Merge branch 'main' into gx2f-actor-shift-more

.github/pull_request_template.md

@@ -8,26 +8,26 @@ REQUEST.
 
     The prefix must be one of:
 
-    - `fix`: for a bugfix
-    - `feat`: for a new feature
-    - `refactor`: for an improvement of an existing feature
-    - `perf`, `test`: for performance- or test-related changes
-    - `docs`: for documentation-related changes
-    - `build`, `ci`, `chore`: as appropriated for infrastructure changes
+  - `fix`: for a bugfix
+  - `feat`: for a new feature
+  - `refactor`: for an improvement of an existing feature
+  - `perf`, `test`: for performance- or test-related changes
+  - `docs`: for documentation-related changes
+  - `build`, `ci`, `chore`: as appropriated for infrastructure changes
 
 - [ ] Does this modify the public API as defined in `docs/versioning.rst`?
 
-    - [ ] Does the PR title contain a `!` to indicate a breaking change?
-    - [ ] Is there section starting with `BREAKING CHANGE:` in the PR body
+  - [ ] Does the PR title contain a `!` to indicate a breaking change?
+  - [ ] Is there section starting with `BREAKING CHANGE:` in the PR body
           that explains the breaking change?
 
 - [ ] Is the PR ready to be merged?
 
-    - [ ] If not: is it marked as a draft PR?
+  - [ ] If not: is it marked as a draft PR?
 
 - [ ] Does this PR close an existing issue?
 
-    - [ ] Is the issue correctly linked so it will be automatically closed
+  - [ ] Is the issue correctly linked so it will be automatically closed
         upon successful merge (See closing keywords link in the sidebar)?
 
 - The CI will initially report a missing milestone. One of the maintainers will
@@ -36,6 +36,6 @@ REQUEST.
 - An automated workflow will assign labels based on changed files, and whether
   or not reference files were changed. These do not have to be set manually.
 
-- If you push updates, and you know they will be superceded later on, consider adding
+- If you push updates, and you know they will be superseded later on, consider adding
   `[skip ci]` in the commit message. This will instruct the CI system not to run any
   jobs on this commit.

.pre-commit-config.yaml

@@ -28,3 +28,61 @@ repos:
     hooks:
     - id: gersemi
       args: ["-i", "--no-warn-about-unknown-commands"]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    - id: codespell
+      args: [
+        "-S", "*.ipynb,*.onnx,_build,*.svg",
+        "-I", "./CI/codespell_ignore.txt"
+      ]
+      exclude: ^CI/.*$
+
+  - repo: local
+    hooks:
+    - id: license
+      name: license
+      language: system
+      entry: CI/check_license.py
+      files: \.(cpp|hpp|ipp|cu|cuh)$
+
+  - repo: local
+    hooks:
+    - id: include_guards
+      name: include_guards
+      language: system
+      entry: CI/check_include_guards.py --fail-global
+      files: \.hpp$
+
+  - repo: local
+    hooks:
+    - id: pragma_once
+      name: pragma_once
+      language: system
+      entry: CI/check_pragma_once.sh
+      files: \.hpp$
+
+  - repo: local
+    hooks:
+    - id: type_t
+      name: type_t
+      language: system
+      entry: CI/check_type_t.py
+      files: \.(cpp|hpp|ipp|cu|cuh)$
+
+  - repo: local
+    hooks:
+    - id: boost_test
+      name: boost_test
+      language: system
+      entry: CI/check_boost_test_macro.sh
+      files: ^Tests\/.*\.(cpp|hpp|ipp|cu|cuh)$
+
+  - repo: local
+    hooks:
+    - id: cmake_options
+      name: cmake_options
+      language: system
+      entry: docs/parse_cmake_options.py --write docs/getting_started.md
+      files: ^CMakeLists.txt$

CI/check_boost_test_macro.sh

@@ -1,14 +1,21 @@
 #!/bin/bash
 
+files="$@"
+
+if [ -z "$files" ]; then
+    files=$(find Tests -name "*.hpp" -or -name "*.cpp" -or -name "*.ipp")
+fi
+
 test_string="BOOST_TEST("
-grep $test_string -n -r Tests --include "*.cpp" --include "*.hpp" --include "*.ipp"
 
-status=$?
+ec=0
+for file in $files; do
+  grep -n "$test_string" "$file"
+  status=$?
+  if [ $status -ne 1 ]; then
+    echo "Found occurrences of '$test_string' in '$file'"
+    ec=1
+  fi
+done
 
