From 7bb86f1f4124787dcd3c4fce5b68a41e73be27be Mon Sep 17 00:00:00 2001
From: zhizhongpu <84325421+zhizhongpu@users.noreply.github.com>
Date: Wed, 18 Mar 2026 17:53:03 -0600
Subject: [PATCH 01/19] #140 bd migrate in github actions

---
 .github/README.md                             |   7 +
 .github/actions/timed-check/action.yml        |  17 ++
 .github/check_eps_savefig.py                  | 147 ++++++++++++++++++
 .github/check_newlines.py                     |  38 +++++
 .github/check_sconscript_log.py               |  27 ++++
 .github/check_sconscripts.py                  | 113 ++++++++++++++
 .github/post_check_results.py                 |  63 ++++++++
 .../post_template_issue_thread_pr_close.md    |  10 ++
 .github/post_template_pr_thread_pr_close.md   |   9 ++
 .github/scripts/pr_close_comment.py           |  47 ++++++
 .github/workflows/checks.yml                  |  94 +++++++++++
 .github/workflows/pr-close-comment.yml        |  36 +++++
 12 files changed, 608 insertions(+)
 create mode 100644 .github/README.md
 create mode 100644 .github/actions/timed-check/action.yml
 create mode 100644 .github/check_eps_savefig.py
 create mode 100644 .github/check_newlines.py
 create mode 100644 .github/check_sconscript_log.py
 create mode 100644 .github/check_sconscripts.py
 create mode 100644 .github/post_check_results.py
 create mode 100644 .github/post_template_issue_thread_pr_close.md
 create mode 100644 .github/post_template_pr_thread_pr_close.md
 create mode 100644 .github/scripts/pr_close_comment.py
 create mode 100644 .github/workflows/checks.yml
 create mode 100644 .github/workflows/pr-close-comment.yml

