downgrade python (theislab/scvelo#1124 (comment))

kevinrue · Aug 30, 2024 · 7c66146 · 7c66146
1 parent ba0dfbb
commit 7c66146
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.11
+Version: 1.15.12
 Date: 2024-08-29
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "kevinrue67@gmail.com", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="infinite.monkeys.with.keyboards@gmail.com", comment = c(ORCID = '0000-0002-3564-4813')),

diff --git a/R/basilisk.R b/R/basilisk.R
@@ -3,30 +3,41 @@
 .scvelo.dependencies.Windows <- list(
   channels = c("bioconda", "conda-forge"),
   packages = c(
-    'anndata==0.10.9',
-    'array-api-compat==1.8',
+    'anndata==0.9.2',
+    'blosc==1.21.6',
     'brotli==1.1.0',
     'brotli-bin==1.1.0',
+    'brotli-python==1.1.0',
     'bzip2==1.0.8',
+    'c-blosc2==2.12.0',
     'ca-certificates==2024.7.4',
     'cached-property==1.5.2',
     'cached_property==1.5.2',
     'certifi==2024.7.4',
+    'cffi==1.17.0',
+    'charset-normalizer==3.3.2',
     'colorama==0.4.6',
-    'contourpy==1.3.0',
+    'contourpy==1.1.1',
     'cycler==0.12.1',
-    'exceptiongroup==1.2.2',
     'fonttools==4.53.1',
     'freetype==2.12.1',
-    'get-annotations==0.1.2',
     'glib==2.80.3',
     'glib-tools==2.80.3',
     'gst-plugins-base==1.24.6',
     'gstreamer==1.24.6',
+    'h2==4.1.0',
     'h5py==3.11.0',
     'hdf5==1.14.3',
+    'hpack==4.0.0',
+    'hyperframe==6.0.1',
     'icu==73.2',
+    'idna==3.8',
+    'importlib-metadata==8.4.0',
+    'importlib-resources==6.4.4',
+    'importlib_metadata==8.4.0',
+    'importlib_resources==6.4.4',
     'intel-openmp==2024.2.1',
+    'jinja2==3.0.3',
     'joblib==1.4.2',
     'kiwisolver==1.4.5',
     'krb5==1.21.3',
@@ -42,7 +53,6 @@
     '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',
@@ -61,53 +71,67 @@
     'libxcb==1.16',
     'libxml2==2.12.7',
     'libzlib==1.3.1',
-    'llvmlite==0.43.0',
+    'llvmlite==0.41.1',
     'loompy==2.0.16',
+    'lz4-c==1.9.4',
     'm2w64-gcc-libgfortran==5.3.0',
     'm2w64-gcc-libs==5.3.0',
     'm2w64-gcc-libs-core==5.3.0',
     'm2w64-gmp==6.1.0',
     'm2w64-libwinpthread-git==5.0.0.4634.697f757',
-    'matplotlib==3.6.3',
-    'matplotlib-base==3.6.3',
+    'markupsafe==2.1.5',
+    'matplotlib==3.7.2',
+    'matplotlib-base==3.7.2',
     'mkl==2024.1.0',
     'msys2-conda-epoch==20160418',
     'munkres==1.0.7',
     'natsort==8.4.0',
-    'networkx==3.3',
-    'numba==0.60.0',
-    'numpy==1.26.4',
