From e33d47470022b06b3bdea26f86569d6cde7df254 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 23 Aug 2024 09:15:56 +0100 Subject: [PATCH 01/14] update environment for windows using micromamba --- R/basilisk.R | 127 +++++++---------- inst/envs/Windows_20240524.txt | 249 +++++++++++++++------------------ inst/envs/format_scvelo_deps.R | 2 +- 3 files changed, 161 insertions(+), 217 deletions(-) diff --git a/R/basilisk.R b/R/basilisk.R index bd120ab..c0ddda7 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -1,37 +1,31 @@ ## Windows ---- .scvelo.dependencies.Windows <- list( - channels = c("bioconda", "conda-forge"), + channels = c("conda-forge", "bioconda"), packages = c( - 'anndata==0.10.5.post1', - 'array-api-compat==1.6', - 'blosc==1.21.5', + 'anndata==0.10.8', + 'array-api-compat==1.8', 'brotli==1.1.0', 'brotli-bin==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', + 'click==8.1.7', 'colorama==0.4.6', 'contourpy==1.2.1', 'cycler==0.12.1', - 'exceptiongroup==1.2.0', - 'fonttools==4.51.0', + 'exceptiongroup==1.2.2', + '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', - 'h5py==3.8.0', - 'hdf5==1.14.0', - 'icu==73.2', - 'importlib-metadata==7.1.0', - 'importlib_metadata==7.1.0', - 'intel-openmp==2024.1.0', + 'get-annotations==0.1.2', + 'h5py==3.11.0', + 'hdf5==1.14.3', + 'intel-openmp==2024.2.1', '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 +35,81 @@ 'libbrotlidec==1.1.0', 'libbrotlienc==1.1.0', 'libcblas==3.9.0', - 'libclang13==18.1.5', - 'libcurl==8.8.0', - 'libdeflate==1.20', + 'libcurl==8.9.1', + 'libdeflate==1.21', + 'libexpat==2.6.2', 'libffi==3.4.2', - 'libglib==2.80.2', - 'libhwloc==2.10.0', + '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', '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', - 'loompy==2.0.16', - 'lz4-c==1.9.4', + 'libzlib==1.3.1', + 'llvmlite==0.43.0', + 'loompy==3.0.6', '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', + 'matplotlib-base==3.9.2', 'mkl==2024.1.0', 'msys2-conda-epoch==20160418', - 'munkres==1.0.7', + 'munkres==1.1.4', 'natsort==8.4.0', - 'networkx==3.2', - 'numba==0.57.1', - 'numexpr==2.7.3', - 'numpy==1.21.1', + 'networkx==3.3', + 'numba==0.60.0', + 'numpy==1.26.4', + 'numpy_groupies==0.11.2', 'openjpeg==2.5.2', - 'openssl==3.3.0', - 'packaging==24.0', - 'pandas==1.5.2', + 'openssl==3.3.1', + 'packaging==24.1', + 'pandas==2.2.2', 'patsy==0.5.6', - 'pcre2==10.43', - 'pillow==10.3.0', - 'pip==24.0', - 'ply==3.11', + 'pillow==10.4.0', + 'pip==24.2', 'pthread-stubs==0.4', 'pthreads-win32==2.9.1', - 'pynndescent==0.5.12', + 'pynndescent==0.5.13', 'pyparsing==3.1.2', - 'pyqt==5.15.9', - 'pyqt5-sip==12.12.2', - 'pytables==3.7.0', - 'python==3.9.12', + 'python==3.12.5', 'python-dateutil==2.9.0', - 'python_abi==3.9', + 'python-tzdata==2024.1', + 'python_abi==3.12', 'pytz==2024.1', - 'qt-main==5.15.8', - 'scanpy==1.7.2', - 'scikit-learn==1.5.0', - 'scipy==1.13.1', + 'qhull==2020.2', + 'scanpy==1.10.2', + 'scikit-learn==1.5.1', + 'scipy==1.14.1', 'scvelo==0.2.5', 'seaborn==0.13.2', 'seaborn-base==0.13.2', - 'setuptools==70.0.0', - 'setuptools-scm==8.1.0', - 'setuptools_scm==8.1.0', - 'sinfo==0.3.1', - 'sip==6.7.12', + 'session-info==1.0.0', + 'setuptools==72.2.0', 'six==1.16.0', - 'snappy==1.2.0', - 'sqlite==3.45.3', 'statsmodels==0.14.2', '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', - 'typing==3.10.0.0', - 'typing-extensions==4.11.0', - 'typing_extensions==4.11.0', + 'tqdm==4.66.5', + 'typing_extensions==4.12.2', 'tzdata==2024a', 'ucrt==10.0.22621.0', - 'umap-learn==0.5.5', - 'unicodedata2==15.1.0', + 'umap-learn==0.5.6', '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', 'xorg-libxau==1.0.11', 'xorg-libxdmcp==1.1.3', 'xz==5.2.6', - 'zipp==3.17.0', 'zstd==1.5.6' ) ) diff --git a/inst/envs/Windows_20240524.txt b/inst/envs/Windows_20240524.txt index 56ab4da..2ac3fb1 100644 --- a/inst/envs/Windows_20240524.txt +++ b/inst/envs/Windows_20240524.txt @@ -1,138 +1,111 @@ -# Name Version Build Channel -anndata 0.10.5.post1 pyhd8ed1ab_0 conda-forge -array-api-compat 1.6 pyhd8ed1ab_0 conda-forge -blosc 1.21.5 hbd69f2e_1 conda-forge -brotli 1.1.0 hcfcfb64_1 conda-forge -brotli-bin 1.1.0 hcfcfb64_1 conda-forge -bzip2 1.0.8 hcfcfb64_5 conda-forge -ca-certificates 2024.2.2 h56e8100_0 conda-forge -cached-property 1.5.2 hd8ed1ab_1 conda-forge -cached_property 1.5.2 pyha770c72_1 conda-forge -certifi 2024.2.2 pyhd8ed1ab_0 conda-forge -colorama 0.4.6 pyhd8ed1ab_0 conda-forge -contourpy 1.2.1 py39h1f6ef14_0 conda-forge -cycler 0.12.1 pyhd8ed1ab_0 conda-forge -exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge -fonttools 4.51.0 py39ha55989b_0 conda-forge -freetype 2.12.1 hdaf720e_2 conda-forge -glib 2.80.2 h0df6a38_0 conda-forge -glib-tools 2.80.2 h2f9d560_0 conda-forge -gst-plugins-base 1.24.3 hba88be7_0 conda-forge -gstreamer 1.24.3 h5006eae_0 conda-forge -h5py 3.8.0 nompi_py39h8a0c37c_101 conda-forge -hdf5 1.14.0 nompi_h918d9b7_103 conda-forge -icu 73.2 h63175ca_0 conda-forge -importlib-metadata 7.1.0 pyha770c72_0 conda-forge -importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge -intel-openmp 2024.1.0 h57928b3_965 conda-forge -joblib 1.4.2 pyhd8ed1ab_0 conda-forge -kiwisolver 1.4.5 py39h1f6ef14_1 conda-forge -krb5 1.21.2 heb0366b_0 conda-forge -lcms2 2.16 h67d730c_0 conda-forge -legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge -lerc 4.0.0 h63175ca_0 conda-forge -libaec 1.1.3 h63175ca_0 conda-forge -libblas 3.9.0 22_win64_mkl conda-forge -libbrotlicommon 1.1.0 hcfcfb64_1 conda-forge -libbrotlidec 1.1.0 hcfcfb64_1 conda-forge -libbrotlienc 1.1.0 hcfcfb64_1 conda-forge -libcblas 3.9.0 22_win64_mkl conda-forge -libclang13 18.1.5 default_hf64faad_0 conda-forge -libcurl 8.8.0 hd5e4a3a_0 conda-forge -libdeflate 1.20 hcfcfb64_0 conda-forge -libffi 3.4.2 h8ffe710_5 conda-forge -libglib 2.80.2 h0df6a38_0 conda-forge -libhwloc 2.10.0 default_h8125262_1001 conda-forge -libiconv 1.17 hcfcfb64_2 conda-forge -libintl 0.22.5 h5728263_2 conda-forge -libintl-devel 0.22.5 h5728263_2 conda-forge -libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge -liblapack 3.9.0 22_win64_mkl conda-forge -libogg 1.3.4 h8ffe710_1 conda-forge -libpng 1.6.43 h19919ed_0 conda-forge -libsqlite 3.45.3 hcfcfb64_0 conda-forge -libssh2 1.11.0 h7dfc565_0 conda-forge -libtiff 4.6.0 hddb2be6_3 conda-forge -libvorbis 1.3.7 h0e60522_0 conda-forge -libwebp-base 1.4.0 hcfcfb64_0 conda-forge -libxcb 1.15 hcd874cb_0 conda-forge -libxml2 2.12.7 h283a6d9_0 conda-forge -libzlib 1.2.13 hcfcfb64_5 conda-forge -llvmlite 0.40.1 py39hd28a505_0 conda-forge -loompy 2.0.16 py_0 bioconda -lz4-c 1.9.4 hcfcfb64_0 conda-forge -m2w64-gcc-libgfortran 5.3.0 6 conda-forge -m2w64-gcc-libs 5.3.0 7 conda-forge -m2w64-gcc-libs-core 5.3.0 7 conda-forge -m2w64-gmp 6.1.0 2 conda-forge -m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge -matplotlib 3.6.3 py39hcbf5309_0 conda-forge -matplotlib-base 3.6.3 py39haf65ace_0 conda-forge -mkl 2024.1.0 h66d3029_692 conda-forge -msys2-conda-epoch 20160418 1 conda-forge -munkres 1.0.7 py_1 bioconda -natsort 8.4.0 pyhd8ed1ab_0 conda-forge -networkx 3.2 pyhd8ed1ab_0 conda-forge -numba 0.57.1 py39hadaa1c4_0 conda-forge -numexpr 2.7.3 py39h2e25243_2 conda-forge -numpy 1.21.1 py39h6635163_0 conda-forge -openjpeg 2.5.2 h3d672ee_0 conda-forge -openssl 3.3.0 h2466b09_3 conda-forge -packaging 24.0 pyhd8ed1ab_0 conda-forge -pandas 1.5.2 py39h2ba5b7c_2 conda-forge -patsy 0.5.6 pyhd8ed1ab_0 conda-forge -pcre2 10.43 h17e33f8_0 conda-forge -pillow 10.3.0 py39h9ee4981_0 conda-forge -pip 24.0 pyhd8ed1ab_0 conda-forge -ply 3.11 pyhd8ed1ab_2 conda-forge -pthread-stubs 0.4 hcd874cb_1001 conda-forge -pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge -pynndescent 0.5.12 pyhca7485f_0 conda-forge -pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge -pyqt 5.15.9 py39hb77abff_5 conda-forge -pyqt5-sip 12.12.2 py39h99910a6_5 conda-forge -pytables 3.7.0 py39h33f4363_4 conda-forge -python 3.9.12 hcf16a7b_1_cpython conda-forge -python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge -python_abi 3.9 4_cp39 conda-forge -pytz 2024.1 pyhd8ed1ab_0 conda-forge -qt-main 5.15.8 hcef0176_21 conda-forge -scanpy 1.7.2 pyhdfd78af_0 bioconda -scikit-learn 1.5.0 py39hdd013cc_1 conda-forge -scipy 1.13.1 py39h1a10956_0 conda-forge -scvelo 0.2.5 pyhdfd78af_0 bioconda -seaborn 0.13.2 hd8ed1ab_2 conda-forge -seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge -setuptools 70.0.0 pyhd8ed1ab_0 conda-forge -setuptools-scm 8.1.0 pyhd8ed1ab_0 conda-forge -setuptools_scm 8.1.0 hd8ed1ab_0 conda-forge -sinfo 0.3.1 py_0 conda-forge -sip 6.7.12 py39h99910a6_0 conda-forge -six 1.16.0 pyh6c4a22f_0 conda-forge -snappy 1.2.0 hfb803bf_1 conda-forge -sqlite 3.45.3 hcfcfb64_0 conda-forge -statsmodels 0.14.2 py39h4b0a98a_0 conda-forge -stdlib-list 0.10.0 pyhd8ed1ab_0 conda-forge -tbb 2021.12.0 hc790b64_1 conda-forge -threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge -tk 8.6.13 h5226925_1 conda-forge -toml 0.10.2 pyhd8ed1ab_0 conda-forge -tomli 2.0.1 pyhd8ed1ab_0 conda-forge -tornado 6.4 py39ha55989b_0 conda-forge -tqdm 4.66.4 pyhd8ed1ab_0 conda-forge -typing 3.10.0.0 pyhd8ed1ab_1 conda-forge -typing-extensions 4.11.0 hd8ed1ab_0 conda-forge -typing_extensions 4.11.0 pyha770c72_0 conda-forge -tzdata 2024a h0c530f3_0 conda-forge -ucrt 10.0.22621.0 h57928b3_0 conda-forge -umap-learn 0.5.5 py39hcbf5309_1 conda-forge -unicodedata2 15.1.0 py39ha55989b_0 conda-forge -vc 14.3 ha32ba9b_20 conda-forge -vc14_runtime 14.38.33135 h835141b_20 conda-forge -vs2015_runtime 14.38.33135 h22015db_20 conda-forge -wheel 0.43.0 pyhd8ed1ab_1 conda-forge -xorg-libxau 1.0.11 hcd874cb_0 conda-forge -xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge -xz 5.2.6 h8d14728_0 conda-forge -zipp 3.17.0 pyhd8ed1ab_0 conda-forge -zstd 1.5.6 h0ea2cb4_0 conda-forge + Name Version Build Channel +------------------------------------------------------------------------------------- + anndata 0.10.8 pyhd8ed1ab_0 conda-forge + array-api-compat 1.8 pyhd8ed1ab_0 conda-forge + brotli 1.1.0 hcfcfb64_1 conda-forge + brotli-bin 1.1.0 hcfcfb64_1 conda-forge + bzip2 1.0.8 h2466b09_7 conda-forge + ca-certificates 2024.7.4 h56e8100_0 conda-forge + cached-property 1.5.2 hd8ed1ab_1 conda-forge + cached_property 1.5.2 pyha770c72_1 conda-forge + certifi 2024.7.4 pyhd8ed1ab_0 conda-forge + click 8.1.7 win_pyh7428d3b_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_0 conda-forge + contourpy 1.2.1 py312h0d7def4_0 conda-forge + cycler 0.12.1 pyhd8ed1ab_0 conda-forge + exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge + fonttools 4.53.1 py312h4389bb4_0 conda-forge + freetype 2.12.1 hdaf720e_2 conda-forge + get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge + h5py 3.11.0 nompi_py312ha036244_102 conda-forge + hdf5 1.14.3 nompi_h2b43c12_105 conda-forge + intel-openmp 2024.2.1 h57928b3_1083 conda-forge + joblib 1.4.2 pyhd8ed1ab_0 conda-forge + kiwisolver 1.4.5 py312h0d7def4_1 conda-forge + krb5 1.21.3 hdf4eb48_0 conda-forge + lcms2 2.16 h67d730c_0 conda-forge + legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge + lerc 4.0.0 h63175ca_0 conda-forge + libaec 1.1.3 h63175ca_0 conda-forge + libblas 3.9.0 23_win64_mkl conda-forge + libbrotlicommon 1.1.0 hcfcfb64_1 conda-forge + libbrotlidec 1.1.0 hcfcfb64_1 conda-forge + libbrotlienc 1.1.0 hcfcfb64_1 conda-forge + libcblas 3.9.0 23_win64_mkl conda-forge + libcurl 8.9.1 h18fefc2_0 conda-forge + libdeflate 1.21 h2466b09_0 conda-forge + libexpat 2.6.2 h63175ca_0 conda-forge + libffi 3.4.2 h8ffe710_5 conda-forge + libhwloc 2.11.1 default_h8125262_1000 conda-forge + libiconv 1.17 hcfcfb64_2 conda-forge + libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge + liblapack 3.9.0 23_win64_mkl conda-forge + libpng 1.6.43 h19919ed_0 conda-forge + libsqlite 3.46.0 h2466b09_0 conda-forge + libssh2 1.11.0 h7dfc565_0 conda-forge + libtiff 4.6.0 hb151862_4 conda-forge + libwebp-base 1.4.0 hcfcfb64_0 conda-forge + libxcb 1.16 hcd874cb_0 conda-forge + libxml2 2.12.7 h0f24e4e_4 conda-forge + libzlib 1.3.1 h2466b09_1 conda-forge + llvmlite 0.43.0 py312h1f7db74_0 conda-forge + loompy 3.0.6 py_0 conda-forge + m2w64-gcc-libgfortran 5.3.0 6 conda-forge + m2w64-gcc-libs 5.3.0 7 conda-forge + m2w64-gcc-libs-core 5.3.0 7 conda-forge + m2w64-gmp 6.1.0 2 conda-forge + m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge + matplotlib-base 3.9.2 py312h90004f6_0 conda-forge + mkl 2024.1.0 h66d3029_694 conda-forge + msys2-conda-epoch 20160418 1 conda-forge + munkres 1.1.4 pyh9f0ad1d_0 conda-forge + natsort 8.4.0 pyhd8ed1ab_0 conda-forge + networkx 3.3 pyhd8ed1ab_1 conda-forge + numba 0.60.0 py312hcccf92d_0 conda-forge + numpy 1.26.4 py312h8753938_0 conda-forge + numpy_groupies 0.11.2 pyhd8ed1ab_0 conda-forge + openjpeg 2.5.2 h3d672ee_0 conda-forge + openssl 3.3.1 h2466b09_2 conda-forge + packaging 24.1 pyhd8ed1ab_0 conda-forge + pandas 2.2.2 py312h72972c8_1 conda-forge + patsy 0.5.6 pyhd8ed1ab_0 conda-forge + pillow 10.4.0 py312h381445a_0 conda-forge + pip 24.2 pyhd8ed1ab_0 conda-forge + pthread-stubs 0.4 hcd874cb_1001 conda-forge + pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge + pynndescent 0.5.13 pyhff2d567_0 conda-forge + pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge + python 3.12.5 h889d299_0_cpython conda-forge + python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge + python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge + python_abi 3.12 5_cp312 conda-forge + pytz 2024.1 pyhd8ed1ab_0 conda-forge + qhull 2020.2 hc790b64_5 conda-forge + scanpy 1.10.2 pyhd8ed1ab_0 conda-forge + scikit-learn 1.5.1 py312h816cc57_0 conda-forge + scipy 1.14.1 py312h1f4e10d_0 conda-forge + scvelo 0.2.5 pyhdfd78af_0 bioconda + seaborn 0.13.2 hd8ed1ab_2 conda-forge + seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge + session-info 1.0.0 pyhd8ed1ab_0 conda-forge + setuptools 72.2.0 pyhd8ed1ab_0 conda-forge + six 1.16.0 pyh6c4a22f_0 conda-forge + statsmodels 0.14.2 py312h1a27103_0 conda-forge + stdlib-list 0.10.0 pyhd8ed1ab_0 conda-forge + tbb 2021.12.0 hc790b64_3 conda-forge + threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge + tk 8.6.13 h5226925_1 conda-forge + tqdm 4.66.5 pyhd8ed1ab_0 conda-forge + typing_extensions 4.12.2 pyha770c72_0 conda-forge + tzdata 2024a h0c530f3_0 conda-forge + ucrt 10.0.22621.0 h57928b3_0 conda-forge + umap-learn 0.5.6 py312h2e8e312_1 conda-forge + vc 14.3 h8a93ad2_20 conda-forge + vc14_runtime 14.40.33810 ha82c5b3_20 conda-forge + vs2015_runtime 14.40.33810 h3bf8584_20 conda-forge + wheel 0.44.0 pyhd8ed1ab_0 conda-forge + xorg-libxau 1.0.11 hcd874cb_0 conda-forge + xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge + xz 5.2.6 h8d14728_0 conda-forge + zstd 1.5.6 h0ea2cb4_0 conda-forge + \ No newline at end of file diff --git a/inst/envs/format_scvelo_deps.R b/inst/envs/format_scvelo_deps.R index 2f3da40..291a404 100644 --- a/inst/envs/format_scvelo_deps.R +++ b/inst/envs/format_scvelo_deps.R @@ -1,7 +1,7 @@ library(dplyr) library(tidyr) -pkg_info <- read.table("Linux_20240523.txt", skip = 2) +pkg_info <- read.table("Windows_20240524.txt", skip = 2) pkg_specs <- pkg_info %>% as_tibble() %>% unite("spec", V1, V2, sep = "==") %>% From 14b87edf75eb76de5cd3859924b53b13db9aab0a Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 23 Aug 2024 09:47:11 +0100 Subject: [PATCH 02/14] try Windows environment resolved using micromamba --- DESCRIPTION | 2 +- R/basilisk.R | 106 +++++++++---- inst/envs/Windows_20240524.txt | 273 +++++++++++++++++++-------------- 3 files changed, 242 insertions(+), 139 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d664f97..59d6261 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.5 +Version: 1.15.6 Date: 2024-08-23 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 index c0ddda7..846b5d4 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -3,113 +3,165 @@ .scvelo.dependencies.Windows <- list( channels = c("conda-forge", "bioconda"), packages = c( - 'anndata==0.10.8', + 'anndata==0.9.2', 'array-api-compat==1.8', 'brotli==1.1.0', 'brotli-bin==1.1.0', + 'brotli-python==1.1.0', 'bzip2==1.0.8', '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', 'click==8.1.7', 'colorama==0.4.6', - 'contourpy==1.2.1', + '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', - 'h5py==3.11.0', - 'hdf5==1.14.3', + 'gettext==0.22.5', + 'gettext-tools==0.22.5', + 'glib==2.80.2', + 'glib-tools==2.80.2', + 'gst-plugins-base==1.21.3', + 'gstreamer==1.21.3', + 'h2==4.1.0', + 'h5py==3.9.0', + 'hdf5==1.14.0', + 'hpack==4.0.0', + 'hyperframe==6.0.1', + 'icu==70.1', + 'idna==3.7', + 'importlib-metadata==8.4.0', + 'importlib-resources==6.4.4', + 'importlib_resources==6.4.4', 'intel-openmp==2024.2.1', 'joblib==1.4.2', + 'jpeg==9e', 'kiwisolver==1.4.5', - 'krb5==1.21.3', - 'lcms2==2.16', + 'krb5==1.20.1', + 'lcms2==2.12', 'legacy-api-wrap==1.4', 'lerc==4.0.0', 'libaec==1.1.3', + 'libasprintf==0.22.5', + 'libasprintf-devel==0.22.5', 'libblas==3.9.0', 'libbrotlicommon==1.1.0', 'libbrotlidec==1.1.0', 'libbrotlienc==1.1.0', 'libcblas==3.9.0', - 'libcurl==8.9.1', + 'libclang==15.0.7', + 'libclang13==15.0.7', + 'libcurl==8.1.2', 'libdeflate==1.21', 'libexpat==2.6.2', 'libffi==3.4.2', + 'libgettextpo==0.22.5', + 'libgettextpo-devel==0.22.5', + 'libglib==2.80.2', 'libhwloc==2.11.1', 'libiconv==1.17', - 'libjpeg-turbo==3.0.0', + 'libintl==0.22.5', + 'libintl-devel==0.22.5', + 'libjpeg-turbo==2.1.4', 'liblapack==3.9.0', + 'libogg==1.3.5', 'libpng==1.6.43', 'libsqlite==3.46.0', - 'libssh2==1.11.0', - 'libtiff==4.6.0', + 'libssh2==1.10.0', + 'libtiff==4.2.0', + 'libvorbis==1.3.7', 'libwebp-base==1.4.0', 'libxcb==1.16', 'libxml2==2.12.7', - 'libzlib==1.3.1', - 'llvmlite==0.43.0', + 'libzlib==1.2.13', + 'llvmlite==0.41.1', 'loompy==3.0.6', '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-base==3.9.2', + 'matplotlib==3.7.2', + 'matplotlib-base==3.7.2', 'mkl==2024.1.0', 'msys2-conda-epoch==20160418', 'munkres==1.1.4', 'natsort==8.4.0', - 'networkx==3.3', - 'numba==0.60.0', - 'numpy==1.26.4', - 'numpy_groupies==0.11.2', - 'openjpeg==2.5.2', - 'openssl==3.3.1', + 'networkx==3.1', + 'numba==0.58.1', + 'numpy==1.24.4', + 'numpy_groupies==0.9.22', + 'olefile==0.47', + 'openjpeg==2.4.0', + 'openssl==1.1.1w', 'packaging==24.1', - 'pandas==2.2.2', + 'pandas==2.0.3', 'patsy==0.5.6', - 'pillow==10.4.0', + 'pcre2==10.43', + 'pillow==8.2.0', 'pip==24.2', + 'platformdirs==4.2.2', + 'ply==3.11', + 'pooch==1.8.2', 'pthread-stubs==0.4', 'pthreads-win32==2.9.1', + 'pycparser==2.22', 'pynndescent==0.5.13', - 'pyparsing==3.1.2', - 'python==3.12.5', + 'pyparsing==3.0.9', + 'pyqt==5.15.7', + 'pyqt5-sip==12.11.0', + 'pysocks==1.7.1', + 'python==3.8.0', 'python-dateutil==2.9.0', 'python-tzdata==2024.1', - 'python_abi==3.12', + 'python_abi==3.8', 'pytz==2024.1', 'qhull==2020.2', + 'qt-main==5.15.6', + 'requests==2.32.3', 'scanpy==1.10.2', - 'scikit-learn==1.5.1', - 'scipy==1.14.1', + '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', + 'sip==6.7.12', 'six==1.16.0', - 'statsmodels==0.14.2', + 'sqlite==3.46.0', + 'statsmodels==0.14.1', '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==6.4.1', 'tqdm==4.66.5', '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==3.20.0', + 'zlib==1.2.13', + 'zstandard==0.23.0', 'zstd==1.5.6' ) ) diff --git a/inst/envs/Windows_20240524.txt b/inst/envs/Windows_20240524.txt index 2ac3fb1..91777d5 100644 --- a/inst/envs/Windows_20240524.txt +++ b/inst/envs/Windows_20240524.txt @@ -1,111 +1,162 @@ - Name Version Build Channel -------------------------------------------------------------------------------------- - anndata 0.10.8 pyhd8ed1ab_0 conda-forge - array-api-compat 1.8 pyhd8ed1ab_0 conda-forge - brotli 1.1.0 hcfcfb64_1 conda-forge - brotli-bin 1.1.0 hcfcfb64_1 conda-forge - bzip2 1.0.8 h2466b09_7 conda-forge - ca-certificates 2024.7.4 h56e8100_0 conda-forge - cached-property 1.5.2 hd8ed1ab_1 conda-forge - cached_property 1.5.2 pyha770c72_1 conda-forge - certifi 2024.7.4 