diff --git a/.github/README.md b/.github/README.md
new file mode 100644
index 0000000..7e971e9
--- /dev/null
+++ b/.github/README.md
@@ -0,0 +1,7 @@
+# GitHub Actions Checks
+
+## Adding a new check
+
+1. Add a step to `checks.yml` with `id: check_<name>`
+2. Add `CHECK_<NAME>_OUTCOME` and `CHECK_<NAME>_TIME` env vars to the `Post results` step in `checks.yml`
+3. Add `("Display Name", "check_<name>")` to `CHECKS` in `post_check_results.py`
diff --git a/.github/actions/timed-check/action.yml b/.github/actions/timed-check/action.yml
new file mode 100644
index 0000000..ac7841a
--- /dev/null
+++ b/.github/actions/timed-check/action.yml
@@ -0,0 +1,17 @@
+name: Timed Python Check
+inputs:
+  script:
+    required: true
+outputs:
+  time:
+    description: Elapsed time in seconds
+    value: ${{ steps.run.outputs.time }}
+runs:
+  using: composite
+  steps:
+    - id: run
+      shell: bash
+      run: |
+        s=$(date +%s%N); python ${{ inputs.script }} || e=$?
+        awk "BEGIN{printf \"time=%.3f\n\",($(date +%s%N)-$s)/1e9}" >> $GITHUB_OUTPUT
+        exit ${e:-0}
diff --git a/.github/check_eps_savefig.py b/.github/check_eps_savefig.py
new file mode 100644
index 0000000..e864ceb
--- /dev/null
+++ b/.github/check_eps_savefig.py
@@ -0,0 +1,147 @@
+#!/usr/bin/env python3
+import os
+import re
+import sys
+
+def IsExcludedPath(path, excluded):
+    norm = os.path.normpath(path)
+    return any(norm == e or norm.startswith(e + os.sep) for e in excluded)
+
+def IsHidden(name):
+    return name.startswith(".")
+
+def IsIgnoredDir(name):
+    return IsHidden(name) or name == "__pycache__"
+
+def ReadFile(path):
+    try:
+        with open(path, "r", encoding="utf-8") as fh:
+            return fh.read()
+    except Exception:
+        return None
+
+def CheckEpsSavefig(file_path, content):
+    """
+    Check if file contains .savefig(*eps*) without remove_eps_info(
+    Returns list of problematic lines with line numbers
+    """
+    problems = []
+    lines = content.split('\n')
+    
+    # Pattern to match .savefig with eps format (both single and double quotes)
+    eps_savefig_patterns = [
+        r'\.savefig\([^)]*[\'"].*eps.*[\'"][^)]*\)',  # matches .savefig(...'...eps...'...)
+        r'\.savefig\([^)]*format\s*=\s*[\'"]eps[\'"][^)]*\)'  # matches format='eps' or format="eps"
+    ]
+    
+    has_remove_eps_info = 'remove_eps_info(' in content
+    
+    for line_num, line in enumerate(lines, 1):
+        for pattern in eps_savefig_patterns:
+            if re.search(pattern, line, re.IGNORECASE):
+                if not has_remove_eps_info:
+                    problems.append(f"Line {line_num}: {line.strip()}")
+                break
+    
+    return problems
+
+def CollectEpsProblems(root, excluded):
+    """Walk through Python files and check for EPS savefig issues"""
+    problems = []
+    
+    for dir_path, dir_names, file_names in os.walk(root):
+        if IsExcludedPath(dir_path, excluded):
+            dir_names[:] = []
+            continue
+            
+        dir_names[:] = [d for d in dir_names if not IsIgnoredDir(d)]
+        
+        for file_name in file_names:
+            if not file_name.endswith('.py'):
+                continue
+                
+            if IsHidden(file_name):
+                continue
+                
+            file_path = os.path.join(dir_path, file_name)
+            content = ReadFile(file_path)
+            
+            if content is None:
+                continue
+                
+            file_problems = CheckEpsSavefig(file_path, content)
+            if file_problems:
+                problems.append({
+                    'file': file_path,
+                    'issues': file_problems
+                })
+    
+    return problems
+
+def CheckEpsCreationDate(content):
+    """
+    Check if any line in an EPS file starts with %%CreationDate.
+    Returns True if it does.
+    """
+    return any(line.startswith("%%CreationDate") for line in content.splitlines())
+
+def CollectEpsCreationDateProblems(root, excluded):
+    """Walk through EPS files and report those that contain %%CreationDate"""
+    eps_files = []
+    
+    for dir_path, dir_names, file_names in os.walk(root):
+        if IsExcludedPath(dir_path, excluded):
+            dir_names[:] = []
+            continue
+            
+        dir_names[:] = [d for d in dir_names if not IsIgnoredDir(d)]
+        
+        for file_name in file_names:
+            if not file_name.endswith('.eps'):
+                continue
+                
+            if IsHidden(file_name):
+                continue
+                
+            eps_path = os.path.join(dir_path, file_name)
+            content = ReadFile(eps_path)
+            
+            if content is None:
+                continue
+                
+            if CheckEpsCreationDate(content):
+                eps_files.append(eps_path)
+    
+    return eps_files
+
+def main():
+    source_root   = "source"
+    output_root   = "output"
+    excluded      = ["source/lib", "source/raw", "source/scrape"]
+
+    problems = CollectEpsProblems(source_root, excluded)
+    creationdate_eps_files = CollectEpsCreationDateProblems(output_root, [])
+    
+    if creationdate_eps_files:
+        print("EPS files containing %%CreationDate:")
+        for eps_file in creationdate_eps_files:
+            print(f"  {eps_file}")
+        print("")
+        return 1
+
+    if problems:
+        print("EPS savefig check failed!")
+        print("\nPython files using .savefig(*eps*) without remove_eps_info():")
+        for problem in problems:
+            print(f"\nFile: {problem['file']}")
+            for issue in problem['issues']:
+                print(f"  {issue}")
+        print("\nTo fix: Add 'from source.lib.JMSLab.remove_eps_info import remove_eps_info'")
+        print("and call 'remove_eps_info(filename)' after each EPS savefig.")
+        return 1
+    else:
+        print("EPS savefig check: all checks passed.")
+        return 0
+
+if __name__ == "__main__":
+    sys.exit(main())
\ No newline at end of file
diff --git a/.github/check_newlines.py b/.github/check_newlines.py
new file mode 100644
index 0000000..2f23cd1
--- /dev/null
+++ b/.github/check_newlines.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+import subprocess
+import sys
+from pathlib import Path
+
+EXCLUDED_EXT = {".log", ".txt"}
+
+INCLUDED_DIRS = {"source", "output"}
+
+def GetTrackedFiles():
+    return [Path(p) for p in subprocess.run(["git","ls-files"], stdout=subprocess.PIPE, check=True).stdout.decode().splitlines() if p.strip() and Path(p).parts[0] in INCLUDED_DIRS]
+
+def IsBinary(p):
+    try:
+        return b"\0" in p.read_bytes()[:4096]
+    except:
+        return True
+
+def NeedsNewline(p):
+    try:
+        d = p.read_bytes()
+        return len(d)==0 or not d.endswith(b"\n")
+    except:
+        return False
+
+def ProcessFiles():
+    missing = [p for p in GetTrackedFiles() if p.exists() and p.suffix not in EXCLUDED_EXT and not IsBinary(p) and NeedsNewline(p)]
+    if not missing:
+        print("No files missing trailing newlines."); return 0
+    print("Files missing trailing newline:")
+    for p in missing: print(" -", p)
+    return 1
+
+def Main():
+    return ProcessFiles()
+
+if __name__=="__main__":
+    sys.exit(Main())
diff --git a/.github/check_sconscript_log.py b/.github/check_sconscript_log.py
new file mode 100644
index 0000000..96742db
--- /dev/null
+++ b/.github/check_sconscript_log.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+import sys
+from pathlib import Path
+
+TARGET = "terminated because of errors."
+
+def Main():
+    bad = []
+    for p in Path(".").rglob("**/*.log"):
+        try:
+            if TARGET in p.read_text(errors="replace"):
+                bad.append(p)
+        except:
+            pass
+
+    if not bad:
+        print("No log files contain the error string.")
+        return 0
+
+    print("Problematic log files:")
+    for p in bad:
+        print(" -", p)
+
+    return 1
+
+if __name__ == "__main__":
+    sys.exit(Main())
diff --git a/.github/check_sconscripts.py b/.github/check_sconscripts.py
new file mode 100644
index 0000000..be10771
--- /dev/null
+++ b/.github/check_sconscripts.py
@@ -0,0 +1,113 @@
+#!/usr/bin/env python3
+import os
+import re
+import sys
+from pathlib import Path
+
+ROOT       = Path("source")
+EXCLUDED   = {Path("source/lib"), Path("source/raw"), Path("source/scrape")}
+PAPER_DIR  = Path("source/paper")
+PAPER_EXTS = {".bib", ".tex", ".lyx"}
+
+
+def Main():
+    missing_dirs, missing_mentions = CollectProblems()
+    missing_in_sconstruct = SourceFoldersMissingInSConstruct()
+    any_problems = bool(missing_dirs or missing_mentions or missing_in_sconstruct)
+    if any_problems:
+        print("SConscript/SConstruct summary of missing items:")
+        if missing_dirs:
+            print("\nFolders missing SConscript:")
+            for p in missing_dirs:
+                print(p)
+        if missing_mentions:
+            print("\nFiles not mentioned in their SConscript:")
+            for p in missing_mentions:
+                print(p)
+        if missing_in_sconstruct:
+            print("\nTop-level source folders missing from root SConstruct:")
+            for p in missing_in_sconstruct:
+                print(p)
+    else:
+        print("SConscript/SConstruct summary: all checks passed.")
+    return 1 if any_problems else 0
+
+
+def CollectProblems():
+    missing_dirs     = []
+    missing_mentions = []
+    for dir_path, dir_names, file_names in os.walk(ROOT):
+        dir_path = Path(dir_path)
+        if IsExcluded(dir_path):
+            dir_names[:] = []
+            continue
+        dir_names[:] = sorted(d for d in dir_names if not IsIgnored(d))
+        file_names   = [f for f in file_names if not IsIgnored(f)]
+        if dir_path == ROOT or (not dir_names and not file_names):
+            continue
+        content = Read(dir_path / "SConscript")
+        if content is None:
+            parent_content = Read(dir_path.parent / "SConscript")
+            if parent_content is None:
+                missing_dirs.append(dir_path)
+            continue
+        for f in sorted(f for f in file_names if f != "SConscript"):
+            if ShouldCheck(dir_path, f) and not IsMentioned(content, f, dir_path):
+                missing_mentions.append(f"{dir_path} -> {f}")
+        for subdir in dir_names:
+            if re.search(rf"\b{re.escape(subdir)}\b", content):
+                continue
+            subdir_path = dir_path / subdir
+            try:
+                subfiles = sorted(
+                    e for e in os.listdir(subdir_path)
+                    if not IsIgnored(e) and (subdir_path / e).is_file() and ShouldCheck(subdir_path, e)
+                )
+            except Exception:
+                missing_dirs.append(subdir_path)
+                continue
+            for f in subfiles:
+                if not IsMentioned(content, f, subdir_path):
+                    missing_mentions.append(f"{dir_path} -> {subdir}/{f}")
+    return missing_dirs, missing_mentions
+
+
+def IsExcluded(dir_path):
+    return any(dir_path == e or dir_path.is_relative_to(e) for e in EXCLUDED)
+
+
+def IsIgnored(name):
+    return name.startswith(".") or name == "__pycache__"
+
+
+def ShouldCheck(dir_path, name):
+    if dir_path.is_relative_to(PAPER_DIR):
+        return Path(name).suffix in PAPER_EXTS
+    return True
+
+
+def Read(path):
+    try:
+        return Path(path).read_text(encoding="utf-8")
+    except Exception:
+        return None
+
+
+def IsMentioned(content, name, dir_path):
+    rel = dir_path.relative_to(ROOT).as_posix()
+    return f"#source/{rel}/{name}" in content
+
+
+def SourceFoldersMissingInSConstruct():
+    content = Read("SConstruct")
+    folders = sorted(
+        e for e in os.listdir(ROOT)
+        if (ROOT / e).is_dir() and not IsIgnored(e) and not IsExcluded(ROOT / e)
+    )
+    if content is None:
+        return folders
+    return [f for f in folders if f"source/{f}/SConscript" not in content]
+
+
+if __name__ == "__main__":
+    sys.exit(Main())
diff --git a/.github/post_check_results.py b/.github/post_check_results.py
new file mode 100644
index 0000000..f66162b
--- /dev/null
+++ b/.github/post_check_results.py
@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+import os
+import subprocess
+import sys
+
+CHECKS = [
+    ("SCons DAG", "check_scons"),
+    ("Newlines",  "check_newlines"),
+    ("EPS data",  "check_eps"),
+    ("Build log", "check_scons_log"),
+]
+
+def Main():
+    repo   = os.environ["GITHUB_REPOSITORY"]
+    run_id = os.environ["GITHUB_RUN_ID"]
+
+    print("Runtime:")
+    rows, failed = CollectResults()
+
+    if "--post" in sys.argv:
+        PostResults(repo, run_id, rows, failed)
+
+    if failed:
+        print(f"Failed checks: {', '.join(failed)}")
+        return 1
+    return 0
+
+def CollectResults():
+    rows, failed = [], []
+    for name, step_id in CHECKS:
+        key     = step_id.upper()
+        outcome = os.environ.get(f"{key}_OUTCOME", "skipped")
+        time    = os.environ.get(f"{key}_TIME", "")
+        print(f"  {step_id}: {time}s")
+        if outcome == "skipped":
+            rows.append(f"| {name} | SKIP | |")
+        elif outcome == "success":
+            rows.append(f"| {name} | ✅ | {time}s |")
+        else:
+            failed.append(name)
+            rows.append(f"| {name} | ❌ | {time}s |")
+    return rows, failed
+
+def PostResults(repo, run_id, rows, failed):
+    run_url    = f"https://github.com/{repo}/actions/runs/{run_id}"
+    table      = "\n".join(["| Check | Result | Time |", "|-------|--------|------|", *rows])
+    body       = f"**Check Results** ([run details]({run_url}))\n\n{table}"
+    pr_num     = os.environ["PR_NUMBER"]
+    pr_sha     = os.environ["PR_SHA"]
+    subprocess.run([
+        "gh", "api", f"repos/{repo}/issues/{pr_num}/comments",
+        "--method", "POST", "-f", f"body={body}",
+    ], check=True)
+    state = "failure" if failed else "success"
+    desc  = f"Failed: {', '.join(failed)}" if failed else "All checks passed"
+    subprocess.run([
+        "gh", "api", f"repos/{repo}/statuses/{pr_sha}",
+        "-f", f"state={state}", "-f", "context=Checks",
+        "-f", f"description={desc}", "-f", f"target_url={run_url}",
+    ], check=True)
+
+if __name__ == "__main__":
+    sys.exit(Main())
diff --git a/.github/post_template_issue_thread_pr_close.md b/.github/post_template_issue_thread_pr_close.md
new file mode 100644
index 0000000..dc49fbf
--- /dev/null
+++ b/.github/post_template_issue_thread_pr_close.md
@@ -0,0 +1,10 @@
+### Summary
+
+In this issue, we:
+
+- WHAT DID YOU DO?
+
+Deliverables:
+- WHAT DID YOU BUILD? IN PERMALINK
+
+[Optional] Issue folder is PERMALINK
diff --git a/.github/post_template_pr_thread_pr_close.md b/.github/post_template_pr_thread_pr_close.md
new file mode 100644
index 0000000..037083e
--- /dev/null
+++ b/.github/post_template_pr_thread_pr_close.md
@@ -0,0 +1,9 @@
+Thanks for closing the PR.
+
+You need to:
+- [ ] edit the issue summary post above
+- [ ] update other issue branches using `main`
+- [ ] update the datastore in the cloud
+- [ ] delete this issue branch 
+
+If you have questions, please ask by tagging the reviewers of this PR.
diff --git a/.github/scripts/pr_close_comment.py b/.github/scripts/pr_close_comment.py
new file mode 100644
index 0000000..36360ec
--- /dev/null
+++ b/.github/scripts/pr_close_comment.py
@@ -0,0 +1,47 @@
+import os
+import re
+from pathlib import Path
+from github import Github
+
+GITHUB_TOKEN = os.environ["GITHUB_TOKEN"]
+REPO_NAME = os.environ["REPO"]
+PR_NUMBER = int(os.environ["PR_NUMBER"])
+PR_AUTHOR = os.environ["PR_AUTHOR"]
+BRANCH_NAME = os.environ["BRANCH_NAME"]
+LAST_COMMIT_SHA = os.environ["LAST_COMMIT_SHA"]
+
+ISSUE_TEMPLATE = Path(".github/post_template_issue_thread_pr_close.md")
+PR_TEMPLATE = Path(".github/post_template_pr_thread_pr_close.md")
+
+
+def Main():
+    repo = Github(GITHUB_TOKEN).get_repo(REPO_NAME)
+    pr = repo.get_pull(PR_NUMBER)
+
+    issue_comment_url = PostIssueComment(repo)
+    PostPrComment(pr, issue_comment_url)
+
+
+def PostIssueComment(repo):
+    issue_match = re.match(r"^(\d+)", BRANCH_NAME)
+    if not issue_match:
+        return None
+
+    issue_number = int(issue_match.group(1))
+    issue_body = ISSUE_TEMPLATE.read_text() + f"\n\nLast commit in issue branch: {LAST_COMMIT_SHA}"
+
+    comment = repo.get_issue(issue_number).create_comment(issue_body)
+    return comment.html_url
+
+
+def PostPrComment(pr, issue_comment_url):
+    pr_body = PR_TEMPLATE.read_text()
+
+    if issue_comment_url:
+        pr_body = f"[Issue summary]({issue_comment_url})\n\n{pr_body}"
+
+    pr.as_issue().create_comment(f"@{PR_AUTHOR} {pr_body}")
+
+
+if __name__ == "__main__":
+    Main()
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
new file mode 100644
index 0000000..e614d2d
--- /dev/null
+++ b/.github/workflows/checks.yml
@@ -0,0 +1,94 @@
+name: Checks
+
+on:
+  push:
+    branches:
+      - "**"
+  issue_comment:
+    types: [created]
+
+jobs:
+  checks:
+    if: |
+      (github.event_name == 'push' && contains(github.event.head_commit.message, '[run-actions-all]')) ||
+      (github.event_name == 'issue_comment' && github.event.issue.pull_request && contains(github.event.comment.body, '/run-actions-'))
+    runs-on: ubuntu-latest
+    timeout-minutes: 1
+    permissions:
+      contents: write
+      statuses: write
+      pull-requests: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) || github.sha }}
+
+      - name: Post pending commit status
+        if: github.event_name == 'issue_comment'
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          PR_SHA=$(gh api repos/${{ github.repository }}/pulls/${{ github.event.issue.number }} --jq '.head.sha')
+          echo "PR_SHA=$PR_SHA" >> $GITHUB_ENV
+          gh api repos/${{ github.repository }}/statuses/$PR_SHA \
+            -f state=pending \
+            -f context="Checks" \
+            -f description="Running..." \
+            -f target_url="https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - id: check_scons
+        name: Check SCons DAG for missing dependencies
+        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-dag') || contains(github.event.comment.body, '/run-actions-all')
+        continue-on-error: true
+        uses: ./.github/actions/timed-check
+        with:
+          script: .github/check_sconscripts.py
+
+      - id: check_newlines
+        name: Check missing newlines
+        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-newlines') || contains(github.event.comment.body, '/run-actions-all')
+        continue-on-error: true
+        uses: ./.github/actions/timed-check
+        with:
+          script: .github/check_newlines.py
+
+      - id: check_eps
+        name: Check extraneous EPS data
+        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-eps') || contains(github.event.comment.body, '/run-actions-all')
+        continue-on-error: true
+        uses: ./.github/actions/timed-check
+        with:
+          script: .github/check_eps_savefig.py
+
+      - id: check_scons_log
+        name: Check build failure
+        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-log') || contains(github.event.comment.body, '/run-actions-all')
+        continue-on-error: true
+        uses: ./.github/actions/timed-check
+        with:
+          script: .github/check_sconscript_log.py
+
+      - name: Post results
+        if: always()
+        env:
+          GH_TOKEN: ${{ github.token }}
+          PR_NUMBER: ${{ github.event.issue.number }}
+          PR_SHA: ${{ env.PR_SHA }}
+          CHECK_SCONS_OUTCOME: ${{ steps.check_scons.outcome }}
+          CHECK_SCONS_TIME: ${{ steps.check_scons.outputs.time }}
+          CHECK_NEWLINES_OUTCOME: ${{ steps.check_newlines.outcome }}
+          CHECK_NEWLINES_TIME: ${{ steps.check_newlines.outputs.time }}
+          CHECK_EPS_OUTCOME: ${{ steps.check_eps.outcome }}
+          CHECK_EPS_TIME: ${{ steps.check_eps.outputs.time }}
+          CHECK_SCONS_LOG_OUTCOME: ${{ steps.check_scons_log.outcome }}
+          CHECK_SCONS_LOG_TIME: ${{ steps.check_scons_log.outputs.time }}
+        run: |
+          python .github/post_check_results.py \
+            ${{ contains(github.event.comment.body, '--post') && '--post' || '' }}
diff --git a/.github/workflows/pr-close-comment.yml b/.github/workflows/pr-close-comment.yml
new file mode 100644
index 0000000..3f787b1
--- /dev/null
+++ b/.github/workflows/pr-close-comment.yml
@@ -0,0 +1,36 @@
+# Post a comment when a PR is closed (merged or unmerged)
+
+name: PR Close Comment
+
+on:
+  pull_request:
+    types: [closed]
+
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: pip install PyGithub
+
+    - name: Comment on PR close
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        REPO: ${{ github.repository }}
+        PR_NUMBER: ${{ github.event.pull_request.number }}
+        PR_AUTHOR: ${{ github.event.pull_request.user.login }}
+        BRANCH_NAME: ${{ github.event.pull_request.head.ref }}
+        LAST_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
+      run: python .github/scripts/pr_close_comment.py

