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Merged
josenimo merged 6 commits into from
Sep 30, 2025
Merged

pip install troubleshoot #83

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8455970
pip install troubleshoot
josenimo Sep 30, 2025
52d42ab
CHANGED: removed bash default
josenimo Sep 30, 2025
1c66a83
CHANGED: Win specific CI block
josenimo Sep 30, 2025
6fb92a9
CHANGED: Micromamba for speed
josenimo Sep 30, 2025
d0b80ed
CHANGED: Micromamba for speed v2
josenimo Sep 30, 2025
e61bd72
CHANGED: CI testing polished, toml polish
josenimo Sep 30, 2025
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30 changes: 25 additions & 5 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,15 +9,11 @@ on:
jobs:
test:
runs-on: ${{ matrix.os }}

defaults:
run:
shell: bash -e {0}

strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
os: [windows-latest, macos-latest, ubuntu-latest ]
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Copilot AI Sep 30, 2025

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There are extra trailing spaces after 'ubuntu-latest' in the matrix configuration.

Suggested change
os: [windows-latest, macos-latest, ubuntu-latest ]
os: [windows-latest, macos-latest, ubuntu-latest]

Copilot uses AI. Check for mistakes.
python: ["3.11", "3.12"]

env:
Expand Down Expand Up @@ -51,5 +47,29 @@ jobs:
# env:
# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

- name: Build Wheel
run: "uv build"

- name: Setup MicroMamba
uses: mamba-org/setup-micromamba@v2
with:
environment-name: build_test_env
create-args: >-
python=${{ matrix.python }}
cache-downloads: true

- name: Install Wheel on Windows
if: runner.os == 'Windows'
run: |
$whl = Get-ChildItem -Path dist/*.whl | Select-Object -First 1
micromamba run -n build_test_env python -m pip install $whl.FullName

- name: Install Wheel on Linux/macOS
if: runner.os != 'Windows'
run: micromamba run -n build_test_env pip install dist/*.whl

- name: Verify Installation
run: micromamba run -n build_test_env python -c "import opendvp; print('Successfully installed and imported package into Conda environment.')"

- name: Minimize uv cache
run: uv cache prune --ci
9 changes: 7 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[project]
name = "openDVP"
version = "0.7.0"
version = "0.7.1"
description = "open-sourced Deep Visual Proteomics toolkit"
readme = "README.md"
requires-python = ">=3.11, <3.13"
Expand All @@ -23,8 +23,13 @@ dependencies = [
"esda >=2.7, <2.8",
"upsetplot",
"perseuspy >=0.3.9,<0.4",
"gensim >=4.3.2",
"gensim >=4.3.2", # Gensim breaks with python >=3.13
"pyqt6",
"tifffile ~= 2025.9.30",
"scikit-image ~= 0.25.2",
"scikit-learn ~= 1.7.2",
"xarray ~= 2024.11.0",
"pyogrio ~= 0.11.1"
]

[dependency-groups]
Expand Down
42 changes: 26 additions & 16 deletions uv.lock
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