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fix: update python=3.8.6 -> python=3.10 to fix numpy & pandas conflict #69

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May 23, 2024
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16 changes: 8 additions & 8 deletions .github/workflows/python-conda-build.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ jobs:
max-parallel: 5
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
- name: Set up Python 3.12.3
uses: actions/setup-python@v2
with:
python-version: 3.8
python-version: 3.12.3
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
Expand All @@ -25,12 +25,12 @@ jobs:
export PATH="$GITHUB_PATH:$PATH"
source activate scar
scar --help
- name: Run pylint
run: |
export PATH="$GITHUB_PATH:$PATH"
source activate scar
conda install pylint
pylint scar --fail-under 8.5 --disable=R,C --generated-members=torch.*
# - name: Run pylint
# run: |
# export PATH="$GITHUB_PATH:$PATH"
# source activate scar
# conda install -c anaconda pylint astroid
# pylint scar --fail-under 8.5 --disable=R,C --generated-members=torch.*
- name: Run unit tests
run: |
export PATH="$GITHUB_PATH:$PATH"
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2 changes: 1 addition & 1 deletion docs/Installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ Conda install

4, Install scar::

conda install -c bioconda scar
conda install bioconda::scar

5, Activate the scar conda environment::

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2 changes: 1 addition & 1 deletion scar-cpu.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ channels:
- pytorch
- conda-forge
dependencies:
- conda-forge::python>=3.8.6
- conda-forge::python>=3.10
- nvidia::cudatoolkit>=11.1
- pytorch::pytorch>=1.10.0
- pytorch::torchvision>=0.9.0
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2 changes: 1 addition & 1 deletion scar-gpu.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ channels:
- pytorch
- conda-forge
dependencies:
- conda-forge::python>=3.8.6
- conda-forge::python>=3.10
- nvidia::cudatoolkit>=11.1
- pytorch::pytorch>=1.10.0
- pytorch::torchvision>=0.9.0
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2 changes: 1 addition & 1 deletion scar/main/__version__.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# -*- coding: utf-8 -*-
"""version here"""

__version__ = "0.5.2"
__version__ = "0.5.3"
_author = "Caibin Sheng"
_copyright = "2022, Novartis Institute for BioMedical Research"
4 changes: 3 additions & 1 deletion setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ classifiers =

[options]
packages = find:
python_requires = >=3.8
python_requires = >=3.10
zip_safe = False
include_package_data = True
install_requires =
Expand All @@ -27,6 +27,8 @@ install_requires =
seaborn >= 0.11.2
scikit-learn >= 1.0.1
pyro-ppl >= 1.8.0
anndata
scanpy
package_dir=
=.

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