[med-svn] [Git][med-team/resfinder][master] 3 commits: Copy .md file as well for autopkgtest

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / resfinder


Commits:
404b968b by Nilesh Patra at 2023-01-22T01:57:22+05:30
Copy .md file as well for autopkgtest

- - - - -
34084876 by Nilesh Patra at 2023-01-21T20:52:04+00:00
Add patch to actually define mut-type as a variable

- - - - -
95f794a7 by Nilesh Patra at 2023-01-21T20:53:14+00:00
Move data to deprecated during autopkgtests

- - - - -


4 changed files:

- + debian/patches/mut-type.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/patches/mut-type.patch
=====================================
@@ -0,0 +1,12 @@
+diff --git a/src/resfinder/cge/phenotype2genotype/res_profile.py b/src/resfinder/cge/phenotype2genotype/res_profile.py
+index 4ca3cc9..12a2b8e 100644
+--- a/src/resfinder/cge/phenotype2genotype/res_profile.py
++++ b/src/resfinder/cge/phenotype2genotype/res_profile.py
+@@ -37,6 +37,7 @@ class PhenoDB(dict):
+         self.id_to_idwithvar = {}
+ 
+         self.ab_class_defs = ABClassDefinition(abclassdef_file)
++        self.mut_type_is_defined = False
+ 
+         if(acquired_file is None and point_file is None
+            and disinf_file is None):


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 fix_path_in_testscript.patch
 fix-shebang.patch
+mut-type.patch


=====================================
debian/rules
=====================================
@@ -11,6 +11,7 @@ override_dh_install:
 	find debian -name '*.nf' -type f | xargs rm -rf
 	mkdir -p debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/$(PYBUILD_NAME)
 	mv debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)/__*.py debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/$(PYBUILD_NAME)
+	mv debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)/*.md debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/$(PYBUILD_NAME)
 	mv debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)/cge    debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/$(PYBUILD_NAME)
 
 override_dh_fixperms:


=====================================
debian/tests/run-unit-test
=====================================
@@ -16,6 +16,9 @@ mkdir -p db_resfinder
 cp -a /usr/share/resfinder/db/* db_resfinder
 find -name '*.gz' -exec gunzip '{}' ';'
 
+# Move data to deprecated dir as functional tests seek relative path
+mv data deprecated/
+
 echo "Indexing files as needed"
 cd db_resfinder
 python3 INSTALL.py 2> /dev/null



View it on GitLab: https://salsa.debian.org/med-team/resfinder/-/compare/99948ea6b05ffd1ba21944eecbc105d83879fe89...95f794a7e066e408cf74385499bf695e7c93212d

-- 
View it on GitLab: https://salsa.debian.org/med-team/resfinder/-/compare/99948ea6b05ffd1ba21944eecbc105d83879fe89...95f794a7e066e408cf74385499bf695e7c93212d
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