deploy: 1d592b5

Author: rcannood

CHANGELOG.md

@@ -1,26 +1,46 @@
-# task_label_projection x.y.z
+# task_label_projection 2.0.0
 
-## BREAKING CHANGES
+A major update to the OpenProblems framework, switching from a Python-based framework to a Viash + Nextflow-based framework. This update features the same concepts as the previous version, but with a new implementation that is more flexible, scalable, and maintainable.
 
-<!-- * Restructured `src` directory (PR #3). -->
+## Migration
 
-## NEW FUNCTIONALITY
+* Added expected input/output interfaces in `src/api` and document them in `README.md`.
 
-* Added `control_methods/true_labels` component (PR #5).
+* Store common resources used across tasks in a git submodule `common`.
 
-* Added `methods/logistic_regression` component (PR #5).
+* Methods, metrics, workflows and other components are implemented as Viash components with a per-component Docker image.
 
-* Added `metrics/accuracy` component (PR #5).
+## New functionality
 
-## MAJOR CHANGES
+* Switched to larger datasets derived from CELLxGENE.
 
-* Updated `api` files (PR #5).
+* Added scGPT zero shot (PR #2).
 
-* Updated configs, components and CI to the latest Viash version (PR #8).
+* Added scGPT fine-tuned (PR #3).
 
-## MINOR CHANGES
+* Added SCimilarity (PR #4).
 
-* Updated `README.md` (PR #5).
+* Added UCE method (PR #6).
 
-## BUGFIXES
+* Added geneformer (PR #7, #16).
 
+* Added scPRINT (PR #8).
+
+## Major changes
+
+* Updated the task API (PR #9).
+
+## Bug fixes
+
+* Convert to dgCMatrix in SingleR (PR #5).
+
+* Multiple fixes prior to release (PR #11, #13, #14, #15, #17).
+
+## Documentation
+
+* Update README (PR #10).
+
+
+# task_label_projection 1.0.0
+
+This version can be found [here](https://github.com/openproblems-bio/openproblems/tree/v1.0.0/openproblems/tasks/label_projection).

_viash.yaml

@@ -72,6 +72,16 @@ authors:
     info:
       github: rcannood
       orcid: "0000-0003-3641-729X"
+  - name: Luke Zappia
+    roles: [author]
+    info:
+      github: lazappi
+      orcid: 0000-0001-7744-8565
+  - name: Sai Nirmayi Yasa
+    roles: [author]
+    info:
+      github: sainirmayi
+      orcid: 0009-0003-6319-9803
 config_mods: |
   .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
 repositories:

target/executable/control_methods/majority_vote/.config.vsh.yaml

@@ -351,7 +351,7 @@ build_info:
   output: "target/executable/control_methods/majority_vote"
   executable: "target/executable/control_methods/majority_vote/majority_vote"
   viash_version: "0.9.0"
-  git_commit: "f52ca0a9c28a6dc72520871de56ed3102c87c840"
+  git_commit: "1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
   git_remote: "https://github.com/openproblems-bio/task_label_projection"
 package_config:
   name: "task_label_projection"
@@ -417,6 +417,18 @@ package_config:
     info:
       github: "rcannood"
       orcid: "0000-0003-3641-729X"
+  - name: "Luke Zappia"
+    roles:
+    - "author"
+    info:
+      github: "lazappi"
+      orcid: "0000-0001-7744-8565"
+  - name: "Sai Nirmayi Yasa"
+    roles:
+    - "author"
+    info:
+      github: "sainirmayi"
+      orcid: "0009-0003-6319-9803"
   keywords:
   - "single-cell"
   - "label projection"

target/executable/control_methods/majority_vote/majority_vote

@@ -474,9 +474,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component control_methods majority_vote"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:36Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_label_projection"
-LABEL org.opencontainers.image.revision="f52ca0a9c28a6dc72520871de56ed3102c87c840"
+LABEL org.opencontainers.image.revision="1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

