Merge pull request #702 from nexusformat/Ticket663_use_gh_pages

Ticket663 use gh pages
nexusformat · Jan 23, 2020 · 622ebff · 622ebff
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-* NeXus: http://www.nexusformat.org/
+* NeXus: https://www.nexusformat.org/
 * citation: [![DOI](https://zenodo.org/badge/19377430.svg)](https://zenodo.org/badge/latestdoi/19377430) (DOI: 10.5281/zenodo.1472392)
-* documentation: http://download.nexusformat.org/doc/html/index.html
+* documentation: https://manual.nexusformat.org/
 * Release Notes: https://github.com/nexusformat/definitions/wiki/Release-Notes
 * build server: http://build.nexusformat.org/
 * travis-ci: syntax check of every NXDL file [![Build Status](https://travis-ci.org/nexusformat/definitions.svg)](https://travis-ci.org/nexusformat/definitions)

diff --git a/base_classes/NXcrystal.nxdl.xml b/base_classes/NXcrystal.nxdl.xml
@@ -75,10 +75,8 @@
               order of their symbol. 
             This is the *Hill* system used by Chemical Abstracts.
             See, for example:
-            http://www.iucr.org/__data/iucr/cif/standard/cifstd15.html,
-            http://www.cas.org/training/stneasytips/subinforformula1.html,
-            or
-            http://www.indiana.edu/~cheminfo/courses/471cnfs.html.
+            http://www.iucr.org/__data/iucr/cif/standard/cifstd15.html or
+            http://www.cas.org/training/stneasytips/subinforformula1.html.
         </doc>
       </item>
     </enumeration>

diff --git a/impatient-guide/index.rst b/impatient-guide/index.rst
@@ -13,9 +13,9 @@ Why NeXus?
 .. seealso:: 
 
    This document is available online in 
-   `HTML <http://download.nexusformat.org/doc/impatient>`_
+   `HTML <https://manual.nexusformat.org/impatient>`_
    and
-   `PDF <http://download.nexusformat.org/doc/NXImpatient.pdf>`_
+   `PDF <https://manual.nexusformat.org/pdf/NXImpatient.pdf>`_
    formats.
 
 The NeXus data format [#NeXus]_ is a tool which has been designed to
@@ -445,10 +445,9 @@ Any program whose aim is to identify plottable data should use the following pro
 #. Plot the *signal* data, given *axes* and *AXISNAME_indices*.
 
 For details of this process, consult this 
-`section <http://download.nexusformat.org/doc/html/datarules.html#version-3>`_ 
+`section <https://manual.nexusformat.org/datarules.html#version-3>`_ 
 of the NeXus manual. [#v3]_
 
-
 NeXus Benefits
 ==============
 
@@ -692,7 +691,7 @@ More Information
 ================
 
 Did we get you interested? Here is where you can get more information.
-Our main entry point is the NeXus WWW-site at http://www.nexusformat.org
+Our main entry point is the NeXus WWW-site at https://www.nexusformat.org/
 where you can find more information, download the NeXus API, 
 NeXus User Manual [#Manual]_ and
 NeXus Reference Documentation. [#RefDoc]_
@@ -717,7 +716,7 @@ which meets once a  year. The NIAC strives to have a representative for
 each participating facility. The NIAC has a constitution which you can
 find on the NeXus WWW site.
 
-.. [#NeXus] NeXus: http://www.nexusformat.org/
+.. [#NeXus] NeXus: https://www.nexusformat.org/
 
   .. shameless self-promotion
 
@@ -729,10 +728,11 @@ find on the NeXus WWW site.
    http://svn.nexusformat.org/definitions/exampledata/IPNS/LRMECS/lrcs3701.nx5
 
 .. [#Manual] NeXus User Manual:
-   http://download.nexusformat.org/doc/html/UserManual.html
+   https://manual.nexusformat.org/user_manual.html
 
 .. [#RefDoc] NeXus Reference Documentation:
-   http://download.nexusformat.org/doc/html/ReferenceDocumentation.html
+   https://manual.nexusformat.org/ref_doc.html
 
