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Set PAML class names in CamelCase

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This commit is contained in:
Thomas Walsh
2025-07-24 15:03:01 +01:00
committed by Peter Cock
parent 392ede471d
commit aceebefbff
3 changed files with 6 additions and 6 deletions
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4
Bio/Phylo/PAML/baseml.py
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@ -69,7 +69,7 @@ class Baseml(Paml):
"""Dynamically build a BASEML control file from the options.
The control file is written to the location specified by the
ctl_file property of the BASEML class.
ctl_file property of the Baseml class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
@ -100,7 +100,7 @@ class Baseml(Paml):
ctl_handle.write(f"{option[0]} = {option[1]}\n")
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the BASEML instance.
"""Parse a control file and load the options into the Baseml instance.
Check that the file exists and that the lines in the file are valid.
Then update each BASEML options to the new option if supplied or None

4
Bio/Phylo/PAML/codeml.py
View File

@ -74,7 +74,7 @@ class Codeml(Paml):
"""Dynamically build a CODEML control file from the options.
The control file is written to the location specified by the
ctl_file property of the CODEML class.
ctl_file property of the Codeml class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
@ -98,7 +98,7 @@ class Codeml(Paml):
ctl_handle.write(f"{option[0]} = {option[1]}\n")
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the CODEML instance.
"""Parse a control file and load the options into the Codeml instance.
Check that the file exists and that the lines in the file are valid.
Then update each CODEML options to the new option if supplied or None

4
Bio/Phylo/PAML/yn00.py
View File

@ -45,7 +45,7 @@ class Yn00(Paml):
"""Dynamically build a yn00 control file from the options.
The control file is written to the location specified by the
ctl_file property of the yn00 class.
ctl_file property of the Yn00 class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
@ -61,7 +61,7 @@ class Yn00(Paml):
ctl_handle.write(f"{option[0]} = {option[1]}\n")
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the yn00 instance."""
"""Parse a control file and load the options into the Yn00 instance."""
temp_options = {}
if not os.path.isfile(ctl_file):
raise FileNotFoundError(f"File not found: {ctl_file!r}")