[med-svn] [Git][med-team/mirtop][master] 4 commits: Revert "Enable experimental in salsa-ci.yml"

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / mirtop


Commits:
f05fad48 by Nilesh Patra at 2024-02-04T14:45:11+05:30
Revert "Enable experimental in salsa-ci.yml"

This reverts commit 22554ec4496d11bbae115ef77c74608eed025690.

- - - - -
a16870eb by Nilesh Patra at 2024-02-04T14:45:19+05:30
Revert "Force pandas >= 2.0 to make sure the version from experimental will be taken"

This reverts commit 3eac0bc2e1bc3140be8321341e7d70c24ea417b3.

- - - - -
74187802 by Nilesh Patra at 2024-02-04T09:53:12+00:00
Add patch to fix FTBFS with pandas 2.0 (Closes: #1044055)

- - - - -
81d0909c by Nilesh Patra at 2024-02-04T09:53:12+00:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/pandas-2.patch
- debian/patches/series
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,9 @@
-mirtop (0.4.25-5) UNRELEASED; urgency=medium
+mirtop (0.4.25-5) unstable; urgency=medium
 
-  * Team upload.
-  * Enable experimental in salsa-ci.yml
+  * Team Upload.
+  * Add patch to fix FTBFS with pandas 2.0 (Closes: #1044055)
 
- -- Andreas Tille <tille at debian.org>  Mon, 29 Jan 2024 09:05:28 +0100
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 04 Feb 2024 14:47:21 +0530
 
 mirtop (0.4.25-4) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-recommonmark,
                python3-pysam,
                python3-pybedtools,
-               python3-pandas (>= 2.0),
+               python3-pandas,
                python3-biopython
 Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/mirtop
@@ -29,7 +29,7 @@ Depends: ${python3:Depends},
          ${sphinxdoc:Depends},
          python3-pysam,
          python3-pybedtools,
-         python3-pandas (>= 2.0),
+         python3-pandas,
          python3-biopython
 Description: annotate miRNAs with a standard mirna/isomir naming (Python 3)
  The main goal of this project is to create a reflection group on metazoan


=====================================
debian/patches/pandas-2.patch
=====================================
@@ -0,0 +1,23 @@
+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/series
=====================================
@@ -2,3 +2,4 @@ spelling
 fix-circular-import.patch
 pytest.patch
 python3-syntax.patch
+pandas-2.patch


=====================================
debian/salsa-ci.yml
=====================================
@@ -2,7 +2,3 @@
 include:
   - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
   - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
-
-variables:
-  # Build against pandas 2.x in experimental to recreate the test failure reported in bug #1044055
-  RELEASE: 'experimental'



View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/3eac0bc2e1bc3140be8321341e7d70c24ea417b3...81d0909c3d41653740aac0d1b9627fad9740216f

-- 
View it on GitLab: https://salsa.debian.org/med-team/mirtop/-/compare/3eac0bc2e1bc3140be8321341e7d70c24ea417b3...81d0909c3d41653740aac0d1b9627fad9740216f
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