From 60b32cb04065d5792407804da4dc383eac5df115 Mon Sep 17 00:00:00 2001
From: kathyxchen <kchen@flatironinstitute.org>
Date: Tue, 9 Jul 2024 15:10:15 -0400
Subject: [PATCH] Adjust lower bound for NumPy/Cython dependency requirements
 (#199)

* adjust dependencies version requirements

* adjust up pytorch for jenkins
---
 RELEASE_NOTES.md      | 3 +++
 pyproject.toml        | 2 +-
 selene-cpu.yml        | 6 +++---
 selene_sdk/version.py | 2 +-
 setup.py              | 6 +++---
 5 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 7258e29e..b9b907c6 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -2,6 +2,9 @@
 
 This is a document describing new functionality, bug fixes, breaking changes, etc. associated with Selene version releases from v0.5.0 onwards. 
 
+## Version 0.5.3
+- Adjust dependency requirements 
+
 ## Version 0.5.2
 - Fix Cython type error causing build issues with Python 3.9+
 
diff --git a/pyproject.toml b/pyproject.toml
index d5a66840..ba58a080 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.26.4", "cython>=3.0.10"]
+requires = ["setuptools", "wheel", "numpy>=1.21.4", "cython>=0.29.24"]
 
 [tool.poetry.dependencies]
 python = ">=3.9"  
diff --git a/selene-cpu.yml b/selene-cpu.yml
index 14910672..fac99da0 100644
--- a/selene-cpu.yml
+++ b/selene-cpu.yml
@@ -5,12 +5,12 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - cython=0.29.3
+  - cython=0.29.24
   - click==7.1.2
   - docopt=0.6.2
   - h5py=2.9.0
   - matplotlib=2.0.2
-  - numpy=1.15.1
+  - numpy=1.21.4
   - pandas=0.20.3
   - python=3.6.2
   - pyyaml=5.1
@@ -19,7 +19,7 @@ dependencies:
   - seaborn=0.8.1
   - setuptools=27.2.0
   - statsmodels=0.8.0
-  - pytorch=0.4.1
+  - pytorch=1.11.0
   - plotly=2.7.0
   - pyfaidx=0.5.5.2
   - pytabix=0.0.2
diff --git a/selene_sdk/version.py b/selene_sdk/version.py
index 72251527..43a1e95b 100644
--- a/selene_sdk/version.py
+++ b/selene_sdk/version.py
@@ -1 +1 @@
-__version__ = "0.5.2"
+__version__ = "0.5.3"
diff --git a/setup.py b/setup.py
index a3737824..cf8140b8 100644
--- a/setup.py
+++ b/setup.py
@@ -25,7 +25,7 @@
 cmdclass = {'build_ext': build_ext}
 
 setup(name="selene-sdk",
-      version="0.5.2",
+      version="0.5.3",
       long_description=long_description,
       long_description_content_type='text/markdown',
       description=("framework for developing sequence-level "
@@ -50,11 +50,11 @@
       cmdclass=cmdclass,
       python_requires='>=3.9',
       install_requires=[
-        "cython>=3.0.10",
+        "cython>=0.29.24",
         'click',
         "h5py",
         "matplotlib>=2.2.3",
-        "numpy>=1.26.4",
+        "numpy>=1.21.4",
         "pandas",
         "plotly",
         "pyfaidx",