From 07324157cea08d8afaab13ed84ef5bc9d1a4375a Mon Sep 17 00:00:00 2001
From: jmshapir <jesse.m.shapiro@gmail.com>
Date: Thu, 19 Mar 2026 14:39:44 -0400
Subject: [PATCH 02/19] Adds datastore to workflow for #140

---
 docs/workflow.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/workflow.md b/docs/workflow.md
index 1b142a3..aee04bf 100644
--- a/docs/workflow.md
+++ b/docs/workflow.md
@@ -29,7 +29,7 @@ We suggest the following adaptation of [Github flow](https://docs.github.com/en/
       * the issue subfolder (ephemeral deliverables)
       * the latest version of the issue branch prior to merging (all deliverables).
     * **Link** to the summary comment in the pull request.
-    * **Update** all open branches from `main`.
+    * **Update** all open branches from `main` and (if needed) the datastore.
       * If you encounter merge conflicts you cannot resolve, check with the _assignee(s)_ of the corresponding issue(s).
 * **Prioritize** work in the order older pull requests > newer pull requests > older issues > newer issues.
   * Age is defined by github numbering.

From d4fc0d9f5f843e673b9b57e6379723a24c1e3bae Mon Sep 17 00:00:00 2001
From: jmshapir <jesse.m.shapiro@gmail.com>
Date: Thu, 19 Mar 2026 14:43:03 -0400
Subject: [PATCH 03/19] Revisions to message for #140

---
 .github/post_template_pr_thread_pr_close.md | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/.github/post_template_pr_thread_pr_close.md b/.github/post_template_pr_thread_pr_close.md
index 037083e..2299dc1 100644
--- a/.github/post_template_pr_thread_pr_close.md
+++ b/.github/post_template_pr_thread_pr_close.md
@@ -1,9 +1,3 @@
-Thanks for closing the PR.
+Thanks for closing this pull. 
 
-You need to:
-- [ ] edit the issue summary post above
-- [ ] update other issue branches using `main`
-- [ ] update the datastore in the cloud
-- [ ] delete this issue branch 
-
-If you have questions, please ask by tagging the reviewers of this PR.
+Before leaving the pull, please be sure you have completed all the required steps in the [workflow](https://github.com/JMSLab/Template/blob/main/docs/workflow.md)!

From 6003fe3f040221f1d0af1ee9f70fd3aa701d5e2d Mon Sep 17 00:00:00 2001
From: jmshapir <jesse.m.shapiro@gmail.com>
Date: Thu, 19 Mar 2026 14:49:26 -0400
Subject: [PATCH 04/19] Documents tests for #140

---
 README.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/README.md b/README.md
index b20b4a7..055ebfa 100644
--- a/README.md
+++ b/README.md
@@ -91,6 +91,14 @@ env.Stata(target, source)
 
 - For tips on batch-specifying targets and sources, see [./docs/batch_specifying.md](./docs/batch_specifying.md).
 
+### Automation
+
+The repository is prebuilt with some automated testing using [Github Actions](./github).
+
+To run all tests, add `[run-actions-all]` to a commit message or type `/run-actions-all` in a comment.
+
+To run a particular test, type `/run-actions-NAMEOFTEST` in a comment (e.g., `/run-actions-log` to run [this test](https://github.com/JMSLab/Template/blob/140-automating-pr-reviews-using-github-actions/.github/check_sconscript_log.py).
+
 ### Citations and expectations for usage
 
 This template is based on [gslab-econ/Template/v4.1.3](https://github.com/gslab-econ/template/releases/tag/4.1.3) and [gslab-python/v4.1.4](https://github.com/gslab-econ/gslab_python/releases/tag/v4.1.4).