pyhd8ed1ab_0 conda-forge - click 8.1.7 win_pyh7428d3b_0 conda-forge - colorama 0.4.6 pyhd8ed1ab_0 conda-forge - contourpy 1.2.1 py312h0d7def4_0 conda-forge - cycler 0.12.1 pyhd8ed1ab_0 conda-forge - exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge - fonttools 4.53.1 py312h4389bb4_0 conda-forge - freetype 2.12.1 hdaf720e_2 conda-forge - get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge - h5py 3.11.0 nompi_py312ha036244_102 conda-forge - hdf5 1.14.3 nompi_h2b43c12_105 conda-forge - intel-openmp 2024.2.1 h57928b3_1083 conda-forge - joblib 1.4.2 pyhd8ed1ab_0 conda-forge - kiwisolver 1.4.5 py312h0d7def4_1 conda-forge - krb5 1.21.3 hdf4eb48_0 conda-forge - lcms2 2.16 h67d730c_0 conda-forge - legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge - lerc 4.0.0 h63175ca_0 conda-forge - libaec 1.1.3 h63175ca_0 conda-forge - libblas 3.9.0 23_win64_mkl conda-forge - libbrotlicommon 1.1.0 hcfcfb64_1 conda-forge - libbrotlidec 1.1.0 hcfcfb64_1 conda-forge - libbrotlienc 1.1.0 hcfcfb64_1 conda-forge - libcblas 3.9.0 23_win64_mkl conda-forge - libcurl 8.9.1 h18fefc2_0 conda-forge - libdeflate 1.21 h2466b09_0 conda-forge - libexpat 2.6.2 h63175ca_0 conda-forge - libffi 3.4.2 h8ffe710_5 conda-forge - libhwloc 2.11.1 default_h8125262_1000 conda-forge - libiconv 1.17 hcfcfb64_2 conda-forge - libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge - liblapack 3.9.0 23_win64_mkl conda-forge - libpng 1.6.43 h19919ed_0 conda-forge - libsqlite 3.46.0 h2466b09_0 conda-forge - libssh2 1.11.0 h7dfc565_0 conda-forge - libtiff 4.6.0 hb151862_4 conda-forge - libwebp-base 1.4.0 hcfcfb64_0 conda-forge - libxcb 1.16 hcd874cb_0 conda-forge - libxml2 2.12.7 h0f24e4e_4 conda-forge - libzlib 1.3.1 h2466b09_1 conda-forge - llvmlite 0.43.0 py312h1f7db74_0 conda-forge - loompy 3.0.6 py_0 conda-forge - m2w64-gcc-libgfortran 5.3.0 6 conda-forge - m2w64-gcc-libs 5.3.0 7 conda-forge - m2w64-gcc-libs-core 5.3.0 7 conda-forge - m2w64-gmp 6.1.0 2 conda-forge - m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge - matplotlib-base 3.9.2 py312h90004f6_0 conda-forge - mkl 2024.1.0 h66d3029_694 conda-forge - msys2-conda-epoch 20160418 1 conda-forge - munkres 1.1.4 pyh9f0ad1d_0 conda-forge - natsort 8.4.0 pyhd8ed1ab_0 conda-forge - networkx 3.3 pyhd8ed1ab_1 conda-forge - numba 0.60.0 py312hcccf92d_0 conda-forge - numpy 1.26.4 py312h8753938_0 conda-forge - numpy_groupies 0.11.2 pyhd8ed1ab_0 conda-forge - openjpeg 2.5.2 h3d672ee_0 conda-forge - openssl 3.3.1 h2466b09_2 conda-forge - packaging 24.1 pyhd8ed1ab_0 conda-forge - pandas 2.2.2 py312h72972c8_1 conda-forge - patsy 0.5.6 pyhd8ed1ab_0 conda-forge - pillow 10.4.0 py312h381445a_0 conda-forge - pip 24.2 pyhd8ed1ab_0 conda-forge - pthread-stubs 0.4 hcd874cb_1001 conda-forge - pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge - pynndescent 0.5.13 pyhff2d567_0 conda-forge - pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge - python 3.12.5 h889d299_0_cpython conda-forge - python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge - python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge - python_abi 3.12 5_cp312 conda-forge - pytz 2024.1 pyhd8ed1ab_0 conda-forge - qhull 2020.2 hc790b64_5 conda-forge - scanpy 1.10.2 pyhd8ed1ab_0 conda-forge - scikit-learn 1.5.1 py312h816cc57_0 conda-forge - scipy 1.14.1 py312h1f4e10d_0 conda-forge - scvelo 0.2.5 pyhdfd78af_0 bioconda - seaborn 0.13.2 hd8ed1ab_2 conda-forge - seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge - session-info 1.0.0 pyhd8ed1ab_0 conda-forge - setuptools 72.2.0 pyhd8ed1ab_0 conda-forge - six 1.16.0 pyh6c4a22f_0 conda-forge - statsmodels 0.14.2 py312h1a27103_0 conda-forge - stdlib-list 0.10.0 pyhd8ed1ab_0 conda-forge - tbb 2021.12.0 hc790b64_3 conda-forge - threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge - tk 8.6.13 h5226925_1 conda-forge - tqdm 4.66.5 pyhd8ed1ab_0 conda-forge - typing_extensions 4.12.2 pyha770c72_0 conda-forge - tzdata 2024a h0c530f3_0 conda-forge - ucrt 10.0.22621.0 h57928b3_0 conda-forge - umap-learn 0.5.6 py312h2e8e312_1 conda-forge - vc 14.3 h8a93ad2_20 conda-forge - vc14_runtime 14.40.33810 ha82c5b3_20 conda-forge - vs2015_runtime 14.40.33810 h3bf8584_20 conda-forge - wheel 0.44.0 pyhd8ed1ab_0 conda-forge - xorg-libxau 1.0.11 hcd874cb_0 conda-forge - xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge - xz 5.2.6 h8d14728_0 conda-forge - zstd 1.5.6 h0ea2cb4_0 conda-forge - \ No newline at end of file + Name Version Build Channel +------------------------------------------------------------------------------------ + anndata 0.9.2 pyhd8ed1ab_0 conda-forge + array-api-compat 1.8 pyhd8ed1ab_0 conda-forge + brotli 1.1.0 hcfcfb64_1 conda-forge + brotli-bin 1.1.0 hcfcfb64_1 conda-forge + brotli-python 1.1.0 py38hd3f51b4_1 conda-forge + bzip2 1.0.8 h2466b09_7 conda-forge + ca-certificates 2024.7.4 h56e8100_0 conda-forge + cached-property 1.5.2 hd8ed1ab_1 conda-forge + cached_property 1.5.2 pyha770c72_1 conda-forge + certifi 2024.7.4 pyhd8ed1ab_0 conda-forge + cffi 1.17.0 py38h4cb3324_0 conda-forge + charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge + click 8.1.7 win_pyh7428d3b_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_0 conda-forge + contourpy 1.1.1 py38hb1fd069_1 conda-forge + cycler 0.12.1 pyhd8ed1ab_0 conda-forge + exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge + fonttools 4.53.1 py38h4cb3324_0 conda-forge + freetype 2.12.1 hdaf720e_2 conda-forge + get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge + gettext 0.22.5 h5728263_3 conda-forge + gettext-tools 0.22.5 h5a7288d_3 conda-forge + glib 2.80.2 h0df6a38_0 conda-forge + glib-tools 2.80.2 h2f9d560_0 conda-forge + gst-plugins-base 1.21.3 h001b923_1 conda-forge + gstreamer 1.21.3 h6b5321d_1 conda-forge + h2 4.1.0 pyhd8ed1ab_0 conda-forge + h5py 3.9.0 nompi_py38h4f44683_100 conda-forge + hdf5 1.14.0 nompi_h97a5375_103 conda-forge + hpack 4.0.0 pyh9f0ad1d_0 conda-forge + hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge + icu 70.1 h0e60522_0 conda-forge + idna 3.7 pyhd8ed1ab_0 conda-forge + importlib-metadata 8.4.0 pyha770c72_0 conda-forge + importlib-resources 6.4.4 pyhd8ed1ab_0 conda-forge + importlib_resources 6.4.4 pyhd8ed1ab_0 conda-forge + intel-openmp 2024.2.1 h57928b3_1083 conda-forge + joblib 1.4.2 pyhd8ed1ab_0 conda-forge + jpeg 9e h8ffe710_2 conda-forge + kiwisolver 1.4.5 py38hb1fd069_1 conda-forge + krb5 1.20.1 h6609f42_0 conda-forge + lcms2 2.12 h2a16943_0 conda-forge + legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge + lerc 4.0.0 h63175ca_0 conda-forge + libaec 1.1.3 h63175ca_0 conda-forge + libasprintf 0.22.5 h5728263_3 conda-forge + libasprintf-devel 0.22.5 h5728263_3 conda-forge + libblas 3.9.0 23_win64_mkl conda-forge + libbrotlicommon 1.1.0 hcfcfb64_1 conda-forge + libbrotlidec 1.1.0 hcfcfb64_1 conda-forge + libbrotlienc 1.1.0 hcfcfb64_1 conda-forge + libcblas 3.9.0 23_win64_mkl conda-forge + libclang 15.0.7 default_h3a3e6c3_5 conda-forge + libclang13 15.0.7 default_hf64faad_5 conda-forge + libcurl 8.1.2 h68f0423_0 conda-forge + libdeflate 1.21 h2466b09_0 conda-forge + libexpat 2.6.2 h63175ca_0 conda-forge + libffi 3.4.2 h8ffe710_5 conda-forge + libgettextpo 0.22.5 h5728263_3 conda-forge + libgettextpo-devel 0.22.5 h5728263_3 conda-forge + libglib 2.80.2 h0df6a38_0 conda-forge + libhwloc 2.11.1 default_h8125262_1000 conda-forge + libiconv 1.17 hcfcfb64_2 conda-forge + libintl 0.22.5 h5728263_3 conda-forge + libintl-devel 0.22.5 h5728263_3 conda-forge + libjpeg-turbo 2.1.4 hcfcfb64_0 conda-forge + liblapack 3.9.0 23_win64_mkl conda-forge + libogg 1.3.5 h2466b09_0 conda-forge + libpng 1.6.43 h19919ed_0 conda-forge + libsqlite 3.46.0 h2466b09_0 conda-forge + libssh2 1.10.0 h680486a_3 conda-forge + libtiff 4.2.0 h0c97f57_3 conda-forge + libvorbis 1.3.7 h0e60522_0 conda-forge + libwebp-base 1.4.0 hcfcfb64_0 conda-forge + libxcb 1.16 hcd874cb_0 conda-forge + libxml2 2.12.7 h283a6d9_1 conda-forge + libzlib 1.2.13 h2466b09_6 conda-forge + llvmlite 0.41.1 py38h19421c1_0 conda-forge + loompy 3.0.6 py_0 conda-forge + m2w64-gcc-libgfortran 5.3.0 6 conda-forge + m2w64-gcc-libs 5.3.0 7 conda-forge + m2w64-gcc-libs-core 5.3.0 7 conda-forge + m2w64-gmp 6.1.0 2 conda-forge + m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge + matplotlib 3.7.2 py38haa244fe_0 conda-forge + matplotlib-base 3.7.2 py38h2d9580e_0 conda-forge + mkl 2024.1.0 h66d3029_694 conda-forge + msys2-conda-epoch 20160418 1 conda-forge + munkres 1.1.4 pyh9f0ad1d_0 conda-forge + natsort 8.4.0 pyhd8ed1ab_0 conda-forge + networkx 3.1 pyhd8ed1ab_0 conda-forge + numba 0.58.1 py38h4a59444_0 conda-forge + numpy 1.24.4 py38h1d91fd2_0 conda-forge + numpy_groupies 0.9.22 pyhd8ed1ab_0 conda-forge + olefile 0.47 pyhd8ed1ab_0 conda-forge + openjpeg 2.4.0 hb211442_1 conda-forge + openssl 1.1.1w hcfcfb64_0 conda-forge + packaging 24.1 pyhd8ed1ab_0 conda-forge + pandas 2.0.3 py38hf08cf0d_1 conda-forge + patsy 0.5.6 pyhd8ed1ab_0 conda-forge + pcre2 10.43 h17e33f8_0 conda-forge + pillow 8.2.0 py38h9273828_1 conda-forge + pip 24.2 pyhd8ed1ab_0 conda-forge + platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge + ply 3.11 pyhd8ed1ab_2 conda-forge + pooch 1.8.2 pyhd8ed1ab_0 conda-forge + pthread-stubs 0.4 hcd874cb_1001 conda-forge + pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge + pycparser 2.22 pyhd8ed1ab_0 conda-forge + pynndescent 0.5.13 pyhff2d567_0 conda-forge + pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge + pyqt 5.15.7 py38hd6c051e_3 conda-forge + pyqt5-sip 12.11.0 py38hd3f51b4_3 conda-forge + pysocks 1.7.1 pyh0701188_6 conda-forge + python 3.8.0 hc9e8b01_5 conda-forge + python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge + python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge + python_abi 3.8 2_cp38 conda-forge + pytz 2024.1 pyhd8ed1ab_0 conda-forge + qhull 2020.2 hc790b64_5 conda-forge + qt-main 5.15.6 h068e40c_6 conda-forge + requests 2.32.3 pyhd8ed1ab_0 conda-forge + scanpy 1.10.2 