Testing GitHub copilot agent mode in browser

profasta/db.py

@@ -63,7 +63,7 @@ class ProteinDatabase:
 
     db: dict[str, AbstractDatabaseEntry]
     added_fasta_files: list[str]
-    skipped_fasta_entries: dict[str, list]
+    skipped_fasta_entries: dict[str, list[str]]
 
     def __init__(self):
         self.db = {}
@@ -128,10 +128,11 @@ def add_fasta(
         if skipped_entry_headers:
             num_skipped = len(skipped_entry_headers)
             num_total = num_skipped + len(parsed_protein_entries)
+            skipped_list = "\n  ".join(skipped_entry_headers)
             logger.warning(
                 f"Skipped {num_skipped}/{num_total} entries while adding "
                 f"'{fasta_name}' to a ProteinDatabase because their headers could not "
-                f"be parsed:"
+                f"be parsed:\n  {skipped_list}"
             )
 
     def add_entry(self, protein_entry: AbstractDatabaseEntry, overwrite: bool = False):
@@ -152,7 +153,7 @@ def add_entry(self, protein_entry: AbstractDatabaseEntry, overwrite: bool = Fals
 
     def write_fasta(
         self,
-        path,
+        path: str,
         append: bool = False,
         header_writer: Optional[str] = None,
         line_width: int = 60,

profasta/io.py

@@ -7,7 +7,7 @@
     FastaRecord: Representation of a protein record in a FASTA file.
 
 Functions:
-    parse_fasta: Parse a FASTA file object and return a list of FastaRecords.
+    parse_fasta: Parse a FASTA file object and yield FastaRecords.
     write_fasta: Write a list of FastaRecords to a file object.
 """
 
@@ -55,14 +55,20 @@ def parse_fasta(file_object: IO[str]) -> Generator[FastaRecord, None, None]:
     Yields:
         Yields FastaRecords.
     """
-    fasta_text = file_object.read()
-    if not fasta_text.startswith("\n"):
-        fasta_text = "\n" + fasta_text
-
-    for block in fasta_text.split("\n>")[1:]:
-        lines = block.split("\n")
-        header = lines[0].strip()
-        sequence = "".join(lines[1:]).replace(" ", "").rstrip("*").upper()
+    header = None
+    sequence_lines: list[str] = []
+    for line in file_object:
+        line = line.rstrip("\n")
+        if line.startswith(">"):
+            if header is not None:
+                sequence = "".join(sequence_lines).replace(" ", "").rstrip("*").upper()
+                yield FastaRecord(header, sequence)
+            header = line[1:].strip()
+            sequence_lines = []
+        else:
+            sequence_lines.append(line)
+    if header is not None:
+        sequence = "".join(sequence_lines).replace(" ", "").rstrip("*").upper()
         yield FastaRecord(header, sequence)
 
 

profasta/parser.py

@@ -16,8 +16,8 @@
     UniprotParser: Parser for Uniprot FASTA headers.
     UniprotLikeParser: Parser for less strict Uniprot like FASTA headers.
     DefaultWriter: Default FASTA header writer.
-    UniprotWriter: Parser for Uniprot FASTA writer.
-    UniprotLikeWriter: Parser for less strict Uniprot like FASTA writer.
+    UniprotWriter: Writer for Uniprot FASTA headers.
+    UniprotLikeWriter: Writer for less strict Uniprot like FASTA headers.
 
 Functions:
     register_parser: Register a custom FASTA header parser by name.
@@ -57,7 +57,7 @@ class AbstractHeaderParser(Protocol):
     """Abstract header parser."""
 
     @classmethod
-    def parse(self, header: str) -> AbstractParsedHeader:
+    def parse(cls, header: str) -> AbstractParsedHeader:
         """Parse a FASTA header string into a ParsedHeader object.
 
         Raises:
@@ -70,7 +70,7 @@ class AbstractHeaderWriter(Protocol):
     """Abstract header writer."""
 
     @classmethod
-    def write(self, parsed_header: AbstractParsedHeader) -> str:
+    def write(cls, parsed_header: AbstractParsedHeader) -> str:
         """Write a FASTA header string from a ParsedHeader object."""
         ...
 
@@ -95,9 +95,9 @@ class DefaultParser:
 
     The `parse` method returns a ParsedHeader object with the identifier being the
     first whitespace-separated word of the header. The rest of the header is stored
-    in the "description" field of the `header_fields` dictionary, which might be an
-    empty string. This parser is guaranteed to work for any FASTA header string and
-    never fail.
+    in the "description" field of the `header_fields` dictionary. If there is no
+    description, the "description" key is absent from `header_fields`. This parser
+    is guaranteed to work for any FASTA header string and never fail.
     """
 
     @classmethod
@@ -315,14 +315,14 @@ def get_parser(parser_name: str) -> AbstractHeaderParser:
     return PARSER_REGISTRY[parser_name]
 
 
-def register_writer(name: str, parser: AbstractHeaderWriter):
+def register_writer(name: str, writer: AbstractHeaderWriter):
     """Register a custom writer by name."""
-    WRITER_REGISTRY[name] = parser
+    WRITER_REGISTRY[name] = writer
 
 
-def get_writer(parser_name: str) -> AbstractHeaderWriter:
+def get_writer(writer_name: str) -> AbstractHeaderWriter:
     """Get a registered writer by name."""
-    return WRITER_REGISTRY[parser_name]
+    return WRITER_REGISTRY[writer_name]
 
 
 PARSER_REGISTRY: dict[str, AbstractHeaderParser] = {

tests/integration/test_integration.py

@@ -15,7 +15,7 @@ def parse(cls, header):
 
 class CustomWriter:
     @classmethod
-    def write(self, parsed_header):
+    def write(cls, parsed_header):
         return parsed_header.header