target/executable/control_methods/random_labels/.config.vsh.yaml

@@ -356,7 +356,7 @@ build_info:
   output: "target/executable/control_methods/random_labels"
   executable: "target/executable/control_methods/random_labels/random_labels"
   viash_version: "0.9.0"
-  git_commit: "f52ca0a9c28a6dc72520871de56ed3102c87c840"
+  git_commit: "1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
   git_remote: "https://github.com/openproblems-bio/task_label_projection"
 package_config:
   name: "task_label_projection"
@@ -422,6 +422,18 @@ package_config:
     info:
       github: "rcannood"
       orcid: "0000-0003-3641-729X"
+  - name: "Luke Zappia"
+    roles:
+    - "author"
+    info:
+      github: "lazappi"
+      orcid: "0000-0001-7744-8565"
+  - name: "Sai Nirmayi Yasa"
+    roles:
+    - "author"
+    info:
+      github: "sainirmayi"
+      orcid: "0009-0003-6319-9803"
   keywords:
   - "single-cell"
   - "label projection"

target/executable/control_methods/random_labels/random_labels

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "scanpy"
 
 LABEL org.opencontainers.image.description="Companion container for running component control_methods random_labels"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:35Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_label_projection"
-LABEL org.opencontainers.image.revision="f52ca0a9c28a6dc72520871de56ed3102c87c840"
+LABEL org.opencontainers.image.revision="1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

target/executable/control_methods/true_labels/.config.vsh.yaml

@@ -350,7 +350,7 @@ build_info:
   output: "target/executable/control_methods/true_labels"
   executable: "target/executable/control_methods/true_labels/true_labels"
   viash_version: "0.9.0"
-  git_commit: "f52ca0a9c28a6dc72520871de56ed3102c87c840"
+  git_commit: "1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
   git_remote: "https://github.com/openproblems-bio/task_label_projection"
 package_config:
   name: "task_label_projection"
@@ -416,6 +416,18 @@ package_config:
     info:
       github: "rcannood"
       orcid: "0000-0003-3641-729X"
+  - name: "Luke Zappia"
+    roles:
+    - "author"
+    info:
+      github: "lazappi"
+      orcid: "0000-0001-7744-8565"
+  - name: "Sai Nirmayi Yasa"
+    roles:
+    - "author"
+    info:
+      github: "sainirmayi"
+      orcid: "0009-0003-6319-9803"
   keywords:
   - "single-cell"
   - "label projection"

target/executable/control_methods/true_labels/true_labels

@@ -474,9 +474,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component control_methods true_labels"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:36Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_label_projection"
-LABEL org.opencontainers.image.revision="f52ca0a9c28a6dc72520871de56ed3102c87c840"
+LABEL org.opencontainers.image.revision="1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

target/executable/data_processors/process_dataset/.config.vsh.yaml

@@ -435,7 +435,7 @@ build_info:
   output: "target/executable/data_processors/process_dataset"
   executable: "target/executable/data_processors/process_dataset/process_dataset"
   viash_version: "0.9.0"
-  git_commit: "f52ca0a9c28a6dc72520871de56ed3102c87c840"
+  git_commit: "1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
   git_remote: "https://github.com/openproblems-bio/task_label_projection"
 package_config:
   name: "task_label_projection"
@@ -501,6 +501,18 @@ package_config:
     info:
       github: "rcannood"
       orcid: "0000-0003-3641-729X"
+  - name: "Luke Zappia"
+    roles:
+    - "author"
+    info:
+      github: "lazappi"
+      orcid: "0000-0001-7744-8565"
+  - name: "Sai Nirmayi Yasa"
+    roles:
+    - "author"
+    info:
+      github: "sainirmayi"
+      orcid: "0009-0003-6319-9803"
   keywords:
   - "single-cell"
   - "label projection"

target/executable/data_processors/process_dataset/process_dataset

@@ -490,9 +490,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component data_processors process_dataset"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:36Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_label_projection"
-LABEL org.opencontainers.image.revision="f52ca0a9c28a6dc72520871de56ed3102c87c840"
+LABEL org.opencontainers.image.revision="1d592b5795139b3cbc3d79cdc9dc6ae220a69b9f"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER