Fix conda environment using micromamba for windows

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.6
-Date: 2024-08-29
+Version: 1.15.7
+Date: 2024-08-30
 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')),
     person("Charlotte", "Soneson", role="aut", email="[email protected]", comment = c(ORCID = '0000-0003-3833-2169')),

NEWS.md

@@ -1,3 +1,7 @@
+# velociraptor 1.15.7
+
+* Update Conda environment using micromamba for Windows. 
+
 # velociraptor 1.15.6
 
 * Update Conda environment to use `anaconda` channel on Linux.

R/basilisk.R

@@ -3,35 +3,41 @@
 .scvelo.dependencies.Windows <- list(
   channels = c("bioconda", "conda-forge"),
   packages = c(
-    'anndata==0.10.5.post1',
-    'array-api-compat==1.6',
-    'blosc==1.21.5',
+    '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',
-    'ca-certificates==2024.2.2',
+    'ca-certificates==2024.7.4',
     'cached-property==1.5.2',
     'cached_property==1.5.2',
-    'certifi==2024.2.2',
+    'certifi==2024.7.4',
+    'cffi==1.17.0',
+    'charset-normalizer==3.3.2',
     'colorama==0.4.6',
-    'contourpy==1.2.1',
+    'contourpy==1.1.1',
     'cycler==0.12.1',
-    'exceptiongroup==1.2.0',
-    'fonttools==4.51.0',
+    'fonttools==4.53.1',
     'freetype==2.12.1',
-    'glib==2.80.2',
-    'glib-tools==2.80.2',
-    'gst-plugins-base==1.24.3',
-    'gstreamer==1.24.3',
+    'glib==2.80.3',
+    'glib-tools==2.80.3',
+    'gst-plugins-base==1.24.6',
+    'gstreamer==1.24.6',
+    'h2==4.1.0',
     'h5py==3.8.0',
     'hdf5==1.14.0',
+    'hpack==4.0.0',
+    'hyperframe==6.0.1',
     'icu==73.2',
-    'importlib-metadata==7.1.0',
-    'importlib_metadata==7.1.0',
-    'intel-openmp==2024.1.0',
+    'idna==3.8',
+    'importlib-metadata==8.4.0',
+    'importlib_metadata==8.4.0',
+    'intel-openmp==2024.2.1',
+    'jinja2==3.0.3',
     'joblib==1.4.2',
     'kiwisolver==1.4.5',
-    'krb5==1.21.2',
+    'krb5==1.21.3',
     'lcms2==2.16',
     'legacy-api-wrap==1.4',
     'lerc==4.0.0',
@@ -41,104 +47,111 @@
     'libbrotlidec==1.1.0',
     'libbrotlienc==1.1.0',
     'libcblas==3.9.0',
-    'libclang13==18.1.5',
-    'libcurl==8.8.0',
-    'libdeflate==1.20',
+    'libclang13==18.1.8',
+    'libcurl==8.9.1',
+    'libdeflate==1.21',
     'libffi==3.4.2',
-    'libglib==2.80.2',
-    'libhwloc==2.10.0',
+    'libglib==2.80.3',
+    'libhwloc==2.11.1',
     'libiconv==1.17',
     'libintl==0.22.5',
     'libintl-devel==0.22.5',
     'libjpeg-turbo==3.0.0',
     'liblapack==3.9.0',
-    'libogg==1.3.4',
+    'libogg==1.3.5',
     'libpng==1.6.43',
-    'libsqlite==3.45.3',
