v0.4.0 (#214)

* cross-platform CI * remove redundant file reads * aqua * docstrings * fix bad dict key in Henry sim auto-save * doctests
SimonEnsemble · Mar 14, 2022 · 3a0ac8e · 3a0ac8e
1 parent edd6d8b
commit 3a0ac8e
Show file tree

Hide file tree

Showing 19 changed files with 237 additions and 136 deletions.
diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -1,11 +1,16 @@
 name: TagBot
 on:
-  schedule:
-    - cron: 0 * * * *
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
 jobs:
   TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+
diff --git a/.github/workflows/ci_testing.yml b/.github/workflows/ci_testing.yml
@@ -12,7 +12,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  julia_version: '1.6.3'
+  julia_version: '1.7.2'
 
 
 
@@ -21,6 +21,7 @@ jobs:
 
   unit-and-doc-tests:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
 
     steps:
       - name: checkout commit
@@ -52,8 +53,70 @@ jobs:
           verbose: true
 
 
+  cross-platform-os:
+    if: github.ref_name == 'master'
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+
+    steps:
+      - name: checkout commit
+        uses: actions/checkout@master
+
+      - name: set up Julia
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ env.julia_version }}
+
+      - name: build package
+        uses: julia-actions/julia-buildpkg@latest
+
+      - name: install dependencies
+        run: julia --project --color=yes -e 'import Pkg; Pkg.add("Documenter")'
+        shell: bash
+
+      - name: run tests
+        run: julia --project --color=yes -e 'import Pkg; Pkg.test()'
+        shell: bash
+
+
+  cross-platform-julia:
+    if: github.ref_name == 'master'
+    strategy:
+      fail-fast: true
+      matrix:
+        julia: ['1.6.4', '1.7.0']
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: checkout commit
+        uses: actions/checkout@master
+
+      - name: set up Julia
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia }}
+
+      - name: build package
+        uses: julia-actions/julia-buildpkg@latest
+
+      - name: install dependencies
+        run: julia --project --color=yes -e 'import Pkg; Pkg.add("Documenter")'
+        shell: bash
+
+      - name: run tests
+        run: julia --project --color=yes -e 'import Pkg; Pkg.test()'
+        shell: bash
+
+
   deploy-docs:
+    if: github.ref_name == 'master'
     runs-on: ubuntu-latest
+    timeout-minutes: 30
 
     env:
       GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
@@ -76,3 +139,26 @@ jobs:
 
       - name: build and deploy docs
         run: julia --project --color=yes ./docs/make.jl
+
+
+  aqua-jl:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: checkout commit
+        uses: actions/checkout@v2
+
+      - name: set up Julia
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ env.julia_version }}
+
+      - name: build package
+        uses: julia-actions/julia-buildpkg@latest
+
+      - name: install dependencies
+        run: julia --project --color=yes -e 'import Pkg; Pkg.add.(["Aqua"])'
+
+      - name: Aqua.jl
+        run: julia --project --color=yes ./test/aqua.jl
diff --git a/Project.toml b/Project.toml
@@ -1,13 +1,13 @@
 name = "PorousMaterials"
 uuid = "68953c7c-a3c7-538e-83d3-73516288599e"
 authors = ["SimonEnsemble <[email protected]>"]
-version = "0.3.4"
+version = "0.4.0"
 
 [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"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FIGlet = "3064a664-84fe-4d92-92c7-ed492f3d8fae"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
@@ -18,7 +18,6 @@ Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
@@ -29,37 +28,27 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Xtals = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 
 [compat]
-CSV = "^0.8"
-DataFrames = "^0.22, 1"
-FIGlet = "^0.2"
-FileIO = "^1.2"
-Graphs = "^1.4"
-JLD2 = "^0.4"
+Aqua = "0.5"
+CSV = "0.8"
+DataFrames = "1"
+FIGlet = "0.2"
+FileIO = "1"
+Graphs = "1"
+JLD2 = "0.4"
 OffsetArrays = "0.11"
-Optim = "^0.19, 1"
-Polynomials = "^0.6"
-ProgressMeter = "^1.2"
-PyCall = "^1.92"
-Reexport = "^1.1"
-Roots = "^0.8"
-SpecialFunctions = "^0.10"
-StatsBase = "~0.32, ^0.33"
-Xtals = "^0.3"
+Optim = "1"
+Polynomials = "0.6"
+ProgressMeter = "1"
+Reexport = "1"
+Roots = "0.8"
+SpecialFunctions = "0.10"
+StatsBase = "0.32"
+Xtals = "0.3"
 julia = "1.6"
 
