Merge pull request #867 from OpenFreeEnergy/fix/update_lock_file_inst…

…ructions

Updated installation instructions for conda-lock

docs/installation.rst

@@ -153,9 +153,59 @@ hardware intended to run openfe jobs, as it will test GPU specific features.
 
 With that, you should be ready to use ``openfe``!
 
+``conda-lock`` file
+-------------------
+
+.. _conda-lock: https://github.com/conda/conda-lock?tab=readme-ov-file#conda-lock
+
+A `conda-lock`_ file is a cross platform way of specifying a conda environment that specifies packages in a reproducible way.
+Unlike the single file installer, an internet connection is required to install from a ``conda-lock`` file.
+We recomend the use of a ``conda-lock`` file when the same conda environment is required across different systems.
+
+
+.. note::
+
+   You will likely need to install ``conda-lock``.
+   We strongly recomend installing ``conda-lock`` in a new virtual environment.
+   This will reduce the chance of dependency conflicts ::
+
+       $ # Install conda lock into a virtual environment
+       $ conda create -n conda-lock -c conda-lock
+       $ # Activate the environment to use the conda-lock command
+       $ conda activate conda-lock
+
+See https://github.com/conda/conda-lock?tab=readme-ov-file#conda-lock for more information on ``conda-lock``.
+
+The latest version of the `conda-lock` file we provide can be downloaded with ::
+
+  $ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/latest/download/conda-lock-openfe.yml
+
+If a particular version is required, the URL will look like this (using the ``openfe 1.0.1`` release as an example) ::
+
+  $ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/download/v1.0.1/conda-lock-openfe-1.0.1.yml
+
+Create a conda environment from the lock file and activate it::
+
+  $ conda-lock install -n openfe conda-lock-openfe.yml
+  $ conda activate openfe
+
+To make sure everything is working, run the tests ::
+
+  $ pytest --pyargs openfe openfecli
+
+The test suite contains several hundred individual tests. This will take a
+few minutes, and all tests should complete with status either passed,
+skipped, or xfailed (expected fail).
+
+With that, you should be ready to use ``openfe``!
+
 Single file installer
 ---------------------
 
+.. warning::
+
+   The single file installer may modify your ``.bashrc`` in a way that requires manual intervention to access your previous ``conda`` installation 
+
 .. _releases on GitHub: https://github.com/OpenFreeEnergy/openfe/releases
 
 Single file installers are available for x86_64 Linux and MacOS. 
@@ -359,43 +409,6 @@ skipped, or xfailed (expected fail).
 
 With that, you should be ready to use ``openfe``!
 
-``conda-lock`` file
--------------------
-
-.. _conda-lock: https://github.com/conda/conda-lock?tab=readme-ov-file#conda-lock
-
-A `conda-lock`_ file is a cross platform way of specifying a conda environment that specifies packages in a reproducible way.
-Unlike the single file installer, an internet connection is required to install from a ``conda-lock`` file.
-We recomend the use of a ``conda-lock`` file when the same conda environment is required across different systems.
-
-See https://github.com/conda/conda-lock?tab=readme-ov-file#installation for instructions on how to install ``conda-lock``.
-
-.. note::
-
-   You will likely need to install ``conda-lock``
-
-The latest version of the `conda-lock` file we provide can be downloaded with ::
-
-  $ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/latest/download/conda-lock-openfe.yml
-
-If a particular version is required, the URL will look like this (using the ``openfe 1.0.1`` release as an example) ::
-
-  $ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/download/v1.0.1/conda-lock-openfe-1.0.1.yml
-
-Create a conda environment from the lock file and activate it::
-
-  $ conda-lock install -n openfe conda-lock-openfe.yml
-  $ conda activate openfe
-
-To make sure everything is working, run the tests ::
-
-  $ pytest --pyargs openfe openfecli
-
-The test suite contains several hundred individual tests. This will take a
-few minutes, and all tests should complete with status either passed,
-skipped, or xfailed (expected fail).
-
-With that, you should be ready to use ``openfe``!
 
 Containers
 ----------