diff --git a/DESCRIPTION b/DESCRIPTION index 161094b..b54c235 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.12 -Date: 2024-09-12 +Version: 1.15.13 +Date: 2024-10-11 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 31c3957..47bd895 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# velociraptor 1.15.13 + +* Add separate environment (untested) for Linux Aarch64. + Cannot break that platform more than it already is. + # velociraptor 1.15.12 * Update Conda environment for Linux to avoid Anaconda channel. diff --git a/R/basilisk.R b/R/basilisk.R index 903981a..aa5a63c 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -156,11 +156,27 @@ ) ) -## MacOSXArm ---- +## LinuxAarch64 ---- -.scvelo.dependencies.MacOSXArm <- list( +.scvelo.dependencies.LinuxAarch64 <- list( channels = c("conda-forge"), packages = c( + 'ipywidgets==8.1.2', + 'libtiff==4.5.1', + 'pillow==10.0.0', + 'scipy==1.13.1', + 'scvelo==0.3.2', + 'tqdm==4.66.5' + ) +) + +## Linux ---- + +.scvelo.dependencies.Linux <- list( + channels = c("conda-forge"), + packages = c( + '_libgcc_mutex==0.1', + '_openmp_mutex==4.5', 'absl-py==2.1.0', 'anndata==0.10.9', 'aom==3.9.1', @@ -192,9 +208,9 @@ 'etils==1.9.4', 'exceptiongroup==1.2.2', 'executing==2.1.0', - 'filelock==3.16.0', + 'filelock==3.16.1', 'flax==0.9.0', - 'fonttools==4.53.1', + 'fonttools==4.54.1', 'freetype==2.12.1', 'fsspec==2024.9.0', 'get-annotations==0.1.2', @@ -206,23 +222,26 @@ 'hpack==4.0.0', 'hyperframe==6.0.1', 'icu==75.1', - 'idna==3.8', - 'importlib-metadata==8.4.0', - 'importlib_resources==6.4.4', + 'idna==3.10', + 'importlib-metadata==8.5.0', + 'importlib_metadata==8.5.0', + 'importlib_resources==6.4.5', 'ipython==8.27.0', - 'ipywidgets==8.1.5', - 'jax==0.4.31', - 'jaxlib==0.4.31', + 'ipywidgets==8.1.2', + 'jax==0.4.27', + 'jaxlib==0.4.23', 'jedi==0.19.1', 'jinja2==3.1.4', 'joblib==1.4.2', 'jupyterlab_widgets==3.0.13', + 'keyutils==1.6.1', 'kiwisolver==1.4.7', 'krb5==1.21.3', - 'lcms2==2.16', + 'lcms2==2.15', + 'ld_impl_linux-64==2.43', 'legacy-api-wrap==1.4', 'lerc==4.0.0', - 'libabseil==20240116.2', + 'libabseil==20230802.1', 'libaec==1.1.3', 'libavif16==1.1.1', 'libblas==3.9.0', @@ -230,38 +249,44 @@ 'libbrotlidec==1.1.0', 'libbrotlienc==1.1.0', 'libcblas==3.9.0', - 'libcurl==8.9.1', - 'libcxx==18.1.8', - 'libdeflate==1.21', + 'libcurl==8.10.1', + 'libdeflate==1.18', 'libedit==3.1.20191231', 'libev==4.33', 'libexpat==2.6.3', 'libffi==3.4.2', - 'libgfortran==5.0.0', - 'libgfortran5==13.2.0', - 'libgrpc==1.62.2', + 'libgcc==14.1.0', + 'libgcc-ng==14.1.0', + 'libgfortran==14.1.0', + 'libgfortran-ng==14.1.0', + 'libgfortran5==14.1.0', + 'libgomp==14.1.0', + 'libgrpc==1.58.2', 'libhwloc==2.11.1', 'libiconv==1.17', - 'libjpeg-turbo==3.0.0', + 'libjpeg-turbo==2.1.5.1', 'liblapack==3.9.0', 'libllvm14==14.0.6', 'libnghttp2==1.58.0', + 'libnsl==2.0.1', 'libopenblas==0.3.27', - 'libpng==1.6.43', - 'libprotobuf==4.25.3', + 'libpng==1.6.44', + 'libprotobuf==4.24.3', 'libre2-11==2023.09.01', 