-if [[ $status -eq 0 ]]; then
-  echo "Found occurrences of '$test_string'"
-  exit 1
-else
-  echo "Did not find occurrences of '$test_string'"
-  exit 0
-fi
+exit $ec

CI/check_include_guards.py

@@ -75,7 +75,7 @@ def main():
     input_help = """
 Input files: either file path, dir path (will glob for headers) or custom glob pattern
     """
-    p.add_argument("input", help=input_help.strip())
+    p.add_argument("input", nargs="+", help=input_help.strip())
     p.add_argument(
         "--fail-local", "-l", action="store_true", help="Fail on local include guards"
     )
@@ -90,15 +90,20 @@ def main():
 
     headers = []
 
-    if os.path.isfile(args.input):
-        headers = [args.input]
-    elif os.path.isdir(args.input):
-        patterns = ["**/*.hpp", "**/*.h"]
-        headers = sum(
-            [glob(os.path.join(args.input, p), recursive=True) for p in patterns], []
-        )
-    else:
-        headers = glob(args.input, recursive=True)
+    if len(args.input) == 1:
+        if os.path.isdir(args.input[0]):
+            patterns = ["**/*.hpp", "**/*.h"]
+            headers = sum(
+                [
+                    glob(os.path.join(args.input[0], p), recursive=True)
+                    for p in patterns
+                ],
+                [],
+            )
+        else:
+            headers = glob(args.input[0], recursive=True)
+    elif all([os.path.isfile(i) for i in args.input]):
+        headers = args.input
 
     valid = True
     nlocal = 0

CI/check_license.py

@@ -80,7 +80,7 @@ def check_git_dates(src):
 
 def main():
     p = argparse.ArgumentParser()
-    p.add_argument("input")
+    p.add_argument("input", nargs="+")
     p.add_argument(
         "--fix", action="store_true", help="Attempt to fix any license issues found."
     )
@@ -99,13 +99,13 @@ def main():
     args = p.parse_args()
     print(args.exclude)
 
-    if os.path.isdir(args.input):
+    if len(args.input) == 1 and os.path.isdir(args.input[0]):
         srcs = (
             str(
                 check_output(
                     [
                         "find",
-                        args.input,
+                        args.input[0],
                         "-iname",
                         "*.cpp",
                         "-or",
@@ -123,7 +123,7 @@ def main():
         )
         srcs = filter(lambda p: not p.startswith("./build"), srcs)
     else:
-        srcs = [args.input]
+        srcs = args.input
 
     year = int(datetime.now().strftime("%Y"))
 

CI/check_pragma_once.sh

@@ -2,7 +2,13 @@
 
 ec=0
 
-for file in $(find Core Examples Tests Plugins -name "*.hpp"); do
+files="$@"
+
+if [ -z "$files" ]; then
+    files=$(find Core Examples Tests Plugins -name "*.hpp")
+fi
+
+for file in $files; do
     res=$(grep -e "^[[:space:]]*#pragma once" $file)
     if [[ "$res" != "#pragma once" ]]; then
         ec=1

CI/check_type_t.py

@@ -48,48 +48,57 @@ def handle_file(file: Path, fix: bool, c_type: str) -> list[tuple[int, str]]:
 
 def main():
     p = argparse.ArgumentParser()
-    p.add_argument("input")
+    p.add_argument("input", nargs="+")
     p.add_argument("--fix", action="store_true", help="Attempt to fix C-style types.")
     p.add_argument("--exclude", "-e", action="append", default=[])
 
     args = p.parse_args()
 
