Remove deprecated datatypes.AlleleCounts class

src/PyPop/_deprecations.py

@@ -64,10 +64,8 @@
 
 deprecated_modules = {
     "PyPop.datatypes.AlleleCounts": {
-        "new": "",
         "reason": "The :class:`~PyPop.datatypes.Genotypes` class now holds allele count data as pseudo-genotype matrix.",
-        "deprecated": "0.6.0",
-        "removal": "1.4.2",
+        "removed": "1.4.2",
     },
     "PyPop.Arlequin": {
         "new": "PyPop.arlequin",

src/PyPop/datatypes.py

@@ -361,72 +361,6 @@ def getIndividualsData(self):
         return self.matrix
 
 
-class AlleleCounts:
-    """Deprecated class to store information in allele count form.
-
-    .. deprecated:: 0.6.0
-         this class is now obsolete, the :class:`Genotypes` class
-         now holds allele count data as pseudo-genotype matrix.
-    """
-
-    def __init__(self, alleleTable=None, locusName=None):
-        self.alleleTable = alleleTable
-        self.locusName = locusName
-        self._genDataStructures()
-
-    def _genDataStructures(self):
-        total = 0
-        self.freqcount = {}
-
-        for allele in self.alleleTable:
-            total += self.alleleTable[allele]
-
-        # store in an iVar for the moment
-        self.totalAlleleCount = total
-
-        logger.debug("alleleTable", self.alleleTable)
-
-        # simply reconstruct the 3-tuple as generated in
-        # ParseGenotypeFile: alleleTable (a map of counts keyed by
-        # allele), total allele count and the number of untyped
-        # individuals (in this case, by definition it is zero).
-        # then store in the same data structure as ParseGenotypeFile
-
-        # even though we only have a single locus, this will make it
-        # easy to generalize later
-
-        self.freqcount[self.locusName] = self.alleleTable, self.totalAlleleCount, 0, 0
-
-    def serializeSubclassMetadataTo(self, stream):
-        """Serialize subclass-specific metadata.
-
-        Specifically, total number of alleles and loci.
-        """
-        stream.opentag("summaryinfo")
-        stream.writeln()
-        stream.tagContents("allelecount", f"{self.totalAlleleCount}")
-        stream.writeln()
-        stream.tagContents("locuscount", f"{1}")
-        stream.writeln()
-        stream.closetag("summaryinfo")
-        stream.writeln()
-
-    def serializeAlleleCountDataAt(self, stream, locus):
-        # call the class-independent function...
-
-        alleleTable, total, untypedIndividuals, unsequencedSites = self.freqcount[locus]
-        _serializeAlleleCountDataAt(
-            stream, alleleTable, total, untypedIndividuals, unsequencedSites
-        )
-
-    def getAlleleCount(self):
-        return self.freqcount[self.locusName]
-
-    def getLocusName(self):
-        # the first key is the name of the locus
-        return self.locusName
-
-
 def _serializeAlleleCountDataAt(
     stream, alleleTable, total, untypedIndividuals, unsequencedSites
 ):