Merge pull request #281 from espressomd/python

Merge Espresso head

.clang-tidy

@@ -3,11 +3,14 @@ Checks: |
    clang-diagnostic-*,
    clang-analyzer-*,
    -clang-analyzer-core.NullDereference,
+   -clang-analyzer-core.uninitialized.UndefReturn,
    -clang-analyzer-optin.mpi.MPI-Checker,
-   -clang-analyzer-security.FloatLoopCounter,
    bugprone-*,
+   -bugprone-easily-swappable-parameters,
+   -bugprone-implicit-widening-of-multiplication-result,
+   -bugprone-macro-parentheses,
+   -bugprone-reserved-identifier,
    clang-analyzer-alpha.*,
-   modernize-avoid-c-arrays,
    modernize-deprecated-headers,
    modernize-make-shared,
    modernize-make-unique,
@@ -36,7 +39,7 @@ Checks: |
    readability-string-compare,
    readability-uniqueptr-delete-release,
    readability-function-size'
-WarningsAsErrors: '*'
+WarningsAsErrors: '*,-clang-analyzer-core.StackAddrEscapeBase,-clang-analyzer-optin.mpi.MPI-Checker'
 HeaderFilterRegex: '.*'
 AnalyzeTemporaryDtors: false
 FormatStyle:     none
@@ -71,15 +74,15 @@ CheckOptions:
   - key:             modernize-make-shared.IgnoreMacros
     value:           '1'
   - key:             modernize-make-shared.IncludeStyle
-    value:           '0'
+    value:           'llvm'
   - key:             modernize-make-shared.MakeSmartPtrFunction
     value:           'std::make_shared'
   - key:             modernize-make-shared.MakeSmartPtrFunctionHeader
     value:           memory
   - key:             modernize-make-unique.IgnoreMacros
     value:           '1'
   - key:             modernize-make-unique.IncludeStyle
-    value:           '0'
+    value:           'llvm'
   - key:             modernize-make-unique.MakeSmartPtrFunction
     value:           'std::make_unique'
   - key:             modernize-make-unique.MakeSmartPtrFunctionHeader

.cmake-format

@@ -0,0 +1,22 @@
+# ------------------------------------------------
+# Options affecting comment reflow and formatting.
+# ------------------------------------------------
+with section("markup"):
+  # If comment markup is enabled, don't reflow the first comment block in each
+  # listfile. Use this to preserve formatting of your copyright/license
+  # statements.
+  first_comment_is_literal = True
+
+# -----------------------------
+# Options affecting formatting.
+# -----------------------------
+with section("format"):
+  # If an argument group contains more than this many sub-groups (parg or kwarg
+  # groups) then force it to a vertical layout.
+  max_subgroups_hwrap = 12
+  # If a positional argument group contains more than this many arguments, then
+  # force it to a vertical layout.
+  max_pargs_hwrap = 12
+  # If a candidate layout is wrapped horizontally but it exceeds this many
+  # lines, then reject the layout.
+  max_lines_hwrap = 6

.codecov.yml

@@ -3,8 +3,6 @@ codecov:
   branch: python
   notify:
     require_ci_to_pass: yes
-  ci:
-    - !travis-ci.org
 
 coverage:
   precision: 0
@@ -14,14 +12,21 @@ coverage:
   status:
     project:
       default: false
-      tests:
+      integration_tests:
         paths:
-          - src/core/unit_tests/
+          - testsuite/python/
+        enabled: yes
+        threshold: 1%
+      unit_tests:
+        paths:
+          - "src/**/*tests/"
         enabled: yes
         threshold: 1%
       core:
         paths:
-          - !src/core/unit_tests/
+          - "src/"
+          - "!src/**/*tests/"
+          - "!src/python/"
         enabled: yes
         threshold: 1%
     patch:
@@ -38,10 +43,13 @@ parsers:
       method: no
       macro: no
 
