Merge remote-tracking branch 'upstream/main' into Solve_seedfilter

.github/workflows/docs.yml

@@ -19,7 +19,7 @@ jobs:
     env:
         DOXYGEN_WARN_AS_ERROR: FAIL_ON_WARNINGS
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Install dependencies
         run: >
           curl -SL https://sourceforge.net/projects/doxygen/files/rel-1.9.4/doxygen-1.9.4.linux.bin.tar.gz/download | tar -xzC .

.gitlab-ci.yml

@@ -12,10 +12,13 @@ clang_tidy:
     - git checkout $HEAD_SHA
     - >
         apt-get update
-        && apt-get install -y clang-10 clang-tidy-10 g++-8 libstdc++-8-dev
-        && ln -s /usr/bin/clang++-10 /usr/bin/clang++
-        && ln -s /usr/bin/clang-10 /usr/bin/clang
-        && ln -s /usr/bin/clang-tidy-10 /usr/bin/clang-tidy
+        && apt-get install -y g++-8 libstdc++-8-dev parallel software-properties-common 
+        && curl -L https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add
+        && add-apt-repository 'deb http://apt.llvm.org/focal/ llvm-toolchain-focal main'
+        && apt-get install -y clang-16 clang-tidy-16
+        && ln -s /usr/bin/clang++-16 /usr/bin/clang++
+        && ln -s /usr/bin/clang-16 /usr/bin/clang
+        && ln -s /usr/bin/clang-tidy-16 /usr/bin/clang-tidy
         && mkdir -p /opt/lib/gcc/x86_64-linux-gnu
         && ln -s /usr/lib/gcc/x86_64-linux-gnu/8/ /opt/lib/gcc/x86_64-linux-gnu/ 
         && clang++ --gcc-toolchain=/opt -v
@@ -30,10 +33,24 @@ clang_tidy:
         -DACTS_RUN_CLANG_TIDY=on
 
     - mkdir clang-tidy
-    - CI/clang_tidy/run_clang_tidy.sh build > clang-tidy/clang-tidy.log
+
+    # Main clang-tidy run during cmake compilation
+    - CI/clang_tidy/run_clang_tidy.sh build | tee clang-tidy/clang-tidy.log
+
+    # Install dependencies for processing scripts
     - pip install -r CI/clang_tidy/requirements.txt
-    - CI/clang_tidy/parse_clang_tidy.py clang-tidy/clang-tidy.log clang-tidy/clang-tidy.json --exclude "*thirdparty*"
+
+    # Parse the main clang-tidy run
+    - >
+        CI/clang_tidy/parse_clang_tidy.py 
+        clang-tidy/clang-tidy.log 
+        clang-tidy/clang-tidy.json 
+        --exclude "*thirdparty*"
+
+    # Check the combined report against the defined limits
     - CI/clang_tidy/check_clang_tidy.py --report clang-tidy/clang-tidy.json --config CI/clang_tidy/limits.yml
+
+    # Generate an html report
     - codereport clang-tidy/clang-tidy.json clang-tidy/html
 
 build:

Alignment/include/ActsAlignment/Kernel/Alignment.ipp

@@ -17,9 +17,12 @@ ActsAlignment::Alignment<fitter_t>::evaluateTrackAlignmentState(
     const std::unordered_map<const Acts::Surface*, size_t>& idxedAlignSurfaces,
     const ActsAlignment::AlignmentMask& alignMask,
     Acts::LoggerWrapper logger) const {
+  // Convert to Acts::SourceLink during iteration
+  Acts::SourceLinkAdapterIterator begin{sourcelinks.begin()};
+  Acts::SourceLinkAdapterIterator end{sourcelinks.end()};
+
   // Perform the fit
-  auto fitRes = m_fitter.fit(sourcelinks.begin(), sourcelinks.end(),
-                             sParameters, fitOptions);
+  auto fitRes = m_fitter.fit(begin, end, sParameters, fitOptions);
   if (not fitRes.ok()) {
     ACTS_WARNING("Fit failure");
     return fitRes.error();
@@ -301,7 +304,6 @@ ActsAlignment::Alignment<fitter_t>::align(
   // Screen out the final aligned parameters
   // @todo
   if (alignmentParametersUpdated) {
-    unsigned int iDetElement = 0;
     for (const auto& det : alignOptions.alignedDetElements) {
       const auto& surface = &det->surface();
       const auto& transform =
@@ -318,7 +320,6 @@ ActsAlignment::Alignment<fitter_t>::align(
       ACTS_VERBOSE(
           "Euler angles (rotZ, rotY, rotX) = " << rotAngles.transpose());
       ACTS_VERBOSE("Rotation marix = \n" << rotation);
-      iDetElement++;
     }
   } else {
     ACTS_DEBUG("Alignment parameters is not updated.");

