fix dependabots and documentation warnings (#138)

* fix dependabots warnings and documentation warnings

* change size

* include missing information for NERSC CI

* Update sync-amrex.json

Author: jeanbez

docs/requirements.txt

@@ -1,4 +1,11 @@
-sphinx==6.2.1
-sphinx-rtd-theme==1.2.2
-sphinxemoji
-urllib3==1.26.15
+Sphinx==8.2.3
+sphinx-rtd-theme==3.0.2
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
+sphinxcontrib-jquery==4.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
+sphinxemoji==0.3.1
+urllib3==2.5.0

docs/source/buildinstructions.rst

@@ -70,7 +70,7 @@ If you want to build your own HDF5, use the following:
 
 .. warning::
 
-    This snippet assumed you had already defined the ``HDF5_HOME`` environment variable to the location where you want HDF5 to be installed. Furthermore, it assumes you have ``mpicc`` available in your path. Notice that in some machines (e.g., Perlmutter), you might want to use ``cc` instead.
+    This snippet assumed you had already defined the ``HDF5_HOME`` environment variable to the location where you want HDF5 to be installed. Furthermore, it assumes you have ``mpicc`` available in your path. Notice that in some machines (e.g., Perlmutter), you might want to use ``cc`` instead.
 
 Compile with CMake
 ---------------------------------------------------

docs/source/macsio.rst

@@ -1,5 +1,5 @@
 MACSio
-====
+======
 
 MACSio (Multi-purpose, Application-Centric, Scalable I/O Proxy Application) is being developed to fill a long existing void in co-design proxy applications that allow for I/O performance testing and evaluation of tradeoffs in data models, I/O library interfaces and parallel I/O paradigms for multi-physics, HPC applications.
 

docs/source/running.rst

@@ -263,7 +263,7 @@ When the ``--debug`` option is enabled, you can expect an output similar to:
    2021-10-25 16:31:49,174 h5bench - INFO - Finishing h5bench Suite
 
 Perlmutter (NERSC)
-^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^
 
 In Perlmutter you need to load Python and its libraries for the main ``h5bench`` script to work. For manual execution of each benchmark, that is not required.