[med-svn] [Git][med-team/gfapy][upstream] New upstream version 1.2.2+dfsg
Sascha Steinbiss (@satta)
gitlab at salsa.debian.org
Fri Jan 21 10:27:54 GMT 2022
Sascha Steinbiss pushed to branch upstream at Debian Med / gfapy
Commits:
d6805080 by Sascha Steinbiss at 2022-01-21T11:24:18+01:00
New upstream version 1.2.2+dfsg
- - - - -
22 changed files:
- CHANGES.txt
- README.rst
- doc/conf.py
- doc/tutorial/errors.rst
- doc/tutorial/positional_fields.rst
- doc/tutorial/references.rst
- gfapy/graph_operations/topology.py
- gfapy/line/edge/containment/containment.py
- gfapy/line/edge/containment/to_gfa2.py
- gfapy/line/edge/gfa1/other.py
- gfapy/line/edge/gfa1/references.py
- gfapy/line/edge/gfa1/to_gfa2.py
- gfapy/line/edge/gfa2/to_gfa1.py
- gfapy/line/edge/link/complement.py
- gfapy/line/edge/link/link.py
- gfapy/line/edge/link/to_gfa2.py
- setup.py
- tests/test_api_lines_finders.py
- tests/test_api_positionals.py
- tests/test_unit_line_connection.py
- tests/test_unit_line_dynamic_fields.py
- tests/test_unit_line_equivalence.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,8 @@
+== 1.2.2 ==
+
+- remove to/from aliases for GFA1 containment/link fields
+ since `to` potentially clashes with a tag name
+
== 1.2.1 ==
- fixed an issue with linear path merging (issue 21)
=====================================
README.rst
=====================================
@@ -1,7 +1,7 @@
Gfapy
~~~~~
-|travis| |readthedocs| |latesttag| |license| |requiresio|
+|travis| |readthedocs| |latesttag| |license|
|bioconda| |pypi| |debian| |ubuntu|
=====================================
doc/conf.py
=====================================
@@ -66,7 +66,7 @@ master_doc = 'index'
# General information about the project.
project = 'Gfapy'
-copyright = '2017--2021, Giorgio Gonnella and others (see CONTRIBUTORS)'
+copyright = '2017--2022, Giorgio Gonnella and others (see CONTRIBUTORS)'
author = 'Giorgio Gonnella and others (see CONTRIBUTORS)'
# The version info for the project you're documenting, acts as replacement for
@@ -76,7 +76,7 @@ author = 'Giorgio Gonnella and others (see CONTRIBUTORS)'
# The short X.Y version.
version = '1.2'
# The full version, including alpha/beta/rc tags.
-release = '1.2.1'
+release = '1.2.2'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
=====================================
doc/tutorial/errors.rst
=====================================
@@ -29,7 +29,7 @@ all library errors.
| `InconsistencyError` | Pieces of information collide | length of sequence and LN tag |
| | with each other | do not match |
+-----------------------+-------------------------------+---------------------------------+
-| `RuntimeError` | The user tried to do | editing from/to field in |
+| `RuntimeError` | The user tried to do | editing from_segment field in |
| | something which is not | connected links |
| | allowed | |
+-----------------------+-------------------------------+---------------------------------+
=====================================
doc/tutorial/positional_fields.rst
=====================================
@@ -23,7 +23,8 @@ Field names
The field names are derived from the specification. Lower case versions
of the field names are used and spaces are substituted with underscores.
In some cases, the field names were changed, as they represent keywords
-in common programming languages (``from``, ``send``).
+in common programming languages or clash with potential tag names
+(``from``, ``to``, ``send``).
The following tables shows the field names used in Gfapy, for each kind
of line. Headers have no positional fields. Comments and custom records
=====================================
doc/tutorial/references.rst
=====================================
@@ -60,9 +60,9 @@ GFA1
+---------------+-------------------+---------------------------+
| Record type | Fields | Type of reference |
+===============+===================+===========================+
-| Link | from, to | Segment |
+| Link | from_segment, to_segment | Segment |
+---------------+-------------------+---------------------------+
-| Containment | from, to | Segment |
+| Containment | from_segment, to_segment | Segment |
+---------------+-------------------+---------------------------+
| Path | segment\_names, | [OrientedLine(Segment)] |
+---------------+-------------------+---------------------------+
@@ -361,7 +361,8 @@ Renaming an element
The name field of a line (e.g. segment ``name``/``sid``) is not a
reference and thus can be edited also in connected lines. When the name
-of the line is changed, no manual editing of references (e.g. from/to
+of the line is changed, no manual editing of references (e.g.