Alignment/include/ActsAlignment/Kernel/detail/AlignmentEngine.hpp

@@ -118,15 +118,17 @@ TrackAlignmentState trackAlignmentState(
   std::vector<std::pair<size_t, bool>> measurementStates;
   measurementStates.reserve(15);
   // Number of smoothed states on the track
-  size_t nSmoothedStates = 0;
+  // size_t nSmoothedStates = 0; // commented because clang-tidy complains about
+  // unused
   // Number of alignable surfaces on the track
   size_t nAlignSurfaces = 0;
 
   // Visit the track states on the track
   multiTraj.visitBackwards(entryIndex, [&](const auto& ts) {
     // Remember the number of smoothed states
     if (ts.hasSmoothed()) {
-      nSmoothedStates++;
+      // nSmoothedStates++; // commented because clang-tidy complains about
+      // unused
     } else {
       // @note: this should in principle never happen now. But still keep it as a note
       return true;

CI/clang_tidy/limits.yml

@@ -1,15 +1,19 @@
 limits:
-  # "readability-inconsistent-declaration-parameter-name": 0
-  # "readability-named-parameter": 0
+  "readability-inconsistent-declaration-parameter-name": 0
+  "readability-named-parameter": 0
   "readability-container-size-empty": 0
-  "modernize-use-using": 0
   "readability-braces-around-statements": 0
-  "modernize-use-override": 0
-  "modernize-use-equals-default" : 0
   "readability-implicit-bool-cast": 0
   "readability-implicit-bool-conversion": 0
-  # "modernize-use-default-member-init": 0
-  # "performance-unnecessary-value-param": 0
-  # "modernize-use-equals-default": 0
+  "modernize-use-using": 0
+  "modernize-use-override": 0
+  "modernize-use-equals-default" : 0
+  "modernize-use-default-member-init": 0
   "modernize-use-nullptr": 0
-  "performance-move-const-arg": 0
+  "performance-unnecessary-value-param": 0
+  "performance-move-const-arg": 0
+  "performance-for-range-copy": 0
+  "cppcoreguidelines-pro-type-member-init": 0
+  "cppcoreguidelines-init-variables": 0
+  "clang-analyzer-optin.cplusplus.UninitializedObject": 0
+  "clang-diagnostic-error": 0

CI/clang_tidy/parse_clang_tidy.py

@@ -24,7 +24,7 @@ def parse_clang_tidy_item(itemstr):
 
     try:
         m = re.match(
-            r"(?P<file>[/.\-+\w]+):(?P<line>\d+):(?P<col>\d+): (?P<sev>.*?):(?P<msg>[\s\S]*?)\[(?P<code>.*)\]\n(?P<info>[\s\S]*)",
+            r"(?P<file>[/.\-+\w]+):(?P<line>\d+):(?P<col>\d+): (?P<sev>.*?):(?P<msg>[\s\S]*)\[(?P<code>.*)\]\n(?P<info>[\s\S]*)",
             itemstr,
         )
 
@@ -35,7 +35,7 @@ def parse_clang_tidy_item(itemstr):
             line=int(m.group("line")),
             col=int(m.group("col")),
             #  message=m.group("msg").strip(),
-            message="\n".join(lines[1:]),
+            message=m.group("msg").strip() + "\n" + "\n".join(lines[1:]),
             code=m.group("code"),
             severity=m.group("sev"),
         )
@@ -101,6 +101,12 @@ def main():
         default=[],
         help="Only include files that match any of these patterns",
     )
+    p.add_argument(
+        "--ignore",
+        action="append",
+        default=[],
+        help="Ignore items with codes matching any of these patterns",
+    )
     p.add_argument("--cwd", type=Path)
     p.add_argument("--strip-common", action="store_true")
 
@@ -116,6 +122,9 @@ def select(item):
             accept = accept and all(fnmatch(item.path, e) for e in args.filter)
 
         accept = accept and not any(fnmatch(item.path, e) for e in args.exclude)
+
+        accept = accept and not any(fnmatch(item.code, i) for i in args.ignore)
+
         return accept
 
     items = list(filter(select, items))

