prettier check (#68)

* prettier check

* add automatic formatting updates

* make script executable

* exclude workflow files

* Automated formatting of files (#69)

Co-authored-by: Philip Top <top1@llnl.gov>
Co-authored-by: HELICS-bot <HELICS-bot@users.noreply.github.com>

* update the markdownlintrc

* add dockerfile linter

* update config location

* update create-file-docker image

* remove markdown from codacy

* fix codacy

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: HELICS-bot <HELICS-bot@users.noreply.github.com>

.ci/azure-build.yml

@@ -1,13 +1,11 @@
 steps:
+  - task: CMake@1
+    inputs:
+      cmakeArgs: .. -DCMAKE_CXX_STANDARD=$(units.std) -DUNITS_HEADER_ONLY=$(units.header) -DCMAKE_BUILD_TYPE=$(units.build_type) $(units.options)
+    displayName: 'Configure'
+    env:
+      GIT_SSL_NO_VERIFY: 1
 
-- task: CMake@1
-  inputs:
-    cmakeArgs: .. -DCMAKE_CXX_STANDARD=$(units.std) -DUNITS_HEADER_ONLY=$(units.header) -DCMAKE_BUILD_TYPE=$(units.build_type) $(units.options)
-  displayName: 'Configure'
-  env:
-    GIT_SSL_NO_VERIFY: 1
-
-- script: cmake --build .
-  displayName: 'Build'
-  workingDirectory: build
-
+  - script: cmake --build .
+    displayName: 'Build'
+    workingDirectory: build

.ci/azure-cmake.yml

@@ -1,16 +1,15 @@
 steps:
+  # Note that silkeh/clang does not include ca-certificates, so check the shasum for verification
+  - bash: |
+      wget --no-check-certificate "https://cmake.org/files/v3.14/cmake-3.14.3-Linux-x86_64.tar.gz"
+      echo "29faa62fb3a0b6323caa3d9557e1a5f1205614c0d4c5c2a9917f16a74f7eff68  cmake-3.14.3-Linux-x86_64.tar.gz" | shasum -sca 256
+    displayName: Download CMake
 
-# Note that silkeh/clang does not include ca-certificates, so check the shasum for verification
-- bash: |
-    wget --no-check-certificate "https://cmake.org/files/v3.14/cmake-3.14.3-Linux-x86_64.tar.gz"
-    echo "29faa62fb3a0b6323caa3d9557e1a5f1205614c0d4c5c2a9917f16a74f7eff68  cmake-3.14.3-Linux-x86_64.tar.gz" | shasum -sca 256
-  displayName: Download CMake
+  - task: ExtractFiles@1
+    inputs:
+      archiveFilePatterns: 'cmake*.tar.gz'
+      destinationFolder: 'cmake_program'
+      displayName: Extract CMake
 
-- task: ExtractFiles@1
-  inputs:
-    archiveFilePatterns: 'cmake*.tar.gz'
-    destinationFolder: 'cmake_program'
-    displayName: Extract CMake
-
-- bash: echo "##vso[task.prependpath]$(Build.SourcesDirectory)/cmake_program/cmake-3.14.3-Linux-x86_64/bin"
-  displayName: Add CMake to PATH
+  - bash: echo "##vso[task.prependpath]$(Build.SourcesDirectory)/cmake_program/cmake-3.14.3-Linux-x86_64/bin"
+    displayName: Add CMake to PATH

.ci/azure-steps.yml

@@ -1,18 +1,17 @@
 steps:
+  - checkout: self
+    fetchDepth: 50
+    submodules: true
 
-- checkout: self
-  fetchDepth: 50
-  submodules: true
+  - task: CMake@1
+    inputs:
+      cmakeArgs: .. -DCMAKE_BUILD_TYPE=Debug
+    displayName: 'Configure'
 
-- task: CMake@1
-  inputs:
-    cmakeArgs: .. -DCMAKE_BUILD_TYPE=Debug
-  displayName: 'Configure'
+  - script: cmake --build . -j
+    displayName: 'Build'
+    workingDirectory: build
 
-- script: cmake --build . -j
-  displayName: 'Build'
-  workingDirectory: build
-
-- script: ctest --output-on-failure -C Debug
-  displayName: 'Test'
-  workingDirectory: build
+  - script: ctest --output-on-failure -C Debug
+    displayName: 'Test'
+    workingDirectory: build

