Merge branch 'main' of https://gitlab.com/dlr-perihub/PeriLab.jl

.github/workflows/CI.yml

@@ -0,0 +1,51 @@
+# SPDX-FileCopyrightText: 2023 Christian Willberg <christian.willberg@dlr.de>, Jan-Timo Hesse <jan-timo.hesse@dlr.de>
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: PeriLab CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the main branch
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - "src/**"
+    branches:
+      - main
+  pull_request:
+    paths:
+      - "src/**"
+    branches-ignore:
+      - release
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 50
+
+    strategy:
+      # Without setting this, a failing test cancels all others
+      fail-fast: false
+      matrix:
+        # We test quite a lot of versions because we do some OS and version specific things unfortunately
+        julia-version: ["1.10"] # "~1.12.0-0"]
+        os: [ubuntu-latest]
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      # Makes the `julia` command available
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: PeriHub/PeriLab.jl
+          files: lcov.info

.github/workflows/CompatHelper.yml

@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: 2023 Christian Willberg <christian.willberg@dlr.de>, Jan-Timo Hesse <jan-timo.hesse@dlr.de>
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: "1"
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Documentation.yml

@@ -0,0 +1,35 @@
+# SPDX-FileCopyrightText: 2023 Christian Willberg <christian.willberg@dlr.de>, Jan-Timo Hesse <jan-timo.hesse@dlr.de>
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: Documentation
+
+on:
+  push:
+    paths:
+      - "src/**"
+      - "docs/**"
+    branches:
+      - main
+    tags: "*"
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+      statuses: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: "1.10"
+      - uses: julia-actions/cache@v1
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -0,0 +1,59 @@
+# SPDX-FileCopyrightText: 2023 Christian Willberg <christian.willberg@dlr.de>, Jan-Timo Hesse <jan-timo.hesse@dlr.de>
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+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 }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
+  DockerHub:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+      - name: Get version from Project.toml
+        id: get_version
+        run: echo "::set-output name=version::$(awk -F'"' '/version/{print $2}' Project.toml)"
+      - name: Build Docker image
+        run: docker build -t perihub/perilab:${{ steps.get_version.outputs.version }} .
+      - name: Publish to Registry
+        run: docker push perihub/perilab${{ steps.get_version.outputs.version }}
+      - name: Retag latest
+        run: docker tag perihub/perilab${{ steps.get_version.outputs.version }} perihub/perilab:latest
+      - name: Publish to Registry
+        run: docker push perihub/perilab:latest

.gitignore

@@ -18,3 +18,4 @@ LocalPreferences.toml
 test/tryout/
 examples/dev/
 LocalPreferences.toml
+.env

CHANGELOG.md

@@ -8,7 +8,23 @@ SPDX-License-Identifier: BSD-3-Clause
 
 All notable changes to this project will be documented in this file.
 
-## [1.0.7] - 2024-
+## [1.1.1] - 2024-
+
+### Changed
+
+## [1.1.0] - 2024-03-19
+
+### Changed
+
+- Julia version
+
+### Fixed
+
+- MPI Issue
+- Logging
+
+
+## [1.0.7] - 2024-03-12
 
 ### Added
 

Dockerfile

@@ -12,16 +12,20 @@ COPY Project.toml ./Project.toml
 
 # Install build dependencies
 RUN apt-get update \
-    && apt-get install -yq build-essential openssh-server \
-    && julia --project=@. -e 'import Pkg; Pkg.add(url="https://github.com/JTHesse/AbaqusReader.jl"); Pkg.add("PackageCompiler"); using PackageCompiler; create_app(".", "build", executables=["PeriLab" => "main", "get_examples" => "get_examples"], incremental=true, force=true)'
+    && apt-get install -yq build-essential\
+    && julia --project=@. -e 'import Pkg; Pkg.add(url="https://github.com/JTHesse/AbaqusReader.jl"); Pkg.add("PackageCompiler")'
+
+RUN julia --project=@. -e 'using PackageCompiler; create_app(".", "build", executables=["PeriLab" => "main", "get_examples" => "get_examples"], force=true)'
 
 #TODO: use alpine
-FROM julia:latest as main 
+FROM debian:bookworm-slim as main 
 
 WORKDIR /app
 
 # Create the destination directory
 RUN mkdir PeriLab
+
+# Assuming /env/build is the build directory from previous stages
 COPY --from=build /env/build /app/PeriLab
 
 # Move the build folder, set permissions, and delete the rest
@@ -30,13 +34,9 @@ RUN chmod +x /app/PeriLab/bin/PeriLab \
 
 ENV PATH="/app/PeriLab/bin:${PATH}"
 
-# RUN apk update && apk add bash && apk add openssh
+# Install SSH server and other dependencies
 RUN apt-get update && apt-get install -yq openssh-server
 
-# Allow mpirun as root, should only be used in container
-ENV OMPI_ALLOW_RUN_AS_ROOT 1
-ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM 1
-
 # Configure SSH server
 RUN mkdir /var/run/sshd \
     && echo 'root:root' | chpasswd \
@@ -46,8 +46,8 @@ RUN mkdir /var/run/sshd \
     && sed -i'' -e's/^UsePAM yes/UsePAM no/' /etc/ssh/sshd_config
 
 # Start SSH service
-RUN service ssh start
+CMD ["/usr/sbin/sshd", "-D"]
 
+# Expose SSH port
 EXPOSE 22
-CMD ["/usr/sbin/sshd", "-D"]
 

Project.toml

@@ -1,7 +1,7 @@
 name = "PeriLab"
 uuid = "2ecefcea-59f0-46dd-9cfd-1d2b8cc5f112"
 authors = ["Christian Willberg <christian.willberg@dlr.de>", "Jan-Timo Hesse <jan-timo.hesse@dlr.de>"]
-version = "1.0.7"
+version = "1.1.1"
 
 [deps]
 AbaqusReader = "bc6b9049-e460-56d6-94b4-a597b2c0390d"