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Merged
merged 1 commit into from
Mar 28, 2022
Merged

Use scvi-colab for installs #56

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14 changes: 3 additions & 11 deletions AutoZI_tutorial.ipynb
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Expand Up @@ -36,17 +36,9 @@
},
"outputs": [],
"source": [
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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17 changes: 4 additions & 13 deletions DestVI_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -36,18 +36,9 @@
},
"outputs": [],
"source": [
"%%capture\n",
"import sys\n",
"\n",
"#if True, will install via pypi, else will install from source\n",
"stable = True\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and stable:\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and not stable:\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@master#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
Expand Down Expand Up @@ -1346,7 +1337,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
"version": "3.9.10"
}
},
"nbformat": 4,
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15 changes: 3 additions & 12 deletions MultiVI_tutorial.ipynb
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Expand Up @@ -25,18 +25,9 @@
},
"outputs": [],
"source": [
"%%capture\n",
"import sys\n",
"\n",
"# If True, will install via pypi, else will install from source\n",
"stable = True\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and stable:\n",
" !pip install --quiet scvi-tools\n",
"elif IN_COLAB and not stable:\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@master#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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64 changes: 28 additions & 36 deletions PeakVI.ipynb
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15 changes: 3 additions & 12 deletions amortized_lda.ipynb
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Expand Up @@ -23,18 +23,9 @@
},
"outputs": [],
"source": [
"%%capture\n",
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"master\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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15 changes: 3 additions & 12 deletions api_overview.ipynb
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Expand Up @@ -27,18 +27,9 @@
},
"outputs": [],
"source": [
"%%capture\n",
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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39 changes: 24 additions & 15 deletions cell2location_lymph_node_spatial_tutorial.ipynb
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14 changes: 3 additions & 11 deletions cellassign_tutorial.ipynb
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Expand Up @@ -52,17 +52,9 @@
},
"outputs": [],
"source": [
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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15 changes: 3 additions & 12 deletions cite_scrna_integration_w_totalVI.ipynb
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Expand Up @@ -23,18 +23,9 @@
},
"outputs": [],
"source": [
"%%capture\n",
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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14 changes: 3 additions & 11 deletions data_loading.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,17 +31,9 @@
},
"outputs": [],
"source": [
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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14 changes: 3 additions & 11 deletions data_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -32,17 +32,9 @@
},
"outputs": [],
"source": [
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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15 changes: 3 additions & 12 deletions gimvi_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,18 +31,9 @@
},
"outputs": [],
"source": [
"%%capture\n",
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]"
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"install()"
]
},
{
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24 changes: 6 additions & 18 deletions harmonization.ipynb
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Expand Up @@ -20,26 +20,14 @@
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"id": "aghHRoYY1HKM"
},
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%capture \n",
"import sys\n",
"\n",
"#if branch is stable, will install via pypi, else will install from source\n",
"branch = \"stable\"\n",
"IN_COLAB = \"google.colab\" in sys.modules\n",
"\n",
"if IN_COLAB and branch == \"stable\":\n",
" !pip install --quiet scvi-tools[tutorials]\n",
" !pip install --quiet git+https://github.com/theislab/scib.git\n",
"elif IN_COLAB and branch != \"stable\":\n",
" !pip install --quiet --upgrade jsonschema\n",
" !pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]\n",
" !pip install --quiet git+https://github.com/theislab/scib.git"
"!pip install --quiet scvi-colab\n",
"!pip install --quiet git+https://github.com/theislab/scib.git\n",
"from scvi_colab import install\n",
"install()"
]
},
{
Expand Down
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