Yet another test of the GHA move-issues.

.Rbuildignore

@@ -16,4 +16,6 @@
 ^inst$
 ^qa$
 ^venv$
+^\.github$
+
 

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

@@ -8,13 +8,13 @@ on:
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }} (R latest)
 
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
+        os: [ubuntu-latest, macos-latest]
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -26,8 +26,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
+          r-version: 'latest'
           use-public-rspm: true
 
       - name: Install dependencies
@@ -37,6 +36,11 @@ jobs:
         shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--no-manual"'
+          error-on: '"error"'
+          check-dir: '"check"'
+
 
       - name: Show testthat output
         if: always()
@@ -47,5 +51,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ matrix.os }}-r-latest-results
           path: check

.github/workflows/move-issues.yml

@@ -1,4 +1,4 @@
-name: Move linked issues through workflow
+name: Chagne status of PR linked issues
 
 on:
   pull_request:
@@ -21,20 +21,22 @@ jobs:
           github-token: ${{ secrets.ORG_PROJECTS_TOKEN }}
           script: |
             // === CONFIG ===
-            const orgLogin = "Seafood-Globalization-Lab"; // hardcoded org
+            const orgLogin = "Seafood-Globalization-Lab"; // org slug
             const projectNumber = 1;                      // from URL
             const fieldName = "Status";                   // field in Project
             const targetStatus = "🧪 QA / Staging";        // target option
             // ==============
 
             const prBody = context.payload.pull_request?.body || "";
-            const issueRefs = prBody.match(/#\d+/g) || [];
+            // Match "#123" or "repo#123" or "org/repo#123"
+            const issueRefs = prBody.match(/([A-Za-z0-9_.-]+\/[A-Za-z0-9_.-]+)?#\d+/g) || [];
+
             if (issueRefs.length === 0) {
-              console.log("No linked issues found in PR body");
+              console.log("ℹ️ No linked issues found in PR body");
               return;
             }
 
-            // Get project and its fields at ORG level
+            // Get project and its fields
             const { organization } = await github.graphql(`
               query($org: String!, $number: Int!) {
                 organization(login: $org) {
@@ -55,35 +57,58 @@ jobs:
             `, { org: orgLogin, number: projectNumber });
 
             if (!organization || !organization.projectV2) {
-              throw new Error(`Project ${projectNumber} not found for org ${orgLogin}`);
+              throw new Error(`❌ Project ${projectNumber} not found for org ${orgLogin}`);
             }
 
             const project = organization.projectV2;
             const statusField = project.fields.nodes.find(f => f.name === fieldName);
-            if (!statusField) throw new Error(`Field '${fieldName}' not found`);
+            if (!statusField) throw new Error(`❌ Field '${fieldName}' not found`);
             const option = statusField.options.find(o => o.name === targetStatus);
-            if (!option) throw new Error(`Option '${targetStatus}' not found`);
+            if (!option) throw new Error(`❌ Option '${targetStatus}' not found`);
+
+            // Process each ref
+            for (const ref of issueRefs) {
+              const match = ref.match(/^(?:(?<owner>[^/]+)\/(?<repo>[^#]+))?#(?<num>\d+)$/);
+              if (!match || !match.groups) {
+                console.log(`⚠️ Skipping invalid ref '${ref}'`);
+                continue;
+              }
 
-            for (const issueRef of issueRefs) {
-              const issueNumber = parseInt(issueRef.replace("#",""));
-              console.log(`Moving issue #${issueNumber} → ${targetStatus}`);
+              const owner = match.groups.owner || context.repo.owner;
+              const repo = match.groups.repo || context.repo.repo;
+              const issueNumber = parseInt(match.groups.num, 10);
 
-              // Get issue node ID
+              if (isNaN(issueNumber)) {
+                console.log(`⚠️ Skipping invalid number in ref '${ref}'`);
+                continue;
+              }
+
+              // Fetch issue or PR
               const { repository } = await github.graphql(`
                 query($owner: String!, $repo: String!, $number: Int!) {
                   repository(owner: $owner, name: $repo) {
-                    issue(number: $number) { id }
+                    issueOrPullRequest(number: $number) {
+                      __typename
+                      ... on Issue { id }
+                    }
                   }
                 }
-              `, {
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                number: issueNumber
-              });
+              `, { owner, repo, number: issueNumber });
+
+              if (!repository || !repository.issueOrPullRequest) {
+                console.log(`⚠️ ${owner}/${repo}#${issueNumber} not found, skipping`);
+                continue;
+              }
 
-              const issueId = repository.issue.id;
+              if (repository.issueOrPullRequest.__typename !== "Issue") {
+                console.log(`ℹ️ ${owner}/${repo}#${issueNumber} is a ${repository.issueOrPullRequest.__typename}, skipping`);
+                continue;
+              }
+
+              const issueId = repository.issueOrPullRequest.id;
+              console.log(`➡️ Processing ${owner}/${repo}#${issueNumber}`);
 
-              // Add to project
+              // Add to project (idempotent if already present)
               const addResp = await github.graphql(`
                 mutation($projectId: ID!, $contentId: ID!) {
                   addProjectV2ItemById(input: {projectId: $projectId, contentId: $contentId}) {
@@ -93,8 +118,9 @@ jobs:
               `, { projectId: project.id, contentId: issueId });
 
               const itemId = addResp.addProjectV2ItemById.item.id;
+              console.log(`   ↳ Added/reused project item ${itemId}`);
 
-              // Update Status
+              // Update Status field
               await github.graphql(`
                 mutation($projectId: ID!, $itemId: ID!, $fieldId: ID!, $optionId: String!) {
                   updateProjectV2ItemFieldValue(input: {
@@ -112,4 +138,6 @@ jobs:
                 fieldId: statusField.id,
                 optionId: option.id
               });
+
+              console.log(`   ✅ Moved ${owner}/${repo}#${issueNumber} → ${targetStatus}`);
             }

DESCRIPTION

@@ -28,23 +28,19 @@ Description: ARTIS (Aquatic Resource Trade in Species) is a global model
     allocate seafood trade and production data, and to compute consumption
     and trade-flow metrics.  Designed to support reproducible research and
     policy-relevant analysis of seafood systems.
-License: Apache License (>= 2.0)
+License: Apache License (>= 2.0) | file LICENSE
 URL: https://github.com/Seafood-Globalization-Lab/artis-model
 BugReports: 
     https://github.com/Seafood-Globalization-Lab/artis-model/issues
 Depends: 
     R (>= 4.1.0)
 Imports:
-    aws.s3,
-    cli,
     aws.s3,
     cli,
     countrycode,
     data.table,
     DBI,
     doParallel,
-    DBI,
-    doParallel,
     dplyr,
     foreach,
     future,
@@ -53,17 +49,15 @@ Imports:
     magrittr,
     parallel,
     qs2,
-    qs2,
     readxl,
     reticulate,
     stringr,
     tibble,
     tidyr,
-    qs2,
-    DBI,
     utils
 Suggests: 
     duckdb,
+    arrow
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2