From 272c3f36b42d2db9cb3eb6d0347adcde8187b7b0 Mon Sep 17 00:00:00 2001
From: Tieqiong Zhang
Date: Thu, 16 Jan 2025 02:10:02 -0500
Subject: [PATCH] fix: fix online manual imag and doc links
---
doc/manual/html/readme.txt | 2 -
doc/{source => manual}/images/Makefile | 0
doc/{source => manual}/images/eq-01.png | Bin
doc/{source => manual}/images/eq-02.png | Bin
doc/{source => manual}/images/fig2-01.png | Bin
doc/{source => manual}/images/fig2-02.png | Bin
doc/{source => manual}/images/fig2-03.png | Bin
doc/{source => manual}/images/fig2-04.png | Bin
doc/{source => manual}/images/fig2-05.png | Bin
doc/{source => manual}/images/fig2-06.png | Bin
doc/{source => manual}/images/fig2-07.png | Bin
doc/{source => manual}/images/fig2-08.png | Bin
doc/{source => manual}/images/fig2-09.png | Bin
doc/{source => manual}/images/fig2-10.png | Bin
doc/{source => manual}/images/fig2-11.png | Bin
doc/{source => manual}/images/fig3-01.png | Bin
doc/{source => manual}/images/fig3-02.png | Bin
doc/{source => manual}/images/fig3-03.png | Bin
doc/{source => manual}/images/fig3-04.png | Bin
doc/{source => manual}/images/fig3-05.png | Bin
doc/{source => manual}/images/fig3-06.png | Bin
doc/{source => manual}/images/fig3-07.png | Bin
doc/{source => manual}/images/fig3-08.png | Bin
doc/{source => manual}/images/fig3-09.png | Bin
doc/{source => manual}/images/fig3-10.png | Bin
doc/{source => manual}/images/fig4-01.png | Bin
doc/{source => manual}/images/fig4-02.png | Bin
.../images/originals/fig2-01.png | Bin
.../images/originals/fig2-01.xcf | Bin
.../images/originals/fig2-02.png | Bin
.../images/originals/fig2-03.png | Bin
.../images/originals/fig2-04.png | Bin
.../images/originals/fig2-05.png | Bin
.../images/originals/fig2-06.png | Bin
.../images/originals/fig2-07.png | Bin
.../images/originals/fig2-08.png | Bin
.../images/originals/fig2-09.png | Bin
.../images/originals/fig2-10.png | Bin
.../images/originals/fig2-11.png | Bin
.../images/originals/fig3-01.png | Bin
.../images/originals/fig3-02.png | Bin
.../images/originals/fig3-03.png | Bin
.../images/originals/fig3-04.png | Bin
.../images/originals/fig3-05.png | Bin
.../images/originals/fig3-06.png | Bin
.../images/originals/fig3-07.png | Bin
.../images/originals/fig3-08.png | Bin
.../images/originals/fig3-09.png | Bin
.../images/originals/fig3-10.png | Bin
.../images/originals/fig4-01.png | Bin
.../images/originals/fig4-02.png | Bin
doc/manual/{html => }/pdfgui.html | 56 +++++++++---------
doc/manual/pdfgui.texinfo | 2 +-
doc/source/conf.py | 2 +-
doc/source/manual.rst | 2 +-
news/html.rst | 23 +++++++
56 files changed, 53 insertions(+), 34 deletions(-)
delete mode 100644 doc/manual/html/readme.txt
rename doc/{source => manual}/images/Makefile (100%)
rename doc/{source => manual}/images/eq-01.png (100%)
rename doc/{source => manual}/images/eq-02.png (100%)
rename doc/{source => manual}/images/fig2-01.png (100%)
rename doc/{source => manual}/images/fig2-02.png (100%)
rename doc/{source => manual}/images/fig2-03.png (100%)
rename doc/{source => manual}/images/fig2-04.png (100%)
rename doc/{source => manual}/images/fig2-05.png (100%)
rename doc/{source => manual}/images/fig2-06.png (100%)
rename doc/{source => manual}/images/fig2-07.png (100%)
rename doc/{source => manual}/images/fig2-08.png (100%)
rename doc/{source => manual}/images/fig2-09.png (100%)
rename doc/{source => manual}/images/fig2-10.png (100%)
rename doc/{source => manual}/images/fig2-11.png (100%)
rename doc/{source => manual}/images/fig3-01.png (100%)
rename doc/{source => manual}/images/fig3-02.png (100%)
rename doc/{source => manual}/images/fig3-03.png (100%)
rename doc/{source => manual}/images/fig3-04.png (100%)
rename doc/{source => manual}/images/fig3-05.png (100%)
rename doc/{source => manual}/images/fig3-06.png (100%)
rename doc/{source => manual}/images/fig3-07.png (100%)
rename doc/{source => manual}/images/fig3-08.png (100%)
rename doc/{source => manual}/images/fig3-09.png (100%)
