From 07b506b9a3d2ea0742a6926442c37f75e4feac94 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Thu, 26 Mar 2020 16:17:10 +0000
Subject: [PATCH] updates to readme.

---
 README.md | 110 +++++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 100 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index c0e83c2..c4b0bc1 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,10 @@
 # Phasecalculator #
 
-Phasecalculator is a python package.
-
-It is designed to automate calculation of FGIPs, solvent similarity and VLE informatio
+Phasecalculator is a python package designed to automate calculation of FGIPs, solvent similarity and VLE informatio
 n using SSIMPLE, pulling together analysis and calculation modules in a higher l
 evel repository for easier use by experimental chemists.
 
-### How do I get set up? ###
+## How do I get set up? ##
 
 * Summary of set up
 * Configuration
@@ -15,17 +13,109 @@ evel repository for easier use by experimental chemists.
 * How to run tests
 * Deployment instructions
 
-### Contribution guidelines ###
+### 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/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
+    * resultsanalysis [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
+    * phasexmlparser [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
+    * phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
+    * resultsanalysis [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
+    * solventmapcreator [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
+    * ssip [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip) 
+    
+### Clone this repository ###
+
+*From bitbucket:*
+
+        git clone https://bitbucket.org/mdd31/phasecalculator.git
+
+
+*From University of Cambridge gitlab:*
+
+
+### Setting up the python environment ###
+
+Change to the repository:
+
+        cd phasecalculator
+
+Details of an anaconda environment is provided in the repository with the required dependencies for this package.
+
+        conda env create -f environment.yml
+
+This creates and environment callled 'resultsanalysis' which can be loaded using:
+
+        conda activate resultsanalysis
+
+### 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.
+
+For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation.
+
+### Using pip to install module ###
+
+To install in your environment using pip run:
+
+        pip install .
+
+This installs it in your current python environment.
 
-* Writing tests
-* Code review
-* Other guidelines
 
 
+### Expected usage ###
+
+This module contains methods for the running of FGIP, similarity and VLE calculations for solvent mixtures at specified temperatures.
+The calculation process can be run through the use of an XML data format.
+For the specification of this format please see the Phase Calculator schema on the [Hunter Group website](http://www-hunter.ch.cam.ac.uk/schema).
+The CLI has been implemented to enable operation in two modes:
+
+1) Run calculations from input XML.
+
+This uses the 
+
+2) Generate input XML for default solvents.
+
+This uses the 
+
+See the help arguments for more information about the options.
+
+#### Example calculations ####
+
+The
+
+
+The csv file of solvent information is in 
+
+Default solvent names for inclusion in the CSV file can be found by running:
+
+    python -m phasecalculator #ADD method- new subprocessor. 
+
+
+### Documentation ###
+
+Documentation can be rendered using sphinx.
+
+        cd docs
+        make html
+
+The rendered HTML can then be found in the build sub folder.
+
+In progress: display of this documentation in a project wiki.
+
+### Contribution guidelines ###
+
+This code has been released under the AGPLv3 license.
+If you find any bugs please file an issue ticket.
+Submission of pull requests for open issues or improvements are welcomed.
+
 ### Who do I talk to? ###
 
-Mark Driver created this repository as a summary of work completed during his PhD.
+Any queries please contact Mark Driver.
 
 ### Licensing ###
 
-This is released under the AGPLv3 license.
\ No newline at end of file
+This is released under the AGPLv3 license.
-- 
GitLab