Merge branch 'main' into exorcise_lv

Author: Moelf

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Keep dependencies for GitHub Actions up-to-date
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      interval: 'weekly'

.github/workflows/CI.yml

@@ -26,16 +26,16 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
             file: lcov.info
             token: ${{ secrets.codecov_token }}

docs/README.md

@@ -0,0 +1,51 @@
+# Generating and Previewing Documentation
+
+## Adding Documentation
+
+`Documenter.jl` is used to generate package documentation. 
+
+The general guidelines are to have documentation split into meaningful sections,
+none of which are too long. If a new functionality is added then create a new
+documentation page in `src`. Then map that markdown file to a section in the
+documentation in `make.jl` in the `pages` map.
+
+## Previewing Documentation
+
+From the `docs` directory:
+
+```julia
+julia --project
+               _
+   _       _ _(_)_     |  Documentation: https://docs.julialang.org
+  (_)     | (_) (_)    |
+   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
+  | | | | | | |/ _` |  |
+  | | |_| | | | (_| |  |  Version 1.11.1 (2024-10-16)
+ _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
+|__/                   |
+
+julia> include("make.jl")
+[ Info: SetupBuildDirectory: setting up build directory.
+[ Info: Doctest: running doctests.
+[ Info: ExpandTemplates: expanding markdown templates.
+[ Info: CrossReferences: building cross-references.
+[ Info: CheckDocument: running document checks.
+[ Info: Populate: populating indices.
+[ Info: RenderDocument: rendering document.
+[ Info: HTMLWriter: rendering HTML pages.
+┌ Warning: Generated HTML over size_threshold_warn limit: lib/internal.md
+│     Generated file size: 128.16 (KiB)
+│     size_threshold_warn: 100.0 (KiB)
+│     size_threshold:      200.0 (KiB)
+│     HTML file:           lib/internal/index.html
+└ @ Documenter.HTMLWriter ~/.julia/packages/Documenter/C1XEF/src/html/HTMLWriter.jl:1828
+[ Info: Automatic `version="0.4.3"` for inventory from ../Project.toml
+┌ Warning: Documenter could not auto-detect the building environment. Skipping deployment.
+└ @ Documenter ~/.julia/packages/Documenter/C1XEF/src/deployconfig.jl:76
+
+julia> using LiveServer
+
+julia> LiveServer.serve(dir="build/")
+✓ LiveServer listening on http://localhost:8000/ ...
+  (use CTRL+C to shut down)
+```

examples/instrumented-jetreco.jl

@@ -59,12 +59,12 @@ function profile_code(profile, jet_reconstruction, events, niters; R = 0.4, p =
             """)
 end
 """
-Top level call funtion for demonstrating the use of jet reconstruction
+Top level call function for demonstrating the use of jet reconstruction
 
 This uses the "jet_reconstruct" wrapper, so algorithm switching
 happens inside the JetReconstruction package itself.
 
-Some other ustilities are also supported here, such as profiling and
+Some other utilities are also supported here, such as profiling and
 serialising the reconstructed jet outputs.
 """
 function jet_process(events::Vector{Vector{T}};

examples/jetreco.jl

@@ -16,7 +16,7 @@ using JetReconstruction
 include(joinpath(@__DIR__, "parse-options.jl"))
 
 """
-Top level call funtion for demonstrating the use of jet reconstruction
+Top level call function for demonstrating the use of jet reconstruction
 
 This uses the "jet_reconstruct" wrapper, so algorithm switching
 happens inside the JetReconstruction package itself.

examples/parse-options.jl

@@ -1,5 +1,5 @@
 """
-Add `parse_item` code for interpeting `JetAlgorithm.Algorithm` and `RecoStrategy.Strategy` types
+Add `parse_item` code for interpreting `JetAlgorithm.Algorithm` and `RecoStrategy.Strategy` types
 from the command line.
 """
 

ext/JetVisualisation.jl

@@ -52,8 +52,8 @@ end
     jetsplot(objects, idx_arrays; barsize_phi=0.1, barsize_eta=0.1, colormap=:glasbey_hv_n256, Module=Main)
 
 Plots a 3d bar chart that represents jets. Takes an `objects` array of objects
-to display and `idx_arrays`, an array of arrays with indeces, where
-`idx_arrays[i]` gives indeces of `objects` that form the jet number `i`. This
+to display and `idx_arrays`, an array of arrays with indices, where
+`idx_arrays[i]` gives indices of `objects` that form the jet number `i`. This
 function's signature might not be the most practical for the current version of
 the JetReconstruction.jl package, as it has been written during the early stage
 of development. There is now an overload of it that takes a `ClusterSequence`
@@ -225,7 +225,7 @@ function JetReconstruction.animatereco(cs::ClusterSequence, filename;
     merge_steps = JetReconstruction.merge_steps(cs)
     jet_ranks = JetReconstruction.jet_ranks(cs)
 
