From 0f84ee39834e65065bf8106c449cf50a5065ebb2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 9 Aug 2024 11:38:55 +0200 Subject: [PATCH 1/3] update base images --- src/control_methods/no_denoising/config.vsh.yaml | 2 +- src/control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/methods/alra/config.vsh.yaml | 2 +- src/methods/knn_smoothing/config.vsh.yaml | 2 +- src/methods/magic/config.vsh.yaml | 2 +- src/methods/saver/config.vsh.yaml | 2 +- src/metrics/mse/config.vsh.yaml | 2 +- src/metrics/poisson/config.vsh.yaml | 2 +- src/process_dataset/config.vsh.yaml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/control_methods/no_denoising/config.vsh.yaml b/src/control_methods/no_denoising/config.vsh.yaml index 366a0f0..c0364df 100644 --- a/src/control_methods/no_denoising/config.vsh.yaml +++ b/src/control_methods/no_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 runners: - type: executable diff --git a/src/control_methods/perfect_denoising/config.vsh.yaml b/src/control_methods/perfect_denoising/config.vsh.yaml index f4c5766..e4f235d 100644 --- a/src/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/control_methods/perfect_denoising/config.vsh.yaml @@ -17,7 +17,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 runners: - type: executable diff --git a/src/methods/alra/config.vsh.yaml b/src/methods/alra/config.vsh.yaml index 32ddc79..4f956b4 100644 --- a/src/methods/alra/config.vsh.yaml +++ b/src/methods/alra/config.vsh.yaml @@ -33,7 +33,7 @@ resources: path: script.R engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix, rsvd ] diff --git a/src/methods/knn_smoothing/config.vsh.yaml b/src/methods/knn_smoothing/config.vsh.yaml index 7ab61ff..fd7aab1 100644 --- a/src/methods/knn_smoothing/config.vsh.yaml +++ b/src/methods/knn_smoothing/config.vsh.yaml @@ -30,7 +30,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/methods/magic/config.vsh.yaml b/src/methods/magic/config.vsh.yaml index cee7046..62b9c87 100644 --- a/src/methods/magic/config.vsh.yaml +++ b/src/methods/magic/config.vsh.yaml @@ -53,7 +53,7 @@ resources: path: script.py engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/methods/saver/config.vsh.yaml b/src/methods/saver/config.vsh.yaml index 5ab4ce0..90717dc 100644 --- a/src/methods/saver/config.vsh.yaml +++ b/src/methods/saver/config.vsh.yaml @@ -23,7 +23,7 @@ resources: path: script.R engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: r github: mohuangx/SAVER diff --git a/src/metrics/mse/config.vsh.yaml b/src/metrics/mse/config.vsh.yaml index 6dd69d1..9068716 100644 --- a/src/metrics/mse/config.vsh.yaml +++ b/src/metrics/mse/config.vsh.yaml @@ -18,7 +18,7 @@ resources: path: script.py engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/metrics/poisson/config.vsh.yaml b/src/metrics/poisson/config.vsh.yaml index 73b02d3..9f8aab8 100644 --- a/src/metrics/poisson/config.vsh.yaml +++ b/src/metrics/poisson/config.vsh.yaml @@ -18,7 +18,7 @@ resources: path: script.py engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/process_dataset/config.vsh.yaml b/src/process_dataset/config.vsh.yaml index 0ae398a..f167d39 100644 --- a/src/process_dataset/config.vsh.yaml +++ b/src/process_dataset/config.vsh.yaml @@ -25,7 +25,7 @@ resources: - path: helper.py engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python packages: From f90e0b67c9dc90ae2893157f47c3beffa29dcfa2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 9 Aug 2024 11:39:40 +0200 Subject: [PATCH 2/3] update submodule --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index fab42b1..25bfdf2 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit fab42b17d1d88317e42bef4849f6ef16687e3531 +Subproject commit 25bfdf258bf7ff4417964eb5647b2dc999f12cfd From 2f2444dc56274ac9211987f8549116ae8cb02db4 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 9 Aug 2024 11:48:01 +0200 Subject: [PATCH 3/3] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c31c80..bb12c68 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,8 @@ * Update `task_name` variable to denoising in component scripts (PR #9). +* Update docker containers used in components (PR #12). + ## transfer from openproblems-v2 repository ### NEW FUNCTIONALITY