[med-svn] [Git][med-team/pyensembl][master] 5 commits: routine-update: New upstream version
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon May 2 20:54:46 BST 2022
Étienne Mollier pushed to branch master at Debian Med / pyensembl
Commits:
d4b248c6 by Étienne Mollier at 2022-05-02T21:37:53+02:00
routine-update: New upstream version
- - - - -
f4768b42 by Étienne Mollier at 2022-05-02T21:37:54+02:00
New upstream version 2.0.0+ds
- - - - -
c9ed0699 by Étienne Mollier at 2022-05-02T21:37:54+02:00
Update upstream source from tag 'upstream/2.0.0+ds'
Update to upstream version '2.0.0+ds'
with Debian dir 9675f59d3a800151dba7f9f1548322403ec23922
- - - - -
080c862f by Étienne Mollier at 2022-05-02T21:38:38+02:00
Refresh do-no-require-tinytimer.patch.
- - - - -
b847a683 by Étienne Mollier at 2022-05-02T21:39:51+02:00
routine-update: Ready to upload to unstable
- - - - -
27 changed files:
- PKG-INFO
- debian/changelog
- debian/patches/do-no-require-tinytimer.patch
- pyensembl.egg-info/PKG-INFO
- pyensembl.egg-info/entry_points.txt
- pyensembl/__init__.py
- pyensembl/common.py
- pyensembl/database.py
- pyensembl/download_cache.py
- pyensembl/ensembl_release_versions.py
- pyensembl/ensembl_url_templates.py
- pyensembl/exon.py
- pyensembl/fasta.py
- pyensembl/gene.py
- pyensembl/genome.py
- pyensembl/locus.py
- pyensembl/locus_with_genome.py
- pyensembl/memory_cache.py
- pyensembl/normalization.py
- pyensembl/reference_name.py
- pyensembl/search.py
- pyensembl/sequence_data.py
- pyensembl/shell.py
- pyensembl/species.py
- pyensembl/transcript.py
- + pyensembl/version.py
- setup.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: pyensembl
-Version: 1.9.4
+Version: 2.0.0
Summary: Python interface to ensembl reference genome metadata
Home-page: https://github.com/openvax/pyensembl
Author: Alex Rubinsteyn
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+pyensembl (2.0.0+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 02 May 2022 21:38:58 +0200
+
pyensembl (1.9.4+ds-1) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/do-no-require-tinytimer.patch
=====================================
@@ -2,10 +2,10 @@ Description: Since tinytimer is needed only for tests, disable it in install_req
Author: Nilesh Patra <nilesh at debian.org>
Forwarded: not-needed
Last-Update: 2021-05-21
---- a/setup.py
-+++ b/setup.py
-@@ -71,7 +71,6 @@
- "six>=1.9.0",
+--- pyensembl.orig/setup.py
++++ pyensembl/setup.py
+@@ -70,7 +70,6 @@
+ "memoized-property>=1.0.2",
"gtfparse>=1.1.0",
"serializable",
- "tinytimer",
=====================================
pyensembl.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: pyensembl
-Version: 1.9.4
+Version: 2.0.0
Summary: Python interface to ensembl reference genome metadata
Home-page: https://github.com/openvax/pyensembl
Author: Alex Rubinsteyn
=====================================
pyensembl.egg-info/entry_points.txt
=====================================
@@ -1,3 +1,2 @@
[console_scripts]
pyensembl = pyensembl.shell:run
-
=====================================
pyensembl/__init__.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from .memory_cache import MemoryCache
from .database import Database
from .download_cache import DownloadCache
@@ -39,10 +37,10 @@ from .species import (
normalize_species_name
)
from .transcript import Transcript
-
-__version__ = '1.9.4'
+from .version import __version__
__all__ = [
+ "__version__",
"MemoryCache",
"DownloadCache",
"Database",
=====================================
pyensembl/common.py
=====================================
@@ -10,11 +10,10 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, absolute_import
+import pickle
from functools import wraps
-from six.moves import cPickle as pickle
def dump_pickle(obj, filepath):
with open(filepath, "wb") as f:
=====================================
pyensembl/database.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
import logging
from os.path import split, join, exists, splitext
import sqlite3
=====================================
pyensembl/download_cache.py
=====================================
@@ -10,7 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
from os import listdir, remove
from os.path import join, exists, split, abspath, isdir
=====================================
pyensembl/ensembl_release_versions.py
=====================================
@@ -10,10 +10,8 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
MIN_ENSEMBL_RELEASE = 54
-MAX_ENSEMBL_RELEASE = 104
+MAX_ENSEMBL_RELEASE = 106
def check_release_number(release):
"""
@@ -25,8 +23,8 @@ def check_release_number(release):
except:
raise ValueError("Invalid Ensembl release: %s" % release)
- if release < MIN_ENSEMBL_RELEASE or release > MAX_ENSEMBL_RELEASE:
+ if release < MIN_ENSEMBL_RELEASE:
raise ValueError(
- "Invalid Ensembl releases %d, must be between %d and %d" % (
- release, MIN_ENSEMBL_RELEASE, MAX_ENSEMBL_RELEASE))
+ "Invalid Ensembl releases %d, must be greater than %d" % (
+ release, MIN_ENSEMBL_RELEASE))
return release
=====================================
pyensembl/ensembl_url_templates.py
=====================================
@@ -19,7 +19,6 @@ For example, the human chromosomal DNA sequences for release 78 are in:
ftp://ftp.ensembl.org/pub/release-78/fasta/homo_sapiens/dna/
"""
-from __future__ import print_function, division, absolute_import
from .species import Species, find_species_by_name
from .ensembl_release_versions import check_release_number
=====================================
pyensembl/exon.py
=====================================
@@ -10,7 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
from .locus import Locus
=====================================
pyensembl/fasta.py
=====================================
@@ -18,13 +18,10 @@ Unfortunately, small errors creep in to different FASTA files on the
Ensembl FTP server that no proper FASTA parser lets you skip over.
