unpin numpy,pandas and pot versions (#155)

* unpin numpy,pandas and pot versions

* Update setup.py

* Update test.yaml

* Update setup.py

* Update setup.py

* Update test_runner.yaml

* Update runner-requirements.txt

Author: atong01

.github/workflows/test.yaml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-20.04, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout

.github/workflows/test_runner.yaml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-20.04, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
 
     steps:
       - name: Checkout

requirements.txt

@@ -3,13 +3,13 @@ torchvision>=0.11.0
 
 lightning-bolts
 matplotlib
-numpy<2.0.0
+numpy
 scipy
 scikit-learn
 scprep
 scanpy
 torchdyn>=1.0.6   # 1.0.4 is broken on pypi
-pot<0.9.5
+pot
 torchdiffeq
 absl-py
 clean-fid

runner-requirements.txt

@@ -38,15 +38,15 @@ pytest            # tests
 # --------- pkg reqs -------- #
 lightning-bolts
 matplotlib
-numpy<2.0.0 # Due to pandas incompatibility
+numpy
 scipy
 scikit-learn
 scprep
 scanpy
 timm
 torchdyn>=1.0.5   # 1.0.4 is broken on pypi
-pot<0.9.5
+pot
 
 # --------- notebook reqs -------- #
 seaborn>=0.12.2
-pandas
+pandas>=2.2.2

setup.py

@@ -6,19 +6,15 @@
 
 install_requires = [
     "torch>=1.11.0",
-    "torchvision>=0.11.0",
-    "lightning-bolts",
     "matplotlib",
-    "numpy<2.0.0",  # Due to pandas incompatibility
+    "numpy",  # Due to pandas incompatibility
     "scipy",
     "scikit-learn",
-    "scprep",
-    "scanpy",
-    "torchdyn",
-    "pot<0.9.5",
+    "torchdyn>=1.0.6",
+    "pot",
     "torchdiffeq",
     "absl-py",
-    "clean-fid",
+    "pandas>=2.2.2",
 ]
 
 version_py = os.path.join(os.path.dirname(__file__), "torchcfm", "version.py")