+``from_segment``/``to_segment``
fields in links) is necessary, as all lines which refer to the line will
still refer to the same instance. The references to the instance in the
Gfa lines collections will be automatically updated. Also, the new name
=====================================
gfapy/graph_operations/topology.py
=====================================
@@ -16,16 +16,16 @@ class Topology:
"""
if link.is_circular():
return False
- if not link.get("from").dovetails_of_end(\
+ if not link.get("from_segment").dovetails_of_end(\
gfapy.invert(link.from_end.end_type)):
return True
- if not link.to.dovetails_of_end(gfapy.invert(link.to_end.end_type)):
+ if not link.to_segment.dovetails_of_end(gfapy.invert(link.to_end.end_type)):
return True
c = {}
for et in ["from", "to"]:
c[et] = set()
visited = set()
- segend = link.get("from") if et == "from" else link.to
+ segend = link.get("from_segment") if et == "from" else link.to_segment
visited.add(segend.name)
visited.add(link.other_end(segend).name)
self.__traverse_component(segend, c[et], visited)
=====================================
gfapy/line/edge/containment/containment.py
=====================================
@@ -17,9 +17,8 @@ class Containment(Containment_ToGFA2, Pos, Canonical, Other,
Note:
from_segment and to_segment are used instead of from/to
- as from is not a valid method name in Python. However, when not
- used as method name (e.g. as argument of get()), from and to can
- be used, as an alias has been defined.
+ as from is not a valid method name in Python and "to" alone
+ potentially clashes with the tag namespace.
Note:
The from segment is considered the container, the to segment the contained
@@ -31,8 +30,6 @@ class Containment(Containment_ToGFA2, Pos, Canonical, Other,
"to_orient", "pos", "overlap"]
FIELD_ALIAS = {"container" : "from_segment",
"contained" : "to_segment",
- "from" : "from_segment",
- "to" : "to_segment",
"container_orient" : "from_orient",
"contained_orient" : "to_orient"}
PREDEFINED_TAGS = ["MQ", "NM", "ID"]
=====================================
gfapy/line/edge/containment/to_gfa2.py
=====================================
@@ -21,7 +21,7 @@ class ToGFA2:
"""
self._check_overlap()
rpos = self.pos + self.overlap.length_on_reference()
- if rpos == self._lastpos_of("from"):
+ if rpos == self._lastpos_of("from_segment"):
rpos = gfapy.LastPos(rpos)
return [self.pos, rpos]
@@ -30,4 +30,4 @@ class ToGFA2:
"""
GFA2 positions of the alignment on the **to** segment
"""
- return [0, self._lastpos_of("to")]
+ return [0, self._lastpos_of("to_segment")]
=====================================
gfapy/line/edge/gfa1/other.py
=====================================
@@ -52,7 +52,7 @@ class Other:
"""
segment_name = str(segment)
if segment_name == str(self.from_segment):
- return self.to
+ return self.to_segment
elif segment_name == str(self.to_segment):
return self.from_segment
elif tolerant:
=====================================
gfapy/line/edge/gfa1/references.py
=====================================
@@ -2,7 +2,7 @@ import gfapy
class References:
def _initialize_references(self):
- for d in ["from", "to"]:
+ for d in ["from_segment", "to_segment"]:
s = self._gfa.segment(self.get(d))
if s is None:
if self._gfa._segments_first_order:
@@ -12,13 +12,14 @@ class References:
version = "gfa1",
virtual = True)
s.connect(self._gfa)
- self._set_existing_field(d+"_segment", s, set_reference = True)
+ self._set_existing_field(d, s, set_reference = True)
if self.record_type == "L":
- et = self.from_end.end_type if d == "from" else self.to_end.end_type
+ et = self.from_end.end_type \
+ if d == "from_segment" else self.to_end.end_type
key = "dovetails_{}".format(et)
else:
- key = \
- "edges_to_contained" if (d == "from") else "edges_to_containers"
+ key = "edges_to_contained" if (d == "from_segment") \
+ else "edges_to_containers"
s._add_reference(self, key)
def _import_field_references(self, previous):
=====================================
gfapy/line/edge/gfa1/to_gfa2.py
=====================================
@@ -83,7 +83,7 @@ class ToGFA2:
length = line.length
if length is None:
raise gfapy.ValueError(
- "Length of segment {} unknown".format(self.to.name))
+ "Length of segment {} unknown".format(self.to_segment.name))
return gfapy.LastPos(length)
def _check_overlap(self):
=====================================
gfapy/line/edge/gfa2/to_gfa1.py
=====================================
@@ -96,7 +96,8 @@ class ToGFA1:
@from_orient.setter
def from_orient(self, value):
- """Set the orientation of the field which will be returned by calling from
+ """Set the orientation of the field which will be returned by calling
+ from_segment
Parameters:
value (str): one of ["+", "-"]
@@ -119,7 +120,7 @@ class ToGFA1:
@to_segment.setter
def to_segment(self, value):
- """Set the field which will be returned by calling ``to``.
