Merge branch 'master' into feat/source-linter

Author: sbryngelson

.claude/settings.json

@@ -0,0 +1,3 @@
+{
+  "allowedTools": ["Bash(*)"]
+}

.github/workflows/claude-code-review.yml

@@ -0,0 +1,44 @@
+name: Claude Code Review
+
+on:
+  pull_request_target:
+    types: [opened, synchronize, ready_for_review, reopened]
+
+jobs:
+  claude-review:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+      issues: read
+      actions: read
+      id-token: write
+
+    steps:
+      - name: Checkout PR head (fork)
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          github_token: ${{ github.token }}
+
+          show_full_output: true
+
+          plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
+          plugins: 'code-review@claude-code-plugins'
+
+          claude_args: |
+            --allowedTools "Bash(*)"
+
+          prompt: |
+            /code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}
+            Post the results as one top-level PR comment titled "Claude Code Review".
+
+          additional_permissions: |
+            actions: read

.github/workflows/claude.yml

@@ -0,0 +1,35 @@
+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
+      id-token: write
+      actions: read
+
+    steps:
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          additional_permissions: |
+            actions: read

.lychee.toml

@@ -12,7 +12,7 @@ retry_wait_time = 4
 
 # Comma-separated list of accepted status codes for valid links.
 # accept = ["200", "206", "403", "429"]
-accept = ["200", "429"]
+accept = ["200", "429", "502"]
 
 verbose = "error"
 

src/common/m_variables_conversion.fpp

@@ -1103,8 +1103,6 @@ contains
                             nbub = 3._wp*q_prim_vf(alf_idx)%sf(j, k, l)/(4._wp*pi*R3tmp)
                         end if
 
-                        if (j == 0 .and. k == 0 .and. l == 0) print *, 'In convert, nbub:', nbub
-
                         do i = bub_idx%beg, bub_idx%end
                             q_cons_vf(i)%sf(j, k, l) = q_prim_vf(i)%sf(j, k, l)*nbub
                         end do

src/post_process/m_data_input.f90

@@ -312,7 +312,6 @@ impure subroutine s_read_serial_data_files(t_step)
                       STATUS='old', ACTION='read')
                 read (1) q_cons_vf(i)%sf(0:m, 0:n, 0:p)
                 close (1)
-                print *, q_cons_vf(i)%sf(:, 0, 0)
             else
                 call s_mpi_abort('File q_cons_vf'//trim(file_num)// &
                                  '.dat is missing in '//trim(t_step_dir)// &