From 456a6d6363fe9bbb13126b2944c4e7bf800300b9 Mon Sep 17 00:00:00 2001
From: Jo Basevi <johanna.basevi@edu.anu.au>
Date: Thu, 3 Aug 2023 11:37:18 +1000
Subject: [PATCH] Update documentation to include module use and load options

---
 .gitignore             |  1 +
 docs/source/config.rst | 16 ++++++++++------
 test/test_payu.py      |  4 ++--
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index 47c37851..808b5549 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,4 +9,5 @@ MANIFEST
 .coverage
 .ipynb_checkpoints
 .vscode
+.idea
 /test/tmp/
\ No newline at end of file
diff --git a/docs/source/config.rst b/docs/source/config.rst
index bc9a9e9d..e9c3c4d9 100644
--- a/docs/source/config.rst
+++ b/docs/source/config.rst
@@ -427,17 +427,21 @@ Miscellaneous
    is generally only used for testing purposes, such as bit reproducibility.
 
 ``modules``
-   Specify a list of environment modules to load at the start of the PBS job,
-   for example::
+   Specify lists of environment modules and/or directories
+   to load/use at the start of the PBS job, for example::
 
       modules:
-         - netcdf-c-4.9.0
-         - parallel-netcdf-1.12.3
-         - xerces-c-3.2.3
+         use:
+            - /path/to/module/directory
+         load:
+            - netcdf-c-4.9.0
+            - parallel-netcdf-1.12.3
+            - xerces-c-3.2.3
 
    This is seldom needed, because payu is good at automatically determining
    the environment modules required by model executables. If the modules
-   require `module use` inorder to be found, do this prior to `payu run`,
+   require `module use` in order to be found, this command can also be run
+   prior to `payu run` instead of listing the directory under the `use` option,
    e.g.::
 
       module use /path/to/module/directory
diff --git a/test/test_payu.py b/test/test_payu.py
index 56835be0..8a6d4065 100644
--- a/test/test_payu.py
+++ b/test/test_payu.py
@@ -245,8 +245,8 @@ def test_parse_ldd_output():
     with open(ldd_output_path, 'r') as f:
         ldd_output = f.read()
     required_libs = payu.fsops.parse_ldd_output(ldd_output)
-    assert(len(required_libs), 4)
-    assert(required_libs['libmpi.so.40'], '/apps/openmpi/4.0.2/lib/libmpi.so.40')
+    assert(len(required_libs) == 4)
+    assert(required_libs['libmpi.so.40'] == '/apps/openmpi/4.0.2/lib/libmpi.so.40')
 
 
 def test_lib_update_lib_if_required():