diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index b2f6d52..37267e4 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -213,13 +213,13 @@ jobs: shell: Rscript {0} - name: Install covr - if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' run: | remotes::install_cran("covr") shell: Rscript {0} - name: Install pkgdown - if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: | remotes::install_cran("pkgdown") shell: Rscript {0} @@ -269,17 +269,17 @@ jobs: shell: Rscript {0} - name: Test coverage - if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' run: | covr::codecov() shell: Rscript {0} - name: Install package - if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: R CMD INSTALL . - name: Build and deploy pkgdown site - if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: | git config --global user.name "$GITHUB_ACTOR" git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com" @@ -299,7 +299,7 @@ jobs: path: check - uses: docker/build-push-action@v1 - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " + if: "github.ref == 'refs/heads/devel' && !contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_PASSWORD }} diff --git a/DESCRIPTION b/DESCRIPTION index d664f97..238bd4f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: velociraptor Title: Toolkit for Single-Cell Velocity -Version: 1.15.5 -Date: 2024-08-23 +Version: 1.15.6 +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')), 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 e0c37e7..c2a2383 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# velociraptor 1.15.6 + +* Update Conda environment to use `anaconda` channel on Linux. + Passed GitHub Action . + # velociraptor 1.15.5 * Update Conda environment to `svelo==0.3.2` on Linux. diff --git a/R/basilisk.R b/R/basilisk.R index bd120ab..3bdd527 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -698,291 +698,154 @@ ## Linux ---- .scvelo.dependencies.Linux <- list( - channels = c("conda-forge", "bioconda"), + channels = c("anaconda", "conda-forge", "bioconda"), packages = c( - c( - '_libgcc_mutex==0.1', - '_openmp_mutex==4.5', - 'absl-py==2.1.0', - 'anndata==0.10.8', - 'annotated-types==0.7.0', - 'anyio==4.4.0', - 'aom==3.9.1', - 'array-api-compat==1.8', - 'arrow==1.3.0', - 'backoff==2.2.1', - 'beautifulsoup4==4.12.3', - 'blessed==1.19.1', - 'blosc==1.21.6', - 'boto3==1.35.3', - 'botocore==1.35.3', - 'brotli==1.1.0', - 'brotli-bin==1.1.0', - 'brotli-python==1.1.0', - 'bzip2==1.0.8', - 'c-ares==1.33.0', - 'ca-certificates==2024.7.4', - 'cachecontrol==0.14.0', - 'cachecontrol-with-filecache==0.14.0', - 