From 5130c79660edd5524b029489ef10ce86ec885dfa Mon Sep 17 00:00:00 2001 From: pavlemarinkovic Date: Thu, 30 May 2024 15:32:39 +0200 Subject: [PATCH 1/2] NF schema is built only if it's missing Use wrabbit 0.1.3 --- .github/dependabot.yml | 0 .github/workflows/codeql-analysis.yml | 0 .github/workflows/tests.yml | 0 .gitignore | 0 LICENSE | 0 MANIFEST.in | 0 Readme.md | 0 requirements.txt | 2 +- sbpack/__init__.py | 0 sbpack/lib.py | 0 sbpack/noncwl/Readme.md | 0 sbpack/noncwl/__init__.py | 0 sbpack/noncwl/constants.py | 0 sbpack/noncwl/copy_app.py | 0 sbpack/noncwl/manifest.py | 0 sbpack/noncwl/nextflow.py | 3 ++- sbpack/noncwl/utils.py | 0 sbpack/noncwl/wdl.py | 0 sbpack/pack.py | 0 sbpack/schemadef.py | 0 sbpack/unpack.py | 0 sbpack/version.py | 0 setup.py | 0 test-requirements.txt | 0 tests/lib.js | 0 tests/remote-cwl/tool1.cwl | 0 tests/remote-cwl/tool2.cwl | 0 tests/remote-cwl/wf1.cwl | 0 tests/test_localpack.py | 0 tests/test_packing.py | 0 tests/test_pulling.py | 0 tests/test_schemadefs.py | 0 tests/test_validation_battery.py | 0 tests/tools/clt1.cwl | 0 tests/tools/clt2.cwl | 0 tests/tools/clt3.cwl | 0 tests/types/array.yml | 0 tests/types/recursive.yml | 0 tests/types/singletype.yml | 0 tests/types/singletype2.yml | 0 tests/types/testtypes.yml | 0 tests/wf2.cwl | 0 tests/workflows/count-lines16-wf.cwl | 0 tests/workflows/import-in-type.cwl | 0 tests/workflows/scatter-wf4.cwl | 0 tests/workflows/type-import.yaml | 0 tests/workflows/wf-with-git.cwl | 0 tests/workflows/wf1.cwl | 0 tests/workflows/wf2.cwl | 0 tests/workflows/wf3.cwl | 0 tests/workflows/wf4.cwl | 0 tests/workflows/wf5.cwl | 0 tests/workflows/wf6.cwl | 0 tests/workflows/wf6.json | 0 tests/workflows/wf6_with_ids.json | 0 55 files changed, 3 insertions(+), 2 deletions(-) mode change 100644 => 100755 .github/dependabot.yml mode change 100644 => 100755 .github/workflows/codeql-analysis.yml mode change 100644 => 100755 .github/workflows/tests.yml mode change 100644 => 100755 .gitignore mode change 100644 => 100755 LICENSE mode change 100644 => 100755 MANIFEST.in mode change 100644 => 100755 Readme.md mode change 100644 => 100755 requirements.txt mode change 100644 => 100755 sbpack/__init__.py mode change 100644 => 100755 sbpack/lib.py mode change 100644 => 100755 sbpack/noncwl/Readme.md mode change 100644 => 100755 sbpack/noncwl/__init__.py mode change 100644 => 100755 sbpack/noncwl/constants.py mode change 100644 => 100755 sbpack/noncwl/copy_app.py mode change 100644 => 100755 sbpack/noncwl/manifest.py mode change 100644 => 100755 sbpack/noncwl/nextflow.py mode change 100644 => 100755 sbpack/noncwl/utils.py mode change 100644 => 100755 sbpack/noncwl/wdl.py mode change 100644 => 100755 sbpack/pack.py mode change 100644 => 100755 sbpack/schemadef.py mode change 100644 => 100755 sbpack/unpack.py mode change 100644 => 100755 sbpack/version.py mode change 100644 => 100755 setup.py mode change 100644 => 100755 test-requirements.txt mode change 100644 => 100755 tests/lib.js mode change 100644 => 100755 tests/remote-cwl/tool1.cwl mode change 100644 => 100755 tests/remote-cwl/tool2.cwl mode change 100644 => 100755 tests/remote-cwl/wf1.cwl mode change 100644 => 100755 tests/test_localpack.py mode change 100644 => 100755 tests/test_packing.py mode change 100644 => 100755 tests/test_pulling.py mode change 100644 => 100755 tests/test_schemadefs.py mode change 100644 => 100755 tests/test_validation_battery.py mode change 100644 => 100755 tests/tools/clt1.cwl mode change 100644 => 100755 tests/tools/clt2.cwl mode change 100644 => 100755 tests/tools/clt3.cwl mode change 100644 => 100755 tests/types/array.yml mode change 100644 => 100755 tests/types/recursive.yml mode change 100644 => 100755 tests/types/singletype.yml mode change 100644 => 100755 tests/types/singletype2.yml mode change 100644 => 100755 tests/types/testtypes.yml mode change 100644 => 100755 tests/wf2.cwl mode change 100644 => 100755 tests/workflows/count-lines16-wf.cwl mode change 100644 => 100755 tests/workflows/import-in-type.cwl mode change 100644 => 100755 tests/workflows/scatter-wf4.cwl mode change 100644 => 100755 tests/workflows/type-import.yaml mode change 100644 => 100755 tests/workflows/wf-with-git.cwl mode change 100644 => 100755 tests/workflows/wf1.cwl mode change 100644 => 100755 tests/workflows/wf2.cwl mode change 100644 => 100755 tests/workflows/wf3.cwl mode change 100644 => 100755 tests/workflows/wf4.cwl mode change 100644 => 100755 tests/workflows/wf5.cwl mode change 100644 => 100755 tests/workflows/wf6.cwl mode change 100644 => 100755 tests/workflows/wf6.json mode change 100644 => 100755 tests/workflows/wf6_with_ids.json diff --git a/.github/dependabot.yml b/.github/dependabot.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml old mode 100644 new mode 100755 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml old mode 100644 new mode 100755 diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/MANIFEST.in b/MANIFEST.in old mode 100644 new mode 100755 diff --git a/Readme.md b/Readme.md old mode 100644 new mode 100755 diff --git a/requirements.txt b/requirements.txt old mode 100644 new mode 100755 index 556065c..268ee49 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ ruamel.yaml >= 0.16 sevenbridges-python >= 2.0 nf-core==2.1 -wrabbit==0.1.2 +wrabbit==0.1.3 cwlformat packaging \ No newline at end of file diff --git a/sbpack/__init__.py b/sbpack/__init__.py old mode 100644 new mode 100755 diff --git a/sbpack/lib.py b/sbpack/lib.py old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/Readme.md b/sbpack/noncwl/Readme.md old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/__init__.py b/sbpack/noncwl/__init__.py old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/constants.py b/sbpack/noncwl/constants.py old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/copy_app.py b/sbpack/noncwl/copy_app.py old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/manifest.py b/sbpack/noncwl/manifest.py old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/nextflow.py b/sbpack/noncwl/nextflow.py old mode 100644 new mode 100755 index 4e2085b..84ec02c --- a/sbpack/noncwl/nextflow.py +++ b/sbpack/noncwl/nextflow.py @@ -250,7 +250,8 @@ def main(): else: # build schema # Do this only if the nextflow_schema.json is missing - nf_wrapper.nf_schema_build() + if not nf_wrapper.nf_schema_path: + nf_wrapper.nf_schema_build() # Create app nf_wrapper.generate_sb_app( diff --git a/sbpack/noncwl/utils.py b/sbpack/noncwl/utils.py old mode 100644 new mode 100755 diff --git a/sbpack/noncwl/wdl.py b/sbpack/noncwl/wdl.py old mode 100644 new mode 100755 diff --git a/sbpack/pack.py b/sbpack/pack.py old mode 100644 new mode 100755 diff --git a/sbpack/schemadef.py b/sbpack/schemadef.py old mode 100644 new mode 100755 diff --git a/sbpack/unpack.py b/sbpack/unpack.py old mode 100644 new mode 100755 diff --git a/sbpack/version.py b/sbpack/version.py old mode 100644 new mode 100755 diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 