update version and README

Project.toml

@@ -2,7 +2,7 @@ name = "DFControl"
 uuid = "1e31e15d-4957-550d-a244-318eced754ae"
 authors = ["Louis Ponet <louisponet@gmail.com>"]
 repo = "https://github.com/louisponet/DFControl.jl.git"
-version = "0.2.1"
+version = "0.3.0"
 
 [deps]
 BinDeps = "9e28174c-4ba2-5203-b857-d8d62c4213ee"

README.md

@@ -2,6 +2,7 @@
 [![Build Status](https://travis-ci.com/louisponet/DFControl.jl.svg?branch=master)](https://travis-ci.com/louisponet/DFControl.jl)
 [![Build status](https://ci.appveyor.com/api/projects/status/05vktbyj39u47usa?svg=true)](https://ci.appveyor.com/project/louisponet/dfcontrol-jl)
 [![Coverage Status](https://coveralls.io/repos/github/louisponet/DFControl.jl/badge.svg?branch=master)](https://coveralls.io/github/louisponet/DFControl.jl?branch=master)
+[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://louisponet.github.io/DFControl.jl/v0.3.0)
 [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://louisponet.github.io/DFControl.jl/dev)
 
 This package is a tool to interact with DFT related packages. Currently best support is for Quantum-Espresso and WANNIER90.
@@ -10,95 +11,9 @@ There is some integration with Juno, namely the display of various Types is spec
 
 ## Installation
 
-This package is registered, but the recommended way to install it is by:
+This package is registered, so as any normal Julia package:
 ```julia
-Pkg.clone("https://github.com/louisponet/DFControl.jl.git")
-Pkg.build("DFControl")
+Pkg.add("DFControl")
 ```
-Since the package has changed quite a lot since the last release.
 
-This will create a directory `user_defaults` with file `user_defaults.jl` inside the `DFControl` source folder. This is done because it allows one to define certain variables and defaults that will get loaded when `using DFControl` is called. The main use for this is to define various defaults, which make a lot of actions more streamlined.
-
-## Defaults/Setup
-
-After installation it is recommended to define a couple of those defaults.
-```julia
-using DFControl
-```
-default server:
-```julia
-setdefault_server("blabla@server.com") #default server
-```
-
-default pseudo potentials:
-this defines a directory on the server to look through for the pseudo potentials for each element. This will be used for certain options when changing atom properties etc.
-```julia
-setdefault_pseudodir(:pbesol,  "pseudos/pbesol/") #change to your pseudo_set_name and directory of choice
-setdefault_pseudodir(:pbesolrel, "pseudos/pbesolrel/")
-#more sets can be defined
-```
-
-followed by the actual loading of the various pseudo filenames:
-```julia
-configuredefault_pseudos()
-```
-This will then connect to the server, look through all the defined pseudo sets inside the `default_pseudos` and tries to link for each element, for each set the correct filename.
-To find out the filename of a certain atom for a certain pseudo set, or to check whether your config worked, you can do:
-```julia
-getdefault_pseudo(:O, :pbesolrel) #again change `pbesolrel` to the set you defined before
-```
-This should return you the filename for the pseudo potential file of Oxygen, `:O`, the format for elements in general is e.g. `:Mn`.
-If multiple pseudos are defined for one set and element, you can specify keyword `pseudo_fuzzy = ...` to pull out the one you want to use.
-For more info on other default functionality please look in the documentation and examples.
-
-## General Usage
-
-The main types in around which the package revolves are the `DFJob`, `DFCalculation`.
-A `DFJob` is comprised of a `Structure`, representing the structure that is simulated in the job, and a collection of calculations to be done. Other fields in `DFJob` are auxiliary properties, such as name, directories, etc.
-
-At this point, the main way the package works is by reading slurm job scripts such as the `test/test_job/job.tt` one.
-What is most important for succesfully parsing these is the format used in the lines that do the actual calculations, i.e. `runcommand exec <input_file.in> output_file.out`, for example: `mpirun -np 24 ~/bin/projwfc.x  <projwfc.in> projwfc.out`.
-The parsing is sort of robust but one should probably stick to this format.
-All other not recognized lines will be saved in the `header` field of the `DFJob`.
-The calculations in commented out lines will also be read and loaded, but they will have a field `DFCalculation.run=false`.
-When the `job.tt` file gets written upon saving of the `DFJob`, calculations which are marked to not run will be written in the `job.tt` file, but be commented out.
-
-As a quick start to see this in action you can do (Juno is highly recommended, for reading clarity)
-```julia
-job = DFJob(joinpath(dirname(pathof("DFControl")), "..", "test/test_job/"))
-```
-
-It will automatically look through the directory for a file which matches the fuzzy `*job*`. This can be specified through kwargs, further info in the documentation and examples.
-
-To do something similar on a directory on a server, you can do
-```julia
-job = DFJob("path/to/job/starting_from_home", "local_dir", server=getdefault_server())
-```
-If the `local_dir` doesn't exist it will be first created before pulling the `job` script and the calculations that it read from this file.
-
-If you ran some calculations, you should be able to pull the outputs into the `local_dir` of the `job`, followed by reading them:
-```julia
-outs = pulloutputs(job)
-outdata= outputdata(job)
-```
-
-If one of the calculations that were performed was a calculation that produced `bands` of some sort (currently both outputs of `nscf` and `bands` calculations count) using Quantum-Espresso, you can do
-```julia
-bands = outdata["name_of_calculation(e.g. nscf)"]
-using Plots
-plot(bands, fermi=outdata["nscf"][:fermi])
-```
-
-Calculations can be set to run or not by
-```julia
-setflow!(job, "" => false) #none will run
-setflow!(job, "nscf" => true, "bands" => true) #args..., and they are matched fuzzily
-```
-
-A job can be submitted by
-```julia
-submit(job)
-```
-If the job had "localhost" as it's server, it will run `qsub job.tt` locally, whereas if server and server_dir are something else, it will push the files and subsequently run them on the server.
-
-This gave just a very small overview of the functionality, please look into the [documentation](https://louisponet.github.io/DFControl.jl/latest) and the examples for more.
+See the [documentation](https://louisponet.github.io/DFControl.jl/) on how to get started.