[med-svn] [Git][med-team/pyensembl][master] Deleted 4 commits: New upstream version 2.2.8+ds
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Tue Jul 25 15:57:48 BST 2023
Lance Lin pushed to branch master at Debian Med / pyensembl
WARNING: The push did not contain any new commits, but force pushed to delete the commits and changes below.
Deleted commits:
437a7832 by Lance Lin at 2023-07-24T21:50:55+07:00
New upstream version 2.2.8+ds
- - - - -
5cb44431 by Lance Lin at 2023-07-24T21:51:04+07:00
Update upstream source from tag 'upstream/2.2.8+ds'
Update to upstream version '2.2.8+ds'
with Debian dir 90829ecf6185ba7fc926f597f7d161a580cc698f
- - - - -
b2e4e07d by Lance Lin at 2023-07-24T22:38:04+07:00
Update copyright
- - - - -
12eac94c by Lance Lin at 2023-07-24T22:38:57+07:00
Update changelog
- - - - -
10 changed files:
- PKG-INFO
- README.md
- debian/changelog
- debian/copyright
- pyensembl.egg-info/PKG-INFO
- pyensembl/ensembl_release_versions.py
- pyensembl/normalization.py
- pyensembl/species.py
- pyensembl/version.py
- requirements.txt
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: pyensembl
-Version: 2.2.4
+Version: 2.2.8
Summary: Python interface to ensembl reference genome metadata
Home-page: https://github.com/openvax/pyensembl
Author: Alex Rubinsteyn
@@ -54,8 +54,7 @@ You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.h
pip install pyensembl
```
-This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and
-[BioPython](http://biopython.org/).
+This should also install any required packages such as [datacache](https://github.com/openvax/datacache).
Before using PyEnsembl, run the following command to download and install
Ensembl data:
=====================================
README.md
=====================================
@@ -36,8 +36,7 @@ You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.h
pip install pyensembl
```
-This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and
-[BioPython](http://biopython.org/).
+This should also install any required packages such as [datacache](https://github.com/openvax/datacache).
Before using PyEnsembl, run the following command to download and install
Ensembl data:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+pyensembl (2.2.8+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * d/copyright: Update copyright to 2023
+
+ -- Lance Lin <lq27267 at gmail.com> Mon, 24 Jul 2023 21:51:14 +0700
+
pyensembl (2.2.4+ds-1) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -13,6 +13,7 @@ License: Apache-2.0
Files: debian/*
Copyright: 2021 Steffen Moeller <moeller at debian.org>
2022 Étienne Mollier <emollier at debian.org>
+ 2023 Lance Lin <lq27267 at gmail.com>
License: Apache-2.0
License: Apache-2.0
=====================================
pyensembl.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: pyensembl
-Version: 2.2.4
+Version: 2.2.8
Summary: Python interface to ensembl reference genome metadata
Home-page: https://github.com/openvax/pyensembl
Author: Alex Rubinsteyn
@@ -54,8 +54,7 @@ You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.h
pip install pyensembl
```
-This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and
-[BioPython](http://biopython.org/).
+This should also install any required packages such as [datacache](https://github.com/openvax/datacache).
Before using PyEnsembl, run the following command to download and install
Ensembl data:
=====================================
pyensembl/ensembl_release_versions.py
=====================================
@@ -11,7 +11,7 @@
# limitations under the License.
MIN_ENSEMBL_RELEASE = 54
-MAX_ENSEMBL_RELEASE = 108
+MAX_ENSEMBL_RELEASE = 109
def check_release_number(release):
"""
=====================================
pyensembl/normalization.py
=====================================
@@ -53,10 +53,8 @@ def normalize_chromosome(c):
def normalize_strand(strand):
- if strand == "+" or strand == "-":
- return strand
- elif strand == 1:
+ if strand == "+" or strand == 1 or strand == "+1" or strand == "1" :
return "+"
- elif strand == -1:
+ elif strand == "-" or strand == -1 or strand == "-1":
return "-"
raise ValueError("Invalid strand: %s" % (strand,))
=====================================
pyensembl/species.py
=====================================
@@ -145,7 +145,7 @@ def normalize_species_name(name):
def find_species_by_name(species_name):
latin_name = normalize_species_name(species_name)
if latin_name not in Species._latin_names_to_species:
- raise ValueError("Species not found: %s" % species_name)
+ raise ValueError("Species not found: %s, for non-Ensembl data see https://github.com/openvax/pyensembl#non-ensembl-data" % (species_name,))
return Species._latin_names_to_species[latin_name]
@@ -211,7 +211,7 @@ brown_rat = Species.register(
"mRatBN7.2": (105, MAX_ENSEMBL_RELEASE)
})
-macaque = cyno = Species.register(
+macaque = Species.register(
latin_name="macaca_fascicularis",
synonyms=["macaque", "Crab-eating macaque"],
reference_assemblies={
@@ -264,3 +264,14 @@ pig = Species.register(
latin_name="sus_scrofa",
synonyms=["pig"],
reference_assemblies={"Sscrofa11.1": (75, MAX_ENSEMBL_RELEASE)})
+
+fly = Species.register(
+ latin_name="drosophila_melanogaster",
+ synonyms=["drosophila", "fruit fly", "fly"],
+ reference_assemblies={
+ "BDGP5": (75, 78),
+ "BDGP6": (79, 95),
+ "BDGP6.22": (96, 98),
+ "BDGP6.28": (99, 102),
+ "BDGP6.32": (103, MAX_ENSEMBL_RELEASE)
+ })
=====================================
pyensembl/version.py
=====================================
@@ -1 +1 @@
-__version__ = '2.2.4'
+__version__ = '2.2.8'
=====================================
requirements.txt
=====================================
@@ -6,3 +6,4 @@ gtfparse>=1.3.0,<2.0.0
serializable
nose>=1.3.3
pylint>=1.4.4
+pandas>=1.3.5
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/5dce7e6decb1af9998de22e7543ec00c52498073...12eac94c460ab1b9c1b85a34981b66b3ff5f738d
--
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/5dce7e6decb1af9998de22e7543ec00c52498073...12eac94c460ab1b9c1b85a34981b66b3ff5f738d
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