'cached-property==1.5.2', - 'cached_property==1.5.2', - 'certifi==2024.7.4', - 'cffi==1.17.0', - 'charset-normalizer==3.3.2', - 'chex==0.1.86', - 'cleo==2.1.0', - 'click==8.1.7', - 'colorama==0.4.6', - 'contextlib2==21.6.0', - 'contourpy==1.2.1', - 'crashtest==0.4.1', - 'croniter==1.4.1', - 'cryptography==43.0.0', - 'cycler==0.12.1', - 'dateutils==0.6.12', - 'dav1d==1.2.1', - 'dbus==1.13.6', - 'deepdiff==7.0.1', - 'distlib==0.3.8', - 'dnspython==2.6.1', - 'docrep==0.3.2', - 'dulwich==0.21.7', - 'email-validator==2.2.0', - 'email_validator==2.2.0', - 'et_xmlfile==1.1.0', - 'etils==1.9.2', - 'exceptiongroup==1.2.2', - 'expat==2.6.2', - 'fastapi==0.112.1', - 'fastapi-cli==0.0.5', - 'filelock==3.15.4', - 'flax==0.8.5', - 'fonttools==4.53.1', - 'freetype==2.12.1', - 'fsspec==2024.6.1', - 'get-annotations==0.1.2', - 'gmp==6.3.0', - 'gmpy2==2.1.5', - 'h11==0.14.0', - 'h2==4.1.0', - 'h5py==3.11.0', - 'hdf5==1.14.3', - 'hpack==4.0.0', - 'httpcore==1.0.5', - 'httpx==0.27.0', - 'hyperframe==6.0.1', - 'icu==75.1', - 'idna==3.7', - 'importlib-metadata==8.4.0', - 'importlib_metadata==8.4.0', - 'importlib_resources==6.4.4', - 'inquirer==3.1.4', - 'itsdangerous==2.2.0', - 'jaraco.classes==3.4.0', - 'jax==0.4.31', - 'jaxlib==0.4.31', - 'jeepney==0.8.0', - 'jinja2==3.1.4', - 'jmespath==1.0.1', - 'joblib==1.4.2', - 'keyring==24.3.1', - 'keyutils==1.6.1', - 'kiwisolver==1.4.5', - 'krb5==1.21.3', - 'lcms2==2.16', - 'ld_impl_linux-64==2.40', - 'legacy-api-wrap==1.4', - 'lerc==4.0.0', - 'libabseil==20240116.2', - 'libaec==1.1.3', - 'libavif16==1.1.1', - 'libblas==3.9.0', - 'libbrotlicommon==1.1.0', - 'libbrotlidec==1.1.0', - 'libbrotlienc==1.1.0', - 'libcblas==3.9.0', - 'libcurl==8.9.1', - 'libdeflate==1.21', - 'libedit==3.1.20191231', - 'libev==4.33', - 'libexpat==2.6.2', - 'libffi==3.4.2', - 'libgcc-ng==14.1.0', - 'libgfortran-ng==14.1.0', - 'libgfortran5==14.1.0', - 'libglib==2.80.3', - 'libgomp==14.1.0', - 'libgrpc==1.62.2', - 'libhwloc==2.11.1', - 'libiconv==1.17', - '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==1.6.43', - 'libprotobuf==4.25.3', - 'libre2-11==2023.09.01', - 'libsqlite==3.46.0', - 'libssh2==1.11.0', - 'libstdcxx-ng==14.1.0', - 'libtiff==4.6.0', - 'libtorch==2.3.1', - 'libuuid==2.38.1', - 'libuv==1.48.0', - 'libwebp-base==1.4.0', - 'libxcb==1.16', - 'libxcrypt==4.4.36', - 'libxml2==2.12.7', - 'libzlib==1.3.1', - 'lightning==2.0.9.post0', - 'lightning-cloud==0.5.70', - 'lightning-utilities==0.11.6', - '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', - 'mdurl==0.1.2', - 'ml-collections==0.1.1', - 'ml_dtypes==0.4.0', - 'more-itertools==10.4.0', - 'mpc==1.3.1', - 