deploy: 3794a92

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

@@ -56,10 +56,15 @@ 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:
@@ -70,11 +75,16 @@ 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" }
 repositories:

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

@@ -338,7 +338,7 @@ build_info:
   output: "target/executable/control_methods/embed_cell_types"
   executable: "target/executable/control_methods/embed_cell_types/embed_cell_types"
   viash_version: "0.9.0"
-  git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
+  git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
   git_remote: "https://github.com/openproblems-bio/task_batch_integration"
 package_config:
   name: "task_batch_integration"
@@ -415,10 +415,16 @@ package_config:
       orcid: "0000-0002-5516-7057"
   - name: "Robrecht Cannoodt"
     roles:
-    - "contributor"
+    - "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"
@@ -431,12 +437,18 @@ package_config:
     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"
   keywords:
   - "batch integration"
   - "scRNA-seq"

target/executable/control_methods/embed_cell_types/embed_cell_types

@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component control_methods embed_cell_types"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:19Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:19:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
-LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
+LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

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

@@ -349,7 +349,7 @@ build_info:
   output: "target/executable/control_methods/embed_cell_types_jittered"
   executable: "target/executable/control_methods/embed_cell_types_jittered/embed_cell_types_jittered"
   viash_version: "0.9.0"
-  git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
+  git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
   git_remote: "https://github.com/openproblems-bio/task_batch_integration"
 package_config:
   name: "task_batch_integration"
@@ -426,10 +426,16 @@ package_config:
       orcid: "0000-0002-5516-7057"
   - name: "Robrecht Cannoodt"
     roles:
-    - "contributor"
+    - "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"
@@ -442,12 +448,18 @@ package_config:
     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"
   keywords:
   - "batch integration"
   - "scRNA-seq"

target/executable/control_methods/embed_cell_types_jittered/embed_cell_types_jittered

@@ -477,9 +477,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component control_methods embed_cell_types_jittered"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:18Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:19:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
-LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
+LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

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

@@ -336,7 +336,7 @@ build_info:
   output: "target/executable/control_methods/no_integration"
   executable: "target/executable/control_methods/no_integration/no_integration"
   viash_version: "0.9.0"
-  git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
+  git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
   git_remote: "https://github.com/openproblems-bio/task_batch_integration"
 package_config:
   name: "task_batch_integration"
@@ -413,10 +413,16 @@ package_config:
       orcid: "0000-0002-5516-7057"
   - name: "Robrecht Cannoodt"
     roles:
-    - "contributor"
+    - "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"
@@ -429,12 +435,18 @@ package_config:
     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"
   keywords:
   - "batch integration"
   - "scRNA-seq"

target/executable/control_methods/no_integration/no_integration

@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component control_methods no_integration"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:18Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:19:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
-LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
+LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

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

@@ -336,7 +336,7 @@ build_info:
   output: "target/executable/control_methods/no_integration_batch"
   executable: "target/executable/control_methods/no_integration_batch/no_integration_batch"
   viash_version: "0.9.0"
-  git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
+  git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
   git_remote: "https://github.com/openproblems-bio/task_batch_integration"
 package_config:
   name: "task_batch_integration"
@@ -413,10 +413,16 @@ package_config:
       orcid: "0000-0002-5516-7057"
   - name: "Robrecht Cannoodt"
     roles:
-    - "contributor"
+    - "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"
@@ -429,12 +435,18 @@ package_config:
     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"
   keywords:
   - "batch integration"
   - "scRNA-seq"

target/executable/control_methods/no_integration_batch/no_integration_batch

@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM openproblems/base_python:1.0.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component control_methods no_integration_batch"
-LABEL org.opencontainers.image.created="2025-02-11T12:19:19Z"
+LABEL org.opencontainers.image.created="2025-02-11T13:19:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
-LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
+LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
 LABEL org.opencontainers.image.version="2.0.0"
 
 VIASHDOCKER

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

@@ -336,7 +336,7 @@ build_info:
   output: "target/executable/control_methods/shuffle_integration"
   executable: "target/executable/control_methods/shuffle_integration/shuffle_integration"
   viash_version: "0.9.0"
-  git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
+  git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
   git_remote: "https://github.com/openproblems-bio/task_batch_integration"
 package_config:
   name: "task_batch_integration"
@@ -413,10 +413,16 @@ package_config:
       orcid: "0000-0002-5516-7057"
   - name: "Robrecht Cannoodt"
     roles:
-    - "contributor"
+    - "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"
@@ -429,12 +435,18 @@ package_config:
     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"
   keywords:
   - "batch integration"
   - "scRNA-seq"