 [extras]
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-Optim = "429524aa-4258-5aef-a3af-852621145aeb"
-Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "Documenter", "CSV", "DataFrames", "FileIO", "JLD2", "LinearAlgebra", "OffsetArrays", "Optim", "Printf", "Random", "Statistics"]
+test = ["Test", "Documenter"]
diff --git a/README.md b/README.md
@@ -2,6 +2,6 @@
 
 | **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) | [![codecov](https://codecov.io/gh/SimonEnsemble/PorousMaterials.jl/branch/master/graph/badge.svg?token=PWsgNnxfZI)](https://codecov.io/gh/SimonEnsemble/PorousMaterials.jl) |
+| [![](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) | [![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).
diff --git a/docs/src/crystal.md b/docs/src/crystal.md
@@ -24,7 +24,7 @@ xtal.bonds                          # Bonding information in the structure. By d
 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
 # output
-Xtals.SymmetryInfo(["x"; "y"; "z"], "P1", true)
+Xtals.SymmetryInfo(["x"; "y"; "z";;], "P1", true)
 ```
 
 ## fixing atom species

diff --git a/docs/src/energy_min.md b/docs/src/energy_min.md
@@ -30,7 +30,7 @@ minimized_molecule, min_E = find_energy_minimum(xtal, minimized_molecule, ljff)
 Computing energy grid of Xe in SBMOF-1.cif
 	Regular grid (in fractional space) of 13 by 7 by 24 points superimposed over the unit cell.
 (Molecule species: Xe
-Center of mass (fractional coords): Frac([0.01749943805846959; 0.9372916114895011; 0.011192272400742498])
+Center of mass (fractional coords): Frac([0.01749943805846959; 0.9372916114895011; 0.011192272400742498;;])
 Atoms:
 
 	atom = Xe, xf = [0.017, 0.937, 0.011], -37.69376112588296)

diff --git a/docs/src/matter.md b/docs/src/matter.md
@@ -59,7 +59,7 @@ length(coords)                 # number of particles, (5)
 ```jldoctest matter
 coords.x = rand(3, 5)
 # output
-ERROR: setfield! immutable struct of type Cart cannot be changed
+ERROR: setfield!: immutable struct of type Cart cannot be changed
 ```
 but we can manipulate the values of `Array{Float64, 2}` where coordinates (through `coords.x` or `coords.xf`) are stored:
 

diff --git a/docs/src/molecule.md b/docs/src/molecule.md
@@ -14,7 +14,7 @@ Molecule input files are stored in `PorousMaterials.PATH_TO_MOLECULES`. Each mol
 molecule = Molecule("CO2")
 # output
 Molecule species: CO2
-Center of mass (fractional coords): Cart([0.0; 0.0; 0.0])
+Center of mass (fractional coords): Cart([0.0; 0.0; 0.0;;])
 Atoms:
 
 	atom = C_CO2, x = [0.000, 0.000, 0.000]

diff --git a/src/PorousMaterials.jl b/src/PorousMaterials.jl
@@ -1,7 +1,7 @@
 module PorousMaterials
 
-using Roots, OffsetArrays, SpecialFunctions, StatsBase, ProgressMeter, Polynomials,
-JLD2, Statistics, Distributed, Optim, Printf, DataFrames, Graphs, CSV, LinearAlgebra
+using CSV, DataFrames, Distributed, FIGlet, Graphs, JLD2, LinearAlgebra, OffsetArrays, Optim, 
+    Polynomials, Printf, ProgressMeter, Roots, SpecialFunctions, Statistics, StatsBase
 
 # extend Xtals
 using Reexport
@@ -36,6 +36,12 @@ function __init__()
     append_atomic_masses()
 end
 
+function banner()
+    font_num = 579
+    FIGlet.render("Porous", FIGlet.availablefonts()[font_num])
+    FIGlet.render("Materials", FIGlet.availablefonts()[font_num])
+end
+
 
 export
     # isotherm_fitting.jl
@@ -54,7 +60,7 @@ export
     lennard_jones, vdw_energy, vdw_energy_no_PBC,
 
     # electrostatics.jl
-    electrostatic_potential, electrostatic_potential_energy, precompute_kvec_wts,
+    electrostatic_potential_energy, precompute_kvec_wts,
     setup_Ewald_sum, total, Eikr, total_electrostatic_potential_energy,
 
     # mc_helpers.jl

diff --git a/src/gcmc.jl b/src/gcmc.jl
@@ -161,6 +161,7 @@ translation.
 - `density_grid_sim_box::Bool`: `true` if we wish for the density grid to be over the 
 entire simulation box as opposed to the box of the crystal passed in. `false` if we wish the
 density grid to be over the original `xtal.box`, before replication, passed in.