CI/clang_tidy/requirements.txt

@@ -6,7 +6,7 @@
 #
 appdirs==1.4.4
     # via fs
-codereport==0.3.0
+codereport==0.3.2
     # via -r CI/clang_tidy/requirements.in
 commonmark==0.9.1
     # via rich

CI/clang_tidy/run_clang_tidy.sh

@@ -6,4 +6,3 @@ export NINJA_STATUS="[ninja][%f/%t] "
 pushd $build_dir
 ninja | grep -v '\[ninja\]'
 popd
-

CI/merge_hashes.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+import argparse
+
+p = argparse.ArgumentParser()
+p.add_argument("output")
+p.add_argument("files", nargs="+")
+
+args = p.parse_args()
+
+items = {}
+
+for file in args.files:
+    with open(file) as fh:
+        for line in fh:
+            key, value = line.split(":", 1)
+            items[key.strip()] = value.strip()
+
+with open(args.output, "w") as fh:
+    for key, value in items.items():
+        fh.write(f"{key}: {value}\n")

CI/physmon/comment_template.md

@@ -1,27 +1,30 @@
 ## :bar_chart: Physics performance monitoring for {{ commit }}
 {% if has_errors %}
-> :red_square: **ERROR** The result has missing elements! 
+> :red_square: **ERROR** The result has missing elements!
 > This is likely a physmon job failure
 {% endif %}
 
 [Full report]({{ url }}/)
-CKF: {{ make_url("seeded", "ckf_seeded.html") }}, {{ make_url("truth smeared", "ckf_truth_smeared.html") }}, {{ make_url("truth estimated", "ckf_truth_estimated.html") }}
-IVF: {{ make_url("seeded", "ivf_seeded.html") }}, {{ make_url("truth smeared", "ivf_truth_smeared.html") }}, {{ make_url("truth estimated", "ivf_truth_estimated.html") }}
-{{ make_url("Ambiguity resolution", "ambi_seeded.html") }}
+Seeding: {{ make_url("seeded", "seeding_seeded.html") }}, {{ make_url("truth estimated", "seeding_truth_estimated.html") }}, {{ make_url("orthogonal", "seeding_orthogonal.html") }}
+CKF: {{ make_url("seeded", "ckf_seeded.html") }}, {{ make_url("truth smeared", "ckf_truth_smeared.html") }}, {{ make_url("truth estimated", "ckf_truth_estimated.html") }}, {{ make_url("orthogonal", "ckf_orthogonal.html") }}
+IVF: {{ make_url("seeded", "ivf_seeded.html") }}, {{ make_url("truth smeared", "ivf_truth_smeared.html") }}, {{ make_url("truth estimated", "ivf_truth_estimated.html") }}, {{ make_url("orthogonal", "ivf_orthogonal.html") }}
+Ambiguity resolution: {{ make_url("seeded", "ambi_seeded.html") }}, {{ make_url("orthogonal", "ambi_orthogonal.html") }}
 {{ make_url("Truth tracking", "truth_tracking.html") }}
+{{ make_url("Truth tracking (GSF)", "gsf.html")}}
 
 ### Vertexing {{ "" if all_exist(
     "vertexing_mu_scan.pdf", 
     "ivf_seeded_plots",
     "ivf_truth_smeared_plots",
     "ivf_truth_estimated_plots",
+    "ivf_orthogonal_plots",
 ) else ":x: "}}
 
 {% call detail_block("Vertexing vs. mu", "vertexing_mu_scan.pdf") %}
 {{ make_image("vertexing_mu_scan.pdf", 350) }}
 {% endcall %}
 
-{% for mode in ["seeded", "truth_smeared", "truth_estimated"] %}
+{% for mode in ["seeded", "truth_smeared", "truth_estimated", "orthogonal"] %}
 
 {% call detail_block("IVF "+mode, "ivf_"+mode+"_plots") %}
 
@@ -40,14 +43,37 @@ IVF: {{ make_url("seeded", "ivf_seeded.html") }}, {{ make_url("truth smeared", "
 
 {% endfor %}
 
+### Seeding {{ "" if all_exist(
+    "seeding_seeded_plots",
+    "seeding_truth_estimated_plots",
+    "seeding_orthogonal_plots",
+) else ":x: "}}
+
+{% for mode in ["seeded", "truth_estimated", "orthogonal"] %}
+
+{% call detail_block("Seeding "+mode, "seeding_"+mode+"_plots") %}
+
+{% for url in [
+    "trackeff_vs_eta.pdf",
+    "trackeff_vs_pT.pdf",
+    "nDuplicated_vs_eta.pdf",
+    "nDuplicated_vs_pT.pdf",
+] -%}
+{{- make_image("seeding_"+mode+"_plots/"+url, "50%") -}}
+{%- endfor %}
+
+{% endcall %}
+
+{% endfor %}
 