.ci/azure-test.yml

@@ -1,12 +1,9 @@
 steps:
-
-- script: ctest --output-on-failure -C $(units.build_type) -T test
-  displayName: 'Test'
-  workingDirectory: build
-
-- task: PublishTestResults@2
-  inputs:
-    testResultsFormat: 'cTest'
-    testResultsFiles: '**/Test.xml'
-
-
+  - script: ctest --output-on-failure -C $(units.build_type) -T test
+    displayName: 'Test'
+    workingDirectory: build
+
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFormat: 'cTest'
+      testResultsFiles: '**/Test.xml'

.circleci/config.yml

@@ -1,6 +1,5 @@
 version: 2
 aliases:
-
   - &run_units
     name: run_units
     environment:
@@ -22,7 +21,6 @@ aliases:
       make QUICK_RAW_FUZZ
 
 jobs:
-
   unitsTSan:
     docker:
       - image: helics/buildenv:sanitizers
@@ -79,5 +77,3 @@ workflows:
       - unitsASan
       - unitsTSan
       - unitsFuzz
-
-

.cmake-format.json

@@ -13,6 +13,6 @@
   "enum_char": ".",
   "bullet_char": "*",
   "line_ending": "unix",
-  "first_comment_is_literal":true,
-  "literal_comment_pattern":"Copyright"
+  "first_comment_is_literal": true,
+  "literal_comment_pattern": "Copyright"
 }

.codacy.yml

@@ -1,18 +1,18 @@
 ---
 engines:
- rubocop:
-   enabled: true
- duplication:
-   enabled: true
- metrics:
-   enabled: true
- coverage:
-   enabled: false
+  rubocop:
+    enabled: true
+  duplication:
+    enabled: true
+  metrics:
+    enabled: true
+  coverage:
+    enabled: false
 languages:
 
 exclude_paths:
-  - ThirdParty/**/*
-  - ThirdParty/*
-  - scripts/**/*
-  - scripts/*
-
+  - 'ThirdParty/**/*'
+  - 'ThirdParty/*'
+  - 'scripts/**/*'
+  - 'scripts/*'
+  - '**.md'

.codecov.yml

@@ -6,7 +6,7 @@ codecov:
 coverage:
   precision: 2
   round: down
-  range: "70...100"
+  range: '70...100'
 
   test:
     target: 100%
@@ -24,12 +24,12 @@ parsers:
       macro: no
 
 comment:
-  layout: "header, diff"
+  layout: 'header, diff'
   behavior: default
   require_changes: no
 
 ignore:
-  - "ThirdParty"
-  - "examples"
-  - "test"
-  - "FuzzTargets"
+  - 'ThirdParty'
+  - 'examples'
+  - 'test'
+  - 'FuzzTargets'

.github/actions/cmake_config/action.yml

@@ -6,7 +6,7 @@ inputs:
   options:
     description: 'The CMake configuration options'
     required: false
-    default: ""
+    default: ''
 name: 'Configure with CMake'
 runs:
   using: 'docker'

.github/actions/create-file-update-pr/Dockerfile

@@ -0,0 +1,15 @@
+FROM alpine:latest
+
+RUN apk add --no-cache \
+    bash \
+    jq \
+    git \
+    ca-certificates \
+    curl
+
+COPY entrypoint.sh /entrypoint.sh
+
+LABEL name="create-file-pr"
+LABEL version="1.0.1"
+
+ENTRYPOINT ["/entrypoint.sh"]

.github/actions/create-file-update-pr/action.yml

@@ -0,0 +1,12 @@
+name: 'Create File Update PR'
+description: 'Pushes a new branch with changed files and opens a PR for updating the changed files in the base branch'
+inputs:
+  no-hash: # turn off inclusion of the hash in the created branch name
+    description: 'Do not include the changed file hash in the PR branch name'
+    default: false
+  replace-branch: # if a PR branch already exists, replaces it with updated contents
+    description: 'Replace the contents of an existing PR branch of the same name'
+    default: false
+runs:
+  using: 'docker'
+  image: 'Dockerfile'