+    'networkx==3.1',
+    'numba==0.58.1',
+    'numexpr==2.7.3',
+    'numpy==1.24.4',
     'openjpeg==2.5.2',
     'openssl==3.3.1',
     'packaging==24.1',
-    'pandas==1.5.2',
+    'pandas==2.0.3',
     'patsy==0.5.6',
     'pcre2==10.44',
     'pillow==10.4.0',
     'pip==24.2',
+    'platformdirs==4.2.2',
     'ply==3.11',
+    'pooch==1.8.2',
     'pthread-stubs==0.4',
     'pthreads-win32==2.9.1',
+    'py-cpuinfo==9.0.0',
+    'pycparser==2.22',
     'pynndescent==0.5.13',
-    'pyparsing==3.1.4',
+    'pyparsing==3.0.9',
     'pyqt==5.15.9',
     'pyqt5-sip==12.12.2',
-    'python==3.11.9',
+    'pysocks==1.7.1',
+    'pytables==3.8.0',
+    'python==3.8.19',
     'python-dateutil==2.9.0',
-    'python_abi==3.11',
+    'python-tzdata==2024.1',
+    'python_abi==3.8',
     'pytz==2024.1',
     'qt-main==5.15.8',
-    'scanpy==1.10.2',
-    'scikit-learn==1.5.1',
-    'scipy==1.13.1',
+    'requests==2.32.3',
+    'scanpy==1.7.2',
+    'scikit-learn==1.3.2',
+    'scipy==1.10.1',
     'scvelo==0.2.5',
     'seaborn==0.13.2',
     'seaborn-base==0.13.2',
-    'session-info==1.0.0',
     'setuptools==72.2.0',
+    'setuptools-scm==8.1.0',
+    'setuptools_scm==8.1.0',
+    'sinfo==0.3.1',
     'sip==6.7.12',
     'six==1.16.0',
-    'statsmodels==0.14.2',
+    'snappy==1.2.1',
+    'statsmodels==0.14.1',
     'stdlib-list==0.10.0',
     'tbb==2021.12.0',
     'threadpoolctl==3.5.0',
@@ -117,17 +141,23 @@
     'tornado==6.4.1',
     'tqdm==4.66.5',
     'typing==3.10.0.0',
+    'typing-extensions==4.12.2',
     'typing_extensions==4.12.2',
-    'tzdata==2024a',
     'ucrt==10.0.22621.0',
     'umap-learn==0.5.6',
+    'unicodedata2==15.1.0',
+    'urllib3==2.2.2',
     'vc==14.3',
     'vc14_runtime==14.40.33810',
     'vs2015_runtime==14.40.33810',
     'wheel==0.44.0',
+    'win_inet_pton==1.1.0',
     'xorg-libxau==1.0.11',
     'xorg-libxdmcp==1.1.3',
     'xz==5.2.6',
+    'zipp==3.20.1',
+    'zlib-ng==2.0.7',
+    'zstandard==0.23.0',
     'zstd==1.5.6'
   )
 )

diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml
@@ -3,32 +3,43 @@ channels:
 - bioconda
 - conda-forge
 dependencies:
-- anndata=0.10.9=pyhd8ed1ab_0
-- array-api-compat=1.8=pyhd8ed1ab_0
+- anndata=0.9.2=pyhd8ed1ab_0
+- blosc=1.21.6=h85f69ea_0
 - brotli=1.1.0=hcfcfb64_1
 - brotli-bin=1.1.0=hcfcfb64_1
+- brotli-python=1.1.0=py38hd3f51b4_1
 - bzip2=1.0.8=h2466b09_7
+- c-blosc2=2.12.0=h183a6f4_0
 - ca-certificates=2024.7.4=h56e8100_0