-    # End point of the catagorical color map
+    # End point of the categorical color map
     # (How to get this programmatically from the CM Symbol?)
     colormap_end = 256
 

src/ClusterSequence.jl

@@ -187,7 +187,7 @@ add_step_to_history!(clusterseq::ClusterSequence, parent1, parent2, jetp_index,
     # retry the clustering with a different strategy.
     @assert parent1 >= 1
     if clusterseq.history[parent1].child != Invalid
-        error("Internal error. Trying to recombine an object that has previsously been recombined. Parent " *
+        error("Internal error. Trying to recombine an object that has previously been recombined. Parent " *
               string(parent1) * "'s child index " *
               string(clusterseq.history[parent1].child) * ". Parent jet index: " *
               string(clusterseq.history[parent1].jetp_index) * ".")
@@ -198,7 +198,7 @@ add_step_to_history!(clusterseq::ClusterSequence, parent1, parent2, jetp_index,
 
     if parent2 >= 1
         clusterseq.history[parent2].child == Invalid ||
-            error("Internal error. Trying to recombine an object that has previsously been recombined.  Parent " *
+            error("Internal error. Trying to recombine an object that has previously been recombined.  Parent " *
                   string(parent2) * "'s child index " *
                   string(clusterseq.history[parent1].child) * ". Parent jet index: " *
                   string(clusterseq.history[parent2].jetp_index) * ".")
@@ -363,7 +363,7 @@ Return the number of exclusive jets of a ClusterSequence that are above a certai
 
 # Arguments
 - `clusterseq::ClusterSequence`: The `ClusterSequence` object containing the clustering history.
-- `dcut::AbstractFloat`: The maximum calue for the distance parameter in the reconstruction.
+- `dcut::AbstractFloat`: The maximum value for the distance parameter in the reconstruction.
 
 # Returns
 The number of exclusive jets in the `ClusterSequence` object.
@@ -502,7 +502,7 @@ based on a given iteration number in the reconstruction.
 
 # Arguments
 - `cs::ClusterSequence`: The `ClusterSequence` object to update.
-- `ranks`: The ranks of the original clusters, that are inherited by peudojets
+- `ranks`: The ranks of the original clusters, that are inherited by pseudojets
  during the reconstruction process.
 - `iteration=0`: The iteration number to consider for updating the
   reconstruction state (0 represents the initial state).

src/GenericAlgo.jl

@@ -33,10 +33,10 @@ these methods are already predefined in the `JetReconstruction` namespace.
 The `recombine` argument is the function used to merge pairs of particles. The
 default is simply `+(jet1,jet2)`, i.e. 4-momenta addition or the *E*-scheme.
 
-## Consitency of `p`, `algorithm` and `R` arguments
+## Consistency of `p`, `algorithm` and `R` arguments
 If an algorithm is explicitly specified the `p` value should be consistent with
 it or `nothing`. If the algorithm is one where `p` can vary, then it has to be
-given, along with the algorithm.``
+given, along with the algorithm.
 
 If the `p` parameter is passed and `algorithm=nothing`, then pp-type
 reconstruction is implied (i.e., AntiKt, CA, Kt or GenKt will be used,
@@ -66,7 +66,7 @@ function jet_reconstruct(particles; p::Union{Real, Nothing} = -1, R = 1.0,
     if (algorithm === nothing) || is_pp(algorithm)
         # We assume a pp reconstruction
         if strategy == RecoStrategy.Best
-            # The breakpoint of ~80 is determined empirically on e+e- -> H and 0.5TeV pp -> 5GeV jets
+            # The breakpoint of ~80 is determined empirically on e+e- -> H and 0.5 TeV pp -> 5 GeV jets
             alg = length(particles) > 80 ? tiled_jet_reconstruct : plain_jet_reconstruct
         elseif strategy == RecoStrategy.N2Plain
             alg = plain_jet_reconstruct

src/HepMC3.jl

@@ -71,7 +71,7 @@ Particle{T}() where {T} = Particle(LorentzVector{T}(0.0, 0.0, 0.0, 0.0), 0, 0, 0
 """ Read a [HepMC3](https://doi.org/10.1016/j.cpc.2020.107310) ascii file.
 
     Each event is passed to the provided function f as a vector of Particles. A
-    maximum number of events to read (value -1 to read all availble events) and
+    maximum number of events to read (value -1 to read all available events) and
     a number of events to skip at the beginning of the file can be provided.
 """