formatting (#178)

* formatting * JuliaFormatter Action Bot (#179) Co-authored-by: eahenle <[email protected]> * JuliaFormatter Action Bot (#180) Co-authored-by: eahenle <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: eahenle <[email protected]>
SimonEnsemble · Oct 12, 2022 · f99aa60 · f99aa60
1 parent 9adbe0d
commit f99aa60
Show file tree

Hide file tree

Showing 31 changed files with 1,802 additions and 1,218 deletions.
diff --git a/.github/workflow_extras/write_load_combos.jl b/.github/workflow_extras/write_load_combos.jl
@@ -1,7 +1,7 @@
 using Combinatorics
 open("load_combos.sh", "w") do f
-    for (a,b,c,d) in permutations(ARGS)
+    for (a, b, c, d) in permutations(ARGS)
         write(f, "julia --project -e 'using $a; using $b; using $c; using $d' && \\\n")
     end
-    write(f, "echo -e \\\\nDone!\n")
-end
+    return write(f, "echo -e \\\\nDone!\n")
+end
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 ![Xtals.jl](logo.jpg)
 
-| **Documentation** | **Build Status** | **Test Coverage** |
-|:---:|:---:|:---:|
+| **Documentation**                                                                                                                                                                                             | **Build Status**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | **Test Coverage**                                                                                                                                                                                                                                                                      |
+|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|
 | [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://SimonEnsemble.github.io/Xtals.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://SimonEnsemble.github.io/Xtals.jl/dev) | [![CI](https://github.com/SimonEnsemble/Xtals.jl/actions/workflows/CI_Build.yml/badge.svg)](https://github.com/SimonEnsemble/Xtals.jl/actions/workflows/CI_Build.yml) [![Docs](https://github.com/SimonEnsemble/Xtals.jl/actions/workflows/doc_deployment.yml/badge.svg)](https://github.com/SimonEnsemble/Xtals.jl/actions/workflows/doc_deployment.yml) [![weekly](https://github.com/SimonEnsemble/Xtals.jl/actions/workflows/weekly.yml/badge.svg)](https://github.com/SimonEnsemble/Xtals.jl/actions/workflows/weekly.yml) | [![codecov](https://codecov.io/gh/SimonEnsemble/Xtals.jl/branch/master/graph/badge.svg?token=QM6XZ3KAW1)](https://codecov.io/gh/SimonEnsemble/Xtals.jl) [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) |
 
 A pure-[Julia](https://julialang.org/) package for importing, manipulating, and working with crystal structures, such as metal-organic frameworks (MOFs).
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,23 +1,23 @@
 using Documenter
 using Xtals, XtalsPyTools
 
-makedocs(
-    root = joinpath(dirname(pathof(Xtals)), "..", "docs"),
-    modules = [Xtals, XtalsPyTools],
-    sitename = "Xtals.jl",
-    clean = true,
-    pages = [
-            "Xtals" => "index.md",
-            "globals" => "globals.md",
-            "matter" => "matter.md",
-            "boxes" => "box.md",
-            "crystals" => "crystal.md",
-            "computing distances" => "distance.md",
-            "bonding" => "bonds.md",
-            "visualization" => "visualization.md",
-            "XtalsPyTools" => "pytools.md"
-            ],
-    format = Documenter.HTML(assets = ["assets/flux.css"])
+makedocs(;
+    root=joinpath(dirname(pathof(Xtals)), "..", "docs"),
+    modules=[Xtals, XtalsPyTools],
+    sitename="Xtals.jl",
+    clean=true,
+    pages=[
+        "Xtals" => "index.md",
+        "globals" => "globals.md",
+        "matter" => "matter.md",
+        "boxes" => "box.md",
+        "crystals" => "crystal.md",
+        "computing distances" => "distance.md",
+        "bonding" => "bonds.md",
+        "visualization" => "visualization.md",
+        "XtalsPyTools" => "pytools.md"
+    ],
+    format=Documenter.HTML(; assets=["assets/flux.css"])
 )
 