'mpfr==4.2.1', - 'mpmath==1.3.0', - 'msgpack-python==1.0.8', - 'mudata==0.3.0', - 'multipledispatch==0.6.0', - 'munkres==1.1.4', - 'natsort==8.4.0', - 'ncurses==6.5', - 'nest-asyncio==1.6.0', - 'networkx==3.3', - 'nomkl==1.0', - 'numba==0.60.0', - 'numpy==1.26.4', - 'numpy_groupies==0.11.2', - 'numpyro==0.15.2', - 'openjpeg==2.5.2', - 'openpyxl==3.1.5', - 'openssl==3.3.1', - 'opt-einsum==3.3.0', - 'opt_einsum==3.3.0', - 'optax==0.2.2', - 'orbax-checkpoint==0.4.4', - 'ordered-set==4.1.0', - 'orjson==3.10.7', - 'packaging==24.1', - 'pandas==2.2.2', - 'patsy==0.5.6', - 'pcre2==10.44', - 'pexpect==4.9.0', - 'pillow==10.4.0', - 'pip==24.2', - 'pkginfo==1.11.1', - 'platformdirs==4.2.2', - 'poetry==1.8.3', - 'poetry-core==1.9.0', - 'poetry-plugin-export==1.8.0', - 'protobuf==4.25.3', - 'psutil==6.0.0', - 'pthread-stubs==0.4', - 'ptyprocess==0.7.0', - 'pybind11-abi==4', - 'pycparser==2.22', - 'pydantic==2.1.1', - 'pydantic-core==2.4.0', - 'pygments==2.18.0', - 'pyjwt==2.9.0', - 'pynndescent==0.5.13', - 'pyparsing==3.1.2', - 'pyproject_hooks==1.1.0', - 'pyro-api==0.1.2', - 'pyro-ppl==1.9.1', - 'pysocks==1.7.1', - 'python==3.11.9', - 'python-build==1.2.1', - 'python-dateutil==2.9.0', - 'python-editor==1.0.4', - 'python-fastjsonschema==2.20.0', - 'python-installer==0.7.0', - 'python-multipart==0.0.9', - 'python-tzdata==2024.1', - 'python_abi==3.11', - 'pytorch==2.3.1', - 'pytorch-lightning==2.4.0', - 'pytz==2024.1', - 'pyyaml==6.0.2', - 'qhull==2020.2', - 'rapidfuzz==3.9.6', - 'rav1e==0.6.6', - 're2==2023.09.01', - 'readchar==4.2.0', - 'readline==8.2', - 'requests==2.32.3', - 'requests-toolbelt==1.0.0', - 'rich==13.7.1', - 's3transfer==0.10.2', - 'scanpy==1.10.2', - 'scikit-learn==1.1.3', - 'scipy==1.13.1', - 'scvelo==0.3.2', - 'scvi-tools==1.1.6', - 'seaborn==0.13.2', - 'seaborn-base==0.13.2', - 'secretstorage==3.3.3', - 'session-info==1.0.0', - 'setuptools==72.2.0', - 'shellingham==1.5.4', - 'six==1.16.0', - 'sleef==3.6.1', - 'snappy==1.2.1', - 'sniffio==1.3.1', - 'soupsieve==2.5', - 'sparse==0.15.4', - 'starlette==0.38.2', - 'starsessions==1.3.0', - 'statsmodels==0.14.2', - 'stdlib-list==0.10.0', - 'svt-av1==2.1.2', - 'sympy==1.13.2', - 'tbb==2021.12.0', - 'tensorstore==0.1.62', - 'threadpoolctl==3.5.0', - 'tk==8.6.13', - 'tomli==2.0.1', - 'tomlkit==0.13.2', - 'toolz==0.12.1', - 'torchmetrics==1.4.0.post0', - 'tqdm==4.66.5', - 'traitlets==5.14.3', - 'trove-classifiers==2024.7.2', - 'typer==0.12.4', - 'typer-slim==0.12.4', - 'typer-slim-standard==0.12.4', - 'types-python-dateutil==2.9.0.20240821', - 'typing-extensions==4.12.2', - 'typing_extensions==4.12.2', - 