ignore 3.12 for now

recursionpharma · Oct 23, 2023 · 2aeb8b2 · 2aeb8b2
1 parent b16df88
commit 2aeb8b2
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Showing 9 changed files with 222 additions and 48 deletions.
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        minor_version: [8, 9, 10, 11, 12]
+        minor_version: [8, 9, 10, 11]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
       - uses: actions/checkout@v3

diff --git a/requirements/dev_3.10.txt b/requirements/dev_3.10.txt
@@ -59,13 +59,13 @@ backcall==0.2.0
     # via ipython
 backoff==2.2.1
     # via lightning
-bandit==1.7.5
+bandit[toml]==1.7.5
     # via efaar-benchmarking (pyproject.toml)
 beautifulsoup4==4.12.2
     # via
     #   lightning
     #   nbconvert
-black==23.10.0
+black==23.10.1
     # via efaar-benchmarking (pyproject.toml)
 bleach==6.1.0
     # via nbconvert
@@ -187,18 +187,37 @@ fsspec[http]==2023.10.0
     #   pytorch-lightning
     #   s3fs
     #   torch
-gcsfs==0.8.0
+gcsfs==2023.10.0
     # via efaar-benchmarking (pyproject.toml)
 gitdb==4.0.11
     # via gitpython
 gitpython==3.1.40
     # via bandit
+google-api-core==2.12.0
+    # via
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth==2.23.3
     # via
     #   gcsfs
+    #   google-api-core
     #   google-auth-oauthlib
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth-oauthlib==1.1.0
     # via gcsfs
+google-cloud-core==2.3.3
+    # via google-cloud-storage
+google-cloud-storage==2.12.0
+    # via gcsfs
+google-crc32c==1.5.0
+    # via
+    #   google-cloud-storage
+    #   google-resumable-media
+google-resumable-media==2.6.0
+    # via google-cloud-storage
+googleapis-common-protos==1.61.0
+    # via google-api-core
 h11==0.14.0
     # via uvicorn
 h5py==3.10.0
@@ -229,6 +248,8 @@ ipython==8.16.1
     # via ipykernel
 isoduration==20.11.0
     # via jsonschema
+isort==5.12.0
+    # via efaar-benchmarking (pyproject.toml)
 itsdangerous==2.1.2
     # via starsessions
 jax==0.4.19
@@ -531,7 +552,10 @@ prometheus-client==0.17.1
 prompt-toolkit==3.0.39
     # via ipython
 protobuf==4.24.4
-    # via orbax-checkpoint
+    # via
+    #   google-api-core
+    #   googleapis-common-protos
+    #   orbax-checkpoint
 psutil==5.9.6
     # via
     #   ipykernel
@@ -639,6 +663,8 @@ requests==2.31.0
     # via
     #   fsspec
     #   gcsfs
+    #   google-api-core
+    #   google-cloud-storage
     #   jupyterlab-server
     #   lightning
     #   lightning-cloud
@@ -674,7 +700,7 @@ scanpy==1.9.5
     # via efaar-benchmarking (pyproject.toml)
 scikit-image==0.22.0
     # via efaar-benchmarking (pyproject.toml)
-scikit-learn==1.3.1
+scikit-learn==1.3.2
     # via
     #   efaar-benchmarking (pyproject.toml)
     #   pynndescent
@@ -759,6 +785,7 @@ tokenize-rt==5.2.0
     # via pyupgrade
 tomli==2.0.1
     # via
+    #   bandit
     #   black
     #   coverage
     #   jupyterlab
@@ -821,6 +848,8 @@ types-pkg-resources==0.1.3
     # via efaar-benchmarking (pyproject.toml)
 types-python-dateutil==2.8.19.14
     # via arrow
+types-setuptools==68.2.0.0
+    # via efaar-benchmarking (pyproject.toml)
 typing-extensions==4.8.0
     # via
     #   async-lru
@@ -840,8 +869,6 @@ typing-extensions==4.8.0
