downgrade pandas (theislab/scvelo#811 (comment))

kevinrue · Aug 30, 2024 · 3c3338d · 3c3338d
1 parent 7d722ab
commit 3c3338d
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Showing 3 changed files with 24 additions and 28 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.7
+Version: 1.15.9
 Date: 2024-08-29
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="[email protected]", comment = c(ORCID = '0000-0002-3564-4813')),

diff --git a/R/basilisk.R b/R/basilisk.R
@@ -1,7 +1,7 @@
 ## Windows ----
 
 .scvelo.dependencies.Windows <- list(
-  channels = c("conda-forge"),
+  channels = c("conda-forge", "defaults"),
   packages = c(
     'brotli==1.1.0',
     'brotli-bin==1.1.0',
@@ -28,7 +28,6 @@
     'libclang13==18.1.8',
     'libcurl==8.9.1',
     'libdeflate==1.21',
-    'libexpat==2.6.2',
     'libffi==3.4.2',
     'libglib==2.80.3',
     'libhwloc==2.11.1',
@@ -62,14 +61,14 @@
     'pthread-stubs==0.4',
     'pthreads-win32==2.9.1',
     'pyqt==5.15.9',
-    'python==3.11.9',
-    'python-tzdata==2024.1',
-    'python_abi==3.11',
+    'python==3.10.14',
+    'python_abi==3.10',
     'qt-main==5.15.8',
     'seaborn-base==0.13.2',
     'tbb==2021.12.0',
     'tk==8.6.13',
     'typing_extensions==4.12.2',
+    'tzdata==2024a',
     'ucrt==10.0.22621.0',
     'vc==14.3',
     'vc14_runtime==14.40.33810',
@@ -80,7 +79,7 @@
     'zstd==1.5.6'
   ),
   pip = c(
-    'anndata==0.10.9',
+    'anndata==0.10.5.post1',
     'array-api-compat==1.8',
     'cached-property==1.5.2',
     'certifi==2024.7.4',
@@ -94,18 +93,17 @@
     'h5py==3.11.0',
     'joblib==1.4.2',
     'kiwisolver==1.4.5',
-    'legacy-api-wrap==1.4',
     'llvmlite==0.43.0',
     'loompy==3.0.6',
     'matplotlib==3.7.3',
     'munkres==1.1.4',
     'natsort==8.4.0',
-    'networkx==3.3',
+    'networkx==3.2',
     'numba==0.60.0',
     'numpy==1.26.4',
     'numpy-groupies==0.11.2',
     'packaging==24.1',
-    'pandas==2.2.2',
+    'pandas==1.3.5',
     'patsy==0.5.6',
     'pillow==10.4.0',
     'pip==24.2',
@@ -116,25 +114,25 @@
     'pyqt5-sip==12.12.2',
     'python-dateutil==2.9.0',
     'pytz==2024.1',
-    'scanpy==1.10.2',
+    'scanpy==1.9.8',
     'scikit-learn==1.5.1',
     'scipy==1.14.1',
     'scvelo==0.2.5',
     'seaborn==0.13.2',
     'session-info==1.0.0',
-    'setuptools==72.2.0',
+    'setuptools==59.8.0',
     'sip==6.7.12',
     'six==1.16.0',
-    'statsmodels==0.14.2',
+    'statsmodels==0.14.1',
     'stdlib-list==0.10.0',
     'threadpoolctl==3.5.0',
     'toml==0.10.2',
     'tomli==2.0.1',
     'tornado==6.4.1',
     'tqdm==4.66.5',
     'typing-extensions==4.12.2',
-    'tzdata==2024.1',
     'umap-learn==0.5.6',
+    'unicodedata2==15.1.0',
     'wheel==0.44.0'
   )
 )

diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml
@@ -28,7 +28,6 @@ dependencies:
   - libclang13=18.1.8=default_ha5278ca_3
   - libcurl=8.9.1=h18fefc2_0
   - libdeflate=1.21=h2466b09_0
-  - libexpat=2.6.2=h63175ca_0
   - libffi=3.4.2=h8ffe710_5
   - libglib=2.80.3=h7025463_2
   - libhwloc=2.11.1=default_h8125262_1000
@@ -52,7 +51,7 @@ dependencies:
   - m2w64-gcc-libs-core=5.3.0=7
   - m2w64-gmp=6.1.0=2
   - m2w64-libwinpthread-git=5.0.0.4634.697f757=2
-  - matplotlib-base=3.7.3=py311h6e989c2_0
+  - matplotlib-base=3.7.3=py310hc9baf74_0
   - mkl=2024.1.0=h66d3029_694
   - msys2-conda-epoch=20160418=1
   - numpy_groupies=0.11.2=pyhd8ed1ab_0
@@ -61,15 +60,15 @@ dependencies:
   - pcre2=10.44=h3d7b363_2
   - pthread-stubs=0.4=hcd874cb_1001
   - pthreads-win32=2.9.1=hfa6e2cd_3
-  - pyqt=5.15.9=py311h125bc19_5
-  - python=3.11.9=h631f459_0_cpython
-  - python-tzdata=2024.1=pyhd8ed1ab_0
-  - python_abi=3.11=5_cp311
+  - pyqt=5.15.9=py310h1fd54f2_5
+  - python=3.10.14=h4de0772_0_cpython
+  - python_abi=3.10=5_cp310
   - qt-main=5.15.8=h06adc49_23
   - seaborn-base=0.13.2=pyhd8ed1ab_2
   - tbb=2021.12.0=hc790b64_4
   - tk=8.6.13=h5226925_1
   - typing_extensions=4.12.2=pyha770c72_0
+  - tzdata=2024a=h8827d51_1
   - ucrt=10.0.22621.0=h57928b3_0
   - vc=14.3=h8a93ad2_20
   - vc14_runtime=14.40.33810=hcc2c482_20
@@ -79,7 +78,7 @@ dependencies:
   - xz=5.2.6=h8d14728_0
   - zstd=1.5.6=h0ea2cb4_0
   - pip:
-    - anndata==0.10.9
+    - anndata==0.10.5.post1
     - array-api-compat==1.8
     - cached-property==1.5.2
     - certifi==2024.7.4
@@ -93,18 +92,17 @@ dependencies:
     - h5py==3.11.0
     - joblib==1.4.2
     - kiwisolver==1.4.5
-    - legacy-api-wrap==1.4
     - llvmlite==0.43.0
     - loompy==3.0.6
     - matplotlib==3.7.3
     - munkres==1.1.4
     - natsort==8.4.0
-    - networkx==3.3
+    - networkx==3.2
     - numba==0.60.0
     - numpy==1.26.4
     - numpy-groupies==0.11.2
     - packaging==24.1
-    - pandas==2.2.2
+    - pandas==1.3.5
     - patsy==0.5.6
     - pillow==10.4.0
     - pip==24.2
@@ -115,23 +113,23 @@ dependencies:
     - pyqt5-sip==12.12.2
     - python-dateutil==2.9.0
     - pytz==2024.1
-    - scanpy==1.10.2
+    - scanpy==1.9.8
     - scikit-learn==1.5.1
     - scipy==1.14.1
     - scvelo==0.2.5
     - seaborn==0.13.2
     - session-info==1.0.0
-    - setuptools==72.2.0
+    - setuptools==59.8.0
     - sip==6.7.12
     - six==1.16.0
-    - statsmodels==0.14.2
+    - statsmodels==0.14.1
     - stdlib-list==0.10.0
     - threadpoolctl==3.5.0
     - toml==0.10.2
     - tomli==2.0.1
     - tornado==6.4.1
     - tqdm==4.66.5
     - typing-extensions==4.12.2
-    - tzdata==2024.1
     - umap-learn==0.5.6
+    - unicodedata2==15.1.0
     - wheel==0.44.0