chore: rename docs files with dash connected

docs/examples/extract_single_peak.py → docs/examples/extract-single-peak.py

@@ -19,9 +19,9 @@
 parameters, running peak extraction, and saving the results.
 
 This script is equivalent to running
-srmise data/Ag_nyquist_qmax30.gr --range 2. 3.5 \
-    --baseline "Polynomial(degree=1)" --save output/extract_single_peak.srmise \
-    --pwa output/extract_single_peak.pwa --plot
+srmise data/Ag-nyquist-qmax30.gr --range 2. 3.5 \
+    --baseline "Polynomial(degree=1)" --save output/extract-single-peak.srmise \
+    --pwa output/extract-single-peak.pwa --plot
 at the command line.
 """
 
@@ -39,7 +39,7 @@ def run(plot=True):
     ppe = PDFPeakExtraction()
 
     # Load the PDF from a file
-    ppe.loadpdf("data/Ag_nyquist_qmax30.gr")
+    ppe.loadpdf("data/Ag-nyquist-qmax30.gr")
 
     # Set up extraction parameters.
     # For convenience, we add all parameters to a dictionary before passing them
@@ -74,8 +74,8 @@ def run(plot=True):
     # half-maximum), and area of extracted peaks.  The reported values
     # are for Gaussians in the radial distribution function (RDF) corresponding
     # to this PDF.
-    ppe.write("output/extract_single_peak.srmise")
-    ppe.writepwa("output/extract_single_peak.pwa")
+    ppe.write("output/extract-single-peak.srmise")
+    ppe.writepwa("output/extract-single-peak.pwa")
 
     # Plot results.
     # Display plot of extracted peak. It is also possible to plot an existing

docs/examples/fit_initial.py → docs/examples/fit-initial.py

@@ -34,7 +34,7 @@ def run(plot=True):
 
     # Initialize peak extraction
     ppe = PDFPeakExtraction()
-    ppe.loadpdf("data/C60_fine_qmax21.gr")
+    ppe.loadpdf("data/C60-fine-qmax21.gr")
 
     # Set up interpolated baseline.
     # The FromSequence baseline creates an interpolated baseline from provided
@@ -98,8 +98,8 @@ def run(plot=True):
     ppe.fit()
 
     # Save results
-    ppe.write("output/fit_initial.srmise")
-    ppe.writepwa("output/fit_initial.pwa")
+    ppe.write("output/fit-initial.srmise")
+    ppe.writepwa("output/fit-initial.pwa")
 
     if plot:
         plt.figure()

docs/examples/multimodel_known_dG1.py → docs/examples/multimodel-known-dG1.py

@@ -52,7 +52,7 @@ def run(plot=True):
 
     # Initialize peak extraction from saved trial
     ppe = PDFPeakExtraction()
-    ppe.read("output/query_results.srmise")
+    ppe.read("output/query-results.srmise")
     ppe.clearcalc()
 
     # Set up extraction parameters
@@ -78,13 +78,13 @@ def run(plot=True):
     ms.run(dgs)
 
     # Save results
-    # The file known_dG_models.dat saves the models generated above.  The file
-    # known_dG_aics.dat saves the value of the AIC of each model when evaluated
+    # The file known-dG-models.dat saves the models generated above.  The file
+    # known-dG-aics.dat saves the value of the AIC of each model when evaluated
     # on a Nyquist-sampled grid using each of the dg values used to generate
     # the models in the first place.
     dr = np.pi / ppe.qmax
-    ms.save("output/known_dG_models.dat")
-    ms.makeaics(dgs, dr, filename="output/known_dG_aics.dat")
+    ms.save("output/known-dG-models.dat")
+    ms.makeaics(dgs, dr, filename="output/known-dG-aics.dat")
 
 
 if __name__ == "__main__":

docs/examples/multimodel_known_dG2.py → docs/examples/multimodel-known-dG2.py

@@ -65,8 +65,8 @@ def run(plot=True):
 
