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Pin version of all dependencies. #100

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ad325d0
add script that prints installed versions
kevinrue Jul 8, 2025
346930a
print package versions
kevinrue Jul 8, 2025
20c0db5
fix code to print python package versions
kevinrue Jul 8, 2025
2c1aa88
pin all packages for all OS'es
kevinrue Jul 8, 2025
53efcc3
update news and description
kevinrue Jul 8, 2025
0410ca0
rephrase
kevinrue Jul 8, 2025
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10 changes: 10 additions & 0 deletions .github/workflows/check-bioc.yml
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Expand Up @@ -226,6 +226,16 @@ jobs:
check_dir = "check"
)
shell: Rscript {0}

- name: Print package versions
run: |
packages_info <- basilisk::listPackages(velociraptor:::velo.env)$full
cat(paste0(
"c(\n",
paste0(sprintf(" '%s'", packages_info), collapse = ",\n"),
"\n)"
))
shell: Rscript {0}

## Might need an to add this to the if: && runner.os == 'Linux'
- name: Reveal testthat details
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4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -1,7 +1,7 @@
Package: velociraptor
Title: Toolkit for Single-Cell Velocity
Version: 1.19.1
Date: 2025-07-07
Version: 1.19.2
Date: 2025-07-08
Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872")),
person("Aaron", "Lun", role="aut", email="[email protected]", comment = c(ORCID = '0000-0002-3564-4813')),
person("Charlotte", "Soneson", role="aut", email="[email protected]", comment = c(ORCID = '0000-0003-3833-2169')),
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4 changes: 4 additions & 0 deletions NEWS.md
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@@ -1,3 +1,7 @@
# velociraptor 1.19.2

* Pin version of all dependencies.

# velociraptor 1.19.1

* Switch import of OS-detecting function to `basilisk`.
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219 changes: 210 additions & 9 deletions R/basilisk.R
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Expand Up @@ -2,44 +2,245 @@

.scvelo.dependencies.Windows <- list(
packages = c(
'scvelo==0.3.3'
'anndata==0.11.4',
'array-api-compat==1.12.0',
'click==8.2.1',
'colorama==0.4.6',
'contourpy==1.3.2',
'cycler==0.12.1',
'fonttools==4.58.5',
'h5py==3.14.0',
'joblib==1.5.1',
'kiwisolver==1.4.8',
'legacy-api-wrap==1.4.1',
'llvmlite==0.44.0',
'loompy==3.0.8',
'matplotlib==3.10.3',
'natsort==8.4.0',
'networkx==3.5',
'numba==0.61.2',
'numpy==2.2.6',
'numpy-groupies==0.11.3',
'packaging==25.0',
'pandas==2.3.1',
'patsy==1.0.1',
'pillow==11.3.0',
'pip==25.1.1',
'pynndescent==0.5.13',
'pyparsing==3.2.3',
'python-dateutil==2.9.0.post0',
'pytz==2025.2',
'scanpy==1.11.3',
'scikit-learn==1.7.0',
'scipy==1.15.3',
'scvelo==0.3.3',
'seaborn==0.13.2',
'session-info2==0.1.2',
'setuptools==80.9.0',
'six==1.17.0',
'statsmodels==0.14.5',
'threadpoolctl==3.6.0',
'tqdm==4.67.1',
'typing_extensions==4.14.1',
'tzdata==2025.2',
'umap-learn==0.5.9.post2',
'wheel==0.45.1'
)
)

## LinuxAarch64 ----

.scvelo.dependencies.LinuxAarch64 <- list(
packages = c(
'ipywidgets==8.1.2',
'libtiff==4.5.1',
'pillow==10.0.0',
'scipy==1.13.1',
'anndata==0.11.4',
'array-api-compat==1.12.0',
'click==8.2.1',
'contourpy==1.3.2',
'cycler==0.12.1',
'fonttools==4.58.5',
'h5py==3.14.0',
'joblib==1.5.1',
'kiwisolver==1.4.8',
'legacy-api-wrap==1.4.1',
'llvmlite==0.44.0',
'loompy==3.0.8',
'matplotlib==3.10.3',
'natsort==8.4.0',
'networkx==3.5',
'numba==0.61.2',
'numpy==2.2.6',
'numpy-groupies==0.11.3',
'packaging==25.0',
'pandas==2.3.1',
'patsy==1.0.1',
'pillow==11.3.0',
'pip==25.1.1',
'pynndescent==0.5.13',
'pyparsing==3.2.3',
'python-dateutil==2.9.0.post0',
'pytz==2025.2',
'scanpy==1.11.3',
'scikit-learn==1.7.0',
'scipy==1.15.3',
'scvelo==0.3.3',
'tqdm==4.66.5'
'seaborn==0.13.2',
'session-info2==0.1.2',
'setuptools==80.9.0',
'six==1.17.0',
'statsmodels==0.14.5',
'threadpoolctl==3.6.0',
'tqdm==4.67.1',
'typing_extensions==4.14.1',
'tzdata==2025.2',
'umap-learn==0.5.9.post2',
'wheel==0.45.1'
)
)

