include pyx, exclude msig

IMTMarburg · Aug 19, 2024 · 05690e3 · 05690e3
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2022 Florian Finkernagel, Philipps University Marburg
+Copyright (c) 2024 Florian Finkernagel, Philipps University Marburg
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/setup.cfg b/setup.cfg
@@ -5,7 +5,7 @@
 [metadata]
 name = mbf
 description = Functionality for genomics
-version = 0.1
+version = 0.1.1
 author = Florian Finkernagel
 author-email = [email protected]
 license = mit

diff --git a/src/mbf/__init__.py b/src/mbf/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.1"
+__version__ = "0.1.1"
 
 
 import mbf_bam as bam  # noqa: F401

diff --git a/src/mbf/functional/datasets/msig/c1.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c1.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c1.all.v3.1.symbols.gmt b/src/mbf/functional/datasets/msig/c1.all.v3.1.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c1.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c1.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c1.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c1.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c1.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c1.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c2.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.all.v3.1.symbols.gmt b/src/mbf/functional/datasets/msig/c2.all.v3.1.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c2.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cgp.v4.0.orig.gmt b/src/mbf/functional/datasets/msig/c2.cgp.v4.0.orig.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cgp.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cgp.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.biocarta.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.biocarta.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.biocarta.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.biocarta.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.kegg.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.kegg.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.kegg.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.kegg.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.reactome.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.reactome.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.reactome.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.reactome.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c2.cp.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c2.cp.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c3.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.all.v3.1.symbols.gmt b/src/mbf/functional/datasets/msig/c3.all.v3.1.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c3.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c3.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c3.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.mir.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c3.mir.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c3.tft.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c3.tft.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c4.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.all.v3.1.symbols.gmt b/src/mbf/functional/datasets/msig/c4.all.v3.1.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c4.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c4.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c4.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.cgn.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c4.cgn.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c4.cm.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c4.cm.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c5.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.all.v3.1.symbols.gmt b/src/mbf/functional/datasets/msig/c5.all.v3.1.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c5.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.bp.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.bp.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.bp.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.bp.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.cc.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.cc.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.cc.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.cc.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.mf.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.mf.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c5.mf.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c5.mf.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c6.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c6.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c6.all.v3.1.symbols.gmt b/src/mbf/functional/datasets/msig/c6.all.v3.1.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c6.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c6.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c6.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c6.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c6.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c6.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c7.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/c7.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c7.all.v4.0.entrez.gmt b/src/mbf/functional/datasets/msig/c7.all.v4.0.entrez.gmt
diff --git a/src/mbf/functional/datasets/msig/c7.all.v4.0.orig.gmt b/src/mbf/functional/datasets/msig/c7.all.v4.0.orig.gmt
diff --git a/src/mbf/functional/datasets/msig/c7.all.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/c7.all.v4.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c7.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/c7.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c7.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c7.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/c8.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/c8.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/h.all.v2023.2.Hs.symbols.gmt b/src/mbf/functional/datasets/msig/h.all.v2023.2.Hs.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/h.all.v5.0.symbols.gmt b/src/mbf/functional/datasets/msig/h.all.v5.0.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/h.all.v7.2.symbols.gmt b/src/mbf/functional/datasets/msig/h.all.v7.2.symbols.gmt
diff --git a/src/mbf/functional/datasets/msig/msigdb.v4.0.symbols.gmt b/src/mbf/functional/datasets/msig/msigdb.v4.0.symbols.gmt