[med-svn] [Git][med-team/umis][master] 6 commits: New upstream version 1.0.7
Steffen Möller
gitlab at salsa.debian.org
Tue May 19 14:07:28 BST 2020
Steffen Möller pushed to branch master at Debian Med / umis
Commits:
2e267bd4 by Steffen Moeller at 2020-05-19T15:01:18+02:00
New upstream version 1.0.7
- - - - -
b48becbd by Steffen Moeller at 2020-05-19T15:01:18+02:00
routine-update: New upstream version
- - - - -
2ca271ca by Steffen Moeller at 2020-05-19T15:01:20+02:00
Update upstream source from tag 'upstream/1.0.7'
Update to upstream version '1.0.7'
with Debian dir a2cb2201ccc75577e60edbaa53feaaa7e1a8e9a0
- - - - -
ff6bfc9c by Steffen Moeller at 2020-05-19T15:01:32+02:00
routine-update: Add salsa-ci file
- - - - -
ffe1caaf by Steffen Moeller at 2020-05-19T15:01:32+02:00
routine-update: Rules-Requires-Root: no
- - - - -
f057d388 by Steffen Moeller at 2020-05-19T15:05:09+02:00
Upload.
- - - - -
12 changed files:
- HISTORY.md
- debian/changelog
- debian/control
- debian/patches/fix_bashism.patch
- + debian/salsa-ci.yml
- + examples/tagcount/tagcount-example.csv
- setup.py
- test.sh
- + tests/correct/test25.mtx
- + tests/correct/test25.mtx.colnames
- + tests/correct/test25.mtx.rownames
- umis/umis.py
Changes:
=====================================
HISTORY.md
=====================================
@@ -1,3 +1,7 @@
+## 1.0.7
+- Ensure headers are not written when writing out a Series, to make us compatible with pandas > 0.24.
+- Fix for deprecated .ix call, .loc is the new replacement. Thanks to @naumenko-sa.
+
## 1.0.6
- Fix for the python3 fix.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+umis (1.0.7-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 19 May 2020 15:01:34 +0200
+
umis (1.0.6-2) unstable; urgency=medium
* Fix clean target
=====================================
debian/control
=====================================
@@ -13,6 +13,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/umis
Vcs-Git: https://salsa.debian.org/med-team/umis.git
Homepage: https://github.com/vals/umis
+Rules-Requires-Root: no
Package: umis
Architecture: any
=====================================
debian/patches/fix_bashism.patch
=====================================
@@ -2,16 +2,18 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Sat, 13 Apr 2019 07:12:50 +0200
Description: Fix bashism in test script
---- a/test.sh
-+++ b/test.sh
+Index: umis/test.sh
+===================================================================
+--- umis.orig/test.sh
++++ umis/test.sh
@@ -1,3 +1,5 @@
+#!/bin/sh
+
rm -r tests/results
mkdir -p tests/results
-@@ -192,7 +194,7 @@ examples/Klein-inDrop/test_cell_demultip
-
+@@ -193,7 +195,7 @@ examples/Klein-inDrop/test_cell_demultip
+ umis sparse examples/tagcount/tagcount-example.csv tests/results/test25.mtx
# only display diff output if there are differences
-if [[ $(diff -rq tests/results tests/correct) ]]; then
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+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
=====================================
examples/tagcount/tagcount-example.csv
=====================================
@@ -0,0 +1,3 @@
+gene,GATAACCATA-GTTACCGC,GATAACCATC-GTTACCGC
+ENSDART00000163675.1,1,2
+ENSDART00000163675.2,0,0
=====================================
setup.py
=====================================
@@ -8,7 +8,7 @@ def read(fname):
setup(
name='umis',
- version='1.0.6',
+ version='1.0.7',
description='Package for estimating UMI counts in Transcript Tag Counting data.',
packages=find_packages(),
install_requires=['click', 'pysam>=0.8.3', 'pandas', 'regex', 'scipy', 'toolz'],
=====================================
test.sh
=====================================
@@ -190,6 +190,7 @@ umis demultiplex_cells \
--out_dir tests/results \
examples/Klein-inDrop/test_cell_demultiplex.fq
+umis sparse examples/tagcount/tagcount-example.csv tests/results/test25.mtx
# only display diff output if there are differences
if [[ $(diff -rq tests/results tests/correct) ]]; then
=====================================
tests/correct/test25.mtx
=====================================
@@ -0,0 +1,5 @@
+%%MatrixMarket matrix coordinate integer general
+%
+2 2 2
+1 1 1
+1 2 2
=====================================
tests/correct/test25.mtx.colnames
=====================================
@@ -0,0 +1,2 @@
+GATAACCATA-GTTACCGC
+GATAACCATC-GTTACCGC
=====================================
tests/correct/test25.mtx.rownames
=====================================
@@ -0,0 +1,2 @@
+ENSDART00000163675.1
+ENSDART00000163675.2
=====================================
umis/umis.py
=====================================
@@ -24,7 +24,7 @@ import numpy as np
import scipy.io, scipy.sparse
import click
-VERSION = "1.0.6"
+VERSION = "1.0.7"
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
@@ -653,7 +653,7 @@ def tagcount(sam, out, genemap, output_evidence_table, positional, minevidence,
genes = pd.Series(index=set(gene_map.values()))
genes = genes.sort_index()
# Now genes is assigned to a DataFrame
- genes = expanded.ix[genes.index]
+ genes = expanded.loc[genes.index]
elif gene_tags:
expanded.sort_index()
@@ -949,8 +949,8 @@ def sparse(csv, sparse):
'''
import pandas as pd
df = pd.read_csv(csv, index_col=0, header=0)
- pd.Series(df.index).to_csv(sparse + ".rownames", index=False)
- pd.Series(df.columns.values).to_csv(sparse + ".colnames", index=False)
+ pd.Series(df.index).to_csv(sparse + ".rownames", index=False, header=False)
+ pd.Series(df.columns.values).to_csv(sparse + ".colnames", index=False, header=False)
with open(sparse, "w+b") as out_handle:
scipy.io.mmwrite(out_handle, scipy.sparse.csr_matrix(df))
View it on GitLab: https://salsa.debian.org/med-team/umis/-/compare/55ca0dd551bff60c146d57dcebfadacad6b0e3c4...f057d388e07a4830dbdb4cdd38c30dbf2bf72817
--
View it on GitLab: https://salsa.debian.org/med-team/umis/-/compare/55ca0dd551bff60c146d57dcebfadacad6b0e3c4...f057d388e07a4830dbdb4cdd38c30dbf2bf72817
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