Upgrade packages

Author: aarmey

pyproject.toml

@@ -8,25 +8,23 @@ requires-python = ">= 3.12"
 
 
 dependencies = [
-    "numpy>=1.26",
-    "scipy>=1.13",
-    "scikit-learn>=1.4",
+    "numpy>=2.1",
+    "scipy>=1.15",
+    "scikit-learn>=1.6",
     "seaborn>=0.13.2",
-    "pandas>=2.2.1",
+    "pandas>=2.2",
     "tensorly>=0.8.1",
     "h5netcdf>=1.3",
     "anndata>=0.10.3",
     "datashader>=0.16",
     "gseapy>=1.1",
-    "scanpy>=1.10",
+    "scanpy @ git+https://github.com/scverse/scanpy.git@c2a7a4b7ec3203121a8d75aa05fbeb602ceecbd4",
     "pacmap>=0.7.1",
     "leidenalg>=0.10.1",
     "tqdm>=4.66.1",
     "tlviz>=0.1.1",
-    "doubletdetection >=4.2",
     "statsmodels>=0.14.1",
-    "dask[dataframe]>=2024.3.1",
-    "scib>=1.1.5",
+    "dask[dataframe]>=2025",
     "ipykernel>=6.29.5",
     "parafac2 @ git+https://github.com/meyer-lab/parafac2.git",
     "wandb>=0.19.9",
@@ -48,7 +46,7 @@ build-backend = "hatchling.build"
 managed = true
 dev-dependencies = [
     "pytest>=8.0",
-    "pytest-cov>=5.0",
+    "pytest-cov>=6.0",
     "pyright>=1.1",
 ]
 