"""
-from __future__ import print_function, division, absolute_import
from gzip import GzipFile
import logging
-from six import binary_type, PY3
-
logger = logging.getLogger(__name__)
@@ -34,9 +31,9 @@ def _parse_header_id(line):
Pull the transcript or protein identifier from the header line
which starts with '>'
"""
- if type(line) is not binary_type:
+ if type(line) is not bytes:
raise TypeError("Expected header line to be of type %s but got %s" % (
- binary_type, type(line)))
+ bytes, type(line)))
if len(line) <= 1:
raise ValueError("No identifier on FASTA line")
@@ -125,12 +122,7 @@ class FastaParser(object):
logger.warn("No sequence data for '%s'", self.current_id)
else:
sequence = b"".join(self.current_lines)
- if PY3:
- # only decoding into an ASCII str for Python 3 since
- # the binary sequence type for Python 2 is already 'str'
- # and the unicode representation is inefficient
- # (using either 16 or 32 bits per character depends on build)
- sequence = sequence.decode("ascii")
+ sequence = sequence.decode("ascii")
return self.current_id, sequence
def _read_header(self, line):
=====================================
pyensembl/gene.py
=====================================
@@ -10,7 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
from memoized_property import memoized_property
=====================================
pyensembl/genome.py
=====================================
@@ -15,13 +15,10 @@ Contains the Genome class, with its millions of accessors and wrappers
around an arbitrary genomic database.
"""
-from __future__ import print_function, division, absolute_import
from os import remove
from os.path import exists, getsize
-from six import string_types
-
from serializable import Serializable
from .memory_cache import MemoryCache
@@ -85,12 +82,12 @@ class Genome(Serializable):
"""
if transcript_fasta_paths_or_urls is None:
transcript_fasta_paths_or_urls = []
- elif isinstance(transcript_fasta_paths_or_urls, string_types):
+ elif isinstance(transcript_fasta_paths_or_urls, str):
transcript_fasta_paths_or_urls = [transcript_fasta_paths_or_urls]
if protein_fasta_paths_or_urls is None:
protein_fasta_paths_or_urls = []
- elif isinstance(protein_fasta_paths_or_urls, string_types):
+ elif isinstance(protein_fasta_paths_or_urls, str):
protein_fasta_paths_or_urls = [protein_fasta_paths_or_urls]
self.reference_name = reference_name
=====================================
pyensembl/locus.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from serializable import Serializable
from .normalization import normalize_chromosome, normalize_strand
=====================================
pyensembl/locus_with_genome.py
=====================================
@@ -10,7 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
from .locus import Locus
=====================================
pyensembl/memory_cache.py
=====================================
@@ -22,7 +22,6 @@ A piece of data is returned from one of three sources:
2) Cache warm on disk. Parse or unpickle the serialized result into memory.
3) Cache warm in memory. Return cached object.
