Author: bugman
Date: Mon Apr 14 19:17:29 2014
New Revision: 22754
URL: http://svn.gna.org/viewcvs/relax?rev=22754&view=rev
Log:
Removed all of the prompt.doc_string.regexp_doc documentation objects from
the user functions.
This is the regular expression documentation which no longer has a purpose.
It was for specifying
multiple parameters simultaneously in user functions such as value.set, but
this functionality has
been removed.
Modified:
trunk/user_functions/dx.py
trunk/user_functions/grace.py
trunk/user_functions/value.py
Modified: trunk/user_functions/dx.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/dx.py?rev=22754&r1=22753&r2=22754&view=diff
==============================================================================
--- trunk/user_functions/dx.py (original)
+++ trunk/user_functions/dx.py Mon Apr 14 19:17:29 2014
@@ -34,7 +34,6 @@
from lib.software.opendx.execute import run
from pipe_control import diffusion_tensor
from pipe_control.opendx import map
-from prompt.doc_string import regexp_doc
from specific_analyses.frame_order.parameter_object import
Frame_order_params; frame_order_params = Frame_order_params()
from specific_analyses.model_free.parameter_object import Model_free_params;
model_free_params = Model_free_params()
from specific_analyses.n_state_model.parameter_object import N_state_params;
n_state_params = N_state_params()
@@ -204,7 +203,6 @@
table.add_row(["3D isosurface", "'Iso3D'"])
uf.desc[-1].add_table(table.label)
# Additional.
-uf.desc.append(regexp_doc)
uf.desc.append(model_free_params.uf_doc(label="table: all model-free
parameters"))
uf.desc.append(n_state_params.uf_doc(label="table: N-state parameters"))
uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion
parameters"))
Modified: trunk/user_functions/grace.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/grace.py?rev=22754&r1=22753&r2=22754&view=diff
==============================================================================
--- trunk/user_functions/grace.py (original)
+++ trunk/user_functions/grace.py Mon Apr 14 19:17:29 2014
@@ -33,7 +33,6 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import grace
-from prompt.doc_string import regexp_doc
from specific_analyses.consistency_tests.parameter_object import
Consistency_tests_params; consistency_test_params = Consistency_tests_params()
from specific_analyses.jw_mapping.parameter_object import Jw_mapping_params;
jw_mapping_params = Jw_mapping_params()
from specific_analyses.model_free.parameter_object import Model_free_params;
model_free_params = Model_free_params()
@@ -190,7 +189,6 @@
uf.desc[-1].add_item_list_element("'error'", "Plot errors.")
uf.desc[-1].add_item_list_element("'sims'", "Plot the simulation values.")
uf.desc[-1].add_paragraph("Normalisation is only allowed for series type
data, for example the R2 exponential curves, and will be ignored for all
other data types. If the norm flag is set to True then the y-value of the
first point of the series will be set to 1. This normalisation is useful for
highlighting errors in the data sets.")
-uf.desc.append(regexp_doc)
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters
and min stats"))
uf.desc.append(noe_params.uf_doc(label="table: NOE parameters"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free parameters
and min stats"))
Modified: trunk/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/value.py?rev=22754&r1=22753&r2=22754&view=diff
==============================================================================
--- trunk/user_functions/value.py (original)
+++ trunk/user_functions/value.py Mon Apr 14 19:17:29 2014
@@ -34,7 +34,6 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pipes, value
-from prompt.doc_string import regexp_doc
from specific_analyses.consistency_tests.parameter_object import
Consistency_tests_params; consistency_test_params = Consistency_tests_params()
from specific_analyses.jw_mapping.parameter_object import Jw_mapping_params;
jw_mapping_params = Jw_mapping_params()
from specific_analyses.model_free.parameter_object import Model_free_params;
model_free_params = Model_free_params()
@@ -89,7 +88,6 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("If this is used to change values of previously
minimised parameters, then the minimisation statistics (chi-squared value,
iteration count, function count, gradient count, and Hessian count) will be
reset.")
# Prompt examples.
-uf.desc.append(regexp_doc)
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free
parameters"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
@@ -131,7 +129,6 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The values corresponding to the given parameter
will be displayed. The scaling argument can be used to scale the parameter
values. This can be useful for example in the case of the model-free Rex
parameter to obtain the spectrometer dependent value from the omega_ex field
strength independent internal value. Or to scale correlation times from
seconds down to nanosecond or picosecond timescales.")
-uf.desc.append(regexp_doc)
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters"))
uf.desc.append(noe_params.uf_doc(label="table: NOE parameters"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter
writing"))
@@ -273,7 +270,6 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The spin system can be identified in the file
using two different formats. The first is the spin ID string column which
can include the molecule name, the residue name and number, and the spin name
and number. Alternatively the molecule name, residue number, residue name,
spin number and/or spin name columns can be supplied allowing this
information to be in separate columns. Note that the numbering of columns
starts at one. The spin ID string can be used to restrict the reading to
certain spin types, for example only 15N spins when only residue information
is in the file.")
uf.desc[-1].add_paragraph("If this is used to change values of previously
minimised parameters, then the minimisation statistics (chi-squared value,
iteration count, function count, gradient count, and Hessian count) will be
reset.")
-uf.desc.append(regexp_doc)
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free
parameters"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
@@ -358,7 +354,6 @@
# Spin identification.
uf.desc.append(Desc_container("Spin identification"))
uf.desc[-1].add_paragraph("If the spin ID is left unset, then this will be
applied to all spins. If the data is global non-spin specific data, such as
diffusion tensor parameters, supplying the spin identifier will terminate the
program with an error.")
-uf.desc.append(regexp_doc)
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter
value setting"))
uf.desc.append(model_free_params.uf_doc(label="table: mf parameter value
setting"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value
setting"))
@@ -456,7 +451,6 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The values corresponding to the given parameter
will be written to file. The scaling argument can be used to scale the
parameter values. This can be useful for example in the case of the
model-free Rex parameter to obtain the spectrometer dependent value from the
omega_ex field strength independent internal value. Or to scale correlation
times from seconds down to nanosecond or picosecond timescales.")
-uf.desc.append(regexp_doc)
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters"))
uf.desc.append(noe_params.uf_doc(label="table: NOE parameters"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter
writing"))
r22754 - in /trunk/user_functions: dx.py grace.py value.py