requirements-dev.lock

@@ -11,11 +11,9 @@
 
 -e file:.
 anndata==0.11.3
-    # via doubletdetection
     # via parafac2
     # via pf2rnaseq
     # via scanpy
-    # via scib
 annotated-types==0.7.0
     # via pydantic
 annoy==1.17.3
@@ -38,7 +36,6 @@ colorcet==3.1.0
     # via datashader
 comm==0.2.2
     # via ipykernel
-    # via ipywidgets
 contourpy==1.3.0
     # via matplotlib
 coverage==7.6.1
@@ -47,26 +44,21 @@ cupy-cuda12x==13.4.0
     # via parafac2
 cycler==0.12.1
     # via matplotlib
-dask==2024.9.0
-    # via dask-expr
+dask==2025.5.0
     # via datashader
     # via pf2rnaseq
-dask-expr==1.1.14
-    # via dask
 datashader==0.16.3
     # via pf2rnaseq
 debugpy==1.8.7
     # via ipykernel
 decorator==5.1.1
     # via ipython
-deprecated==1.2.14
-    # via scib
 docker-pycreds==0.4.0
     # via wandb
-doubletdetection==4.2
-    # via pf2rnaseq
 executing==2.1.0
     # via stack-data
+fast-array-utils==1.2.1
+    # via scanpy
 fastrlock==0.8.3
     # via cupy-cuda12x
 fonttools==4.53.1
@@ -85,22 +77,16 @@ h5py==3.11.0
     # via anndata
     # via h5netcdf
     # via scanpy
-    # via scib
 idna==3.8
     # via requests
 igraph==0.11.6
     # via leidenalg
-    # via louvain
-    # via scib
 iniconfig==2.0.0
     # via pytest
 ipykernel==6.29.5
     # via pf2rnaseq
 ipython==8.27.0
     # via ipykernel
-    # via ipywidgets
-ipywidgets==8.1.5
-    # via doubletdetection
 jedi==0.19.1
     # via ipython
 joblib==1.4.2
@@ -112,30 +98,20 @@ jupyter-client==8.6.3
 jupyter-core==5.7.2
     # via ipykernel
     # via jupyter-client
-jupyterlab-widgets==3.0.13
-    # via ipywidgets
 kiwisolver==1.4.7
     # via matplotlib
 legacy-api-wrap==1.4
     # via scanpy
 leidenalg==0.10.2
-    # via doubletdetection
     # via pf2rnaseq
-    # via phenograph
-    # via scib
 llvmlite==0.44.0
     # via numba
     # via pynndescent
-    # via scib
 locket==1.0.0
     # via partd
-louvain==0.8.2
-    # via doubletdetection
 matplotlib==3.9.2
-    # via doubletdetection
     # via gseapy
     # via scanpy
-    # via scib
     # via seaborn
     # via tlviz
 matplotlib-inline==0.1.7
@@ -154,18 +130,18 @@ nodeenv==1.9.1
     # via pyright
 numba==0.61.0
     # via datashader
+    # via fast-array-utils
     # via pacmap
     # via pynndescent
     # via scanpy
-    # via scib
     # via umap-learn
 numpy==2.1.3
     # via anndata
     # via contourpy
     # via cupy-cuda12x
     # via dask
     # via datashader
-    # via doubletdetection
+    # via fast-array-utils
     # via gseapy
     # via h5py
     # via matplotlib
@@ -175,12 +151,9 @@ numpy==2.1.3
     # via parafac2
     # via patsy
     # via pf2rnaseq
-    # via phenograph
     # via pyarrow
     # via scanpy
-    # via scib
     # via scikit-learn
-    # via scikit-misc
     # via scipy
     # via seaborn
     # via statsmodels
@@ -204,13 +177,10 @@ pacmap==0.7.3
 pandas==2.2.2
     # via anndata
     # via dask
-    # via dask-expr
     # via datashader
-    # via doubletdetection
     # via gseapy
     # via pf2rnaseq
     # via scanpy
-    # via scib
     # via seaborn
     # via statsmodels
     # via tlviz
@@ -229,8 +199,6 @@ patsy==0.5.6
     # via statsmodels
 pexpect==4.9.0
     # via ipython
-phenograph==1.5.7
-    # via doubletdetection
 pillow==10.4.0
     # via datashader
     # via matplotlib
@@ -245,34 +213,30 @@ protobuf==5.29.4
     # via wandb
 psutil==6.0.0
     # via ipykernel
-    # via phenograph
     # via wandb
 ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
 pyarrow==17.0.0
-    # via dask-expr
+    # via dask
 pyct==0.5.0
     # via datashader
 pydantic==2.11.2
     # via wandb
 pydantic-core==2.33.1
     # via pydantic
-pydot==3.0.1
-    # via scib
 pygments==2.18.0
     # via ipython
 pynndescent==0.5.13
     # via scanpy
     # via umap-learn
 pyparsing==3.1.4
     # via matplotlib
-    # via pydot
 pyright==1.1.380
 pytest==8.3.3
     # via pytest-cov
-pytest-cov==5.0.0
+pytest-cov==6.1.1
 python-dateutil==2.9.0.post0
     # via jupyter-client
     # via matplotlib
@@ -290,34 +254,24 @@ requests==2.32.3
     # via gseapy
     # via tlviz
     # via wandb
-scanpy==1.10.4
-    # via doubletdetection
-    # via pf2rnaseq
-    # via scib
-scib==1.1.5
+scanpy @ git+https://github.com/scverse/scanpy.git@c2a7a4b7ec3203121a8d75aa05fbeb602ceecbd4
     # via pf2rnaseq
 scikit-learn==1.6.1
     # via pacmap
     # via parafac2
     # via pf2rnaseq
-    # via phenograph
     # via pynndescent
     # via scanpy
-    # via scib
     # via umap-learn
-scikit-misc==0.5.1
-    # via scib
 scipy==1.15.2
     # via anndata
     # via datashader
-    # via doubletdetection
+    # via fast-array-utils
     # via gseapy
     # via parafac2
     # via pf2rnaseq
-    # via phenograph
     # via pynndescent
     # via scanpy
-    # via scib
     # via scikit-learn
     # via statsmodels
     # via tensorly
@@ -326,15 +280,13 @@ scipy==1.15.2
 seaborn==0.13.2
     # via pf2rnaseq
     # via scanpy
-    # via scib
 sentry-sdk==2.25.1
     # via wandb
-session-info==1.0.0
+session-info2==0.1.2
     # via scanpy
 setproctitle==1.3.5
     # via wandb
 setuptools==74.1.2
-    # via phenograph
     # via wandb
 six==1.16.0
     # via asttokens
@@ -349,8 +301,6 @@ statsmodels==0.14.2
     # via pf2rnaseq
     # via scanpy
     # via tlviz
-stdlib-list==0.10.0
-    # via session-info
 tensorly==0.8.1
     # via parafac2
     # via pf2rnaseq
@@ -368,7 +318,6 @@ tornado==6.4.1
     # via ipykernel
     # via jupyter-client
 tqdm==4.66.5
-    # via doubletdetection
     # via parafac2
     # via pf2rnaseq
     # via scanpy
@@ -377,13 +326,13 @@ traitlets==5.14.3
     # via comm
     # via ipykernel
     # via ipython
-    # via ipywidgets
     # via jupyter-client
     # via jupyter-core
     # via matplotlib-inline
 typing-extensions==4.12.2
     # via pydantic
     # via pydantic-core
+    # via scanpy
     # via typing-inspection
     # via wandb
 typing-inspection==0.4.0
@@ -392,18 +341,13 @@ tzdata==2024.1
     # via pandas
 umap-learn==0.5.6
     # via scanpy
-    # via scib
 urllib3==2.2.3
     # via requests
     # via sentry-sdk
 wandb==0.19.9
     # via pf2rnaseq
 wcwidth==0.2.13
     # via prompt-toolkit
-widgetsnbextension==4.0.13
-    # via ipywidgets
-wrapt==1.16.0
-    # via deprecated
 xarray==2024.9.0
     # via datashader
     # via tlviz