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 <[email protected]> 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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