'libsqlite==3.46.1', 'libssh2==1.11.0', - 'libtiff==4.6.0', - 'libtorch==2.4.0', - 'libuv==1.48.0', + 'libstdcxx==14.1.0', + 'libstdcxx-ng==14.1.0', + 'libtiff==4.5.1', + 'libuuid==2.38.1', + 'libuv==1.49.0', 'libwebp-base==1.4.0', - 'libxcb==1.16', + 'libxcb==1.15', + 'libxcrypt==4.4.36', 'libxml2==2.12.7', 'libzlib==1.3.1', - 'lightning==2.4.0', + 'lightning==2.3.3', 'lightning-utilities==0.11.7', - 'llvm-openmp==18.1.8', 'llvmlite==0.43.0', 'loompy==3.0.6', 'lz4-c==1.9.4', @@ -271,11 +296,11 @@ 'matplotlib-inline==0.1.7', 'mdurl==0.1.2', 'ml-collections==0.1.1', - 'ml_dtypes==0.4.0', + 'ml_dtypes==0.5.0', 'mpc==1.3.1', 'mpfr==4.2.1', 'mpmath==1.3.0', - 'msgpack-python==1.0.8', + 'msgpack-python==1.1.0', 'mudata==0.3.1', 'multipledispatch==0.6.0', 'munkres==1.1.4', @@ -287,8 +312,8 @@ 'numba==0.60.0', 'numpy==1.26.4', 'numpy_groupies==0.11.2', - 'numpyro==0.15.2', - 'openjpeg==2.5.2', + 'numpyro==0.15.3', + 'openjpeg==2.5.0', 'openpyxl==3.1.5', 'openssl==3.3.2', 'opt-einsum==3.3.0', @@ -296,15 +321,15 @@ 'optax==0.2.2', 'orbax-checkpoint==0.4.4', 'packaging==24.1', - 'pandas==2.2.2', + 'pandas==2.2.3', 'parso==0.8.4', 'patsy==0.5.6', 'pexpect==4.9.0', 'pickleshare==0.7.5', - 'pillow==10.4.0', + 'pillow==10.0.0', 'pip==24.2', - 'prompt-toolkit==3.0.47', - 'protobuf==4.25.3', + 'prompt-toolkit==3.0.48', + 'protobuf==4.24.3', 'pthread-stubs==0.4', 'ptyprocess==0.7.0', 'pure_eval==0.2.3', @@ -316,12 +341,12 @@ 'pyro-api==0.1.2', 'pyro-ppl==1.9.1', 'pysocks==1.7.1', - 'python==3.11.9', + 'python==3.11.10', 'python-dateutil==2.9.0', - 'python-tzdata==2024.1', + 'python-tzdata==2024.2', 'python_abi==3.11', - 'pytorch==2.4.0', - 'pytorch-lightning==2.4.0', + 'pytorch==2.0.0', + 'pytorch-lightning==2.3.3', 'pytz==2024.1', 'pyyaml==6.0.2', 'qhull==2020.2', @@ -329,61 +354,62 @@ 're2==2023.09.01', 'readline==8.2', 'requests==2.32.3', - 'rich==13.7.1', - 'scanpy==1.10.2', + 'rich==13.8.1', + 'scanpy==1.10.3', 'scikit-learn==1.1.3', 'scipy==1.13.1', 'scvelo==0.3.2', - 'scvi-tools==1.1.6', + 'scvi-tools==1.1.6.post1', 'seaborn==0.13.2', 'seaborn-base==0.13.2', 'session-info==1.0.0', - 'setuptools==73.0.1', + 'setuptools==75.1.0', 'six==1.16.0', - 'sleef==3.6.1', + 'sleef==3.7', 'snappy==1.2.1', 'sparse==0.15.4', 'stack_data==0.6.2', - 'statsmodels==0.14.2', + 'statsmodels==0.14.3', 'stdlib-list==0.10.0', 'svt-av1==2.2.1', 'sympy==1.13.2', 'tbb==2021.13.0', - 'tensorstore==0.1.62', + 'tensorstore==0.1.44', 'threadpoolctl==3.5.0', 'tk==8.6.13', 'toolz==0.12.1', - 'torchmetrics==1.4.0.post0', + 'torchmetrics==1.4.2', 'tqdm==4.66.5', 'traitlets==5.14.3', 'typing-extensions==4.12.2', 'typing_extensions==4.12.2', 'tzdata==2024a', 'umap-learn==0.5.6', - 'urllib3==2.2.2', + 'urllib3==2.2.3', 'wcwidth==0.2.13', 'wheel==0.44.0', 'widgetsnbextension==4.0.13', - 'xarray==2024.7.0', + 'xarray==2024.9.0', 'xorg-libxau==1.0.11', 'xorg-libxdmcp==1.1.3', 'xz==5.2.6', 'yaml==0.2.5', - 'zipp==3.20.1', + 'zipp==3.20.2', 'zstandard==0.23.0', 