-deploydocs(repo = "github.com/SimonEnsemble/Xtals.jl.git")
+deploydocs(; repo="github.com/SimonEnsemble/Xtals.jl.git")
diff --git a/docs/src/bonds.md b/docs/src/bonds.md
@@ -11,42 +11,48 @@ The nodes of the graph correspond to the [`Crystal`](@ref)'s [`Atoms`](@ref), an
 
 ## Bonding Rules
 
-`Xtals` uses an array of [`BondingRule`](@ref) structs stored in `rc` for deciding if two [`Atoms`](@ref) are an appropriate distance to be chemically bonded.  
-The default rules are based on the [Cordero covalent radii](https://doi.org/10.1039/B801115J), modified based on the work of [Thomas Manz](https://doi.org/10.1039/c9ra07327b).  
+`Xtals` uses an array of [`BondingRule`](@ref) structs stored in `rc` for deciding if two [`Atoms`](@ref) are an appropriate distance to be chemically bonded.
+The default rules are based on the [Cordero covalent radii](https://doi.org/10.1039/B801115J), modified based on the work of [Thomas Manz](https://doi.org/10.1039/c9ra07327b).
 Each [`BondingRule`](@ref) is composed of two chemical species symbols and a floating point value, the maximum distance for inferring a bond between the indicated species.
 
 ```jldoctest; output=false
 BondingRule(:C, :C, 1.77)
+
 # output
+
 BondingRule(:C, :C, 1.77)
 ```
 
-The global bonding rules may be augmented with [`add_bonding_rules`](@ref) or written to/read from disk with [`write_bonding_rules`](@ref) and [`read_bonding_rules`](@ref).  
-The default rules are determined from `rc[:covalent_radii]` at module load, but *are not recalculated upon changes to the covalent radii.*  
+The global bonding rules may be augmented with [`add_bonding_rules`](@ref) or written to/read from disk with [`write_bonding_rules`](@ref) and [`read_bonding_rules`](@ref).
+The default rules are determined from `rc[:covalent_radii]` at module load, but *are not recalculated upon changes to the covalent radii.*
 If `rc[:covalent_radii]` is altered and new bonding rules should be calculated, the user must do `rc[:bonding_rules] = bondingrules()`.
 
 ## Adding Bonds to Crystals
 
-By default, bonding information is not added to a [`Crystal`](@ref). 
-Bonds may be inferred at the time of loading structure data by using the `infer_bonds` keyword argument.  
+By default, bonding information is not added to a [`Crystal`](@ref).
+Bonds may be inferred at the time of loading structure data by using the `infer_bonds` keyword argument.
 See [`Crystal`](@ref) for more details.
 
 ```jldoctest bonds
-xtal = Crystal("SBMOF-1.cif", infer_bonds=true, periodic_boundaries=true)
+xtal = Crystal("SBMOF-1.cif"; infer_bonds=true, periodic_boundaries=true)
 xtal.bonds
+
 # output
+
 {120, 144} undirected Int64 metagraph with Float64 weights defined by :weight (default weight 1.0)
 ```
 
-The first number is the number of nodes, and the second is the number of edges.  
+The first number is the number of nodes, and the second is the number of edges.
 The `:weight` attribute is not used, and can be ignored.
 
 [`remove_bonds!`](@ref) clears the bonding information from a [`Crystal`](@ref):
 
 ```jldoctest bonds
 remove_bonds!(xtal)
 xtal.bonds
+
 # output
+
 {120, 0} undirected Int64 metagraph with Float64 weights defined by :weight (default weight 1.0)
 ```
 
@@ -55,46 +61,54 @@ Use [`infer_bonds!`](@ref) to infer plausible bonds using the global bonding rul
 ```jldoctest bonds
 infer_bonds!(xtal, true)
 xtal.bonds
+
 # output
+
 {120, 144} undirected Int64 metagraph with Float64 weights defined by :weight (default weight 1.0)
 ```
 
