Missing test file tests/test_datatable.ini

countess/plugins/fastq.py

@@ -4,8 +4,8 @@
 from typing import Iterable, Optional
 
 import pandas as pd
-from fqfa.fastq.fastq import parse_fastq_reads # type: ignore
 from fqfa.fasta.fasta import parse_fasta_records # type: ignore
+from fqfa.fastq.fastq import parse_fastq_reads # type: ignore
 
 from countess import VERSION
 from countess.core.parameters import BooleanParam, FloatParam, StringParam
@@ -24,6 +24,7 @@ def _fastq_reader(
  "filename": clean_filename(filename),
  }
 
+
 class LoadFastqPlugin(PandasInputFilesPlugin):
  """Load counts from one or more FASTQ files, by first building a dask dataframe of raw sequences
  with count=1 and then grouping by sequence and summing counts. It supports counting
@@ -80,15 +81,14 @@ def read_file_to_dataframe(self, file_params, row_limit=None):
  return dataframe
 
 
-def _fasta_reader(
- file_handle, row_limit: Optional[int] = None
-) -> Iterable[dict[str, str]]:
+def _fasta_reader(file_handle, row_limit: Optional[int] = None) -> Iterable[dict[str, str]]:
  for header, sequence in islice(parse_fasta_records(file_handle), 0, row_limit):
  yield {
  "__s": sequence,
  "__h": header,
  }
 
+
 class LoadFastaPlugin(PandasInputFilesPlugin):
  name = "FASTA Load"
  description = "Loads sequences from FASTA files"

tests/test_datatable.ini

@@ -0,0 +1,36 @@
+[DataTable]
+_module = countess.plugins.data_table
+_class = DataTablePlugin
+_version = 0.0.69
+_hash = 5d54face788a55338e1873cd0c29820317e805c06f2fe9d95450f3f38153392c
+_sort = 0 0
+_position = 500 500
+columns.0.name = 'aaa'
+columns.0.type = 'string'
+columns.0.index = False
+columns.1.name = 'bbb'
+columns.1.type = 'number'
+columns.1.index = False
+columns.2.name = 'ccc'
+columns.2.type = 'boolean'
+columns.2.index = False
+rows.0.aaa = ''
+rows.0.bbb = None
+rows.0.ccc = False
+rows.1.aaa = ''
+rows.1.bbb = None
+rows.1.ccc = False
+
+[CSV Save]
+_module = countess.plugins.csv
+_class = SaveCsvPlugin
+_version = 0.0.69
+_hash = eeb7325e4c7649ab971759c5120eb0ffc8684495a4ddc7a4dfb395c3b9cf1e60
+_sort = 0 0
+_position = 581 559
+_parent.0 = DataTable
+header = True
+filename = None
+delimiter = ','
+quoting = False
+