From 90ccf639d9e0634f432040eb1eac057e6f5b1055 Mon Sep 17 00:00:00 2001
From: zhizhongpu <84325421+zhizhongpu@users.noreply.github.com>
Date: Thu, 19 Mar 2026 14:42:59 -0600
Subject: [PATCH 05/19] #140 bd extra line

---
 .github/check_eps_savefig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/check_eps_savefig.py b/.github/check_eps_savefig.py
index e864ceb..423214b 100644
--- a/.github/check_eps_savefig.py
+++ b/.github/check_eps_savefig.py
@@ -144,4 +144,4 @@ def main():
         return 0
 
 if __name__ == "__main__":
-    sys.exit(main())
\ No newline at end of file
+    sys.exit(main())

From df96e64bb269990855ea78139ceb0ba7e4700eb5 Mon Sep 17 00:00:00 2001
From: zhizhongpu <84325421+zhizhongpu@users.noreply.github.com>
Date: Thu, 19 Mar 2026 14:45:29 -0600
Subject: [PATCH 06/19] #140 rename README

---
 .github/{README.md => readme.md} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/{README.md => readme.md} (100%)

diff --git a/.github/README.md b/.github/readme.md
similarity index 100%
rename from .github/README.md
rename to .github/readme.md

From 79ee7b972def17f5e901a2505d84e03c21035dd9 Mon Sep 17 00:00:00 2001
From: zhizhongpu <84325421+zhizhongpu@users.noreply.github.com>
Date: Thu, 19 Mar 2026 14:51:15 -0600
Subject: [PATCH 07/19] #140 reorg rename github_action_checks.md

---
 .github/{readme.md => github_action_checks.md} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/{readme.md => github_action_checks.md} (100%)

diff --git a/.github/readme.md b/.github/github_action_checks.md
similarity index 100%
rename from .github/readme.md
rename to .github/github_action_checks.md

From 46e832037f7c530036d8cbb10a16b5a2967b010b Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 18:58:58 -0400
Subject: [PATCH 08/19] Improve how we add actions [run-actions-all] #141

---
 .github/actions/timed-check/action.yml | 19 ++++++-----
 .github/checks.json                    |  6 ++++
 .github/github_action_checks.md        |  7 ++--
 .github/post_check_results.py          | 46 ++++++++++++++------------
 .github/workflows/checks.yml           | 12 +++----
 5 files changed, 48 insertions(+), 42 deletions(-)
 create mode 100644 .github/checks.json

diff --git a/.github/actions/timed-check/action.yml b/.github/actions/timed-check/action.yml
index ac7841a..0d03791 100644
--- a/.github/actions/timed-check/action.yml
+++ b/.github/actions/timed-check/action.yml
@@ -2,16 +2,17 @@ name: Timed Python Check
 inputs:
   script:
     required: true
-outputs:
-  time:
-    description: Elapsed time in seconds
-    value: ${{ steps.run.outputs.time }}
+  display:
+    required: true
 runs:
   using: composite
   steps:
-    - id: run
-      shell: bash
+    - shell: bash
       run: |
-        s=$(date +%s%N); python ${{ inputs.script }} || e=$?
-        awk "BEGIN{printf \"time=%.3f\n\",($(date +%s%N)-$s)/1e9}" >> $GITHUB_OUTPUT
-        exit ${e:-0}
+        mkdir -p "$RUNNER_TEMP/check_results"
+        s=$(date +%s%N)
+        python ${{ inputs.script }} && outcome=success || outcome=failure
+        time=$(awk "BEGIN{printf \"%.3f\",($(date +%s%N)-$s)/1e9}")
+        printf '{"outcome":"%s","time":"%s"}' "$outcome" "$time" \
+          > "$RUNNER_TEMP/check_results/${{ inputs.display }}.json"
+        [ "$outcome" = "success" ]
diff --git a/.github/checks.json b/.github/checks.json
new file mode 100644
index 0000000..4811be2
--- /dev/null
+++ b/.github/checks.json
@@ -0,0 +1,6 @@
+[
+  {"name": "SCons DAG"},
+  {"name": "Newlines"},
+  {"name": "EPS data"},
+  {"name": "Build log"}
+]
diff --git a/.github/github_action_checks.md b/.github/github_action_checks.md
index 7e971e9..046b96b 100644
--- a/.github/github_action_checks.md
+++ b/.github/github_action_checks.md
@@ -2,6 +2,7 @@
 
 ## Adding a new check
 
-1. Add a step to `checks.yml` with `id: check_<name>`
-2. Add `CHECK_<NAME>_OUTCOME` and `CHECK_<NAME>_TIME` env vars to the `Post results` step in `checks.yml`
-3. Add `("Display Name", "check_<name>")` to `CHECKS` in `post_check_results.py`
+1. Add a step to `checks.yml` with a unique `id` and `display` (e.g. `id: check_newlines`, `display: Newlines`)
+2. Add `{"name": "Newlines"}` (i.e. matching `display`) to `checks.json`
+
+The order of entries in `checks.json` controls the row order in the results table.
diff --git a/.github/post_check_results.py b/.github/post_check_results.py
index f66162b..20c39c6 100644
--- a/.github/post_check_results.py
+++ b/.github/post_check_results.py
@@ -1,14 +1,10 @@
 #!/usr/bin/env python3
+import json
 import os
 import subprocess
 import sys
 
-CHECKS = [
-    ("SCons DAG", "check_scons"),
-    ("Newlines",  "check_newlines"),
-    ("EPS data",  "check_eps"),
-    ("Build log", "check_scons_log"),
-]
+CHECKS_JSON = os.path.join(os.path.dirname(__file__), 'checks.json')
 
 def Main():
     repo   = os.environ["GITHUB_REPOSITORY"]
@@ -26,27 +22,33 @@ def Main():
     return 0
 
 def CollectResults():
+    checks      = json.load(open(CHECKS_JSON))
+    results_dir = os.path.join(os.environ["RUNNER_TEMP"], "check_results")
     rows, failed = [], []
-    for name, step_id in CHECKS:
-        key     = step_id.upper()
-        outcome = os.environ.get(f"{key}_OUTCOME", "skipped")
-        time    = os.environ.get(f"{key}_TIME", "")
-        print(f"  {step_id}: {time}s")
-        if outcome == "skipped":
-            rows.append(f"| {name} | SKIP | |")
-        elif outcome == "success":
-            rows.append(f"| {name} | ✅ | {time}s |")
+    for check in checks:
+        name        = check["name"]
+        result_file = os.path.join(results_dir, f"{name}.json")
+        if os.path.exists(result_file):
+            result  = json.load(open(result_file))
+            outcome = result["outcome"]
+            time    = result["time"]
+            print(f"  {name}: {time}s")
+            if outcome == "success":
+                rows.append(f"| {name} | ✅ | {time}s |")
+            else:
+                failed.append(name)
+                rows.append(f"| {name} | ❌ | {time}s |")
         else:
-            failed.append(name)
-            rows.append(f"| {name} | ❌ | {time}s |")
+            print(f"  {name}: skipped")
+            rows.append(f"| {name} | SKIP | |")
     return rows, failed
 
 def PostResults(repo, run_id, rows, failed):
-    run_url    = f"https://github.com/{repo}/actions/runs/{run_id}"
-    table      = "\n".join(["| Check | Result | Time |", "|-------|--------|------|", *rows])
-    body       = f"**Check Results** ([run details]({run_url}))\n\n{table}"
-    pr_num     = os.environ["PR_NUMBER"]
-    pr_sha     = os.environ["PR_SHA"]
+    run_url = f"https://github.com/{repo}/actions/runs/{run_id}"
+    table   = "\n".join(["| Check | Result | Time |", "|-------|--------|------|", *rows])
+    body    = f"**Check Results** ([run details]({run_url}))\n\n{table}"
+    pr_num  = os.environ["PR_NUMBER"]
+    pr_sha  = os.environ["PR_SHA"]
     subprocess.run([
         "gh", "api", f"repos/{repo}/issues/{pr_num}/comments",
         "--method", "POST", "-f", f"body={body}",
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index e614d2d..c0c70e7 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -50,6 +50,7 @@ jobs:
         uses: ./.github/actions/timed-check
         with:
           script: .github/check_sconscripts.py
+          display: SCons DAG
 
       - id: check_newlines
         name: Check missing newlines
@@ -58,6 +59,7 @@ jobs:
         uses: ./.github/actions/timed-check
         with:
           script: .github/check_newlines.py
+          display: Newlines
 
       - id: check_eps
         name: Check extraneous EPS data
@@ -66,6 +68,7 @@ jobs:
         uses: ./.github/actions/timed-check
         with:
           script: .github/check_eps_savefig.py
+          display: EPS data
 
       - id: check_scons_log
         name: Check build failure
@@ -74,6 +77,7 @@ jobs:
         uses: ./.github/actions/timed-check
         with:
           script: .github/check_sconscript_log.py
+          display: Build log
 
       - name: Post results
         if: always()
@@ -81,14 +85,6 @@ jobs:
           GH_TOKEN: ${{ github.token }}
           PR_NUMBER: ${{ github.event.issue.number }}
           PR_SHA: ${{ env.PR_SHA }}
-          CHECK_SCONS_OUTCOME: ${{ steps.check_scons.outcome }}
-          CHECK_SCONS_TIME: ${{ steps.check_scons.outputs.time }}
-          CHECK_NEWLINES_OUTCOME: ${{ steps.check_newlines.outcome }}
-          CHECK_NEWLINES_TIME: ${{ steps.check_newlines.outputs.time }}
-          CHECK_EPS_OUTCOME: ${{ steps.check_eps.outcome }}
-          CHECK_EPS_TIME: ${{ steps.check_eps.outputs.time }}
-          CHECK_SCONS_LOG_OUTCOME: ${{ steps.check_scons_log.outcome }}
-          CHECK_SCONS_LOG_TIME: ${{ steps.check_scons_log.outputs.time }}
         run: |
           python .github/post_check_results.py \
             ${{ contains(github.event.comment.body, '--post') && '--post' || '' }}

