[med-svn] [Git][med-team/mirtop][master] 3 commits: add explicity dependency on python3-six (Closes: #1084347)

[Alexandre Detiste (@detiste-guest)]

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 <tchet at debian.org>  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 <nilesh at debian.org>
 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 <nilesh at debian.org>
-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 <tille at debian.org>
-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
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