[med-svn] [Git][med-team/igdiscover][master] 10 commits: New upstream version 0.12.3
Andreas Tille
gitlab at salsa.debian.org
Fri Oct 2 13:48:16 BST 2020
Andreas Tille pushed to branch master at Debian Med / igdiscover
Commits:
11f77113 by Andreas Tille at 2020-10-02T14:31:20+02:00
New upstream version 0.12.3
- - - - -
80ab7857 by Andreas Tille at 2020-10-02T14:31:20+02:00
routine-update: New upstream version
- - - - -
21471bb7 by Andreas Tille at 2020-10-02T14:31:22+02:00
Update upstream source from tag 'upstream/0.12.3'
Update to upstream version '0.12.3'
with Debian dir 8ff9fb5e78ae663ad812bee62d87692103c8211e
- - - - -
32159080 by Andreas Tille at 2020-10-02T14:31:22+02:00
routine-update: debhelper-compat 13
- - - - -
109ecdf3 by Andreas Tille at 2020-10-02T14:35:02+02:00
routine-update: Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
4268e8c1 by Andreas Tille at 2020-10-02T14:37:11+02:00
routine-update: Do not parse d/changelog
- - - - -
20cea4b6 by Andreas Tille at 2020-10-02T14:37:11+02:00
routine-update: Add salsa-ci file
- - - - -
156a485d by Andreas Tille at 2020-10-02T14:37:11+02:00
routine-update: Rules-Requires-Root: no
- - - - -
b1c53709 by Andreas Tille at 2020-10-02T14:44:52+02:00
Update copyright
- - - - -
8dad23e2 by Andreas Tille at 2020-10-02T14:48:00+02:00
DEP3
- - - - -
13 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/adjusting_tests_for_python3.patch
- debian/patches/avoidTroubleWithPkgResources.patch
- debian/patches/dontusetagsforversion.patch
- debian/rules
- + debian/salsa-ci.yml
- src/igdiscover/Snakefile
- src/igdiscover/cli/clonoquery.py
- src/igdiscover/cli/clonotypes.py
- tests/test_commands.py
- tests/utils.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,19 @@
-igdiscover (0.12.2-1) UNRELEASED; urgency=medium
+igdiscover (0.12.3-1) UNRELEASED; urgency=medium
+ [ Steffen Moeller ]
* New upstream version
BLOCKER: Still needs igblast to test
+ [ Andreas Tille ]
+ * debhelper-compat 13 (routine-update)
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+ update)
+ * Do not parse d/changelog (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Update copyright
+ * DEP3
+
-- Steffen Moeller <moeller at debian.org> Sun, 26 Jan 2020 01:47:18 +0100
igdiscover (0.12-1) UNRELEASED; urgency=medium
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
python3-setuptools,
@@ -30,6 +30,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/igdiscover
Vcs-Git: https://salsa.debian.org/med-team/igdiscover.git
Homepage: http://docs.igdiscover.se/en/stable/
+Rules-Requires-Root: no
Package: igdiscover
Architecture: all
=====================================
debian/copyright
=====================================
@@ -36,14 +36,6 @@ License: Apache-2.0
On Debian systems, the complete text of the Apache version 2.0 license
can be found in "/usr/share/common-licenses/Apache-2.0".
-
-Files: versioneer.py
-Copyright: Brian Warner
-License: Public-Domain
- Available from https://github.com/warner/python-versioneer, the
- authors waives his copyrights for this work.
-
-
Files: debian/*
Copyright: 2019 Steffen Moeller <moeller at debian.org>
License: MIT
=====================================
debian/patches/adjusting_tests_for_python3.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-02-03 02:13:16 +0100
+Description: Python3 fix
+
Index: igdiscover/src/igdiscover/__main__.py
===================================================================
--- igdiscover.orig/src/igdiscover/__main__.py
=====================================
debian/patches/avoidTroubleWithPkgResources.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-02-03 02:13:16 +0100
+Description: Avoid issue with pkg_resources
+
Index: igdiscover/doc/conf.py
===================================================================
--- igdiscover.orig/doc/conf.py
=====================================
debian/patches/dontusetagsforversion.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-02-03 02:13:16 +0100
+Description: Do not use tags to obtain version number
+
Index: igdiscover/setup.py
===================================================================
--- igdiscover.orig/setup.py
=====================================
debian/rules
=====================================
@@ -4,12 +4,14 @@ export DH_VERBOSE = 1
export PYBUILD_NAME=igdiscover
+include /usr/share/dpkg/default.mk
+
%:
dh $@ --with python3,sphinxdoc --buildsystem=pybuild
override_dh_auto_build:
- echo "version=\"$$(dpkg-parsechangelog |grep ^Version|cut -f2 -d' ' | cut -f1 -d-)\"" > src/igdiscover/__version__.py
+ echo "$(DEB_VERSION_UPSTREAM)" > src/igdiscover/__version__.py
dh_auto_build
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/ build/html # HTML generator
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman doc/ build/man # Manpage generator
@@ -25,4 +27,6 @@ override_dh_auto_clean:
#rm -rf src/igdiscover.egg-info/
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo "**** NOT TESTING ******"
+endif
=====================================
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
=====================================
src/igdiscover/Snakefile
=====================================
@@ -330,7 +330,12 @@ else:
input: fastaq='reads/3-forward-primer-trimmed.{ext}.gz'
resources: time=1
run:
- relative_symlink(input.fastaq, output.fastaq, force=True)
+ if config.forward_primers:
+ # The target is marked as temp().