"""
-from __future__ import print_function, division, absolute_import
import logging
from os import remove, stat
=====================================
pyensembl/normalization.py
=====================================
@@ -10,9 +10,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
-from six.moves import intern
+from sys import intern
from typechecks import is_string, is_integer
# Manually memoizing here, since our simple common.memoize function has
=====================================
pyensembl/reference_name.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from .ensembl_release import EnsemblRelease
from .species import Species, find_species_by_name
=====================================
pyensembl/search.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
"""
Helper functions for searching over collections of PyEnsembl objects
"""
=====================================
pyensembl/sequence_data.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from os import remove
from os.path import exists, abspath, split, join
import logging
=====================================
pyensembl/shell.py
=====================================
@@ -38,10 +38,7 @@ To install a genome from source files:
--protein-fasta URL_OR_PATH
"""
-from __future__ import print_function, division, absolute_import
-
import argparse
-import logging
import logging.config
import pkg_resources
import os
=====================================
pyensembl/species.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, absolute_import, division
-
from serializable import Serializable
from .ensembl_release_versions import MAX_ENSEMBL_RELEASE
@@ -204,5 +202,60 @@ brown_rat = Species.register(
synonyms=["brown rat", "lab rat", "rat"],
reference_assemblies={
"Rnor_5.0": (75, 79),
- "Rnor_6.0": (80, MAX_ENSEMBL_RELEASE),
+ "Rnor_6.0": (80, 104),
+ "mRatBN7.2": (105, MAX_ENSEMBL_RELEASE)
+ })
+
+macaque = cyno = Species.register(
+ latin_name="macaca_fascicularis",
+ synonyms=["macaque", "Crab-eating macaque"],
+ reference_assemblies={
+ "Macaca_fascicularis_6.0": (103, MAX_ENSEMBL_RELEASE),
})
+
+green_monkey = Species.register(
+ latin_name="chlorocebus_sabaeus",
+ synonyms=["green_monkey", "african_green_monkey"],
+ reference_assemblies={
+ "ChlSab1.1": (86, MAX_ENSEMBL_RELEASE),
+ })
+
+rhesus = Species.register(
+ latin_name="macaca_mulatta",
+ synonyms=["rhesus"],
+ reference_assemblies={"Mmul_10": (75, MAX_ENSEMBL_RELEASE)})
+
+rabbit = Species.register(
+ latin_name="oryctolagus_cuniculus",
+ synonyms=["rabbit"],
+ reference_assemblies={"OryCun2.0": (75, MAX_ENSEMBL_RELEASE)})
+
+gerbil = Species.register(
+ latin_name="meriones_unguiculatus",
+ synonyms=["gerbil"],
+ reference_assemblies={"MunDraft-v1.0": (75, MAX_ENSEMBL_RELEASE)})
+
+syrian_hamster = Species.register(
+ latin_name="mesocricetus_auratus",
+ synonyms=["syrian_hamster"],
+ reference_assemblies={"MesAur1.0": (75, MAX_ENSEMBL_RELEASE)})
+
+chinese_hamster = Species.register(
+ latin_name="cricetulus_griseus_chok1gshd",
+ synonyms=["chinese_hamster"],
+ reference_assemblies={"CHOK1GS_HDv1": (75, MAX_ENSEMBL_RELEASE)})
+
+naked_mole_rat = Species.register(
+ latin_name="heterocephalus_glaber_female",
+ synonyms=["naked_mole_rat"],
+ reference_assemblies={"HetGla_female_1.0": (75, MAX_ENSEMBL_RELEASE)})
+
+guinea_pig = Species.register(
+ latin_name="cavia_porcellus",
+ synonyms=["guinea_pig"],
+ reference_assemblies={"Cavpor3.0": (75, MAX_ENSEMBL_RELEASE)})
+
+pig = Species.register(
+ latin_name="sus_scrofa",
+ synonyms=["pig"],
+ reference_assemblies={"Sscrofa11.1": (75, MAX_ENSEMBL_RELEASE)})
=====================================
pyensembl/transcript.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from memoized_property import memoized_property
from .common import memoize
=====================================
pyensembl/version.py
=====================================
@@ -0,0 +1 @@
+__version__ = '2.0.0'
\ No newline at end of file
=====================================
setup.py
=====================================
@@ -31,7 +31,7 @@ except IOError as e:
readme_markdown = ""
-with open('%s/__init__.py' % package_name, 'r') as f:
+with open('%s/version.py' % package_name, 'r') as f:
version = re.search(
r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
f.read(),
@@ -68,7 +68,6 @@ if __name__ == '__main__':
"pandas>=0.15",
"datacache>=1.1.4",
"memoized-property>=1.0.2",
- "six>=1.9.0",
"gtfparse>=1.1.0",
"serializable",
"tinytimer",
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/fcea494a8a8d5c7718141726359be9b731f92b58...b847a6835231bfc6c984e22dfdc43cda746d8ed2
--
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/fcea494a8a8d5c7718141726359be9b731f92b58...b847a6835231bfc6c984e22dfdc43cda746d8ed2
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