository code
Expand All @@ -19,21 +21,21 @@ jobs:
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.9
python-version: ${{ matrix.python-version }}

- name: Basic dependencies install
shell: bash -l {0}
run: |
conda create --yes -n qiita-files python=3.9 h5py pandas scipy numpy
conda create --yes -n qiita-files python=${{ matrix.python-version }} h5py pandas scipy numpy
conda activate qiita-files
pip install .
pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
pip install sphinx sphinx-bootstrap-theme pytest-cov codecov Click

- name: Main tests
shell: bash -l {0}
run: |
conda activate qiita-files
nosetests --with-doctest --with-coverage --cover-package=qiita_files
pytest --doctest-modules --cov=qiita_files --cov-report=lcov

lint:
runs-on: ubuntu-latest
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5 changes: 4 additions & 1 deletion qiita_files/parse/workflow.py
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Expand Up @@ -9,7 +9,10 @@
from copy import deepcopy
from time import time
from functools import update_wrapper
from collections import Iterable
try:
from collections.abc import Iterable
except ImportError:
from collections import Iterable
from types import MethodType


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4 changes: 4 additions & 0 deletions setup.py
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Expand Up @@ -20,6 +20,10 @@
Programming Language :: Python
Programming Language :: Python :: 3.5
Programming Language :: Python :: 3.6
Comment on lines 21 to 22
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Thank you for adding those, just to confirm, is it OK to leave these?

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If I recall correctly, older plugins (qp-deblur) still run on py3.5 - so we should not remove.
Unfortunately, the test framework breaks, as pytest is not available in this old py version. I suggest to NOT test, but keep these lines

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found a way to avoid running coverage reports for older py versions, while still executing tests :-)

Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.10
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This needs to be updated, no?

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good catch!

Programming Language :: Python :: 3.11
Programming Language :: Python :: 3.12
Programming Language :: Python :: Implementation :: CPython
Operating System :: POSIX :: Linux
Operating System :: MacOS :: MacOS X
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