Create formatter.yml

.github/workflows/formatter.yml

@@ -0,0 +1,87 @@
+name: formatter
+
+on:
+  pull_request:
+    branches: [ master ]
+
+concurrency: # only allow the most recent workflow to execute
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env: # environment variables
+  julia_version: '1.8.2' # julia version to use on all runners (except cross-platform-julia)
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: mdecoleman/[email protected]
+        id: vars
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ env.julia_version }}
+
+      - uses: actions/checkout@main
+
+      - name: Install JuliaFormatter
+        run: julia  -e 'using Pkg; Pkg.add("JuliaFormatter")'
+
+      - name: Run JuliaFormatter
+        run: | 
+          julia  -e '
+            using JuliaFormatter; 
+            format(
+              ".", 
+              verbose=true,
+              always_for_in=true,
+              whitespace_typedefs=true,
+              whitespace_ops_in_indices=true,
+              remove_extra_newlines=true,
+              short_to_long_function_def=true,
+              long_to_short_function_def=true,
+              always_use_return=true,
+              whitespace_in_kwargs=false,
+              format_docstrings=true,
+              conditional_to_if=true,
+              normalize_line_endings="unix",
+              trailing_comma=false,
+              separate_kwargs_with_semicolon=true,
+              format_markdown=true
+            )'
+
+      - name: Formatting Check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'
+
+      - if: ${{ failure() }}
+        id: cpr
+        name: Formatting PR
+        uses: peter-evans/create-pull-request@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          base: ${{ steps.vars.outputs.branch }}
+          commit-message: JuliaFormatter Action Bot
+          title: 'Automatic JuliaFormatter.jl run'
+          branch: auto-juliaformatter-pr
+          delete-branch: true
+          labels: formatting, automated pr, no changelog
+
+      - if: ${{ failure() }}
+        name: comment on PR
+        uses: thollander/actions-comment-pull-request@v1
+        with:
+          message: 'Code formatting requirements not met.  See PR #${{ steps.cpr.outputs.pull-request-number }}'
+          pr_number: ${{ github.event.issue.number }}
+          comment_includes: "Code formatting requirements not met.  See PR #"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -1,7 +1,7 @@
 ![PorousMaterials.jl](PMlogo.png)
 
-| **Documentation** | **DOI** | **Build Status** | **Test Coverage** |
-|:---:|:---:|:---:|:---:|
+| **Documentation**                                                                                                                                                                                                                 | **DOI**                                                                                        | **Build Status**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | **Test Coverage**                                                                                                                                                                                                                                                                                          |
+|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|
 | [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://simonensemble.github.io/PorousMaterials.jl/dev) [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://simonensemble.github.io/PorousMaterials.jl/stable) | [![DOI](https://zenodo.org/badge/102691401.svg)](https://zenodo.org/badge/latestdoi/102691401) | [![Build](https://github.com/SimonEnsemble/PorousMaterials.jl/actions/workflows/ci_testing.yml/badge.svg)](https://github.com/SimonEnsemble/PorousMaterials.jl/actions/workflows/ci_testing.yml) [![Docs](https://github.com/SimonEnsemble/PorousMaterials.jl/actions/workflows/doc_deployment.yml/badge.svg)](https://github.com/SimonEnsemble/PorousMaterials.jl/actions/workflows/doc_deployment.yml) [![Weekly](https://github.com/SimonEnsemble/PorousMaterials.jl/actions/workflows/weekly.yml/badge.svg)](https://github.com/SimonEnsemble/PorousMaterials.jl/actions/workflows/weekly.yml) | [![codecov](https://codecov.io/gh/SimonEnsemble/PorousMaterials.jl/branch/master/graph/badge.svg?token=PWsgNnxfZI)](https://codecov.io/gh/SimonEnsemble/PorousMaterials.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 classical molecular modeling of adsorption in porous crystals such as metal-organic frameworks (MOFs).

docs/README.md

@@ -1,7 +1,9 @@
 notes:
-- all documentation files are in `docs/src`
-- `make.jl` automatically pulls doc strings from code in `src`
 
