From 14a4e39053fa71b3026ad8dd7022e3f8ecdbd3cd Mon Sep 17 00:00:00 2001
From: Adrian Henle <eahenle@gmail.com>
Date: Fri, 28 Jun 2024 16:06:48 -0700
Subject: [PATCH] update Project.toml (#196)

* update Project.toml

* JuliaFormatter Action Bot (#197)

Co-authored-by: eahenle <eahenle@users.noreply.github.com>

* fix compats

* atomsbase interface and printing fix

* fix

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: eahenle <eahenle@users.noreply.github.com>
---
 Project.toml   | 16 ++++++++--------
 src/crystal.jl | 46 +++++++++++++++++++++++++++++++++++++---------
 2 files changed, 45 insertions(+), 17 deletions(-)

diff --git a/Project.toml b/Project.toml
index a089534..e793e84 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 = "0.5.0"
+version = "0.5.1"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -20,17 +20,17 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 Aqua = "0.5"
-AtomsBase = "0.2.0"
-Bio3DView = "0.1"
+AtomsBase = "0.2, 0.3, 0.4"
+Bio3DView = "0.1, 1, 2"
 CSV = "0.10"
-DataFrames = "1.0"
+DataFrames = "1"
 Graphs = "1.4"
 JLD2 = "0.4"
 MetaGraphs = "0.7"
-PeriodicTable = "1.1"
-PrecompileSignatures = "3.0"
-StaticArrays = "1.3"
-Unitful = "1.11"
+PeriodicTable = "1"
+PrecompileSignatures = "3"
+StaticArrays = "1"
+Unitful = "1"
 julia = "1.6"
 
 [extras]
diff --git a/src/crystal.jl b/src/crystal.jl
index 01bc5f2..55be594 100644
--- a/src/crystal.jl
+++ b/src/crystal.jl
@@ -1,3 +1,7 @@
+# AtomsBase interface things
+import Base: position, length, getindex, keys, display, show, print, println
+import AtomsBase: velocity, bounding_box, boundary_conditions, atomic_symbol, species_type, atomic_number
+
 """
     SymmetryInfo(symmetry, space_group, is_p1)
 
@@ -157,7 +161,7 @@ function Crystal(
 
             # Make sure the space group is P1
             if line[1] == "_symmetry_space_group_name_H-M" ||
-               line[1] == "_space_group_name_Hall"         ||
+               line[1] == "_space_group_name_Hall" ||
                line[1] == "_space_group_name_H-M_alt"
                 # use anonymous function to combine all terms past the first
                 #   to extract space group name
@@ -1194,7 +1198,31 @@ crystal and adding new ones...\n",
     return new_crystal
 end
 
-function Base.show(io::IO, crystal::Crystal)
+function Base.show(io::IO, mime::MIME"text/plain", system::Crystal)
+    print(io, system)
+end
+
+print(xtal::Crystal) = show(xtal)
+
+print(io::IO, xtal::Crystal) = show(io, xtal)
+
+function println(xtal::Crystal)
+    println("")
+    show(xtal)
+end
+
+function println(io::IO, xtal::Crystal)
+    println(io, "")
+    show(io, xtal)
+end
+
+display(xtal::Crystal) = show(xtal)
+
+display(io::IO, xtal::Crystal) = show(io, xtal)
+
+show(xtal::Crystal) = show(stdout, xtal)
+
+function show(io::IO, crystal::Crystal)
     println(io, "Name: ", crystal.name)
     println(io, crystal.box)
     @printf(io, "\t# atoms = %d\n", crystal.atoms.n)
@@ -1329,13 +1357,11 @@ function Base.:+(
     return crystal
 end
 
-# AtomsBase interface things
-import Base.position
-import AtomsBase.velocity
-import AtomsBase.bounding_box
-import AtomsBase.boundary_conditions
-import Base.length, Base.getindex
-import AtomsBase.atomic_symbol
+keys(xtal::Crystal) = 1:xtal.atoms.n
+
+atomic_number(xtal::Crystal) = [elements[x].number for x in xtal.atoms.species]
+
+species_type(xtal::Crystal) = xtal.atoms.species
 
 length(xtal::Crystal) = xtal.atoms.n
 
@@ -1343,6 +1369,8 @@ getindex(xtal::Crystal, index::Int) = xtal.atoms[index]
 
 atomic_symbol(atom::Atoms) = atom.species[1]
 
+atomic_symbol(xtal::Crystal) = xtal.atoms.species
+
 function position(crystal::Crystal)
     pos = Cart(crystal.atoms.coords, crystal.box).x
     return [pos[:, i] for i in 1:size(pos, 2)] * u"Å"