Prepare pcatR 1.0.1 for CRAN (#2)

* Prepare pcatR 1.0.1 for CRAN

* Record passing GitHub Actions checks

* Address CRAN submission review feedback

* Diagnose full R-devel manual checks

* Expose R TeX macros to full manual checks

* Install TeX index tool for R manuals

* Record successful candidate archive checks

* Record joint software copyright ownership

* Update TinyTeX before installing manual tools

* Record joint-copyright archive validation

* Address final CRAN review corrections

Author: JaeManP

.Rbuildignore

@@ -5,7 +5,6 @@
 ^\.editorconfig$
 ^_pkgdown\.yml$
 ^README\.Rmd$
-^TECHNICAL_USER_GUIDE\.md$
 ^RELEASE_CHECKLIST\.md$
 ^PUBLISHING\.md$
 ^ROADMAP\.md$
@@ -26,3 +25,7 @@
 ^LICENSE\.md$
 ^REFERENCES\.md$
 ^RELEASE_VALIDATION\.md$
+^CRAN_SUBMISSION\.md$
+^pcatR_.*\.tar\.gz$
+^pcatR\.Rcheck$
+^tmp$

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -10,7 +10,7 @@ body:
     id: version
     attributes:
       label: pcatR version
-      placeholder: "1.0.0"
+      placeholder: "1.0.1"
     validations:
       required: true
   - type: textarea

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

@@ -22,6 +22,7 @@ jobs:
           - {os: ubuntu-latest, r: devel, http-user-agent: release}
           - {os: ubuntu-latest, r: release}
           - {os: ubuntu-latest, r: oldrel-1}
+          - {os: ubuntu-22.04, r: '4.1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -47,3 +48,118 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual")'
+
+  cran-build:
+    name: Build exact CRAN source archive (R release)
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: check
+
+      - name: Build and identify the exact archive
+        run: |
+          R CMD build .
+          test -f pcatR_1.0.1.tar.gz
+          sha256sum pcatR_1.0.1.tar.gz | tee pcatR_1.0.1.sha256
+
+      - name: Upload exact source archive
+        uses: actions/upload-artifact@v7
+        with:
+          name: pcatR-1.0.1-source
+          path: |
+            pcatR_1.0.1.tar.gz
+            pcatR_1.0.1.sha256
+          if-no-files-found: error
+
+  cran-check:
+    name: Exact archive, full manual (R ${{ matrix.config.r }})
+    needs: cran-build
+    runs-on: ubuntu-latest
+    timeout-minutes: 40
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {r: release}
+          - {r: devel, http-user-agent: release}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: actions/download-artifact@v8
+        with:
+          name: pcatR-1.0.1-source
+          path: dist
+
+      - name: Verify the downloaded archive checksum
+        working-directory: dist
+        run: sha256sum --check pcatR_1.0.1.sha256
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install the PDF manual index tool
+        run: |
+          tlmgr update --self
+          tlmgr install makeindex
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: check
+
+      - name: Configure R manual TeX macros
+        run: |
+          R_TEXMF="$(R RHOME)/share/texmf/tex/latex"
+          test -f "$R_TEXMF/Rd.sty"
+          echo "TEXINPUTS=$R_TEXMF//:" >> "$GITHUB_ENV"
+
+      - name: Check the downloaded archive with CRAN settings
+        id: cran-check
+        continue-on-error: true
+        run: R CMD check --as-cran dist/pcatR_1.0.1.tar.gz
+
+      - name: Diagnose a failed PDF manual build
+        if: steps.cran-check.outcome == 'failure'
+        continue-on-error: true
+        working-directory: pcatR.Rcheck
+        run: texi2dvi --pdf --batch pcatR-manual.tex
+
+      - name: Upload check logs
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: cran-check-${{ matrix.config.r }}
+          path: |
+            pcatR.Rcheck/00check.log
+            pcatR.Rcheck/00install.out
+            pcatR.Rcheck/pcatR-manual.*
+          if-no-files-found: warn
+
+      - name: Confirm the CRAN check passed
+        if: always()
+        run: test "${{ steps.cran-check.outcome }}" = "success"

.github/workflows/pkgdown.yaml

@@ -1,20 +1,22 @@
 name: pkgdown
 
 on:
+  pull_request:
   push:
     branches: [main]
   release:
     types: [published]
   workflow_dispatch:
 
 permissions:
-  contents: write
+  contents: read
 
 jobs:
-  pkgdown:
+  build:
+    name: pkgdown
     runs-on: ubuntu-latest
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    permissions:
+      contents: read
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
@@ -30,9 +32,39 @@ jobs:
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
+
+      - name: Upload built site
+        uses: actions/upload-artifact@v7
+        with:
+          name: pkgdown-site
+          path: docs
+          include-hidden-files: true
+          if-no-files-found: error
+
+  deploy:
+    name: Deploy pkgdown site
+    if: github.event_name != 'pull_request'
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    concurrency:
+      group: pkgdown-deploy
+      cancel-in-progress: false
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+
+      - name: Download built site
+        uses: actions/download-artifact@v8
+        with:
+          name: pkgdown-site
+          path: site
+
       - name: Deploy to GitHub Pages
         uses: JamesIves/github-pages-deploy-action@v4
         with:
-          folder: docs
+          folder: site
           branch: gh-pages
           clean: true