-comment:
-  layout: "reach, diff, flags, files, footer"
-  behavior: default
-  require_changes: no
+comment: false
 
 ignore:
   - "libs"
+  - "doc/tutorials"
+  - "samples"
+  - "maintainer"
+  - "src/walberla_bridge/**/generated_kernels/*"
+  - "src/walberla_bridge/myintrin.h"
+  - "src/walberla_bridge/philox_rand.h"

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+parallel = True

.cppcheck

@@ -0,0 +1,9 @@
+// clang-format off
+constParameter
+unusedFunction
+missingIncludeSystem
+noConstructor
+noExplicitConstructor
+redundantAssignment
+uselessAssignmentPtrArg
+preprocessorErrorDirective

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,12 +1,4 @@
 Fixes #
 
 Description of changes:
- - 
-
-
-PR Checklist
-------------
- - [ ] Tests?
-   - [ ] Interface
-   - [ ] Core 
- - [ ] Docs?
+- 

.github/actions/build_and_check/action.yml

@@ -0,0 +1,19 @@
+name: 'Build and check'
+description: 'Build espresso and run checks'
+runs:
+  using: "composite"
+  steps:
+    - run: |
+       brew install boost boost-mpi fftw
+       brew install hdf5-mpi
+       pip3 install -c requirements.txt numpy cython h5py scipy
+      shell: bash
+      if: runner.os == 'macOS'
+    - run: |
+        export myconfig=maxset with_cuda=false with_gsl=false test_timeout=800 check_skip_long=true
+        bash maintainer/CI/build_cmake.sh
+      shell: bash
+      # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4
+      # See https://github.com/open-mpi/ompi/issues/6518
+      env:
+        OMPI_MCA_btl: "self,tcp"

.github/actions/deploy_docs/action.yml

@@ -0,0 +1,53 @@
+name: 'Deploy documentation'
+description: 'Deploy ESPResSo documentation'
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        # checkout github pages
+        cd "${HOME}"
+        git clone --quiet git@github.com:espressomd/espressomd.github.io.git
+        cd espressomd.github.io
+        # check if already up-to-date (i.e. the commit SHA of the
+        # generated docs is identical to the current commit SHA)
+        LAST_COMMIT=$(git log -1 --pretty=format:"%s" remotes/origin/main)
+        NEXT_COMMIT="Documentation for ${GITHUB_SHA}"
+        if [ "${NEXT_COMMIT}" = "${LAST_COMMIT}" ]; then
+          echo "Documentation already up-to-date.";
+          exit 0;
+        fi
+        # download artifacts
+        curl https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/-/jobs/artifacts/python/download?job=run_tutorials --fail -L -o tutorials.zip
+        curl https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/-/jobs/artifacts/python/download?job=run_doxygen   --fail -L -o doxygen.zip
+        curl https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/-/jobs/artifacts/python/download?job=check_sphinx  --fail -L -o sphinx.zip
+        if grep -F '<!DOCTYPE html>' *.zip; then
+          echo "The artifacts could not be downloaded.";
+          exit 1;
+        fi
+        unzip -q '*.zip'
+        # create a fresh main branch containing the docs of old releases
+        git config --global user.email "noreply@icp.uni-stuttgart.de"
+        git config --global user.name "espresso-ci"
+        git checkout -b new_main remotes/origin/releases
+        # generate the landing page by merging the branch containing the
+        # HTML theme and Markdown files, then convert them to HTML files
+        git merge --quiet --commit --no-edit --allow-unrelated-histories remotes/origin/landing_page
+        make tutorials.md
+        make videos.md
+        for filename in *.md; do
+          make "${filename%.md}.html";
+        done
+        rm *_header.html
+        git add *.html
+        git clean -f
+        git rm *.md *.py Makefile
+        git commit --quiet -m "Generate landing page"
+        # add devel documentation
+        rsync -a --delete --exclude='*.md5' --exclude='*.map' "build/doc/doxygen/html/" dox/
+        rsync -a --delete --exclude='.buildinfo' "build/doc/sphinx/html/" doc/
+        rsync -a --delete "build/doc/tutorials/html/" tutorials/
+        git add doc dox tutorials
+        git commit --quiet -m "${NEXT_COMMIT}"
+        # deploy
+        git push -f origin new_main:main
+      shell: bash