rename doc/{source => manual}/images/fig3-10.png (100%)
rename doc/{source => manual}/images/fig4-01.png (100%)
rename doc/{source => manual}/images/fig4-02.png (100%)
rename doc/{source => manual}/images/originals/fig2-01.png (100%)
rename doc/{source => manual}/images/originals/fig2-01.xcf (100%)
rename doc/{source => manual}/images/originals/fig2-02.png (100%)
rename doc/{source => manual}/images/originals/fig2-03.png (100%)
rename doc/{source => manual}/images/originals/fig2-04.png (100%)
rename doc/{source => manual}/images/originals/fig2-05.png (100%)
rename doc/{source => manual}/images/originals/fig2-06.png (100%)
rename doc/{source => manual}/images/originals/fig2-07.png (100%)
rename doc/{source => manual}/images/originals/fig2-08.png (100%)
rename doc/{source => manual}/images/originals/fig2-09.png (100%)
rename doc/{source => manual}/images/originals/fig2-10.png (100%)
rename doc/{source => manual}/images/originals/fig2-11.png (100%)
rename doc/{source => manual}/images/originals/fig3-01.png (100%)
rename doc/{source => manual}/images/originals/fig3-02.png (100%)
rename doc/{source => manual}/images/originals/fig3-03.png (100%)
rename doc/{source => manual}/images/originals/fig3-04.png (100%)
rename doc/{source => manual}/images/originals/fig3-05.png (100%)
rename doc/{source => manual}/images/originals/fig3-06.png (100%)
rename doc/{source => manual}/images/originals/fig3-07.png (100%)
rename doc/{source => manual}/images/originals/fig3-08.png (100%)
rename doc/{source => manual}/images/originals/fig3-09.png (100%)
rename doc/{source => manual}/images/originals/fig3-10.png (100%)
rename doc/{source => manual}/images/originals/fig4-01.png (100%)
rename doc/{source => manual}/images/originals/fig4-02.png (100%)
rename doc/manual/{html => }/pdfgui.html (99%)
create mode 100644 news/html.rst
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%
rename from doc/source/images/eq-01.png
rename to doc/manual/images/eq-01.png
diff --git a/doc/source/images/eq-02.png b/doc/manual/images/eq-02.png
similarity index 100%
rename from doc/source/images/eq-02.png
rename to doc/manual/images/eq-02.png
diff --git a/doc/source/images/fig2-01.png b/doc/manual/images/fig2-01.png
similarity index 100%
rename from doc/source/images/fig2-01.png
rename to doc/manual/images/fig2-01.png
diff --git a/doc/source/images/fig2-02.png b/doc/manual/images/fig2-02.png
similarity index 100%
rename from doc/source/images/fig2-02.png
rename to doc/manual/images/fig2-02.png
diff --git a/doc/source/images/fig2-03.png b/doc/manual/images/fig2-03.png
similarity index 100%
rename from doc/source/images/fig2-03.png
rename to doc/manual/images/fig2-03.png
diff --git a/doc/source/images/fig2-04.png b/doc/manual/images/fig2-04.png
similarity index 100%
rename from doc/source/images/fig2-04.png
rename to doc/manual/images/fig2-04.png
diff --git a/doc/source/images/fig2-05.png b/doc/manual/images/fig2-05.png
similarity index 100%
rename from doc/source/images/fig2-05.png
rename to doc/manual/images/fig2-05.png
diff --git a/doc/source/images/fig2-06.png b/doc/manual/images/fig2-06.png
similarity index 100%
rename from doc/source/images/fig2-06.png
rename to doc/manual/images/fig2-06.png
diff --git a/doc/source/images/fig2-07.png b/doc/manual/images/fig2-07.png
similarity index 100%
rename from doc/source/images/fig2-07.png
rename to doc/manual/images/fig2-07.png
diff --git a/doc/source/images/fig2-08.png b/doc/manual/images/fig2-08.png
similarity index 100%
rename from doc/source/images/fig2-08.png
rename to doc/manual/images/fig2-08.png
diff --git a/doc/source/images/fig2-09.png b/doc/manual/images/fig2-09.png
similarity index 100%
rename from doc/source/images/fig2-09.png
rename to doc/manual/images/fig2-09.png
diff --git a/doc/source/images/fig2-10.png b/doc/manual/images/fig2-10.png
similarity index 100%
rename from doc/source/images/fig2-10.png
rename to doc/manual/images/fig2-10.png
diff --git a/doc/source/images/fig2-11.png b/doc/manual/images/fig2-11.png