From bf0edefa0bd2b332844e8ff2e4db00ed2cf0ec71 Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:10:50 -0400
Subject: [PATCH 09/19] reorganize folder structure #141

---
 .github/checks.json                           |  6 -----
 .github/{ => checks}/check_eps_savefig.py     |  0
 .github/{ => checks}/check_newlines.py        |  0
 .github/{ => checks}/check_sconscript_log.py  |  0
 .github/{ => checks}/check_sconscripts.py     |  0
 .github/checks/checks.json                    |  6 +++++
 .github/github_action_checks.md               |  2 +-
 .github/helper_scripts/parse_commands.py      |  8 +++++++
 .../post_check_results.py                     |  6 +++--
 .../pr_close_comment.py                       |  0
 .github/workflows/checks.yml                  | 24 ++++++++++++-------
 .github/workflows/pr-close-comment.yml        |  2 +-
 12 files changed, 35 insertions(+), 19 deletions(-)
 delete mode 100644 .github/checks.json
 rename .github/{ => checks}/check_eps_savefig.py (100%)
 rename .github/{ => checks}/check_newlines.py (100%)
 rename .github/{ => checks}/check_sconscript_log.py (100%)
 rename .github/{ => checks}/check_sconscripts.py (100%)
 create mode 100644 .github/checks/checks.json
 create mode 100644 .github/helper_scripts/parse_commands.py
 rename .github/{ => helper_scripts}/post_check_results.py (88%)
 rename .github/{scripts => helper_scripts}/pr_close_comment.py (100%)

diff --git a/.github/checks.json b/.github/checks.json
deleted file mode 100644
index 4811be2..0000000
--- a/.github/checks.json
+++ /dev/null
@@ -1,6 +0,0 @@
-[
-  {"name": "SCons DAG"},
-  {"name": "Newlines"},
-  {"name": "EPS data"},
-  {"name": "Build log"}
-]
diff --git a/.github/check_eps_savefig.py b/.github/checks/check_eps_savefig.py
similarity index 100%
rename from .github/check_eps_savefig.py
rename to .github/checks/check_eps_savefig.py
diff --git a/.github/check_newlines.py b/.github/checks/check_newlines.py
similarity index 100%
rename from .github/check_newlines.py
rename to .github/checks/check_newlines.py
diff --git a/.github/check_sconscript_log.py b/.github/checks/check_sconscript_log.py
similarity index 100%
rename from .github/check_sconscript_log.py
rename to .github/checks/check_sconscript_log.py
diff --git a/.github/check_sconscripts.py b/.github/checks/check_sconscripts.py
similarity index 100%
rename from .github/check_sconscripts.py
rename to .github/checks/check_sconscripts.py
diff --git a/.github/checks/checks.json b/.github/checks/checks.json
new file mode 100644
index 0000000..a0f40dc
--- /dev/null
+++ b/.github/checks/checks.json
@@ -0,0 +1,6 @@
+[
+  {"name": "SCons DAG", "command": "/run-actions-dag"},
+  {"name": "Newlines",  "command": "/run-actions-newlines"},
+  {"name": "EPS data",  "command": "/run-actions-eps"},
+  {"name": "Build log", "command": "/run-actions-log"}
+]
diff --git a/.github/github_action_checks.md b/.github/github_action_checks.md
index 046b96b..126391c 100644
--- a/.github/github_action_checks.md
+++ b/.github/github_action_checks.md
@@ -3,6 +3,6 @@
 ## Adding a new check
 
 1. Add a step to `checks.yml` with a unique `id` and `display` (e.g. `id: check_newlines`, `display: Newlines`)
-2. Add `{"name": "Newlines"}` (i.e. matching `display`) to `checks.json`
+2. Add `{"name": "Newlines", "command": "/run-actions-newlines"}` (i.e. matching `display`) to `checks.json`
 
 The order of entries in `checks.json` controls the row order in the results table.
diff --git a/.github/helper_scripts/parse_commands.py b/.github/helper_scripts/parse_commands.py
new file mode 100644
index 0000000..b300b75
--- /dev/null
+++ b/.github/helper_scripts/parse_commands.py
@@ -0,0 +1,8 @@
+import json, os
+checks  = json.load(open(os.path.join(os.path.dirname(__file__), '../checks/checks.json')))
+comment = os.environ.get('COMMENT_BODY', '')
+run = [c['name'] for c in checks
+       if os.environ.get('GITHUB_EVENT_NAME') == 'push'
+       or '/run-actions-all' in comment
+       or c.get('command', '') in comment]
+print(json.dumps(run))
diff --git a/.github/post_check_results.py b/.github/helper_scripts/post_check_results.py
similarity index 88%
rename from .github/post_check_results.py
rename to .github/helper_scripts/post_check_results.py
index 20c39c6..d920bb4 100644
--- a/.github/post_check_results.py
+++ b/.github/helper_scripts/post_check_results.py
@@ -4,7 +4,7 @@
 import subprocess
 import sys
 
-CHECKS_JSON = os.path.join(os.path.dirname(__file__), 'checks.json')
+CHECKS_JSON = os.path.join(os.path.dirname(__file__), '../checks/checks.json')
 
 def Main():
     repo   = os.environ["GITHUB_REPOSITORY"]
@@ -44,9 +44,11 @@ def CollectResults():
     return rows, failed
 
 def PostResults(repo, run_id, rows, failed):
+    checks  = json.load(open(CHECKS_JSON))
     run_url = f"https://github.com/{repo}/actions/runs/{run_id}"
     table   = "\n".join(["| Check | Result | Time |", "|-------|--------|------|", *rows])
-    body    = f"**Check Results** ([run details]({run_url}))\n\n{table}"
+    commands = " · ".join(f"`{c['command']}`" for c in checks if "command" in c) + " · `/run-actions-all`"
+    body    = f"**Check Results** ([run details]({run_url}))\n\n{table}\n\nRun individually: {commands}"
     pr_num  = os.environ["PR_NUMBER"]
     pr_sha  = os.environ["PR_SHA"]
     subprocess.run([
diff --git a/.github/scripts/pr_close_comment.py b/.github/helper_scripts/pr_close_comment.py
similarity index 100%
rename from .github/scripts/pr_close_comment.py
rename to .github/helper_scripts/pr_close_comment.py
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index c0c70e7..ee63ccd 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -43,40 +43,46 @@ jobs:
         with:
           python-version: "3.x"
 
+      - id: parse_commands
+        env:
+          COMMENT_BODY: ${{ github.event.comment.body }}
+        run: echo "run=$(python .github/helper_scripts/parse_commands.py)" >> $GITHUB_OUTPUT
+        shell: bash
+
       - id: check_scons
         name: Check SCons DAG for missing dependencies
-        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-dag') || contains(github.event.comment.body, '/run-actions-all')
+        if: contains(fromJSON(steps.parse_commands.outputs.run), 'SCons DAG')
         continue-on-error: true
         uses: ./.github/actions/timed-check
         with:
-          script: .github/check_sconscripts.py
+          script: .github/checks/check_sconscripts.py
           display: SCons DAG
 
       - id: check_newlines
         name: Check missing newlines
-        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-newlines') || contains(github.event.comment.body, '/run-actions-all')
+        if: contains(fromJSON(steps.parse_commands.outputs.run), 'Newlines')
         continue-on-error: true
         uses: ./.github/actions/timed-check
         with:
-          script: .github/check_newlines.py
+          script: .github/checks/check_newlines.py
           display: Newlines
 
       - id: check_eps
         name: Check extraneous EPS data
-        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-eps') || contains(github.event.comment.body, '/run-actions-all')
+        if: contains(fromJSON(steps.parse_commands.outputs.run), 'EPS data')
         continue-on-error: true
         uses: ./.github/actions/timed-check
         with:
-          script: .github/check_eps_savefig.py
+          script: .github/checks/check_eps_savefig.py
           display: EPS data
 
       - id: check_scons_log
         name: Check build failure
-        if: github.event_name == 'push' || contains(github.event.comment.body, '/run-actions-log') || contains(github.event.comment.body, '/run-actions-all')
+        if: contains(fromJSON(steps.parse_commands.outputs.run), 'Build log')
         continue-on-error: true
         uses: ./.github/actions/timed-check
         with:
-          script: .github/check_sconscript_log.py
+          script: .github/checks/check_sconscript_log.py
           display: Build log
 
       - name: Post results
@@ -86,5 +92,5 @@ jobs:
           PR_NUMBER: ${{ github.event.issue.number }}
           PR_SHA: ${{ env.PR_SHA }}
         run: |
-          python .github/post_check_results.py \
+          python .github/helper_scripts/post_check_results.py \
             ${{ contains(github.event.comment.body, '--post') && '--post' || '' }}
diff --git a/.github/workflows/pr-close-comment.yml b/.github/workflows/pr-close-comment.yml
index 3f787b1..9a0ddf7 100644
--- a/.github/workflows/pr-close-comment.yml
+++ b/.github/workflows/pr-close-comment.yml
@@ -33,4 +33,4 @@ jobs:
         PR_AUTHOR: ${{ github.event.pull_request.user.login }}
         BRANCH_NAME: ${{ github.event.pull_request.head.ref }}
         LAST_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
-      run: python .github/scripts/pr_close_comment.py
+      run: python .github/helper_scripts/pr_close_comment.py

