From f2992d17cc6e29175ef41ea58d4f77fc6c431a30 Mon Sep 17 00:00:00 2001
From: Adrian Henle <eahenle@gmail.com>
Date: Sat, 12 Jun 2021 10:38:14 -0700
Subject: [PATCH] set_paths (#85)

---
 Project.toml        |  6 +++---
 docs/src/globals.md | 15 +++++++++++++++
 src/Xtals.jl        | 10 ++++++----
 src/misc.jl         | 29 +++++++++++++++++++++++++++++
 test/paths.jl       | 15 ++++++++++-----
 5 files changed, 63 insertions(+), 12 deletions(-)

diff --git a/Project.toml b/Project.toml
index ad91fa0..7aaad7a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "Xtals"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 authors = ["SimonEnsemble <cory.simon@oregonstate.edu>"]
-version = "0.3.0"
+version = "0.3.1"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -17,10 +17,10 @@ PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [compat]
-JLD2 = "^0.4.9"
-FIGlet = "^0.2.1"
 CSV = "^0.8.0"
 DataFrames = "^0.22.1"
+FIGlet = "^0.2.1"
+JLD2 = "^0.4.9"
 LightGraphs = "^1.3.0"
 MetaGraphs = "^0.6.6"
 PyCall = "^1.92"
diff --git a/docs/src/globals.md b/docs/src/globals.md
index ac88249..b8692a8 100644
--- a/docs/src/globals.md
+++ b/docs/src/globals.md
@@ -8,7 +8,22 @@ In `Xtals.jl`, global variables are stored in a dictionary called `rc`.  The ent
 - `rc[:covalent_radii]` : a dictionary which maps atomic species to their covalent radii in Å
 - `rc[:paths]` : a dictionary of paths to directories to search for input data
 
+## Paths
+
 The `rc[:paths]` dictionary holds the following:
 
 - `rc[:paths][:crystals]` : the path to find crystallographic files (`.cif`, `.cssr`) to read in
 - `rc[:paths][:data]` : not directly used by `Xtals.jl`, but important for other packages which use `Xtals`, e.g. [PorousMaterials.jl](https://simonensemble.github.io/PorousMaterials.jl/dev/)
+
+When `Xtals` is first loaded, the paths are set based on the present working directory.  `Xtals` expects to find a folder named `data` in the working directory, and assumes that crystallographic data will be present in `data/crystals`.  To change the location of the crystal inputs, either set `rc[:paths][:crystals]` directly, or use `set_paths`:
+
+```julia
+rc[:paths][:crystals] = "other_crystals" # crystals are now loaded from "other_crystals"
+set_paths("other_data") # crystals are now loaded from "other_data/crystals"
+```
+
+# Docs
+
+```@docs
+set_paths
+```
diff --git a/src/Xtals.jl b/src/Xtals.jl
index d297933..167a41c 100644
--- a/src/Xtals.jl
+++ b/src/Xtals.jl
@@ -32,9 +32,11 @@ include("pydeps.jl")
 function __init__()
     # load Python dependencies
     init_pydeps()
-    # sets paths to data and crystals relative to pwd() at import
-    rc[:paths][:data] = joinpath(pwd(), "data")
-    rc[:paths][:crystals] = joinpath(rc[:paths][:data], "crystals")
+    # create path entries in global dictionary
+    rc[:paths][:crystals] = ""
+    rc[:paths][:data] = ""
+    # set paths to data and crystals relative to pwd() at import
+    set_paths(joinpath(pwd(), "data"))
 end
 
 
@@ -52,7 +54,7 @@ export
     nearest_image!, distance, overlap, remove_duplicates, pairwise_distances,
 
     # misc.jl
-    read_xyz, write_xyz, read_mol, write_mol2, assert_P1_symmetry,
+    read_xyz, write_xyz, read_mol, write_mol2, assert_P1_symmetry, set_paths,
 
     # crystal.jl
     Crystal, strip_numbers_from_atom_labels!, assign_charges, chemical_formula, molecular_weight, 
diff --git a/src/misc.jl b/src/misc.jl
index be593da..282839f 100644
--- a/src/misc.jl
+++ b/src/misc.jl
@@ -154,3 +154,32 @@ function write_mol2(xtal::Crystal; filename::String="")
 	# flush the buffer
 	close(f)
 end
+
+
+"""
+    `set_paths("path_to_data", print_paths=true)`
+
+Sets all paths in `rc[:paths]` relative to `path_to_data`.  Paths follow the standard format of 
+`rc[:paths][:foo] = "path_to_data/foo"`, except for `rc[:paths][:data]` which is `"path_to_data"`.
+Warnings are issued if any chosen paths are not valid folders.
+# Arguments
+- `path_to_data::String` : an absolute or relative path to use as the root of the data folder tree. Defaults to present working directory.
+- `print_paths::Bool` : Optional.  If `true`, prints contents of `rc[:paths]` to console.  Defaults to `false`.
+- `no_warn::Bool` : Optional.  Set `true` to suppress invalid path warnings.  Default to `false`.
+"""
+function set_paths(path_to_data::String=pwd(); print_paths::Bool=false, no_warn::Bool=false)
+    for (key, path) ∈ rc[:paths] # set all relative paths
+        rc[:paths][key] = joinpath(path_to_data, String(key))
+    end
+    rc[:paths][:data] = path_to_data # correct data root path
+    if print_paths
+        @info rc[:paths]
+    end
+    if !no_warn
+        for (key, path) ∈ rc[:paths]
+            if !isdir(path)
+                @warn "$key path directory not found" path
+            end
+        end
+    end
+end
diff --git a/test/paths.jl b/test/paths.jl
index 48b045a..28c0def 100644
--- a/test/paths.jl
+++ b/test/paths.jl
@@ -5,10 +5,15 @@ using Test
 
 @testset "Path Tests" begin
     @test rc[:atomic_masses][:He] == 4.0026
-    oldpath = rc[:paths][:crystals]
-    rc[:paths][:crystals] = joinpath(pwd(), "other_data", "other_crystals")
-    Crystal("other_SBMOF-1.cif")
-    rc[:paths][:crystals] = oldpath
-    @test true # if made it this far :)
+    oldpath = rc[:paths][:data]
+    newpath = joinpath(pwd(), "other_data")
+    set_paths(newpath, print_paths=true)
+    @test rc[:paths][:crystals] == joinpath(newpath, "crystals")
+    rc[:paths][:crystals] = joinpath(newpath, "other_crystals")
+    xtal = Crystal("SBMOF-1.cif")
+    @test xtal.atoms.n == 120
+    rc[:paths][:foo] = "bar"
+    set_paths(oldpath)
+    @test rc[:paths][:foo] == joinpath(oldpath, "foo")
 end
 end