 ### CKF {{ "" if all_exist(
     "ckf_seeded_plots",
     "ckf_truth_smeared_plots",
     "ckf_truth_estimated_plots",
+    "ckf_orthogonal_plots",
 ) else ":x: "}}
 
-{% for mode in ["seeded", "truth_smeared", "truth_estimated"] %}
+{% for mode in ["seeded", "truth_smeared", "truth_estimated", "orthogonal"] %}
 
 {% call detail_block("CKF "+mode, "ckf_"+mode+"_plots") %}
 
@@ -79,7 +105,7 @@ IVF: {{ make_url("seeded", "ivf_seeded.html") }}, {{ make_url("truth smeared", "
 
 {% endcall %}
 
-### Truth tracking {{ "" if exists("truth_tracking_plots") else ":x: "}}
+### Truth tracking (Kalman Filter) {{ "" if exists("truth_tracking_plots") else ":x: "}}
 
 {% call detail_block("Truth tracking", "truth_tracking_plots") %}
 
@@ -97,3 +123,18 @@ IVF: {{ make_url("seeded", "ivf_seeded.html") }}, {{ make_url("truth smeared", "
 {%- endfor %}
 
 {% endcall %}
+
+### Truth tracking (GSF) {{ "" if exists("truth_tracking_plots") else ":x: "}}
+
+{% call detail_block("Truth tracking", "truth_tracking_plots") %}
+
+{% for url in [
+    "pull_d0.pdf",
+    "res_d0.pdf",
+    "pull_qop.pdf",
+    "res_qop.pdf",
+] -%}
+{{- make_image("gsf_plots/"+url, "50%") -}}
+{%- endfor %}
+
+{% endcall %}

CI/physmon/gsf.yml

@@ -0,0 +1,13 @@
+checks:
+  "*":
+    Chi2Test:
+      threshold: 0.01
+    KolmogorovTest:
+      threshold: 0.68
+    RatioCheck:
+      threshold: 3
+    ResidualCheck:
+      threshold: 3
+    IntegralCheck:
+      threshold: 3
+

CI/physmon/phys_perf_mon.sh

@@ -44,6 +44,16 @@ function full_chain() {
     fi
     echo $config
 
+    if [ $suffix != truth_smeared ]; then
+	    run \
+  	      $outdir/performance_seeding_hists_${suffix}.root \
+    	    $refdir/performance_seeding_hists_${suffix}.root \
+      	  --title "Seeding ${suffix}" \
+        	-c $config \
+        	-o $outdir/seeding_${suffix}.html \
+        	-p $outdir/seeding_${suffix}_plots
+    fi
+
     run \
         $outdir/performance_ckf_${suffix}.root \
         $refdir/performance_ckf_${suffix}.root \
@@ -71,6 +81,15 @@ function full_chain() {
 full_chain truth_smeared
 full_chain truth_estimated
 full_chain seeded
+full_chain orthogonal
+
+run \
+    $outdir/performance_gsf.root \
+    $refdir/performance_gsf.root \
+    --title "Truth tracking (GSF)" \
+    -c CI/physmon/gsf.yml \
+    -o $outdir/gsf.html \
+    -p $outdir/gsf_plots
 
 run \
     $outdir/performance_truth_tracking.root \
@@ -86,13 +105,13 @@ run \
     --title "Ambisolver seeded" \
     -o $outdir/ambi_seeded.html \
     -p $outdir/ambi_seeded_plots
-
+    
 run \
-    $outdir/acts_analysis_residuals_and_pulls.root \
-    $refdir/acts_analysis_residuals_and_pulls.root \
-    --title "analysis_residuals_and_pulls" \
-#    -o $outdir/analysis_residuals_and_pulls.html \
-#    -p $outdir/analysis_residuals_and_pulls
+    $outdir/performance_ambi_orthogonal.root \
+    $refdir/performance_ambi_orthogonal.root \
+    --title "Ambisolver orthogonal" \
+    -o $outdir/ambi_orthogonal.html \
+    -p $outdir/ambi_orthogonal_plots
 
 Examples/Scripts/vertex_mu_scan.py \
     $outdir/performance_vertexing_*mu*.root \