From 215a26ec103aff061898acc88f170647235738fd Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Sat, 28 Mar 2020 11:50:43 +0000
Subject: [PATCH] update readme.
---
README.md | 35 ++++++++++++++++++++---------------
1 file changed, 20 insertions(+), 15 deletions(-)
diff --git a/README.md b/README.md
index 9ccdbde..9da9f12 100644
--- a/README.md
+++ b/README.md
@@ -6,17 +6,6 @@ evel repository for easier use by experimental chemists.
## How do I get set up? ##
-### Required modules ###
-
-The other modules produced by Mark Driver required for this work to function are:
-
-* xmlvalidator [bitbucket](https://bitbucket.org/mdd31/xmlvalidator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/xmlvalidator)
-* puresolventinformation [bitbucket](https://bitbucket.org/mdd31/puresolventinformation) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/puresolventinformation)
-* resultsanalysis [bitbucket](https://bitbucket.org/mdd31/resultsanalysis) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/resultsanalysis)
-* phasexmlparser [bitbucket](https://bitbucket.org/mdd31/phasexmlparser) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlparser)
-* phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/phasexmlcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlcreator)
-* solventmapcreator [bitbucket](https://bitbucket.org/mdd31/solventmapcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/solventmapcreator)
-* ssip (specifically phasetransfer module) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip)
### Clone this repository ###
@@ -31,6 +20,8 @@ The other modules produced by Mark Driver required for this work to function are
If you have not already set up ssh access to the gitlab server please look through the instructions on the gitlab help page [https://gitlab.developers.cam.ac.uk/help/ssh/README](https://gitlab.developers.cam.ac.uk/help/ssh/README).
+
+
### Setting up the python environment ###
Change to the repository:
@@ -47,20 +38,34 @@ This creates and environment callled 'resultsanalysis' which can be loaded using
### Install dependencies ###
-Before installing this module please make sure that the required modules listed previously are installed in the current python environment. Before cloning the dependent repositories please change up a directory and follow install instructions to install in this environment.
+Before installing this module please make sure that the required modules listed below are installed in the current python environment (resultsanalysis).
+
+Before cloning the dependent repositories please change up a directory and follow install instructions to install within the readme files for the repository.
+Do not follow the instructions to create a python environment.
-For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation (This requires version 6.0.0 or greater). A pre-compiled jar with dependencies may be available on the repository \_\_\_ page.
+#### Required modules ####
+
+The other modules produced by Mark Driver required for this work to function are listed below. Please install them in the below order.
+
+* xmlvalidator [bitbucket](https://bitbucket.org/mdd31/xmlvalidator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/xmlvalidator)
+* puresolventinformation [bitbucket](https://bitbucket.org/mdd31/puresolventinformation) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/puresolventinformation)
+* resultsanalysis [bitbucket](https://bitbucket.org/mdd31/resultsanalysis) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/resultsanalysis)
+* phasexmlparser [bitbucket](https://bitbucket.org/mdd31/phasexmlparser) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlparser)
+* phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/phasexmlcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlcreator)
+* solventmapcreator [bitbucket](https://bitbucket.org/mdd31/solventmapcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/solventmapcreator)
+* ssip (specifically phasetransfer module) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip)
+
+For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation (This requires version 6.0.0 or greater).
### Using pip to install module ###
-To install in your environment using pip run:
+In the top level phasecalculator folder (where environment.yml and README.md files are located) using pip run the following command in your chosen python environment:
pip install .
This installs it in your current python environment.
-
### Expected usage ###
This module contains methods for the running of FGIP, similarity and VLE calculations for solvent mixtures at specified temperatures.
--
GitLab