 ## Bonds from Input File
 
-Some chemical information formats, like `.cif` and `.mol`, can store not only the cartesian coordinates of atoms, but also the graph of bonds between atoms in molecules and crystals.  
-The `read_bonds_from_file` keyword argument for [`Crystal`](@ref) enables loading these bonds when reading the data.  
+Some chemical information formats, like `.cif` and `.mol`, can store not only the cartesian coordinates of atoms, but also the graph of bonds between atoms in molecules and crystals.
+The `read_bonds_from_file` keyword argument for [`Crystal`](@ref) enables loading these bonds when reading the data.
 [`read_mol`](@ref) also returns bond information.
 
 ## Bonds for Atoms
 
-In the case that atomic coordinates are loaded from XYZ format, there will be no unit cell information.  
+In the case that atomic coordinates are loaded from XYZ format, there will be no unit cell information.
 To infer bonds between atoms in this case, use the [`infer_bonds`](@ref) function:
 
 ```jldoctest bonds
 atoms = Cart(xtal.atoms, xtal.box) # get atoms in Cartesian coords
 bonds = infer_bonds(atoms) # infer bonding graph
+
 # output
+
 {120, 110} undirected Int64 metagraph with Float64 weights defined by :weight (default weight 1.0)
 ```
 
 ## Bond Distances, Vectors, and Angles
 
-Bonds may be labeled with several additional pieces of information.  
+Bonds may be labeled with several additional pieces of information.
 The first is the center-to-center distance between the bonded atoms, accessible via [`bond_distance`](@ref):
 
 ```jldoctest bonds
 bond_distance(xtal, 1, 5)
+
 # output
+
 1.5233240952030063
 ```
 
-The bond distance is automatically added by [`infer_bonds!`](@ref). 
+The bond distance is automatically added by [`infer_bonds!`](@ref).
 Applying [`calculate_bond_vectors!`](@ref) (or passing `calculate_vectors=true` to [`infer_bonds!`](@ref)) labels each edge in the bonding graph with a vector, accessible via [`get_bond_vector`](@ref):
 
 ```jldoctest bonds
 calculate_bond_vectors!(xtal)
 get_bond_vector(xtal, 1, 5)
+
 # output
+
 3-element Vector{Float64}:
  -1.2460713575602618
  -0.26441824999999985
@@ -105,7 +119,9 @@ While the bond graph itself is undirected, the vectors returned by [`get_bond_ve
 
 ```jldoctest bonds
 get_bond_vector(xtal, 5, 1)
+
 # output
+
 3-element Vector{Float64}:
   1.2460713575602618
   0.26441824999999985
@@ -117,7 +133,9 @@ To get the angle (in radians) between two bonds, use [`bond_angle`](@ref):
 
 ```jldoctest bonds
 bond_angle(xtal, 1, 5, 9)
+
 # output
+
 2.089762039489374
 ```
 

diff --git a/docs/src/box.md b/docs/src/box.md
@@ -18,9 +18,9 @@ For example, given the unit cell of Co-MOF-74, we can define its [`Box`](@ref):
 a = 26.13173 # Å
 b = 26.13173
 c = 6.722028
-α = π/2 # radians
-β = π/2
-γ = 2*π/3
+α = π / 2 # radians
+β = π / 2
+γ = 2 * π / 3
 box = Box(a, b, c, α, β, γ)
 ```
 
@@ -40,7 +40,6 @@ To quickly get a simple unit-cubic [`Box`](@ref), use the [`unit_cube`](@ref) fu
 #└       Volume of unit cell: 1.000000 Å³
 ```
 
-
 ## Transforming Coordinates
 
 Conversions are provided for switching between [`Frac`](@ref)tional and [`Cart`](@ref)esian [`Coords`](@ref) using the [`Box`](@ref) (works for [`Atoms`](@ref) and [`Charges`](@ref), too).
@@ -53,14 +52,13 @@ Cart(xtal.atoms.coords, xtal.box)
 # 1.231811631 0.32198514120000005 … 6.2082409932000004 2.2119953472])
 ```
 
-
 ## Replicating a Box
 
 For simulations in larger volumes than a single crystallograhic unit cell, the [`Box`](@ref) may be replicated along each or any of the three crystallographic axes.
 See [`replicate`](@ref).
 
