Rely on AtomsIO for structure parsing (#802)

JuliaMolSim · Dec 20, 2022 · a9764b4 · a9764b4
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -19,19 +19,17 @@ jobs:
   # Unit tests
   #
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.payload }}
+    name: Julia stable - ${{ matrix.os }} - ${{ matrix.payload }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         include:
-          - {version: '1.6',   os: ubuntu-latest,  payload: serial}
-          - {version: '1.6',   os: macOS-latest,   payload: serial}
-          - {version: '1.6',   os: windows-latest, payload: serial}
-          - {version: '1.6',   os: ubuntu-latest,  payload: mpi   }
-          - {version: nightly, os: ubuntu-latest,  payload: serial}
+          - {os: ubuntu-latest,  payload: "fast,example" }
+          - {os: macOS-latest,   payload: fast           }
+          - {os: windows-latest, payload: fast           }
+          - {os: ubuntu-latest,  payload: mpi            }
     env:
-      PYTHON: ""          # Force using Conda in PyCall
       GKS_ENCODING: "utf8"
       GKSwstype: "100"    # Needed for Plots-related tests
       PLOTS_TEST: "true"  # Needed for Plots-related tests
@@ -40,34 +38,15 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.version }}
+          version: '1.6'
           arch: x64
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - name: Install Conda dependencies
-        shell: bash
-        run: |
-          julia -e '
-            using Pkg; Pkg.add("Conda"); using Conda
-            pkgs = ["ase", "pymatgen"]
-            !Sys.iswindows() && (pkgs = append!(["libblas=*=*netlib", "nomkl"], pkgs))
-            Conda.add(pkgs; channel="conda-forge")
-          '
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
 
-      - name: Execute serial tests
-        uses: julia-actions/julia-runtest@v1
-        if: ${{ matrix.payload == 'serial' }}
-        continue-on-error: ${{ matrix.version == 'nightly' }}
-
+      - uses: julia-actions/julia-runtest@v1
+        if: ${{ matrix.payload != 'mpi' }}
+        env:
+          DFTK_TEST_ARGS: ${{ matrix.payload }}
       - name: Execute MPI-parallel tests
         run: |
           julia --project -e '
@@ -77,40 +56,38 @@ jobs:
           '
           $HOME/.julia/bin/mpiexecjl -np 2 julia --check-bounds=yes --depwarn=yes --project --color=yes -e 'using Pkg; Pkg.test(coverage=true)'
         if: ${{ matrix.payload == 'mpi' }}
-        continue-on-error: ${{ matrix.version == 'nightly' }}
+        env:
+          DFTK_TEST_ARGS: fast
 
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v2
         with:
           file: lcov.info
   #
-  # Examples
+  # Nightly
   #
-  examples:
-    name: Run examples
+  nightly:
+    name: Julia nightly - ubuntu-latest
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
     env:
       GKS_ENCODING: "utf8"
       GKSwstype: "100"    # Needed for Plots-related tests
       PLOTS_TEST: "true"  # Needed for Plots-related tests
+
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.7'
-      - name: Install python dependencies
-        run: pip install ase
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.6'
-      - uses: actions/cache@v1
+          version: nightly
+          arch: x64
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
         env:
-          cache-name: cache-artifacts
+          DFTK_TEST_ARGS: fast
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v2
         with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - run: julia --color=yes --project -e 'using Pkg; Pkg.test(test_args=["example"])'
+          file: lcov.info
diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -18,33 +18,29 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.7'
-      - name: Install python dependencies
-        run: pip install ase pymatgen
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
-      - name: Instantiate and build packages
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        timeout-minutes: 40
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+      - name: Setup PyCall to use python executable from PythonCall
+        # Note: This is needed to ensure PyCall and PythonCall are using
+        #       exactly the same python version.
         run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()
-            Pkg.precompile()
-            Pkg.build("DFTK")
-          '
+          julia --project -e '
+            import Pkg
+            Pkg.add(["PyCall", "PythonCall"])
+            import PythonCall
+            ENV["PYTHON"] = PythonCall.C.CTX.exe_path
+            Pkg.build("PyCall")'
       - name: Run doctests
         run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
             using DFTK
             DocMeta.setdocmeta!(DFTK, :DocTestSetup, :(using DFTK); recursive=true)
             doctest(DFTK)'
-      - name: Generate docs
-        run: julia --project=docs docs/make.jl
-        timeout-minutes: 30
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@
 deps/deps.jl
 Manifest.toml
 .vscode
+.CondaPkg
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,27 +1,21 @@
 stages:
   - test
 
-# TODO More fine-grained rule setup
-
 # This job tests DFTK.jl with Julia 1.8 on Noctua 2
+# It only runs when:
+#    - Commit in master
+#    - PR from branch with name ending in "gpu"
+#    - Manual run triggered
 julia/1.8-n2:
   stage: test
   variables:
-    SCHEDULER_PARAMETERS: "-N 1 -n 1 -c 16 --gres=gpu:a100:1 -t 00:15:00 -A hpc-prf-dftkjl -p gpu"
+    SCHEDULER_PARAMETERS: "-N 1 -n 1 -c 16 --gres=gpu:a100:1 --qos=devel -p dgx -t 00:15:00 -A hpc-prf-dftkjl"
     JULIA_NUM_THREADS: "1"  # GPU and multi-threading not yet compatible
   coverage: '/\(\d+.\d+\%\) covered/'
-  only:
-    - external_pull_requests
-    - tags
-    - master
-  # rules:
-  #   - changes:
-  #     - "README.md"
-  #   #   - "docs/**/*.md"
-  #   #   - "docs/make.jl"
-  #   #   - "docs/build_docs.jl"
-  #   #   when: never
-  #   - when: on_success
+  rules:
+    - if: $CI_COMMIT_BRANCH == "master"
+    - if: $CI_PIPELINE_SOURCE == "external_pull_request_event" && $CI_EXTERNAL_PULL_REQUEST_SOURCE_BRANCH_NAME =~ /gpu$/
+    - when: manual
   script:
     - module load lang/JuliaHPC/1.8.3-foss-2022a-CUDA-11.7.0
     - julia --color=yes --project=. -e '

diff --git a/Project.toml b/Project.toml
@@ -4,11 +4,12 @@ authors = ["Michael F. Herbst <[email protected]>", "Antoine Levitt <antoi
 version = "0.5.15"
 
 [deps]
+ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
 Brillouin = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DftFunctionals = "6bd331d2-b28d-4fd3-880e-1a1c7f37947f"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -33,7 +34,6 @@ Primes = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 PseudoPotentialIO = "cb339c56-07fa-4cb2-923a-142469552264"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
@@ -48,11 +48,12 @@ UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 spglib_jll = "ac4a9f1e-bdb2-5204-990c-47c8b2f70d4e"
 
 [compat]
+ASEconvert = "0.1"
 AbstractFFTs = "1"
 AtomsBase = "0.2.2"
-Brillouin = "0.5.10"
+AtomsIO = "0.1.1"
+Brillouin = "0.5.11"
 ChainRulesCore = "1.15"
-Conda = "1"
 DftFunctionals = "0.2"
 FFTW = "1"
 ForwardDiff = "0.10"
@@ -72,7 +73,6 @@ Polynomials = "3"
 Primes = "0.5"
 ProgressMeter = "1"
 PseudoPotentialIO = "0.1"
-PyCall = "1"
 Requires = "1"
 Roots = "2"
 SpecialFunctions = "2"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,7 @@
 [deps]
+ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
 Brillouin = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 DFTK = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,6 +1,5 @@
 # To manually generate the docs:
-#     1. Install all python dependencies from the PYDEPS array below.
-#     2. Run "julia make.jl"
+#     1. Run "julia make.jl"
 #
 # To add a new example to the docs:
 #     1. Add the *.jl file to /examples, along with assets you require (e.g. input files,
@@ -85,9 +84,7 @@ PAGES = [
 
 # Files from the /examples folder that need to be copied over to the docs
 # (typically images, input or data files etc.)
-EXAMPLE_ASSETS = [
-    "examples/Fe_afm.pwi",
-]
+EXAMPLE_ASSETS = ["examples/Fe_afm.pwi", "examples/Si.extxyz"]
 
 #
 # Configuration and setup
@@ -105,9 +102,6 @@ DFTKREV    = LibGit2.head(ROOTPATH)
 DFTKBRANCH = try LibGit2.branch(LibGit2.GitRepo(ROOTPATH)) catch end
 DFTKREPO   = "github.com/JuliaMolSim/DFTK.jl.git"
 
-# Python dependencies needed for running the notebooks
-PYDEPS = ["ase"]
-
 # Setup julia dependencies for docs generation if not yet done
 Pkg.activate(@__DIR__)
 if !isfile(joinpath(@__DIR__, "Manifest.toml"))
@@ -185,20 +179,16 @@ end
 # Generate the docs in BUILDPATH
 makedocs(;
     modules=[DFTK],
+    repo="https://" * DFTKREPO * "/blob/{commit}{path}#{line}",
     format=Documenter.HTML(
         # Use clean URLs, unless built as a "local" build
         prettyurls = CONTINUOUS_INTEGRATION,
         canonical = "https://docs.dftk.org/stable/",
+        edit_link = "master",
         assets = ["assets/favicon.ico"],
     ),
     sitename = "DFTK.jl",
     authors = "Michael F. Herbst, Antoine Levitt and contributors.",
-    linkcheck = false,  # TODO
-    linkcheck_ignore = [
-        # Ignore links that point to GitHub's edit pages, as they redirect to the
-        # login screen and cause a warning:
-        r"https://github.com/([A-Za-z0-9_.-]+)/([A-Za-z0-9_.-]+)/edit(.*)",
-    ],
     pages=transform_to_md(PAGES),
     checkdocs=:exports,
     strict=!DEBUG,
@@ -207,20 +197,6 @@ makedocs(;
 # Dump files for managing dependencies in binder
 if CONTINUOUS_INTEGRATION && DFTKBRANCH == "master"
     cd(BUILDPATH) do
-        open("environment.yml", "w") do io
-            print(io,
-                  """
-                  name: dftk
-                  channels:
-                    - defaults
-                    - conda-forge
-                  dependencies:
-                  """)
-            for dep in PYDEPS
-                println(io, "  - " * dep)
-            end
-        end
-
         # Install Julia dependencies into build
         Pkg.activate(".")
         Pkg.add(Pkg.PackageSpec(url="https://" * DFTKREPO, rev=DFTKREV))
@@ -230,7 +206,7 @@ if CONTINUOUS_INTEGRATION && DFTKBRANCH == "master"
 end
 
 # Deploy docs to gh-pages branch
-deploydocs(; repo=DFTKREPO)
+deploydocs(; repo=DFTKREPO, devbranch="master")
 
 # Remove generated example files
 if !DEBUG

diff --git a/docs/src/features.md b/docs/src/features.md
@@ -41,7 +41,7 @@
     - Seamless integration with many standard [Input and output formats](@ref).
     - Integration with [ASE](https://wiki.fysik.dtu.dk/ase/) and
       [AtomsBase](https://github.com/JuliaMolSim/AtomsBase.jl) for passing
-      atomic structures.
+      atomic structures (see [AtomsBase integration](@ref)).
     - [Wannierization using Wannier90](@ref)