From 2a929c4b905e69b8b0f31c8d908b52a3c0ac9fb3 Mon Sep 17 00:00:00 2001 From: "Lewis Winterberger (RIT Student)" Date: Sun, 30 Aug 2026 17:06:01 -0400 Subject: [PATCH 1/4] ruff_test --- urgap/uftypes/proteomics.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/urgap/uftypes/proteomics.py b/urgap/uftypes/proteomics.py index 8bb8a1e..fdb864e 100644 --- a/urgap/uftypes/proteomics.py +++ b/urgap/uftypes/proteomics.py @@ -20,6 +20,8 @@ proteomics.dbsearch.XTANDEM_XML = ".xtandem.xml" proteomics.dbsearch.DIANN_QUANT = ".diann.quant" proteomics.dbsearch.DIANN_REPORT = ".diann_report.tsv" +proteomics.dbsearch.SAGE_TSV = ".sage_report.tsv" +proteomics.dbsearch.SAGE_JSON = ".sage_report.json" proteomics.diannlibrary = types.SimpleNamespace() proteomics.diannlibrary.ANY = "proteomics.diannlibrary.ANY" @@ -61,3 +63,8 @@ proteomics.qc = types.SimpleNamespace() proteomics.qc.ANY = "proteomics.qc.ANY" proteomics.qc.OFFSET_CSV = ".offset.csv" + +proteomics.params = types.SimpleNamespace() +proteomics.params.ANY = ".msgfplus.params.ANY" +proteomics.params.MSGFPLUS_TXT = ".msgfplus_params.txt" +proteomics.params.SAGE_JSON = ".sage.json" \ No newline at end of file From 737c63ddcd1ea9f01904791dcea5faa768b15e5c Mon Sep 17 00:00:00 2001 From: StSchulze Date: Mon, 31 Aug 2026 22:34:24 -0400 Subject: [PATCH 2/4] Update pyproject.toml Add ignore tags to ruff configuration --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 5f7fb20..95463a1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,6 +54,8 @@ ignore = [ "PLC0415", # Avoid unnecessary imports, "UP047", # Only available 3.13+ "INP001", # Namespace packages intentionally have no __init__.py (PEP 420) + "CPY001", # Missing copyright notices + "PLR0917", # Too many positional arguments ] From d6a7e501dd69660cd600163bf5d0093034ffdb89 Mon Sep 17 00:00:00 2001 From: StSchulze Date: Mon, 31 Aug 2026 22:42:24 -0400 Subject: [PATCH 3/4] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 95463a1..01ca8bc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ dependencies = [ [project.optional-dependencies] dev = [ "pytest", - "pytest-asyncio>=0.23", + "pytest-asyncio>=0.23.6", "urgap[dev]", ] From 39ff711b0be9eb0cf5c00fde24308e9891670378 Mon Sep 17 00:00:00 2001 From: StSchulze Date: Mon, 31 Aug 2026 22:51:17 -0400 Subject: [PATCH 4/4] Update pyproject.toml --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 01ca8bc..29e70bc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,8 +15,8 @@ dependencies = [ [project.optional-dependencies] dev = [ - "pytest", - "pytest-asyncio>=0.23.6", + "pytest>=8.2", + "pytest-asyncio>=0.24", "urgap[dev]", ]