+ # To avoid a dangling symlink, use a hardlink.
+ os.link(input.fastaq, output.fastaq)
+ else:
+ relative_symlink(input.fastaq, output.fastaq, force=True)
rule trimmed_fasta_stats:
=====================================
src/igdiscover/cli/clonoquery.py
=====================================
@@ -30,7 +30,6 @@ def add_arguments(parser):
arg = parser.add_argument
arg('--minimum-count', '-c', metavar='N', default=1, type=int,
help='Discard all rows with count less than N. Default: %(default)s')
- arg('--v-shm-threshold', default=5, type=float, help='V SHM threshold for _mindiffrate computations')
arg('--cdr3-core', default=None,
type=slice_arg, metavar='START:END',
help='START:END defines the non-junction region of CDR3 '
@@ -93,7 +92,7 @@ def collect(querytable, reftable, mismatches, cdr3_core_slice, cdr3_column):
yield ([query_row], reftable.head(0))
continue
- similar_group = vjlen_group.iloc[list(indices), :]
+ similar_group = vjlen_group.iloc[list(indices), :].copy()
yield (query_rows, similar_group)
# Yield result tuples for all the queries that have not been found
@@ -138,13 +137,11 @@ def main(args):
else:
summary_file = None
- # Print header
+ # Header
print(*reftable.columns, sep='\t')
- # Do the actual work
for query_rows, result_table in collect(querytable, reftable, args.mismatches,
args.cdr3_core, cdr3_column):
- result_table = augment_group(result_table, v_shm_threshold=args.v_shm_threshold)
assert len(query_rows) >= 1
if summary_file:
for query_row in query_rows:
=====================================
src/igdiscover/cli/clonotypes.py
=====================================
@@ -234,9 +234,8 @@ def augment_group(table, v_shm_threshold=5, suffix='_mindiffrate'):
for column in columns:
root_seq = root[column]
- table[column + suffix] = [
+ table[column + suffix] = table[column].apply(lambda s:
round(edit_distance(root_seq, s, maxdiff=int(0.2 * len(root_seq))) / len(root_seq) * 100., 1)
- for s in table[column]
- ]
+ )
return table
=====================================
tests/test_commands.py
=====================================
@@ -1,12 +1,14 @@
import os
import sys
-import pytest
import contextlib
import shutil
+from pathlib import Path
+from xopen import xopen
+import pytest
from igdiscover.__main__ import main
-from .utils import datapath, resultpath, files_equal
+from .utils import datapath, resultpath, files_equal, convert_fastq_to_fasta
from igdiscover.cli.init import run_init
from igdiscover.cli.config import print_configuration, modify_configuration
from igdiscover.cli.run import run_snakemake
@@ -154,6 +156,27 @@ def test_primers(pipeline_dir):
run_snakemake(dryrun=True)
+# TODO slow
+def test_only_forward_primer(pipeline_dir):
+ # issue #107 (broken symlink)
+ with chdir(pipeline_dir):
+ modify_configuration(settings=[("forward_primers", "['CGTGA']")])
+ # Create some dummy files so we don’t need to run irrelevant steps of the pipeline
+ r = Path("reads")
+ r.mkdir()
+ with xopen(r / "2-merged.fastq.gz", "w") as f:
+ pass
+ s = Path("stats")
+ s.mkdir()
+ with open(s / "merging-successful", "w") as f:
+ pass
+ with open(s / "reads.json", "w") as f:
+ f.write('{"total": 0}')
+ with open(s / "trimmed.json", "w") as f:
+ f.write('{"trimmed": 0}')
+ run_snakemake(targets=["reads/sequences.fasta.gz"])
+
+
def test_flash(pipeline_dir):
# Test using FLASH and parsing its log output
with chdir(pipeline_dir):
@@ -218,11 +241,3 @@ def test_fasta_input(has_filtered_tab, tmp_path):
with chdir(directory):
modify_configuration([("barcode_length_3prime", "21")])
run_snakemake(targets=["stats/reads.json"])
-
-
-def convert_fastq_to_fasta(fastq, fasta):
- import dnaio
- with dnaio.open(fastq) as inf:
- with dnaio.open(fasta, mode="w") as outf:
- for record in inf:
- outf.write(record)
=====================================
tests/utils.py
=====================================
@@ -4,6 +4,8 @@ import subprocess
from contextlib import contextmanager
from io import StringIO
+import dnaio
+
@contextmanager
def capture_stdout():
@@ -25,3 +27,9 @@ def resultpath(path):
def files_equal(path1, path2):
return subprocess.call(['diff', '-u', path1, path2]) == 0
+
+def convert_fastq_to_fasta(fastq, fasta):
+ with dnaio.open(fastq) as inf:
+ with dnaio.open(fasta, mode="w") as outf:
+ for record in inf:
+ outf.write(record)
View it on GitLab: https://salsa.debian.org/med-team/igdiscover/-/compare/08a96059b27df21da373e719bda4214cf59a4a39...8dad23e25697f7e747988ed894e3fda0750151f0
--
View it on GitLab: https://salsa.debian.org/med-team/igdiscover/-/compare/08a96059b27df21da373e719bda4214cf59a4a39...8dad23e25697f7e747988ed894e3fda0750151f0
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