diff --git a/test-requirements.txt b/test-requirements.txt old mode 100644 new mode 100755 diff --git a/tests/lib.js b/tests/lib.js old mode 100644 new mode 100755 diff --git a/tests/remote-cwl/tool1.cwl b/tests/remote-cwl/tool1.cwl old mode 100644 new mode 100755 diff --git a/tests/remote-cwl/tool2.cwl b/tests/remote-cwl/tool2.cwl old mode 100644 new mode 100755 diff --git a/tests/remote-cwl/wf1.cwl b/tests/remote-cwl/wf1.cwl old mode 100644 new mode 100755 diff --git a/tests/test_localpack.py b/tests/test_localpack.py old mode 100644 new mode 100755 diff --git a/tests/test_packing.py b/tests/test_packing.py old mode 100644 new mode 100755 diff --git a/tests/test_pulling.py b/tests/test_pulling.py old mode 100644 new mode 100755 diff --git a/tests/test_schemadefs.py b/tests/test_schemadefs.py old mode 100644 new mode 100755 diff --git a/tests/test_validation_battery.py b/tests/test_validation_battery.py old mode 100644 new mode 100755 diff --git a/tests/tools/clt1.cwl b/tests/tools/clt1.cwl old mode 100644 new mode 100755 diff --git a/tests/tools/clt2.cwl b/tests/tools/clt2.cwl old mode 100644 new mode 100755 diff --git a/tests/tools/clt3.cwl b/tests/tools/clt3.cwl old mode 100644 new mode 100755 diff --git a/tests/types/array.yml b/tests/types/array.yml old mode 100644 new mode 100755 diff --git a/tests/types/recursive.yml b/tests/types/recursive.yml old mode 100644 new mode 100755 diff --git a/tests/types/singletype.yml b/tests/types/singletype.yml old mode 100644 new mode 100755 diff --git a/tests/types/singletype2.yml b/tests/types/singletype2.yml old mode 100644 new mode 100755 diff --git a/tests/types/testtypes.yml b/tests/types/testtypes.yml old mode 100644 new mode 100755 diff --git a/tests/wf2.cwl b/tests/wf2.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/count-lines16-wf.cwl b/tests/workflows/count-lines16-wf.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/import-in-type.cwl b/tests/workflows/import-in-type.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/scatter-wf4.cwl b/tests/workflows/scatter-wf4.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/type-import.yaml b/tests/workflows/type-import.yaml old mode 100644 new mode 100755 diff --git a/tests/workflows/wf-with-git.cwl b/tests/workflows/wf-with-git.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf1.cwl b/tests/workflows/wf1.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf2.cwl b/tests/workflows/wf2.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf3.cwl b/tests/workflows/wf3.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf4.cwl b/tests/workflows/wf4.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf5.cwl b/tests/workflows/wf5.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf6.cwl b/tests/workflows/wf6.cwl old mode 100644 new mode 100755 diff --git a/tests/workflows/wf6.json b/tests/workflows/wf6.json old mode 100644 new mode 100755 diff --git a/tests/workflows/wf6_with_ids.json b/tests/workflows/wf6_with_ids.json old mode 100644 new mode 100755 From 45a1689dbc9b4bbc0d2f13d50be3dd5cd196bd06 Mon Sep 17 00:00:00 2001 From: pavlemarinkovic Date: Mon, 3 Jun 2024 13:46:13 +0200 Subject: [PATCH 2/2] NF schema is built only if it's missing Use wrabbit 0.1.3 --- sbpack/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sbpack/version.py b/sbpack/version.py index cc96978..6588dfc 100755 --- a/sbpack/version.py +++ b/sbpack/version.py @@ -1 +1 @@ -__version__ = "2024.5.21rc1" +__version__ = "2024.6.3rc1"