diff --git a/README.md b/README.md index a0d77f1e..3346ad9a 100644 --- a/README.md +++ b/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 -c mantid/label/nightly mvesuvio` + +To activate the conda environment: +- `conda activate ` + +### 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 \ No newline at end of file + 6. Analysis of bootstrap data works only with stored data in directories mentioned in point 5, it does not run any bootstrap diff --git a/mvesuvio/__init__.py b/mvesuvio/__init__.py index abbaac84..2ffce353 100644 --- a/mvesuvio/__init__.py +++ b/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):