'tzdata==2024a', - 'umap-learn==0.5.6', - 'urllib3==2.2.2', - 'uvicorn==0.30.6', - 'virtualenv==20.26.3', - 'wcwidth==0.2.13', - 'websocket-client==1.8.0', - 'websockets==12.0', - 'wheel==0.44.0', - 'xarray==2024.7.0', - 'xorg-libxau==1.0.11', - 'xorg-libxdmcp==1.1.3', - 'xz==5.2.6', - 'yaml==0.2.5', - 'zipp==3.20.0', - 'zstandard==0.23.0', - 'zstd==1.5.6' - ) + '_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', + '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', + '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', + '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', + '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-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==2.2.2', + 'patsy==0.5.6', + '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', + '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', + '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==72.1.0', + 'six==1.16.0', + 'sqlite==3.45.3', + 'statsmodels==0.14.2', + 'stdlib-list==0.10.0', + 'sympy==1.12', + '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', + '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' ) ) diff --git a/inst/envs/Linux_x86_64.yaml b/inst/envs/Linux_x86_64.yaml new file mode 100644 index 0000000..de51350 --- /dev/null +++ b/inst/envs/Linux_x86_64.yaml @@ -0,0 +1,209 @@ +name: scvelo_032 +channels: +- conda-forge +dependencies: +- _libgcc_mutex=0.1=conda_forge +- _openmp_mutex=4.5=2_gnu +- absl-py=2.1.0=pyhd8ed1ab_0 +- anndata=0.10.8=pyhd8ed1ab_0 +- aom=3.9.1=hac33072_0 +- array-api-compat=1.8=pyhd8ed1ab_0 +- blosc=1.21.6=hef167b5_0 +- brotli=1.1.0=hd590300_1 +- brotli-bin=1.1.0=hd590300_1 +- brotli-python=1.1.0=py311hb755f60_1 +- bzip2=1.0.8=h4bc722e_7 +- c-ares=1.33.1=heb4867d_0 +- ca-certificates=2024.7.4=hbcca054_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=py311ha8e6434_0 +- charset-normalizer=3.3.2=pyhd8ed1ab_0 +- chex=0.1.86=pyhd8ed1ab_0 +- click=8.1.7=unix_pyh707e725_0 +- colorama=0.4.6=pyhd8ed1ab_0 +- contextlib2=21.6.0=pyhd8ed1ab_0 +- contourpy=1.2.1=py311h9547e67_0 +- cycler=0.12.1=pyhd8ed1ab_0 +- dav1d=1.2.1=hd590300_0 +- docrep=0.3.2=pyh44b312d_0 +- et_xmlfile=1.1.0=pyhd8ed1ab_0 +- etils=1.9.2=pyhd8ed1ab_0 +- exceptiongroup=1.2.2=pyhd8ed1ab_0 +- filelock=3.15.4=pyhd8ed1ab_0 +- flax=0.9.0=pyhd8ed1ab_0 +- fonttools=4.53.1=py311h61187de_0 +- freetype=2.12.1=h267a509_2 +- fsspec=2024.6.1=pyhff2d567_0 +- get-annotations=0.1.2=pyhd8ed1ab_0 +- gmp=6.3.0=hac33072_2 +- gmpy2=2.1.5=py311hc4f1f91_1 +- h2=4.1.0=pyhd8ed1ab_0 +- h5py=3.11.0=nompi_py311h439e445_102 +- hdf5=1.14.3=nompi_hdf9ad27_105 +- hpack=4.0.0=pyh9f0ad1d_0 +- hyperframe=6.0.1=pyhd8ed1ab_0 +- icu=75.1=he02047a_0 +- idna=3.8=pyhd8ed1ab_0 +- importlib-metadata=8.4.0=pyha770c72_0 +- importlib_metadata=8.4.0=hd8ed1ab_0 +- importlib_resources=6.4.4=pyhd8ed1ab_0 +- jax=0.4.31=pyhd8ed1ab_0 +- jaxlib=0.4.31=cpu_py311hb2c720c_0 +- jinja2=3.1.4=pyhd8ed1ab_0 +- joblib=1.4.2=pyhd8ed1ab_0 +- keyutils=1.6.1=h166bdaf_0 +- kiwisolver=1.4.5=py311h9547e67_1 +- krb5=1.21.3=h659f571_0 +- lcms2=2.16=hb7c19ff_0 +- ld_impl_linux-64=2.40=hf3520f5_7 +- legacy-api-wrap=1.4=pyhd8ed1ab_1 +- lerc=4.0.0=h27087fc_0 +- libabseil=20240116.2=cxx17_he02047a_1 +- libaec=1.1.3=h59595ed_0 +- libavif16=1.1.1=h104a339_1 +- libblas=3.9.0=23_linux64_openblas +- libbrotlicommon=1.1.0=hd590300_1 +- libbrotlidec=1.1.0=hd590300_1 +- libbrotlienc=1.1.0=hd590300_1 +- libcblas=3.9.0=23_linux64_openblas +- libcurl=8.9.1=hdb1bdb2_0 +- libdeflate=1.21=h4bc722e_0 +- libedit=3.1.20191231=he28a2e2_2 +- libev=4.33=hd590300_2 +- libexpat=2.6.2=h59595ed_0 +- libffi=3.4.2=h7f98852_5 +- libgcc=14.1.0=h77fa898_1 +- libgcc-ng=14.1.0=h69a702a_1 +- libgfortran=14.1.0=h69a702a_1 +- libgfortran-ng=14.1.0=h69a702a_1 +- libgfortran5=14.1.0=hc5f4f2c_1 +- libgomp=14.1.0=h77fa898_1 +- libgrpc=1.62.2=h15f2491_0 +- libhwloc=2.11.1=default_hecaa2ac_1000 +- libiconv=1.17=hd590300_2 +- libjpeg-turbo=3.0.0=hd590300_1 +- liblapack=3.9.0=23_linux64_openblas +- libllvm14=14.0.6=hcd5def8_4 +- libnghttp2=1.58.0=h47da74e_1 +- libnsl=2.0.1=hd590300_0 +- libopenblas=0.3.27=pthreads_hac2b453_1 +- libpng=1.6.43=h2797004_0 +- libprotobuf=4.25.3=h08a7969_0 +- libre2-11=2023.09.01=h5a48ba9_2 +- libsqlite=3.46.0=hde9e2c9_0 +- libssh2=1.11.0=h0841786_0 +- libstdcxx=14.1.0=hc0a3c3a_1 +- libstdcxx-ng=14.1.0=h4852527_1 +- libtiff=4.6.0=h46a8edc_4 +- libtorch=2.4.0=cpu_generic_h4a3044c_1 +- libuuid=2.38.1=h0b41bf4_0 +- libuv=1.48.0=hd590300_0 +- libwebp-base=1.4.0=hd590300_0 +- libxcb=1.16=hb9d3cd8_1 +- libxcrypt=4.4.36=hd590300_1 +- libxml2=2.12.7=he7c6b58_4 +- libzlib=1.3.1=h4ab18f5_1 +- lightning=2.4.0=pyhd8ed1ab_0 +- lightning-utilities=0.11.6=pyhd8ed1ab_0 +- llvmlite=0.43.0=py311hbde99c3_0 +- loompy=3.0.6=py_0 +- lz4-c=1.9.4=hcb278e6_0 +- markdown-it-py=3.0.0=pyhd8ed1ab_0 +- markupsafe=2.1.5=py311h459d7ec_0 +- matplotlib-base=3.9.2=py311h74b4f7c_0 +- mdurl=0.1.2=pyhd8ed1ab_0 +- ml-collections=0.1.1=pyhd8ed1ab_0 +- ml_dtypes=0.4.0=py311h14de704_1 +- mpc=1.3.1=hfe3b2da_0 +- mpfr=4.2.1=h38ae2d0_2 +- mpmath=1.3.0=pyhd8ed1ab_0 +- msgpack-python=1.0.8=py311h52f7536_0 +- mudata=0.3.0=pyhd8ed1ab_0 +- multipledispatch=0.6.0=pyhd8ed1ab_1 +- munkres=1.1.4=pyh9f0ad1d_0 +- natsort=8.4.0=pyhd8ed1ab_0 +- ncurses=6.5=he02047a_1 +- nest-asyncio=1.6.0=pyhd8ed1ab_0 +- networkx=3.3=pyhd8ed1ab_1 +- nomkl=1.0=h5ca1d4c_0 +- numba=0.60.0=py311h4bc866e_0 +- numpy=1.26.4=py311h64a7726_0 +- numpy_groupies=0.11.2=pyhd8ed1ab_0 +- numpyro=0.15.2=pyhd8ed1ab_0 +- openjpeg=2.5.2=h488ebb8_0 +- openpyxl=3.1.5=py311h459d7ec_0 +- openssl=3.3.1=hb9d3cd8_3 +- opt-einsum=3.3.0=hd8ed1ab_2 +- opt_einsum=3.3.0=pyhc1e730c_2 +- optax=0.2.2=pyhd8ed1ab_1 +- orbax-checkpoint=0.4.4=pyhd8ed1ab_0 +- packaging=24.1=pyhd8ed1ab_0 +- pandas=2.2.2=py311h14de704_1 +- patsy=0.5.6=pyhd8ed1ab_0 +- pillow=10.4.0=py311h82a398c_0 +- pip=24.2=pyhd8ed1ab_0 +- protobuf=4.25.3=py311h7b78aeb_0 +- pthread-stubs=0.4=h36c2ea0_1001 +- pybind11-abi=4=hd8ed1ab_3 +- pycparser=2.22=pyhd8ed1ab_0 +- pygments=2.18.0=pyhd8ed1ab_0 +- pynndescent=0.5.13=pyhff2d567_0 +- pyparsing=3.1.4=pyhd8ed1ab_0 +- pyro-api=0.1.2=pyhd8ed1ab_0 +- pyro-ppl=1.9.1=pyhd8ed1ab_0 +- pysocks=1.7.1=pyha2e5f31_6 +- python=3.11.9=hb806964_0_cpython +- python-dateutil=2.9.0=pyhd8ed1ab_0 +- python-tzdata=2024.1=pyhd8ed1ab_0 +- python_abi=3.11=5_cp311 +- pytorch=2.4.0=cpu_generic_py311h7a8ff39_1 +- pytorch-lightning=2.4.0=pyhd8ed1ab_0 +- pytz=2024.1=pyhd8ed1ab_0 +- pyyaml=6.0.2=py311h61187de_0 +- qhull=2020.2=h434a139_5 +- rav1e=0.6.6=he8a937b_2 +- re2=2023.09.01=h7f4b329_2 +- readline=8.2=h8228510_1 +- requests=2.32.3=pyhd8ed1ab_0 +- rich=13.7.1=pyhd8ed1ab_0 +- scanpy=1.10.2=pyhd8ed1ab_0 +- scikit-learn=1.1.3=py311h3b52e38_1 +- scipy=1.13.1=py311h517d4fd_0 +- scvelo=0.3.2=pyhd8ed1ab_1 +- scvi-tools=1.1.6=pyhd8ed1ab_1 +- 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 +- six=1.16.0=pyh6c4a22f_0 +- sleef=3.6.1=h1b44611_3 +- snappy=1.2.1=ha2e4443_0 +- sparse=0.15.4=pyhd8ed1ab_0 +- statsmodels=0.14.2=py311h18e1886_0 +- stdlib-list=0.10.0=pyhd8ed1ab_0 +- svt-av1=2.2.1=h5888daf_0 +- sympy=1.13.2=pypyh2585a3b_103 +- tbb=2021.12.0=h434a139_3 +- tensorstore=0.1.62=py311h865b1b2_0 +- threadpoolctl=3.5.0=pyhc1e730c_0 +- tk=8.6.13=noxft_h4845f30_101 +- toolz=0.12.1=pyhd8ed1ab_0 +- torchmetrics=1.4.0.post0=pyhd8ed1ab_0 +- tqdm=4.66.5=pyhd8ed1ab_0 +- typing-extensions=4.12.2=hd8ed1ab_0 +- typing_extensions=4.12.2=pyha770c72_0 +- tzdata=2024a=h8827d51_1 +- umap-learn=0.5.6=py311h38be061_1 +- urllib3=2.2.2=pyhd8ed1ab_1 +- wheel=0.44.0=pyhd8ed1ab_0 +- xarray=2024.7.0=pyhd8ed1ab_0 +- xorg-libxau=1.0.11=hd590300_0 +- xorg-libxdmcp=1.1.3=h7f98852_0 +- xz=5.2.6=h166bdaf_0 +- yaml=0.2.5=h7f98852_2 +- zipp=3.20.1=pyhd8ed1ab_0 +- zstandard=0.23.0=py311h5cd10c7_0 +- zstd=1.5.6=ha6fb4c9_0 + diff --git a/inst/envs/Linux_x86_64_anaconda.yaml b/inst/envs/Linux_x86_64_anaconda.yaml