Merge pull request #20 from cesmix-mit/refactor

First refactoring iteration

.github/workflows/CI.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-    tags: '*'
+    tags: "*"
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -13,8 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
-          - 'nightly'
+          - "1.7"
         os:
           - ubuntu-latest
           - macOS-latest
@@ -37,32 +36,18 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
+      - name: add CESMIX registry
+        run: |
+          julia -e '
+            using Pkg
+            Pkg.Registry.add("General")
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git"))
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/JuliaMolSim/MolSim.git"))
+          '
+        shell: bash
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1
         with:
           file: lcov.info
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: |
-          julia --project=docs -e '
-            using Documenter: DocMeta, doctest
-            using PotentialLearning
-            DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true)
-            doctest(PotentialLearning)'
-      - run: julia --project=docs docs/make.jl
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/Documentation.yml

@@ -0,0 +1,49 @@
+name: Documentation
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+    tags: "*"
+jobs:
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: "1.7"
+      - name: add CESMIX registry
+        run: |
+          julia -e '
+            using Pkg
+            Pkg.Registry.add("General")
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git"))
+            Pkg.Registry.add(RegistrySpec(url = "https://github.com/JuliaMolSim/MolSim.git"))
+          '
+        shell: bash
+      - name: instantiate docs
+        run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()
+          '
+      - name: run doctests
+        run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.activate("./")
+            Pkg.add("Documenter")
+            using Documenter: DocMeta, doctest
+            using PotentialLearning
+            DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true)
+            doctest(PotentialLearning)
+          '
+      - name: generate docs
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/PreviewCleanup.yml

@@ -0,0 +1,26 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.gitignore

@@ -1 +1,5 @@
 Manifest.toml
+
+# generated docs
+docs/build/
+docs/src/generated/

Project.toml

@@ -0,0 +1,30 @@
+name = "PotentialLearning"
+uuid = "82b0a93c-c2e3-44bc-a418-f0f89b0ae5c2"
+authors = ["CESMIX Team"]
+version = "0.1.0"
+
+[deps]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+GalacticOptim = "a75be94c-b780-496d-a8a9-0878b188d577"
+InteratomicBasisPotentials = "37c59853-c2ad-4e3a-930c-a41b2395fb19"
+InteratomicPotentials = "a9efe35a-c65d-452d-b8a8-82646cd5cb04"
+IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
+LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+
+[compat]
+julia = "1.7"

README.md

@@ -1,9 +1,33 @@
-## [WIP] PotentialLearning.jl: an open source library for the active learning and fast calculation of interatomic potentials in atomistic simulations of materials.
+## [WIP] PotentialLearning.jl
 
-Developed as part of [CESMIX](https://cesmix.mit.edu).
+An open source library for the active learning and fast calculation of interatomic potentials in atomistic simulations of materials.
+
+<!-- Information badges -->
+<p align="center">
+  <a href="https://mit-license.org">
+    <img alt="MIT license" src="https://img.shields.io/badge/License-MIT-blue.svg?style=flat-square">
+  </a>
+  <a href="https://github.com/cesmix-mit/PotentialLearning.jl/issues/new">
+    <img alt="Ask us anything" src="https://img.shields.io/badge/Ask%20us-anything-1abc9c.svg?style=flat-square">
+  </a>
+  <a href="https://github.com/cesmix-mit/PotentialLearning.jl/releases">
+    <img alt="GitHub tag (latest SemVer pre-release)" src="https://img.shields.io/github/v/tag/cesmix-mit/PotentialLearning.jl?include_prereleases&label=latest%20version&logo=github&sort=semver&style=flat-square">
+  </a>
+</p>
 
-This package is currently being refactored. See [Atomistic Composable Workflows](https://github.com/cesmix-mit/AtomisticComposableWorkflows) for current Julia case studies.
+<!-- CI and documentation badges -->
+<p align="center">
+  <a href="https://cesmix-mit.github.io/PotentialLearning.jl/stable">
+    <img alt="Stable documentation" src="https://img.shields.io/badge/documentation-stable%20release-blue?style=flat-square">
+  </a>
+  <a href="https://cesmix-mit.github.io/PotentialLearning.jl/dev">
+    <img alt="Development documentation" src="https://img.shields.io/badge/documentation-in%20development-orange?style=flat-square">
+  </a>
+</p>
 
 
+Developed as part of [CESMIX](https://cesmix.mit.edu).
+
+See [Atomistic Composable Workflows](https://github.com/cesmix-mit/AtomisticComposableWorkflows) for current Julia case studies.
 
 

docs/Project.toml

@@ -0,0 +1,7 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"

docs/make.jl

@@ -0,0 +1,49 @@
+    pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..")) # add PotentialLearning to environment stack
+
+using PotentialLearning
+using Documenter
+using DocumenterCitations
+using Literate
+
+DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive = true)
+
+bib = CitationBibliography(joinpath(@__DIR__, "citations.bib"))
+
+# Generate examples
+
+#const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
+#const OUTPUT_DIR = joinpath(@__DIR__, "src/generated")
+
+#examples = Pair{String,String}[]
+
+#for (_, name) in examples
+#    example_filepath = joinpath(EXAMPLES_DIR, string(name, ".jl"))
+#    Literate.markdown(example_filepath, OUTPUT_DIR, documenter = true)
+#end
+
+#examples = [title => joinpath("generated", string(name, ".md")) for (title, name) in examples]
+
+makedocs(bib;
+    modules = [PotentialLearning],
+    authors = "CESMIX-MIT",
+    repo = "https://github.com/cesmix-mit/PotentialLearning.jl/blob/{commit}{path}#{line}",
+    sitename = "PotentialLearning.jl",
+    format = Documenter.HTML(;
+        prettyurls = get(ENV, "CI", "false") == "true",
+        canonical = "https://cesmix-mit.github.io/PotentialLearning.jl",
+        assets = String[],
+    ),
+    pages = [
+        "Home" => "index.md",
+        "API" => "api.md",
+    ],
+    doctest = true,
+    linkcheck = true,
+    strict = false
+)
+
+deploydocs(;
+    repo = "github.com/cesmix-mit/PotentialLearning.jl",
+    devbranch = "main",
+    push_preview = true
+)

docs/src/api.md

@@ -0,0 +1,9 @@
+# API Reference
+
+This page provides a list of all documented types and functions and in PotentialLearning.jl.
+
+
+```@autodocs
+Modules = [PotentialLearning]
+Order   = [:type, :function, :constant]
+```

docs/src/index.md

@@ -0,0 +1,2 @@
+# PotentialLearning.jl
+

examples/README.md

@@ -0,0 +1 @@
+See https://github.com/cesmix-mit/AtomisticComposableWorkflows