     #   uvicorn
 tzdata==2023.3
     # via pandas
-ujson==5.8.0
-    # via gcsfs
 umap-learn==0.5.4
     # via scanpy
 uri-template==1.3.0
@@ -858,7 +885,7 @@ uvicorn==0.23.2
     #   lightning-cloud
 validate-pyproject[all]==0.15
     # via efaar-benchmarking (pyproject.toml)
-virtualenv==20.24.5
+virtualenv==20.24.6
     # via
     #   pre-commit
     #   tox

diff --git a/requirements/dev_3.11.txt b/requirements/dev_3.11.txt
@@ -59,13 +59,13 @@ backcall==0.2.0
     # via ipython
 backoff==2.2.1
     # via lightning
-bandit==1.7.5
+bandit[toml]==1.7.5
     # via efaar-benchmarking (pyproject.toml)
 beautifulsoup4==4.12.2
     # via
     #   lightning
     #   nbconvert
-black==23.10.0
+black==23.10.1
     # via efaar-benchmarking (pyproject.toml)
 bleach==6.1.0
     # via nbconvert
@@ -181,18 +181,37 @@ fsspec[http]==2023.10.0
     #   pytorch-lightning
     #   s3fs
     #   torch
-gcsfs==0.8.0
+gcsfs==2023.10.0
     # via efaar-benchmarking (pyproject.toml)
 gitdb==4.0.11
     # via gitpython
 gitpython==3.1.40
     # via bandit
+google-api-core==2.12.0
+    # via
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth==2.23.3
     # via
     #   gcsfs
+    #   google-api-core
     #   google-auth-oauthlib
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth-oauthlib==1.1.0
     # via gcsfs
+google-cloud-core==2.3.3
+    # via google-cloud-storage
+google-cloud-storage==2.12.0
+    # via gcsfs
+google-crc32c==1.5.0
+    # via
+    #   google-cloud-storage
+    #   google-resumable-media
+google-resumable-media==2.6.0
+    # via google-cloud-storage
+googleapis-common-protos==1.61.0
+    # via google-api-core
 h11==0.14.0
     # via uvicorn
 h5py==3.10.0
@@ -223,6 +242,8 @@ ipython==8.16.1
     # via ipykernel
 isoduration==20.11.0
     # via jsonschema
+isort==5.12.0
+    # via efaar-benchmarking (pyproject.toml)
 itsdangerous==2.1.2
     # via starsessions
 jax==0.4.19
@@ -525,7 +546,10 @@ prometheus-client==0.17.1
 prompt-toolkit==3.0.39
     # via ipython
 protobuf==4.24.4
-    # via orbax-checkpoint
+    # via
+    #   google-api-core
+    #   googleapis-common-protos
+    #   orbax-checkpoint
 psutil==5.9.6
     # via
     #   ipykernel
@@ -633,6 +657,8 @@ requests==2.31.0
     # via
     #   fsspec
     #   gcsfs
+    #   google-api-core
+    #   google-cloud-storage
     #   jupyterlab-server
     #   lightning
     #   lightning-cloud
@@ -668,7 +694,7 @@ scanpy==1.9.5
     # via efaar-benchmarking (pyproject.toml)
 scikit-image==0.22.0
     # via efaar-benchmarking (pyproject.toml)
-scikit-learn==1.3.1
+scikit-learn==1.3.2
     # via
     #   efaar-benchmarking (pyproject.toml)
     #   pynndescent
@@ -805,6 +831,8 @@ types-pkg-resources==0.1.3
     # via efaar-benchmarking (pyproject.toml)
 types-python-dateutil==2.8.19.14
     # via arrow
+types-setuptools==68.2.0.0
+    # via efaar-benchmarking (pyproject.toml)
 typing-extensions==4.8.0
     # via
     #   chex
@@ -821,8 +849,6 @@ typing-extensions==4.8.0
     #   torch
 tzdata==2023.3
     # via pandas
-ujson==5.8.0
-    # via gcsfs
 umap-learn==0.5.4
     # via scanpy
 uri-template==1.3.0
@@ -839,7 +865,7 @@ uvicorn==0.23.2
     #   lightning-cloud
 validate-pyproject[all]==0.15
