Merging develop

.github/dependabot.yml

@@ -1,6 +1,14 @@
-versions: 2
+version: 2
 updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "daily"
+  - package-ecosystem: "pip"
+    directory: "/.github/workflows/requirements"
+    schedule:
+      interval: "weekly"
+    ignore:
+      # setuptools releases new versions almost daily
+      - dependency-name: "setuptools"
+        update-types: ["version-update:semver-patch"]

.github/labeler.yml

@@ -0,0 +1,31 @@
+application:
+- changed-files:
+  - any-glob-to-any-file:
+    - repo/**
+
+ci:
+- changed-files:
+  - any-glob-to-any-file:
+    - .github/**
+
+configs:
+- changed-files:
+  - any-glob-to-any-file:
+    - configs/**
+
+dependencies:
+- changed-files:
+  - any-glob-to-any-file:
+    - .github/worklflows/requirements/**
+    - pyproject.toml
+
+docs:
+- changed-files:
+  - any-glob-to-any-file:
+    - docs/**
+    - README.rst
+
+experiment:
+- changed-files:
+  - any-glob-to-any-file:
+    - experiments/**

.github/workflows/bin/license

@@ -0,0 +1,184 @@
+#!/bin/env python3
+#
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from __future__ import print_function
+
+import os
+import re
+import sys
+from collections import defaultdict
+
+#: SPDX license id must appear in the first <license_lines> lines of a file
+license_lines = 7
+
+#: Benchpark's license identifier
+apache_spdx = "Apache-2.0"
+
+#: regular expressions for licensed files.
+licensed_files = [
+    r"^bin\/benchpark",
+    r"^configs\/[^\/]*\/[^\/]*",
+    r"^docs\/[^\/]*\.rst$",
+    r"^experiments\/[^\/]*\/[^\/]*",
+    r"^repo\/[^\/]*\/[^\/]*",
+]
+
+
+def _all_files(root="."):
+    """Generates root-relative paths of all files in the repository."""
+    visited = set()
+    for cur_root, folders, files in os.walk(root):
+        for filename in files:
+            path = os.path.realpath(os.path.join(cur_root, filename))
+
+            if path not in visited:
+                yield os.path.relpath(path, root)
+                visited.add(path)
+
+
+def _licensed_files(root):
+    for relpath in _all_files(root):
+        if any(regex.match(relpath) for regex in licensed_files):
+            yield relpath
+
+
+def list_files(root):
+    """List files that should have license headers"""
+    for relpath in sorted(_licensed_files(root)):
+        print(os.path.join(".", relpath))
+
+
+# Error codes for license verification. All values are chosen such that
+# bool(value) evaluates to True
+SPDX_MISMATCH, GENERAL_MISMATCH, COPYRIGHT_YEAR_MISMATCH = range(1, 4)
+
+#: Latest year that copyright applies. UPDATE THIS when bumping copyright.
+latest_year = 2023
+strict_date = r"Copyright %s" % latest_year
+
+#: regexes for valid license lines at tops of files
+license_line_regexes = [
+    r"Copyright (%d|[0-9]{4}) Lawrence Livermore National Security, LLC and other"
+    % latest_year,
+    r"Benchpark Project Developers. See the top-level COPYRIGHT file for details.",
+    r"SPDX-License-Identifier: Apache-2.0",
+]
+
+
+class LicenseError(object):
+    def __init__(self):
+        self.error_counts = defaultdict(int)
+
+    def add_error(self, error):
+        self.error_counts[error] += 1
+
+    def has_errors(self):
+        return sum(self.error_counts.values()) > 0
+
+    def error_messages(self):
+        total = sum(self.error_counts.values())
+        missing = self.error_counts[GENERAL_MISMATCH]
+        spdx_mismatch = self.error_counts[SPDX_MISMATCH]
+        copyright_year_mismatch = self.error_counts[COPYRIGHT_YEAR_MISMATCH]
+        return (
+            "%d improperly licensed files\n" % (total),
+            "files with wrong SPDX-License-Identifier:   %d\n" % spdx_mismatch,
+            "files not containing expected license:      %d\n" % missing,
+            "files with wrong copyright year:            %d\n" % copyright_year_mismatch,
+        )
+
+
+def _check_license(lines, path):
+    found = []
+
+    for line in lines:
+        line = re.sub(r"^[\s#\%\.\!\/\/]*", "", line)
+        line = line.rstrip()
+        for i, line_regex in enumerate(license_line_regexes):
+            if re.match(line_regex, line):
+                # The first line of the license contains the copyright date.
+                # We allow it to be out of date but print a warning if it is
+                # out of date.
+                if i == 0:
+                    if not re.search(strict_date, line):
+                        print("{0}: Copyright date mismatch".format(path))
+                        return COPYRIGHT_YEAR_MISMATCH
+                found.append(i)
+
+    if len(found) == len(license_line_regexes) and found == list(sorted(found)):
+        return
+
+    # If the SPDX identifier is present, then there is a mismatch (since it
+    # did not match the above regex)
+    def wrong_spdx_identifier(line, path):
+        m = re.search(r"SPDX-License-Identifier: [^\n]*", line)
+        if m and m.group(1) != apache_spdx:
+            print(
+                "{0}: SPDX license identifier mismatch"
+                "(expecting {1}, found {2})".format(path, apache_spdx, m.group(1))
+            )
+            return SPDX_MISMATCH
+        else:
+            print("{0}: SPDX license identifier missing".format(path))
+            return GENERAL_MISMATCH
+
+    checks = [wrong_spdx_identifier]
+
+    for line in lines:
+        for check in checks:
+            error = check(line, path)
+            if error:
+                return error
+
+    print(
+        "{0}: the license header at the top of the file does not match the"
+        " expected format".format(path)
+    )
+    return GENERAL_MISMATCH
+
+
+def verify(root):
+    """Verify that files have the right license header"""
+
+    license_errors = LicenseError()
+
+    for relpath in _licensed_files(root):
+        path = os.path.join(root, relpath)
+        with open(path) as f:
+            lines = [line for line in f][:license_lines]
+
+        error = _check_license(lines, path)
+        if error:
+            license_errors.add_error(error)
+
+    if license_errors.has_errors():
+        print(*license_errors.error_messages())
+        sys.exit(1)
+    else:
+        print("No license issues found.")
+        return
+
+
+if __name__ == "__main__":
+    valid_options = ["list-files", "verify"]
+
+    if len(sys.argv) != 2:
+        print("Please specify a valid option: {}".format(valid_options))
+        sys.exit()
+
+    cmd = sys.argv[1]
+    if cmd not in valid_options:
+        print("Invalid argument. Valid options are {}".format(valid_options))
+        sys.exit()
+
+    licensed_files[:] = [re.compile(regex) for regex in licensed_files]
+    root = os.path.abspath(os.curdir)
+
+    if cmd == "list-files":
+        list_files(root)
+    elif cmd == "verify":
+        verify(root)

