diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml
index e56e7010..38f24b62 100644
--- a/.github/workflows/publish-docs-on-release.yml
+++ b/.github/workflows/publish-docs-on-release.yml
@@ -1,6 +1,7 @@
name: Deploy Documentation on Release
on:
+ push:
release:
types: [published]
workflow_dispatch:
diff --git a/doc/manual/html/readme.txt b/doc/manual/html/readme.txt
deleted file mode 100644
index cf60cf43..00000000
--- a/doc/manual/html/readme.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-This directory need to be relatively the same as doc/build/html/manual from
-doc/source/_static/images
diff --git a/doc/source/images/Makefile b/doc/manual/images/Makefile
similarity index 100%
rename from doc/source/images/Makefile
rename to doc/manual/images/Makefile
diff --git a/doc/source/images/eq-01.png b/doc/manual/images/eq-01.png
similarity index 100%
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diff --git a/doc/source/images/eq-02.png b/doc/manual/images/eq-02.png
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diff --git a/doc/source/images/fig2-01.png b/doc/manual/images/fig2-01.png
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similarity index 100%
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similarity index 100%
rename from doc/source/images/originals/fig4-01.png
rename to doc/manual/images/originals/fig4-01.png
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diff --git a/doc/manual/html/pdfgui.html b/doc/manual/pdfgui.html
similarity index 99%
rename from doc/manual/html/pdfgui.html
rename to doc/manual/pdfgui.html
index 5c4a963f..24219aeb 100644
--- a/doc/manual/html/pdfgui.html
+++ b/doc/manual/pdfgui.html
@@ -1069,7 +1069,7 @@ 2.2 Creating a simple fit using a preexisting structure file
exercise a preexisting structure file Ni.stru is to be loaded.
-
+
Figure 2.1: PDFgui window with fit tree and Plot Control panels to the left and
current action panel to the right. The fit tree panel features the current fit
@@ -1103,7 +1103,7 @@ 2.2 Creating a simple fit using a preexisting structure file
were collected at 300 K.
-
+
Figure 2.2: Appearance of a PDFgui window after a PDF dataset is loaded. The Fit
Tree panel features the current fit, loaded Ni structure, and loaded Ni PDF
@@ -1137,7 +1137,7 @@ 2.2 Creating a simple fit using a preexisting structure file
rightmost “quick-plot” button in the tool bar.
-
+
Figure 2.3: Adjusting data set related configuration.
@@ -1168,7 +1168,7 @@
2.2 Creating a simple fit using a preexisting structure file
Figure 2.4.
-
+
Figure 2.4: Setting up the refinement parameters and constraints.
@@ -1187,7 +1187,7 @@
2.2 Creating a simple fit using a preexisting structure file
-
+
Figure 2.5: Setting up the refinement parameters and constraints.
@@ -1210,7 +1210,7 @@
2.2 Creating a simple fit using a preexisting structure file
that the parameter assignment is done correctly.
-
+
Figure 2.6: Reviewing the fit parameters and conditions.
@@ -1231,7 +1231,7 @@
2.2 Creating a simple fit using a preexisting structure file
illustrated in Figure 2.7.
-
+
Figure 2.7: While the refinement is running, the refinement progress is
displayed in the PDFfit2 Output panel.
@@ -1252,7 +1252,7 @@ 2.2 Creating a simple fit using a preexisting structure file
may make it difficult to reproduce the fit.
-
+
Figure 2.8: Updating the set of initial values of refined parameters.
@@ -1267,13 +1267,13 @@
2.2 Creating a simple fit using a preexisting structure file
fitting is in progress, the content will be updated after each fit iteration.
-
+
Figure 2.9: An example of PDFgui plotting capabilities: displaying a fit.
-
+
Figure 2.10: An example of PDFgui plotting capabilities: displaying a parameter.
@@ -1284,7 +1284,7 @@
2.2 Creating a simple fit using a preexisting structure file
file, or saved along with the entire project for future reference.
-
+
Figure 2.11: Using “Journal” feature can be a convenient way for taking notes.
@@ -1406,7 +1406,7 @@
3.1 Building structure model using crystal symmetry
sites with the proper symmetry.
-
+
Figure 3.1: Expanding the unit cell using space group information.
@@ -1435,7 +1435,7 @@
3.1 Building structure model using crystal symmetry
identical to these described in Creating a simple fit using a preexisting structure file.
-
+
Figure 3.2: Setting up symmetry constraints to be used in a refinement.
@@ -1472,7 +1472,7 @@
3.2 Calculating PDF from a structure
set is loaded, as shown in Figure 3.3.
-
+
Figure 3.3: An example of the calculation configuration panel.
@@ -1582,7 +1582,7 @@
3.3.1 Multistage fitting
parameter is not yet refined. An example of this is shown in Figure 3.4.
-
+
Figure 3.4: An example of linked fits. The output of a converged fit will
be fed into the succeeding fit in the sequence as an input.
@@ -1678,7 +1678,7 @@ 3.3.2 Sequential fitting of incremental r-series
is done, you can review the results using the plot control.
-
+
Figure 3.5: Appearance of the setup panel for specifying an incremental r-series
fit conditions.
@@ -1741,7 +1741,7 @@ 3.3.3 Sequential fitting of temperature series
The data can be ordered by temperature by clicking the “Temperature” header.
-
+
Figure 3.6: Setting up a T-series sequential refinement for LaMnO3. Ordering
by temperature will ensure that the fits are linked correctly.
@@ -1768,7 +1768,7 @@ 3.3.3 Sequential fitting of temperature series
the plot of Uiso(20) vs T.
-
+
Figure 3.7: Displaying the refinement results as a function of external
parameter: T-series refinement of LaMnO3, example of isotropic ADP of
@@ -1828,7 +1828,7 @@ 3.3.4 Sequential fitting of doping series
previous example.
-
+
Figure 3.8: After loading of the Ca-doping data series of LaMnO3 system, proper
doping assignment needs to be carried out, as the doping levels introspected
@@ -1872,7 +1872,7 @@ 3.3.4 Sequential fitting of doping series
sequential refinement of the doping series.
-
+
Figure 3.9: Sequence of refined parameters, such as lattice constants, can be
plotted vs doping using PDFgui plotting facilities. Figure features lattice
@@ -2049,7 +2049,7 @@ 3.4 Nanoparticle structure
Quantitative size-dependent structure and strain determination of CdSe nanoparticles using atomic pair distribution function analysis.
-
+
Figure 3.10: Fitting the structure of a nanoparticle: 3nm CdSe
nanoparticle example.
@@ -2141,7 +2141,7 @@ 4.1 PDF plotting
-
+
Figure 4.1: Plotting window featuring Rw vs refinement step for Ni example.
The basic functionality for manipulating the plot is provided through icons
@@ -2185,7 +2185,7 @@ 4.2 Displaying the structure
An example Ni structure visualization with AtomEye is shown in Figure 4.2.
-
+
Figure 4.2: Using AtomEye functionality (if installed on your system) for 3D
visualization of the initial and refined PDF structures: example of Ni
@@ -2511,7 +2511,7 @@ Renamed variables
(float Å^-1, default 0 Å^-1, qsig in PDFFIT)
PDF Gaussian dampening envelope due to limited Q-resolution.
Not applied when equal to zero. The Gaussian envelope is of the form
-
+
- Dataset: qbroad
@@ -2627,7 +2627,7 @@ 5.4 PDF peak width
the motion can be strongly correlated leading to a sharpening of the first
peak(s) in the observed PDF. PDFfit2 provides three different correction terms
for the PDF peak width. The final width is given by
-
+
Here the primed sigma is the peak width without correlation, which is
computed from the anisotropic displacement parameters. The first two terms
correct for the effects of correlated motion. Within the scope of the users
diff --git a/doc/source/conf.py b/doc/source/conf.py
index cc57882a..e4d1788a 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -158,7 +158,7 @@
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
-# html_extra_path = []
+html_extra_path = ["../manual"]
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
diff --git a/doc/source/manual.rst b/doc/source/manual.rst
index 9667d818..158bda6e 100644
--- a/doc/source/manual.rst
+++ b/doc/source/manual.rst
@@ -13,4 +13,4 @@ Resources used
- :download:`Nanoparticle structure `
.. raw:: html
- :file: ../manual/html/pdfgui.html
+ :file: ../manual/pdfgui.html
diff --git a/news/doc.rst b/news/doc.rst
new file mode 100644
index 00000000..176aaf08
--- /dev/null
+++ b/news/doc.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+*
+
+**Changed:**
+
+*
+
+**Deprecated:**
+
+*
+
+**Removed:**
+
+*
+
+**Fixed:**
+
+* Fixed online manual not showing images.
+
+**Security:**
+
+*