[med-svn] [Git][med-team/paleomix][upstream] New upstream version 1.3.8

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / paleomix


Commits:
5e9f38ab by Étienne Mollier at 2023-06-11T23:36:25+02:00
New upstream version 1.3.8
- - - - -


7 changed files:

- CHANGES.md
- docs/conf.py
- paleomix/__init__.py
- paleomix/pipelines/bam/parts/lane.py
- paleomix/pipelines/phylo/pipeline.py
- paleomix_environment.yaml
- tests/node_test.py


Changes:

=====================================
CHANGES.md
=====================================
@@ -1,5 +1,12 @@
 # Changelog
 
+## [1.3.8] - 2023-05-19
+
+#### Fixed
+  - Added 'genotyping' alias to match phylo pipeline documentation (issue #48).
+  - Fixed options for BWA `aln` being applied to `samse` and `sampe` (issue #49).
+
+
 ## [1.3.7] - 2022-08-22
 
 #### Added


=====================================
docs/conf.py
=====================================
@@ -26,7 +26,7 @@ author = "Mikkel Schubert"
 # The short X.Y version
 version = "1.3"
 # The full version, including alpha/beta/rc tags
-release = "1.3.6"
+release = "1.3.8"
 
 
 # -- General configuration ---------------------------------------------------


=====================================
paleomix/__init__.py
=====================================
@@ -21,5 +21,5 @@
 # SOFTWARE.
 #
 
-__version_info__ = (1, 3, 7)
+__version_info__ = (1, 3, 8)
 __version__ = "%i.%i.%i" % __version_info__


=====================================
paleomix/pipelines/bam/parts/lane.py
=====================================
@@ -168,7 +168,8 @@ class Lane:
             output_file=output_file_bam,
             prefix=parameters["prefix"],
             reference=parameters["reference"],
-            mapping_options=self.options["Aligners"]["BWA"],
+            # FIXME: There needs to be a way to set BWASamse options
+            # mapping_options=self.options["Aligners"]["BWA"],
             cleanup_options=self._cleanup_options("BWA"),
             dependencies=aln_node,
         )
@@ -199,7 +200,8 @@ class Lane:
             output_file=output_bam,
             prefix=parameters["prefix"],
             reference=parameters["reference"],
-            mapping_options=self.options["Aligners"]["BWA"],
+            # FIXME: There needs to be a way to set BWASamse options
+            # mapping_options=self.options["Aligners"]["BWA"],
             cleanup_options=self._cleanup_options("BWA"),
             dependencies=(aln_node_1, aln_node_2),
         )


=====================================
paleomix/pipelines/phylo/pipeline.py
=====================================
@@ -38,6 +38,7 @@ from paleomix.pipelines.phylo.makefile import MakefileError, read_makefiles
 
 _COMMANDS = {
     "genotype": genotype.chain,
+    "genotyping": genotype.chain,
     "msa": msa.chain,
     "phylogeny": phylo.chain_examl,
 }


=====================================
paleomix_environment.yaml
=====================================
@@ -17,4 +17,4 @@ dependencies:
   - r-gam
   - r-inline
   - pip:
-      - paleomix==1.3.7
+      - paleomix==1.3.9


=====================================
tests/node_test.py
=====================================
@@ -42,12 +42,12 @@ from paleomix.node import (
 from paleomix.common.utilities import safe_coerce_to_frozenset
 
 
-def test_dir():
+def create_test_dir():
     return os.path.dirname(__file__)
 
 
-def test_file(*args):
-    return os.path.join(test_dir(), "data", *args)
+def create_test_file(*args):
+    return os.path.join(create_test_dir(), "data", *args)
 
 
 def first(values):
@@ -62,14 +62,18 @@ _NODE_TYPES = (Node, _CommandNodeWrap)
 
 
 _DESCRIPTION = "My description of a node"
-_IN_FILES = frozenset((test_file("empty_file_1"), test_file("empty_file_2")))
+_IN_FILES = frozenset(
+    (create_test_file("empty_file_1"), create_test_file("empty_file_2"))
+)
 _OUT_FILES = frozenset(
-    (test_file("missing_out_file_1"), test_file("missing_out_file_2"))
+    (create_test_file("missing_out_file_1"), create_test_file("missing_out_file_2"))
 )
 _EXEC_FILES = frozenset(("ls", "sh"))
-_AUX_FILES = frozenset((test_file("rCRS.fasta"), test_file("rCRS.fasta.fai")))
+_AUX_FILES = frozenset(
+    (create_test_file("rCRS.fasta"), create_test_file("rCRS.fasta.fai"))
+)
 _REQUIREMENTS = frozenset((id, str))
-_EMPTY_FILE = test_file("empty_file_1")
+_EMPTY_FILE = create_test_file("empty_file_1")
 
 
 def _build_cmd_mock(



View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/5e9f38abb902993bf47e1b734f3df2be780ab671

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View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/5e9f38abb902993bf47e1b734f3df2be780ab671
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