Merge branch 'develop'

noclocks · Sep 14, 2024 · 130e30b · 130e30b
2 parents ceb270e + f74d660
commit 130e30b
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,4 +1,4 @@
-^noclocksR\.Rproj$
+^noclocksr\.Rproj$
 ^\.Rproj\.user$
 ^cliff\.toml$
 ^CHANGELOG\.md$

diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml
@@ -0,0 +1,9 @@
+name: Dependencies
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Install package dependencies 📄
+      run: |
+        pak::local_install_deps(".", upgrade=FALSE, ask=FALSE, dependencies = TRUE)
+      shell: Rscript {0}
diff --git a/.github/cliff.toml b/.github/cliff.toml
@@ -1,64 +1,120 @@
-# configuration file for git-cliff
-# see <https://github.com/orhun/git-cliff/blob/main/config/cliff.toml> for default
-# see also: <https://www.conventionalcommits.org>
+# No Clocks, LLC Custom Configuration Template File for `git-cliff`
+
 [changelog]
+
+# remove the leading and trailing whitespace from the template
+trim = true
+
+# header
 header = """
-# Changelog
-*All notable changes to this project will be documented in this file.*\n
+# Changelog\n
+> All notable changes to this project will be documented in this file. The format is based on
+[Keep a Changelog](http://keepachangelog.com/) and this project adheres to
+[Semantic Versioning](http://semver.org/).\n
 """
+
+# body - see https://tera.netlify.app/docs/#introduction
 body = """
 {% if version %}\
-    ## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }}
+    ## [{{ version | trim_start_matches(pat="v") }}]\
+    {% if previous %}\
+		{% if previous.version %}\
+			(REPOSITORY_URL/compare/{{ previous.version }}...{{ version }})\
+		{% else %}\
+			(REPOSITORY_URL/tree/{{ version }})\
+		{% endif %}\
+	{% endif %}\
+	- ({{ timestamp | date(format="%Y-%m-%d") }})
 {% else %}\
     ## [Unreleased]
 {% endif %}\
 {% for group, commits in commits | group_by(attribute="group") %}
-    ### {{ group | upper_first }}
-    {% for commit in commits %}
-        - {% if commit.breaking %}[**breaking**] {% endif %}{{ commit.message | upper_first }}\
-    {% endfor %}
+	## {{ group | upper_first }}
+	{% for commit in commits %}
+		- {% if commit.scope %}\
+			**{{commit.scope}}:** \
+		  {% endif %}\
+		  {% if '```' in commit.message %}\
+		    {{ commit.message | upper_first }}\n\
+		    ([{{ commit.id | truncate(length=7, end="") }}](REPOSITORY_URL/commit/{{ commit.id }}))  - ({{ commit.author.name }})\
+          {% else %}\
+			{{ commit.message | upper_first  }} ([{{ commit.id | truncate(length=7, end="") }}](REPOSITORY_URL/commit/{{ commit.id }}))  - ({{ commit.author.name }})\
+          {% endif %}\
+		{% if commit.breaking %}\
+			{% for breakingChange in commit.footers %}\
+				\n{% raw %}  {% endraw %}- **{{ breakingChange.token }}{{ breakingChange.separator }}** {{ breakingChange.value }}\
+			{% endfor %}\
+		{% endif %}\
+	{% endfor %}
 {% endfor %}\n
 """
-trim = true
+
 footer = """
 ***
 *Changelog generated by [git-cliff](https://github.com/orhun/git-cliff).*
+***
 """
+
 [git]
 conventional_commits = true
 filter_unconventional = true
-commit_parsers = [
-    { message = "^feat", group = "Features"},
-    { message = "^fix", group = "Bug Fixes"},
-    { message = "^bug", group = "Bug Fixes"},
-    { message = "^doc", group = "Documentation"},
-    { message = "^docs", group = "Documentation"},
-    { message = "^perf", group = "Performance"},
-    { message = "^app", group = "Application"},
-    { message = "^api", group = "API"},
-    { message = "^data", group = "Data"},
-    { message = "^db", group = "Database"},
-    { message = "^refactor", group = "Refactoring"},
-    { message = "^style", group = "Styling"},
-    { message = "^test", group = "Testing"},
-    { message = "^setup", group = "Infrastructure"},
-    { message = "^infra", group = "Infrastructure"},
-    { message = "^meta", group = "Meta"},
-    { message = "^config", group = "Configuration"},
-    { message = "^design", group = "Design"},
-    { message = "^clean", group = "Cleanup"},
-    { message = "^unit", group = "Testing"},
-    { message = "^enhance", group = "Features"},
-    { message = "^cicd", group = "DevOps"},
-    { message = "^config", group = "Configuration"},
-    { message = "^deploy", group = "Deployment"},
-    { message = "^chore\\(release\\): prepare for", skip = true},
-    { message = "^chore", group = "Miscellaneous Tasks"},
-    { body = ".*security", group = "Security"},
-]
-filter_commits = false
+filter_commits = true
 tag_pattern = "v[0-9]*"
-skip_tags = "v0.1.0-beta.1"
+skip_tags = "v0.0.0.9999"       # "v0.1.0-beta.1"
 ignore_tags = ""
-topo_order = false
-sort_commits = "oldest"
+date_order = true
+topo_order = true
+sort_commits = "newest"         # "oldest"
+split_commits = false
+protect_breaking_commits = true
+# limit_commits = 42
+commit_preprocessors = [
+    { pattern = '\((\w+\s)?#([0-9]+)\)', replace = "([#${2}](REPOSITORY_URL/issues/${2}))"},