similarity index 100%
rename from doc/source/images/fig2-11.png
rename to doc/manual/images/fig2-11.png
diff --git a/doc/source/images/fig3-01.png b/doc/manual/images/fig3-01.png
similarity index 100%
rename from doc/source/images/fig3-01.png
rename to doc/manual/images/fig3-01.png
diff --git a/doc/source/images/fig3-02.png b/doc/manual/images/fig3-02.png
similarity index 100%
rename from doc/source/images/fig3-02.png
rename to doc/manual/images/fig3-02.png
diff --git a/doc/source/images/fig3-03.png b/doc/manual/images/fig3-03.png
similarity index 100%
rename from doc/source/images/fig3-03.png
rename to doc/manual/images/fig3-03.png
diff --git a/doc/source/images/fig3-04.png b/doc/manual/images/fig3-04.png
similarity index 100%
rename from doc/source/images/fig3-04.png
rename to doc/manual/images/fig3-04.png
diff --git a/doc/source/images/fig3-05.png b/doc/manual/images/fig3-05.png
similarity index 100%
rename from doc/source/images/fig3-05.png
rename to doc/manual/images/fig3-05.png
diff --git a/doc/source/images/fig3-06.png b/doc/manual/images/fig3-06.png
similarity index 100%
rename from doc/source/images/fig3-06.png
rename to doc/manual/images/fig3-06.png
diff --git a/doc/source/images/fig3-07.png b/doc/manual/images/fig3-07.png
similarity index 100%
rename from doc/source/images/fig3-07.png
rename to doc/manual/images/fig3-07.png
diff --git a/doc/source/images/fig3-08.png b/doc/manual/images/fig3-08.png
similarity index 100%
rename from doc/source/images/fig3-08.png
rename to doc/manual/images/fig3-08.png
diff --git a/doc/source/images/fig3-09.png b/doc/manual/images/fig3-09.png
similarity index 100%
rename from doc/source/images/fig3-09.png
rename to doc/manual/images/fig3-09.png
diff --git a/doc/source/images/fig3-10.png b/doc/manual/images/fig3-10.png
similarity index 100%
rename from doc/source/images/fig3-10.png
rename to doc/manual/images/fig3-10.png
diff --git a/doc/source/images/fig4-01.png b/doc/manual/images/fig4-01.png
similarity index 100%
rename from doc/source/images/fig4-01.png
rename to doc/manual/images/fig4-01.png
diff --git a/doc/source/images/fig4-02.png b/doc/manual/images/fig4-02.png
similarity index 100%
rename from doc/source/images/fig4-02.png
rename to doc/manual/images/fig4-02.png
diff --git a/doc/source/images/originals/fig2-01.png b/doc/manual/images/originals/fig2-01.png
similarity index 100%
rename from doc/source/images/originals/fig2-01.png
rename to doc/manual/images/originals/fig2-01.png
diff --git a/doc/source/images/originals/fig2-01.xcf b/doc/manual/images/originals/fig2-01.xcf
similarity index 100%
rename from doc/source/images/originals/fig2-01.xcf
rename to doc/manual/images/originals/fig2-01.xcf
diff --git a/doc/source/images/originals/fig2-02.png b/doc/manual/images/originals/fig2-02.png
similarity index 100%
rename from doc/source/images/originals/fig2-02.png
rename to doc/manual/images/originals/fig2-02.png
diff --git a/doc/source/images/originals/fig2-03.png b/doc/manual/images/originals/fig2-03.png
similarity index 100%
rename from doc/source/images/originals/fig2-03.png
rename to doc/manual/images/originals/fig2-03.png
diff --git a/doc/source/images/originals/fig2-04.png b/doc/manual/images/originals/fig2-04.png
similarity index 100%
rename from doc/source/images/originals/fig2-04.png
rename to doc/manual/images/originals/fig2-04.png
diff --git a/doc/source/images/originals/fig2-05.png b/doc/manual/images/originals/fig2-05.png
similarity index 100%
rename from doc/source/images/originals/fig2-05.png
rename to doc/manual/images/originals/fig2-05.png
diff --git a/doc/source/images/originals/fig2-06.png b/doc/manual/images/originals/fig2-06.png
similarity index 100%
rename from doc/source/images/originals/fig2-06.png
rename to doc/manual/images/originals/fig2-06.png
diff --git a/doc/source/images/originals/fig2-07.png b/doc/manual/images/originals/fig2-07.png
similarity index 100%
rename from doc/source/images/originals/fig2-07.png
rename to doc/manual/images/originals/fig2-07.png
diff --git a/doc/source/images/originals/fig2-08.png b/doc/manual/images/originals/fig2-08.png
similarity index 100%
rename from doc/source/images/originals/fig2-08.png
rename to doc/manual/images/originals/fig2-08.png
diff --git a/doc/source/images/originals/fig2-09.png b/doc/manual/images/originals/fig2-09.png
similarity index 100%
rename from doc/source/images/originals/fig2-09.png
rename to doc/manual/images/originals/fig2-09.png
diff --git a/doc/source/images/originals/fig2-10.png b/doc/manual/images/originals/fig2-10.png
similarity index 100%
rename from doc/source/images/originals/fig2-10.png
rename to doc/manual/images/originals/fig2-10.png
diff --git a/doc/source/images/originals/fig2-11.png b/doc/manual/images/originals/fig2-11.png
similarity index 100%
rename from doc/source/images/originals/fig2-11.png
rename to doc/manual/images/originals/fig2-11.png
diff --git a/doc/source/images/originals/fig3-01.png b/doc/manual/images/originals/fig3-01.png
similarity index 100%
rename from doc/source/images/originals/fig3-01.png
rename to doc/manual/images/originals/fig3-01.png
diff --git a/doc/source/images/originals/fig3-02.png b/doc/manual/images/originals/fig3-02.png
similarity index 100%
rename from doc/source/images/originals/fig3-02.png
rename to doc/manual/images/originals/fig3-02.png
diff --git a/doc/source/images/originals/fig3-03.png b/doc/manual/images/originals/fig3-03.png
similarity index 100%
rename from doc/source/images/originals/fig3-03.png
rename to doc/manual/images/originals/fig3-03.png
diff --git a/doc/source/images/originals/fig3-04.png b/doc/manual/images/originals/fig3-04.png
similarity index 100%
rename from doc/source/images/originals/fig3-04.png
rename to doc/manual/images/originals/fig3-04.png
diff --git a/doc/source/images/originals/fig3-05.png b/doc/manual/images/originals/fig3-05.png
similarity index 100%
rename from doc/source/images/originals/fig3-05.png
rename to doc/manual/images/originals/fig3-05.png
diff --git a/doc/source/images/originals/fig3-06.png b/doc/manual/images/originals/fig3-06.png
similarity index 100%
rename from doc/source/images/originals/fig3-06.png
rename to doc/manual/images/originals/fig3-06.png
diff --git a/doc/source/images/originals/fig3-07.png b/doc/manual/images/originals/fig3-07.png
similarity index 100%
rename from doc/source/images/originals/fig3-07.png
rename to doc/manual/images/originals/fig3-07.png
diff --git a/doc/source/images/originals/fig3-08.png b/doc/manual/images/originals/fig3-08.png
similarity index 100%
rename from doc/source/images/originals/fig3-08.png
rename to doc/manual/images/originals/fig3-08.png
diff --git a/doc/source/images/originals/fig3-09.png b/doc/manual/images/originals/fig3-09.png
similarity index 100%
rename from doc/source/images/originals/fig3-09.png
rename to doc/manual/images/originals/fig3-09.png
diff --git a/doc/source/images/originals/fig3-10.png b/doc/manual/images/originals/fig3-10.png
similarity index 100%
rename from doc/source/images/originals/fig3-10.png
rename to doc/manual/images/originals/fig3-10.png
diff --git a/doc/source/images/originals/fig4-01.png b/doc/manual/images/originals/fig4-01.png
similarity index 100%
rename from doc/source/images/originals/fig4-01.png
rename to doc/manual/images/originals/fig4-01.png
diff --git a/doc/source/images/originals/fig4-02.png b/doc/manual/images/originals/fig4-02.png
similarity index 100%
rename from doc/source/images/originals/fig4-02.png
rename to doc/manual/images/originals/fig4-02.png
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 8d7eaacd..50c9c499 100644
--- a/doc/manual/html/pdfgui.html
+++ b/doc/manual/pdfgui.html
@@ -1793,7 +1793,7 @@
-
![images/fig2-01](../../source/images/fig2-01.png)
+
-
![images/fig2-02](../../source/images/fig2-02.png)
+
-
![images/fig2-03](../../source/images/fig2-03.png)
+
Figure 2.3: Adjusting data set related configuration.