 .. [#v3] Finding the plottable data:
-   http://download.nexusformat.org/doc/html/datarules.html#version-3
+   https://manual.nexusformat.org/datarules.html#version-3
+
diff --git a/jenkins_build b/jenkins_build
@@ -1,7 +1,6 @@
 #!/bin/sh
 set -o errexit -x
 
-
 # jenkins job name
 job_name="$1"
 
@@ -59,6 +58,56 @@ if test "${job_name}" = "master branch"; then
 
 
     ( cd impatient-guide && cp -f _build/latex/NXImpatient.pdf ${WWW_ROOT}/doc/NXImpatient.pdf && rm -rf ${WWW_ROOT}/doc/impatient && cp -rf _build/html ${WWW_ROOT}/doc/impatient )
+
 fi
+    ## new gh-pages stuff
+
+    git_rev=`git rev-parse --short HEAD`
+    export DIST_ROOT=`pwd`/dist
+
+    rm -fr ${DIST_ROOT}
+    git clone https://github.com/nexusformat/definitions.git --branch gh-pages ${DIST_ROOT}
+    rm -fr ${DIST_ROOT}/*
+
+    mkdir ${DIST_ROOT}/pdf
+
+    cd manual
+    cd source
+
+    cp -fr examples ${DIST_ROOT}
+
+    cd ..
+    # be more deliberate about building the PDF
+    # first, build all intermediate content, indices, etc.
+    make latex
+    cd build/latex/
+    # next, build the PDF
+    # extra option needed to satisfy "levels nested too deeply" error
+    # expect it to fail (thus exit 0) since nexus.ind not found first time
+    ( pdflatex --interaction=nonstopmode nexus.tex || exit 0 )
+    # make the .ind file now
+    makeindex nexus.idx
+    # run again with fresh nexus.ind
+    ( pdflatex --interaction=nonstopmode nexus.tex || exit 0 )
+    cd ..
+
+    #pdf
+    cp -f latex/nexus.pdf ${DIST_ROOT}/pdf/NeXusManual.pdf
+    wget https://github.com/nexusformat/code/blob/master/doc/api/NeXusIntern.pdf -O ${DIST_ROOT}/pdf/NeXusIntern.pdf
+
+    #html
+    cp -fr html/* ${DIST_ROOT}
+
+    cd ../../..
+
+    cp -fr /isis/www/nexus/doxygen ${DIST_ROOT}
+
+    ( cd impatient-guide && cp -f _build/latex/NXImpatient.pdf ${DIST_ROOT}/pdf/NXImpatient.pdf && cp -rf _build/html ${DIST_ROOT}/impatient )
+
+    cd ${DIST_ROOT}
+    git add .
+    git commit -m "Update docs for ${git_rev}"
+    git push origin gh-pages
+
 
 exit 0
diff --git a/legacy_docs/README.md b/legacy_docs/README.md
@@ -1,6 +1,6 @@
 # Legacy versions of NeXus definitions documentation
 
-Per the [NeXus release procedure](http://download.nexusformat.org/doc/html/installation.html?highlight=semantic#nexus-definitions), 
+Per the [NeXus release procedure](http://manual.nexusformat.org/installation.html?highlight=semantic#nexus-definitions), 
 this directory contains legacy copies of the PDF rendition of the NeXus definitions documentation.  (Retaining multiple versions
 of the HTML would become tedious and clutter the current repository.)
 

diff --git a/manual/source/NeXusIntern.pdf b/manual/source/NeXusIntern.pdf
diff --git a/manual/source/_templates/google_search.html b/manual/source/_templates/google_search.html
@@ -22,7 +22,7 @@ <h3>{{ _('Google search') }}</h3>
 				<td align="center" style="font-size:75%">
 					<input type="radio"  name="sitesearch" value="" />global
 					<input type="radio"  name="sitesearch"
-						value="download.nexusformat.org" 
+						value="manual.nexusformat.org" 
 						checked />NeXus manual
 					<input type="submit" value="{{ _('Go') }}" />
 					<br />

diff --git a/manual/source/community.rst b/manual/source/community.rst
@@ -35,7 +35,7 @@ NeXus Webpage
 =============
 
 First of all, there is the NeXus webpage,
-http://www.nexusformat.org/,
+https://www.nexusformat.org/,
 which provides all kinds of information, including membership, minutes, and 
 discussions from the meetings of the NIAC, Code Camps, and Tele Conferences, 
 as well as some proposed designs for consideration by NeXus.

diff --git a/manual/source/copyright.rst b/manual/source/copyright.rst
@@ -7,7 +7,7 @@ Copyright and Licenses
 .. index:: license, copyright
 
 Published by NeXus International Advisory Committee, 
-http://www.nexusformat.org
+https://www.nexusformat.org
 
 Copyright (C) 1996-2020 NeXus International Advisory Committee (NIAC)
 

diff --git a/manual/source/datarules.rst b/manual/source/datarules.rst
@@ -900,12 +900,12 @@ is specified using attributes attached to the :ref:`NXdata` group.
    "strict writer, liberal reader". 
 
 .. [#] Summary of the discussion at NIAC2014 to revise how to find default data: 
-       http://www.nexusformat.org/2014_How_to_find_default_data.html
+       https://www.nexusformat.org/2014_How_to_find_default_data.html
 .. [#aa]  Note on array attributes:
           Attributes potentially containing multiple values 
           (axes and _indices) are to be written as string or integer arrays, 
           to avoid string parsing in reading applications.
-.. [#axes] NIAC2014 proposition: http://www.nexusformat.org/2014_axes_and_uncertainties.html
+.. [#axes] NIAC2014 proposition: https://www.nexusformat.org/2014_axes_and_uncertainties.html
 
 
 Examples
@@ -1057,7 +1057,7 @@ attribute for the other scales is optional.
 
 .. 2016-01-23,PRJ: not necessary
    Perhaps substitute with the discussion from NIAC2014?
-   http://www.nexusformat.org/2014_axes_and_uncertainties.html
+   https://www.nexusformat.org/2014_axes_and_uncertainties.html
    
    .. _Design-Linking-Discussion:
    

diff --git a/manual/source/design.rst b/manual/source/design.rst
@@ -282,7 +282,7 @@ path [#absolute_address]_ to the *original* dataset.
       such as: ``detector/polar_angle``).
 
    .. [#hdf5_hard_link] HDF5 hard link:
-      https://support.hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateHard
+      https://portal.hdfgroup.org/display/HDF5/H5L_CREATE_HARD
 
 NeXus links are best understood with an example.
 The canonical location (expressed as a NeXus class path) to store wavelength
@@ -378,7 +378,7 @@ a URL to a group in another file.  More information about the
 ``@napimount`` attribute is described in the
 *NeXus Programmers Reference*. [#]_
 
-.. [#] http://download.nexusformat.org/doc/NeXusIntern.pdf
+.. [#] https://manual.nexusformat.org/pdf/NeXusIntern.pdf
 
 .. index:: link; external file, NeXus link
 

diff --git a/manual/source/examples/NX__template__.nxdl.xml b/manual/source/examples/NX__template__.nxdl.xml
@@ -18,7 +18,7 @@
 # License along with this library; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 #
-# For further information, see http://www.nexusformat.org
+# For further information, see https://www.nexusformat.org/
 -->
 <definition name="NX__template__" extends="NXobject" type="group"
     category="application"

diff --git a/manual/source/examples/epics/index.rst b/manual/source/examples/epics/index.rst
@@ -298,7 +298,7 @@ Footnotes
 .. [#] EPICS Area Detector: http://cars9.uchicago.edu/software/epics/areaDetector.html
 .. [#] HDF5 File Writer: http://cars9.uchicago.edu/software/epics/NDFileHDF5.html
 .. [#] EPICS SimDetector: http://cars9.uchicago.edu/software/epics/simDetectorDoc.html
-.. [#] NeXus manual: http://download.nexusformat.org/doc/html/index.html
+.. [#] NeXus manual: https://manual.nexusformat.org/
 .. [#] caQtDM: http://epics.web.psi.ch/software/caqtdm/
 .. [#] h5py: http://docs.h5py.org
 .. [#] nexusformat: This Python package is described on the NeXPy web site

diff --git a/manual/source/examples/h5py/index.rst b/manual/source/examples/h5py/index.rst
@@ -279,8 +279,8 @@ Here is an example of the structure:
         two_theta --> file="external_angles.hdf5", path="/angles"
 
 .. [#] see these URLs for further guidance on HDF5 external links:
-   http://www.hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateExternal, 
-   http://www.h5py.org/docs-1.3/guide/group.html#external-links
+   https://portal.hdfgroup.org/display/HDF5/H5L_CREATE_EXTERNAL, 
+   http://docs.h5py.org/en/stable/high/group.html#external-links
 
 file: external_master.hdf5
 ==========================

diff --git a/manual/source/examples/lrmecs/index.rst b/manual/source/examples/lrmecs/index.rst
@@ -45,7 +45,7 @@ Visualize Using *HDFview*
 
 For many, the simplest way to view the data content 
 of an HDF5 file is to use the  *HDFview* program 
-(http://www.hdfgroup.org/hdf-java-html/hdfview)
+(https://portal.hdfgroup.org/display/HDFVIEW/HDFView)
 from The HDF Group.  After starting *HDFview*, the data file 
 may be loaded by dragging it into the main HDF window.
 On opening up to the first ``NXdata`` group */Histogram1/data*

diff --git a/manual/source/faq.rst b/manual/source/faq.rst
@@ -19,7 +19,7 @@ This is a list of commonly asked questions concerning the NeXus data format.
 
     This is not easy to say, not all facilities using NeXus actively
     participate in the committee. Some facilities have reported their
-    adoption status on the `Facilities web page <http://www.nexusformat.org/Facilities.html>`_.
+    adoption status on the `Facilities web page <https://www.nexusformat.org/Facilities.html>`_.
     Please have a look at this list. Keep in mind that it is never fully complete or up to date.
 
 #. NeXus files are binary? This is crazy! How am I supposed to see my data?
@@ -78,7 +78,7 @@ This is a list of commonly asked questions concerning the NeXus data format.
 
     If you encounter any problems because the classes are not
     sufficient to describe your experiment, please contact the
-    `mailing list <http://download.nexusformat.org/doc/html/MailingLists.html>`_.
+    :ref:`mailing list<NeXus.mailinglist.main>`.
     Pull requests for the defintions repository (for example adding contributed defintions) 
     are also welcome (see next question).
     The NIAC is always willing to consider new proposals.
@@ -88,7 +88,7 @@ This is a list of commonly asked questions concerning the NeXus data format.
 
     Read the :index:`NXDL` Tutorial in :ref:`NXDL_Tutorial-CreatingNxdlSpec`
     and have a try. You can ask for help on the 
-    `mailing lists <http://download.nexusformat.org/doc/html/MailingLists.html>`_.
+    :ref:`mailing lists<NeXus.mailinglist.main>`.
     Once you have a definition that is working well for at least your case,
     you can submit it to the NIAC for acceptance as a standard.
     The procedures for acceptance are defined in the NIAC :index:`constitution`. [#]_
@@ -97,7 +97,7 @@ This is a list of commonly asked questions concerning the NeXus data format.
 	.. [#]
 	    Refer to the most recent version of the NIAC constitution on the
 	    NIAC web page:
-	    http://www.nexusformat.org/NIAC.html#constitution
+	    https://www.nexusformat.org/NIAC.html#constitution
 
 
 #. What is the purpose of ``NXdata``?

diff --git a/manual/source/history.rst b/manual/source/history.rst
@@ -33,7 +33,7 @@ Two things to note about the development and history of NeXus:
     and the NXentry and NXdata groups. 
     See the description in :ref:`Design-FindPlottable-NIAC2014`
     and the proposal:
-    http://www.nexusformat.org/2014_How_to_find_default_data.html
+    https://www.nexusformat.org/2014_How_to_find_default_data.html
 
 2012-05:
     first release (3.1.0) of NXDL (NeXus Definition Language)
@@ -127,7 +127,7 @@ Two things to note about the development and history of NeXus:
 
