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🚚 Replace ln.track() with ln.context.track()
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@falexwolf
falexwolf committed Aug 16, 2024
1 parent f26c162 commit df93ae1
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Showing 4 changed files with 32 additions and 36 deletions.
5 changes: 2 additions & 3 deletions docs/notebooks/01-rxrx1-ingest.ipynb
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Expand Up @@ -30,9 +30,8 @@
"import bionty as bt\n",
"import wetlab as wl\n",
"\n",
"ln.settings.transform.stem_uid = \"Zo0qJt4IQPsb\"\n",
"ln.settings.transform.version = \"1\"\n",
"run = ln.track()"
"ln.context.uid = \"Zo0qJt4IQPsb0000\"\n",
"run = ln.context.track()"
]
},
{
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27 changes: 13 additions & 14 deletions docs/static/2024-04-02-marshall-2022.ipynb
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Expand Up @@ -16,7 +16,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"💡 connected lamindb: scverse/spatial\n"
"\ud83d\udca1 connected lamindb: scverse/spatial\n"
]
}
],
Expand All @@ -33,19 +33,18 @@
"name": "stdout",
"output_type": "stream",
"text": [
"💡 connected lamindb: scverse/spatial\n",
"💡 notebook imports: anndata==0.10.7 lamindb==0.70.3 numpy==1.26.4 scanpy==1.10.1 vitessce==3.2.5\n",
"💡 loaded: Transform(uid='VwUYGOmA3koC65cN', name='marshall-2022', key='2024-04-02-marshall-2022', version='2', type='notebook', updated_at=2024-04-23 12:40:36 UTC, created_by_id=2)\n",
"💡 loaded: Run(uid='v6SbqImFKgQZdOBlsUcW', started_at=2024-04-23 13:45:52 UTC, is_consecutive=True, transform_id=20, created_by_id=2)\n"
"\ud83d\udca1 connected lamindb: scverse/spatial\n",
"\ud83d\udca1 notebook imports: anndata==0.10.7 lamindb==0.70.3 numpy==1.26.4 scanpy==1.10.1 vitessce==3.2.5\n",
"\ud83d\udca1 loaded: Transform(uid='VwUYGOmA3koC65cN', name='marshall-2022', key='2024-04-02-marshall-2022', version='2', type='notebook', updated_at=2024-04-23 12:40:36 UTC, created_by_id=2)\n",
"\ud83d\udca1 loaded: Run(uid='v6SbqImFKgQZdOBlsUcW', started_at=2024-04-23 13:45:52 UTC, is_consecutive=True, transform_id=20, created_by_id=2)\n"
]
}
],
"source": [
"import lamindb as ln\n",
"\n",
"ln.settings.transform.stem_uid = \"VwUYGOmA3koC\"\n",
"ln.settings.transform.version = \"2\"\n",
"ln.track()"
"ln.context.uid = \"VwUYGOmA3koC0000\"\n",
"ln.context.track()"
]
},
{
Expand Down Expand Up @@ -334,7 +333,7 @@
"output_type": "stream",
"text": [
"... uploading config.vitessce.json: 100.0%\n",
"💡 go to: https://lamin.ai/scverse/spatial/artifact/sKxat1sh8unY0n0IkqNb\n"
"\ud83d\udca1 go to: https://lamin.ai/scverse/spatial/artifact/sKxat1sh8unY0n0IkqNb\n"
]
}
],
Expand All @@ -351,14 +350,14 @@
"name": "stdout",
"output_type": "stream",
"text": [
"❗ cells [(9, 11)] were not run consecutively\n",
"\u2757 cells [(9, 11)] were not run consecutively\n",
"... uploading 2024-04-02-marshall-2022.ipynb: 100.0%\n",
"✅ saved transform.source_code: Artifact(uid='uOM8vBTTl3u72AyybkwW', suffix='.ipynb', description='Source of transform VwUYGOmA3koC65cN', version='2', size=7404, hash='NXzsZfmqWWpsTk-wIDa8Yg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-23 13:55:20 UTC, storage_id=2, created_by_id=2)\n",
"\u2705 saved transform.source_code: Artifact(uid='uOM8vBTTl3u72AyybkwW', suffix='.ipynb', description='Source of transform VwUYGOmA3koC65cN', version='2', size=7404, hash='NXzsZfmqWWpsTk-wIDa8Yg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-23 13:55:20 UTC, storage_id=2, created_by_id=2)\n",
