[med-svn] [Git][med-team/pyensembl][upstream] Deleted 1 commit: New upstream version 2.2.8+ds

[Lance Lin (@linqigang)]

Lance Lin pushed to branch upstream 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
- - - - -


8 changed files:

- PKG-INFO
- README.md
- 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:


=====================================
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/-/commit/437a78322832faba3febef7adbf6ccb0cab5e6ea

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/commit/437a78322832faba3febef7adbf6ccb0cab5e6ea
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230725/8605bfdb/attachment-0001.htm>