 - cached-property=1.5.2=hd8ed1ab_1
 - cached_property=1.5.2=pyha770c72_1
 - certifi=2024.7.4=pyhd8ed1ab_0
+- cffi=1.17.0=py38h4cb3324_0
+- charset-normalizer=3.3.2=pyhd8ed1ab_0
 - colorama=0.4.6=pyhd8ed1ab_0
-- contourpy=1.3.0=py311h3257749_0
+- contourpy=1.1.1=py38hb1fd069_1
 - cycler=0.12.1=pyhd8ed1ab_0
-- exceptiongroup=1.2.2=pyhd8ed1ab_0
-- fonttools=4.53.1=py311he736701_0
+- fonttools=4.53.1=py38h4cb3324_0
 - freetype=2.12.1=hdaf720e_2
-- get-annotations=0.1.2=pyhd8ed1ab_0
 - glib=2.80.3=h7025463_2
 - glib-tools=2.80.3=h4394cf3_2
 - gst-plugins-base=1.24.6=hb0a98b8_0
 - gstreamer=1.24.6=h5006eae_0
-- h5py=3.11.0=nompi_py311h67016bb_102
+- h2=4.1.0=pyhd8ed1ab_0
+- h5py=3.11.0=nompi_py38hd93224d_102
 - hdf5=1.14.3=nompi_h2b43c12_105
+- hpack=4.0.0=pyh9f0ad1d_0
+- hyperframe=6.0.1=pyhd8ed1ab_0
 - icu=73.2=h63175ca_0
+- idna=3.8=pyhd8ed1ab_0
+- importlib-metadata=8.4.0=pyha770c72_0
+- importlib-resources=6.4.4=pyhd8ed1ab_0
+- importlib_metadata=8.4.0=hd8ed1ab_0
+- importlib_resources=6.4.4=pyhd8ed1ab_0
 - intel-openmp=2024.2.1=h57928b3_1083
+- jinja2=3.0.3=pyhd8ed1ab_0
 - joblib=1.4.2=pyhd8ed1ab_0
-- kiwisolver=1.4.5=py311h3257749_2
+- kiwisolver=1.4.5=py38hb1fd069_1
 - krb5=1.21.3=hdf4eb48_0
 - lcms2=2.16=h67d730c_0
 - legacy-api-wrap=1.4=pyhd8ed1ab_1
@@ -42,7 +53,6 @@ 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
@@ -61,71 +71,91 @@ dependencies:
 - libxcb=1.16=h013a479_1
 - libxml2=2.12.7=h0f24e4e_4
 - libzlib=1.3.1=h2466b09_1
-- llvmlite=0.43.0=py311h7deaa30_0
+- llvmlite=0.41.1=py38h19421c1_0
 - loompy=2.0.16=py_0
+- lz4-c=1.9.4=hcfcfb64_0
 - m2w64-gcc-libgfortran=5.3.0=6
 - m2w64-gcc-libs=5.3.0=7
 - m2w64-gcc-libs-core=5.3.0=7
 - m2w64-gmp=6.1.0=2
 - m2w64-libwinpthread-git=5.0.0.4634.697f757=2
-- matplotlib=3.6.3=py311h1ea47a8_0
-- matplotlib-base=3.6.3=py311h6e989c2_0
+- markupsafe=2.1.5=py38h91455d4_0
+- matplotlib=3.7.2=py38haa244fe_0
+- matplotlib-base=3.7.2=py38h2d9580e_0
 - mkl=2024.1.0=h66d3029_694
 - msys2-conda-epoch=20160418=1
 - munkres=1.0.7=py_1
 - natsort=8.4.0=pyhd8ed1ab_0
-- networkx=3.3=pyhd8ed1ab_1
-- numba=0.60.0=py311h0673bce_0
-- numpy=1.26.4=py311h0b4df5a_0
+- networkx=3.1=pyhd8ed1ab_0
+- numba=0.58.1=py38h4a59444_0
+- numexpr=2.7.3=py38h5d928e2_2
+- numpy=1.24.4=py38h1d91fd2_0
 - openjpeg=2.5.2=h3d672ee_0
 - openssl=3.3.1=h2466b09_3
 - packaging=24.1=pyhd8ed1ab_0
-- pandas=1.5.2=py311hf63dbb6_2
+- pandas=2.0.3=py38hf08cf0d_1
 - patsy=0.5.6=pyhd8ed1ab_0
 - pcre2=10.44=h3d7b363_2
-- pillow=10.4.0=py311h5592be9_0