 ```julia
-replicated_box = replicate(box, (2,2,2))
+replicated_box = replicate(box, (2, 2, 2))
 ```
 
 ## Exporting a Box
@@ -69,7 +67,9 @@ For visualization of the unit cell boundaries, the [`Box`](@ref) may be written
 
 ```jldoctest; setup=:(box = Box([26.1317 -13.0659 0; 0 22.6307 0; 0 0 6.72203])), output=false
 write_vtk(box, "box.vtk"; verbose=true)
+
 # output
+
 See box.vtk
 ```
 

diff --git a/docs/src/crystal.md b/docs/src/crystal.md
@@ -10,8 +10,8 @@ end
 
 ## Reading in a Crystal Structure File
 
-Currently, the crystal structure file reader accepts `.cif` and `.cssr` file formats. 
-`Xtals.jl` looks for the crystal structure files in `rc[:paths][:crystals]` which is by default `./data/crystals` (relative to `pwd()` at module loading). 
+Currently, the crystal structure file reader accepts `.cif` and `.cssr` file formats.
+`Xtals.jl` looks for the crystal structure files in `rc[:paths][:crystals]` which is by default `./data/crystals` (relative to `pwd()` at module loading).
 By typing `rc[:paths][:crystals] = "my_crystal_dir"`, `Xtals.jl` now looks for the crystal structure file in `my_crystal_dir`.
 The files can be read as:
 
@@ -22,37 +22,43 @@ xtal.box                            # The unit cell information
 xtal.atoms                          # The atom coordinates (in fractional space) and the atom identities
 xtal.charges                        # The charge magnitude and coordinates (in fractional space)
 xtal.bonds                          # Bonding information in the structure. By default this is an empty graph,
-                                    #  but use `read_bonds_from_file=true` argument in `Crystal` to read from crystal structure file
+#  but use `read_bonds_from_file=true` argument in `Crystal` to read from crystal structure file
 xtal.symmetry                       # Symmetry information of the crystal. By default converts the symmetry to P1 symmetry.
-                                    #  Use `convert_to_p1=false` argument in `Crystal` to keep original symmetry
+#  Use `convert_to_p1=false` argument in `Crystal` to keep original symmetry
+
 # output
+
 Xtals.SymmetryInfo(["x"; "y"; "z";;], "P1", true)
 ```
 
 ## Fixing Atom Species Labels
 
-Often, the atoms species are appended by numbers. 
+Often, the atoms species are appended by numbers.
 This messes with the internal workings of `Xtals.jl`.
 To circumvent this problem, the function [`strip_numbers_from_atom_labels!`](@ref) removes the appended numbers.
 It is important to use this function prior to GCMC or Henry coefficient calculations and bond inference operations.
 
 ```jldoctest crystal
-xtal = Crystal("IRMOF-1.cif", species_col=["_atom_site_label"])
+xtal = Crystal("IRMOF-1.cif"; species_col=["_atom_site_label"])
 xtal.atoms.species[1]
+
 # output
+
 :Zn1
 ```
 
 ```jldoctest crystal
 strip_numbers_from_atom_labels!(xtal)
 xtal.atoms.species[1]
+
 # output
+
 :Zn
 ```
 
 ## Converting the Coordinates to Cartesian Space
 
-The coordinates of the [`Crystal`](@ref)'s [`Atoms`](@ref) are stored in [`Frac`](@ref)tional coordinates. 
+The coordinates of the [`Crystal`](@ref)'s [`Atoms`](@ref) are stored in [`Frac`](@ref)tional coordinates.
 If one needs to analyze the [`Cart`](@ref)esian coordinates of the [`Crystal`](@ref), that can be done by using the unit cell ([`Box`](@ref)) information.
 
 ```julia
@@ -66,9 +72,11 @@ For many simulations, one needs to replicate the unit cell multiple times to cre
 This is done with [`replicate`](@ref):
 
