Alexandre Detiste pushed to branch master at Debian Med / mirtop
Commits: c8656ac4 by Alexandre Detiste at 2024-10-12T14:52:46+02:00 add explicity dependency on python3-six (Closes: #1084347) - - - - - 065bc417 by Alexandre Detiste at 2024-10-12T14:56:29+02:00 refresh patches - - - - - 3c055e56 by Alexandre Detiste at 2024-10-12T15:07:14+02:00 release - - - - - 6 changed files: - debian/changelog - debian/control - debian/patches/fix-circular-import.patch - − debian/patches/pandas-2.patch - − debian/patches/python3-syntax.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +mirtop (0.4.28-1) unstable; urgency=medium + + * Team Upload. + * New upstream version 0.4.28 + * Add explicity dependency on python3-six (Closes: #1084347) + + [ Andreas Tille ] + * Add hint for better testing + + -- Alexandre Detiste <[email protected]> Sat, 12 Oct 2024 15:06:38 +0200 + mirtop (0.4.25-5) unstable; urgency=medium * Team Upload. ===================================== debian/control ===================================== @@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, + python3-six, python3-sphinx, python3-recommonmark, python3-pysam, @@ -27,6 +28,7 @@ Section: python Depends: ${python3:Depends}, ${misc:Depends}, ${sphinxdoc:Depends}, + python3-six, python3-pysam, python3-pybedtools, python3-pandas, ===================================== debian/patches/fix-circular-import.patch ===================================== @@ -3,7 +3,7 @@ Author: Nilesh Patra <[email protected]> Last-Update: 2021-06-30 --- a/mirtop/bam/bam.py +++ b/mirtop/bam/bam.py -@@ -15,7 +15,6 @@ +@@ -16,7 +16,6 @@ from mirtop.mirna.realign import isomir, hits, reverse_complement from mirtop.mirna.mapper import get_primary_transcript, guess_database from mirtop.bam import filter @@ -11,7 +11,7 @@ Last-Update: 2021-06-30 from mirtop.mirna.annotate import annotate from mirtop.libs import sql -@@ -72,6 +71,7 @@ +@@ -73,6 +72,7 @@ def low_memory_bam(bam_fn, sample, out_handle, args): if args.genomic: raise ValueError("low-memory option is not compatible with genomic coordinates.") @@ -19,7 +19,7 @@ Last-Update: 2021-06-30 precursors = args.precursors bam_fn = _sam_to_bam(bam_fn) bam_fn = _bam_sort(bam_fn) -@@ -100,6 +100,7 @@ +@@ -101,6 +101,7 @@ 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.") ===================================== debian/patches/pandas-2.patch deleted ===================================== @@ -1,23 +0,0 @@ -Description: Replace append with concat as per pandas changed API -Author: Nilesh Patra <[email protected]> -Last-Update: 2024-02-04 ---- a/mirtop/gff/stats.py -+++ b/mirtop/gff/stats.py -@@ -107,13 +107,13 @@ - # ref_miRNA_mean - category = "ref_miRNA_mean" - if sum(df['category']==category) == 0: -- df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0} -- df = df.append(df2, ignore_index = True) -+ df2 = pd.DataFrame({'category': category, 'sample': df['sample'].iat[0], 'counts': 0}, index=[0]) -+ df = pd.concat([df, df2], ignore_index = True) - - category = "isomiR_sum" - if sum(df['category']==category) == 0: -- df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0} -- df = df.append(df2, ignore_index = True) -+ df2 = pd.DataFrame({'category': category, 'sample': df['sample'].iat[0], 'counts': 0}, index=[0]) -+ df = pd.concat([df, df2], ignore_index = True) - - return df - ===================================== debian/patches/python3-syntax.patch deleted ===================================== @@ -1,16 +0,0 @@ -Descriptiosn: Fix Python3 syntax -Bug-Debian: https://bugs.debian.org/1040287 -Author: Andreas Tille <[email protected]> -Last-Update: Mon, 10 Jul 2023 14:11:25 +0200 - ---- a/mirtop/mirna/mintplates.py -+++ b/mirtop/mirna/mintplates.py -@@ -509,7 +509,7 @@ def encode_sequence(sequence, prefix): - """ - length = len(sequence) - # Encode label -- if prefix is '': -+ if prefix == '': - final_result = [(str(length) + '-')] - else: - final_result = [prefix + "-" + str(length) + "-"] ===================================== debian/patches/series ===================================== @@ -1,5 +1,3 @@ spelling fix-circular-import.patch -pytest.patch -python3-syntax.patch -pandas-2.patch +#pytest.patch View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/c0a2829c3f62e8bd1206c7ba6e01e9e4698d400f...3c055e56e668580616fd263ec69400a655e4642a -- View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/c0a2829c3f62e8bd1206c7ba6e01e9e4698d400f...3c055e56e668580616fd263ec69400a655e4642a You're receiving this email because of your account on salsa.debian.org.
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