morie 0.9.5.2 — CRAN-Policy fix + rOpenSci #770 audit (supersedes 0.9.4 archived)

.github/workflows/ci-numba-bench.yml

@@ -9,6 +9,9 @@ on:
     - cron: "37 4 * * *"   # nightly at 04:37 UTC
   workflow_dispatch:
 
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 permissions:
   contents: read
 

.github/workflows/docker-publish.yml

@@ -109,7 +109,12 @@ jobs:
           sbom: true
 
       - name: Generate build provenance attestation
-        uses: actions/attest-build-provenance@e8998f949152b193b063cb0ec769d69d929409be # v2
+        # v4.1.0 — composite action that internally uses
+        # actions/attest@v4.1.0 with `using: node24`. Bumped from v2
+        # (Node-20-targeting sub-actions) on 2026-05-21 to clear the
+        # "Node.js 20 deprecated" annotation that appeared on the
+        # v0.9.4 Docker publish run (26019670710).
+        uses: actions/attest-build-provenance@a2bbfa25375fe432b6a289bc6b6cd05ecd0c4c32 # v4.1.0
         with:
           subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           subject-digest: ${{ steps.build.outputs.digest }}

.github/workflows/r-cmd-check.yml

@@ -2,6 +2,10 @@ name: R CMD check
 
 env:
   FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+  # Parallel compile for source-installed dependencies (notably duckdb,
+  # which has ~50 MB of C++ source and otherwise takes 20-25 min single-
+  # threaded). GitHub-hosted runners are 4-vCPU / 16 GB RAM so -j4 fits.
+  MAKEFLAGS: "-j4"
 
 
 # Run R CMD check across the supported OS x R-version matrix. Required
@@ -17,6 +21,11 @@ on:
     paths:
       - 'r-package/morie/**'
       - '.github/workflows/r-cmd-check.yml'
+  pull_request:
+    branches: [main]
+    paths:
+      - 'r-package/morie/**'
+      - '.github/workflows/r-cmd-check.yml'
   workflow_dispatch:
 
 permissions:
@@ -33,7 +42,9 @@ jobs:
       matrix:
         config:
           - { os: macos-latest,   r: 'release' }
-          - { os: windows-latest, r: 'release' }
+          # Pin Windows runner explicitly (windows-latest auto-redirects to
+          # windows-2025-vs2026 by 2026-06-15; pre-pin removes ambiguity).
+          - { os: windows-2025,   r: 'release' }
           - { os: ubuntu-latest,  r: 'release' }
           - { os: ubuntu-latest,  r: 'devel'   }
           - { os: ubuntu-latest,  r: 'oldrel-1' }
@@ -72,3 +83,65 @@ jobs:
           # vignettes/PDFs in CI.
           args: 'c("--no-manual")'
           error-on: '"error"'
+
+  # Separate Linux-only job that spins up a live PostgreSQL service and
+  # exercises the PG branch of the DBI cache layer. The PG testthat
+  # block in tests/testthat/test-db-backends.R is gated on
+  # MORIE_PG_TEST=true; this job sets that env var so the tests run.
+  # The default R-CMD-check matrix above does NOT set MORIE_PG_TEST,
+  # so the PG block correctly skips there.
+  R-CMD-check-postgres:
+    runs-on: ubuntu-latest
+    name: ubuntu-latest (release) + postgres-15
+
+    services:
+      postgres:
+        image: postgres:15
+        env:
+          POSTGRES_DB: testdb
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: password
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+    env:
+      _R_CHECK_FORCE_SUGGESTS_: false
+      R_KEEP_PKG_SOURCE: yes
+      MORIE_PG_TEST: "true"
+      PGHOST: localhost
+      PGPORT: "5432"
+      PGUSER: postgres
+      PGPASSWORD: password
+      PGDATABASE: testdb
+
+    defaults:
+      run:
+        working-directory: r-package/morie
+
+    steps:
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+
+      - uses: r-lib/actions/setup-pandoc@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          working-directory: r-package/morie
+          extra-packages: any::rcmdcheck any::RPostgres any::duckdb any::withr
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          working-directory: r-package/morie
+          upload-snapshots: true
+          args: 'c("--no-manual")'
+          error-on: '"error"'

.github/workflows/r-coverage-and-lint.yml

@@ -0,0 +1,178 @@
+name: R coverage + lint + goodpractice
+
+# Runs covr (with codecov.io upload), lintr, and goodpractice on every
+# push to main / PR. Complements r-cmd-check.yml — which only runs
+# R CMD check across the OS × R-version matrix. Together they cover
+# the full rOpenSci pkgcheck surface (rcmdcheck + covr + cyclocomp +
+# lintr + goodpractice).
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'r-package/morie/**'
+      - '.github/workflows/r-coverage-and-lint.yml'
+  pull_request:
+    branches: [main]
+    paths:
+      - 'r-package/morie/**'
+  workflow_dispatch:
+
+env:
+  # Force every JavaScript-based action (codecov, upload-artifact, etc.)
+  # to use Node.js 24 instead of the deprecated Node.js 20.
+  # Node 20 is scheduled for removal from runners on 2026-09-16.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+  # Parallel compile for source-installed Suggests (notably duckdb,
+  # which has ~50 MB of C++ source). 4-vCPU runners + -j4 cuts the
+  # dependency-install step from ~25 min single-threaded to ~5 min.
+  MAKEFLAGS: "-j4"
+
+permissions:
+  contents: read
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    name: covr + codecov upload
+
+    env:
+      _R_CHECK_FORCE_SUGGESTS_: false
+      R_KEEP_PKG_SOURCE: yes
+
+    defaults:
+      run:
+        working-directory: r-package/morie
+
+    steps:
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          working-directory: r-package/morie
+          extra-packages: any::covr any::xml2
+          needs: coverage
+
+      - name: Run covr
+        run: |
+          Rscript -e 'cov <- covr::package_coverage(type = "tests", quiet = TRUE); covr::to_cobertura(cov, filename = "coverage.xml"); cat(sprintf("Coverage: %.2f%%\n", covr::percent_coverage(cov)))'
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: r-package/morie/coverage.xml
+          flags: r-tests
+          fail_ci_if_error: false  # don't block on codecov outages
+        continue-on-error: true
+
+  lint:
+    runs-on: ubuntu-latest
+    name: lintr
+
+    defaults:
+      run:
+        working-directory: r-package/morie
+
+    steps:
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          working-directory: r-package/morie
+          extra-packages: any::lintr
+
+      - name: Run lintr
+        run: |
+          Rscript -e 'lintr::lint_package()'
+
+  goodpractice:
+    runs-on: ubuntu-latest
+    name: goodpractice (covr + cyclocomp + lintr + rcmdcheck)
+
+    env:
+      _R_CHECK_FORCE_SUGGESTS_: false
+
+    defaults:
+      run:
+        working-directory: r-package/morie
+
+    steps:
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: r-lib/actions/setup-pandoc@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          working-directory: r-package/morie
+          extra-packages: any::goodpractice any::rcmdcheck any::covr any::cyclocomp any::lintr
+
+      - name: Run goodpractice
+        run: |
+          Rscript -e 'g <- goodpractice::gp("."); print(g)'
+
+  pkgcheck:
+    # rOpenSci's own check — runs pkgstats + covr + goodpractice + rcmdcheck
+    # internally and produces the markdown comment the rOpenSci bot uses.
+    runs-on: ubuntu-latest
+    name: rOpenSci pkgcheck
+
+    defaults:
+      run:
+        working-directory: r-package/morie
+
+    steps:
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: r-lib/actions/setup-pandoc@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      # pkgcheck's internal rcmdcheck builds the PDF manual, which needs
+      # the `inconsolata` LaTeX font. Without it pkgcheck reports a
+      # spurious "R CMD check found 1 warning" against a package that
+      # otherwise has 0 warnings in the dedicated r-cmd-check.yml matrix.
+      - uses: r-lib/actions/setup-tinytex@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+      - name: Install inconsolata + helpers for PDF manual build
+        run: |
+          tlmgr update --self
+          tlmgr install inconsolata helvetic times courier ec parskip url upquote
+
+      - name: Install system deps for pkgstats (universal-ctags)
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y universal-ctags
+
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
+        with:
+          working-directory: r-package/morie
+          extra-packages: |
+            any::rcmdcheck
+            any::goodpractice
+            any::cyclocomp
+            ropensci-review-tools/pkgstats
+            ropensci-review-tools/pkgcheck
+
+      - name: Run pkgcheck::pkgcheck() + checks_to_markdown()
+        env:
+          # pkgcheck queries the GitHub GraphQL API for repo metadata. Use
+          # the runner's auto-provided token instead of unauthenticated
+          # requests (which hit the 60-req/hr rate limit instantly).
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          Rscript -e 'cks <- pkgcheck::pkgcheck("."); md <- pkgcheck::checks_to_markdown(cks); writeLines(md, "pkgcheck.md"); cat(md)'
+
+      - name: Upload pkgcheck markdown
+        uses: actions/upload-artifact@v5
+        with:
+          name: pkgcheck-markdown
+          path: r-package/morie/pkgcheck.md

.gitignore

@@ -114,3 +114,4 @@ papers/PAPERS_*.txt
 RELEASE-EMAILS-*.md
 *-EMAILS-*.md
 morie-private/
+data-snapshots/

.zenodo.json

@@ -55,5 +55,5 @@
     "Goffman, E. (1961). Asylums: Essays on the Social Situation of Mental Patients and Other Inmates. Anchor Books."
   ],
   "notes": "MORIE is licensed AGPL-3.0-or-later (strong copyleft; see LICENSE). The optional Linux-kernel adjuncts under kernel-module/ and daemon/ are GPL-2.0-only (kernel ABI requirement). The Ontario SIU scraper is additionally subject to the Ontario open-government licence on the source corpus.",
-  "version": "0.9.4"
+  "version": "0.9.5"
 }

CITATION.cff

@@ -8,7 +8,7 @@ authors:
     name-particle: "Singh"
     # morie pronunciation: /ˈmɔɪraɪ/ -- "MOY-rye", like the Greek Moirai (the Fates)
     # IPA: /ʋənʃ sɪŋ ɾʊˈɦeːlɑː/
-version: "0.9.4"
+version: "0.9.5.2"
 date-released: "2026-05-18"
 url: "https://github.com/hadesllm/morie"
 repository-code: "https://github.com/hadesllm/morie"
@@ -37,7 +37,7 @@ preferred-citation:
       given-names: "Vansh Singh"
       orcid: "https://orcid.org/0009-0004-1750-3592"
   year: "2026"
-  version: "0.9.4"
+  version: "0.9.5.2"
   doi: "10.5281/zenodo.20111233"
   url: "https://doi.org/10.5281/zenodo.20111233"
 references:
@@ -48,7 +48,7 @@ references:
         given-names: "Vansh Singh"
         orcid: "https://orcid.org/0009-0004-1750-3592"
     year: "2026"
-    version: "0.9.4"
+    version: "0.9.5.2"
     doi: "10.5281/zenodo.20096350"
     url: "https://doi.org/10.5281/zenodo.20096350"
     notes: "Python companion software paper (same toolkit, Python implementation)."

Dockerfile

@@ -79,7 +79,7 @@ RUN R CMD INSTALL --library=/usr/local/lib/R/site-library /build/r-package/morie
 # ─── Stage 3: Runtime ────────────────────────────────────────────────────────
 FROM python:${PYTHON_VERSION}-slim AS runtime
 
-ARG VERSION=0.9.4
+ARG VERSION=0.9.5
 ARG VCS_REF=unknown
 ARG BUILD_DATE=unknown