.github/actions/create-file-update-pr/entrypoint.sh

@@ -0,0 +1,72 @@
+#!/bin/bash
+
+PR_URL=$(jq --raw-output .repository.pulls_url "$GITHUB_EVENT_PATH")
+PR_URL=${PR_URL%\{*}
+API_VERSION=v3
+API_HEADER="Accept: application/vnd.github.${API_VERSION}+json; application/vnd.github.shadow-cat-preview+json; application/vnd.github.symmetra-preview+json; application/vnd.github.sailor-v-preview+json"
+AUTH_HEADER="Authorization: token ${GITHUB_TOKEN}"
+
+# Only commit and open a PR if files have changed
+files_changed=$(git diff --staged --name-only)
+if [[ "$files_changed" != "" ]];
+then
+  hash=$(sha256sum "${files_changed}" | sha256sum | cut -c 1-12 -)
+  if [[ "${GITHUB_REF}" == "refs/pull/"* ]];
+  then
+    current_branch="${GITHUB_HEAD_REF}"
+  else
+    current_branch="${GITHUB_REF#refs/heads/}"
+  fi
+
+  # Set the git origin url for committing using a GITHUB_TOKEN
+  git remote set-url origin "https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}"
+  git config user.name "${INPUT_GIT_NAME}"
+  git config user.email "${INPUT_GIT_EMAIL}"
+
+  # Construct the branch name with the changes for a PR
+  pr_branch="${INPUT_BRANCH_PREFIX}update-${current_branch}"
+  if [[ "${INPUT_NO_HASH}" != "true" ]];
+  then
+    pr_branch="${pr_branch}-${hash}"
+  fi
+
+  # Make sure a branch with the same name doesn't already exist, unless INPUT_REPLACE_BRANCH is true
+  git ls-remote --exit-code . "origin/${pr_branch}"
+  rv=$?
+  if [[ "$rv" == "0" ]];
+  then
+    if [[ "${INPUT_REPLACE_BRANCH}" != "true" ]];
+    then
+      exit 0
+    fi
+    pr_branch_exists="true"
+  fi
+
+  if [[ "${pr_branch_exists}" == "true" ]];
+  then
+      # delete any existing local branch with the same name
+      git branch -D "${pr_branch}" >/dev/null 2>&1
+  fi
+
+  # Commit the changed files and push the branch to GitHub
+  git checkout -b "${pr_branch}"
+  git commit -m "${INPUT_COMMIT_MSG}"
+  git push -f -u origin "${pr_branch}"
+
+  if [[ "$pr_branch_exists" != "true" ]];
+  then
+    # Format string values for GitHub API JSON payload
+    PR_TITLE="$(echo -n "${INPUT_PR_TITLE}" | jq --raw-input --slurp ".")"
+    PR_BODY="$(echo -n "${INPUT_PR_BODY}" | jq --raw-input --slurp ".")"
+    PR_BASE="$(echo -n "${current_branch}" | jq --raw-input --slurp ".")"
+    PR_HEAD="$(echo -n "${pr_branch}" | jq --raw-input --slurp ".")"
+    pr_api_data="{\"title\":${PR_TITLE}, \"body\":${PR_BODY}, \"base\":${PR_BASE}, \"head\":${PR_HEAD}, \"draft\":false}"
+
+    # Open up the GitHub PR
+    curl -XPOST -fsSL \
+         -H "${AUTH_HEADER}" \
+         -H "${API_HEADER}" \
+         --data "${pr_api_data}" \
+         "${PR_URL}"
+  fi
+fi

.github/workflows/tests.yml

@@ -22,6 +22,30 @@ jobs:
         path: ~/.cache/pre-commit
         key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
     - uses: pre-commit/action@v1.0.0
+    - name: Stage changed files
+      if: failure() && github.event.pull_request.draft != true && github.event.pull_request.head.repo.full_name == github.repository
+      shell: bash --noprofile --norc {0}
+      run: |
+        git diff --name-only
+        if [[ "$?" == "0" ]];
+        then
+          git add --all
+        fi
+        exit 0
+    - name: Create/update a file update PR with no hash
+      if: failure() && github.event.pull_request.draft != true && github.event.pull_request.head.repo.full_name == github.repository
+      uses: ./.github/actions/create-file-update-pr
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        COMMIT_MSG: "Automated formatting of files"
+        PR_TITLE: "Automated formatting of files"
+        PR_BODY: "Automated formatting of files in commit /~https://github.com/${{ github.event.pull_request.head.repo.full_name }}/commit/${{ github.sha }} from ${{ github.ref }}."
+        GIT_EMAIL: "HELICS-bot@users.noreply.github.com"
+        GIT_NAME: "HELICS-bot"
+        BRANCH_PREFIX: "pre-commit/"
+        NO_HASH: "true"
+        REPLACE_BRANCH: "true"
 
   cmake-config:
     name: CMake config check