 ```jldoctest crystal
-super_xtal = replicate(xtal, (2,2,2))       # Replicates the original unit cell once in each dimension
+super_xtal = replicate(xtal, (2, 2, 2))       # Replicates the original unit cell once in each dimension
 xtal.atoms.n, super_xtal.atoms.n
+
 # output
+
 (424, 3392)
 ```
 
@@ -87,12 +95,20 @@ If the structure file does not contain partial charges, we provide methods to as
 ```jldoctest crystal; output=false
 species_to_charge = Dict(:Zn => 2.0, :C => 0.0, :H => 0.0, :O => -0.61538)  # This method assigns a static charge to atom species
 charged_xtal = assign_charges(xtal, species_to_charge, 1e-3)                # This function creates a new charged `Crystal` object.
-                                                                            #   The function checks for charge neutrality with a tolerance of 1e-3
+#   The function checks for charge neutrality with a tolerance of 1e-3
 new_charges = Charges(zeros(xtal.atoms.n), xtal.atoms.coords)
-other_charged_xtal = Crystal(xtal.name, xtal.box, xtal.atoms,               # Here we create a new `Charges` object using an array of new charges.
-                             new_charges, xtal.bonds, xtal.symmetry)        #   The number of charges in the array has to be equal to the number of atoms
-                                                                            #   and finally a new `Crystal` object is manually created
+other_charged_xtal = Crystal(
+    xtal.name,
+    xtal.box,
+    xtal.atoms,               # Here we create a new `Charges` object using an array of new charges.
+    new_charges,
+    xtal.bonds,
+    xtal.symmetry
+)        #   The number of charges in the array has to be equal to the number of atoms
+#   and finally a new `Crystal` object is manually created
+
 # output
+
 Name: IRMOF-1.cif
 Bravais unit cell of a crystal.
 	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg.
@@ -117,11 +133,11 @@ We provide methods to write both `.xyz` and `.cif` files.
 ```jldoctest crystal; output=false
 write_cif(xtal, "my_new_cif_file.cif")      # Stored in the current directory
 write_xyz(xtal, "my_new_xyz_file.xyz")      # stored in the current directory
+
 # output
 
 ```
 
-
 # Detailed Docs
 
 ```@docs

diff --git a/docs/src/distance.md b/docs/src/distance.md
@@ -6,29 +6,35 @@ end
 
 # Distances
 
-The distance between two [`Atoms`](@ref) in a [`Crystal`](@ref) is central to many operations within `Xtals.jl`.  
+The distance between two [`Atoms`](@ref) in a [`Crystal`](@ref) is central to many operations within `Xtals.jl`.
 The [`distance`](@ref) function calculates the [`Cart`](@ref)esian displacement between the [`Coords`](@ref) ([`Cart`](@ref) or [`Frac`](@ref)) of two points, `i` and `j`, within a given [`Box`](@ref), in units of Å.
 
 ```jldoctest distance
 xtal = Crystal("IRMOF-1.cif")
 distance(xtal.atoms.coords, xtal.box, 1, 2, false)
+
 # output
+
 18.538930020700434
 ```
 
 The `apply_pbc` argument allows for calculation of distances across the periodic boundaries of the [`Box`](@ref).
 
 ```jldoctest distance
 distance(xtal.atoms.coords, xtal.box, 1, 2, true)
+
 # output
+
 15.096469110488975
 ```
 
 [`distance`](@ref) also works on [`Atoms`](@ref) and [`Charges`](@ref).
 
 ```jldoctest distance
 distance(xtal.atoms, xtal.box, 3, 5, true)
+
 # output
+
 16.90555095103936
 ```