CITATION.cff

@@ -1,8 +1,7 @@
 cff-version: 1.2.0
 message: "Please cite the software and the original pCAT article. Cite the 2026 article when using updated CFIR mappings."
 title: "pcatR: Analyze and Visualize Pragmatic Context Assessment Tool Data"
-version: 1.0.0
-date-released: 2026-07-12
+version: 1.0.1
 type: software
 authors:
   - family-names: Li
@@ -45,6 +44,20 @@ references:
         given-names: Jessica
       - family-names: Pfeiffer
         given-names: Paul N.
+      - family-names: Robinson
+        given-names: Claire H.
+      - family-names: Evans
+        given-names: Lacey
+      - family-names: Damschroder
+        given-names: Laura J.
+      - family-names: Stewart
+        given-names: Madison A.
+      - family-names: Garlick
+        given-names: Brittani
+      - family-names: Sussman
+        given-names: Jeremy B.
+      - family-names: Nevedal
+        given-names: Andrea L.
     journal: Implementation Science Communications
     year: 2026
     volume: 7

CRAN_SUBMISSION.md

@@ -0,0 +1,67 @@
+# pcatR 1.0.1 CRAN submission record
+
+This file tracks the initial CRAN submission separately from the immutable
+GitHub `v1.0.0` release.
+
+## Completed in the source tree
+
+- Package version advanced to 1.0.1.
+- DESCRIPTION cites both source articles by DOI.
+- Source-derived content and adaptations are documented in `LICENSE.note` and
+  installed `inst/COPYRIGHTS`.
+- Package citation is generated from DESCRIPTION metadata; both source articles
+  have complete author lists.
+- Installed technical guides include PDF and self-contained HTML plus editable
+  R Markdown source, CSS, and rendering instructions.
+- Unreleased-version metadata identifies the guide as a CRAN submission
+  candidate rather than assigning version 1.0.1 a release date.
+- The documented minimum R version is exercised by an R 4.1 CI job.
+
+## Required evidence before submission
+
+- [x] Local source spelling and URL checks reviewed.
+- [x] `R CMD build` produces exactly `pcatR_1.0.1.tar.gz`.
+- [x] `R CMD check --as-cran pcatR_1.0.1.tar.gz` reviewed with no errors or
+      warnings and all notes explained.
+- [x] Archive contents inspected for excluded development and release files.
+- [x] GitHub Actions pass on Windows, macOS, Linux, R devel, release, oldrel,
+      and R 4.1.
+- [x] The exact uploaded source archive passes full-manual `--as-cran` checks
+      under current R-release and R-devel.
+- [x] A clean local pkgdown build was inspected for its home, reference,
+      article, citation, author, license, attribution, and release pages.
+- [x] Joint software copyright ownership is implemented consistently in
+      `Authors@R`, `LICENSE`, `LICENSE.md`, and `inst/COPYRIGHTS`.
+- [ ] Retain Lilac Li's written approval of her authorship and copyright-holder
+      role, Jae Man Park's maintainer role, the MIT and CC BY 4.0 licensing
+      treatment, public distribution, and submission to CRAN.
+- [ ] Win-builder R-devel and R-release results reviewed.
+- [ ] Freeze one final source archive and retain its generated `.sha256` file;
+      send those exact archive bytes to Win-builder and CRAN without rebuilding.
+- [ ] Maintainer obtains confirmation of the package name and source-content
+      treatment from the original instrument authors before submission.
+- [ ] Maintainer submits only the source archive through CRAN's submission form
+      and responds to CRAN's confirmation email.
+
+Registry searches can show that a name is currently unused, but they do not
+reserve it. Recheck CRAN and Bioconductor immediately before submission.
+
+## Pre-freeze automated evidence
+
+Candidate workflows have successfully checked exact uploaded archives under
+current R-release and R-devel with full PDF manuals. The workflow now stores a
+generated `.sha256` file beside each archive and verifies it before both checks.
+
+The final source head, run IDs, and SHA-256 are deliberately pending. Record
+them only after the external approvals are retained, the source is frozen, and
+one exact archive is selected for Win-builder and CRAN submission.
+
+## Registry check recorded July 12, 2026
+
+- `pcatR` was absent from the current CRAN package index.
+- CRAN's exact `src/contrib/Archive/pcatR/` path returned HTTP 404, indicating
+  no historical archive at that exact case-sensitive name.
+- The exact package name was absent from Bioconductor's release package page.
+
+These observations are point-in-time checks, not a reservation or acceptance
+decision.

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: pcatR
 Type: Package
 Title: Analyze and Visualize Pragmatic Context Assessment Tool Data
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
     person(
       given = "Lilac",
       family = "Li",
       email = "lix@unk.edu",
-      role = "aut",
+      role = c("aut", "cph"),
       comment = c(
         URL = "https://www.unk.edu/academics/management/lilac-li.php"
       )
@@ -16,7 +16,7 @@ Authors@R: c(
       given = "Jae Man",
       family = "Park",
       email = "jaemanblp2@gmail.com",
-      role = c("aut", "cre"),
+      role = c("aut", "cre", "cph"),
       comment = c(
         URL = "https://www.linkedin.com/in/jae-man-park/"
       )
@@ -29,7 +29,10 @@ Description: Provides a reproducible workflow for importing, validating,
     updated Consolidated Framework for Implementation Research ('CFIR')
     mappings, describes team agreement and disagreement, compares repeated
     assessments, and creates implementation action-planning outputs. It does
-    not calculate or claim a validated total pCAT scale score.
+    not calculate or claim a validated total pCAT scale score. The instrument
+    is described by Robinson and Damschroder (2023)
+    <doi:10.1186/s43058-022-00380-5>; updated 'CFIR' mappings are from Domlyn
+    et al. (2026) <doi:10.1186/s43058-026-00956-5>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Language: en-US

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2026
-COPYRIGHT HOLDER: Jae Man Park
+COPYRIGHT HOLDER: Lilac Li and Jae Man Park

LICENSE.md

@@ -1,6 +1,6 @@
-MIT License
+# MIT License
 
-Copyright (c) 2026 Jae Man Park
+Copyright (c) 2026 Lilac Li and Jae Man Park
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal