Prep ROpenSci submission

.Rbuildignore

@@ -1,3 +1,13 @@
 ^renv$
 ^renv\.lock$
 ^LICENSE\.md$
+^codemeta\.json$
+^README\.Rmd$
+^\.github$
+^\.pre-commit-config.yaml$
+^\.pixi$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^newsfragments$
+^pixi\.*$
+^\.covrignore$

.covrignore

@@ -0,0 +1,4 @@
+inst/include/fast_matrix_market/*
+inst/include/fast_matrix_market/app/*
+inst/include/fast_matrix_market/third_party/*
+.pixi/*

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,16 @@
+---
+name: Bug report or feature request
+about: Describe a bug you've seen or make a case for a new feature
+---
+
+Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on our discussions page <https://github.com/HaoZeke/fastMatMR/discussions/>.
+
+Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+
+For more advice on how to write a great issue, see <https://code-review.tidyverse.org/issues/>.
+
+Brief description of the problem
+
+```r
+# insert reprex here
+```

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,53 @@
+# 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:
+  push:
+    branches: main
+  pull_request:
+    branches: main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/document.yaml

@@ -0,0 +1,42 @@
+# 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:
+  push:
+    paths: ["R/**"]
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "BOT: Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

.github/workflows/pkgcheck.yaml

@@ -1,17 +1,16 @@
 name: pkgcheck
 
-# This will cancel running jobs once a new run is triggered
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref }}
   cancel-in-progress: true
 
 on:
-  # Manually trigger the Action under Actions/pkgcheck
   workflow_dispatch:
-  # Run on every push to main
   push:
     branches:
       - main
+  # pull_request:
+  #   branches: main
 
 jobs:
   pkgcheck:

.github/workflows/pr-commands.yaml

@@ -0,0 +1,79 @@
+# 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:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'BOT: Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'BOT: Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/render-rmarkdown.yaml

@@ -0,0 +1,33 @@
+# 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:
+  push:
+    paths: ['**.Rmd']
+
+name: render-rmarkdown
+
+jobs:
+  render-rmarkdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Render Rmarkdown files and Commit Results
+        run: |
+          RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '[.]Rmd$'))
+          Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]}
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git commit ${RMD_PATH[*]/.Rmd/.md} -m 'Re-build Rmarkdown files' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.gitignore

@@ -1,8 +1,6 @@
 # Added
 .pixi/
-## Generated files
-R/cpp11.R
-src/cpp11.cpp
+*.mtx
 ### Generated by gibo (https://github.com/simonwhitaker/gibo)
 ### https://raw.github.com/github/gitignore/4488915eec0b3a45b5c63ead28f286819c0917de/Global/macOS.gitignore
 

.pre-commit-config.yaml

@@ -5,34 +5,11 @@ repos:
   - id: trailing-whitespace
     exclude: ^(.lintr/)|^(renv/)
   - id: end-of-file-fixer
-    exclude: ^(inst/)|^(renv/)
+    exclude: ^(renv/)
   - id: check-yaml
   - id: check-added-large-files
 - repo: https://github.com/pre-commit/mirrors-clang-format
   rev: v16.0.6
   hooks:
   - id: clang-format
     exclude: ^(inst)
-- repo: https://github.com/lorenzwalthert/precommit
-  rev: v0.2.0
-  hooks:
-  # any R project
-  # - id: codemeta-description-updated
-  - id: style-files
-    args: [--style_pkg=styler, --style_fun=tidyverse_style]
-  - id: lintr
-    args: [--warn_only]
-    verbose: True
-  - id: parsable-R
-  - id: no-browser-statement
-  - id: readme-rmd-rendered
-  - id: roxygenize
-    additional_dependencies:
-      - git2r
-      - pkgbuild
-      - brio
-      - decor
-      - vctrs
-      - tibble
-  - id: use-tidy-description
-  - id: deps-in-desc