+    'libsqlite==3.46.0',
     'libssh2==1.11.0',
     'libtiff==4.6.0',
     'libvorbis==1.3.7',
     'libwebp-base==1.4.0',
-    'libxcb==1.15',
+    'libxcb==1.16',
     'libxml2==2.12.7',
-    'libzlib==1.2.13',
-    'llvmlite==0.40.1',
+    'libzlib==1.3.1',
+    'llvmlite==0.39.1',
     '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',
+    'markupsafe==2.1.5',
     'matplotlib==3.6.3',
     'matplotlib-base==3.6.3',
     'mkl==2024.1.0',
     'msys2-conda-epoch==20160418',
     'munkres==1.0.7',
     'natsort==8.4.0',
-    'networkx==3.2',
-    'numba==0.57.1',
+    'networkx==3.1',
+    'numba==0.56.4',
     'numexpr==2.7.3',
     'numpy==1.21.1',
     'openjpeg==2.5.2',
-    'openssl==3.3.0',
-    'packaging==24.0',
+    'openssl==3.3.1',
+    'packaging==24.1',
     'pandas==1.5.2',
     'patsy==0.5.6',
-    'pcre2==10.43',
-    'pillow==10.3.0',
-    'pip==24.0',
+    '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',
-    'pynndescent==0.5.12',
-    'pyparsing==3.1.2',
+    'pycparser==2.22',
+    'pynndescent==0.5.13',
+    'pyparsing==3.1.4',
     'pyqt==5.15.9',
     'pyqt5-sip==12.12.2',
+    'pysocks==1.7.1',
     'pytables==3.7.0',
-    'python==3.9.12',
+    'python==3.8.19',
     'python-dateutil==2.9.0',
-    'python_abi==3.9',
+    'python_abi==3.8',
     'pytz==2024.1',
     'qt-main==5.15.8',
+    'requests==2.32.3',
     'scanpy==1.7.2',
-    'scikit-learn==1.5.0',
-    'scipy==1.13.1',
+    'scikit-learn==1.2.2',
+    'scipy==1.10.1',
     'scvelo==0.2.5',
     'seaborn==0.13.2',
     'seaborn-base==0.13.2',
-    'setuptools==70.0.0',
+    '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',
-    'snappy==1.2.0',
-    'sqlite==3.45.3',
-    'statsmodels==0.14.2',
+    'snappy==1.2.1',
+    'statsmodels==0.13.5',
     'stdlib-list==0.10.0',
     'tbb==2021.12.0',
     'threadpoolctl==3.5.0',
     'tk==8.6.13',
     'toml==0.10.2',
     'tomli==2.0.1',
-    'tornado==6.4',
-    'tqdm==4.66.4',
+    'tornado==6.4.1',
+    'tqdm==4.66.5',
     'typing==3.10.0.0',
-    'typing-extensions==4.11.0',
-    'typing_extensions==4.11.0',
-    'tzdata==2024a',
+    'typing-extensions==4.12.2',
+    'typing_extensions==4.12.2',
     'ucrt==10.0.22621.0',
-    'umap-learn==0.5.5',
+    'umap-learn==0.5.6',
     'unicodedata2==15.1.0',
+    'urllib3==2.2.2',
     'vc==14.3',
-    'vc14_runtime==14.38.33135',
-    'vs2015_runtime==14.38.33135',
-    'wheel==0.43.0',
+    '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==3.17.0',
+    'zipp==3.20.1',
+    'zstandard==0.23.0',
     'zstd==1.5.6'
   )
 )

