Merge pull request #124 from cgat-developers/AC-codeclean

deprication of Blat and gff2psl

cgat/Blat.py

@@ -1,11 +1,18 @@
 '''Blat.py - tools for working with PSL formatted files and data
 =============================================================
 
+IMPORTANT NOTICE:
+Several functions within this module are scheduled for
+deprecation in May 2024.
+Details regarding the specific functions to be deprecated
+can be found in the documentation of each function.
+
+
 This module provides a class to parse :term:`PSL` formatted
 files such as those output by the BLAT tool.
 
 This module defines the :class:`Blat.Match` class representing a
-single entry and a series of iterators to iterate of :term:`PSL`
+single entry and a series of iterators to iterate of :term:`SL`
 formatted files (:func:`iterator`, :func:`iterator_target_overlap`,
 ...).
 
@@ -16,6 +23,8 @@
 import copy
 import string
 import collections
+import warnings
+import functools
 
 try:
     import alignlib_lite
@@ -26,6 +35,19 @@
 from cgatcore import experiment as E
 
 
+def deprecated_class(cls):
+    orig_init = cls.__init__
+
+    @functools.wraps(orig_init)
+    def new_init(self, *args, **kwargs):
+        warnings.warn(f"{cls.__name__} is deprecated and will be removed in May 2024.", DeprecationWarning)
+        orig_init(self, *args, **kwargs)
+
+    cls.__init__ = new_init
+    return cls
+
+
+@deprecated_class
 class Error(Exception):
     """Base class for exceptions in this module."""
 
@@ -40,6 +62,7 @@ def _set_message(self, message):
     message = property(_get_message, _set_message)
 
 
+@deprecated_class
 class ParsingError(Error):
 
     """Exception raised for errors while parsing
@@ -61,6 +84,7 @@ def __init__(self, message, line=None):
 ---------------------------------------------------------------------------------------------------------------------------------------------------------------"""
 
 
+@deprecated_class
 class Match:
 
     """a :term:`psl` formatted alignment.
@@ -479,6 +503,7 @@ def getHeaders(self):
                 "qStarts", "tStarts")
 
 
+@deprecated_class
 class MatchPSLX(Match):
 
     def __init__(self):
@@ -601,6 +626,7 @@ def _iterate(infile):
         yield match
 
 
+@deprecated_class
 class BlatIterator:
 
     def __init__(self, f, *args, **kwargs):

cgat/IndexedFasta.py

@@ -36,7 +36,6 @@
 
 '''
 
-from __future__ import generator_stop
 import os
 import sys
 import array

cgat/SequenceProperties.py

@@ -42,7 +42,6 @@
 import hashlib
 import base64
 import itertools
-import six
 
 from cgat import Genomics as Genomics
 
@@ -137,7 +136,7 @@ def loadSequence(self, sequence, seqtype="na"):
         SequenceProperties.loadSequence(self, sequence, seqtype)
 
         # do the encryption
-        h = hashlib.md5(six.b(sequence)).digest()
+        h = hashlib.md5(sequence.encode()).digest()
         # map to printable letters: hid has length 22, so the padded '=' are
         # truncated. You have to add them, if you ever want to decode,
         # but who would do such a thing :=)

cgat/tools/gff2psl.py

@@ -4,6 +4,8 @@
 
 :Tags: Genomics Intervals GFF PSL Conversion
 
+Note: This script is scheduled for deprecation in May 2024.
+
 Purpose
 -------
 
@@ -47,12 +49,19 @@
 import cgat.Intervals as Intervals
 
 
+def print_deprecation_warning():
+    warning_message = ("""WARNING: 'gff2psl.py' is deprecated and will be removed in May 2024.""")
+    print(warning_message, file=sys.stderr)
+
+
 def main(argv=None):
     """script main.
 
     parses command line options in sys.argv, unless *argv* is given.
     """
 
+    print_deprecation_warning()
+
     if argv is None:
         argv = sys.argv
 

conda/environments/cgat-apps.yml

@@ -15,7 +15,6 @@ dependencies:
 - alignlib-lite
 - biopython
 - cython
-- jinja2
 - cgatcore
 - matplotlib
 - nose
@@ -31,7 +30,6 @@ dependencies:
 - scikit-learn
 - scipy
 - setuptools
-- six
 - sortedcontainers
 - bedtools
 - grep

tests/test_scripts.py

@@ -19,8 +19,6 @@
 
 """
 
-from __future__ import print_function
-
 import subprocess
 import tempfile
 import os