Remove anndata for now

cellcommunicationpf2/cc-pf2.py

@@ -1,4 +1,3 @@
-import anndata
 import numpy as np
 import cupy as cp
 import tensorly as tl

cellcommunicationpf2/figures/common.py

@@ -5,7 +5,6 @@
 import sys
 import time
 
-from anndata import AnnData
 import datashader as ds
 import datashader.transfer_functions as tf
 import matplotlib

cellcommunicationpf2/figures/figure1.py

@@ -2,7 +2,6 @@
 Figure 1: XX
 """
 
-import anndata
 import pandas as pd
 from .common import getSetup, subplotLabel
 

pyproject.toml

@@ -12,7 +12,6 @@ dependencies = [
     "tensorly>=0.8.1",
     "tqdm>=4.66",
     "cupy-cuda12x>=13.0",
-    "anndata>=0.10",
     "scikit-learn>=1.4.2",
     "pacmap>=0.7.2",
     "tlviz>=0.1.1",

requirements-dev.lock

@@ -5,52 +5,117 @@
 #   pre: false
 #   features: []
 #   all-features: false
+#   with-sources: false
+#   generate-hashes: false
+#   universal: false
 
 -e file:.
-anndata==0.10.9
 annoy==1.17.3
-array-api-compat==1.9
+    # via pacmap
 certifi==2024.8.30
+    # via requests
 charset-normalizer==3.3.2
+    # via requests
 contourpy==1.3.0
+    # via matplotlib
 coverage==7.6.1
+    # via pytest-cov
 cupy-cuda12x==13.3.0
+    # via cellcommunicationpf2
 cycler==0.12.1
+    # via matplotlib
 fastrlock==0.8.2
+    # via cupy-cuda12x
 fonttools==4.54.1
-h5py==3.12.1
+    # via matplotlib
 idna==3.10
+    # via requests
 iniconfig==2.0.0
+    # via pytest
 joblib==1.4.2
+    # via scikit-learn
 kiwisolver==1.4.7
+    # via matplotlib
 llvmlite==0.43.0
+    # via numba
 matplotlib==3.9.2
-natsort==8.4.0
+    # via tlviz
 nodeenv==1.9.1
+    # via pyright
 numba==0.60.0
+    # via pacmap
 numpy==2.0.2
+    # via cellcommunicationpf2
+    # via contourpy
+    # via cupy-cuda12x
+    # via matplotlib
+    # via numba
+    # via pacmap
+    # via pandas
+    # via patsy
+    # via scikit-learn
+    # via scipy
+    # via statsmodels
+    # via tensorly
+    # via tlviz
+    # via xarray
 packaging==24.1
+    # via matplotlib
+    # via pytest
+    # via statsmodels
+    # via xarray
 pacmap==0.7.3
+    # via cellcommunicationpf2
 pandas==2.2.3
+    # via statsmodels
+    # via tlviz
+    # via xarray
 patsy==0.5.6
+    # via statsmodels
 pillow==10.4.0
+    # via matplotlib
 pluggy==1.5.0
+    # via pytest
 pyparsing==3.1.4
+    # via matplotlib
 pyright==1.1.383
 pytest==8.3.3
+    # via pytest-cov
 pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
+    # via matplotlib
+    # via pandas
 pytz==2024.2
+    # via pandas
 requests==2.32.3
+    # via tlviz
 scikit-learn==1.5.2
+    # via cellcommunicationpf2
+    # via pacmap
 scipy==1.14.1
+    # via cellcommunicationpf2
+    # via scikit-learn
+    # via statsmodels
+    # via tensorly
+    # via tlviz
 six==1.16.0
+    # via patsy
+    # via python-dateutil
 statsmodels==0.14.4
+    # via tlviz
 tensorly==0.8.1
+    # via cellcommunicationpf2
 threadpoolctl==3.5.0
+    # via scikit-learn
 tlviz==0.1.1
+    # via cellcommunicationpf2
 tqdm==4.66.5
+    # via cellcommunicationpf2
 typing-extensions==4.12.2
+    # via pyright
 tzdata==2024.2
+    # via pandas
 urllib3==2.2.3
+    # via requests
 xarray==2024.9.0
+    # via tlviz

requirements.lock

@@ -5,44 +5,102 @@
 #   pre: false
 #   features: []
 #   all-features: false
+#   with-sources: false
+#   generate-hashes: false
+#   universal: false
 
 -e file:.
-anndata==0.10.9
 annoy==1.17.3
-array-api-compat==1.9
+    # via pacmap
 certifi==2024.8.30
+    # via requests
 charset-normalizer==3.3.2
+    # via requests
 contourpy==1.3.0
+    # via matplotlib
 cupy-cuda12x==13.3.0
+    # via cellcommunicationpf2
 cycler==0.12.1
+    # via matplotlib
 fastrlock==0.8.2
+    # via cupy-cuda12x
 fonttools==4.54.1
-h5py==3.12.1
+    # via matplotlib
 idna==3.10
+    # via requests
 joblib==1.4.2
+    # via scikit-learn
 kiwisolver==1.4.7
+    # via matplotlib
 llvmlite==0.43.0
+    # via numba
 matplotlib==3.9.2
-natsort==8.4.0
+    # via tlviz
 numba==0.60.0
+    # via pacmap
 numpy==2.0.2
+    # via cellcommunicationpf2
+    # via contourpy
+    # via cupy-cuda12x
+    # via matplotlib
+    # via numba
+    # via pacmap
+    # via pandas
+    # via patsy
+    # via scikit-learn
+    # via scipy
+    # via statsmodels
+    # via tensorly
+    # via tlviz
+    # via xarray
 packaging==24.1
+    # via matplotlib
+    # via statsmodels
+    # via xarray
 pacmap==0.7.3
+    # via cellcommunicationpf2
 pandas==2.2.3
+    # via statsmodels
+    # via tlviz
+    # via xarray
 patsy==0.5.6
+    # via statsmodels
 pillow==10.4.0
+    # via matplotlib
 pyparsing==3.1.4
+    # via matplotlib
 python-dateutil==2.9.0.post0
+    # via matplotlib
+    # via pandas
 pytz==2024.2
+    # via pandas
 requests==2.32.3
+    # via tlviz
 scikit-learn==1.5.2
+    # via cellcommunicationpf2
+    # via pacmap
 scipy==1.14.1
+    # via cellcommunicationpf2
+    # via scikit-learn
+    # via statsmodels
+    # via tensorly
+    # via tlviz
 six==1.16.0
+    # via patsy
+    # via python-dateutil
 statsmodels==0.14.4
+    # via tlviz
 tensorly==0.8.1
+    # via cellcommunicationpf2
 threadpoolctl==3.5.0
+    # via scikit-learn
 tlviz==0.1.1
+    # via cellcommunicationpf2
 tqdm==4.66.5
+    # via cellcommunicationpf2
 tzdata==2024.2
+    # via pandas
 urllib3==2.2.3
+    # via requests
 xarray==2024.9.0
+    # via tlviz