Merge branch 'dev'

PyEED · May 25, 2024 · 3ee56e9 · 3ee56e9
2 parents da550b6 + c7645e8
commit 3ee56e9
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diff --git a/.github/scripts/env.toml b/.github/scripts/env.toml
diff --git a/.github/scripts/example.py b/.github/scripts/example.py
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -4,11 +4,10 @@ on: pull_request
 
 jobs:
   build:
-
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest]
         python-version: ["3.10", "3.11", "3.12"]
 
     steps:

diff --git a/docs/examples/alignment.ipynb b/docs/examples/alignment.ipynb
diff --git a/docs/examples/basics.ipynb b/docs/examples/basics.ipynb
@@ -14,60 +14,6 @@
     "The `ProteinRecord` object contains the sequence as a string and additional information such as information on the `Organism`, `Region` or `Site` annotations of the sequence.\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[4mProteinRecord\u001b[0m\n",
-      "├── \u001b[94mid\u001b[0m = E300_wefef\n",
-      "├── \u001b[94mname\u001b[0m = my sequence\n",
-      "├── \u001b[94morganism\u001b[0m\n",
-      "│   └── \u001b[4mOrganism\u001b[0m\n",
-      "│       ├── \u001b[94mid\u001b[0m = f1e41f5c-3e17-477f-a453-837f4fd09ca7\n",
-      "│       ├── \u001b[94mtaxonomy_id\u001b[0m = 9094\n",
-      "│       └── \u001b[94mname\u001b[0m = E. coli\n",
-      "├── \u001b[94msequence\u001b[0m = SDFSGWRSB\n",
-      "└── \u001b[94msites\u001b[0m\n",
-      "    └── 0\n",
-      "        └── \u001b[4mSite\u001b[0m\n",
-      "            ├── \u001b[94mid\u001b[0m = 277fed27-a7b4-451a-a822-cbfe3e88c1a2\n",
-      "            ├── \u001b[94mname\u001b[0m = active site\n",
-      "            └── \u001b[94mpositions\u001b[0m = [1, 2, 3, ...]\n",
-      "\n"
-     ]
-    }
-   ],
-   "source": [
-    "from pyeed.core import ProteinRecord\n",
-    "from pyeed.core import Organism\n",
-    "\n",
-    "my_organism = Organism(name=\"E. coli\", taxonomy_id=9094)\n",
-    "\n",
-    "E300 = ProteinRecord(id=\"E300_wefef\", sequence=\"SDFSGWRSB\", organism=my_organism, name=\"my sequence\")\n",
-    "\n",
-    "E300.add_to_sites(\n",
-    "    positions=[1,2,3],\n",
-    "    name=\"active site\"\n",
-    ")\n",
-    "\n",
-    "E300.\n",
-    "\n",
-    "print(E300)\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/examples/alignment.ipynb b/examples/alignment.ipynb
diff --git a/examples/basics.ipynb b/examples/basics.ipynb
diff --git a/pyeed/align/msa.py b/pyeed/align/msa.py
@@ -47,8 +47,8 @@ def _map_alignment(self, alignment: MultipleSeqAlignment) -> AlignmentResult:
         """
 
         result = AlignmentResult()
-        [result.add_to_sequences(seq.id, seq.sequence) for seq in self.sequences]
-        [result.add_to_aligned_sequences(seq.id, str(seq.seq)) for seq in alignment]
+        [result.add_to_sequences(id=seq.id, sequence=seq.sequence, sequence_id=seq.id) for seq in self.sequences]
+        [result.add_to_aligned_sequences(id=seq.id, sequence=str(seq.seq), sequence_id=seq.id) for seq in alignment]
 
         return result
 

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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/proteinrecord.py b/pyeed/core/proteinrecord.py
@@ -74,7 +74,7 @@ class ProteinRecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _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="b67f8aac7619d462d1e346822b9153a10996d11c"
+        default="ff1fb2064e9efbdf71ccde1d8f08b9af434150bb"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyeed"
-version = "0.3.2"
+version = "0.3.3"
 description = "Toolkit to create, annotate, and analyze sequence data"
 authors = ["haeussma <[email protected]>"]
 license = "MIT"