[med-svn] [Git][med-team/mirtop][master] 2 commits: d/p/fix-circular-import.patch: Fix circular import

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / mirtop


Commits:
6a00a05f by Nilesh Patra at 2021-06-30T18:17:21+00:00
d/p/fix-circular-import.patch: Fix circular import

- - - - -
9943c4fb by Nilesh Patra at 2021-06-30T18:19:26+00:00
Update changelog

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix-circular-import.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
 mirtop (0.4.23-1) UNRELEASED; urgency=medium
 
+  * Team Upload.
   [ Matúš Kalaš ]
   * Update citations
   * Fixed citations
@@ -7,10 +8,14 @@ mirtop (0.4.23-1) UNRELEASED; urgency=medium
   * Pretty-printed metadata & removed double-quotes
 
   [ Shruti Sridhar ]
-  * team Upload.
   * Add autopkgtests
+  * Update changelog
+  * Add salsa-ci.yml
 
- -- Shruti Sridhar <shruti.sridhar99 at gmail.com>  Wed, 30 Jun 2021 20:46:37 +0530
+  [ Nilesh Patra ]
+  * d/p/fix-circular-import.patch: Fix circular import
+
+ -- Nilesh Patra <nilesh at debian.org>  Wed, 30 Jun 2021 18:18:19 +0000
 
 mirtop (0.4.23-1) unstable; urgency=medium
 


=====================================
debian/patches/fix-circular-import.patch
=====================================
@@ -0,0 +1,29 @@
+Description: import module in needed functions to fix circular import
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-06-30
+--- a/mirtop/bam/bam.py
++++ b/mirtop/bam/bam.py
+@@ -15,7 +15,6 @@
+ from mirtop.mirna.realign import isomir, hits, reverse_complement
+ from mirtop.mirna.mapper import get_primary_transcript, guess_database
+ from mirtop.bam import filter
+-from mirtop.gff import body
+ from mirtop.mirna.annotate import annotate
+ from mirtop.libs import sql
+ 
+@@ -72,6 +71,7 @@
+ def low_memory_bam(bam_fn, sample, out_handle, args):
+     if args.genomic:
+         raise ValueError("low-memory option is not compatible with genomic coordinates.")
++    from mirtop.gff import body
+     precursors = args.precursors
+     bam_fn = _sam_to_bam(bam_fn)
+     bam_fn = _bam_sort(bam_fn)
+@@ -100,6 +100,7 @@
+ def low_memory_genomic_bam(bam_fn, sample, out_handle, args):
+     logger.info("Reading BAM file in low memory mode.")
+     logger.warning("This is under development and variants can be unexact.")
++    from mirtop.gff import body
+     precursors = args.precursors
+     bam_fn = _sam_to_bam(bam_fn)
+     bam_fn = _bam_sort(bam_fn)


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 spelling
+fix-circular-import.patch



View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/7894173e72878c5eed9c065f98c736e32ee9b57f...9943c4fbbf173de4810d6e97af4fbc0c611e73a6

-- 
View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/7894173e72878c5eed9c065f98c736e32ee9b57f...9943c4fbbf173de4810d6e97af4fbc0c611e73a6
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