-to deploy locally: 
-- run `julia make.jl` from `docs` directory.
-- open `build/index.html` in your browswer
+  - all documentation files are in `docs/src`
+  - `make.jl` automatically pulls doc strings from code in `src`
+
+to deploy locally:
+
+  - run `julia make.jl` from `docs` directory.
+  - open `build/index.html` in your browswer

docs/make.jl

@@ -1,27 +1,27 @@
 using Documenter
 using PorousMaterials
 
-makedocs(
-    root = joinpath(dirname(pathof(PorousMaterials)), "..", "docs"),
-    modules = [PorousMaterials],
-    sitename = "PorousMaterials.jl",
-    clean = true,
-    pages = [
-            "PorousMaterials" => "index.md",
-            "paths" => "paths.md",
-            "matter" => "matter.md",
-            "boxes" => "box.md",
-            "crystals" => "crystal.md",
-            "molecules" => "molecule.md",
-            "computing distances" => "distance.md",
-            "forcefields" => "force_field.md",
-            "equations of state" => "eos.md",
-            "Henry coefficients" => "henry.md",
-            "grand-canonical Monte Carlo simulations" => "gcmc.md",
-            "energy minimum" => "energy_min.md",
-            "grids" => "grid.md"
-            ],
-    format = Documenter.HTML(assets = ["assets/flux.css"])
+makedocs(;
+    root=joinpath(dirname(pathof(PorousMaterials)), "..", "docs"),
+    modules=[PorousMaterials],
+    sitename="PorousMaterials.jl",
+    clean=true,
+    pages=[
+        "PorousMaterials" => "index.md",
+        "paths" => "paths.md",
+        "matter" => "matter.md",
+        "boxes" => "box.md",
+        "crystals" => "crystal.md",
+        "molecules" => "molecule.md",
+        "computing distances" => "distance.md",
+        "forcefields" => "force_field.md",
+        "equations of state" => "eos.md",
+        "Henry coefficients" => "henry.md",
+        "grand-canonical Monte Carlo simulations" => "gcmc.md",
+        "energy minimum" => "energy_min.md",
+        "grids" => "grid.md"
+    ],
+    format=Documenter.HTML(; assets=["assets/flux.css"])
 )
 
-deploydocs(repo="github.com/SimonEnsemble/PorousMaterials.jl.git")
+deploydocs(; repo="github.com/SimonEnsemble/PorousMaterials.jl.git")

docs/src/box.md

@@ -22,11 +22,13 @@ A `Box` is most conveniently constructed from its basic spatial data (`a` `b` `c
 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)
+
 # output
+
 Bravais unit cell of a crystal.
 	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000000 deg.
 	Unit cell dimensions a = 26.131730 Å. b = 26.131730 Å, c = 6.722028 Å
@@ -35,26 +37,31 @@ Bravais unit cell of a crystal.
 
 A `Box` may also be defined by providing only the `Frac`tional-to-`Cart`esian conversion
 matrix:
+
 ```jldoctest box
 box = Box([26.1317 -13.0659 0; 0 22.6307 0; 0 0 6.72203])
+
 # output
+
 Bravais unit cell of a crystal.
 	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg.
 	Unit cell dimensions a = 26.131700 Å. b = 26.131711 Å, c = 6.722030 Å
 	Volume of unit cell: 3975.265115 ų
 ```
 
 To quickly get a simple unit-cubic `Box`, use the `unit_cube` function.
+
 ```jldoctest
 unit_cube()
+
 # output
+
 Bravais unit cell of a crystal.
 	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg.
 	Unit cell dimensions a = 1.000000 Å. b = 1.000000 Å, c = 1.000000 Å
 	Volume of unit cell: 1.000000 ų
 ```
 
-
 ## transforming coordinates
 
 Conversions are provided for switching between `Frac`tional and `Cart`esian `Coords`
@@ -63,38 +70,40 @@ using the `Box` (works for `Atoms` and `Charges`, too)
 ```jldoctest box
 xtal = Crystal("SBMOF-1.cif")
 Cart(xtal.atoms.coords, xtal.box)
+
 # output
+
 Cart([4.594867082350715 -0.952720283971488 … 0.8392490029633858 -1.5321086078257065; 1.4395486200000005 4.2228986200000005 … 1.4289162230000012 4.212266223; 5.89964228469024 5.359217037237699 … 17.537474811394276 16.239103154389543])
 ```
 
-
 ## replicating a box
 
 For simulations in larger volumes than a single crystallograhic unit cell, the
 `Box` may be replicated along each or any of the three crystallographic axes.
 
 ```jldoctest box
-replicated_box = replicate(box, (2,2,2))
+replicated_box = replicate(box, (2, 2, 2))
+
 # output
+
 Bravais unit cell of a crystal.
 	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg.
 	Unit cell dimensions a = 52.263400 Å. b = 52.263422 Å, c = 13.444060 Å
 	Volume of unit cell: 31802.120923 ų
 ```
 