'zstd==1.5.6' ) ) -## MacOSX ---- +## MacOSXArm ---- -.scvelo.dependencies.MacOSX <- list( - channels = c("conda-forge", "bioconda"), +.scvelo.dependencies.MacOSXArm <- list( + channels = c("conda-forge"), packages = c( 'absl-py==2.1.0', 'anndata==0.10.9', 'aom==3.9.1', 'array-api-compat==1.8', + 'asttokens==2.4.1', 'blosc==1.21.6', 'brotli==1.1.0', 'brotli-bin==1.1.0', @@ -393,25 +419,28 @@ 'ca-certificates==2024.8.30', 'cached-property==1.5.2', 'cached_property==1.5.2', - 'certifi==2024.7.4', - 'cffi==1.17.0', + 'certifi==2024.8.30', + 'cffi==1.17.1', 'charset-normalizer==3.3.2', 'chex==0.1.86', 'click==8.1.7', 'colorama==0.4.6', + 'comm==0.2.2', 'contextlib2==21.6.0', 'contourpy==1.3.0', 'cycler==0.12.1', 'dav1d==1.2.1', + 'decorator==5.1.1', 'docrep==0.3.2', 'et_xmlfile==1.1.0', - 'etils==1.9.2', + 'etils==1.9.4', 'exceptiongroup==1.2.2', - 'filelock==3.15.4', + 'executing==2.1.0', + 'filelock==3.16.0', 'flax==0.9.0', 'fonttools==4.53.1', 'freetype==2.12.1', - 'fsspec==2024.6.1', + 'fsspec==2024.9.0', 'get-annotations==0.1.2', 'gmp==6.3.0', 'gmpy2==2.1.5', @@ -423,13 +452,16 @@ 'icu==75.1', 'idna==3.8', 'importlib-metadata==8.4.0', - 'importlib_metadata==8.4.0', 'importlib_resources==6.4.4', + 'ipython==8.27.0', + 'ipywidgets==8.1.5', 'jax==0.4.31', 'jaxlib==0.4.31', + 'jedi==0.19.1', 'jinja2==3.1.4', 'joblib==1.4.2', - 'kiwisolver==1.4.5', + 'jupyterlab_widgets==3.0.13', + 'kiwisolver==1.4.7', 'krb5==1.21.3', 'lcms2==2.16', 'legacy-api-wrap==1.4', @@ -447,7 +479,7 @@ 'libdeflate==1.21', 'libedit==3.1.20191231', 'libev==4.33', - 'libexpat==2.6.2', + 'libexpat==2.6.3', 'libffi==3.4.2', 'libgfortran==5.0.0', 'libgfortran5==13.2.0', @@ -462,7 +494,7 @@ 'libpng==1.6.43', 'libprotobuf==4.25.3', 'libre2-11==2023.09.01', - 'libsqlite==3.46.0', + 'libsqlite==3.46.1', 'libssh2==1.11.0', 'libtiff==4.6.0', 'libtorch==2.4.0', @@ -472,7 +504,7 @@ 'libxml2==2.12.7', 'libzlib==1.3.1', 'lightning==2.4.0', - 'lightning-utilities==0.11.6', + 'lightning-utilities==0.11.7', 'llvm-openmp==18.1.8', 'llvmlite==0.43.0', 'loompy==3.0.6', @@ -480,6 +512,7 @@ 'markdown-it-py==3.0.0', 'markupsafe==2.1.5', 'matplotlib-base==3.9.2', + 'matplotlib-inline==0.1.7', 'mdurl==0.1.2', 'ml-collections==0.1.1', 'ml_dtypes==0.4.0', @@ -501,18 +534,24 @@ 'numpyro==0.15.2', 'openjpeg==2.5.2', 'openpyxl==3.1.5', - 'openssl==3.3.1', + 'openssl==3.3.2', 'opt-einsum==3.3.0', 'opt_einsum==3.3.0', 'optax==0.2.2', 'orbax-checkpoint==0.4.4', 'packaging==24.1', 'pandas==2.2.2', + 'parso==0.8.4', 'patsy==0.5.6', + 'pexpect==4.9.0', + 'pickleshare==0.7.5', 'pillow==10.4.0', 'pip==24.2', + 'prompt-toolkit==3.0.47', 'protobuf==4.25.3', 'pthread-stubs==0.4', + 'ptyprocess==0.7.0', + 'pure_eval==0.2.3', 'pybind11-abi==4', 'pycparser==2.22', 'pygments==2.18.0', @@ -543,28 +582,32 @@ 'seaborn==0.13.2', 'seaborn-base==0.13.2', 'session-info==1.0.0', - 'setuptools==72.2.0', + 'setuptools==73.0.1', 'six==1.16.0', 'sleef==3.6.1', 'snappy==1.2.1', 'sparse==0.15.4', + 'stack_data==0.6.2', 