update api and readme

Author: rcannood

README.md

@@ -3,7 +3,8 @@ example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.
 label: "Raw dataset RNA"
 summary: "The RNA modality of the raw dataset."
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts

README.qmd

@@ -3,7 +3,8 @@ example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.
 label: "Raw dataset mod2"
 summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset"
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts

src/api/file_common_dataset_mod1.yaml

@@ -3,7 +3,8 @@ example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swa
 label: "Prediction"
 summary: "A prediction of the mod2 expression values of the test cells"
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: double
         name: normalized

src/api/file_common_dataset_mod2.yaml

@@ -3,7 +3,8 @@ example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swa
 label: "Score"
 summary: "Metric score file"
 info:
-  slots:
+  format:
+    type: h5ad
     uns:
       - type: string
         name: dataset_id

src/api/file_prediction.yaml

@@ -3,7 +3,8 @@ example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swa
 label: "Test mod1"
 summary: "The mod1 expression values of the test cells."
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts

src/api/file_score.yaml

@@ -3,7 +3,8 @@ example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swa
 label: "Test mod2"
 summary: "The mod2 expression values of the test cells."
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts

src/api/file_test_mod1.yaml

@@ -3,7 +3,8 @@ example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swa
 label: "Train mod1"
 summary: "The mod1 expression values of the train cells."
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts

src/api/file_test_mod2.yaml

@@ -3,7 +3,8 @@ example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swa
 label: "Train mod2"
 summary: "The mod2 expression values of the train cells."
 info:
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts