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Update long docstrings in PAML class methods

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This commit is contained in:
Thomas Walsh
2025-07-24 15:10:28 +01:00
committed by Peter Cock
parent aceebefbff
commit f6e56e5061
3 changed files with 20 additions and 18 deletions
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18
Bio/Phylo/PAML/baseml.py
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@ -102,9 +102,9 @@ class Baseml(Paml):
def read_ctl_file(self, ctl_file):
"""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
if not supplied. Otherwise raise an exception.
Update each BASEML option to the new option if supplied or None if
not supplied. Raise an exception if the control file does not exist,
a line is malformed, or an option is invalid.
"""
temp_options = {}
if not os.path.isfile(ctl_file):
@ -171,9 +171,10 @@ class Baseml(Paml):
def run(self, ctl_file=None, verbose=False, command="baseml", parse=True):
"""Run baseml using the current configuration.
Check that the tree attribute is specified and exists, and then
run BASEML. If parse is True then read and return the result. If
parse is False return None. Otherwise raise an exception.
Check that the tree file is specified and exists, and then
run BASEML. If parse is True then read and return the results,
otherwise return None. An exception is raised if the return code
of the BASEML command is non-zero.
The arguments may be passed as either absolute or relative paths,
despite the fact that BASEML requires relative paths.
@ -191,9 +192,8 @@ class Baseml(Paml):
def read(results_file):
"""Parse a BASEML results file.
Check that the file exits, that the results file is not empty, and then
parse the file. Check there is a version in the results and then return
the results. Otherwise raise an exception.
Parse the file and return the results. Raise an exception if
the results file does not exist, is empty, or is invalid.
"""
results = {}
if not os.path.exists(results_file):

17
Bio/Phylo/PAML/codeml.py
View File

@ -100,9 +100,9 @@ class Codeml(Paml):
def read_ctl_file(self, ctl_file):
"""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
if not supplied. Otherwise raise an exception.
Update each CODEML option to the new option if supplied or None if
not supplied. Raise an exception if the control file does not exist,
a line is malformed, or an option is invalid.
"""
temp_options = {}
if not os.path.isfile(ctl_file):
@ -182,9 +182,10 @@ class Codeml(Paml):
def run(self, ctl_file=None, verbose=False, command="codeml", parse=True):
"""Run CODEML using the current configuration.
Check that the tree attribute is specified and exists, and then
run CODEML. If parse is True then read and return the results. If
parse is false return None. Otherwise raise an exception.
Check that the tree file is specified and exists, and then
run CODEML. If parse is True then read and return the results,
otherwise return None. An exception is raised if the return code
of the CODEML command is non-zero.
The arguments may be passed as either absolute or relative
paths, despite the fact that CODEML requires relative paths.
@ -202,8 +203,8 @@ class Codeml(Paml):
def read(results_file):
"""Parse a CODEML results file.
Check that the file exists and is not empty. Return the results
if there are any. Otherwise raise an exception.
Return the results if there are any. Raise an exception if
the results file does not exist, is empty, or is invalid.
"""
results = {}
if not os.path.exists(results_file):

3
Bio/Phylo/PAML/yn00.py
View File

@ -106,7 +106,8 @@ class Yn00(Paml):
"""Run yn00 using the current configuration.
If parse is True then read and return the result, otherwise
return None.
return None. An exception is raised if the return code of
the yn00 command is non-zero.
"""
Paml.run(self, ctl_file, verbose, command)
if parse: