From de5b9c2838768de2c86fa0f524a3507f98eb4094 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 6 Aug 2025 11:18:13 +0200 Subject: [PATCH 1/6] experiment with python helpers --- _viash.yaml | 5 ++++- common | 2 +- pyproject.toml | 16 ++++++++++++++++ target/executable/__init__.py | 0 4 files changed, 21 insertions(+), 2 deletions(-) create mode 100644 pyproject.toml create mode 100644 target/executable/__init__.py diff --git a/_viash.yaml b/_viash.yaml index 626b71f8..dcbc7ea6 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -97,7 +97,10 @@ authors: github: jkobject orcid: 0000-0002-2818-9728 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" } + .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" }; + .resources += { path: "/common/python_helpers/run.py" }; + .resources += { path: "/common/python_helpers/__init__.txt", dest: "__init__.py" } + repositories: - name: openproblems diff --git a/common b/common index b60eda08..f40cc0ea 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit b60eda085e9cd505ec169fa30cc7e919e8563ad2 +Subproject commit f40cc0eae423e43955072e44b8b2da240b14040e diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..b71fbe9f --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,16 @@ +[build-system] +requires = ["setuptools>=70"] +build-backend = "setuptools.build_meta" + +[project] +name = "task_batch_integration" +authors = [{name = "Robrecht Cannoodt", email = "robrecht@data-intuitive.com"}] +readme = "README.md" +version = "0.1.0" +description = "A test python wrapper for viash" + +[tool.setuptools.package-data] +"*" = ["*", ".*"] + +[tool.setuptools.package-dir] +task_batch_integration = "target/executable" diff --git a/target/executable/__init__.py b/target/executable/__init__.py new file mode 100644 index 00000000..e69de29b From 6f51577b8e553c2a5324247cca13f17f575a0f80 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 6 Aug 2025 11:39:02 +0200 Subject: [PATCH 2/6] update submodule --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index f40cc0ea..b841d7ff 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit f40cc0eae423e43955072e44b8b2da240b14040e +Subproject commit b841d7ff6285ba3929d7c8a4174744c2a01ecdae From 515e781b521d2afb7279f3309510f918140df865 Mon Sep 17 00:00:00 2001 From: Luke Zappia Date: Mon, 11 Aug 2025 15:07:12 +0200 Subject: [PATCH 3/6] Update submodule --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index b841d7ff..ee1c6ba2 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit b841d7ff6285ba3929d7c8a4174744c2a01ecdae +Subproject commit ee1c6ba2d22e53025cdf2a0279f33fb7d7984c47 From c464a8c68a1211c0517e465a20f4d0979ab42ec1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 Aug 2025 16:51:59 +0200 Subject: [PATCH 4/6] update common --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index ee1c6ba2..130c81bf 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit ee1c6ba2d22e53025cdf2a0279f33fb7d7984c47 +Subproject commit 130c81bf0dff67a1940fa12d2df4fc43fe961325 From 0afe22e83ba1db3b8025cc597a44f79eeebf9f70 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 14 Aug 2025 09:09:59 +0200 Subject: [PATCH 5/6] iterate on helper functions --- _viash.yaml | 3 +-- common | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/_viash.yaml b/_viash.yaml index dcbc7ea6..1bd4ecc9 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -98,8 +98,7 @@ authors: orcid: 0000-0002-2818-9728 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" }; - .resources += { path: "/common/python_helpers/run.py" }; - .resources += { path: "/common/python_helpers/__init__.txt", dest: "__init__.py" } + .resources += { path: "/common/python_helpers/__init__.py"} repositories: diff --git a/common b/common index 130c81bf..21751190 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 130c81bf0dff67a1940fa12d2df4fc43fe961325 +Subproject commit 2175119053d6587516a7ca9d374e8722509d3333 From 12c7c192d3faf10b59a45c4631db965dbec7a009 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 14 Aug 2025 09:25:52 +0200 Subject: [PATCH 6/6] update submodule --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index 21751190..ce2eae99 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 2175119053d6587516a7ca9d374e8722509d3333 +Subproject commit ce2eae9957152dd8e7a1c5a8ba250aabca2f4a74