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Merged
merged 8 commits into from
Sep 23, 2022
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DEV: Use requirements.txt in setup.py #467

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7e9f2ad
DEV: Use requirements.txt in setup.py
shaneahmed Sep 12, 2022
41df20d
DEV: Copy requirements.txt in GitHub workflow
shaneahmed Sep 12, 2022
2335c1e
DEV: Add pytorch cu113 link
shaneahmed Sep 12, 2022
9ef74cd
DEV: Add pytorch cu113 link
shaneahmed Sep 12, 2022
7fc92db
DEV: Update requirements_dev file
shaneahmed Sep 12, 2022
e750285
REV: Revert requirements_dev changes
shaneahmed Sep 12, 2022
26c3078
Merge remote-tracking branch 'origin/develop' into dev-use-requiremen…
shaneahmed Sep 16, 2022
b8ba636
[skip ci] DOC: Update requirements.txt
shaneahmed Sep 16, 2022
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1 change: 1 addition & 0 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ include CONTRIBUTING.rst
include HISTORY.md
include LICENSE
include README.md
include requirements.txt
include make.bat
include Makefile
include conf.py
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4 changes: 3 additions & 1 deletion requirements.txt
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@@ -1,3 +1,5 @@
# torch installation
--extra-index-url https://download.pytorch.org/whl/cu113; sys_platform != "darwin"
albumentations>=1.0.3
Click>=8.1.2
defusedxml>=0.7.1
Expand All @@ -20,7 +22,7 @@ scipy>=1.7.3
shapely>=1.8.1
sphinx>=4.3.2
tifffile>=2021.11.2
torch>=1.11.0, <1.12 #pytorch 1.12 has several issues
torch>=1.11.0
torchvision>=0.12.0
tqdm>=4.63.1
umap-learn>=0.5.2
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30 changes: 2 additions & 28 deletions setup.py
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Expand Up @@ -10,34 +10,8 @@
with open("HISTORY.md") as history_file:
history = history_file.read()

requirements = [
"albumentations>=1.0.3",
"Click>=8.1.2",
"defusedxml>=0.7.1",
"flask>=2.1.1",
"glymur>=0.9.9",
"imagecodecs>=2021.11.20",
"matplotlib>=3.5.1",
"numpy>=1.21.5",
"opencv-python>=4.5.5",
"openslide-python>=1.1.2",
"pandas>=1.3.5",
"pillow>=9.0.1",
"pydicom>=2.3.0",
"pyyaml>=6.0",
"requests>=2.27.1",
"scikit-image>=0.19.2",
"scikit-learn>=1.0.2",
"scipy>=1.7.3",
"shapely>=1.8.1",
"tifffile>=2021.11.2",
"torch>=1.11.0",
"torchvision>=0.12.0",
"tqdm>=4.63.1",
"umap-learn>=0.5.2",
"wsidicom>=0.2.0",
"zarr>=2.11.1",
]
with open("requirements.txt") as requirements_file:
requirements = requirements_file.read().splitlines()

setup_requirements = [
"pytest-runner",
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