update changelog and author list

Author: rcannood

CHANGELOG.md

@@ -1,26 +1,66 @@
-# task_batch_integration x.y.z
+# task_batch_integration 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 SCimilarity (PR #3).
 
-* Updated configs, components and CI to the latest Viash version (PR #8).
+* Added Geneformer (PR #6).
 
-## MINOR CHANGES
+* Added UCE method (PR #7).
 
-* Updated `README.md` (PR #5).
+* Added scGPT zero shot (PR #8, #16).
 
-## BUGFIXES
+* Added scPRINT (PR #13).
 
+* Added scGPT fine-tuned (PR #17).
+
+
+## Major changes
+
+* Prefilter batches in HVG overlap metric (PR #9).
+
+* Precompute clustering for some metrics (PR #18).
+
+
+## Minor changes
+
+* Add arguments for filtering methods in benchmarking workflow (PR #4).
+
+* Update compute environment (PR #5).
+
+* Adjust resources (PR #10).
+
+* Update dependency components (PR #10).
+
+* Update API formats (PR #21, #28, #31).
+
+* Add support for zebrafish and C. elegans (PR #22).
+
+* Bump scIB to v1.1.7 (PR #30).
+
+* Update common submodule (PR #29).
+
+## Bug fixes
+
+* Multiple fixes prior to release (PR #24, #25, #26, #27, #32, #34, #36, #37, #39, #41, #42, #43, #44).
+
+## Documentation
+
+* Update documentation (PR #45).
+
+
+# task_batch_integration 1.0.0
+
+This version can be found [here](https://github.com/openproblems-bio/openproblems/tree/v1.0.0/openproblems/tasks/_batch_integration).

_viash.yaml

@@ -62,10 +62,15 @@ authors:
       github: danielStrobl
       orcid: 0000-0002-5516-7057
   - name: Robrecht Cannoodt
-    roles: [ contributor ]
+    roles: [ author ]
     info:
       github: rcannood
       orcid: "0000-0003-3641-729X"
+  - name: Luke Zappia
+    roles: [author]
+    info:
+      github: lazappi
+      orcid: 0000-0001-7744-8565
   - name: "Scott Gigante"
     roles: [ contributor ]
     info:
@@ -76,11 +81,16 @@ authors:
     info:
       github: KaiWaldrant
       orcid: "0009-0003-8555-1361"
-  - name: Nartin Kim
+  - name: Martin Kim
     roles: [ contributor ]
     info:
       github: martinkim0
       orcid: "0009-0003-8555-1361"
+  - name: Sai Nirmayi Yasa
+    roles: [contributor]
+    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" }