Merge branch 'master' of github.com:nufeb/NUFEB-2 into mutation

.readthedocs.yml

@@ -7,10 +7,15 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: "ubuntu-22.04"
   tools:
-    python: "latest"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
+
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: docs/requirements.txt

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx==5.3.0
+sphinx_rtd_theme==1.1.1
+readthedocs-sphinx-search==0.1.1

docs/source/conf.py

@@ -12,9 +12,9 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
-import sys
-sys.path.insert(0, os.path.abspath('../../'))
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('../../'))
 
 
 # -- Project information -----------------------------------------------------
@@ -87,7 +87,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = [""]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

docs/source/install.rst

@@ -124,8 +124,7 @@ will allow NUFEB simulation to output both vtk and hdf5 data formats.
 
 When the installation finished, you should have an executable ``nufeb_mpi`` or
 ``nufeb_serial`` or ``nufeb_gpu`` in 
-``NUFEB-2`` directory deponeding on configuration. The path to the executable 
-will be automatically added to the system (.bashrc).
+``NUFEB-2`` directory deponeding on configuration.
 
  .. note::
    For convenience, the executables built from install.sh are limited to mpi, gpu (cuda + mpi), and serial versions.

docs/source/run_nufeb.rst

@@ -25,23 +25,23 @@ NUFEB provides numbers of examples available in the ``NUFEB-2/examples`` directo
 For example: 
 
  .. parsed-literal::
-   cd NUFEB-2/examples/biofilm-het
-   mpirun -np 4 nufeb_mpi -in nufeb.in
+   cd NUFEB-2/examples/biofilm-heterotroph
+   mpirun -np 4 ../../nufeb_mpi -in inputscript.nufeb
 
-The above commands will run the input script ``nufeb.in`` in the ``NUFEB-dev/biofilm-het`` directory using NUFEB MPI executable with 4 CPU processors.
+The above commands will run the input script ``inputscript.nufeb`` in the ``NUFEB-dev/biofilm-heterotroph`` directory using NUFEB MPI executable with 4 CPU processors.
 `mpirun -np X` command-line switch to specify the numbers of processors to run the simulation.
 
  .. parsed-literal::
-  cd NUFEB-2/examples/biofilm-het/
-  nufeb_serial -in nufeb.in
+  cd NUFEB-2/examples/biofilm-heterotroph
+  ../../nufeb_serial -in inputscript.nufeb
 
-The above commands will run the ``NUFEB-dev/biofilm-het`` example using NUFEB serial executable with single processor.
+The above commands will run the ``NUFEB-dev/biofilm-heterotroph`` example using NUFEB serial executable with single processor.
 
  .. parsed-literal::
-  cd NUFEB-2/examples/biofilm-het/  
-  mpirun -np 2 nufeb_gpu -k on g 2 -sf kk -pk kokkos newton off neigh half binsize 2e-6 -in nufeb.in
+  cd NUFEB-2/examples/biofilm-heterotroph
+  mpirun -np 2 ../../nufeb_gpu -k on g 2 -sf kk -pk kokkos newton off neigh half binsize 2e-6 -in inputscript.nufeb
 
-The above commands will run the ``NUFEB-dev/biofilm-het`` examaple using NUFEB GPU executable with 2 GPUs and 2 CPUs.
+The above commands will run the ``NUFEB-dev/biofilm-heterotroph`` example using NUFEB GPU executable with 2 GPUs and 2 CPUs.
 In particular, the `-k on` command-line switch enable Kokkos support; `g 2` specify the use of 2 GPUs to run the simulation.
 `-sf kk` enables NUFEB to use Kokkos variant styles of any commands defined in the inputscript; 
 `-pk kokkos newton off neigh half binsize 2e-6` re-define the setting in the inputscript.