 1994-10:
     :index:`Ray Osborn <single: Osborn, Raymond>` convened a series of three workshops called
-    *SoftNeSS*. [#softness]_
+    *SoftNeSS*.
     In the first meeting,
     Mark Könnecke and Jon Tischler were invited to meet with representatives
     from all the major U.S. neutron scattering laboratories
@@ -145,13 +145,11 @@ Two things to note about the development and history of NeXus:
     for the European neutron scattering community while working at ISIS
 
 
-.. [#NeXus_Proposal] http://www.nexusformat.org/pdfs/NeXus_Proposal.pdf
+.. [#NeXus_Proposal] https://www.nexusformat.org/pdfs/NeXus_Proposal.pdf
 
-.. [#softness] http://www.neutron.anl.gov/softness
+.. [#aps] https://www.nexusformat.org/pdfs/Proposed_Data_Standard_for_the_APS.pdf
 
-.. [#aps] http://www.nexusformat.org/pdfs/Proposed_Data_Standard_for_the_APS.pdf
-
-.. [#netCDF] http:/wwww.nexusformat.org/pdfs/European-Formats.pdf
+.. [#netCDF] https://www.nexusformat.org/pdfs/European-Formats.pdf
 
 
 .. comment from here moved to file: history-unpublished-comment.txt

diff --git a/manual/source/index.rst b/manual/source/index.rst
@@ -5,7 +5,7 @@
 User Manual and Reference Documentation
 =======================================
 
-http://www.nexusformat.org/
+https://www.nexusformat.org/
 
 .. toctree::
     :maxdepth: 2
@@ -32,19 +32,19 @@ This manual built |today|.
    This document is available in these formats online:
 
    :HTML:
-   	http://download.nexusformat.org/doc/html/index.html
+   	https://manual.nexusformat.org/
 
    :PDF:
-   	http://download.nexusformat.org/doc/NeXusManual.pdf
+   	https://manual.nexusformat.org/pdf/NeXusManual.pdf
 
    A very brief overview (title: *NeXus for the Impatient*) 
    is also available (separate from the manual).
 
    :HTML:
-      http://download.nexusformat.org/doc/impatient
+      https://manual.nexusformat.org/impatient/
 
    :PDF:
-      http://download.nexusformat.org/doc/NXImpatient.pdf
+      https://manual.nexusformat.org/pdf/NXImpatient.pdf
 
 ..  Suggestions for adding to this manual:
 

diff --git a/manual/source/installation.rst b/manual/source/installation.rst
@@ -41,7 +41,7 @@ Linux RPM Distribution Kits
    see: RPM; NAPI installation
 
 An installation kit (source or binary) can be downloaded from:
-http://download.nexusformat.org/kits/
+https://github.com/nexusformat/code/releases/tag/4.3.0
 
 A NeXus binary RPM (nexus-\*.i386.rpm) contains ready compiled NeXus libraries whereas a
 source RPM (nexus-\*.src.rpm) needs to be compiled into a binary RPM before it can be
@@ -89,7 +89,7 @@ Microsoft Windows Installation Kit
    see: Windows; NAPI installation
 
 A Windows MSI based installation kit is available and can be downloaded from: 
-http://download.nexusformat.org/kits/windows/
+https://github.com/nexusformat/code/releases/tag/4.3.0
 
 .. _Installation-MacOS:
 
@@ -102,7 +102,7 @@ Mac OS X Installation Kit
 
 
 An installation disk image (.dmg) can be downloaded from: 
-http://download.nexusformat.org/kits/macosx/
+https://github.com/nexusformat/code/releases/tag/4.3.0
 
 .. _Installation-Source:
 
@@ -157,8 +157,7 @@ state of the NeXus standard).
 Each new *release* of the definitions
 will be posted to the definitions GitHub repository
 and announced to the community via the
-NeXus mailing list: ``nexus@nexusformat.org``
-(http://download.nexusformat.org/doc/html/mailinglist.html#nexus-mailing-list)
+NeXus mailing list: :ref:`nexus@nexusformat.org<NeXus.mailinglist.main>`
 
 NeXus definitions
 =================