[med-svn] [Git][med-team/python-screed][master] 5 commits: New upstream version 1.1.3
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jan 13 18:28:47 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / python-screed
Commits:
fd07693a by Étienne Mollier at 2024-01-13T19:25:27+01:00
New upstream version 1.1.3
- - - - -
9092fea4 by Étienne Mollier at 2024-01-13T19:25:27+01:00
routine-update: New upstream version
- - - - -
283f69bb by Étienne Mollier at 2024-01-13T19:25:28+01:00
Update upstream source from tag 'upstream/1.1.3'
Update to upstream version '1.1.3'
with Debian dir 938b840213312b6c98d17beb0120a02639f23a5e
- - - - -
ce0e2b7e by Étienne Mollier at 2024-01-13T19:25:31+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
b2f0b13f by Étienne Mollier at 2024-01-13T19:27:46+01:00
routine-update: Ready to upload to unstable
- - - - -
17 changed files:
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/python.yml
- .readthedocs.yaml
- debian/changelog
- debian/control
- debian/rules
- screed/openscreed.py
- screed/tests/test_attriberror.py
- screed/tests/test_convert.py
- screed/tests/test_dictionary.py
- screed/tests/test_fasta.py
- screed/tests/test_fasta_recover.py
- screed/tests/test_fastq.py
- screed/tests/test_fastq_recover.py
- screed/tests/test_hava_methods.py
- screed/tests/test_shell.py
- tox.ini
Changes:
=====================================
.github/PULL_REQUEST_TEMPLATE.md
=====================================
@@ -1,9 +0,0 @@
-- [ ] Is it mergeable?
-- [ ] `make test` Did it pass the tests?
-- [ ] `make clean diff-cover` If it introduces new functionality, is it tested?
-- [ ] `make format diff_pylint_report doc` Is it well formatted?
-- [ ] For substantial changes or changes to the command-line interface, is it
- documented in `CHANGELOG.md`? See [keepachangelog](http://keepachangelog.com/)
- for more details.
-- [ ] Was a spellchecker run on the source code and documentation after
- changes were made?
=====================================
.github/workflows/python.yml
=====================================
@@ -6,24 +6,24 @@ on:
pull_request:
branches: [latest]
schedule:
- - cron: "0 0 * * *" # daily
+ - cron: "0 0 7 * *" # monthly
jobs:
test:
runs-on: ${{ matrix.os }}
strategy:
matrix:
- os: [ubuntu-18.04, macos-latest]
+ os: [ubuntu-latest, macos-latest]
py: ["3.10", 3.9, 3.8]
fail-fast: false
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.py }}
- uses: actions/setup-python at v4
+ uses: actions/setup-python at v5
with:
python-version: ${{ matrix.py }}
@@ -57,3 +57,10 @@ jobs:
run: tox
env:
PYTHONDEVMODE: 1
+
+ - name: Upload Python coverage to codecov
+ uses: codecov/codecov-action at v3
+ with:
+ flags: python
+ fail_ci_if_error: true
+ files: coverage.xml
=====================================
.readthedocs.yaml
=====================================
@@ -14,4 +14,3 @@ python:
install:
- method: pip
path: .
- system_packages: true
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-screed (1.1.3-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 13 Jan 2024 19:26:31 +0100
+
python-screed (1.1.2-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <crusoe at debian.org>
Section: python
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
python3-all,
python3-pytest,
python3-sphinx,
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ export DH_VERBOSE=1
export PYBUILD_NAME=screed
%:
- dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+ dh $@ --with sphinxdoc --buildsystem=pybuild
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
=====================================
screed/openscreed.py
=====================================
@@ -76,6 +76,7 @@ class Open(object):
try:
first_char = peek[0]
except IndexError as err:
+ sequencefile.close()
return [] # empty file
try:
@@ -89,6 +90,7 @@ class Open(object):
iter_fn = fastq_iter
if iter_fn is None:
+ sequencefile.close()
raise ValueError("unknown file format for '%s'" % filename)
self.sequencefile = sequencefile
=====================================
screed/tests/test_attriberror.py
=====================================
@@ -15,7 +15,7 @@ class nostring:
class test_comparisons():
- def setup(self):
+ def setup_method(self):
self._testfile = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfile)
screed.read_fasta_sequences(self._testfile)
=====================================
screed/tests/test_convert.py
=====================================
@@ -15,7 +15,7 @@ class Test_fasta_to_fastq(test_fasta.Test_fasta):
db and then run the fasta suite
"""
- def setup(self):
+ def setup_method(self):
self._fqName = utils.get_temp_filename('fa_to_fq')
self._faName = utils.get_temp_filename('fq_to_fa')
@@ -29,7 +29,7 @@ class Test_fasta_to_fastq(test_fasta.Test_fasta):
screed.read_fasta_sequences(self._faName) # Fasta file -> fasta db
self.db = screed.ScreedDB(self._faName)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._fqName)
os.unlink(self._fqName + fileExtension)
os.unlink(self._faName)
=====================================
screed/tests/test_dictionary.py
=====================================
@@ -13,14 +13,14 @@ class Test_dict_methods(object):
queries.