new file mode 100644 index 0000000..653d1cd --- /dev/null +++ b/inst/envs/Linux_x86_64_anaconda.yaml @@ -0,0 +1,151 @@ +name: scvelo_libjpegturbo303 +channels: +- anaconda +- conda-forge +dependencies: +- _libgcc_mutex=0.1=conda_forge +- _openmp_mutex=4.5=2_gnu +- absl-py=2.1.0=py311h06a4308_0 +- anndata=0.10.9=pyhd8ed1ab_0 +- array-api-compat=1.8=pyhd8ed1ab_0 +- blas=1.0=openblas +- bottleneck=1.3.7=py311hf4808d0_0 +- brotli=1.0.9=h5eee18b_8 +- brotli-bin=1.0.9=h5eee18b_8 +- bzip2=1.0.8=h5eee18b_6 +- c-ares=1.19.1=h5eee18b_0 +- ca-certificates=2024.7.2=h06a4308_0 +- chex=0.1.5=py311h06a4308_0 +- click=8.1.7=py311h06a4308_0 +- contextlib2=21.6.0=py311h06a4308_0 +- contourpy=1.2.0=py311hdb19cb5_0 +- cycler=0.11.0=pyhd3eb1b0_0 +- dm-tree=0.1.7=py311h6a678d5_1 +- docrep=0.3.2=pyh44b312d_0 +- et_xmlfile=1.1.0=py311h06a4308_0 +- exceptiongroup=1.2.0=py311h06a4308_0 +- filelock=3.13.1=py311h06a4308_0 +- flax=0.6.1=pyhd8ed1ab_1 +- fonttools=4.51.0=py311h5eee18b_0 +- freetype=2.12.1=h4a9f257_0 +- fsspec=2024.3.1=py311h06a4308_0 +- get-annotations=0.1.2=pyhd8ed1ab_0 +- gmp=6.2.1=h295c915_3 +- gmpy2=2.1.2=py311hc9b5ff0_0 +- h5py=3.11.0=py311h865a13c_0 +- hdf5=1.12.1=h2b7332f_3 +- jax=0.3.25=py311h06a4308_0 +- jaxlib=0.3.25=py311h6a678d5_2 +- jinja2=3.1.4=py311h06a4308_0 +- joblib=1.4.2=py311h06a4308_0 +- jpeg=9e=h5eee18b_3 +- kiwisolver=1.4.4=py311h6a678d5_0 +- krb5=1.20.1=h143b758_1 +- lcms2=2.12=h3be6417_0 +- ld_impl_linux-64=2.38=h1181459_1 +- legacy-api-wrap=1.4=pyhd8ed1ab_1 +- lerc=3.0=h295c915_0 +- libblas=3.9.0=16_linux64_openblas +- libbrotlicommon=1.0.9=h5eee18b_8 +- libbrotlidec=1.0.9=h5eee18b_8 +- libbrotlienc=1.0.9=h5eee18b_8 +- libcblas=3.9.0=16_linux64_openblas +- libcurl=7.88.1=h251f7ec_2 +- libdeflate=1.17=h5eee18b_1 +- libedit=3.1.20230828=h5eee18b_0 +- libev=4.33=h7f8727e_1 +- libffi=3.4.4=h6a678d5_1 +- libgcc=14.1.0=h77fa898_1 +- libgcc-ng=14.1.0=h69a702a_1 +- libgfortran-ng=11.2.0=h00389a5_1 +- libgfortran5=11.2.0=h1234567_1 +- libgomp=14.1.0=h77fa898_1 +- libllvm14=14.0.6=hdb19cb5_3 +- libnghttp2=1.57.0=h2d74bed_0 +- libopenblas=0.3.21=h043d6bf_0 +- libpng=1.6.39=h5eee18b_0 +- libprotobuf=3.20.3=he621ea3_0 +- libssh2=1.11.0=h251f7ec_0 +- libstdcxx=14.1.0=hc0a3c3a_1 +- libstdcxx-ng=14.1.0=h4852527_1 +- libtiff=4.5.1=h6a678d5_0 +- libuuid=1.41.5=h5eee18b_0 +- libwebp-base=1.3.2=h5eee18b_0 +- lightning-utilities=0.9.0=py311h06a4308_0 +- llvmlite=0.43.0=py311h6a678d5_0 +- loompy=3.0.6=py_0 +- lz4-c=1.9.4=h6a678d5_1 +- markdown-it-py=2.2.0=py311h06a4308_1 +- markupsafe=2.1.3=py311h5eee18b_0 +- matplotlib-base=3.8.4=py311ha02d727_0 +- mdurl=0.1.0=py311h06a4308_0 +- ml-collections=0.1.1=pyhd8ed1ab_0 +- mpc=1.1.0=h10f8cd9_1 +- mpfr=4.0.2=hb69a4c5_1 +- mpmath=1.3.0=py311h06a4308_0 +- msgpack-python=1.0.3=py311hdb19cb5_0 +- mudata=0.3.0=pyhd8ed1ab_0 +- multipledispatch=0.6.0=py311h06a4308_0 +- natsort=7.1.1=pyhd3eb1b0_0 +- ncurses=6.4=h6a678d5_0 +- networkx=3.3=py311h06a4308_0 +- numba=0.60.0=py311h4bc866e_0 +- numexpr=2.8.7=py311h812550d_0 +- numpy=1.26.4=py311h24aa872_0 +- numpy-base=1.26.4=py311hbfb1bba_0 +- numpy_groupies=0.11.2=pyhd8ed1ab_0 +- numpyro=0.13.2=pyhd8ed1ab_0 +- openjpeg=2.5.2=he7f1fd0_0 +- openpyxl=3.1.5=py311h5eee18b_0 +- openssl=3.0.14=h5eee18b_0 +- opt_einsum=3.3.0=pyhd3eb1b0_1 +- optax=0.1.4=py311h06a4308_0 +- packaging=24.1=py311h06a4308_0 +- pandas=2.2.2=py311ha02d727_0 +- patsy=0.5.6=py311h06a4308_0 +- pillow=10.4.0=py311h5eee18b_0 +- pip=24.2=py311h06a4308_0 +- pybind11-abi=4=hd3eb1b0_1 +- pygments=2.15.1=py311h06a4308_1 +- pynndescent=0.5.10=py311h06a4308_0 +- pyparsing=3.0.9=py311h06a4308_0 +- pyro-api=0.1.2=pyhd8ed1ab_0 +- pyro-ppl=1.9.1=pyhd8ed1ab_0 +- python=3.11.9=h955ad1f_0 +- python-dateutil=2.9.0post0=py311h06a4308_2 +- python-tzdata=2023.3=pyhd3eb1b0_0 +- python_abi=3.11=2_cp311 +- pytorch=2.3.0=cpu_py311h991c31c_0 +- pytorch-lightning=1.9.5=py311h06a4308_1 +- pytz=2024.1=py311h06a4308_0 +- pyyaml=6.0.1=py311h5eee18b_0 +- readline=8.2=h5eee18b_0 +- rich=13.7.1=py311h06a4308_0 +- scanpy=1.10.2=pyhd8ed1ab_0 +- scikit-learn=1.1.3=py311h3b52e38_1 +- scipy=1.13.1=py311h24aa872_0 +- scvelo=0.3.2=pyhd8ed1ab_1 +- scvi-tools=0.20.3=pyhd8ed1ab_0 +- seaborn=0.13.2=py311h06a4308_0 +- session-info=1.0.0=pyhd8ed1ab_0 +- setuptools=72.1.0=py311h06a4308_0 +- six=1.16.0=pyhd3eb1b0_1 +- sqlite=3.45.3=h5eee18b_0 +- statsmodels=0.14.2=py311hf4808d0_0 +- stdlib-list=0.10.0=py311h06a4308_0 +- sympy=1.12=py311h06a4308_0 +- threadpoolctl=3.5.0=py311h92b7b1e_0 +- tk=8.6.14=h39e8969_0 +- toolz=0.12.0=py311h06a4308_0 +- torchmetrics=1.4.0.post0=py311h06a4308_0 +- tqdm=4.66.4=py311h92b7b1e_0 +- typing-extensions=4.11.0=py311h06a4308_0 +- typing_extensions=4.11.0=py311h06a4308_0 +- tzdata=2024a=h04d1e81_0 +- umap-learn=0.5.3=py311h06a4308_0 +- unicodedata2=15.1.0=py311h5eee18b_0 +- wheel=0.43.0=py311h06a4308_0 +- xz=5.4.6=h5eee18b_1 +- yaml=0.2.5=h7b6447c_0 +- zlib=1.2.13=h5eee18b_1 +- zstd=1.5.5=hc292b87_2 diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R new file mode 100644 index 0000000..d147eb2 --- /dev/null +++ b/inst/envs/format_yaml_to_r.R @@ -0,0 +1,11 @@ +library(yaml) +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(" ", "'", r_data, "'", collapse = ",\n"), + "\n", + ")", + "\n" +))