From 76cd84d5607b5d462f679971823238b8b2acfcc3 Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:14:53 -0400
Subject: [PATCH 10/19] new url #141

---
 .github/github_action_checks.md | 4 ++--
 README.md                       | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/github_action_checks.md b/.github/github_action_checks.md
index 126391c..cc37aaf 100644
--- a/.github/github_action_checks.md
+++ b/.github/github_action_checks.md
@@ -2,7 +2,7 @@
 
 ## Adding a new check
 
-1. Add a step to `checks.yml` with a unique `id` and `display` (e.g. `id: check_newlines`, `display: Newlines`)
-2. Add `{"name": "Newlines", "command": "/run-actions-newlines"}` (i.e. matching `display`) to `checks.json`
+1. Add a step to `workflows/checks.yml` with a unique `id` and `display` (e.g. `id: check_newlines`, `display: Newlines`), and a `script` pointing to your script in `checks/`
+2. Add `{"name": "Newlines", "command": "/run-actions-newlines"}` (i.e. matching `display`) to `checks/checks.json`
 
 The order of entries in `checks.json` controls the row order in the results table.
diff --git a/README.md b/README.md
index 055ebfa..8e5d5e1 100644
--- a/README.md
+++ b/README.md
@@ -97,7 +97,7 @@ The repository is prebuilt with some automated testing using [Github Actions](./
 
 To run all tests, add `[run-actions-all]` to a commit message or type `/run-actions-all` in a comment.
 
-To run a particular test, type `/run-actions-NAMEOFTEST` in a comment (e.g., `/run-actions-log` to run [this test](https://github.com/JMSLab/Template/blob/140-automating-pr-reviews-using-github-actions/.github/check_sconscript_log.py).
+To run a particular test, type `/run-actions-NAMEOFTEST` in a comment (e.g., `/run-actions-log` to run [this test](https://github.com/JMSLab/Template/blob/master/.github/checks/check_sconscript_log.py).
 
 ### Citations and expectations for usage
 

From 729443dca07912999bbf1cf58d10f6274eea6a6c Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:21:05 -0400
Subject: [PATCH 11/19] remove footer i dislike #141

---
 .github/helper_scripts/post_check_results.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/helper_scripts/post_check_results.py b/.github/helper_scripts/post_check_results.py
index d920bb4..6246e47 100644
--- a/.github/helper_scripts/post_check_results.py
+++ b/.github/helper_scripts/post_check_results.py
@@ -44,11 +44,9 @@ def CollectResults():
     return rows, failed
 
 def PostResults(repo, run_id, rows, failed):
-    checks  = json.load(open(CHECKS_JSON))
     run_url = f"https://github.com/{repo}/actions/runs/{run_id}"
     table   = "\n".join(["| Check | Result | Time |", "|-------|--------|------|", *rows])
-    commands = " · ".join(f"`{c['command']}`" for c in checks if "command" in c) + " · `/run-actions-all`"
-    body    = f"**Check Results** ([run details]({run_url}))\n\n{table}\n\nRun individually: {commands}"
+    body    = f"**Check Results** ([run details]({run_url}))\n\n{table}"
     pr_num  = os.environ["PR_NUMBER"]
     pr_sha  = os.environ["PR_SHA"]
     subprocess.run([

From f39e9c0d5c7709d0ae95312610f5e6eb56d4d98c Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:23:11 -0400
Subject: [PATCH 12/19] improve code quality #141

---
 .github/helper_scripts/parse_commands.py | 32 ++++++++++++++++++------
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/.github/helper_scripts/parse_commands.py b/.github/helper_scripts/parse_commands.py
index b300b75..650eb97 100644
--- a/.github/helper_scripts/parse_commands.py
+++ b/.github/helper_scripts/parse_commands.py
@@ -1,8 +1,24 @@
-import json, os
-checks  = json.load(open(os.path.join(os.path.dirname(__file__), '../checks/checks.json')))
-comment = os.environ.get('COMMENT_BODY', '')
-run = [c['name'] for c in checks
-       if os.environ.get('GITHUB_EVENT_NAME') == 'push'
-       or '/run-actions-all' in comment
-       or c.get('command', '') in comment]
-print(json.dumps(run))
+#!/usr/bin/env python3
+import json
+import os
+import sys
+from pathlib import Path
+
+def LoadChecks():
+    checks_path = Path(__file__).parent.parent / 'checks' / 'checks.json'
+    return json.loads(checks_path.read_text())
+
+def ParseCommands():
+    checks = LoadChecks()
+    comment = os.environ.get('COMMENT_BODY', '')
+    return [c['name'] for c in checks
+            if os.environ.get('GITHUB_EVENT_NAME') == 'push'
+            or '/run-actions-all' in comment
+            or c.get('command', '') in comment]
+
+def Main():
+    print(json.dumps(ParseCommands()))
+    return 0
+
+if __name__ == '__main__':
+    sys.exit(Main())

From 3a55df2ffe88afcd9e4e849d40f79130f13989ae Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:41:58 -0400
Subject: [PATCH 13/19] minor improvements [run-actions-all] #141

thank you claude senior swe
---
 .github/actions/timed-check/action.yml       | 2 +-
 .github/checks/check_newlines.py             | 4 ++--
 .github/checks/check_sconscript_log.py       | 2 +-
 .github/helper_scripts/post_check_results.py | 6 ++++--
 .github/workflows/checks.yml                 | 1 -
 .github/workflows/pytest.yml                 | 4 ++--
 6 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/actions/timed-check/action.yml b/.github/actions/timed-check/action.yml
index 0d03791..8294b6a 100644
--- a/.github/actions/timed-check/action.yml
+++ b/.github/actions/timed-check/action.yml
@@ -11,7 +11,7 @@ runs:
       run: |
         mkdir -p "$RUNNER_TEMP/check_results"
         s=$(date +%s%N)
-        python ${{ inputs.script }} && outcome=success || outcome=failure
+        python "${{ inputs.script }}" && outcome=success || outcome=failure
         time=$(awk "BEGIN{printf \"%.3f\",($(date +%s%N)-$s)/1e9}")
         printf '{"outcome":"%s","time":"%s"}' "$outcome" "$time" \
           > "$RUNNER_TEMP/check_results/${{ inputs.display }}.json"
diff --git a/.github/checks/check_newlines.py b/.github/checks/check_newlines.py
index 2f23cd1..59cd9b1 100644
--- a/.github/checks/check_newlines.py
+++ b/.github/checks/check_newlines.py
@@ -13,14 +13,14 @@ def GetTrackedFiles():
 def IsBinary(p):
     try:
         return b"\0" in p.read_bytes()[:4096]
-    except:
+    except Exception:
         return True
 
 def NeedsNewline(p):
     try:
         d = p.read_bytes()
         return len(d)==0 or not d.endswith(b"\n")
-    except:
+    except Exception:
         return False
 
 def ProcessFiles():
diff --git a/.github/checks/check_sconscript_log.py b/.github/checks/check_sconscript_log.py
index 96742db..67310ea 100644
--- a/.github/checks/check_sconscript_log.py
+++ b/.github/checks/check_sconscript_log.py
@@ -10,7 +10,7 @@ def Main():
         try:
             if TARGET in p.read_text(errors="replace"):
                 bad.append(p)
-        except:
+        except Exception:
             pass
 
     if not bad:
diff --git a/.github/helper_scripts/post_check_results.py b/.github/helper_scripts/post_check_results.py
index 6246e47..ec2d1da 100644
--- a/.github/helper_scripts/post_check_results.py
+++ b/.github/helper_scripts/post_check_results.py
@@ -22,14 +22,16 @@ def Main():
     return 0
 
 def CollectResults():
-    checks      = json.load(open(CHECKS_JSON))
+    with open(CHECKS_JSON) as f:
+        checks = json.load(f)
     results_dir = os.path.join(os.environ["RUNNER_TEMP"], "check_results")
     rows, failed = [], []
     for check in checks:
         name        = check["name"]
         result_file = os.path.join(results_dir, f"{name}.json")
         if os.path.exists(result_file):
-            result  = json.load(open(result_file))
+            with open(result_file) as f:
+                result = json.load(f)
             outcome = result["outcome"]
             time    = result["time"]
             print(f"  {name}: {time}s")
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index ee63ccd..db190e2 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -15,7 +15,6 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 1
     permissions:
-      contents: write
       statuses: write
       pull-requests: write
 
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index f7c5d65..c0d400c 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -20,9 +20,9 @@ jobs:
         os: [ ubuntu-latest, windows-latest, macos-latest ]
         python-version: [ "3.10", "3.11", "3.12", "3.13", "3.14" ]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

From 02b212745b4045d542a605d73c1ac9f5b23885df Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:44:20 -0400
Subject: [PATCH 14/19] more swe fixes #141 [run-actions-all]

---
 .github/checks/check_eps_savefig.py        | 12 ++++----
 .github/helper_scripts/pr_close_comment.py | 32 +++++++++++-----------
 2 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/.github/checks/check_eps_savefig.py b/.github/checks/check_eps_savefig.py
index 423214b..2064960 100644
--- a/.github/checks/check_eps_savefig.py
+++ b/.github/checks/check_eps_savefig.py
@@ -34,15 +34,17 @@ def CheckEpsSavefig(file_path, content):
         r'\.savefig\([^)]*format\s*=\s*[\'"]eps[\'"][^)]*\)'  # matches format='eps' or format="eps"
     ]
     