+- pillow=10.4.0=py38h8d10685_0
 - pip=24.2=pyh8b19718_1
+- platformdirs=4.2.2=pyhd8ed1ab_0
 - ply=3.11=pyhd8ed1ab_2
+- pooch=1.8.2=pyhd8ed1ab_0
 - pthread-stubs=0.4=hcd874cb_1001
 - pthreads-win32=2.9.1=hfa6e2cd_3
+- py-cpuinfo=9.0.0=pyhd8ed1ab_0
+- pycparser=2.22=pyhd8ed1ab_0
 - pynndescent=0.5.13=pyhff2d567_0
-- pyparsing=3.1.4=pyhd8ed1ab_0
-- pyqt=5.15.9=py311h125bc19_5
-- pyqt5-sip=12.12.2=py311h12c1d0e_5
-- python=3.11.9=h631f459_0_cpython
+- pyparsing=3.0.9=pyhd8ed1ab_0
+- pyqt=5.15.9=py38hd6c051e_5
+- pyqt5-sip=12.12.2=py38hd3f51b4_5
+- pysocks=1.7.1=pyh0701188_6
+- pytables=3.8.0=py38h4c0c689_4
+- python=3.8.19=h4de0772_0_cpython
 - python-dateutil=2.9.0=pyhd8ed1ab_0
-- python_abi=3.11=5_cp311
+- python-tzdata=2024.1=pyhd8ed1ab_0
+- python_abi=3.8=5_cp38
 - pytz=2024.1=pyhd8ed1ab_0
 - qt-main=5.15.8=h06adc49_23
-- scanpy=1.10.2=pyhd8ed1ab_0
-- scikit-learn=1.5.1=py311hdcb8d17_0
-- scipy=1.13.1=py311hd4686c6_0
+- requests=2.32.3=pyhd8ed1ab_0
+- scanpy=1.7.2=pyhdfd78af_0
+- scikit-learn=1.3.2=py38h4f736e5_2
+- scipy=1.10.1=py38h1aea9ed_3
 - scvelo=0.2.5=pyhdfd78af_0
 - seaborn=0.13.2=hd8ed1ab_2
 - seaborn-base=0.13.2=pyhd8ed1ab_2
-- session-info=1.0.0=pyhd8ed1ab_0
 - setuptools=72.2.0=pyhd8ed1ab_0
-- sip=6.7.12=py311h12c1d0e_0
+- setuptools-scm=8.1.0=pyhd8ed1ab_0
+- setuptools_scm=8.1.0=hd8ed1ab_0
+- sinfo=0.3.1=py_0
+- sip=6.7.12=py38hd3f51b4_0
 - six=1.16.0=pyh6c4a22f_0
-- statsmodels=0.14.2=py311h0a17f05_0
+- snappy=1.2.1=h23299a8_0
+- statsmodels=0.14.1=py38he7056a7_0
 - stdlib-list=0.10.0=pyhd8ed1ab_0
 - tbb=2021.12.0=hc790b64_4
 - threadpoolctl=3.5.0=pyhc1e730c_0
 - tk=8.6.13=h5226925_1
 - toml=0.10.2=pyhd8ed1ab_0
 - tomli=2.0.1=pyhd8ed1ab_0
-- tornado=6.4.1=py311he736701_1
+- tornado=6.4.1=py38h4cb3324_0
 - tqdm=4.66.5=pyhd8ed1ab_0
 - typing=3.10.0.0=pyhd8ed1ab_1
+- typing-extensions=4.12.2=hd8ed1ab_0
 - typing_extensions=4.12.2=pyha770c72_0
-- tzdata=2024a=h8827d51_1
 - ucrt=10.0.22621.0=h57928b3_0
-- umap-learn=0.5.6=py311h1ea47a8_1
+- umap-learn=0.5.6=py38haa244fe_1
+- unicodedata2=15.1.0=py38h91455d4_0
+- urllib3=2.2.2=pyhd8ed1ab_1
 - vc=14.3=h8a93ad2_20
 - vc14_runtime=14.40.33810=hcc2c482_20
 - vs2015_runtime=14.40.33810=h3bf8584_20
 - wheel=0.44.0=pyhd8ed1ab_0
+- win_inet_pton=1.1.0=pyhd8ed1ab_6
 - xorg-libxau=1.0.11=hcd874cb_0
 - xorg-libxdmcp=1.1.3=hcd874cb_0
 - xz=5.2.6=h8d14728_0
+- zipp=3.20.1=pyhd8ed1ab_0
+- zlib-ng=2.0.7=hcfcfb64_0
+- zstandard=0.23.0=py38hf92978b_0
 - zstd=1.5.6=h0ea2cb4_0