     exit_code = 0
 
-    # walk over all files
-    for root, _, files in os.walk("."):
-        root = Path(root)
-        for filename in files:
-            # get the full path of the file
-            filepath = root / filename
-            if filepath.suffix not in (
-                ".hpp",
-                ".cpp",
-                ".ipp",
-                ".h",
-                ".C",
-                ".c",
-                ".cu",
-                ".cuh",
-            ):
-                continue
-
-            if any([fnmatch(str(filepath), e) for e in args.exclude]):
-                continue
-
-            for c_type in type_list:
-                changed_lines = handle_file(file=filepath, fix=args.fix, c_type=c_type)
-                if len(changed_lines) > 0:
-                    exit_code = 1
-                    print()
-                    print(filepath)
-                    for i, oline in changed_lines:
-                        print(f"{i}: {oline}")
-
-                        if github:
-                            print(
-                                f"::error file={filepath},line={i+1},title=Do not use C-style {c_type}::Replace {c_type} with std::{c_type}"
-                            )
+    inputs = []
+
+    if len(args.input) == 1 and os.path.isdir(args.input[0]):
+        # walk over all files
+        for root, _, files in os.walk(args.input[0]):
+            root = Path(root)
+            for filename in files:
+                # get the full path of the file
+                filepath = root / filename
+                if filepath.suffix not in (
+                    ".hpp",
+                    ".cpp",
+                    ".ipp",
+                    ".h",
+                    ".C",
+                    ".c",
+                    ".cu",
+                    ".cuh",
+                ):
+                    continue
+
+                if any([fnmatch(str(filepath), e) for e in args.exclude]):
+                    continue
+
+                inputs.append(filepath)
+    else:
+        for file in args.input:
+            inputs.append(Path(file))
+
+    for filepath in inputs:
+        for c_type in type_list:
+            changed_lines = handle_file(file=filepath, fix=args.fix, c_type=c_type)
+            if len(changed_lines) > 0:
+                exit_code = 1
+                print()
+                print(filepath)
+                for i, oline in changed_lines:
+                    print(f"{i}: {oline}")
+
+                    if github:
+                        print(
+                            f"::error file={filepath},line={i+1},title=Do not use C-style {c_type}::Replace {c_type} with std::{c_type}"
+                        )
 
     return exit_code
 

CI/codespell_ignore.txt

@@ -22,3 +22,5 @@ dthe
 dthe
 vart
 pixelx
+millepede
+dependees

CITATION.cff

@@ -23,7 +23,6 @@ authors:
   affiliation: Universite Paris-Saclay / CNRS/IN2P3
 - given-names: Robert
   family-names: Langenberg
-  affiliation: University of Massachussets
 - given-names: Corentin
   family-names: Allaire
   affiliation: CERN

CMakeLists.txt

@@ -90,7 +90,7 @@ option(ACTS_BUILD_DOCS "Build documentation" OFF)
 option(ACTS_SETUP_BOOST "Explicitly set up Boost for the project" ON)
 option(ACTS_SETUP_EIGEN3 "Explicitly set up Eigen3 for the project" ON)
 option(ACTS_BUILD_ODD "Build the OpenDataDetector" OFF)
-# profiling related optios
+# profiling related options
 option(ACTS_ENABLE_CPU_PROFILING "Enable CPU profiling using gperftools" OFF)
 option(ACTS_ENABLE_MEMORY_PROFILING "Enable memory profiling using gperftools" OFF)
 set(ACTS_GPERF_INSTALL_DIR "" CACHE STRING "Hint to help find gperf if profiling is enabled")
@@ -298,7 +298,7 @@ find_package(Filesystem REQUIRED)
 
 # the `<project_name>_VERSION` variables set by `setup(... VERSION ...)` have
 # only local scope, i.e. they are not accessible her for dependencies added
-# via `add_subdirectory`. this overrides the `project(...)` funcion for
+# via `add_subdirectory`. this overrides the `project(...)` function for
 # sub-projects such that the resulting `<project_name>_VERSION` has
 # global scope and is accessible within the main project later on.
 cmake_policy(SET CMP0048 NEW)

CONTRIBUTING.rst

@@ -220,7 +220,7 @@ bugfix should happen in a different branch. The recommended procedure
 for handling this situation is the following:
 
 #. Get into a clean state of your working directory on your feature
-   branch (either by commiting open changes or by stashing them).
+   branch (either by committing open changes or by stashing them).
 #. Checkout the branch the bugfix should be merged into (either *main*
    or *release/X.Y.Z*) and get the most recent version.
 #. Create a new branch for the bugfix.
@@ -238,7 +238,7 @@ Example: Backporting a feature or bugfix
 
 Suppose you have a bugfix or feature branch that is eventually going to
 be merged in ``main``. You might want to have the feature/bugfix
-avilable in a patch (say ``0.25.1``) tag. To to that, find the
+available in a patch (say ``0.25.1``) tag. To to that, find the
 corresponding release branch, for this example that would be
 ``release/v0.25.X``. You must create a dedicated branch that **only**
 contains the commits that relate to your feature/bugfix, otherwise the