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update GA and dependencies #32

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17 changes: 10 additions & 7 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@

name: spora

# Controls when the workflow will run
on:
push:
branches:
Expand All @@ -14,21 +13,25 @@ jobs:
build:
name: spora test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
env:
CONDA_OVERRIDE_CUDA: "11.8"
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest"]
python-version: ["3.8"]
python-version: ["3.9"]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- if: runner.os == 'Linux'
run: sudo apt-get -y update && sudo apt-get install -y libgl1-mesa-dev libglfw3-dev
- uses: conda-incubator/setup-miniconda@v2
with:
environment-file: environments/environment.yml
activate-environment: ncov_spora
channels: conda-forge,bioconda,defaults,r
mamba-version: "*"
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
miniconda-version: "latest"
- name: Install spora
run: pip install .
- name: Check spora version
Expand Down
3 changes: 2 additions & 1 deletion environments/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,12 @@ dependencies:
- fasttree=2.1.10
- iqtree=2.1.2
- mafft=7.480
- numpy=1.20.3
- numpy==1.24.3
- pandas=1.2.4
- pandoc=>2.1.3
- pango=1.48.5
- pip=21.1.2
- pulp==2.7.0
- pytest=6.2.4
- python=3.8.10
- raxml=8.2.12
Expand Down
6 changes: 3 additions & 3 deletions setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,12 @@
},
license='',
author='Matthew Watson',
author_email='matthew.watson@oahpp.ca',
author_email='matt.sd.watson@gmail.com',
description='spora: Streamlined Phylogenomic Outbreak Report Analysis',
long_description_content_type="text/markdown",
long_description = long_description,
install_requires = ["pandas>=1.1.5", "numpy>=1.19", "biopython>=1.79", "snakemake>=7.0.0", "pypandoc>=1.8",
"pytest>=7.1.2", "click>=8.0.3"],
install_requires = ["pandas>=1.1.5", "numpy>=1.24.3", "biopython>=1.79", "snakemake>=7.0.0", "pypandoc>=1.8",
"pytest>=7.1.2", "click>=8.0.3", "pulp==2.7.0"],
entry_points="""
[console_scripts]
{program} = spora.main:main
Expand Down
2 changes: 1 addition & 1 deletion spora/__init__.py
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
_program = "spora"
__version__ = "0.7.0"
__version__ = "0.7.1"
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