+ """Set the field which will be returned by calling ``to_segment``.
Parameters:
value (str or gfapy.line.segment.GFA2)
@@ -142,7 +143,8 @@ class ToGFA1:
@to_orient.setter
def to_orient(self, value):
- """Set the orientation of the field which will be returned by calling ``to``.
+ """Set the orientation of the field which will be returned by calling
+ ``to_segment``.
Parameters:
value (str): one of ["+", "-"]
=====================================
gfapy/line/edge/link/complement.py
=====================================
@@ -20,7 +20,7 @@ class Complement:
gfapy.line.edge.Link: The inverted link.
"""
l = self.clone()
- l.from_segment = self.to
+ l.from_segment = self.to_segment
l.from_orient = gfapy.invert(self.to_orient)
l.to_segment = self.from_segment
l.to_orient = gfapy.invert(self.from_orient)
=====================================
gfapy/line/edge/link/link.py
=====================================
@@ -19,16 +19,14 @@ class Link(Link_ToGFA2, GFA1_ToGFA2, Link_References, Equivalence, Complement, \
Note:
from_segment and to_segment are used instead of from/to
- as from is not a valid method name in Python. However, when not
- used as method name (e.g. as argument of get()), from and to can
- be used, as an alias has been defined.
+ as from is not a valid method name in Python and "to" alone
+ potentially clashes with the tag namespace.
"""
RECORD_TYPE = "L"
POSFIELDS = ["from_segment", "from_orient", "to_segment", "to_orient",
"overlap"]
PREDEFINED_TAGS = ["MQ", "NM", "RC", "FC", "KC", "ID"]
- FIELD_ALIAS = {"from": "from_segment", "to": "to_segment"}
DATATYPE = {
"from_segment" : "segment_name_gfa1",
"from_orient" : "orientation",
=====================================
gfapy/line/edge/link/to_gfa2.py
=====================================
@@ -2,7 +2,7 @@ class ToGFA2:
@property
def from_coords(self):
- """GFA2 positions of the alignment on the from segment.
+ """GFA2 positions of the alignment on the **from** segment.
Returns
-------
@@ -20,7 +20,7 @@ class ToGFA2:
"""
self._check_overlap()
if self.from_orient == "+":
- from_l = self._lastpos_of("from")
+ from_l = self._lastpos_of("from_segment")
return [from_l - self.overlap.length_on_reference(), from_l]
else:
return [0, self.overlap.length_on_reference()]
@@ -32,5 +32,5 @@ class ToGFA2:
if self.to_orient == "+":
return [0, self.overlap.length_on_query()]
else:
- to_l = self._lastpos_of("to")
+ to_l = self._lastpos_of("to_segment")
return [to_l - self.overlap.length_on_query(), to_l]
=====================================
setup.py
=====================================
@@ -9,7 +9,7 @@ if not sys.version_info[0] == 3:
sys.exit("Sorry, only Python 3 is supported")
setup(name='gfapy',
- version='1.2.1',
+ version='1.2.2',
description='Library for handling data in the GFA1 and GFA2 formats',
long_description=readme(),
url='https://github.com/ggonnella/gfapy',
=====================================
tests/test_api_lines_finders.py
=====================================
@@ -112,20 +112,22 @@ class TestAPILinesFinders(unittest.TestCase):
"name":"1"}))
# search links
self.assertEqual(TestAPILinesFinders.l_gfa1[4:5], TestAPILinesFinders.gfa1.select({"record_type":"L",
- "from":"1",
+ "from_segment":"1",
"from_orient":"+"}))
# search containments
self.assertEqual(TestAPILinesFinders.l_gfa1[6:7], TestAPILinesFinders.gfa1.select({"record_type":"C",
- "from":"1",
+ "from_segment":"1",
"pos":1}))
# search paths
self.assertEqual(TestAPILinesFinders.l_gfa1[7:8], TestAPILinesFinders.gfa1.select({"record_type":"P",
