Merge pull request #96 from mantidproject/update_readme_with_package_…

…instructions

Update readme following addition of mvesuvio package

README.md

@@ -1,7 +1,78 @@
-# scatt_scripts
+# VESUIVO REPOSITORY
 
-## Repository for the optimized NCP analysis procedures on VESUVIO
+This repository contains:
+- `mvesuvio` package containing the Optimized NCP analysis procedures, published nightly.
+- Vesuvio calibration script
 
+## mvesuvio package
+
+### Install mamba
+
+To use the `mvesuvio` package you will need to use the `conda` package manager (or preferably  `mamba`, a much faster implementation of `conda`).
+
+This is also the recommended best practice way of using the mantid packages.
+
+To download and install mamba:
+- https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html
+
+### Create and activate an environment
+
+To create a conda environment for `mvesuvio`:
+- `mamba env create -n <environment_name> -c mantid/label/nightly mvesuvio`
+
+To activate the conda environment:
+- `conda activate <environment_name>`
+
+### Using mvesuvio via the command line
+
+You can use `mvesuvio` via the command line. There are two commands available: `config` and `run`.
+
+#### config
+
+The `config` command has three optional arguments:
+- `--set-cache` - Sets the location `mvesuvio` will set up the experiment directory.
+- `--set-experiment` - Sets the current experiment. This creates a new directory in the experiment directory (if not existing) which contains an input file. `mvesuvio` caches and outputs workspaces here.
+- `--set-ipfolder` - Sets the directory in which `mvesuvio` will look for instrument parameter files.
+
+If any of these arguments are not provided a default location/experiment will be selected. These will be output on the running of `mvesuvo config`
+
+Usage examples:
+- `mvesuvio config --set-cache C:\Vesuvio --set-experiment example1 --set-ipfolder C:\IPFolder` - Set cache and IP folder, create a new experiment directory called `example1`.
+- `mvesuvio config --set-experiment example2` - Creates a new experiment directory in `C:\Vesuvio` called `example2`.
+
+#### run
+
+The `run` command has one optional argument:
+- `--yes` - If provided, this argument automatically inputs `Y` when prompted for user input.
+
+Usage example:
+- `mvesuvio run --yes` - Run the vesuvio analysis, automatically providing `Y` when prompted.
+- `mvesuvio run`- Run the vesuvio analysis, will wait for user input when prompted.
+
+### Using mvesuvio via workbench
+
+You can also use `mvesuvio` via `mantidworkbench` if you desire a higher degree of interaction with the output workspaces.
+
+To do this, install workbench into your existing vesuvio conda environment:
+- `mamba install mantidworkbench`
+
+Start workbench using the command line:
+- `workbench`
+
+In the workbench script editor you must first import mvesuvio:
+
+- `import mvesuvio as mv`
+
+After this you can set the config if desired, as above in the command line example. All arguments are optional.
+
+- `mv.set_config(cache_directory='C:\Vesuvio', experiment_id='example3', ip_folder='C:\IPFolder')`
+
+Following the setting of the config, you can use workbench to open and edit the analysis input file created in the relevant experiment directory.
+Once the inputs have been ammended and the file saved, run the analysis:
+
+- `mv.run(yes_to_all=True)`
+
+## Outdated documentation (To Review):
 ### Currently in development, daily updates and corrections.
 
 Three example scripts are provided, BaH2_500C, D_HMT and starch_80_RD, each detailing the initial conditions for each sample.
@@ -20,4 +91,4 @@ How to use for a new sample:
 
     5. Bootstrap option is still under development, but any data from running bootstrap is stored under experiments/sample/bootstrap_data/ or experiments/sample/jackknife_data
 
-    6. Analysis of bootstrap data works only with stored data in directories mentioned in point 5, it does not run any bootstrap
+    6. Analysis of bootstrap data works only with stored data in directories mentioned in point 5, it does not run any bootstrap

mvesuvio/__init__.py

@@ -50,8 +50,8 @@ def yes(self):
         return self.__yes
 
 
-def set_config(cache_directory="", experiment_id="", ip_folder_dirctory=""):
-    config_args = ConfigArgInputs(cache_directory, experiment_id, ip_folder_dirctory)
+def set_config(cache_directory="", experiment_id="", ip_folder=""):
+    config_args = ConfigArgInputs(cache_directory, experiment_id, ip_folder)
     main(config_args)
 
 def run(yes_to_all=False):