     # Create multimodeling object and load diffpy.srmise results from file.
     ms = MultimodelSelection()
-    ms.load("output/known_dG_models.dat")
-    ms.loadaics("output/known_dG_aics.dat")
+    ms.load("output/known-dG-models.dat")
+    ms.loadaics("output/known-dG-aics.dat")
 
     # Use Nyquist sampling
     # Standard AIC analysis assumes the data have independent uncertainties.

docs/examples/multimodel_unknown_dG1.py → docs/examples/multimodel-unknown-dG1.py

@@ -52,7 +52,7 @@ def run(plot=True):
 
     # Initialize peak extraction
     ppe = PDFPeakExtraction()
-    ppe.loadpdf("data/C60_fine_qmax21.gr")
+    ppe.loadpdf("data/C60-fine-qmax21.gr")
 
     # Set up extraction parameters
     # The FromSequence baseline interpolates (r, G(r)) values read from a
@@ -87,8 +87,8 @@ def run(plot=True):
     # on a Nyquist-sampled grid using each of the dg values used to generate
     # the models in the first place.
     dr = np.pi / ppe.qmax
-    ms.save("output/unknown_dG_models.dat")
-    ms.makeaics(dgs, dr, filename="output/unknown_dG_aics.dat")
+    ms.save("output/unknown-dG-models.dat")
+    ms.makeaics(dgs, dr, filename="output/unknown-dG-aics.dat")
 
 
 if __name__ == "__main__":

docs/examples/multimodel_unknown_dG2.py → docs/examples/multimodel-unknown-dG2.py

@@ -80,8 +80,8 @@ def run(plot=True):
 
     # Create multimodeling object and load diffpy.srmise results from file.
     ms = MultimodelSelection()
-    ms.load("output/unknown_dG_models.dat")
-    ms.loadaics("output/unknown_dG_aics.dat")
+    ms.load("output/unknown-dG-models.dat")
+    ms.loadaics("output/unknown-dG-aics.dat")
 
     # Use Nyquist sampling
     # Standard AIC analysis assumes the data have independent uncertainties.

docs/examples/parameter_summary.py → docs/examples/parameter-summary.py

@@ -43,7 +43,7 @@ def run(plot=True):
     ppe = PDFPeakExtraction()
 
     # Load the PDF from a file
-    ppe.loadpdf("data/TiO2_fine_qmax26.gr")
+    ppe.loadpdf("data/TiO2-fine-qmax26.gr")
 
     # Set up extraction parameters.
     # In this section we'll examine the major extraction parameters in detail.
@@ -220,8 +220,8 @@ def run(plot=True):
     # half-maximum), and area of of extracted peaks.  The reported values
     # are for Gaussians in the radial distribution function (RDF) corresponding
     # to this PDF.
-    ppe.write("output/parameter_summary.srmise")
-    ppe.writepwa("output/parameter_summary.pwa")
+    ppe.write("output/parameter-summary.srmise")
+    ppe.writepwa("output/parameter-summary.pwa")
 
     # Plot results.
     # Display plot of extracted peak.  It is also possible to plot an existing

docs/examples/query_results.py → docs/examples/query-results.py

@@ -20,10 +20,10 @@
 to evaluate the model on an arbitrary grid.
 
 The peaks extracted by this script are equivalent to those obtained running
-srmise data/Ag_nyquist_qmax30.gr --range 2. 10. \
-    --bsrmise output/extract_single_peak.srmise \
-    --save output/query_results.srmise \
-    --pwa output/query_results.pwa --plot
+srmise data/Ag-nyquist-qmax30.gr --range 2. 10. \
+    --bsrmise output/extract-single-peak.srmise \
+    --save output/query-results.srmise \
+    --pwa output/query-results.pwa --plot
 at the command line.
 """
 
@@ -41,13 +41,13 @@ def run(plot=True):
     ppe = PDFPeakExtraction()
 