'statsmodels==0.14.2', 'stdlib-list==0.10.0', 'svt-av1==2.2.1', 'sympy==1.13.2', - 'tbb==2021.12.0', + 'tbb==2021.13.0', 'tensorstore==0.1.62', 'threadpoolctl==3.5.0', 'tk==8.6.13', 'toolz==0.12.1', 'torchmetrics==1.4.0.post0', 'tqdm==4.66.5', + 'traitlets==5.14.3', 'typing-extensions==4.12.2', 'typing_extensions==4.12.2', 'tzdata==2024a', 'umap-learn==0.5.6', 'urllib3==2.2.2', + 'wcwidth==0.2.13', 'wheel==0.44.0', + 'widgetsnbextension==4.0.13', 'xarray==2024.7.0', 'xorg-libxau==1.0.11', 'xorg-libxdmcp==1.1.3', @@ -576,18 +619,15 @@ ) ) -## Linux ---- +## MacOSX ---- -.scvelo.dependencies.Linux <- list( - channels = c("conda-forge"), +.scvelo.dependencies.MacOSX <- list( + channels = c("conda-forge", "bioconda"), packages = c( - '_libgcc_mutex==0.1', - '_openmp_mutex==4.5', 'absl-py==2.1.0', 'anndata==0.10.9', 'aom==3.9.1', 'array-api-compat==1.8', - 'asttokens==2.4.1', 'blosc==1.21.6', 'brotli==1.1.0', 'brotli-bin==1.1.0', @@ -597,28 +637,25 @@ 'ca-certificates==2024.8.30', 'cached-property==1.5.2', 'cached_property==1.5.2', - 'certifi==2024.8.30', - 'cffi==1.17.1', + 'certifi==2024.7.4', + 'cffi==1.17.0', 'charset-normalizer==3.3.2', 'chex==0.1.86', 'click==8.1.7', 'colorama==0.4.6', - 'comm==0.2.2', 'contextlib2==21.6.0', 'contourpy==1.3.0', 'cycler==0.12.1', 'dav1d==1.2.1', - 'decorator==5.1.1', 'docrep==0.3.2', 'et_xmlfile==1.1.0', - 'etils==1.9.4', + 'etils==1.9.2', 'exceptiongroup==1.2.2', - 'executing==2.1.0', - 'filelock==3.16.1', + 'filelock==3.15.4', 'flax==0.9.0', - 'fonttools==4.54.1', + 'fonttools==4.53.1', 'freetype==2.12.1', - 'fsspec==2024.9.0', + 'fsspec==2024.6.1', 'get-annotations==0.1.2', 'gmp==6.3.0', 'gmpy2==2.1.5', @@ -628,26 +665,20 @@ 'hpack==4.0.0', 'hyperframe==6.0.1', 'icu==75.1', - 'idna==3.10', - 'importlib-metadata==8.5.0', - 'importlib_metadata==8.5.0', - 'importlib_resources==6.4.5', - 'ipython==8.27.0', - 'ipywidgets==8.1.2', - 'jax==0.4.27', - 'jaxlib==0.4.23', - 'jedi==0.19.1', + 'idna==3.8', + 'importlib-metadata==8.4.0', + 'importlib_metadata==8.4.0', + 'importlib_resources==6.4.4', + 'jax==0.4.31', + 'jaxlib==0.4.31', 'jinja2==3.1.4', 'joblib==1.4.2', - 'jupyterlab_widgets==3.0.13', - 'keyutils==1.6.1', - 'kiwisolver==1.4.7', + 'kiwisolver==1.4.5', 'krb5==1.21.3', - 'lcms2==2.15', - 'ld_impl_linux-64==2.43', + 'lcms2==2.16', 'legacy-api-wrap==1.4', 'lerc==4.0.0', - 'libabseil==20230802.1', + 'libabseil==20240116.2', 'libaec==1.1.3', 'libavif16==1.1.1', 'libblas==3.9.0', @@ -655,58 +686,51 @@ 'libbrotlidec==1.1.0', 'libbrotlienc==1.1.0', 'libcblas==3.9.0', - 'libcurl==8.10.1', - 'libdeflate==1.18', + 'libcurl==8.9.1', + 'libcxx==18.1.8', + 'libdeflate==1.21', 'libedit==3.1.20191231', 'libev==4.33', - 'libexpat==2.6.3', + 'libexpat==2.6.2', 'libffi==3.4.2', - 'libgcc==14.1.0', - 'libgcc-ng==14.1.0', - 'libgfortran==14.1.0', - 'libgfortran-ng==14.1.0', - 'libgfortran5==14.1.0', - 'libgomp==14.1.0', - 'libgrpc==1.58.2', + 'libgfortran==5.0.0', + 'libgfortran5==13.2.0', + 