pyhd8ed1ab_0 conda-forge + scikit-learn 1.3.2 py38h4f736e5_2 conda-forge + scipy 1.10.1 py38h1aea9ed_3 conda-forge + scvelo 0.2.5 pyhdfd78af_0 bioconda + seaborn 0.13.2 hd8ed1ab_2 conda-forge + seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge + session-info 1.0.0 pyhd8ed1ab_0 conda-forge + setuptools 72.2.0 pyhd8ed1ab_0 conda-forge + sip 6.7.12 py38hd3f51b4_0 conda-forge + six 1.16.0 pyh6c4a22f_0 conda-forge + sqlite 3.46.0 h2466b09_0 conda-forge + statsmodels 0.14.1 py38he7056a7_0 conda-forge + stdlib-list 0.10.0 pyhd8ed1ab_0 conda-forge + tbb 2021.12.0 hc790b64_3 conda-forge + threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge + tk 8.6.13 h5226925_1 conda-forge + toml 0.10.2 pyhd8ed1ab_0 conda-forge + tomli 2.0.1 pyhd8ed1ab_0 conda-forge + tornado 6.4.1 py38h4cb3324_0 conda-forge + tqdm 4.66.5 pyhd8ed1ab_0 conda-forge + typing_extensions 4.12.2 pyha770c72_0 conda-forge + tzdata 2024a h0c530f3_0 conda-forge + ucrt 10.0.22621.0 h57928b3_0 conda-forge + umap-learn 0.5.6 py38haa244fe_1 conda-forge + unicodedata2 15.1.0 py38h91455d4_0 conda-forge + urllib3 2.2.2 pyhd8ed1ab_1 conda-forge + vc 14.3 h8a93ad2_20 conda-forge + vc14_runtime 14.40.33810 ha82c5b3_20 conda-forge + vs2015_runtime 14.40.33810 h3bf8584_20 conda-forge + wheel 0.44.0 pyhd8ed1ab_0 conda-forge + win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge + xorg-libxau 1.0.11 hcd874cb_0 conda-forge + xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge + xz 5.2.6 h8d14728_0 conda-forge + zipp 3.20.0 pyhd8ed1ab_0 conda-forge + zlib 1.2.13 h2466b09_6 conda-forge + zstandard 0.23.0 py38hf92978b_0 conda-forge + zstd 1.5.6 h0ea2cb4_0 conda-forge \ No newline at end of file From c46195e9e9f0d9a4a46d189e9f48678d3cf73ada Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 08:09:31 +0100 Subject: [PATCH 03/14] add pip dependencies --- R/basilisk.R | 180 +++++++++++++---------------------- inst/envs/Windows.yaml | 121 +++++++---------------- inst/envs/format_yaml_to_r.R | 27 +++++- 3 files changed, 126 insertions(+), 202 deletions(-) diff --git a/R/basilisk.R b/R/basilisk.R index 9c81a79..765784d 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -1,168 +1,121 @@ ## Windows ---- .scvelo.dependencies.Windows <- list( - channels = c("conda-forge", "bioconda"), + channels = c("conda-forge"), packages = c( - 'anndata==0.9.2', - 'array-api-compat==1.8', 'brotli==1.1.0', 'brotli-bin==1.1.0', - 'brotli-python==1.1.0', 'bzip2==1.0.8', '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', - 'click==8.1.7', - 'colorama==0.4.6', - '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', - 'gettext==0.22.5', - 'gettext-tools==0.22.5', - 'glib==2.80.2', - 'glib-tools==2.80.2', - 'gst-plugins-base==1.21.3', - 'gstreamer==1.21.3', - 'h2==4.1.0', - 'h5py==3.9.0', - 'hdf5==1.14.0', - 'hpack==4.0.0', - 'hyperframe==6.0.1', - 'icu==70.1', - 'idna==3.7', - 'importlib-metadata==8.4.0', - 'importlib-resources==6.4.4', - 'importlib_resources==6.4.4', + 'hdf5==1.14.3', 'intel-openmp==2024.2.1', - 'joblib==1.4.2', - 'jpeg==9e', - 'kiwisolver==1.4.5', - 'krb5==1.20.1', - 'lcms2==2.12', - 'legacy-api-wrap==1.4', + 'krb5==1.21.3', + 'lcms2==2.16', 'lerc==4.0.0', 'libaec==1.1.3', - 'libasprintf==0.22.5', - 'libasprintf-devel==0.22.5', 'libblas==3.9.0', 'libbrotlicommon==1.1.0', 'libbrotlidec==1.1.0', 'libbrotlienc==1.1.0', 'libcblas==3.9.0', - 'libclang==15.0.7', - 'libclang13==15.0.7', - 'libcurl==8.1.2', + 'libcurl==8.9.1', 'libdeflate==1.21', 'libexpat==2.6.2', 'libffi==3.4.2', - 'libgettextpo==0.22.5', - 'libgettextpo-devel==0.22.5', - 'libglib==2.80.2', 'libhwloc==2.11.1', 'libiconv==1.17', - 'libintl==0.22.5', - 'libintl-devel==0.22.5', - 'libjpeg-turbo==2.1.4', + 'libjpeg-turbo==3.0.0', 'liblapack==3.9.0', - 'libogg==1.3.5', 'libpng==1.6.43', 'libsqlite==3.46.0', - 'libssh2==1.10.0', - 'libtiff==4.2.0', - 'libvorbis==1.3.7', + 'libssh2==1.11.0', + 'libtiff==4.6.0', 'libwebp-base==1.4.0', 'libxcb==1.16', 'libxml2==2.12.7', - 'libzlib==1.2.13', - 'llvmlite==0.41.1', - 'loompy==3.0.6', + 'libzlib==1.3.1', '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==3.7.2', - 'matplotlib-base==3.7.2', + 'matplotlib-base==3.9.2', 'mkl==2024.1.0', 'msys2-conda-epoch==20160418', + 'numpy_groupies==0.11.2', + 'openjpeg==2.5.2', + 'openssl==3.3.1', + 'pthread-stubs==0.4', + 'pthreads-win32==2.9.1', + 'python==3.12.5', + 'python-tzdata==2024.1', + 'python_abi==3.12', + 'qhull==2020.2', + 'seaborn-base==0.13.2', + 'tbb==2021.12.0', + 'tk==8.6.13', + 'typing_extensions==4.12.2', + 'ucrt==10.0.22621.0', + 'vc==14.3', + 'vc14_runtime==14.40.33810', + 'vs2015_runtime==14.40.33810', + 'xorg-libxau==1.0.11', + 'xorg-libxdmcp==1.1.3', + 'xz==5.2.6', + 'zstd==1.5.6' + ), + pip = c( + 'anndata==0.10.9', + 'array-api-compat==1.8', + 'cached-property==1.5.2', + 'certifi==2024.7.4', + 'click==8.1.7', + 'colorama==0.4.6', + 'contourpy==1.3.0', + 'cycler==0.12.1', + 'exceptiongroup==1.2.2', + 'fonttools==4.53.1', + 'get-annotations==0.1.2', + '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==3.9.2', 'munkres==1.1.4', 'natsort==8.4.0', - 'networkx==3.1', - 'numba==0.58.1', - 'numpy==1.24.4', - 'numpy_groupies==0.9.22', - 'olefile==0.47', - 'openjpeg==2.4.0', - 'openssl==1.1.1w', + 'networkx==3.3', + 'numba==0.60.0', + 'numpy==1.26.4', + 'numpy-groupies==0.11.2', 'packaging==24.1', - 'pandas==2.0.3', + 'pandas==2.2.2', 'patsy==0.5.6', - 'pcre2==10.43', - 'pillow==8.2.0', + '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', - 'pycparser==2.22', 'pynndescent==0.5.13', - 'pyparsing==3.0.9', - 'pyqt==5.15.7', - 'pyqt5-sip==12.11.0', - 'pysocks==1.7.1', - 'python==3.8.0', + 'pyparsing==3.1.4', 'python-dateutil==2.9.0', - 'python-tzdata==2024.1', - 'python_abi==3.8', 'pytz==2024.1', - 'qhull==2020.2', - 'qt-main==5.15.6', - 'requests==2.32.3', 'scanpy==1.10.2', - 'scikit-learn==1.3.2', - 'scipy==1.10.1', + 'scikit-learn==1.5.1', + 'scipy==1.14.1', 'scvelo==0.2.5', 'seaborn==0.13.2', - 'seaborn-base==0.13.2', 'session-info==1.0.0', 'setuptools==72.2.0', - 'sip==6.7.12', 'six==1.16.0', - 'sqlite==3.46.0', - 'statsmodels==0.14.1', + 'statsmodels==0.14.2', '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==6.4.1', 'tqdm==4.66.5', - 'typing_extensions==4.12.2', - 'tzdata==2024a', - 'ucrt==10.0.22621.0', + 'typing-extensions==4.12.2', + 'tzdata==2024.1', '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==3.20.0', - 'zlib==1.2.13', - 'zstandard==0.23.0', - 'zstd==1.5.6' + 'wheel==0.44.0' ) ) @@ -170,6 +123,7 @@ .scvelo.dependencies.MacOSXArm <- list( channels = c("conda-forge", "bioconda"), + pip = character(0), packages = c( 'absl-py==2.1.0', 'anndata==0.10.7', @@ -446,6 +400,7 @@ .scvelo.dependencies.MacOSX <- list( channels = c("conda-forge", "bioconda"), + pip = character(0), packages = c( 'absl-py==2.1.0', 'anndata==0.10.7', @@ -722,6 +677,7 @@ .scvelo.dependencies.Linux <- list( channels = c("anaconda", "conda-forge", "bioconda"), + pip = character(0), packages = c( '_libgcc_mutex==0.1', '_openmp_mutex==4.5', @@ -889,4 +845,4 @@ if (basilisk.utils::isWindows()) { #' @importFrom basilisk BasiliskEnvironment #' @importFrom zellkonverter AnnDataDependencies velo.env <- BasiliskEnvironment("env", "velociraptor", - packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels) + packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels, pip = .scvelo_dependencies$pip) diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml index 0f5321f..98d6283 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -3,168 +3,115 @@ channels: - conda-forge - defaults dependencies: + - 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=pyha770c72_1 - freetype=2.12.1=hdaf720e_2 - - gettext=0.22.5=h5728263_3 - - gettext-tools=0.22.5=h5a7288d_3 - - glib=2.80.2=h0df6a38_0 - - glib-tools=2.80.2=h2f9d560_0 - - gst-plugins-base=1.21.3=h001b923_1 - - gstreamer=1.21.3=h6b5321d_1 - - hdf5=1.14.0=nompi_h97a5375_103 - - icu=70.1=h0e60522_0 - - importlib_resources=6.4.4=pyhd8ed1ab_0 + - hdf5=1.14.3=nompi_h2b43c12_105 - intel-openmp=2024.2.1=h57928b3_1083 - - jpeg=9e=h8ffe710_2 - - krb5=1.20.1=h6609f42_0 - - lcms2=2.12=h2a16943_0 + - krb5=1.21.3=hdf4eb48_0 + - lcms2=2.16=h67d730c_0 - lerc=4.0.0=h63175ca_0 - libaec=1.1.3=h63175ca_0 - - libasprintf=0.22.5=h5728263_3 - - libasprintf-devel=0.22.5=h5728263_3 - 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 - - libclang=15.0.7=default_h3a3e6c3_5 - - libclang13=15.0.7=default_hf64faad_5 - - libcurl=8.1.2=h68f0423_0 + - libcurl=8.9.1=h18fefc2_0 - libdeflate=1.21=h2466b09_0 - libexpat=2.6.2=h63175ca_0 - libffi=3.4.2=h8ffe710_5 - - libgettextpo=0.22.5=h5728263_3 - - libgettextpo-devel=0.22.5=h5728263_3 - - libglib=2.80.2=h0df6a38_0 - 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=2.1.4=hcfcfb64_0 + - 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=1.10.0=h680486a_3 - - libtiff=4.2.0=h0c97f57_3 - - libvorbis=1.3.7=h0e60522_0 + - libssh2=1.11.0=h7dfc565_0 + - libtiff=4.6.0=hb151862_4 - libwebp-base=1.4.0=hcfcfb64_0 - - libxcb=1.16=hcd874cb_0 - - libxml2=2.12.7=h283a6d9_1 - - libzlib=1.2.13=h2466b09_6 + - libxcb=1.16=h013a479_1 + - libxml2=2.12.7=h0f24e4e_4 + - libzlib=1.3.1=h2466b09_1 - 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-base=3.7.2=py38h2d9580e_0 + - matplotlib-base=3.9.2=py312h90004f6_0 - mkl=2024.1.0=h66d3029_694 - msys2-conda-epoch=20160418=1 - - numpy_groupies=0.9.22=pyhd8ed1ab_0 - - openjpeg=2.4.0=hb211442_1 - - openssl=1.1.1w=hcfcfb64_0 - - pcre2=10.43=h17e33f8_0 + - numpy_groupies=0.11.2=pyhd8ed1ab_0 + - openjpeg=2.5.2=h3d672ee_0 + - openssl=3.3.1=h2466b09_3 - pthread-stubs=0.4=hcd874cb_1001 - pthreads-win32=2.9.1=hfa6e2cd_3 - - pyqt=5.15.7=py38hd6c051e_3 - - python=3.8.0=hc9e8b01_5 + - python=3.12.5=h889d299_0_cpython - python-tzdata=2024.1=pyhd8ed1ab_0 - - python_abi=3.8=2_cp38 + - python_abi=3.12=5_cp312 - qhull=2020.2=hc790b64_5 - - qt-main=5.15.6=h068e40c_6 - seaborn-base=0.13.2=pyhd8ed1ab_2 - - sqlite=3.46.0=h2466b09_0 - - tbb=2021.12.0=hc790b64_3 + - tbb=2021.12.0=hc790b64_4 - tk=8.6.13=h5226925_1 - typing_extensions=4.12.2=pyha770c72_0 - ucrt=10.0.22621.0=h57928b3_0 - vc=14.3=h8a93ad2_20 - - vc14_runtime=14.40.33810=ha82c5b3_20 + - vc14_runtime=14.40.33810=hcc2c482_20 - vs2015_runtime=14.40.33810=h3bf8584_20 - - 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 - - zlib=1.2.13=h2466b09_6 - zstd=1.5.6=h0ea2cb4_0 - pip: - - anndata==0.9.2 + - anndata==0.10.9 - array-api-compat==1.8 - - brotli==1.1.0 - cached-property==1.5.2 - certifi==2024.7.4 - - cffi==1.17.0 - - charset-normalizer==3.3.2 - click==8.1.7 - colorama==0.4.6 - - contourpy==1.1.1 + - contourpy==1.3.0 - cycler==0.12.1 - exceptiongroup==1.2.2 - fonttools==4.53.1 - get-annotations==0.1.2 - - h2==4.1.0 - - h5py==3.9.0 - - hpack==4.0.0 - - hyperframe==6.0.1 - - idna==3.7 - - importlib-metadata==8.4.0 - - importlib-resources==6.4.4 + - h5py==3.11.0 - joblib==1.4.2 - kiwisolver==1.4.5 - legacy-api-wrap==1.4 - - llvmlite==0.41.1 + - llvmlite==0.43.0 - loompy==3.0.6 - - matplotlib==3.7.2 + - matplotlib==3.9.2 - munkres==1.1.4 - natsort==8.4.0 - - networkx==3.1 - - numba==0.58.1 - - numpy==1.24.4 - - numpy-groupies==0.9.22 - - olefile==0.47 + - networkx==3.3 + - numba==0.60.0 + - numpy==1.26.4 + - numpy-groupies==0.11.2 - packaging==24.1 - - pandas==2.0.3 + - pandas==2.2.2 - patsy==0.5.6 - - pillow==8.2.0 + - pillow==10.4.0 - pip==24.2 - - platformdirs==4.2.2 - - ply==3.11 - - pooch==1.8.2 - - pycparser==2.22 - pynndescent==0.5.13 - - pyparsing==3.0.9 - - pyqt5==5.15.7 - - pyqt5-sip==12.11.0 - - pysocks==1.7.1 + - pyparsing==3.1.4 - python-dateutil==2.9.0 - pytz==2024.1 - - requests==2.32.3 - scanpy==1.10.2 - - scikit-learn==1.3.2 - - scipy==1.10.1 + - 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 - - sip==6.7.12 - six==1.16.0 - - statsmodels==0.14.1 + - statsmodels==0.14.2 - 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 - - urllib3==2.2.2 - wheel==0.44.0 - - win-inet-pton==1.1.0 - - zipp==3.20.0 - - zstandard==0.23.0 \ No newline at end of file diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R index d147eb2..7eb0776 100644 --- a/inst/envs/format_yaml_to_r.R +++ b/inst/envs/format_yaml_to_r.R @@ -1,11 +1,32 @@ library(yaml) -yaml_data <- yaml::read_yaml("Linux_x86_64_anaconda.yaml") -r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies) +yaml_data <- yaml::read_yaml("Windows.yaml") + +which_pip_dependencies <- which(sapply(yaml_data$dependencies, function(x) any(names(x) %in% "pip"))) + +conda_dependencies <- yaml_data$dependencies[-c(which_pip_dependencies)] + +conda_dependencies <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , conda_dependencies) + + +message("Conda dependencies:") cat(paste0( "c(", "\n", - paste0(" ", "'", r_data, "'", collapse = ",\n"), + paste0(" ", "'", conda_dependencies, "'", collapse = ",\n"), "\n", ")", "\n" )) + +message("pip dependencies:") +if (length(which_pip_dependencies)) { + pip_dependencies <- yaml_data$dependencies[[which_pip_dependencies]]$pip + cat(paste0( + "c(", + "\n", + paste0(" ", "'", pip_dependencies, "'", collapse = ",\n"), + "\n", + ")", + "\n" + )) +} From 7d722ab10d344057999ffb428cba38743cba039d Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 08:23:49 +0100 Subject: [PATCH 04/14] downgrade matplotlib to 3.7.3 (https://stackoverflow.com/questions/77128061/ydata-profiling-profilereport-attributeerror-module-matplotlib-cbook-has-no) --- R/basilisk.R | 30 +++++++++++++++++++++++++----- inst/envs/Windows.yaml | 30 +++++++++++++++++++++++++----- 2 files changed, 50 insertions(+), 10 deletions(-) diff --git a/R/basilisk.R b/R/basilisk.R index 765784d..01b3f6d 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -9,7 +9,12 @@ 'ca-certificates==2024.7.4', 'cached_property==1.5.2', 'freetype==2.12.1', + 'glib==2.80.3', + 'glib-tools==2.80.3', + 'gst-plugins-base==1.24.6', + 'gstreamer==1.24.6', 'hdf5==1.14.3', + 'icu==73.2', 'intel-openmp==2024.2.1', 'krb5==1.21.3', 'lcms2==2.16', @@ -20,18 +25,24 @@ 'libbrotlidec==1.1.0', 'libbrotlienc==1.1.0', 'libcblas==3.9.0', + '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', 'libiconv==1.17', + 'libintl==0.22.5', + 'libintl-devel==0.22.5', 'libjpeg-turbo==3.0.0', 'liblapack==3.9.0', + 'libogg==1.3.5', 'libpng==1.6.43', 'libsqlite==3.46.0', 'libssh2==1.11.0', 'libtiff==4.6.0', + 'libvorbis==1.3.7', 'libwebp-base==1.4.0', 'libxcb==1.16', 'libxml2==2.12.7', @@ -41,18 +52,20 @@ 'm2w64-gcc-libs-core==5.3.0', 'm2w64-gmp==6.1.0', 'm2w64-libwinpthread-git==5.0.0.4634.697f757', - 'matplotlib-base==3.9.2', + 'matplotlib-base==3.7.3', 'mkl==2024.1.0', 'msys2-conda-epoch==20160418', 'numpy_groupies==0.11.2', 'openjpeg==2.5.2', 'openssl==3.3.1', + 'pcre2==10.44', 'pthread-stubs==0.4', 'pthreads-win32==2.9.1', - 'python==3.12.5', + 'pyqt==5.15.9', + 'python==3.11.9', 'python-tzdata==2024.1', - 'python_abi==3.12', - 'qhull==2020.2', + 'python_abi==3.11', + 'qt-main==5.15.8', 'seaborn-base==0.13.2', 'tbb==2021.12.0', 'tk==8.6.13', @@ -84,7 +97,7 @@ 'legacy-api-wrap==1.4', 'llvmlite==0.43.0', 'loompy==3.0.6', - 'matplotlib==3.9.2', + 'matplotlib==3.7.3', 'munkres==1.1.4', 'natsort==8.4.0', 'networkx==3.3', @@ -96,8 +109,11 @@ 'patsy==0.5.6', 'pillow==10.4.0', 'pip==24.2', + 'ply==3.11', 'pynndescent==0.5.13', 'pyparsing==3.1.4', + 'pyqt5==5.15.9', + 'pyqt5-sip==12.12.2', 'python-dateutil==2.9.0', 'pytz==2024.1', 'scanpy==1.10.2', @@ -107,10 +123,14 @@ 'seaborn==0.13.2', 'session-info==1.0.0', 'setuptools==72.2.0', + 'sip==6.7.12', 'six==1.16.0', 'statsmodels==0.14.2', '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', diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml index 98d6283..0fc59b9 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -9,7 +9,12 @@ dependencies: - ca-certificates=2024.7.4=h56e8100_0 - cached_property=1.5.2=pyha770c72_1 - 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 - hdf5=1.14.3=nompi_h2b43c12_105 + - icu=73.2=h63175ca_0 - intel-openmp=2024.2.1=h57928b3_1083 - krb5=1.21.3=hdf4eb48_0 - lcms2=2.16=h67d730c_0 @@ -20,18 +25,24 @@ dependencies: - 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 - 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 - 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 @@ -41,18 +52,20 @@ 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=3.9.2=py312h90004f6_0 + - matplotlib-base=3.7.3=py311h6e989c2_0 - mkl=2024.1.0=h66d3029_694 - msys2-conda-epoch=20160418=1 - numpy_groupies=0.11.2=pyhd8ed1ab_0 - openjpeg=2.5.2=h3d672ee_0 - openssl=3.3.1=h2466b09_3 + - pcre2=10.44=h3d7b363_2 - pthread-stubs=0.4=hcd874cb_1001 - pthreads-win32=2.9.1=hfa6e2cd_3 - - python=3.12.5=h889d299_0_cpython + - pyqt=5.15.9=py311h125bc19_5 + - python=3.11.9=h631f459_0_cpython - python-tzdata=2024.1=pyhd8ed1ab_0 - - python_abi=3.12=5_cp312 - - qhull=2020.2=hc790b64_5 + - python_abi=3.11=5_cp311 + - 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 @@ -83,7 +96,7 @@ dependencies: - legacy-api-wrap==1.4 - llvmlite==0.43.0 - loompy==3.0.6 - - matplotlib==3.9.2 + - matplotlib==3.7.3 - munkres==1.1.4 - natsort==8.4.0 - networkx==3.3 @@ -95,8 +108,11 @@ dependencies: - patsy==0.5.6 - pillow==10.4.0 - pip==24.2 + - ply==3.11 - pynndescent==0.5.13 - pyparsing==3.1.4 + - pyqt5==5.15.9 + - pyqt5-sip==12.12.2 - python-dateutil==2.9.0 - pytz==2024.1 - scanpy==1.10.2 @@ -106,10 +122,14 @@ dependencies: - seaborn==0.13.2 - session-info==1.0.0 - setuptools==72.2.0 + - sip==6.7.12 - six==1.16.0 - statsmodels==0.14.2 - 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 From 3c3338dbfcf6b66d8a6f967ba0893a80236f44dc Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 08:44:59 +0100 Subject: [PATCH 05/14] downgrade pandas (https://github.com/theislab/scvelo/issues/811#issuecomment-1026555408) --- DESCRIPTION | 2 +- R/basilisk.R | 24 +++++++++++------------- inst/envs/Windows.yaml | 26 ++++++++++++-------------- 3 files changed, 24 insertions(+), 28 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7abe31c..a6c59f3 100644 --- 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 = "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 index 01b3f6d..2e64ede 100644 --- 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', @@ -116,16 +114,16 @@ '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', @@ -133,8 +131,8 @@ '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 index 0fc59b9..bbf990f 100644 --- 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 @@ -115,16 +113,16 @@ 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 @@ -132,6 +130,6 @@ dependencies: - 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 From 471dfd37ec507c74a9db352e919531b579333e15 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 08:56:56 +0100 Subject: [PATCH 06/14] remove pip section --- R/basilisk.R | 243 +++++++++++++++++--------------- inst/envs/Windows.yaml | 262 +++++++++++++++++------------------ inst/envs/format_yaml_to_r.R | 27 +--- 3 files changed, 260 insertions(+), 272 deletions(-) diff --git a/R/basilisk.R b/R/basilisk.R index 2e64ede..29860f4 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -1,139 +1,154 @@ ## Windows ---- .scvelo.dependencies.Windows <- list( - channels = c("conda-forge", "defaults"), + channels = c("bioconda", "conda-forge"), packages = c( - 'brotli==1.1.0', - 'brotli-bin==1.1.0', - 'bzip2==1.0.8', - 'ca-certificates==2024.7.4', - 'cached_property==1.5.2', - 'freetype==2.12.1', - 'glib==2.80.3', - 'glib-tools==2.80.3', - 'gst-plugins-base==1.24.6', - 'gstreamer==1.24.6', - 'hdf5==1.14.3', - 'icu==73.2', - 'intel-openmp==2024.2.1', - 'krb5==1.21.3', - 'lcms2==2.16', - 'lerc==4.0.0', - 'libaec==1.1.3', - 'libblas==3.9.0', - 'libbrotlicommon==1.1.0', - 'libbrotlidec==1.1.0', - 'libbrotlienc==1.1.0', - 'libcblas==3.9.0', - 'libclang13==18.1.8', - 'libcurl==8.9.1', - 'libdeflate==1.21', - 'libffi==3.4.2', - '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==1.3.5', - 'libpng==1.6.43', - 'libsqlite==3.46.0', - 'libssh2==1.11.0', - 'libtiff==4.6.0', - 