"... uploading run_env_pip_v6SbqImFKgQZdOBlsUcW.txt: 100.0%\n",
"✅ saved run.environment: Artifact(uid='iWaFLxrJN9TDrBZhCqrf', suffix='.txt', description='requirements.txt', size=10914, hash='WMhSDgtH_xsYI0nHNDNzuA', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-23 13:55:20 UTC, storage_id=2, created_by_id=2)\n",
"\u2705 saved run.environment: Artifact(uid='iWaFLxrJN9TDrBZhCqrf', suffix='.txt', description='requirements.txt', size=10914, hash='WMhSDgtH_xsYI0nHNDNzuA', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-23 13:55:20 UTC, storage_id=2, created_by_id=2)\n",
"... uploading 2024-04-02-marshall-2022.html: 100.0%\n",
"✅ saved transform.latest_report: Artifact(uid='xGaILnIF0wJNiu6Evv7a', suffix='.html', description='Report of run v6SbqImFKgQZdOBlsUcW', version='2', size=301331, hash='KF9Z0Cc9eCDFuuxS9hsPRg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-23 13:55:20 UTC, storage_id=2, created_by_id=2)\n",
"✅ go to: https://lamin.ai/scverse/spatial/transform/VwUYGOmA3koC65cN\n"
"\u2705 saved transform.latest_report: Artifact(uid='xGaILnIF0wJNiu6Evv7a', suffix='.html', description='Report of run v6SbqImFKgQZdOBlsUcW', version='2', size=301331, hash='KF9Z0Cc9eCDFuuxS9hsPRg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-23 13:55:20 UTC, storage_id=2, created_by_id=2)\n",
"\u2705 go to: https://lamin.ai/scverse/spatial/transform/VwUYGOmA3koC65cN\n"
]
}
],
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31 changes: 15 additions & 16 deletions docs/static/mudata-vitessce.ipynb
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Expand Up @@ -16,7 +16,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"💡 connected lamindb: laminlabs/lamindata\n"
"\ud83d\udca1 connected lamindb: laminlabs/lamindata\n"
]
}
],
Expand All @@ -33,25 +33,24 @@
"name": "stdout",
"output_type": "stream",
"text": [
"💡 connected lamindb: laminlabs/lamindata\n"
"\ud83d\udca1 connected lamindb: laminlabs/lamindata\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"💡 notebook imports: lamindb==0.70.3 mudata==0.2.3 scanpy==1.10.1 vitessce==3.2.5\n",
"💡 saved: Transform(uid='aCrfeVoAaDr95zKv', name='Visualize MuData in Vitessce', key='mudata-vitessce', version='1', type='notebook', updated_at=2024-04-30 12:46:10 UTC, created_by_id=2)\n",
"💡 saved: Run(uid='VPYyibO30e6mHkw7DC7r', transform_id=82, created_by_id=2)\n"
"\ud83d\udca1 notebook imports: lamindb==0.70.3 mudata==0.2.3 scanpy==1.10.1 vitessce==3.2.5\n",
"\ud83d\udca1 saved: Transform(uid='aCrfeVoAaDr95zKv', name='Visualize MuData in Vitessce', key='mudata-vitessce', version='1', type='notebook', updated_at=2024-04-30 12:46:10 UTC, created_by_id=2)\n",
"\ud83d\udca1 saved: Run(uid='VPYyibO30e6mHkw7DC7r', transform_id=82, created_by_id=2)\n"
]
}
],
"source": [
"import lamindb as ln\n",
"\n",
"ln.settings.transform.stem_uid = \"aCrfeVoAaDr9\"\n",
"ln.settings.transform.version = \"1\"\n",
"ln.track()"
"ln.context.uid = \"aCrfeVoAaDr90000\"\n",
"ln.context.track()"
]
},
{
Expand Down Expand Up @@ -92,7 +91,7 @@
{
"data": {
"text/html": [
"<pre>MuData object with n_obs × n_vars = 20729 × 18776\n",
"<pre>MuData object with n_obs \u00d7 n_vars = 20729 \u00d7 18776\n",
" 4 modalities\n",
" rna:\t20729 x 18649\n",
" obs:\t&#x27;orig.ident&#x27;, &#x27;nCount_RNA&#x27;, &#x27;nFeature_RNA&#x27;, &#x27;nCount_HTO&#x27;, &#x27;nFeature_HTO&#x27;, &#x27;nCount_GDO&#x27;, &#x27;nCount_ADT&#x27;, &#x27;nFeature_ADT&#x27;, &#x27;percent.mito&#x27;, &#x27;MULTI_ID&#x27;, &#x27;HTO_classification&#x27;, &#x27;guide_ID&#x27;, &#x27;gene_target&#x27;, &#x27;NT&#x27;, &#x27;perturbation&#x27;, &#x27;replicate&#x27;, &#x27;S.Score&#x27;, &#x27;G2M.Score&#x27;, &#x27;Phase&#x27;\n",