inst/envs/Windows.yaml

@@ -0,0 +1,155 @@
+name: scvelo
+channels:
+- bioconda
+- conda-forge
+dependencies:
+- 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
+- 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=1.1.1=py38hb1fd069_1
+- cycler=0.12.1=pyhd8ed1ab_0
+- fonttools=4.53.1=py38h4cb3324_0
+- freetype=2.12.1=hdaf720e_2
+- 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
+- h2=4.1.0=pyhd8ed1ab_0
+- h5py=3.8.0=nompi_py38h442309b_101
+- hdf5=1.14.0=nompi_h918d9b7_103
+- 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_metadata=8.4.0=hd8ed1ab_0
+- intel-openmp=2024.2.1=h57928b3_1083
+- jinja2=3.0.3=pyhd8ed1ab_0
+- joblib=1.4.2=pyhd8ed1ab_0
+- kiwisolver=1.4.5=py38hb1fd069_1
+- krb5=1.21.3=hdf4eb48_0
+- lcms2=2.16=h67d730c_0
+- legacy-api-wrap=1.4=pyhd8ed1ab_1
+- lerc=4.0.0=h63175ca_0
+- libaec=1.1.3=h63175ca_0
+- libblas=3.9.0=23_win64_mkl
+- libbrotlicommon=1.1.0=hcfcfb64_1
+- libbrotlidec=1.1.0=hcfcfb64_1
+- libbrotlienc=1.1.0=hcfcfb64_1
+- libcblas=3.9.0=23_win64_mkl
+- libclang13=18.1.8=default_ha5278ca_3
+- libcurl=8.9.1=h18fefc2_0
+- libdeflate=1.21=h2466b09_0
+- libffi=3.4.2=h8ffe710_5
+- libglib=2.80.3=h7025463_2
+- libhwloc=2.11.1=default_h8125262_1000
+- libiconv=1.17=hcfcfb64_2
+- libintl=0.22.5=h5728263_3
+- libintl-devel=0.22.5=h5728263_3
+- libjpeg-turbo=3.0.0=hcfcfb64_1
+- liblapack=3.9.0=23_win64_mkl
+- libogg=1.3.5=h2466b09_0
+- libpng=1.6.43=h19919ed_0
+- libsqlite=3.46.0=h2466b09_0
+- libssh2=1.11.0=h7dfc565_0
+- libtiff=4.6.0=hb151862_4
+- libvorbis=1.3.7=h0e60522_0
+- libwebp-base=1.4.0=hcfcfb64_0
+- libxcb=1.16=h013a479_1
+- libxml2=2.12.7=h0f24e4e_4
+- libzlib=1.3.1=h2466b09_1
+- llvmlite=0.39.1=py38h19421c1_1
+- 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
+- markupsafe=2.1.5=py38h91455d4_0
+- matplotlib=3.6.3=py38haa244fe_0
+- matplotlib-base=3.6.3=py38h528a6c7_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=3.1=pyhd8ed1ab_0
+- numba=0.56.4=py38h3873db4_0
+- numexpr=2.7.3=py38h5d928e2_2
+- numpy=1.21.1=py38h09042cb_0
+- openjpeg=2.5.2=h3d672ee_0
+- openssl=3.3.1=h2466b09_3
+- packaging=24.1=pyhd8ed1ab_0
+- pandas=1.5.2=py38h5846ac1_2
+- patsy=0.5.6=pyhd8ed1ab_0
+- pcre2=10.44=h3d7b363_2
+- 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
+- pycparser=2.22=pyhd8ed1ab_0
+- pynndescent=0.5.13=pyhff2d567_0
+- pyparsing=3.1.4=pyhd8ed1ab_0
+- pyqt=5.15.9=py38hd6c051e_5
+- pyqt5-sip=12.12.2=py38hd3f51b4_5
+- pysocks=1.7.1=pyh0701188_6
+- pytables=3.7.0=py38hdec0819_4
+- python=3.8.19=h4de0772_0_cpython
+- python-dateutil=2.9.0=pyhd8ed1ab_0
+- python_abi=3.8=5_cp38
+- pytz=2024.1=pyhd8ed1ab_0
+- qt-main=5.15.8=h06adc49_23
+- requests=2.32.3=pyhd8ed1ab_0
+- scanpy=1.7.2=pyhdfd78af_0
+- scikit-learn=1.2.2=py38h42e183d_1
+- scipy=1.10.1=py38h0f6ee2a_0
+- scvelo=0.2.5=pyhdfd78af_0
+- seaborn=0.13.2=hd8ed1ab_2
+- seaborn-base=0.13.2=pyhd8ed1ab_2
+- setuptools=72.2.0=pyhd8ed1ab_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
+- snappy=1.2.1=h23299a8_0
+- statsmodels=0.13.5=py38hbaf524b_2
+- 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=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
+- ucrt=10.0.22621.0=h57928b3_0
+- 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
+- zstandard=0.23.0=py38hf92978b_0
+- zstd=1.5.6=h0ea2cb4_0