## Linux ----

.scvelo.dependencies.Linux <- list(
packages = c(
'scvelo==0.3.3'
'anndata==0.11.4',
'array-api-compat==1.12.0',
'click==8.2.1',
'contourpy==1.3.2',
'cycler==0.12.1',
'fonttools==4.58.5',
'h5py==3.14.0',
'joblib==1.5.1',
'kiwisolver==1.4.8',
'legacy-api-wrap==1.4.1',
'llvmlite==0.44.0',
'loompy==3.0.8',
'matplotlib==3.10.3',
'natsort==8.4.0',
'networkx==3.5',
'numba==0.61.2',
'numpy==2.2.6',
'numpy-groupies==0.11.3',
'packaging==25.0',
'pandas==2.3.1',
'patsy==1.0.1',
'pillow==11.3.0',
'pip==25.1.1',
'pynndescent==0.5.13',
'pyparsing==3.2.3',
'python-dateutil==2.9.0.post0',
'pytz==2025.2',
'scanpy==1.11.3',
'scikit-learn==1.7.0',
'scipy==1.15.3',
'scvelo==0.3.3',
'seaborn==0.13.2',
'session-info2==0.1.2',
'setuptools==80.9.0',
'six==1.17.0',
'statsmodels==0.14.5',
'threadpoolctl==3.6.0',
'tqdm==4.67.1',
'typing_extensions==4.14.1',
'tzdata==2025.2',
'umap-learn==0.5.9.post2',
'wheel==0.45.1'
)
)

## MacOSXArm ----

.scvelo.dependencies.MacOSXArm <- list(
packages = c(
'scvelo==0.3.3'
'anndata==0.11.4',
'array-api-compat==1.12.0',
'click==8.2.1',
'contourpy==1.3.2',
'cycler==0.12.1',
'fonttools==4.58.5',
'h5py==3.14.0',
'joblib==1.5.1',
'kiwisolver==1.4.8',
'legacy-api-wrap==1.4.1',
'llvmlite==0.44.0',
'loompy==3.0.8',
'matplotlib==3.10.3',
'natsort==8.4.0',
'networkx==3.5',
'numba==0.61.2',
'numpy==2.2.6',
'numpy-groupies==0.11.3',
'packaging==25.0',
'pandas==2.3.1',
'patsy==1.0.1',
'pillow==11.3.0',
'pip==25.1.1',
'pynndescent==0.5.13',
'pyparsing==3.2.3',
'python-dateutil==2.9.0.post0',
'pytz==2025.2',
'scanpy==1.11.3',
'scikit-learn==1.7.0',
'scipy==1.15.3',
'scvelo==0.3.3',
'seaborn==0.13.2',
'session-info2==0.1.2',
'setuptools==80.9.0',
'six==1.17.0',
'statsmodels==0.14.5',
'threadpoolctl==3.6.0',
'tqdm==4.67.1',
'typing_extensions==4.14.1',
'tzdata==2025.2',
'umap-learn==0.5.9.post2',
'wheel==0.45.1'
)
)

## MacOSX ----

.scvelo.dependencies.MacOSX <- list(
packages = c(
'scvelo==0.3.3'
'anndata==0.11.4',
'array-api-compat==1.12.0',
'click==8.2.1',
'contourpy==1.3.2',
'cycler==0.12.1',
'fonttools==4.58.5',
'h5py==3.14.0',
'joblib==1.5.1',
'kiwisolver==1.4.8',
'legacy-api-wrap==1.4.1',
'llvmlite==0.44.0',
'loompy==3.0.8',
'matplotlib==3.10.3',
'natsort==8.4.0',
'networkx==3.5',
'numba==0.61.2',
'numpy==2.2.6',
'numpy-groupies==0.11.3',
'packaging==25.0',
'pandas==2.3.1',
'patsy==1.0.1',
'pillow==11.3.0',
'pip==25.1.1',
'pynndescent==0.5.13',
'pyparsing==3.2.3',
'python-dateutil==2.9.0.post0',
'pytz==2025.2',
'scanpy==1.11.3',
'scikit-learn==1.7.0',
'scipy==1.15.3',
'scvelo==0.3.3',
'seaborn==0.13.2',
'session-info2==0.1.2',
'setuptools==80.9.0',
'six==1.17.0',
'statsmodels==0.14.5',
'threadpoolctl==3.6.0',
'tqdm==4.67.1',
'typing_extensions==4.14.1',
'tzdata==2025.2',
'umap-learn==0.5.9.post2',
'wheel==0.45.1'
)
)

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6 changes: 6 additions & 0 deletions inst/envs/pyenv-package-versions.R
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@@ -0,0 +1,6 @@
packages_info <- basilisk::listPackages(velociraptor:::velo.env)$full
cat(paste0(
"c\n",
paste0(sprintf(" '%s'", packages_info), collapse = ",\n"),
"\n)"
))
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