Merge branch 'main' into add-simple-mlp

openproblems-bio · Jan 8, 2025 · 042fc55 · 042fc55
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,24 +1,15 @@
-# task_predict_modality x.y.z
+# task_predict_modality 0.1.0
 
-## BREAKING CHANGES
-
-<!-- * Restructured `src` directory (PR #3). -->
+Initial release after migrating the codebase.
 
 ## NEW FUNCTIONALITY
 
-* Added `control_methods/true_labels` component (PR #5).
+* Control methods: Solution, Mean per gene, Random Predictions, Zeros.
 
-* Added `methods/logistic_regression` component (PR #5).
+* Methods: Guanlab-dengkw, KNNR, Linear Model
 
-* Added `metrics/accuracy` component (PR #5).
+* Metrics: MAE, Mean pearson / spearman, RMSE
 
 ## MAJOR CHANGES
 
-* Updated `api` files (PR #5).
-
-## MINOR CHANGES
-
-* Updated `README.md` (PR #5).
-
-## BUGFIXES
-
+* Refactored the API schema.
diff --git a/README.md b/README.md
@@ -35,50 +35,49 @@ data shows that this is not trivial.
 | Alejandro Granados | author             |
 | Alex Tong          | author             |
 | Bastian Rieck      | author             |
+| Christopher Lance  | author             |
 | Daniel Burkhardt   | author             |
 | Kai Waldrant       | contributor        |
 | Kaiwen Deng        | contributor        |
 | Louise Deconinck   | author             |
 | Robrecht Cannoodt  | author, maintainer |
-| Xueer Chen         | contributor        |
-| Jiwei Liu          | contributor        |
 
 ## API
 
 ``` mermaid
-flowchart LR
-  file_common_dataset_mod1("Raw dataset RNA")
-  comp_process_datasets[/"Process Dataset"/]
-  file_test_mod1("Test mod1")
-  file_test_mod2("Test mod2")
-  file_train_mod1("Train mod1")
-  file_train_mod2("Train mod2")
-  comp_control_method[/"Control method"/]
-  comp_method_predict[/"Predict"/]
-  comp_method_train[/"Train"/]
-  comp_method[/"Method"/]
-  comp_metric[/"Metric"/]
-  file_prediction("Prediction")
-  file_pretrained_model("Pretrained model")
-  file_score("Score")
-  file_common_dataset_mod2("Raw dataset mod2")
+flowchart TB
+  file_common_dataset_mod1("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-raw-dataset-rna'>Raw dataset RNA</a>")
+  comp_process_datasets[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-process-dataset'>Process Dataset</a>"/]
+  file_test_mod1("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-test-mod1'>Test mod1</a>")
+  file_test_mod2("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-test-mod2'>Test mod2</a>")
+  file_train_mod1("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-train-mod1'>Train mod1</a>")
+  file_train_mod2("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-train-mod2'>Train mod2</a>")
+  comp_control_method[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-control-method'>Control method</a>"/]
+  comp_method_predict[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-predict'>Predict</a>"/]
+  comp_method_train[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-train'>Train</a>"/]
+  comp_method[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-method'>Method</a>"/]
+  comp_metric[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-metric'>Metric</a>"/]
+  file_prediction("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-prediction'>Prediction</a>")
+  file_pretrained_model("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-pretrained-model'>Pretrained model</a>")
+  file_score("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-score'>Score</a>")
+  file_common_dataset_mod2("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-raw-dataset-mod2'>Raw dataset mod2</a>")
   file_common_dataset_mod1---comp_process_datasets
   comp_process_datasets-->file_test_mod1
   comp_process_datasets-->file_test_mod2
   comp_process_datasets-->file_train_mod1
   comp_process_datasets-->file_train_mod2
   file_test_mod1---comp_control_method
   file_test_mod1---comp_method_predict
-  file_test_mod1---comp_method_train
+  file_test_mod1-.-comp_method_train
   file_test_mod1---comp_method
   file_test_mod2---comp_control_method
   file_test_mod2---comp_metric
   file_train_mod1---comp_control_method
-  file_train_mod1---comp_method_predict
+  file_train_mod1-.-comp_method_predict
   file_train_mod1---comp_method_train
   file_train_mod1---comp_method
   file_train_mod2---comp_control_method
-  file_train_mod2---comp_method_predict
+  file_train_mod2-.-comp_method_predict
   file_train_mod2---comp_method_train
   file_train_mod2---comp_method
   comp_control_method-->file_prediction

diff --git a/_viash.yaml b/_viash.yaml
@@ -45,6 +45,11 @@ authors:
     roles: [ author ]
     info:
       github: Pseudomanifold
+  - name: Christopher Lance
+    roles: [ author ]
+    info:
+      github: xlancelottx
+      orcid: "0000-0002-1275-9802"
   - name: Daniel Burkhardt
     roles: [ author ]
     info:

diff --git a/scripts/create_readme.sh b/scripts/create_readme.sh
@@ -2,4 +2,4 @@
 
 set -e
 
-common/scripts/create_task_readme
+common/scripts/create_task_readme --input src
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,4 @@

		set -e

		common/scripts/create_task_readme
		common/scripts/create_task_readme --input src