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Support python 3.13 #95

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233c590
Support python 3.13
poshul Aug 11, 2025
0e189f1
Update ci.yml
poshul Aug 11, 2025
0e76422
Update static.yml
poshul Aug 11, 2025
7232408
Update execute_notebooks.yml
poshul Aug 11, 2025
71cf474
bump versions
poshul Aug 11, 2025
4345693
update requirements
poshul Aug 11, 2025
c9fe996
Update ci.yml
poshul Aug 11, 2025
4d34f9c
Merge branch 'main' into poshul-patch-1
poshul Nov 3, 2025
0090e51
update snapshots for new bokeh
poshul Nov 3, 2025
7f2db37
add building with 3.14 in CI
poshul Nov 3, 2025
3b607cd
stabilize UUIDs generated during testing to make less brittle
poshul Nov 3, 2025
6bfb3c3
push stabilized uuids
poshul Nov 3, 2025
51abde0
Update test/conftest.py
poshul Nov 3, 2025
b8d95b8
allow small differences between snapshots to handle different platforms
poshul Nov 3, 2025
14be8a8
increase test tolerance
poshul Nov 3, 2025
a040bcf
consistant UUID for a run
poshul Nov 3, 2025
0c8cd37
canonicalize json before doing snapshot comparisons
poshul Nov 3, 2025
927f4ad
fix canonicalization
poshul Nov 3, 2025
0339566
decode base64 arrays in the BokehSnapshotExtension before doing a com…
poshul Nov 3, 2025
6b898ac
apply fix from suggestion
poshul Nov 3, 2025
335fca1
more debugging output on failed test
poshul Nov 3, 2025
8863690
decode bas64 dicts before comparing them.
poshul Nov 3, 2025
fc1b504
sort arrays before comparison
poshul Nov 3, 2025
948d826
handle tuples in plotly snapshot properly.
poshul Nov 3, 2025
ada0ce0
Handle customData
poshul Nov 3, 2025
2067db2
address code review
poshul Nov 3, 2025
5010aa3
Apply suggestion from @coderabbitai[bot]
poshul Nov 3, 2025
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2 changes: 1 addition & 1 deletion .binder/runtime.txt
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
python-3.12
python-3.13
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -8,7 +8,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest, windows-latest] # note mac-latest tests fail due to slight differences in images
python-version: ["3.12"]
python-version: ["3.12", "3.13", "3.14"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
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2 changes: 1 addition & 1 deletion .github/workflows/execute_notebooks.yml
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Expand Up @@ -30,7 +30,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.12'
python-version: '3.13'
cache: 'pip'

- name: Install dependencies
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2 changes: 1 addition & 1 deletion .github/workflows/static.yml
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Expand Up @@ -38,7 +38,7 @@ jobs:
- name: Set up python
uses: actions/setup-python@v4
with:
python-version: '3.12'
python-version: '3.13'

- name: Install dependencies
run: |
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4 changes: 2 additions & 2 deletions .readthedocs.yaml
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@@ -1,9 +1,9 @@
version: 2
# Set the OS, Python version and other tools you might need
build:
os: ubuntu-22.04
os: ubuntu-24.04
tools:
python: "3.12"
python: "3.13"
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@jcharkow jcharkow Aug 13, 2025

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Would keep testing at 3.12 for now, see above

# Build documentation in the "docs/" directory with Sphinx
sphinx:
configuration: docs/conf.py
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -39,7 +39,7 @@ The recommended way of installing pyopenms_viz is through the Python Package Ind
First create a new environemnt:

```bash
conda create --name=pyopenms_viz python=3.12
conda create --name=pyopenms_viz python=3.13
conda activate pyopenms_viz
```
Then in the new environment install pyopenms_viz.
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2 changes: 1 addition & 1 deletion docs/Installation.rst
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Expand Up @@ -10,7 +10,7 @@ First create a new environment:

.. code-block:: bash

conda create --name=pyopenms-viz python=3.12
conda create --name=pyopenms-viz python=3.13
conda activate pyopenms-viz

Then in the new environment install pyOpenMS-viz.
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6 changes: 4 additions & 2 deletions pyproject.toml
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Expand Up @@ -7,7 +7,7 @@ name = "pyopenms_viz"
module = "pyopenms_viz"
dist-name = "pyopenms_viz"
author = "OpenMS Team"
version = "1.0.0"
version = "1.0.1"
author-email = "[email protected]"
home-page = "https://github.com/OpenMS/pyopenms_viz/"
description = "A package for visualizing mass spectrometry data using pandas dataframes"
Expand All @@ -19,10 +19,12 @@ classifiers = [
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Chemistry",
]
requires-python = ">=3.10, <=3.13"
requires-python = ">=3.10, <=3.14"
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@coderabbitai coderabbitai bot Aug 11, 2025

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💡 Verification agent

🧩 Analysis chain

Re-evaluate requires-python upper bound vs CI coverage

You allow installation on 3.14 but do not test it in CI. Either:

  • Add 3.14 (or 3.14-dev) to CI matrices, or
  • Change to "<3.14" until you officially support it.
-requires-python = ">=3.10, <=3.14"
+# Option A: tighten until CI covers 3.14
+requires-python = ">=3.10, <3.14"

Alternatively, add Python 3.14 to classifiers and CI once available.

🏁 Script executed:

#!/bin/bash
# Search for python-version entries in GitHub Actions workflows to verify CI coverage
grep -R "python-version" -n .github/workflows

Length of output: 554

Re-evaluate requires-python upper bound vs CI coverage

Our GitHub Actions only run on Python 3.12 and 3.13, but pyproject.toml currently allows installation on 3.14. Please choose one of the following:

• Tighten the upper bound until we add CI for 3.14:

- requires-python = ">=3.10, <=3.14"
+ requires-python = ">=3.10, <3.14"

• Or add Python 3.14 (or 3.14-dev) to your CI matrices in:
– .github/workflows/ci.yml (matrix.python-version)
– .github/workflows/static.yml
– .github/workflows/execute_notebooks.yml
– (and any other workflow using python-version)

Once CI passes on 3.14, don’t forget to update your PyPI classifiers to include it.

dependencies = ["pandas>=0.17"]

[project.optional-dependencies]
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