     # via efaar-benchmarking (pyproject.toml)
-virtualenv==20.24.5
+virtualenv==20.24.6
     # via
     #   pre-commit
     #   tox

diff --git a/requirements/dev_3.8.txt b/requirements/dev_3.8.txt
@@ -48,11 +48,11 @@ babel==2.13.0
     # via jupyterlab-server
 backcall==0.2.0
     # via ipython
-bandit==1.7.5
+bandit[toml]==1.7.5
     # via efaar-benchmarking (pyproject.toml)
 beautifulsoup4==4.12.2
     # via nbconvert
-black==23.10.0
+black==23.10.1
     # via efaar-benchmarking (pyproject.toml)
 bleach==6.1.0
     # via nbconvert
@@ -154,18 +154,37 @@ fsspec[http]==2023.10.0
     #   pytorch-lightning
     #   s3fs
     #   torch
-gcsfs==0.8.0
+gcsfs==2023.10.0
     # via efaar-benchmarking (pyproject.toml)
 gitdb==4.0.11
     # via gitpython
 gitpython==3.1.40
     # via bandit
+google-api-core==2.12.0
+    # via
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth==2.23.3
     # via
     #   gcsfs
+    #   google-api-core
     #   google-auth-oauthlib
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth-oauthlib==1.1.0
     # via gcsfs
+google-cloud-core==2.3.3
+    # via google-cloud-storage
+google-cloud-storage==2.12.0
+    # via gcsfs
+google-crc32c==1.5.0
+    # via
+    #   google-cloud-storage
+    #   google-resumable-media
+google-resumable-media==2.6.0
+    # via google-cloud-storage
+googleapis-common-protos==1.61.0
+    # via google-api-core
 h5py==3.10.0
     # via
     #   anndata
@@ -206,6 +225,8 @@ ipython==8.13.0
     # via ipykernel
 isoduration==20.11.0
     # via jsonschema
+isort==5.12.0
+    # via efaar-benchmarking (pyproject.toml)
 jax==0.4.13
     # via
     #   chex
@@ -492,6 +513,10 @@ prometheus-client==0.17.1
     # via jupyter-server
 prompt-toolkit==3.0.39
     # via ipython
+protobuf==4.24.4
+    # via
+    #   google-api-core
+    #   googleapis-common-protos
 psutil==5.9.6
     # via ipykernel
 ptyprocess==0.7.0
@@ -580,6 +605,8 @@ requests==2.31.0
     # via
     #   fsspec
     #   gcsfs
+    #   google-api-core
+    #   google-cloud-storage
     #   jupyterlab-server
     #   requests-oauthlib
 requests-oauthlib==1.3.1
@@ -609,7 +636,7 @@ scanpy==1.9.5
     # via efaar-benchmarking (pyproject.toml)
 scikit-image==0.21.0
     # via efaar-benchmarking (pyproject.toml)
-scikit-learn==1.3.1
+scikit-learn==1.3.2
     # via
     #   efaar-benchmarking (pyproject.toml)
     #   pynndescent
@@ -682,6 +709,7 @@ tokenize-rt==5.2.0
     # via pyupgrade
 tomli==2.0.1
     # via
+    #   bandit
     #   black
     #   coverage
     #   jupyterlab
@@ -740,6 +768,8 @@ types-pkg-resources==0.1.3
     # via efaar-benchmarking (pyproject.toml)
 types-python-dateutil==2.8.19.14
     # via arrow
+types-setuptools==68.2.0.0
+    # via efaar-benchmarking (pyproject.toml)
 typing-extensions==4.8.0
     # via
     #   aioitertools
@@ -757,8 +787,6 @@ typing-extensions==4.8.0
     #   torchmetrics
 tzdata==2023.3
     # via pandas
-ujson==5.8.0
-    # via gcsfs
 umap-learn==0.5.4
     # via scanpy
 uri-template==1.3.0
@@ -769,7 +797,7 @@ urllib3==1.26.18
     #   requests
 validate-pyproject[all]==0.15
     # via efaar-benchmarking (pyproject.toml)
-virtualenv==20.24.5
+virtualenv==20.24.6
     # via
     #   pre-commit
     #   tox