@@ -1914,7 +1914,7 @@
-
![images/fig2-04](../../source/images/fig2-04.png)
+
-
![images/fig2-05](../../source/images/fig2-05.png)
+
-
![images/fig2-06](../../source/images/fig2-06.png)
+
Figure 2.6: Reviewing the fit parameters and conditions.
@@ -1993,7 +1993,7 @@
-
![images/fig2-07](../../source/images/fig2-07.png)
+
-
![images/fig2-08](../../source/images/fig2-08.png)
+
-
![images/fig2-09](../../source/images/fig2-09.png)
+
-
![images/fig2-10](../../source/images/fig2-10.png)
+
-
![images/fig2-11](../../source/images/fig2-11.png)
+
3.1 Building structure model using crystal symmetry
-
![images/fig3-01](../../source/images/fig3-01.png)
+
3.1 Building structure model using crystal symmetry
-
![images/fig3-02](../../source/images/fig3-02.png)
+
3.2 Calculating PDF from a structure
-
![images/fig3-03](../../source/images/fig3-03.png)
+
3.3.1 Multistage fitting
-
![images/fig3-04](../../source/images/fig3-04.png)
+
3.3.2 Sequential fitting of incremental r-series
-
![images/fig3-05](../../source/images/fig3-05.png)
+
3.3.3 Sequential fitting of temperature series
-
![images/fig3-06](../../source/images/fig3-06.png)
+
3.3.3 Sequential fitting of temperature series
-
![images/fig3-07](../../source/images/fig3-07.png)
+
3.3.4 Sequential fitting of doping series
-
![images/fig3-08](../../source/images/fig3-08.png)
+
3.3.4 Sequential fitting of doping series
-
![images/fig3-09](../../source/images/fig3-09.png)
+
To learn more about the tui module and about the objects and functions
that it returns, please see the API documentation for diffpy.pdfgui at
- http://docs.danse.us/diffraction/diffpy.pdfgui/https://diffpy.github.io/diffpy.pdfgui.
@@ -3342,7 +3342,7 @@
3.4 Nanoparticle structure
-
![images/fig3-10](../../source/images/fig3-10.png)
+
4.1 PDF plotting
-
![images/fig4-01](../../source/images/fig4-01.png)
+
4.2 Displaying the structure
-
![images/fig4-02](../../source/images/fig4-02.png)
+
Renamed variables
applied when equal to zero. The Gaussian envelope is of the form
-
+
@@ -4366,9 +4366,7 @@ 5.4 PDF peak width
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
-
-
-
+ ![images/eq-02.png](images/eq-02.png)
Here the primed sigma is the peak width without correlation, which is
computed from the anisotropic displacement parameters. The first two terms
diff --git a/doc/manual/pdfgui.texinfo b/doc/manual/pdfgui.texinfo
index 8c79bbe7..14bd3834 100644
--- a/doc/manual/pdfgui.texinfo
+++ b/doc/manual/pdfgui.texinfo
@@ -1446,7 +1446,7 @@ the comments in the script for detailed explanation.
To learn more about the tui module and about the objects
and functions that it returns, please see the API
documentation for diffpy.pdfgui at
-@url{http://docs.danse.us/diffraction/diffpy.pdfgui/}.
+@url{https://diffpy.github.io/diffpy.pdfgui}.
Feel free to ask at the
@url{https://groups.google.com/d/forum/diffpy-users, diffpy-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/html.rst b/news/html.rst
new file mode 100644
index 00000000..176aaf08
--- /dev/null
+++ b/news/html.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+*
+
+**Changed:**
+
+*
+
+**Deprecated:**
+
+*
+
+**Removed:**
+
+*
+
+**Fixed:**
+
+* Fixed online manual not showing images.
+
+**Security:**
+
+*