     # Load the PDF from a file
-    ppe.loadpdf("data/Ag_nyquist_qmax30.gr")
+    ppe.loadpdf("data/Ag-nyquist-qmax30.gr")
 
     # Obtain baseline from a saved diffpy.srmise trial.  This is not the
     # initial baseline estimate from the previous example, but the baseline
     # after both it and the extracted peaks have been fit to the data.
     ppebl = PDFPeakExtraction()
-    ppebl.read("output/extract_single_peak.srmise")
+    ppebl.read("output/extract-single-peak.srmise")
     baseline = ppebl.extracted.baseline
 
     # Set up extraction parameters.
@@ -196,8 +196,8 @@ def run(plot=True):
     print("%i: %f" % (total_ideal_intensity, total_observed_intensity))
 
     # Save output
-    ppe.write("output/query_results.srmise")
-    ppe.writepwa("output/query_results.pwa")
+    ppe.write("output/query-results.srmise")
+    ppe.writepwa("output/query-results.pwa")
 
     # Evaluating a model.
     # Although the ModelCovariance object is useful, the model used for fitting

docs/source/tutorial/abbreviations.txt

@@ -10,18 +10,18 @@
 .. |tar.gz| replace:: :source-release:`tar.gz`
 
 .. Image substitutions
-.. |images/extract_single_peak1.png| image:: ../../examples/images/extract_single_peak1.png
-.. |images/extract_single_peak2.png| image:: ../../examples/images/extract_single_peak2.png
-.. |images/extract_single_peak3.png| image:: ../../examples/images/extract_single_peak3.png
-.. |images/parameter_summary1.png| image:: ../../examples/images/parameter_summary1.png
-.. |images/parameter_summary2.png| image:: ../../examples/images/parameter_summary2.png
-.. |images/parameter_summary3.png| image:: ../../examples/images/parameter_summary3.png
-.. |images/parameter_summary4.png| image:: ../../examples/images/parameter_summary4.png
-.. |images/fit_initial1.png| image:: ../../examples/images/fit_initial1.png
-.. |images/fit_initial2.png| image:: ../../examples/images/fit_initial2.png
-.. |images/query_results1.png| image:: ../../examples/images/query_results1.png
-.. |images/query_results2.png| image:: ../../examples/images/query_results2.png
-.. |images/query_results3.png| image:: ../../examples/images/query_results3.png
+.. |images/extract_single_peak1.png| image:: ../../examples/images/extract-single-peak1.png
+.. |images/extract_single_peak2.png| image:: ../../examples/images/extract-single-peak2.png
+.. |images/extract_single_peak3.png| image:: ../../examples/images/extract-single-peak3.png
+.. |images/parameter_summary1.png| image:: ../../examples/images/parameter-summary1.png
+.. |images/parameter_summary2.png| image:: ../../examples/images/parameter-summary2.png
+.. |images/parameter_summary3.png| image:: ../../examples/images/parameter-summary3.png
+.. |images/parameter_summary4.png| image:: ../../examples/images/parameter-summary4.png
+.. |images/fit_initial1.png| image:: ../../examples/images/fit-initial1.png
+.. |images/fit_initial2.png| image:: ../../examples/images/fit-initial2.png
+.. |images/query_results1.png| image:: ../../examples/images/query-results1.png
+.. |images/query_results2.png| image:: ../../examples/images/query-results2.png
+.. |images/query_results3.png| image:: ../../examples/images/query-results3.png
 
 .. External links
 .. _ParSCAPE algorithm: https://dx.doi.org/10.1107/S2053273315005276
@@ -38,5 +38,5 @@
 .. |d_c| replace:: d\ :sub:`c`
 .. |pi/Qmax| replace:: π/Q\ :sub:`max`
 