'libvorbis==1.3.7', - 'libwebp-base==1.4.0', - 'libxcb==1.16', - 'libxml2==2.12.7', - 'libzlib==1.3.1', - '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-base==3.7.3', - 'mkl==2024.1.0', - 'msys2-conda-epoch==20160418', - 'numpy_groupies==0.11.2', - 'openjpeg==2.5.2', - 'openssl==3.3.1', - 'pcre2==10.44', - 'pthread-stubs==0.4', - 'pthreads-win32==2.9.1', - 'pyqt==5.15.9', - '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', - 'vs2015_runtime==14.40.33810', - 'xorg-libxau==1.0.11', - 'xorg-libxdmcp==1.1.3', - 'xz==5.2.6', - 'zstd==1.5.6' - ), - pip = c( - 'anndata==0.10.5.post1', + '_libgcc_mutex==0.1', + '_openmp_mutex==4.5', + 'absl-py==2.1.0', + 'anndata==0.10.9', 'array-api-compat==1.8', - 'cached-property==1.5.2', - 'certifi==2024.7.4', + 'blas==1.0', + 'bottleneck==1.3.7', + 'brotli==1.0.9', + 'brotli-bin==1.0.9', + 'bzip2==1.0.8', + 'c-ares==1.19.1', + 'ca-certificates==2024.7.2', + 'chex==0.1.5', 'click==8.1.7', - 'colorama==0.4.6', - 'contourpy==1.3.0', - 'cycler==0.12.1', - 'exceptiongroup==1.2.2', - 'fonttools==4.53.1', + 'contextlib2==21.6.0', + 'contourpy==1.2.0', + 'cycler==0.11.0', + 'dm-tree==0.1.7', + 'docrep==0.3.2', + 'et_xmlfile==1.1.0', + 'exceptiongroup==1.2.0', + 'filelock==3.13.1', + 'flax==0.6.1', + 'fonttools==4.51.0', + 'freetype==2.12.1', + 'fsspec==2024.3.1', 'get-annotations==0.1.2', + 'gmp==6.2.1', + 'gmpy2==2.1.2', 'h5py==3.11.0', + 'hdf5==1.12.1', + 'jax==0.3.25', + 'jaxlib==0.3.25', + 'jinja2==3.1.4', 'joblib==1.4.2', - 'kiwisolver==1.4.5', + 'jpeg==9e', + 'kiwisolver==1.4.4', + 'krb5==1.20.1', + 'lcms2==2.12', + 'ld_impl_linux-64==2.38', + 'legacy-api-wrap==1.4', + 'lerc==3.0', + 'libblas==3.9.0', + 'libbrotlicommon==1.0.9', + 'libbrotlidec==1.0.9', + 'libbrotlienc==1.0.9', + 'libcblas==3.9.0', + 'libcurl==7.88.1', + 'libdeflate==1.17', + 'libedit==3.1.20230828', + 'libev==4.33', + 'libffi==3.4.4', + 'libgcc==14.1.0', + 'libgcc-ng==14.1.0', + 'libgfortran-ng==11.2.0', + 'libgfortran5==11.2.0', + 'libgomp==14.1.0', + 'libllvm14==14.0.6', + 'libnghttp2==1.57.0', + 'libopenblas==0.3.21', + 'libpng==1.6.39', + 'libprotobuf==3.20.3', + 'libssh2==1.11.0', + 'libstdcxx==14.1.0', + 'libstdcxx-ng==14.1.0', + 'libtiff==4.5.1', + 'libuuid==1.41.5', + 'libwebp-base==1.3.2', + 'lightning-utilities==0.9.0', 'llvmlite==0.43.0', 'loompy==3.0.6', - 'matplotlib==3.7.3', - 'munkres==1.1.4', - 'natsort==8.4.0', - 'networkx==3.2', + 'lz4-c==1.9.4', + 'markdown-it-py==2.2.0', + 'markupsafe==2.1.3', + 'matplotlib-base==3.8.4', + 'mdurl==0.1.0', + 'ml-collections==0.1.1', + 'mpc==1.1.0', + 'mpfr==4.0.2', + 'mpmath==1.3.0', + 'msgpack-python==1.0.3', + 'mudata==0.3.0', + 'multipledispatch==0.6.0', + 'natsort==7.1.1', + 'ncurses==6.4', + 'networkx==3.3', 'numba==0.60.0', + 'numexpr==2.8.7', 'numpy==1.26.4', - 'numpy-groupies==0.11.2', + 'numpy-base==1.26.4', + 'numpy_groupies==0.11.2', + 'numpyro==0.13.2', + 'openjpeg==2.5.2', + 'openpyxl==3.1.5', + 'openssl==3.0.14', + 'opt_einsum==3.3.0', + 'optax==0.1.4', 'packaging==24.1', - 'pandas==1.3.5', + 'pandas==2.2.2', 'patsy==0.5.6', 'pillow==10.4.0', 'pip==24.2', - 'ply==3.11', - 'pynndescent==0.5.13', - 'pyparsing==3.1.4', - 'pyqt5==5.15.9', - 'pyqt5-sip==12.12.2', - 'python-dateutil==2.9.0', + 'pybind11-abi==4', + 'pygments==2.15.1', + 'pynndescent==0.5.10', + 'pyparsing==3.0.9', + 'pyro-api==0.1.2', + 'pyro-ppl==1.9.1', + 'python==3.11.9', + 'python-dateutil==2.9.0post0', + 'python-tzdata==2023.3', + 'python_abi==3.11', + 'pytorch==2.3.0', + 'pytorch-lightning==1.9.5', 'pytz==2024.1', - 'scanpy==1.9.8', - 'scikit-learn==1.5.1', - 'scipy==1.14.1', - 'scvelo==0.2.5', + 'pyyaml==6.0.1', + 'readline==8.2', + 'rich==13.7.1', + 'scanpy==1.10.2', + 'scikit-learn==1.1.3', + 'scipy==1.13.1', + 'scvelo==0.3.2', + 'scvi-tools==0.20.3', 'seaborn==0.13.2', 'session-info==1.0.0', - 'setuptools==59.8.0', - 'sip==6.7.12', + 'setuptools==72.1.0', 'six==1.16.0', - 'statsmodels==0.14.1', + 'sqlite==3.45.3', + 'statsmodels==0.14.2', 'stdlib-list==0.10.0', + 'sympy==1.12', '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', - 'umap-learn==0.5.6', + 'tk==8.6.14', + 'toolz==0.12.0', + 'torchmetrics==1.4.0.post0', + 'tqdm==4.66.4', + 'typing-extensions==4.11.0', + 'typing_extensions==4.11.0', + 'tzdata==2024a', + 'umap-learn==0.5.3', 'unicodedata2==15.1.0', - 'wheel==0.44.0' + 'wheel==0.43.0', + 'xz==5.4.6', + 'yaml==0.2.5', + 'zlib==1.2.13', + 'zstd==1.5.5' ) ) @@ -418,7 +433,6 @@ .scvelo.dependencies.MacOSX <- list( channels = c("conda-forge", "bioconda"), - pip = character(0), packages = c( 'absl-py==2.1.0', 'anndata==0.10.7', @@ -695,7 +709,6 @@ .scvelo.dependencies.Linux <- list( channels = c("anaconda", "conda-forge", "bioconda"), - pip = character(0), packages = c( '_libgcc_mutex==0.1', '_openmp_mutex==4.5', @@ -863,4 +876,4 @@ if (basilisk.utils::isWindows()) { #' @importFrom basilisk BasiliskEnvironment #' @importFrom zellkonverter AnnDataDependencies velo.env <- BasiliskEnvironment("env", "velociraptor", - packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels, pip = .scvelo_dependencies$pip) + packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels) diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml index bbf990f..26fa8ad 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -1,135 +1,131 @@ -name: null +name: scvelo channels: - - conda-forge - - defaults +- bioconda +- conda-forge dependencies: - - brotli=1.1.0=hcfcfb64_1 - - brotli-bin=1.1.0=hcfcfb64_1 - - bzip2=1.0.8=h2466b09_7 - - ca-certificates=2024.7.4=h56e8100_0 - - cached_property=1.5.2=pyha770c72_1 - - 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 - - hdf5=1.14.3=nompi_h2b43c12_105 - - icu=73.2=h63175ca_0 - - intel-openmp=2024.2.1=h57928b3_1083 - - krb5=1.21.3=hdf4eb48_0 - - lcms2=2.16=h67d730c_0 - - 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 - - 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-base=3.7.3=py310hc9baf74_0 - - mkl=2024.1.0=h66d3029_694 - - msys2-conda-epoch=20160418=1 - - numpy_groupies=0.11.2=pyhd8ed1ab_0 - - openjpeg=2.5.2=h3d672ee_0 - - openssl=3.3.1=h2466b09_3 - - pcre2=10.44=h3d7b363_2 - - pthread-stubs=0.4=hcd874cb_1001 - - pthreads-win32=2.9.1=hfa6e2cd_3 - - 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 - - vs2015_runtime=14.40.33810=h3bf8584_20 - - xorg-libxau=1.0.11=hcd874cb_0 - - xorg-libxdmcp=1.1.3=hcd874cb_0 - - xz=5.2.6=h8d14728_0 - - zstd=1.5.6=h0ea2cb4_0 - - pip: - - anndata==0.10.5.post1 - - array-api-compat==1.8 - - cached-property==1.5.2 - - certifi==2024.7.4 - - click==8.1.7 - - colorama==0.4.6 - - contourpy==1.3.0 - - cycler==0.12.1 - - exceptiongroup==1.2.2 - - fonttools==4.53.1 - - get-annotations==0.1.2 - - h5py==3.11.0 - - joblib==1.4.2 - - kiwisolver==1.4.5 - - llvmlite==0.43.0 - - loompy==3.0.6 - - matplotlib==3.7.3 - - munkres==1.1.4 - - natsort==8.4.0 - - networkx==3.2 - - numba==0.60.0 - - numpy==1.26.4 - - numpy-groupies==0.11.2 - - packaging==24.1 - - pandas==1.3.5 - - patsy==0.5.6 - - pillow==10.4.0 - - pip==24.2 - - ply==3.11 - - pynndescent==0.5.13 - - pyparsing==3.1.4 - - pyqt5==5.15.9 - - pyqt5-sip==12.12.2 - - python-dateutil==2.9.0 - - pytz==2024.1 - - 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==59.8.0 - - sip==6.7.12 - - six==1.16.0 - - 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 - - umap-learn==0.5.6 - - unicodedata2==15.1.0 - - wheel==0.44.0 +- anndata=0.10.5.post1=pyhd8ed1ab_0 +- array-api-compat=1.8=pyhd8ed1ab_0 +- brotli=1.1.0=hcfcfb64_1 +- brotli-bin=1.1.0=hcfcfb64_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 +- click=8.1.7=win_pyh7428d3b_0 +- colorama=0.4.6=pyhd8ed1ab_0 +- contourpy=1.3.0=py310hc19bc0b_0 +- cycler=0.12.1=pyhd8ed1ab_0 +- exceptiongroup=1.2.2=pyhd8ed1ab_0 +- fonttools=4.53.1=py310ha8f682b_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_py310h2b0be38_102 +- hdf5=1.14.3=nompi_h2b43c12_105 +- icu=73.2=h63175ca_0 +- intel-openmp=2024.2.1=h57928b3_1083 +- joblib=1.4.2=pyhd8ed1ab_0 +- kiwisolver=1.4.5=py310hc19bc0b_2 +- krb5=1.21.3=hdf4eb48_0 +- lcms2=2.16=h67d730c_0 +- 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=0.43.0=py310h0288bfe_0 +- loompy=3.0.6=py_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=3.7.3=py310h5588dad_0 +- matplotlib-base=3.7.3=py310hc9baf74_0 +- mkl=2024.1.0=h66d3029_694 +- msys2-conda-epoch=20160418=1 +- munkres=1.1.4=pyh9f0ad1d_0 +- natsort=8.4.0=pyhd8ed1ab_0 +- networkx=3.2=pyhd8ed1ab_0 +- numba=0.60.0=py310h7793332_0 +- numpy=1.26.4=py310hf667824_0 +- numpy_groupies=0.11.2=pyhd8ed1ab_0 +- openjpeg=2.5.2=h3d672ee_0 +- openssl=3.3.1=h2466b09_3 +- packaging=24.1=pyhd8ed1ab_0 +- pandas=1.3.5=py310hf5e1058_0 +- patsy=0.5.6=pyhd8ed1ab_0 +- pcre2=10.44=h3d7b363_2 +- pillow=10.4.0=py310h3e38d90_0 +- pip=24.2=pyh8b19718_1 +- ply=3.11=pyhd8ed1ab_2 +- pthread-stubs=0.4=hcd874cb_1001 +- pthreads-win32=2.9.1=hfa6e2cd_3 +- pynndescent=0.5.13=pyhff2d567_0 +- pyparsing=3.1.4=pyhd8ed1ab_0 +- pyqt=5.15.9=py310h1fd54f2_5 +- pyqt5-sip=12.12.2=py310h00ffb61_5 +- python=3.10.14=h4de0772_0_cpython +- python-dateutil=2.9.0=pyhd8ed1ab_0 +- python_abi=3.10=5_cp310 +- pytz=2024.1=pyhd8ed1ab_0 +- qt-main=5.15.8=h06adc49_23 +- scanpy=1.9.8=pyhd8ed1ab_0 +- scikit-learn=1.5.1=py310hf2a6c47_0 +- scipy=1.14.1=py310h46043a1_0 +- 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=59.8.0=py310h5588dad_1 +- sip=6.7.12=py310h00ffb61_0 +- six=1.16.0=pyh6c4a22f_0 +- statsmodels=0.14.1=py310h3e78b6c_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=py310ha8f682b_1 +- tqdm=4.66.5=pyhd8ed1ab_0 +- typing_extensions=4.12.2=pyha770c72_0 +- tzdata=2024a=h8827d51_1 +- ucrt=10.0.22621.0=h57928b3_0 +- umap-learn=0.5.6=py310h5588dad_1 +- unicodedata2=15.1.0=py310h8d17308_0 +- 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 +- xorg-libxau=1.0.11=hcd874cb_0 +- xorg-libxdmcp=1.1.3=hcd874cb_0 +- xz=5.2.6=h8d14728_0 +- zstd=1.5.6=h0ea2cb4_0 diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R index 7eb0776..d147eb2 100644 --- a/inst/envs/format_yaml_to_r.R +++ b/inst/envs/format_yaml_to_r.R @@ -1,32 +1,11 @@ library(yaml) -yaml_data <- yaml::read_yaml("Windows.yaml") - -which_pip_dependencies <- which(sapply(yaml_data$dependencies, function(x) any(names(x) %in% "pip"))) - -conda_dependencies <- yaml_data$dependencies[-c(which_pip_dependencies)] - -conda_dependencies <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , conda_dependencies) - - -message("Conda dependencies:") +yaml_data <- yaml::read_yaml("Linux_x86_64_anaconda.yaml") +r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies) cat(paste0( "c(", "\n", - paste0(" ", "'", conda_dependencies, "'", collapse = ",\n"), + paste0(" ", "'", r_data, "'", collapse = ",\n"), "\n", ")", "\n" )) - -message("pip dependencies:") -if (length(which_pip_dependencies)) { - pip_dependencies <- yaml_data$dependencies[[which_pip_dependencies]]$pip - cat(paste0( - "c(", - "\n", - paste0(" ", "'", pip_dependencies, "'", collapse = ",\n"), - "\n", - ")", - "\n" - )) -} From 17afe4ffb28bc5f2951b4af162ce5cf2531cba73 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 09:20:32 +0100 Subject: [PATCH 07/14] https://github.com/kevinrue/velociraptor/issues/80#issuecomment-2320454366 --- DESCRIPTION | 2 +- inst/envs/Windows.yaml | 60 +++++++++++++++++++++--------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a6c59f3..d9ee319 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.9 +Version: 1.15.11 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/inst/envs/Windows.yaml b/inst/envs/Windows.yaml index 26fa8ad..e1e44f7 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -3,7 +3,7 @@ channels: - bioconda - conda-forge dependencies: -- anndata=0.10.5.post1=pyhd8ed1ab_0 +- anndata=0.10.9=pyhd8ed1ab_0 - array-api-compat=1.8=pyhd8ed1ab_0 - brotli=1.1.0=hcfcfb64_1 - brotli-bin=1.1.0=hcfcfb64_1 @@ -12,26 +12,26 @@ dependencies: - cached-property=1.5.2=hd8ed1ab_1 - cached_property=1.5.2=pyha770c72_1 - certifi=2024.7.4=pyhd8ed1ab_0 -- click=8.1.7=win_pyh7428d3b_0 - colorama=0.4.6=pyhd8ed1ab_0 -- contourpy=1.3.0=py310hc19bc0b_0 +- contourpy=1.3.0=py311h3257749_0 - cycler=0.12.1=pyhd8ed1ab_0 - exceptiongroup=1.2.2=pyhd8ed1ab_0 -- fonttools=4.53.1=py310ha8f682b_0 +- fonttools=4.53.1=py311he736701_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_py310h2b0be38_102 +- h5py=3.11.0=nompi_py311h67016bb_102 - hdf5=1.14.3=nompi_h2b43c12_105 - icu=73.2=h63175ca_0 - intel-openmp=2024.2.1=h57928b3_1083 - joblib=1.4.2=pyhd8ed1ab_0 -- kiwisolver=1.4.5=py310hc19bc0b_2 +- kiwisolver=1.4.5=py311h3257749_2 - 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 @@ -42,6 +42,7 @@ 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 @@ -60,67 +61,66 @@ dependencies: - libxcb=1.16=h013a479_1 - libxml2=2.12.7=h0f24e4e_4 - libzlib=1.3.1=h2466b09_1 -- llvmlite=0.43.0=py310h0288bfe_0 -- loompy=3.0.6=py_0 +- llvmlite=0.43.0=py311h7deaa30_0 +- loompy=2.0.16=py_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=3.7.3=py310h5588dad_0 -- matplotlib-base=3.7.3=py310hc9baf74_0 +- matplotlib=3.6.3=py311h1ea47a8_0 +- matplotlib-base=3.6.3=py311h6e989c2_0 - mkl=2024.1.0=h66d3029_694 - msys2-conda-epoch=20160418=1 -- munkres=1.1.4=pyh9f0ad1d_0 +- munkres=1.0.7=py_1 - natsort=8.4.0=pyhd8ed1ab_0 -- networkx=3.2=pyhd8ed1ab_0 -- numba=0.60.0=py310h7793332_0 -- numpy=1.26.4=py310hf667824_0 -- numpy_groupies=0.11.2=pyhd8ed1ab_0 +- networkx=3.3=pyhd8ed1ab_1 +- numba=0.60.0=py311h0673bce_0 +- numpy=1.26.4=py311h0b4df5a_0 - openjpeg=2.5.2=h3d672ee_0 - openssl=3.3.1=h2466b09_3 - packaging=24.1=pyhd8ed1ab_0 -- pandas=1.3.5=py310hf5e1058_0 +- pandas=1.5.2=py311hf63dbb6_2 - patsy=0.5.6=pyhd8ed1ab_0 - pcre2=10.44=h3d7b363_2 -- pillow=10.4.0=py310h3e38d90_0 +- pillow=10.4.0=py311h5592be9_0 - pip=24.2=pyh8b19718_1 - ply=3.11=pyhd8ed1ab_2 - pthread-stubs=0.4=hcd874cb_1001 - pthreads-win32=2.9.1=hfa6e2cd_3 - pynndescent=0.5.13=pyhff2d567_0 - pyparsing=3.1.4=pyhd8ed1ab_0 -- pyqt=5.15.9=py310h1fd54f2_5 -- pyqt5-sip=12.12.2=py310h00ffb61_5 -- python=3.10.14=h4de0772_0_cpython +- pyqt=5.15.9=py311h125bc19_5 +- pyqt5-sip=12.12.2=py311h12c1d0e_5 +- python=3.11.9=h631f459_0_cpython - python-dateutil=2.9.0=pyhd8ed1ab_0 -- python_abi=3.10=5_cp310 +- python_abi=3.11=5_cp311 - pytz=2024.1=pyhd8ed1ab_0 - qt-main=5.15.8=h06adc49_23 -- scanpy=1.9.8=pyhd8ed1ab_0 -- scikit-learn=1.5.1=py310hf2a6c47_0 -- scipy=1.14.1=py310h46043a1_0 +- scanpy=1.10.2=pyhd8ed1ab_0 +- scikit-learn=1.5.1=py311hdcb8d17_0 +- scipy=1.13.1=py311hd4686c6_0 - 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=59.8.0=py310h5588dad_1 -- sip=6.7.12=py310h00ffb61_0 +- setuptools=72.2.0=pyhd8ed1ab_0 +- sip=6.7.12=py311h12c1d0e_0 - six=1.16.0=pyh6c4a22f_0 -- statsmodels=0.14.1=py310h3e78b6c_0 +- statsmodels=0.14.2=py311h0a17f05_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=py310ha8f682b_1 +- tornado=6.4.1=py311he736701_1 - tqdm=4.66.5=pyhd8ed1ab_0 +- typing=3.10.0.0=pyhd8ed1ab_1 - typing_extensions=4.12.2=pyha770c72_0 - tzdata=2024a=h8827d51_1 - ucrt=10.0.22621.0=h57928b3_0 -- umap-learn=0.5.6=py310h5588dad_1 -- unicodedata2=15.1.0=py310h8d17308_0 +- umap-learn=0.5.6=py311h1ea47a8_1 - vc=14.3=h8a93ad2_20 - vc14_runtime=14.40.33810=hcc2c482_20 - vs2015_runtime=14.40.33810=h3bf8584_20 From ba0dfbb90b8504cce92d20980ab9fc8f4a03bc3f Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 09:21:25 +0100 Subject: [PATCH 08/14] woops updated env in R code too --- R/basilisk.R | 208 ++++++++++++++++------------------- inst/envs/format_yaml_to_r.R | 2 +- 2 files changed, 95 insertions(+), 115 deletions(-) diff --git a/R/basilisk.R b/R/basilisk.R index 29860f4..5b6c4cb 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -3,152 +3,132 @@ .scvelo.dependencies.Windows <- list( channels = c("bioconda", "conda-forge"), packages = c( - '_libgcc_mutex==0.1', - '_openmp_mutex==4.5', - 'absl-py==2.1.0', 'anndata==0.10.9', 'array-api-compat==1.8', - 'blas==1.0', - 'bottleneck==1.3.7', - 'brotli==1.0.9', - 'brotli-bin==1.0.9', + 'brotli==1.1.0', + 'brotli-bin==1.1.0', 'bzip2==1.0.8', - 'c-ares==1.19.1', - 'ca-certificates==2024.7.2', - 'chex==0.1.5', - 'click==8.1.7', - 'contextlib2==21.6.0', - 'contourpy==1.2.0', - 'cycler==0.11.0', - 'dm-tree==0.1.7', - 'docrep==0.3.2', - 'et_xmlfile==1.1.0', - 'exceptiongroup==1.2.0', - 'filelock==3.13.1', - 'flax==0.6.1', - 'fonttools==4.51.0', + 'ca-certificates==2024.7.4', + 'cached-property==1.5.2', + 'cached_property==1.5.2', + 'certifi==2024.7.4', + 'colorama==0.4.6', + 'contourpy==1.3.0', + 'cycler==0.12.1', + 'exceptiongroup==1.2.2', + 'fonttools==4.53.1', 'freetype==2.12.1', - 'fsspec==2024.3.1', 'get-annotations==0.1.2', - 'gmp==6.2.1', - 'gmpy2==2.1.2', + 'glib==2.80.3', + 'glib-tools==2.80.3', + 'gst-plugins-base==1.24.6', + 'gstreamer==1.24.6', 'h5py==3.11.0', - 'hdf5==1.12.1', - 'jax==0.3.25', - 'jaxlib==0.3.25', - 'jinja2==3.1.4', + 'hdf5==1.14.3', + 'icu==73.2', + 'intel-openmp==2024.2.1', 'joblib==1.4.2', - 'jpeg==9e', - 'kiwisolver==1.4.4', - 'krb5==1.20.1', - 'lcms2==2.12', - 'ld_impl_linux-64==2.38', + 'kiwisolver==1.4.5', + 'krb5==1.21.3', + 'lcms2==2.16', 'legacy-api-wrap==1.4', - 'lerc==3.0', + 'lerc==4.0.0', + 'libaec==1.1.3', 'libblas==3.9.0', - 'libbrotlicommon==1.0.9', - 'libbrotlidec==1.0.9', - 'libbrotlienc==1.0.9', + 'libbrotlicommon==1.1.0', + 'libbrotlidec==1.1.0', + 'libbrotlienc==1.1.0', 'libcblas==3.9.0', - 'libcurl==7.88.1', - 'libdeflate==1.17', - 'libedit==3.1.20230828', - 'libev==4.33', - 'libffi==3.4.4', - 'libgcc==14.1.0', - 'libgcc-ng==14.1.0', - 'libgfortran-ng==11.2.0', - 'libgfortran5==11.2.0', - 'libgomp==14.1.0', - 'libllvm14==14.0.6', - 'libnghttp2==1.57.0', - 'libopenblas==0.3.21', - 'libpng==1.6.39', - 'libprotobuf==3.20.3', + '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', + 'libiconv==1.17', + 'libintl==0.22.5', + 'libintl-devel==0.22.5', + 'libjpeg-turbo==3.0.0', + 'liblapack==3.9.0', + 'libogg==1.3.5', + 'libpng==1.6.43', + 'libsqlite==3.46.0', 'libssh2==1.11.0', - 'libstdcxx==14.1.0', - 'libstdcxx-ng==14.1.0', - 'libtiff==4.5.1', - 'libuuid==1.41.5', - 'libwebp-base==1.3.2', - 'lightning-utilities==0.9.0', + 'libtiff==4.6.0', + 'libvorbis==1.3.7', + 'libwebp-base==1.4.0', + 'libxcb==1.16', + 'libxml2==2.12.7', + 'libzlib==1.3.1', 'llvmlite==0.43.0', - 'loompy==3.0.6', - 'lz4-c==1.9.4', - 'markdown-it-py==2.2.0', - 'markupsafe==2.1.3', - 'matplotlib-base==3.8.4', - 'mdurl==0.1.0', - 'ml-collections==0.1.1', - 'mpc==1.1.0', - 'mpfr==4.0.2', - 'mpmath==1.3.0', - 'msgpack-python==1.0.3', - 'mudata==0.3.0', - 'multipledispatch==0.6.0', - 'natsort==7.1.1', - 'ncurses==6.4', + 'loompy==2.0.16', + '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', + 'mkl==2024.1.0', + 'msys2-conda-epoch==20160418', + 'munkres==1.0.7', + 'natsort==8.4.0', 'networkx==3.3', 'numba==0.60.0', - 'numexpr==2.8.7', 'numpy==1.26.4', - 'numpy-base==1.26.4', - 'numpy_groupies==0.11.2', - 'numpyro==0.13.2', 'openjpeg==2.5.2', - 'openpyxl==3.1.5', - 'openssl==3.0.14', - 'opt_einsum==3.3.0', - 'optax==0.1.4', + 'openssl==3.3.1', 'packaging==24.1', - 'pandas==2.2.2', + 'pandas==1.5.2', 'patsy==0.5.6', + 'pcre2==10.44', 'pillow==10.4.0', 'pip==24.2', - 'pybind11-abi==4', - 'pygments==2.15.1', - 'pynndescent==0.5.10', - 'pyparsing==3.0.9', - 'pyro-api==0.1.2', - 'pyro-ppl==1.9.1', + 'ply==3.11', + 'pthread-stubs==0.4', + 'pthreads-win32==2.9.1', + 'pynndescent==0.5.13', + 'pyparsing==3.1.4', + 'pyqt==5.15.9', + 'pyqt5-sip==12.12.2', 'python==3.11.9', - 'python-dateutil==2.9.0post0', - 'python-tzdata==2023.3', + 'python-dateutil==2.9.0', 'python_abi==3.11', - 'pytorch==2.3.0', - 'pytorch-lightning==1.9.5', 'pytz==2024.1', - 'pyyaml==6.0.1', - 'readline==8.2', - 'rich==13.7.1', + 'qt-main==5.15.8', 'scanpy==1.10.2', - 'scikit-learn==1.1.3', + 'scikit-learn==1.5.1', 'scipy==1.13.1', - 'scvelo==0.3.2', - 'scvi-tools==0.20.3', + 'scvelo==0.2.5', 'seaborn==0.13.2', + 'seaborn-base==0.13.2', 'session-info==1.0.0', - 'setuptools==72.1.0', + 'setuptools==72.2.0', + 'sip==6.7.12', 'six==1.16.0', - 'sqlite==3.45.3', 