From 1077b6383469c37d51c90ff365b62443fabe3be1 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Sun, 18 Apr 2021 23:44:15 +0200
Subject: [PATCH 1/2] [Module] OpenPathSampling CLI MD Command

This module adds an ``md`` command to the OpenPathSampling CLI, which runs
molecular dynamics for either a fixed time or until a subtrajectory of
satsfies a given ensemble.
---
 .../modules/ops_cli_md_command/readme.rst     | 111 ++++++++++++++++++
 1 file changed, 111 insertions(+)
 create mode 100644 Classical-MD-Modules/modules/ops_cli_md_command/readme.rst

diff --git a/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst b/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst
new file mode 100644
index 00000000..5bb8ac2d
--- /dev/null
+++ b/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst
@@ -0,0 +1,111 @@
+.. _ops_cli_md_command:
+
+###############################
+OpenPathSampling CLI MD Command
+###############################
+
+.. sidebar:: Software Technical Information
+
+  The information in this section describes OpenPathSampling as a whole.
+  Information specific to the additions in this module are in subsequent
+  sections.
+
+  Language
+    Python (3.6+)
+
+  Documentation Tool
+    Sphinx, numpydoc format (ReST)
+
+  Application Documentation
+    http://openpathsampling-cli.readthedocs.io/
+
+  Relevant Training Material
+    http://openpathsampling.org/
+
+  Licence
+    MIT
+
+  Software module developed by
+    David W.H. Swenson
+
+.. contents:: :local:
+
+The module adds an ``md`` command to the OpenPathSampling CLI, which runs
+molecular dynamics for either a fixed time or until a subtrajectory of
+satsfies a given ensemble.
+
+
+Purpose of Module
+_________________
+
+.. TODO
+
+OpenPathSampling introduced the idea of generalized path ensembles, which
+allow users to define the charactistic function of an ensemble from
+
+
+Background Information
+______________________
+
+This module builds on OpenPathSampling, a Python package for path sampling
+simulations. To learn more about OpenPathSampling, you might be interested in
+reading:
+
+* OPS documentation: http://openpathsampling.org
+* OPS source code: http://github.com/openpathsampling/openpathsampling
+
+Detailed documentation on the CLI can be found at
+https://openpathsampling-cli.readthedocs.io/
+
+Testing
+_______
+
+The OPS CLI can be installed with either pip or conda:
+
+.. code:: bash
+
+   pip install openpathsampling-cli
+   # or
+   conda install -c conda-forge openpathsampling-cli
+
+Tests in the OpenPathSampling CLI use `pytest`_, which can be installed with
+either ``pip`` or ``conda``.
+
+With the package and its testing tools installed, tests can be run with:
+
+.. code:: bash
+
+   py.test --pyargs paths_cli
+
+Examples
+________
+
+Basic examples of how to use the OPS CLI can be found in:
+
+.. TODO
+
+Source Code
+___________
+
+This module is composed of the following pull request:
+
+* https://github.com/openpathsampling/openpathsampling-cli/pull/35
+
+.. link the source code
+
+.. IF YOUR MODULE IS IN OPS CORE
+
+.. This module has been merged into OpenPathSampling. It is composed of the
+.. following pull requests:
+
+.. * link PRs
+
+.. IF YOUR MODULE IS A SEPARATE REPOSITORY
+
+.. The source code for this module can be found in: URL.
+
+.. CLOSING MATERIAL -------------------------------------------------------
+
+.. Here are the URL references used
+
+.. _pytest: http://pytest.org/
-- 
GitLab


From c71c99e4b90d9fba09797f20028bde03a9154bfc Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 20 Apr 2021 03:01:20 +0200
Subject: [PATCH 2/2] add orphan

---
 Classical-MD-Modules/modules/ops_cli_md_command/readme.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst b/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst
index 5bb8ac2d..8ab1120e 100644
--- a/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst
+++ b/Classical-MD-Modules/modules/ops_cli_md_command/readme.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 .. _ops_cli_md_command:
 
 ###############################
-- 
GitLab