Merge branch 'dev' of https://github.com/PyEED/pyeed into dev

PyEED · May 28, 2024 · 168d235 · 168d235
2 parents 3c058ca + 905f283
commit 168d235
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Showing 15 changed files with 16 additions and 16 deletions.
diff --git a/pyeed/core/abstractannotation.py b/pyeed/core/abstractannotation.py
@@ -49,7 +49,7 @@ class AbstractAnnotation(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/alignmentresult.py b/pyeed/core/alignmentresult.py
@@ -53,7 +53,7 @@ class AlignmentResult(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/blastdata.py b/pyeed/core/blastdata.py
@@ -90,7 +90,7 @@ class BlastData(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/clustalomegaresult.py b/pyeed/core/clustalomegaresult.py
@@ -32,7 +32,7 @@ class ClustalOmegaResult(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/dnarecord.py b/pyeed/core/dnarecord.py
@@ -32,7 +32,7 @@ class DNARecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/organism.py b/pyeed/core/organism.py
@@ -108,7 +108,7 @@ class Organism(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/pairwisealignmentresult.py b/pyeed/core/pairwisealignmentresult.py
@@ -60,7 +60,7 @@ class PairwiseAlignmentResult(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/proteinrecord.py b/pyeed/core/proteinrecord.py
@@ -75,7 +75,7 @@ class ProteinRecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
@@ -145,7 +145,6 @@ def get_id(cls, protein_id: str) -> "ProteinRecord":
 
         import nest_asyncio
 
-
         nest_asyncio.apply()
 
         if isinstance(protein_id, list) and all(isinstance(x, str) for x in protein_id):
@@ -166,7 +165,6 @@ def get_ids(cls, accession_ids: List[str]) -> List["ProteinRecord"]:
 
         import nest_asyncio
 
-
         nest_asyncio.apply()
 
         return asyncio.run(

diff --git a/pyeed/core/region.py b/pyeed/core/region.py
@@ -43,7 +43,7 @@ class Region(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/regionset.py b/pyeed/core/regionset.py
@@ -35,7 +35,7 @@ class RegionSet(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _object_terms: Set[str] = PrivateAttr(

diff --git a/pyeed/core/sequence.py b/pyeed/core/sequence.py
@@ -38,7 +38,7 @@ class Sequence(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/sequencerecord.py b/pyeed/core/sequencerecord.py
@@ -103,7 +103,7 @@ class SequenceRecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/site.py b/pyeed/core/site.py
@@ -35,7 +35,7 @@ class Site(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/standardnumbering.py b/pyeed/core/standardnumbering.py
@@ -47,7 +47,7 @@ class StandardNumbering(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="63f43b11e0d359e1d0a1f541cea25dd484ad0072"
+        default="8a37de9455d136d5661c7cc077ce66512dedfac8"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/schemes/pyeed_schema.md b/pyeed/schemes/pyeed_schema.md
@@ -125,6 +125,8 @@ classDiagram
         +FAMILY
         +MOTIVE
         +CODING_SEQ
+        +ALPHAHELIX
+        +BETASTRAND
     }
     
     class SequenceType {