'statsmodels==0.14.2', 'stdlib-list==0.10.0', - 'sympy==1.12', + 'tbb==2021.12.0', 'threadpoolctl==3.5.0', - 'tk==8.6.14', - 'toolz==0.12.0', - 'torchmetrics==1.4.0.post0', - 'tqdm==4.66.4', - 'typing-extensions==4.11.0', - 'typing_extensions==4.11.0', + 'tk==8.6.13', + 'toml==0.10.2', + 'tomli==2.0.1', + 'tornado==6.4.1', + 'tqdm==4.66.5', + 'typing==3.10.0.0', + 'typing_extensions==4.12.2', 'tzdata==2024a', - 'umap-learn==0.5.3', - 'unicodedata2==15.1.0', - 'wheel==0.43.0', - 'xz==5.4.6', - 'yaml==0.2.5', - 'zlib==1.2.13', - 'zstd==1.5.5' + 'ucrt==10.0.22621.0', + 'umap-learn==0.5.6', + 'vc==14.3', + 'vc14_runtime==14.40.33810', + 'vs2015_runtime==14.40.33810', + 'wheel==0.44.0', + 'xorg-libxau==1.0.11', + 'xorg-libxdmcp==1.1.3', + 'xz==5.2.6', + 'zstd==1.5.6' ) ) diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R index d147eb2..9120aa8 100644 --- a/inst/envs/format_yaml_to_r.R +++ b/inst/envs/format_yaml_to_r.R @@ -1,5 +1,5 @@ library(yaml) -yaml_data <- yaml::read_yaml("Linux_x86_64_anaconda.yaml") +yaml_data <- yaml::read_yaml("Windows.yaml") r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies) cat(paste0( "c(", From 7c661460c0e82749d7b48c3c66f1b77bf3a276d0 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 09:52:18 +0100 Subject: [PATCH 09/14] downgrade python (https://github.com/theislab/scvelo/issues/1124#issuecomment-1802261666) --- DESCRIPTION | 2 +- R/basilisk.R | 74 +++++++++++++++++++++++---------- inst/envs/Windows.yaml | 92 ++++++++++++++++++++++++++++-------------- 3 files changed, 114 insertions(+), 54 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d9ee319..62b5579 100644 --- 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 index 5b6c4cb..1f83583 100644 --- 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 index e1e44f7..030532a 100644 --- 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 From 81fa558c8cceddc21574d6c0e6518be61bedb989 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 10:01:09 +0100 Subject: [PATCH 10/14] matplotlib 3.6.3 --- DESCRIPTION | 2 +- R/basilisk.R | 8 +++----- inst/envs/Windows.yaml | 8 +++----- 3 files changed, 7 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 62b5579..ee529d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.12 +Version: 1.15.13 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 index 1f83583..c01b57b 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -33,9 +33,7 @@ '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', @@ -80,8 +78,8 @@ 'm2w64-gmp==6.1.0', 'm2w64-libwinpthread-git==5.0.0.4634.697f757', 'markupsafe==2.1.5', - 'matplotlib==3.7.2', - 'matplotlib-base==3.7.2', + 'matplotlib==3.6.3', + 'matplotlib-base==3.6.3', 'mkl==2024.1.0', 'msys2-conda-epoch==20160418', 'munkres==1.0.7', @@ -106,7 +104,7 @@ 'py-cpuinfo==9.0.0', 'pycparser==2.22', 'pynndescent==0.5.13', - 'pyparsing==3.0.9', + 'pyparsing==3.1.4', 'pyqt==5.15.9', 'pyqt5-sip==12.12.2', 'pysocks==1.7.1', diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml index 030532a..8920273 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -33,9 +33,7 @@ dependencies: - 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 @@ -80,8 +78,8 @@ dependencies: - m2w64-gmp=6.1.0=2 - m2w64-libwinpthread-git=5.0.0.4634.697f757=2 - markupsafe=2.1.5=py38h91455d4_0 -- matplotlib=3.7.2=py38haa244fe_0 -- matplotlib-base=3.7.2=py38h2d9580e_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 @@ -106,7 +104,7 @@ dependencies: - py-cpuinfo=9.0.0=pyhd8ed1ab_0 - pycparser=2.22=pyhd8ed1ab_0 - pynndescent=0.5.13=pyhff2d567_0 -- pyparsing=3.0.9=pyhd8ed1ab_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 From e661635e994417e5987f0016ee1a0f9b8413e1fe Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 10:09:56 +0100 Subject: [PATCH 11/14] pandas 1.5.2 --- DESCRIPTION | 2 +- R/basilisk.R | 3 +-- inst/envs/Windows.yaml | 3 +-- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ee529d3..5d3eaa1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.13 +Version: 1.15.14 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 index c01b57b..8acea4b 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -91,7 +91,7 @@ 'openjpeg==2.5.2', 'openssl==3.3.1', 'packaging==24.1', - 'pandas==2.0.3', + 'pandas==1.5.2', 'patsy==0.5.6', 'pcre2==10.44', 'pillow==10.4.0', @@ -111,7 +111,6 @@ 'pytables==3.8.0', 'python==3.8.19', 'python-dateutil==2.9.0', - 'python-tzdata==2024.1', 'python_abi==3.8', 'pytz==2024.1', 'qt-main==5.15.8', diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml index 8920273..8c6a8c9 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -91,7 +91,7 @@ dependencies: - openjpeg=2.5.2=h3d672ee_0 - openssl=3.3.1=h2466b09_3 - packaging=24.1=pyhd8ed1ab_0 -- pandas=2.0.3=py38hf08cf0d_1 +- pandas=1.5.2=py38h5846ac1_2 - patsy=0.5.6=pyhd8ed1ab_0 - pcre2=10.44=h3d7b363_2 - pillow=10.4.0=py38h8d10685_0 @@ -111,7 +111,6 @@ dependencies: - pytables=3.8.0=py38h4c0c689_4 - python=3.8.19=h4de0772_0_cpython - python-dateutil=2.9.0=pyhd8ed1ab_0 -- python-tzdata=2024.1=pyhd8ed1ab_0 - python_abi=3.8=5_cp38 - pytz=2024.1=pyhd8ed1ab_0 - qt-main=5.15.8=h06adc49_23 From 785835d3811041acc13b3daba76b104076e2c26a Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 10:16:29 +0100 Subject: [PATCH 12/14] numpy 1.21.1 --- DESCRIPTION | 2 +- R/basilisk.R | 19 ++++++++----------- inst/envs/Windows.yaml | 21 +++++++++------------ 3 files changed, 18 insertions(+), 24 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5d3eaa1..20dafe4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.14 +Version: 1.15.15 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 index 8acea4b..cd540e9 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -9,7 +9,6 @@ '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', @@ -26,8 +25,8 @@ 'gst-plugins-base==1.24.6', 'gstreamer==1.24.6', 'h2==4.1.0', - 'h5py==3.11.0', - 'hdf5==1.14.3', + 'h5py==3.8.0', + 'hdf5==1.14.0', 'hpack==4.0.0', 'hyperframe==6.0.1', 'icu==73.2', @@ -69,7 +68,7 @@ 'libxcb==1.16', 'libxml2==2.12.7', 'libzlib==1.3.1', - 'llvmlite==0.41.1', + 'llvmlite==0.39.1', 'loompy==2.0.16', 'lz4-c==1.9.4', 'm2w64-gcc-libgfortran==5.3.0', @@ -85,9 +84,9 @@ 'munkres==1.0.7', 'natsort==8.4.0', 'networkx==3.1', - 'numba==0.58.1', + 'numba==0.56.4', 'numexpr==2.7.3', - 'numpy==1.24.4', + 'numpy==1.21.1', 'openjpeg==2.5.2', 'openssl==3.3.1', 'packaging==24.1', @@ -101,14 +100,13 @@ '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', 'pyqt==5.15.9', 'pyqt5-sip==12.12.2', 'pysocks==1.7.1', - 'pytables==3.8.0', + 'pytables==3.7.0', 'python==3.8.19', 'python-dateutil==2.9.0', 'python_abi==3.8', @@ -116,7 +114,7 @@ 'qt-main==5.15.8', 'requests==2.32.3', 'scanpy==1.7.2', - 'scikit-learn==1.3.2', + 'scikit-learn==1.2.2', 'scipy==1.10.1', 'scvelo==0.2.5', 'seaborn==0.13.2', @@ -128,7 +126,7 @@ 'sip==6.7.12', 'six==1.16.0', 'snappy==1.2.1', - 'statsmodels==0.14.1', + 'statsmodels==0.13.5', 'stdlib-list==0.10.0', 'tbb==2021.12.0', 'threadpoolctl==3.5.0', @@ -153,7 +151,6 @@ '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 index 8c6a8c9..169531b 100644 --- a/inst/envs/Windows.yaml +++ b/inst/envs/Windows.yaml @@ -9,7 +9,6 @@ dependencies: - 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 @@ -26,8 +25,8 @@ dependencies: - gst-plugins-base=1.24.6=hb0a98b8_0 - gstreamer=1.24.6=h5006eae_0 - h2=4.1.0=pyhd8ed1ab_0 -- h5py=3.11.0=nompi_py38hd93224d_102 -- hdf5=1.14.3=nompi_h2b43c12_105 +- 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 @@ -69,7 +68,7 @@ dependencies: - libxcb=1.16=h013a479_1 - libxml2=2.12.7=h0f24e4e_4 - libzlib=1.3.1=h2466b09_1 -- llvmlite=0.41.1=py38h19421c1_0 +- 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 @@ -85,9 +84,9 @@ dependencies: - munkres=1.0.7=py_1 - natsort=8.4.0=pyhd8ed1ab_0 - networkx=3.1=pyhd8ed1ab_0 -- numba=0.58.1=py38h4a59444_0 +- numba=0.56.4=py38h3873db4_0 - numexpr=2.7.3=py38h5d928e2_2 -- numpy=1.24.4=py38h1d91fd2_0 +- numpy=1.21.1=py38h09042cb_0 - openjpeg=2.5.2=h3d672ee_0 - openssl=3.3.1=h2466b09_3 - packaging=24.1=pyhd8ed1ab_0 @@ -101,14 +100,13 @@ dependencies: - 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=py38hd6c051e_5 - pyqt5-sip=12.12.2=py38hd3f51b4_5 - pysocks=1.7.1=pyh0701188_6 -- pytables=3.8.0=py38h4c0c689_4 +- 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 @@ -116,8 +114,8 @@ dependencies: - qt-main=5.15.8=h06adc49_23 - 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 +- 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 @@ -128,7 +126,7 @@ dependencies: - sip=6.7.12=py38hd3f51b4_0 - six=1.16.0=pyh6c4a22f_0 - snappy=1.2.1=h23299a8_0 -- statsmodels=0.14.1=py38he7056a7_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 @@ -153,6 +151,5 @@ dependencies: - 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 From 8d8b7e1966a1e27f546684db51d73cc4d82b6990 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 10:22:30 +0100 Subject: [PATCH 13/14] fix version bump --- DESCRIPTION | 4 ++-- NEWS.md | 4 ++++ 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 20dafe4..d61dc72 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.15 -Date: 2024-08-29 +Version: 1.15.7 +Date: 2024-08-30 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')), person("Charlotte", "Soneson", role="aut", email="charlottesoneson@gmail.com", comment = c(ORCID = '0000-0003-3833-2169')), diff --git a/NEWS.md b/NEWS.md index c2a2383..9f1c65b 100644 --- a/NEWS.md +++ b/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. From 0f6b96e7e506308061817be8b4f4d42792f85203 Mon Sep 17 00:00:00 2001 From: Kevin Rue Date: Fri, 30 Aug 2024 11:05:46 +0100 Subject: [PATCH 14/14] remove useless pip --- R/basilisk.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/basilisk.R b/R/basilisk.R index cd540e9..6b043d6 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -160,7 +160,6 @@ .scvelo.dependencies.MacOSXArm <- list( channels = c("conda-forge", "bioconda"), - pip = character(0), packages = c( 'absl-py==2.1.0', 'anndata==0.10.7',