'libgrpc==1.62.2', 'libhwloc==2.11.1', 'libiconv==1.17', - 'libjpeg-turbo==2.1.5.1', + 'libjpeg-turbo==3.0.0', 'liblapack==3.9.0', 'libllvm14==14.0.6', 'libnghttp2==1.58.0', - 'libnsl==2.0.1', 'libopenblas==0.3.27', - 'libpng==1.6.44', - 'libprotobuf==4.24.3', + 'libpng==1.6.43', + 'libprotobuf==4.25.3', 'libre2-11==2023.09.01', - 'libsqlite==3.46.1', + 'libsqlite==3.46.0', 'libssh2==1.11.0', - 'libstdcxx==14.1.0', - 'libstdcxx-ng==14.1.0', - 'libtiff==4.5.1', - 'libuuid==2.38.1', - 'libuv==1.49.0', + 'libtiff==4.6.0', + 'libtorch==2.4.0', + 'libuv==1.48.0', 'libwebp-base==1.4.0', - 'libxcb==1.15', - 'libxcrypt==4.4.36', + 'libxcb==1.16', 'libxml2==2.12.7', 'libzlib==1.3.1', - 'lightning==2.3.3', - 'lightning-utilities==0.11.7', + 'lightning==2.4.0', + 'lightning-utilities==0.11.6', + 'llvm-openmp==18.1.8', 'llvmlite==0.43.0', 'loompy==3.0.6', 'lz4-c==1.9.4', 'markdown-it-py==3.0.0', 'markupsafe==2.1.5', 'matplotlib-base==3.9.2', - 'matplotlib-inline==0.1.7', 'mdurl==0.1.2', 'ml-collections==0.1.1', - 'ml_dtypes==0.5.0', + 'ml_dtypes==0.4.0', 'mpc==1.3.1', 'mpfr==4.2.1', 'mpmath==1.3.0', - 'msgpack-python==1.1.0', + 'msgpack-python==1.0.8', 'mudata==0.3.1', 'multipledispatch==0.6.0', 'munkres==1.1.4', @@ -718,27 +742,21 @@ 'numba==0.60.0', 'numpy==1.26.4', 'numpy_groupies==0.11.2', - 'numpyro==0.15.3', - 'openjpeg==2.5.0', + 'numpyro==0.15.2', + 'openjpeg==2.5.2', 'openpyxl==3.1.5', - 'openssl==3.3.2', + 'openssl==3.3.1', 'opt-einsum==3.3.0', 'opt_einsum==3.3.0', 'optax==0.2.2', 'orbax-checkpoint==0.4.4', 'packaging==24.1', - 'pandas==2.2.3', - 'parso==0.8.4', + 'pandas==2.2.2', 'patsy==0.5.6', - 'pexpect==4.9.0', - 'pickleshare==0.7.5', - 'pillow==10.0.0', + 'pillow==10.4.0', 'pip==24.2', - 'prompt-toolkit==3.0.48', - 'protobuf==4.24.3', + 'protobuf==4.25.3', 'pthread-stubs==0.4', - 'ptyprocess==0.7.0', - 'pure_eval==0.2.3', 'pybind11-abi==4', 'pycparser==2.22', 'pygments==2.18.0', @@ -747,12 +765,12 @@ 'pyro-api==0.1.2', 'pyro-ppl==1.9.1', 'pysocks==1.7.1', - 'python==3.11.10', + 'python==3.11.9', 'python-dateutil==2.9.0', - 'python-tzdata==2024.2', + 'python-tzdata==2024.1', 'python_abi==3.11', - 'pytorch==2.0.0', - 'pytorch-lightning==2.3.3', + 'pytorch==2.4.0', + 'pytorch-lightning==2.4.0', 'pytz==2024.1', 'pyyaml==6.0.2', 'qhull==2020.2', @@ -760,47 +778,43 @@ 're2==2023.09.01', 'readline==8.2', 'requests==2.32.3', - 'rich==13.8.1', - 'scanpy==1.10.3', + 'rich==13.7.1', + 'scanpy==1.10.2', 'scikit-learn==1.1.3', 'scipy==1.13.1', 'scvelo==0.3.2', - 'scvi-tools==1.1.6.post1', + 'scvi-tools==1.1.6', 'seaborn==0.13.2', 'seaborn-base==0.13.2', 'session-info==1.0.0', - 'setuptools==75.1.0', + 'setuptools==72.2.0', 'six==1.16.0', - 'sleef==3.7', + 'sleef==3.6.1', 'snappy==1.2.1', 'sparse==0.15.4', - 'stack_data==0.6.2', - 'statsmodels==0.14.3', + 'statsmodels==0.14.2', 'stdlib-list==0.10.0', 'svt-av1==2.2.1', 'sympy==1.13.2', - 'tbb==2021.13.0', - 'tensorstore==0.1.44', + 'tbb==2021.12.0', + 'tensorstore==0.1.62', 