Expand All @@ -115,7 +114,7 @@
" var:\t&#x27;name&#x27;</pre>"
],
"text/plain": [
"MuData object with n_obs × n_vars = 20729 × 18776\n",
"MuData object with n_obs \u00d7 n_vars = 20729 \u00d7 18776\n",
" 4 modalities\n",
" rna:\t20729 x 18649\n",
" obs:\t'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'nCount_HTO', 'nFeature_HTO', 'nCount_GDO', 'nCount_ADT', 'nFeature_ADT', 'percent.mito', 'MULTI_ID', 'HTO_classification', 'guide_ID', 'gene_target', 'NT', 'perturbation', 'replicate', 'S.Score', 'G2M.Score', 'Phase'\n",
Expand Down Expand Up @@ -354,7 +353,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"💡 go to: https://lamin.ai/laminlabs/lamindata/artifact/sRapK07mMtToihzFeTaf\n"
"\ud83d\udca1 go to: https://lamin.ai/laminlabs/lamindata/artifact/sRapK07mMtToihzFeTaf\n"
]
}
],
Expand All @@ -373,11 +372,11 @@
"name": "stdout",
"output_type": "stream",
"text": [
"✅ cell execution numbers increase consecutively\n",
"✅ saved transform.source_code: Artifact(uid='j6zQfam6cVBHlOR1dTde', suffix='.ipynb', description='Source of transform aCrfeVoAaDr95zKv', version='1', size=4511, hash='cmD2CwZCSebUjDXlzngfmQ', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-30 12:52:46 UTC, storage_id=2, created_by_id=2)\n",
"✅ saved run.environment: Artifact(uid='nYO2R3tM4rhqB7mZHZnl', suffix='.txt', description='requirements.txt', size=10821, hash='Iu7Isnon8g7iS-XUyNFD7w', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-30 12:52:47 UTC, storage_id=2, created_by_id=2)\n",
"✅ saved transform.latest_report: Artifact(uid='NEuTTW4HAIX9ORtCuDOe', suffix='.html', description='Report of run VPYyibO30e6mHkw7DC7r', size=293911, hash='ADqBuImn9seir0EPXhGOcg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-30 12:52:48 UTC, storage_id=2, created_by_id=2)\n",
"✅ go to: https://lamin.ai/laminlabs/lamindata/transform/aCrfeVoAaDr95zKv\n"
"\u2705 cell execution numbers increase consecutively\n",
"\u2705 saved transform.source_code: Artifact(uid='j6zQfam6cVBHlOR1dTde', suffix='.ipynb', description='Source of transform aCrfeVoAaDr95zKv', version='1', size=4511, hash='cmD2CwZCSebUjDXlzngfmQ', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-30 12:52:46 UTC, storage_id=2, created_by_id=2)\n",
"\u2705 saved run.environment: Artifact(uid='nYO2R3tM4rhqB7mZHZnl', suffix='.txt', description='requirements.txt', size=10821, hash='Iu7Isnon8g7iS-XUyNFD7w', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-30 12:52:47 UTC, storage_id=2, created_by_id=2)\n",
"\u2705 saved transform.latest_report: Artifact(uid='NEuTTW4HAIX9ORtCuDOe', suffix='.html', description='Report of run VPYyibO30e6mHkw7DC7r', size=293911, hash='ADqBuImn9seir0EPXhGOcg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-04-30 12:52:48 UTC, storage_id=2, created_by_id=2)\n",
"\u2705 go to: https://lamin.ai/laminlabs/lamindata/transform/aCrfeVoAaDr95zKv\n"
]
}
],
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5 changes: 2 additions & 3 deletions docs/vitessce.ipynb
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Expand Up @@ -75,9 +75,8 @@
"outputs": [],
"source": [
"# [optional] track the current notebook or script\n",
"ln.settings.transform.stem_uid = \"BZhZQ6uIbkWv\"\n",
"ln.settings.transform.version = \"2.1\"\n",
"ln.track()"
"ln.context.uid = \"BZhZQ6uIbkWv0000\"\n",
"ln.context.track()"
]
},
{
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