-    has_remove_eps_info = 'remove_eps_info(' in content
-    
+    eps_lines = []
     for line_num, line in enumerate(lines, 1):
         for pattern in eps_savefig_patterns:
             if re.search(pattern, line, re.IGNORECASE):
-                if not has_remove_eps_info:
-                    problems.append(f"Line {line_num}: {line.strip()}")
+                eps_lines.append(f"Line {line_num}: {line.strip()}")
                 break
-    
+
+    remove_count = content.count('remove_eps_info(')
+    if len(eps_lines) != remove_count:
+        problems.extend(eps_lines)
+
     return problems
 
 def CollectEpsProblems(root, excluded):
diff --git a/.github/helper_scripts/pr_close_comment.py b/.github/helper_scripts/pr_close_comment.py
index 36360ec..c73cc7c 100644
--- a/.github/helper_scripts/pr_close_comment.py
+++ b/.github/helper_scripts/pr_close_comment.py
@@ -3,44 +3,44 @@
 from pathlib import Path
 from github import Github
 
-GITHUB_TOKEN = os.environ["GITHUB_TOKEN"]
-REPO_NAME = os.environ["REPO"]
-PR_NUMBER = int(os.environ["PR_NUMBER"])
-PR_AUTHOR = os.environ["PR_AUTHOR"]
-BRANCH_NAME = os.environ["BRANCH_NAME"]
-LAST_COMMIT_SHA = os.environ["LAST_COMMIT_SHA"]
-
 ISSUE_TEMPLATE = Path(".github/post_template_issue_thread_pr_close.md")
 PR_TEMPLATE = Path(".github/post_template_pr_thread_pr_close.md")
 
 
 def Main():
-    repo = Github(GITHUB_TOKEN).get_repo(REPO_NAME)
-    pr = repo.get_pull(PR_NUMBER)
+    github_token    = os.environ["GITHUB_TOKEN"]
+    repo_name       = os.environ["REPO"]
+    pr_number       = int(os.environ["PR_NUMBER"])
+    pr_author       = os.environ["PR_AUTHOR"]
+    branch_name     = os.environ["BRANCH_NAME"]
+    last_commit_sha = os.environ["LAST_COMMIT_SHA"]
+
+    repo = Github(github_token).get_repo(repo_name)
+    pr = repo.get_pull(pr_number)
 
-    issue_comment_url = PostIssueComment(repo)
-    PostPrComment(pr, issue_comment_url)
+    issue_comment_url = PostIssueComment(repo, branch_name, last_commit_sha)
+    PostPrComment(pr, pr_author, issue_comment_url)
 
 
-def PostIssueComment(repo):
-    issue_match = re.match(r"^(\d+)", BRANCH_NAME)
+def PostIssueComment(repo, branch_name, last_commit_sha):
+    issue_match = re.match(r"^(\d+)", branch_name)
     if not issue_match:
         return None
 
     issue_number = int(issue_match.group(1))
-    issue_body = ISSUE_TEMPLATE.read_text() + f"\n\nLast commit in issue branch: {LAST_COMMIT_SHA}"
+    issue_body = ISSUE_TEMPLATE.read_text() + f"\n\nLast commit in issue branch: {last_commit_sha}"
 
     comment = repo.get_issue(issue_number).create_comment(issue_body)
     return comment.html_url
 
 
-def PostPrComment(pr, issue_comment_url):
+def PostPrComment(pr, pr_author, issue_comment_url):
     pr_body = PR_TEMPLATE.read_text()
 
     if issue_comment_url:
         pr_body = f"[Issue summary]({issue_comment_url})\n\n{pr_body}"
 
-    pr.as_issue().create_comment(f"@{PR_AUTHOR} {pr_body}")
+    pr.as_issue().create_comment(f"@{pr_author} {pr_body}")
 
 
 if __name__ == "__main__":

From 523f6186e998e82707082c16df5c57946ce126dc Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Thu, 19 Mar 2026 19:48:31 -0400
Subject: [PATCH 15/19] remove node js warnings #141 [run-actions-all]

---
 .github/workflows/checks.yml           | 4 ++--
 .github/workflows/pr-close-comment.yml | 4 ++--
 .github/workflows/pytest.yml           | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index db190e2..bd246bc 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) || github.sha }}
 
@@ -38,7 +38,7 @@ jobs:
             -f target_url="https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
 
diff --git a/.github/workflows/pr-close-comment.yml b/.github/workflows/pr-close-comment.yml
index 9a0ddf7..4a66d97 100644
--- a/.github/workflows/pr-close-comment.yml
+++ b/.github/workflows/pr-close-comment.yml
@@ -15,10 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.12'
 
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index c0d400c..b33128d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -20,9 +20,9 @@ jobs:
         os: [ ubuntu-latest, windows-latest, macos-latest ]
         python-version: [ "3.10", "3.11", "3.12", "3.13", "3.14" ]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

From 9f81d0ba5c1f89cf39b2f86b5915d0e5e32833d7 Mon Sep 17 00:00:00 2001
From: jmshapir <jesse.m.shapiro@gmail.com>
Date: Fri, 20 Mar 2026 08:11:42 -0400
Subject: [PATCH 16/19] Rename for #141

---
 .github/{github_action_checks.md => readme_for_checks.md} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/{github_action_checks.md => readme_for_checks.md} (100%)

diff --git a/.github/github_action_checks.md b/.github/readme_for_checks.md
similarity index 100%
rename from .github/github_action_checks.md
rename to .github/readme_for_checks.md

From 7f63852d6f44d06eb299c68790999a0983df99ff Mon Sep 17 00:00:00 2001
From: jmshapir <jesse.m.shapiro@gmail.com>
Date: Fri, 20 Mar 2026 08:14:49 -0400
Subject: [PATCH 17/19] Readme for #141

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 8e5d5e1..6b2694b 100644
--- a/README.md
+++ b/README.md
@@ -93,11 +93,11 @@ env.Stata(target, source)
 
 ### Automation
 
-The repository is prebuilt with some automated testing using [Github Actions](./github).
+The repository is prebuilt with some automated testing using [Github Actions](./.github).
 
 To run all tests, add `[run-actions-all]` to a commit message or type `/run-actions-all` in a comment.
 
-To run a particular test, type `/run-actions-NAMEOFTEST` in a comment (e.g., `/run-actions-log` to run [this test](https://github.com/JMSLab/Template/blob/master/.github/checks/check_sconscript_log.py).
+To run a particular test, type `/run-actions-NAMEOFTEST` in a comment (e.g., `/run-actions-log` to run [this test](./.github/checks/check_sconscript_log.py); see [commands](./.github/checks/checks.json) for others).
 
 ### Citations and expectations for usage
 

From 847de72d0dcb6cb65f20a4fc6403f41db3d3657e Mon Sep 17 00:00:00 2001
From: jmshapir <jesse.m.shapiro@gmail.com>
Date: Fri, 20 Mar 2026 08:19:38 -0400
Subject: [PATCH 18/19] Clarifies docs for #141

---
 .github/post_template_pr_thread_pr_close.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/post_template_pr_thread_pr_close.md b/.github/post_template_pr_thread_pr_close.md
index 2299dc1..a4488dd 100644
--- a/.github/post_template_pr_thread_pr_close.md
+++ b/.github/post_template_pr_thread_pr_close.md
@@ -1,3 +1,6 @@
 Thanks for closing this pull. 
 
-Before leaving the pull, please be sure you have completed all the required steps in the [workflow](https://github.com/JMSLab/Template/blob/main/docs/workflow.md)!
+Before leaving the pull, please be sure you have completed all the required steps in the [workflow](https://github.com/JMSLab/Template/blob/main/docs/workflow.md).
+
+This includes filling in the issue summary linked at the top of this comment.
+

From c44ac14dd6300eff8addd0cd1b53cc1f9bd13441 Mon Sep 17 00:00:00 2001
From: Chris Liao <33707455+liaochris@users.noreply.github.com>
Date: Fri, 20 Mar 2026 15:34:50 -0400
Subject: [PATCH 19/19] [run-actions-all] #141 improve style, remove eps output
 check

---
 .github/checks/check_eps_savefig.py          | 118 ++++---------------
 .github/checks/check_sconscript_log.py       |   2 +-
 .github/helper_scripts/post_check_results.py |  37 +++---
 .github/helper_scripts/pr_close_comment.py   |   4 +-
 .github/workflows/checks.yml                 |   3 +-
 .github/workflows/pr-close-comment.yml       |   4 +-
 6 files changed, 51 insertions(+), 117 deletions(-)

diff --git a/.github/checks/check_eps_savefig.py b/.github/checks/check_eps_savefig.py
index 2064960..7d89454 100644
--- a/.github/checks/check_eps_savefig.py
+++ b/.github/checks/check_eps_savefig.py
@@ -20,116 +20,50 @@ def ReadFile(path):
     except Exception:
         return None
 