.github/workflows/deploy.yml

@@ -0,0 +1,25 @@
+name: deploy
+
+on:
+  schedule:
+    - cron: '0 7 * * *'
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+jobs:
+  deploy_docs:
+    runs-on: ubuntu-22.04
+    if: github.repository == 'espressomd/espresso'
+    environment: deploy_documentation
+    steps:
+      - name: Install pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+      - name: Setup SSH agent
+        uses: webfactory/ssh-agent@v0.7.0
+        with:
+          ssh-private-key: ${{ secrets.GH_PAGES_SSH_PRIVATE_KEY }}
+      - name: Checkout
+        uses: actions/checkout@main
+      - name: Deploy documentation
+        uses: ./.github/actions/deploy_docs

.github/workflows/push_pull.yml

@@ -0,0 +1,110 @@
+name: run tests
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+jobs:
+  macos:
+    runs-on: macos-12
+    if: ${{ github.repository == 'espressomd/espresso' }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+      - name: Setup ccache
+        uses: hendrikmuhs/ccache-action@v1.2
+        with:
+          key: macos
+          save: ${{ github.ref == 'refs/heads/python' }}
+      - name: Setup Python environment
+        uses: actions/setup-python@v4.3.1
+        with:
+          python-version: '3.9'
+      - name: Get runner specifications
+        run: system_profiler SPHardwareDataType
+      - name: Build and check
+        uses: ./.github/actions/build_and_check
+        env:
+          build_procs: 3
+          check_procs: 3
+          with_ccache: 'true'
+
+  debian:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/espressomd/docker/debian:fbdf2f2f9d76b761c0aa1308f17fb17e38501850-base-layer
+      credentials:
+         username: ${{ github.actor }}
+         password: ${{ secrets.github_token }}
+      options: --cpus 2
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+      - name: Setup ccache
+        uses: hendrikmuhs/ccache-action@v1.2
+        with:
+          key: debian
+          save: ${{ github.ref == 'refs/heads/python' || ( github.repository != 'espressomd/espresso' && ! startsWith(github.ref, 'refs/pull') ) }}
+      - name: Setup Git environment
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+      - name: Get runner specifications
+        run: lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)'
+      - name: Build and check
+        uses: ./.github/actions/build_and_check
+        env:
+          build_procs: 2
+          check_procs: 2
+          myconfig: 'maxset'
+          with_ccache: 'true'
+          with_cuda: 'false'
+          with_hdf5: 'true'
+          with_fftw: 'true'
+          with_gsl: 'false'
+          with_scafacos: 'false'
+          with_stokesian_dynamics: 'false'
+          make_check_unit_tests: 'true'
+          make_check_python: 'false'
+          OMPI_ALLOW_RUN_AS_ROOT: 1
+          OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+
+  ubuntu:
+    runs-on: ubuntu-latest
+    if: ${{ github.repository == 'espressomd/espresso' }}
+    container:
+      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:fbdf2f2f9d76b761c0aa1308f17fb17e38501850-base-layer
+      credentials:
+         username: ${{ github.actor }}
+         password: ${{ secrets.github_token }}
+      options: --cpus 2
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+      - name: Setup ccache
+        uses: hendrikmuhs/ccache-action@v1.2
+        with:
+          key: ubuntu
+          save: ${{ github.ref == 'refs/heads/python' }}
+      - name: Setup Git environment
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+      - name: Get runner specifications
+        run: lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)'
+      - name: Build and check
+        uses: ./.github/actions/build_and_check
+        env:
+          build_procs: 2
+          check_procs: 2
+          myconfig: 'maxset'
+          with_ccache: 'true'
+          with_cuda: 'false'
+          with_hdf5: 'false'
+          with_fftw: 'false'
+          with_gsl: 'false'
+          with_scafacos: 'false'
+          with_stokesian_dynamics: 'false'
+          make_check_unit_tests: 'false'
+          make_check_python: 'false'
+          OMPI_ALLOW_RUN_AS_ROOT: 1
+          OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1