"segment_names":"1+,2+"}))
# no record type specified
self.assertEqual(TestAPILinesFinders.l_gfa1[0:1], TestAPILinesFinders.gfa1.select({"name":"1"}))
- self.assertEqual(TestAPILinesFinders.l_gfa1[4:7], TestAPILinesFinders.gfa1.select({"from":"1"}))
+ self.assertEqual(TestAPILinesFinders.l_gfa1[4:7],
+ TestAPILinesFinders.gfa1.select({"from_segment":"1"}))
# reference as value
- self.assertEqual(TestAPILinesFinders.l_gfa1[4:7], TestAPILinesFinders.gfa1.select({"from":TestAPILinesFinders.l_gfa1[0]}))
+ self.assertEqual(TestAPILinesFinders.l_gfa1[4:7],
+ TestAPILinesFinders.gfa1.select({"from_segment":TestAPILinesFinders.l_gfa1[0]}))
# placeholder is equal to any value
self.assertEqual(set(TestAPILinesFinders.l_gfa1_a[0:3]),
set([str(x) for x in TestAPILinesFinders.gfa1.select({"sequence":"ACC"})]))
=====================================
tests/test_api_positionals.py
=====================================
@@ -86,7 +86,6 @@ class TestAPIPositionals(unittest.TestCase):
"S1":{"name":"sid"}, "P":{"path_name":"name"},
"S2":{"sid":"name"}, "E":{"eid":"name"}, "G":{"gid":"name"},
"U":{"pid":"name"}, "O":{"pid":"name"},
- "L":{"from_segment": "from", "to_segment": "to"},
"C":{"from_segment":"container", "from_orient":"container_orient",
"to_segment":"contained", "to_orient":"contained_orient"}
}
=====================================
tests/test_unit_line_connection.py
=====================================
@@ -62,10 +62,10 @@ class TestUnitLineConnection(unittest.TestCase):
g = gfapy.Gfa()
g.append(s1)
g.append(l)
- assert(l.get("from") is s1)
+ assert(l.get("from_segment") is s1)
l.disconnect()
- assert(not l.get("from") is s1)
- self.assertEqual("1", l.get("from"))
+ assert(not l.get("from_segment") is s1)
+ self.assertEqual("1", l.get("from_segment"))
def test_disconnect_disconnects_depent_lines(self):
s1 = gfapy.Line("S\t1\tACCAT")
=====================================
tests/test_unit_line_dynamic_fields.py
=====================================
@@ -8,8 +8,8 @@ class TestUnitLineDynamicFields(unittest.TestCase):
# record_type
self.assertTrue(hasattr(l, "record_type"))
# reqfields
- self.assertTrue(hasattr(l, "from"))
- self.assertIsInstance(object.__getattribute__(l, "from"),
+ self.assertTrue(hasattr(l, "from_segment"))
+ self.assertIsInstance(object.__getattribute__(l, "from_segment"),
gfapy.line.common.dynamic_fields.DynamicField)
# predefined tags
self.assertTrue(hasattr(l, "KC"))
=====================================
tests/test_unit_line_equivalence.py
=====================================
@@ -94,7 +94,8 @@ class TestUnitLineEquivalence(unittest.TestCase):
assert(TestUnitLineEquivalence.a._has_eql_fields(TestUnitLineEquivalence.a.clone()))
# positional field difference
assert(not TestUnitLineEquivalence.l._has_eql_fields(TestUnitLineEquivalence.l_from))
- assert(TestUnitLineEquivalence.l._has_eql_fields(TestUnitLineEquivalence.l_from, ["from"]))
+ assert(TestUnitLineEquivalence.l._has_eql_fields(TestUnitLineEquivalence.l_from,
+ ["from_segment"]))
# positional field difference: name alias
assert(not TestUnitLineEquivalence.e._has_eql_fields(TestUnitLineEquivalence.e_name))
assert(TestUnitLineEquivalence.e._has_eql_fields(TestUnitLineEquivalence.e_name, ["eid"]))
View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/commit/d6805080f3fc41ca93ecd5bcee5f40378d6012f7
--
View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/commit/d6805080f3fc41ca93ecd5bcee5f40378d6012f7
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