+- `autosave::Bool`: `true` if we wish to automatically save the simulation results to the standard path/filename.
 - `results_filename_comment::AbstractString`: An optional comment that will be appended to the name of the saved file (if autosaved)
 """
 function μVT_sim(xtal::Crystal, molecule::Molecule, temperature::Float64,

diff --git a/test/aqua.jl b/test/aqua.jl
@@ -0,0 +1,15 @@
+using PorousMaterials
+import Aqua
+
+# ambiguity testing finds many "problems" outside the scope of this package
+ambiguities=false
+
+# to skip when checking for stale dependencies and missing compat entries
+#   Aqua is added in a separate CI job, so (ironically) does not work w/ itself
+stale_deps = (ignore=[:Aqua],)
+
+Aqua.test_all(
+    PorousMaterials;
+    ambiguities=ambiguities, 
+    stale_deps=stale_deps
+)
diff --git a/test/energy_min.jl b/test/energy_min.jl
@@ -6,10 +6,13 @@ using JLD2
 using Statistics
 using Random
 
+FIQCEN_clean = Crystal("FIQCEN_clean.cif")
+Xe = Molecule("Xe")
+
 @testset "Energy Minimizaiton Tests" begin
-    xtal = Crystal("FIQCEN_clean.cif")
+    xtal = deepcopy(FIQCEN_clean)
     strip_numbers_from_atom_labels!(xtal)
-    molecule  = Molecule("Xe")
+    molecule  = deepcopy(Xe)
     ljff = LJForceField("UFF")
     n_pts = (15, 15, 15)
 
@@ -30,9 +33,9 @@ using Random
     @test isapprox(vdw_energy(xtal, min_mol, ljff) * 8.314 / 1000, min_E, atol=0.1)
 
     # make sure it works with cart coords too.
-    xtal = Crystal("FIQCEN_clean.cif")
+    xtal = deepcopy(FIQCEN_clean)
     strip_numbers_from_atom_labels!(xtal)
-    molecule = Molecule("Xe")
+    molecule = deepcopy(Xe)
     translate_to!(molecule, Cart(Frac([0.785, 0.785, 0.785]), xtal.box))
     min_mol, min_E = find_energy_minimum(xtal, molecule, ljff)
     @test isapprox(min_E, -27.0269, atol=0.01)

diff --git a/test/forcefield.jl b/test/forcefield.jl
@@ -30,8 +30,9 @@ using Random
     @test rep_factors == (25, 25, 25)
 
     # test check for force field coverage
-    @test forcefield_coverage(Crystal("SBMOF-1.cif").atoms, ljforcefield)
-    @test forcefield_coverage(Crystal("SBMOF-1.cif"), ljforcefield)
-    @test ! forcefield_coverage(Crystal("SBMOF-1.cif").atoms, LJForceField("bogus"))
+    SBMOF1 = Crystal("SBMOF-1.cif")
+    @test forcefield_coverage(SBMOF1.atoms, ljforcefield)
+    @test forcefield_coverage(SBMOF1, ljforcefield)
+    @test ! forcefield_coverage(SBMOF1.atoms, LJForceField("bogus"))
 end
 end
diff --git a/test/grid.jl b/test/grid.jl
@@ -8,6 +8,9 @@ using JLD2
 using Statistics
 using Random
 
+CH4 = Molecule("CH4")
+UFF = LJForceField("UFF")
+
 @testset "Grid Tests" begin
     # required number of pts
     box = Box(1.0, 10.0, 5.0, π/2, π/2, π/2)
@@ -40,8 +43,8 @@ using Random
     for zeolite in ["LTA", "SOD"]
         crystal = Crystal(zeolite * ".cif")
         write_xyz(crystal)
-        molecule = Molecule("CH4")
-        forcefield = LJForceField("UFF")
+        molecule = deepcopy(CH4)
+        forcefield = deepcopy(UFF)
         grid = energy_grid(crystal, molecule, forcefield, resolution=5.)
 
         # endpoints included, ensure periodic since endpoints of grid pts included
@@ -98,8 +101,8 @@ using Random
 
     # test accessibility interpolator when there are replications
     crystal = Crystal("LTA.cif")
-    molecule = Molecule("CH4")
-    forcefield = LJForceField("UFF")
+    molecule = deepcopy(CH4)
+    forcefield = deepcopy(UFF)
     accessibility_grid, nb_segments_blocked, porosity = compute_accessibility_grid(crystal,
         molecule, forcefield, resolution=2., energy_tol=0.0, verbose=false,
         write_b4_after_grids=true)
@@ -122,8 +125,8 @@ using Random
     @test same_accessibility_repfactors
 
     # SBMOF-1, CAXVILL_clean hv no pockets blocked. test accessibility grid w./o pocket blocking
-    molecule = Molecule("CH4")
-    forcefield = LJForceField("UFF")
+    molecule = deepcopy(CH4)
+    forcefield = deepcopy(UFF)
     for crystal in [Crystal("SBMOF-1.cif"), Crystal("CAXVII_clean.cif")]
 
         # w./ blocking