+    { pattern = "Merge pull request #([0-9]+) from [^ ]+", replace = "PR [#${1}](REPOSITORY_URL/pull/${1}):"},
+]
+commit_parsers = [
+    { message = "^feat", group = "Features" },
+    { message = "^fix", group = "Bug Fixes" },
+    { message = "^bug", group = "Bug Fixes" },
+    { message = "^doc", group = "Documentation" },
+    { message = "^docs", group = "Documentation" },
+    { message = "^perf", group = "Performance" },
+    { message = "^app", group = "Application" },
+    { message = "^api", group = "API" },
+    { message = "^data", group = "Data" },
+    { message = "^db", group = "Database" },
+    { message = "^refactor", group = "Refactoring" },
+    { message = "^style", group = "Styling" },
+    { message = "^test", group = "Testing" },
+    { message = "^setup", group = "Setup" },
+    { message = "^infra", group = "Infrastructure" },
+    { message = "^meta", group = "Meta" },
+    { message = "^config", group = "Configuration" },
+    { message = "^design", group = "Design" },
+    { message = "^clean", group = "Cleanup" },
+    { message = "^unit", group = "Testing" },
+    { message = "^enhance", group = "Features" },
+    { message = "^cicd", group = "DevOps" },
+    { message = "^config", group = "Configuration" },
+    { message = "^deploy", group = "Deployment" },
+    { message = "^chore\\(release\\): prepare for", skip = true },
+    { message = "^chore", group = "Miscellaneous Tasks", skip = true },
+    { body = ".*security", group = "Security" },
+]
+
+
+# ------------------------------------------------------------------------------
+# parse the commits based on https://www.conventionalcommits.org
+# filter out the commits that are not conventional
+# process each line of a commit as an individual commit
+# regex for preprocessing the commit messages
+# regex for parsing and grouping commits
+# protect breaking changes from being skipped due to matching a skipping commit_parser
+# filter out the commits that are not matched by commit parsers
+# glob pattern for matching git tags
+# regex for skipping tags
+# regex for ignoring tags
+# sort the tags chronologically
+# sort the commits inside sections by oldest/newest order
+# limit the number of commits included in the changelog
+# ------------------------------------------------------------------------------
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    assignees:
+      - "jimbrig"
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -1,34 +1,38 @@
-name: Generate CHANGELOG.md
+name: Generate Changelog
 on:
   workflow_dispatch:
+  workflow_call:
   push:
-    branches:
-      - main
-      - develop
+    branches: [ "main" ]
+  pull_request:
 jobs:
   changelog:
-    name: Generate changelog
+    name: Generate Changelog
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Generate a changelog
-        uses: orhun/git-cliff-action@v1
+      - name: Run Git Cliff
+        uses: tj-actions/[email protected]
         id: git-cliff
         with:
-          config: ./.github/cliff.toml
-          args: --verbose
-        env:
-          OUTPUT: ./CHANGELOG.md
-
-      - name: Print the changelog
-        run: cat "${{ steps.git-cliff.outputs.changelog }}"
-
-      - name: Commit and Push Changes
-        uses: actions-js/push@master
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          args: "--verbose"
+          output: "CHANGELOG.md"
+          template-config: "./.github/cliff.toml"
+      - name: Print Changelog
+        id: print-changelog
+        run: |
+          cat "CHANGELOG.md"
+      # Commit and push the updated changelog, IF not a pull request
+      - name: Commit and Push Changelog
+        if: github.event_name != 'pull_request'
+        run: |
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
+          set +e
+          git add CHANGELOG.md
+          git commit -m "[chore]: update changelog"
+          git push https://${{ secrets.GITHUB_TOKEN }}@github.com/${GITHUB_REPOSITORY}.git "main"
diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -0,0 +1,30 @@
+name: Check 📦
+
+on:
+  workflow_call:
+
+concurrency:
+  group: check-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check:
+    name: ${{ vars.CI_IMAGE }}
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout project ⬇️
+        uses: actions/checkout@v4
+
+      - name: Install package dependencies 📄
+        uses: noclocks/noclocksr/.github/actions/dependencies@main
+
+      - name: Check 📦
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(error_on = "error", args = "--no-tests")
+        shell: Rscript {0}
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_dispatch:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Test Coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.github/workflows/document.yml b/.github/workflows/document.yml
@@ -0,0 +1,47 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_dispatch:
+  push:
+    paths: ["R/**"]
+
+name: Document (Roxygen)
+
+permissions: read-all
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin