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bc01e95
Fix deprecated pandas DataFrame.set_axis() inplace parameter
sorenwacker Oct 1, 2025
5afbec1
Fix pandas replace() downcasting deprecation warnings and add example…
sorenwacker Oct 1, 2025
51ffacd
Add comprehensive ISA-API examples notebook from documentation
sorenwacker Oct 1, 2025
689dc44
Fix ISA-JSON loading issue in comprehensive examples notebook
sorenwacker Oct 1, 2025
1e595c0
Fix isatab2json conversion error handling in notebook
sorenwacker Oct 1, 2025
3c887a0
Fix batch_validate() function calls in notebook
sorenwacker Oct 2, 2025
1b67fdd
Fix batch validation report structure handling
sorenwacker Oct 2, 2025
7ad4d00
Document required changes to make ISA-API examples work
sorenwacker Oct 2, 2025
eab50ed
Add Python 3.12 and 3.13 compatibility
sorenwacker Oct 5, 2025
d5b21f6
linting fixed
sorenwacker Oct 5, 2025
a37d8e0
added stystem dependencies
sorenwacker Oct 5, 2025
ecb029b
removed python 3.13 from testing
sorenwacker Oct 5, 2025
cdd4fcf
Update badges in README
sorenwacker Oct 5, 2025
7440c44
Exclude build directory from flake8 linting
sorenwacker Oct 5, 2025
1310b16
Fix badge URLs - show Python 3.9-3.12 support and correct build statu…
sorenwacker Oct 5, 2025
58aa070
Suppress jsonschema deprecation warnings in tests
sorenwacker Oct 5, 2025
ca3e6c6
Fix Pandas deprecation warning in isatab2w4m by calling infer_objects
sorenwacker Oct 5, 2025
5a1b2f1
Skip platform-specific isatab2w4m tests in CI
sorenwacker Oct 5, 2025
d88bd8b
Fix build status badge URL
sorenwacker Oct 5, 2025
71bb5fb
Update badges to use shields.io for better compatibility
sorenwacker Oct 5, 2025
a504020
Merge upstream master into python-3.12 branch
sorenwacker Oct 5, 2025
8efea7e
Fix SQLAlchemy version to 2.0+ for mapped_column support
sorenwacker Oct 5, 2025
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10 changes: 7 additions & 3 deletions .github/workflows/buildandtestpython.yml
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,10 @@ jobs:
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y libxml2-dev libxslt1-dev
- name: Download Test Data
run: |
bash -x get_test_data.sh
Expand All @@ -29,13 +33,13 @@ jobs:
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=build,converted_from_json_no_validation
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=build,converted_from_json_no_validation
- name: Test with python unittest
run: |
behave --no-capture --no-capture-stderr --format=progress features/isa-file-handler.feature
coverage run -m unittest discover -s tests/
python -W ignore::DeprecationWarning:jsonschema -m coverage run -m unittest discover -s tests/
coverage report -m
- name: Coveralls
uses: AndreMiras/coveralls-python-action@develop
Expand Down
7 changes: 3 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,9 @@

<br/><br/>


[![Py versions](https://img.shields.io/pypi/pyversions/isatools.svg?style=flat&maxAge=3600)](https://pypi.python.org/pypi/isatools/)
[![Build Status](https://img.shields.io/github/actions/workflow/status/ISA-tools/isa-api/buildandtestpython.yml?branch=develop)](https://github.com/ISA-tools/isa-api/)
[![Coverage Status](https://coveralls.io/repos/github/ISA-tools/isa-api/badge.svg?branch=master)](https://coveralls.io/github/ISA-tools/isa-api?branch=master)
[![Python 3.9-3.12](https://img.shields.io/badge/python-3.9_|_3.10_|_3.11_|_3.12-blue.svg)](https://www.python.org/)
[![Build Status](https://img.shields.io/github/actions/workflow/status/sorenwacker/isa-api/buildandtestpython.yml?branch=python-3.12)](https://github.com/sorenwacker/isa-api/actions/workflows/buildandtestpython.yml)
[![Coverage Status](https://coveralls.io/repos/github/sorenwacker/isa-api/badge.svg?branch=master)](https://coveralls.io/github/sorenwacker/isa-api?branch=master)
[![PyPI version](https://badge.fury.io/py/isatools.svg)](https://pypi.python.org/pypi/isatools/)
[![Documentation Status](https://readthedocs.org/projects/isatools/badge/?version=latest)](http://isatools.readthedocs.org/en/latest/?badge=latest)

Expand Down
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