.github/workflows/ci.yml

@@ -20,6 +20,7 @@ jobs:
       docs: ${{ steps.filter.outputs.docs }}
       style: ${{ steps.filter.outputs.style }}
       run: ${{ steps.filter.outputs.run }}
+      license: ${{ steps.filter.outputs.license }}
 
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
@@ -49,6 +50,13 @@ jobs:
               - 'configs/**'
               - 'experiments/**'
               - 'repo/**'
+            license:
+              - '.github/**'
+              - 'bin/**'
+              - 'configs/**'
+              - 'docs/**'
+              - 'experiments/**'
+              - 'repo/**'
 
   docs:
     if: ${{ needs.changes.outputs.docs == 'true' }}
@@ -64,3 +72,8 @@ jobs:
     if: ${{ needs.changes.outputs.run == 'true' }}
     needs: changes
     uses: ./.github/workflows/run.yml
+
+  license:
+    if: ${{ needs.changes.outputs.license == 'true' }}
+    needs: changes
+    uses: ./.github/workflows/license.yml

.github/workflows/docs.yml

@@ -1,7 +1,5 @@
 name: Build & Deploy docs site to GitHub Pages
 on:
-  # This Workflow can be triggered manually
-  workflow_dispatch:
   workflow_call:
 
 jobs:
@@ -12,15 +10,15 @@ jobs:
       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
 
     - name: Setup Python
-      uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: '3.11'
         cache: 'pip'
         cache-dependency-path: '.github/workflows/requirements/docs.txt'
 
     - name: Setup GitHub Pages
       id: pages
-      uses: actions/configure-pages@f156874f8191504dae5b037505266ed5dda6c382
+      uses: actions/configure-pages@1f0c5cde4bc74cd7e1254d0cb4de8d49e9068c7d
 
     - name: Install Sphinx and Theme via Pip
       run: |
@@ -30,8 +28,12 @@ jobs:
       run: |
         sphinx-build docs/ _build
 
+    - name: Check for Typos using Codespell
+      run: |
+        codespell
+
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@a753861a5debcf57bf8b404356158c8e1e33150c
+      uses: actions/upload-pages-artifact@0252fc4ba7626f0298f0cf00902a25c6afc77fa8
       if: github.ref == 'refs/heads/develop'
       with:
         path: ./_build
@@ -52,4 +54,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@9dbe3824824f8a1377b8e298bafde1a50ede43e5
+        uses: actions/deploy-pages@7a9bd943aa5e5175aeb8502edcc6c1c02d398e10

.github/workflows/label.yml

@@ -0,0 +1,21 @@
+#-----------------------------------------------------------------------
+# DO NOT modify unless you really know what you are doing.
+#
+# See https://stackoverflow.com/a/74959635 for more info.
+# Talk to @alecbcs if you have questions/are not sure of a change's
+# possible impact to security.
+#-----------------------------------------------------------------------
+name: label
+on:
+  pull_request_target:
+    branches:
+      - develop
+
+jobs:
+  pr:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+    steps:
+      - uses: actions/labeler@8558fd74291d67161a8a78ce36a881fa63b766a9

.github/workflows/license.yml

@@ -0,0 +1,19 @@
+name: License Checks
+on:
+  workflow_call:
+
+jobs:
+  verify-license:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Verify license headers
+        run: |
+          python .github/workflows/bin/license verify

.github/workflows/nightly.yml

@@ -0,0 +1,13 @@
+name: nightly
+on:
+  schedule:
+    - cron: '0 14 * * *'
+
+#------------------------------------------------------------------------
+# Execute a nightly CI run to verify benchmarks continue to build & run
+# sucessfully. Will also update the CI buildcache to minimize build
+# times in PRs.
+#------------------------------------------------------------------------
+jobs:
+  run:
+    uses: ./.github/workflows/run.yml

.github/workflows/requirements/docs.txt

@@ -1,3 +1,4 @@
 # docs
 sphinx==7.2.6
-sphinx-rtd-theme==1.3.0
+sphinx-rtd-theme==2.0.0
+codespell==2.2.6

.github/workflows/requirements/style.txt

@@ -1,2 +1,4 @@
-black==23.10.1
-flake8==6.1.0
+black==23.12.1
+flake8==7.0.0
+isort==5.13.2
+codespell==2.2.6