"""
- def setup(self):
+ def setup_method(self):
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
screed.read_fasta_sequences(self._testfa)
self.db = screed.ScreedDB(self._testfa)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfa + fileExtension)
def test_iter_stuff(self):
=====================================
screed/tests/test_fasta.py
=====================================
@@ -29,14 +29,14 @@ def test_new_record():
class Test_fasta(object):
- def setup(self):
+ def setup_method(self):
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
screed.read_fasta_sequences(self._testfa)
self.db = screed.ScreedDB(self._testfa)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfa + fileExtension)
def test_length(self):
@@ -111,7 +111,7 @@ class Test_fasta(object):
class Test_fasta_whitespace(object):
- def setup(self):
+ def setup_method(self):
self._testfa = utils.get_temp_filename('test-whitespace.fa')
shutil.copy(utils.get_test_data('test-whitespace.fa'), self._testfa)
@@ -121,7 +121,7 @@ class Test_fasta_whitespace(object):
def test_for_omitted_record(self):
assert 'ENSMICT00000012401' in self.db
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfa + fileExtension)
=====================================
screed/tests/test_fasta_recover.py
=====================================
@@ -9,7 +9,7 @@ import shutil
class test_fa_recover(test_fasta.Test_fasta):
- def setup(self):
+ def setup_method(self):
self._fileName = utils.get_temp_filename('fastaRecovery')
self._testfa = utils.get_temp_filename('test.fa')
@@ -20,7 +20,7 @@ class test_fa_recover(test_fasta.Test_fasta):
screed.read_fasta_sequences(self._fileName)
self.db = screed.ScreedDB(self._fileName)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._fileName)
os.unlink(self._fileName + fileExtension)
os.unlink(self._testfa + fileExtension)
=====================================
screed/tests/test_fastq.py
=====================================
@@ -60,14 +60,14 @@ def test_parse_description_false():
class Test_fastq(object):
- def setup(self):
+ def setup_method(self):
self._testfq = utils.get_temp_filename('test.fastq')
shutil.copy(utils.get_test_data('test.fastq'), self._testfq)
screed.read_fastq_sequences(self._testfq)
self.db = screed.ScreedDB(self._testfq)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfq + fileExtension)
def test_length(self):
=====================================
screed/tests/test_fastq_recover.py
=====================================
@@ -9,7 +9,7 @@ import shutil
class test_fq_recover(test_fastq.Test_fastq):
- def setup(self):
+ def setup_method(self):
self._fileName = utils.get_temp_filename('fastqRecovery')
self._testfq = utils.get_temp_filename('test.fastq')
@@ -20,7 +20,7 @@ class test_fq_recover(test_fastq.Test_fastq):
screed.read_fastq_sequences(self._fileName)
self.db = screed.ScreedDB(self._fileName)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._fileName)
os.unlink(self._fileName + fileExtension)
os.unlink(self._testfq + fileExtension)
=====================================
screed/tests/test_hava_methods.py
=====================================
@@ -12,11 +12,11 @@ shutil.copy(utils.get_test_data('test.hava'), testha)
class test_hava(object):
- def setup(self):
+ def setup_method(self):
screed.seqparse.read_hava_sequences(testha)
self._db = screed.ScreedDB(testha)
- def teardown(self):
+ def teardown_method(self):
b = 7
# os.unlink(testha + fileExtension)
=====================================
screed/tests/test_shell.py
=====================================
@@ -15,7 +15,7 @@ class Test_fa_shell_command(test_fasta.Test_fasta):
screed database correctly from the shell
"""
- def setup(self):
+ def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfa = utils.get_temp_filename('test.fa')
@@ -26,7 +26,7 @@ class Test_fa_shell_command(test_fasta.Test_fasta):
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfa)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfa + fileExtension)
@@ -37,7 +37,7 @@ class Test_fq_shell_command(test_fastq.Test_fastq):
screed database correctly from the shell
"""
- def setup(self):
+ def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfq = utils.get_temp_filename('test.fastq')
@@ -48,7 +48,7 @@ class Test_fq_shell_command(test_fastq.Test_fastq):
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfq)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfq + fileExtension)
@@ -59,7 +59,7 @@ class Test_fa_shell_module(test_fasta.Test_fasta):
screed database correctly from the shell
"""
- def setup(self):
+ def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfa = utils.get_temp_filename('test.fa')
@@ -70,7 +70,7 @@ class Test_fa_shell_module(test_fasta.Test_fasta):
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfa)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfa + fileExtension)
@@ -81,7 +81,7 @@ class Test_fq_shell_module(test_fastq.Test_fastq):
screed database correctly from the shell
"""
- def setup(self):
+ def setup_method(self):
thisdir = os.path.dirname(__file__)
self._testfq = utils.get_temp_filename('test.fastq')
@@ -92,7 +92,7 @@ class Test_fq_shell_module(test_fastq.Test_fastq):
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfq)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._testfq + fileExtension)
@@ -104,7 +104,7 @@ class Test_convert_shell(test_fasta.Test_fasta):
db and then run the fasta suite, all from the command line.
"""
- def setup(self):
+ def setup_method(self):
self._fqName = utils.get_temp_filename('fa_to_fq')
self._faName = utils.get_temp_filename('fq_to_fa')
@@ -133,7 +133,7 @@ class Test_convert_shell(test_fasta.Test_fasta):
self.db = screed.ScreedDB(self._faName)
- def teardown(self):
+ def teardown_method(self):
os.unlink(self._fqName)
os.unlink(self._fqName + fileExtension)
os.unlink(self._faName)
=====================================
tox.ini
=====================================
@@ -16,14 +16,12 @@ passenv =
allowlist_externals = make
commands =
make install-dependencies
- pytest --cov -m 'not known_failing'
- codecov
+ pytest --cov -m 'not known_failing' --cov-report xml
make pep8
make doc
deps =
pytest
pytest-cov
- codecov
sphinx
[gh-actions]
View it on GitLab: https://salsa.debian.org/med-team/python-screed/-/compare/0513642d3a31db5b15dcbfc7678f15ad594f9dd7...b2f0b13f9883340ae5529dca1abc220122c1db41
--
View it on GitLab: https://salsa.debian.org/med-team/python-screed/-/compare/0513642d3a31db5b15dcbfc7678f15ad594f9dd7...b2f0b13f9883340ae5529dca1abc220122c1db41
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