scdataloader 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

scdataloader/utils.py

@@ -433,7 +433,7 @@ def populate_my_ontology(
         names = bt.Phenotype.public().df().index if not sex else sex
         records = [
             bt.Phenotype.from_source(
-                ontology_id=i,
+                ontology_id=i, source=bt.PublicSource.filter(name="pato").first()
             )
             for i in names
         ]
@@ -472,9 +472,12 @@ def populate_my_ontology(
 
         names = bt.DevelopmentalStage.public(organism="mouse").df().index
         records = [
-            bt.DevelopmentalStage.from_source(ontology_id=i) for i in names.tolist()
+            bt.DevelopmentalStage.from_source(
+                ontology_id=i,
+                source=bt.PublicSource.filter(organism="mouse", name="mmusdv").first(),
+            )
+            for i in names.tolist()
         ]
-        records[-4] = records[-4][0]
         ln.save(records)
     # Disease
     if diseases is not None:

{scdataloader-1.0.5.dist-info → scdataloader-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scdataloader
-Version: 1.0.5
+Version: 1.0.6
 Summary: a dataloader for single cell data in lamindb
 Home-page: https://github.com/jkobject/scDataLoader
 License: GPL3
@@ -82,13 +82,41 @@ I needed to create this Data Loader for my PhD project. I am using it to load &
 
 ```bash
 pip install scdataloader
+# or
+pip install scDataLoader[dev] # for dev dependencies
+
+lamin login <email> --key <API-key>
+lamin init --storage [folder-name-where-lamin-data-will-be-stored] --schema bionty
 ```
 
-### Install it locally and run the notebooks:
+if you start with lamin and had to do a `lamin init`, you will also need to populate your ontologies. This is because scPRINT is using ontologies to define its cell types, diseases, sexes, ethnicities, etc.
+
+you can do it manually or with our function:
+
+```python
+from scdataloader.utils import populate_my_ontology
+
+populate_my_ontology() #to populate everything (recommended) (can take 2-10mns)
+
+populate_my_ontology( #the minimum for scprint to run some inferences (denoising, grn inference)
+organisms: List[str] = ["NCBITaxon:10090", "NCBITaxon:9606"],
+    sex: List[str] = ["PATO:0000384", "PATO:0000383"],
+    celltypes = None,
+    ethnicities = None,
+    assays = None,
+    tissues = None,
+    diseases = None,
+    dev_stages = None,
+)
+```
+
+### Dev install
+
+If you want to use the latest version of scDataLoader and work on the code yourself use `git clone` and `pip -e` instead of `pip install`.
 
 ```bash
 git clone https://github.com/jkobject/scDataLoader.git
-pip install -e scDataLoader
+pip install -e scDataLoader[dev]
 ```
 
 ## Usage

{scdataloader-1.0.5.dist-info → scdataloader-1.0.6.dist-info}/RECORD

@@ -8,9 +8,9 @@ scdataloader/data.py,sha256=3a9jUhREIzbxC797COGNSn6QqbRiiC30FzxXCoYsTNo,13773
 scdataloader/datamodule.py,sha256=JZq8g274ce3ARW59qwg5GKAt2SzOTaMPGh3CySGQS70,16893
 scdataloader/mapped.py,sha256=s_Fg-lwaXjHFyQcKnp9El2IceMoaEajynyUgOnpVnXQ,20750
 scdataloader/preprocess.py,sha256=9dgsq7c5jD2l-CUGfwC2uG98MCIgnrYFkqknqAyu5dU,28841
-scdataloader/utils.py,sha256=aXIdnJGrANL5Q4Kcpq2_HNZOT8TcnvyoZgLiLuzchDA,21306
-scdataloader-1.0.5.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-scdataloader-1.0.5.dist-info/METADATA,sha256=ypdRTtPWFQz_Y4YQeZlrRsGmU6b4_xbAttUEAwIPxwg,42295
-scdataloader-1.0.5.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-scdataloader-1.0.5.dist-info/entry_points.txt,sha256=nLqucZaa5wiF7-1FCgMXO916WDQ9Qm0TcxQp0f1DwE4,59
-scdataloader-1.0.5.dist-info/RECORD,,
+scdataloader/utils.py,sha256=8YIVpqJzNKkIIpAS5p01gyt57X2CrfaMEsC1EJs-q_A,21451
+scdataloader-1.0.6.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+scdataloader-1.0.6.dist-info/METADATA,sha256=LhqbssiiI5Y-GZeYk1nXnHFNo2SNhuc6W9LwlIX_OCo,43336
+scdataloader-1.0.6.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+scdataloader-1.0.6.dist-info/entry_points.txt,sha256=nLqucZaa5wiF7-1FCgMXO916WDQ9Qm0TcxQp0f1DwE4,59
+scdataloader-1.0.6.dist-info/RECORD,,