'threadpoolctl==3.5.0', 'tk==8.6.13', 'toolz==0.12.1', - 'torchmetrics==1.4.2', + 'torchmetrics==1.4.0.post0', 'tqdm==4.66.5', - 'traitlets==5.14.3', 'typing-extensions==4.12.2', 'typing_extensions==4.12.2', 'tzdata==2024a', 'umap-learn==0.5.6', - 'urllib3==2.2.3', - 'wcwidth==0.2.13', + 'urllib3==2.2.2', 'wheel==0.44.0', - 'widgetsnbextension==4.0.13', - 'xarray==2024.9.0', + 'xarray==2024.7.0', 'xorg-libxau==1.0.11', 'xorg-libxdmcp==1.1.3', 'xz==5.2.6', 'yaml==0.2.5', - 'zipp==3.20.2', + 'zipp==3.20.1', 'zstandard==0.23.0', 'zstd==1.5.6' ) @@ -810,6 +824,8 @@ if (basilisk.utils::isWindows()) { .scvelo_dependencies <- .scvelo.dependencies.Windows +} else if (basilisk.utils::isLinuxAarch64()) { + .scvelo_dependencies <- .scvelo.dependencies.LinuxAarch64 } else if (basilisk.utils::isLinux()) { .scvelo_dependencies <- .scvelo.dependencies.Linux } else if (basilisk.utils::isMacOSXArm()) { diff --git a/R/scvelo.R b/R/scvelo.R index a86eb52..132366e 100644 --- a/R/scvelo.R +++ b/R/scvelo.R @@ -107,18 +107,31 @@ #' As of the latest \pkg{velociraptor} update (24 May 2024): #' #' \describe{ -#' \item{Linux}{\pkg{scVelo} v0.3.2 from bioconda is used. +#' \item{All environments}{ +#' \pkg{tqdm} and \pkg{ipywidgets} are installed to suppress the message "Unable to create progress bar". +#' } +#' \item{Linux}{\pkg{scVelo} v0.3.2 from conda-forge is used. +#' This is the latest version available to date. +#' \pkg{libtiff} is pinned to v4.5.1 and \pkg{pillow} is pinned to v10.0.0 (\url{https://github.com/conda-forge/libtiff-feedstock/issues/104#issuecomment-2375893029}), +#' \pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). +#' } +#' \item{Linux AArch64}{\pkg{scVelo} v0.3.2 from conda-forge is used. #' This is the latest version available to date. #' \pkg{libtiff} is pinned to v4.5.1 and \pkg{pillow} is pinned to v10.0.0 (\url{https://github.com/conda-forge/libtiff-feedstock/issues/104#issuecomment-2375893029}), #' \pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). +#' Please note that this environment has not been validated yet; it is derived from the environment from Linux (above) and requires additional testing to identify a working environment before pinning all the packages and versions in the environment. #' } -#' \item{MacOS Arm}{\pkg{scVelo} v0.3.2 from conda-forge is used. +#' \item{macOS}{\pkg{scVelo} v0.3.2 from conda-forge is used. #' This is the latest version available to date. -#' \pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}) +#' \pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). +#' } +#' \item{macOS ARM}{\pkg{scVelo} v0.3.2 from conda-forge is used. +#' This is the latest version available to date. +#' \pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). #' } #' \item{Windows}{\pkg{scVelo} v0.2.5 from bioconda is used. #' Later versions of \pkg{scVelo} depend on \pkg{jaxlib} which is not supported on Windows (\url{https://github.com/google/jax/issues/438}). -#' Note that \pkg{matplotlib} is pinned to v3.6.3 (\url{https://github.com/scverse/scanpy/issues/2411}), +#' \pkg{matplotlib} is pinned to v3.6.3 (\url{https://github.com/scverse/scanpy/issues/2411}), #' \pkg{pandas} is pinned to v1.5.2 (\url{https://stackoverflow.com/questions/76234312/importerror-cannot-import-name-is-categorical-from-pandas-api-types}), #' and \pkg{numpy} is pinned to v1.21.1 (\url{https://github.com/theislab/scvelo/issues/1109}). #' } diff --git a/man/scvelo.Rd b/man/scvelo.Rd index 51db3de..7626412 100644 --- a/man/scvelo.Rd +++ b/man/scvelo.Rd @@ -177,18 +177,31 @@ Differences in packages and versions available from Conda require different envi As of the latest \pkg{velociraptor} update (24 May 2024): \describe{ -\item{Linux}{\pkg{scVelo} v0.3.2 from bioconda is used. +\item{All environments}{ +\pkg{tqdm} and \pkg{ipywidgets} are installed to suppress the message "Unable to create progress bar". +} +\item{Linux}{\pkg{scVelo} v0.3.2 from conda-forge is used. +This is the latest version available to date. +\pkg{libtiff} is pinned to v4.5.1 and \pkg{pillow} is pinned to v10.0.0 (\url{https://github.com/conda-forge/libtiff-feedstock/issues/104#issuecomment-2375893029}), +\pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). +} +\item{Linux AArch64}{\pkg{scVelo} v0.3.2 from conda-forge is used. This is the latest version available to date. \pkg{libtiff} is pinned to v4.5.1 and \pkg{pillow} is pinned to v10.0.0 (\url{https://github.com/conda-forge/libtiff-feedstock/issues/104#issuecomment-2375893029}), \pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). +Please note that this environment has not been validated yet; it is derived from the environment from Linux (above) and requires additional testing to identify a working environment before pinning all the packages and versions in the environment. } -\item{MacOS Arm}{\pkg{scVelo} v0.3.2 from conda-forge is used. +\item{macOS}{\pkg{scVelo} v0.3.2 from conda-forge is used. This is the latest version available to date. -\pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}) +\pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). +} +\item{macOS ARM}{\pkg{scVelo} v0.3.2 from conda-forge is used. +This is the latest version available to date. +\pkg{scipy} is pinned to v1.13.1 (\url{https://github.com/theislab/scvelo/issues/1260}). } \item{Windows}{\pkg{scVelo} v0.2.5 from bioconda is used. Later versions of \pkg{scVelo} depend on \pkg{jaxlib} which is not supported on Windows (\url{https://github.com/google/jax/issues/438}). -Note that \pkg{matplotlib} is pinned to v3.6.3 (\url{https://github.com/scverse/scanpy/issues/2411}), +\pkg{matplotlib} is pinned to v3.6.3 (\url{https://github.com/scverse/scanpy/issues/2411}), \pkg{pandas} is pinned to v1.5.2 (\url{https://stackoverflow.com/questions/76234312/importerror-cannot-import-name-is-categorical-from-pandas-api-types}), and \pkg{numpy} is pinned to v1.21.1 (\url{https://github.com/theislab/scvelo/issues/1109}). }