-
 ## exporting a box
 
 For visualization of the unit cell boundaries, the `Box` may be written out to a
 `.vtk` file for use in [Visit](https://wci.llnl.gov/simulation/computer-codes/visit/)
 
 ```jldoctest box
 write_vtk(box, "box.vtk")
+
 # output
 
 ```
 
-
 # detailed docs
 
 ```@docs

docs/src/crystal.md

@@ -20,10 +20,12 @@ 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)
 ```
 
@@ -37,6 +39,7 @@ It is important to use this function prior to GCMC or Henry coefficient calculat
 strip_numbers_from_atom_labels!(xtal)
 
 # output
+
 ```
 
 ## converting the coordinates to cartesian space
@@ -47,7 +50,9 @@ that can be done by using the unit cell information of the crystal.
 ```jldoctest crystal
 xtal.atoms.coords.xf                                    # array of fractional coordinates
 cart_coords = xtal.box.f_to_c * xtal.atoms.coords.xf    # array of cartesian coordinates
+
 # output
+
 3×120 Matrix{Float64}:
  4.59487  -0.95272   2.68943   8.23701  …  8.8164    0.839249  -1.53211
  1.43955   4.2229    4.12715   1.3438      1.35443   1.42892    4.21227
@@ -59,23 +64,14 @@ cart_coords = xtal.box.f_to_c * xtal.atoms.coords.xf    # array of cartesian coo
 For many simulations, one needs to replicate the unit cell multiple times to create a bigger super cell.
 
 ```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
+
 # output
-Name: SBMOF-1.cif
-Bravais unit cell of a crystal.
-	Unit cell angles α = 90.000000 deg. β = 100.897000 deg. γ = 90.000000 deg.
-	Unit cell dimensions a = 23.238600 Å. b = 11.133400 Å, c = 45.862400 Å
-	Volume of unit cell: 11651.776815 ų
-
-	# atoms = 960
-	# charges = 960
-	chemical formula: Ca₃₂C₄₄₈H₂₅₆O₁₉₂S₃₂
-	space Group: P1
-	symmetry Operations:
-		'x, y, z'
-	bonding graph:
-		# vertices = 960
-		# edges = 0
+
+Crystal(Ca₃₂C₄₄₈H₂₅₆O₁₉₂S₃₂, periodic = TTT):
+    bounding_box      : [ 23.2386        0        0;
+                         6.81724e-16  11.1334        0;
+                         -8.67001 3.33915e-15  45.0354]u"Å"
 ```
 
 ## finding other properties
@@ -84,7 +80,9 @@ Bravais unit cell of a crystal.
 rho = crystal_density(xtal)         # Crystal density of the crystal in kg/m^2
 mw = molecular_weight(xtal)         # The molecular weight of the unit cell in amu
 formula = chemical_formula(xtal)    # The irreducible chemical formula of the crystal
+
 # output
+
 "Ca₄C₅₆H₃₂O₂₄S₄"
 ```
 
@@ -95,11 +93,17 @@ If the crystal structure file does not contains partial charges, we provide meth
 ```julia
 species_to_charges = Dict(:Ca => 2.0, :C => 1.0, :H => -1.0)                # This method assigns a static charge to atom species
 charged_xtal = assign_charges(xtal, species_to_charges, 1e-5)                # This function creates a new charged `Crystal` object.
-                                                                            #   The function checks for charge neutrality with a tolerance of 1e-5
+#   The function checks for charge neutrality with a tolerance of 1e-5
 new_charges = Charges([2.0, 1.0, -1.0, -1.0, ...], 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
 ```
 
 ## writing crystal files
@@ -109,11 +113,11 @@ 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

docs/src/distance.md

@@ -14,7 +14,9 @@ within a given `box`.
 ```jldoctest distance
 xtal = Crystal("SBMOF-1.cif")
 distance(xtal.atoms.coords, xtal.box, 1, 10, false) # Cartesian distance within the unit cell
+
 # output
+
 4.962373067546231
 ```
 
@@ -23,15 +25,19 @@ across the periodic boundaries of the `box`.
 
 ```jldoctest distance
 distance(xtal.atoms.coords, xtal.box, 1, 10, true) # Cartesian distance accounting for periodic boundary
+
 # output
+
 4.143597209982431
 ```
 
 `distance` also works on `Atoms` and `Charges`.
 
 ```jldoctest distance
 distance(xtal.atoms, xtal.box, 3, 5, true)
+
 # output
+
 10.244292605252747
 ```