-def CheckEpsSavefig(file_path, content):
-    """
-    Check if file contains .savefig(*eps*) without remove_eps_info(
-    Returns list of problematic lines with line numbers
-    """
-    problems = []
-    lines = content.split('\n')
-    
-    # Pattern to match .savefig with eps format (both single and double quotes)
+def WalkFiles(root, excluded, extension):
+    for dir_path, dir_names, file_names in os.walk(root):
+        if IsExcludedPath(dir_path, excluded):
+            dir_names[:] = []
+            continue
+
+        dir_names[:] = [d for d in dir_names if not IsIgnoredDir(d)]
+
+        for file_name in file_names:
+            if file_name.endswith(extension) and not IsHidden(file_name):
+                yield os.path.join(dir_path, file_name)
+
+def CheckEpsSavefig(content):
     eps_savefig_patterns = [
-        r'\.savefig\([^)]*[\'"].*eps.*[\'"][^)]*\)',  # matches .savefig(...'...eps...'...)
-        r'\.savefig\([^)]*format\s*=\s*[\'"]eps[\'"][^)]*\)'  # matches format='eps' or format="eps"
+        r'\.savefig\([^)]*[\'"].*eps.*[\'"][^)]*\)',
+        r'\.savefig\([^)]*format\s*=\s*[\'"]eps[\'"][^)]*\)'
     ]
-    
+
     eps_lines = []
-    for line_num, line in enumerate(lines, 1):
+    for line_num, line in enumerate(content.split('\n'), 1):
         for pattern in eps_savefig_patterns:
             if re.search(pattern, line, re.IGNORECASE):
                 eps_lines.append(f"Line {line_num}: {line.strip()}")
                 break
 
     remove_count = content.count('remove_eps_info(')
-    if len(eps_lines) != remove_count:
-        problems.extend(eps_lines)
-
-    return problems
+    return eps_lines if len(eps_lines) != remove_count else []
 
 def CollectEpsProblems(root, excluded):
-    """Walk through Python files and check for EPS savefig issues"""
     problems = []
-    
-    for dir_path, dir_names, file_names in os.walk(root):
-        if IsExcludedPath(dir_path, excluded):
-            dir_names[:] = []
+    for file_path in WalkFiles(root, excluded, '.py'):
+        content = ReadFile(file_path)
+        if content is None:
             continue
-            
-        dir_names[:] = [d for d in dir_names if not IsIgnoredDir(d)]
-        
-        for file_name in file_names:
-            if not file_name.endswith('.py'):
-                continue
-                
-            if IsHidden(file_name):
-                continue
-                
-            file_path = os.path.join(dir_path, file_name)
-            content = ReadFile(file_path)
-            
-            if content is None:
-                continue
-                
-            file_problems = CheckEpsSavefig(file_path, content)
-            if file_problems:
-                problems.append({
-                    'file': file_path,
-                    'issues': file_problems
-                })
-    
+        file_problems = CheckEpsSavefig(content)
+        if file_problems:
+            problems.append({'file': file_path, 'issues': file_problems})
     return problems
 
-def CheckEpsCreationDate(content):
-    """
-    Check if any line in an EPS file starts with %%CreationDate.
-    Returns True if it does.
-    """
-    return any(line.startswith("%%CreationDate") for line in content.splitlines())
-
-def CollectEpsCreationDateProblems(root, excluded):
-    """Walk through EPS files and report those that contain %%CreationDate"""
-    eps_files = []
-    
-    for dir_path, dir_names, file_names in os.walk(root):
-        if IsExcludedPath(dir_path, excluded):
-            dir_names[:] = []
-            continue
-            
-        dir_names[:] = [d for d in dir_names if not IsIgnoredDir(d)]
-        
-        for file_name in file_names:
-            if not file_name.endswith('.eps'):
-                continue
-                
-            if IsHidden(file_name):
-                continue
-                
-            eps_path = os.path.join(dir_path, file_name)
-            content = ReadFile(eps_path)
-            
-            if content is None:
-                continue
-                
-            if CheckEpsCreationDate(content):
-                eps_files.append(eps_path)
-    
-    return eps_files
-
-def main():
+def Main():
     source_root   = "source"
-    output_root   = "output"
     excluded      = ["source/lib", "source/raw", "source/scrape"]
 
     problems = CollectEpsProblems(source_root, excluded)
-    creationdate_eps_files = CollectEpsCreationDateProblems(output_root, [])
-    
-    if creationdate_eps_files:
-        print("EPS files containing %%CreationDate:")
-        for eps_file in creationdate_eps_files:
-            print(f"  {eps_file}")
-        print("")
-        return 1
 
     if problems:
         print("EPS savefig check failed!")
@@ -146,4 +80,4 @@ def main():
         return 0
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(Main())
diff --git a/.github/checks/check_sconscript_log.py b/.github/checks/check_sconscript_log.py
index 67310ea..f3e12c9 100644
--- a/.github/checks/check_sconscript_log.py
+++ b/.github/checks/check_sconscript_log.py
@@ -6,7 +6,7 @@
 
 def Main():
     bad = []
-    for p in Path(".").rglob("**/*.log"):
+    for p in Path(".").rglob("*.log"):
         try:
             if TARGET in p.read_text(errors="replace"):
                 bad.append(p)
diff --git a/.github/helper_scripts/post_check_results.py b/.github/helper_scripts/post_check_results.py
index ec2d1da..cbf7b32 100644
--- a/.github/helper_scripts/post_check_results.py
+++ b/.github/helper_scripts/post_check_results.py
@@ -3,8 +3,9 @@
 import os
 import subprocess
 import sys
+from pathlib import Path
 
-CHECKS_JSON = os.path.join(os.path.dirname(__file__), '../checks/checks.json')
+CHECKS_JSON = Path(__file__).parent.parent / 'checks' / 'checks.json'
 
 def Main():
     repo   = os.environ["GITHUB_REPOSITORY"]
@@ -22,27 +23,25 @@ def Main():
     return 0
 
 def CollectResults():
-    with open(CHECKS_JSON) as f:
-        checks = json.load(f)
-    results_dir = os.path.join(os.environ["RUNNER_TEMP"], "check_results")
+    checks      = json.loads(CHECKS_JSON.read_text())
+    results_dir = Path(os.environ["RUNNER_TEMP"]) / "check_results"
     rows, failed = [], []
+    STATUS = {"success": "✅", "failure": "❌"}
     for check in checks:
-        name        = check["name"]
-        result_file = os.path.join(results_dir, f"{name}.json")
-        if os.path.exists(result_file):
-            with open(result_file) as f:
-                result = json.load(f)
-            outcome = result["outcome"]
-            time    = result["time"]
-            print(f"  {name}: {time}s")
-            if outcome == "success":
-                rows.append(f"| {name} | ✅ | {time}s |")
-            else:
-                failed.append(name)
-                rows.append(f"| {name} | ❌ | {time}s |")
+        check_name  = check["name"]
+        result_file = results_dir / f"{check_name}.json"
+        if result_file.exists():
+            result      = json.loads(result_file.read_text())
+            outcome     = result["outcome"]
+            elapsed     = result["time"]
+            print(f"  {check_name}: {elapsed}s")
+            status_icon = STATUS.get(outcome, "❌")
+            if outcome != "success":
+                failed.append(check_name)
+            rows.append(f"| {check_name} | {status_icon} | {elapsed}s |")
         else:
-            print(f"  {name}: skipped")
-            rows.append(f"| {name} | SKIP | |")
+            print(f"  {check_name}: skipped")
+            rows.append(f"| {check_name} | SKIP | |")
     return rows, failed
 
 def PostResults(repo, run_id, rows, failed):
diff --git a/.github/helper_scripts/pr_close_comment.py b/.github/helper_scripts/pr_close_comment.py
index c73cc7c..7d93594 100644
--- a/.github/helper_scripts/pr_close_comment.py
+++ b/.github/helper_scripts/pr_close_comment.py
@@ -1,5 +1,6 @@
 import os
 import re
+import sys
 from pathlib import Path
 from github import Github
 
@@ -20,6 +21,7 @@ def Main():
 
     issue_comment_url = PostIssueComment(repo, branch_name, last_commit_sha)
     PostPrComment(pr, pr_author, issue_comment_url)
+    return 0
 
 
 def PostIssueComment(repo, branch_name, last_commit_sha):
@@ -44,4 +46,4 @@ def PostPrComment(pr, pr_author, issue_comment_url):
 
 
 if __name__ == "__main__":
-    Main()
+    sys.exit(Main())
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index bd246bc..44e3cc6 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -43,6 +43,7 @@ jobs:
           python-version: "3.x"
 
       - id: parse_commands
+        name: Parse requested checks
         env:
           COMMENT_BODY: ${{ github.event.comment.body }}
         run: echo "run=$(python .github/helper_scripts/parse_commands.py)" >> $GITHUB_OUTPUT
@@ -76,7 +77,7 @@ jobs:
           display: EPS data
 
       - id: check_scons_log
-        name: Check build failure
+        name: Check SCons build log for errors
         if: contains(fromJSON(steps.parse_commands.outputs.run), 'Build log')
         continue-on-error: true
         uses: ./.github/actions/timed-check
diff --git a/.github/workflows/pr-close-comment.yml b/.github/workflows/pr-close-comment.yml
index 4a66d97..6f5db5e 100644
--- a/.github/workflows/pr-close-comment.yml
+++ b/.github/workflows/pr-close-comment.yml
@@ -1,5 +1,3 @@
-# Post a comment when a PR is closed (merged or unmerged)
-
 name: PR Close Comment
 
 on:
@@ -20,7 +18,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
-        python-version: '3.12'
+        python-version: "3.x"
 
     - name: Install dependencies
       run: pip install PyGithub