-.. Links to PDF information defined in sample_links.txt
+.. Links to PDF information defined in sample-links.txt
 .. |Extending SrMise| replace:: :ref:`extending-srmise`

docs/source/tutorial/extract_single_peak.rst → docs/source/tutorial/extract-single-peak.rst

@@ -1,6 +1,6 @@
 .. include:: abbreviations.txt
 
-.. include:: sample_links.txt
+.. include:: sample-links.txt
 
 
 .. include:: ../../examples/README.rst
@@ -13,4 +13,4 @@
 Script (extract_single_peak.py)
 -------------------------------
 
-.. literalinclude:: ../../examples/extract_single_peak.py
+.. literalinclude:: ../../examples/extract-single-peak.py

docs/source/tutorial/fit_initial.rst → docs/source/tutorial/fit-initial.rst

@@ -1,6 +1,6 @@
 .. include:: abbreviations.txt
 
-.. include:: sample_links.txt
+.. include:: sample-links.txt
 
 
 .. include:: ../../examples/README.rst
@@ -13,4 +13,4 @@
 Script (fit_initial.py)
 ---------------------------
 
-.. literalinclude:: ../../examples/fit_initial.py
+.. literalinclude:: ../../examples/fit-initial.py

docs/source/tutorial/index.rst

@@ -15,12 +15,12 @@ Tutorial
 .. toctree::
    :maxdepth: 1
 
-   extract_single_peak
-   parameter_summary
-   fit_initial
-   query_results
-   multimodel_known_uncertainties
-   multimodel_unknown_uncertainties
+   extract-single-peak
+   parameter-summary
+   fit-initial
+   query-results
+   multimodel-known-uncertainties
+   multimodel-unknown-uncertainties
 
 
 .. Now add information about the samples

docs/source/tutorial/multimodel-known-uncertainties.rst

@@ -0,0 +1,25 @@
+.. include:: abbreviations.txt
+
+.. include:: sample-links.txt
+
+
+.. include:: ../../examples/README.rst
+   :start-after: ~Example 5~
+   :end-before: ~Example 6~
+
+
+
+.. _multimodel-known-dG1.py:
+
+Extraction Script (multimodel-known-dG1.py)
+---------------------------------------------
+
+.. literalinclude:: ../../examples/multimodel-known-dG1.py
+
+
+.. _multimodel-known-dG2.py:
+
+Analysis Script (multimodel-known-dG2.py)
+-----------------------------------------
+
+.. literalinclude:: ../../examples/multimodel-known-dG2.py

docs/source/tutorial/multimodel-unknown-uncertainties.rst

@@ -0,0 +1,25 @@
+.. include:: abbreviations.txt
+
+.. include:: sample_links.txt
+
+
+.. include:: ../../examples/README.rst
+   :start-after: ~Example 6~
+   :end-before: ~PDF Info~
+
+
+
+.. _multimodel-unknown-dG1.py:
+
+Extraction Script (multimodel-unknown-dG1.py)
+---------------------------------------------
+
+.. literalinclude:: ../../examples/multimodel-unknown-dG1.py
+
+
+.. _multimodel-unknown-dG2.py:
+
+Analysis Script (multimodel-unknown-dG2.py)
+-------------------------------------------
+
+.. literalinclude:: ../../examples/multimodel-unknown-dG2.py

docs/source/tutorial/parameter_summary.rst → docs/source/tutorial/parameter-summary.rst

@@ -1,16 +1,16 @@
 .. include:: abbreviations.txt
 
-.. include:: sample_links.txt
+.. include:: sample-links.txt
 
 
 .. include:: ../../examples/README.rst
    :start-after: ~Example 2~
    :end-before: ~Example 3~
 
 
-.. _parameter_summary.py:
+.. _parameter-summary.py:
 
-Script (parameter_summary.py)
+Script (parameter-summary.py)
 -----------------------------
 
-.. literalinclude:: ../../examples/parameter_summary.py
+.. literalinclude:: ../../examples/parameter-summary.py