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Jul 9, 2025
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chore: rename doc → docs, update references, and fix test.txt #171

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0 doc/Makefile → docs/Makefile
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2 changes: 1 addition & 1 deletion doc/examples/README.rst → docs/examples/README.rst
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Expand Up @@ -82,7 +82,7 @@ directory, ::

tar xvzf archivename.tar.gz

From a command window change to the *doc/examples* directory of the new
From a command window change to the *docs/examples* directory of the new
folder. For example, a Windows' user who extracted *archivename.zip* in the
folder *C:\\Research* would type ::

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0 doc/examples/data/Ag_nyquist_qmax30.gr → docs/examples/data/Ag_nyquist_qmax30.gr
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0 doc/examples/data/C60_fine_qmax21.gr → docs/examples/data/C60_fine_qmax21.gr
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0 doc/examples/data/C60baseline.dat → docs/examples/data/C60baseline.dat
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0 doc/examples/data/TiO2_fine_qmax26.gr → docs/examples/data/TiO2_fine_qmax26.gr
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0 doc/examples/extract_single_peak.py → docs/examples/extract_single_peak.py
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0 doc/examples/fit_initial.py → docs/examples/fit_initial.py
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0 doc/examples/images/extract_single_peak1.png → .../examples/images/extract_single_peak1.png
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0 doc/examples/images/extract_single_peak2.png → .../examples/images/extract_single_peak2.png
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0 doc/examples/images/extract_single_peak3.png → .../examples/images/extract_single_peak3.png
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0 doc/examples/images/fit_initial1.png → docs/examples/images/fit_initial1.png
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0 doc/examples/images/fit_initial2.png → docs/examples/images/fit_initial2.png
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0 doc/examples/images/parameter_summary1.png → docs/examples/images/parameter_summary1.png
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0 doc/examples/images/parameter_summary2.png → docs/examples/images/parameter_summary2.png
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0 doc/examples/images/query_results1.png → docs/examples/images/query_results1.png
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0 doc/examples/multimodel_known_dG1.py → docs/examples/multimodel_known_dG1.py
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0 doc/examples/multimodel_known_dG2.py → docs/examples/multimodel_known_dG2.py
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0 doc/examples/multimodel_unknown_dG1.py → docs/examples/multimodel_unknown_dG1.py
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0 doc/examples/multimodel_unknown_dG2.py → docs/examples/multimodel_unknown_dG2.py
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2 changes: 1 addition & 1 deletion doc/examples/output/extract_single_peak.pwa → docs/examples/output/extract_single_peak.pwa
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Expand Up @@ -6,7 +6,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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2 changes: 1 addition & 1 deletion ...xamples/output/extract_single_peak.srmise → ...xamples/output/extract_single_peak.srmise
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Expand Up @@ -38,7 +38,7 @@ cres=0.10472
ModelEvaluator=AIC
Range=[2.0, 3.5]
# Metadata
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr'
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr'
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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2 changes: 1 addition & 1 deletion doc/examples/output/fit_initial.pwa → docs/examples/output/fit_initial.pwa
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Expand Up @@ -6,7 +6,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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2 changes: 1 addition & 1 deletion doc/examples/output/fit_initial.srmise → docs/examples/output/fit_initial.srmise
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Expand Up @@ -130,7 +130,7 @@ cres=0.05
ModelEvaluator=AIC
Range=[1.0, 7.25]
# Metadata
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr'
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr'
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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0 doc/examples/output/known_dG_aics.dat → docs/examples/output/known_dG_aics.dat
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2 changes: 1 addition & 1 deletion doc/examples/output/known_dG_m0.pwa → docs/examples/output/known_dG_m0.pwa
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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2 changes: 1 addition & 1 deletion doc/examples/output/known_dG_m1.pwa → docs/examples/output/known_dG_m1.pwa
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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2 changes: 1 addition & 1 deletion doc/examples/output/known_dG_m12.pwa → docs/examples/output/known_dG_m12.pwa
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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2 changes: 1 addition & 1 deletion doc/examples/output/known_dG_m8.pwa → docs/examples/output/known_dG_m8.pwa
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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2 changes: 1 addition & 1 deletion doc/examples/output/known_dG_models.dat → docs/examples/output/known_dG_models.dat
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2 changes: 1 addition & 1 deletion doc/examples/output/parameter_summary.pwa → docs/examples/output/parameter_summary.pwa
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Expand Up @@ -6,7 +6,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/TiO2_fine_qmax26.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/TiO2_fine_qmax26.gr
nyquist=True
qmax=26.0
qmax_reportedbypdf=26.0
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2 changes: 1 addition & 1 deletion doc/examples/output/parameter_summary.srmise → .../examples/output/parameter_summary.srmise
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Expand Up @@ -73,7 +73,7 @@ cres=0.05
ModelEvaluator=AIC
Range=[1.5, 10.0]
# Metadata
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/TiO2_fine_qmax26.gr'
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/TiO2_fine_qmax26.gr'
nyquist=True
qmax=26.0
qmax_reportedbypdf=26.0
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2 changes: 1 addition & 1 deletion doc/examples/output/query_results.pwa → docs/examples/output/query_results.pwa
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Expand Up @@ -6,7 +6,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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Expand Up @@ -38,7 +38,7 @@ cres=0.10472
ModelEvaluator=AIC
Range=[2.0, 10.0]
# Metadata
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr'
filename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/Ag_nyquist_qmax30.gr'
nyquist=True
qmax=30.0
qmax_reportedbypdf=30.0
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0 doc/examples/output/unknown_dG_aics.dat → docs/examples/output/unknown_dG_aics.dat
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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2 changes: 1 addition & 1 deletion doc/examples/output/unknown_dG_m5.pwa → docs/examples/output/unknown_dG_m5.pwa
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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Expand Up @@ -12,7 +12,7 @@ diffpy.srmise version 0.5.2
##### PDF Peak Extraction Summary
# The information below is not sufficient to replicate extraction.
## PDF metadata
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr
filename=/home/luke/Workspaces/MSU_Research/diffpy.srmise/docs/examples/data/C60_fine_qmax21.gr
nyquist=True
qmax=21.299999
qmax_reportedbypdf=21.299999
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0 doc/examples/parameter_summary.py → docs/examples/parameter_summary.py
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0 doc/examples/query_results.py → docs/examples/query_results.py
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0 doc/make.bat → docs/make.bat
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0 doc/source/_static/.placeholder → docs/source/_static/.placeholder
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0 ...source/api/diffpy.srmise.applications.rst → ...source/api/diffpy.srmise.applications.rst
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0 doc/source/api/diffpy.srmise.baselines.rst → docs/source/api/diffpy.srmise.baselines.rst
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0 ...rce/api/diffpy.srmise.modelevaluators.rst → ...rce/api/diffpy.srmise.modelevaluators.rst
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0 doc/source/api/diffpy.srmise.peaks.rst → docs/source/api/diffpy.srmise.peaks.rst
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0 doc/source/api/diffpy.srmise.rst → docs/source/api/diffpy.srmise.rst
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2 changes: 1 addition & 1 deletion doc/source/conf.py → docs/source/conf.py
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Expand Up @@ -139,7 +139,7 @@
"github_user": "diffpy",
"github_repo": "diffpy.srmise",
"github_version": "main",
"conf_py_path": "/doc/source/",
"conf_py_path": "/docs/source/",
}

# Theme options are theme-specific and customize the look and feel of a theme
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0 doc/source/extending.rst → docs/source/extending.rst
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0 doc/source/index.rst → docs/source/index.rst
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0 doc/source/license.rst → docs/source/license.rst
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0 doc/source/release.rst → docs/source/release.rst
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0 doc/source/snippets/.placeholder → docs/source/snippets/.placeholder
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2 changes: 1 addition & 1 deletion doc/source/tutorial/abbreviations.txt → docs/source/tutorial/abbreviations.txt
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@@ -1,6 +1,6 @@
.. Abbreviations and definitions for SrMise tutorial.

.. The README file in the doc/examples directory of the SrMise source
.. The README file in the docs/examples directory of the SrMise source
distribution should be readable without generating the full Sphinx docs.
To do this, the amount of markup is kept to a bare minimum, and the markup
that does appear shouldn't get in the way of understanding.
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0 doc/source/tutorial/index.rst → docs/source/tutorial/index.rst
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0 ...torial/multimodel_known_uncertainties.rst → ...torial/multimodel_known_uncertainties.rst
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0 ...rial/multimodel_unknown_uncertainties.rst → ...rial/multimodel_unknown_uncertainties.rst
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0 requirements/test.txt → requirements/tests.txt
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