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 <[email protected]> Wed, 30 Jun 2021 20:46:37 +0530 + [ Nilesh Patra ] + * d/p/fix-circular-import.patch: Fix circular import + + -- Nilesh Patra <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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