v0.5

.github/workflows/CI_Build.yml

@@ -33,7 +33,7 @@ jobs:
         uses: julia-actions/julia-buildpkg@latest
 
       - name: install dependencies
-        run: julia --project --color=yes -e 'import Pkg; Pkg.add.(["FIGlet", "Coverage"])'
+        run: julia --project --color=yes -e 'import Pkg; Pkg.add.(["Coverage"])'
 
       - name: run tests
         run: julia --project --color=yes --code-coverage -e 'import Pkg; Pkg.test(coverage=true)'

.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 }}

Project.toml

@@ -1,21 +1,19 @@
 name = "PorousMaterials"
 uuid = "68953c7c-a3c7-538e-83d3-73516288599e"
 authors = ["SimonEnsemble <[email protected]>"]
-version = "0.4.2"
+version = "0.5.0"
 
 [deps]
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-FIGlet = "3064a664-84fe-4d92-92c7-ed492f3d8fae"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
+PrecompileSignatures = "91cefc8d-f054-46dc-8f8c-26e11d7c5411"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -24,31 +22,25 @@ Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Xtals = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 
 [compat]
-Aqua = "0.5.5"
-CSV = "0.10.4"
+Aqua = "0.5"
+CSV = "0.10"
 DataFrames = "1"
-FIGlet = "0.2.1"
-FileIO = "1"
 Graphs = "1"
-JLD2 = "0.4.22"
+JLD2 = "0.4"
 OffsetArrays = "1"
 Optim = "1"
 Polynomials = "3"
+PrecompileSignatures = "3"
 ProgressMeter = "1"
 Reexport = "1"
 Roots = "2"
 SpecialFunctions = "2"
-StatsBase = "0.33.16"
-Xtals = "0.4"
-julia = "1.7, 1.8"
+StatsBase = "0.34"
+Xtals = "0.5"
+julia = "1.6"
 
 [extras]
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test", "Documenter"]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

README.md

@@ -1,7 +1,7 @@
-![PorousMaterials.jl](PMlogo.png)
+![PorousMaterials.jl](logo.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

@@ -1,6 +1,6 @@
 ```@meta
 DocTestSetup = quote
-  using Xtals
+  using PorousMaterials
 end
 ```
 
@@ -22,39 +22,46 @@ 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
-	Volume of unit cell: 3975.275878 ų
+    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
+    Volume of unit cell: 3975.275878 ų
 ```
 
 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
+    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
+    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
+    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