treewide: fix codespell issues (#1724)

Fixes codespell:
https://results.pre-commit.ci/run/github/512187504/1738308139.YIrmyPXzSpaFmHjIt5yjgA

Enable calorimeter hit merging by functions (#1668)

### Briefly, what does this PR introduce?

This PR extends the functionality of the `CalorimeterHitsMerger`
algorithm. Previously, reconstructed hits could only be merged across a
given field of the readout of a calorimeter. This presents a challenge
for calorimeters such as the Barrel HCal where

1. our readout has no segmentation beyond just eta  & phi, and
2. it could be useful to study the response of the detector as a
function of how many readout channels we gang together after
reconstruction.

This PR addresses this point by utilizing the `EvaluatorSvc` in a manner
similar to the `adjacencyMatrix`, `peakNeighbourhoodMatrix` of the
`CalorimeterIslandClustering` and the `sampFrac` of
`CalorimeterHitReco`. Now the user has the ability to specify an
(almost) arbitrarily complex transformation for a specific field of the
readout via the `fieldTransformations` parameter, which defines both the
field to transform and the function to map the indices of that field
onto the desired reference indices.

For example:

```
app->Add(new JOmniFactoryGeneratorT<CalorimeterHitsMerger_factory>(
  "HcalBarrelMergedHits", {"HcalBarrelRecHits"}, {"HcalBarrelMergedHits"},
  {
    .readout = "HcalBarrelHits",
    .fieldTransformations = {"phi:phi-(5*((phi/5)-floor(phi/5)))"}
  },
  app   // TODO: Remove me once fixed
));
```

Here, the `HcalBarrelMergedHits` collection will merge 5 hits (i.e.
scintillator tiles for the BHCal) adjacent in phi into a one with the
position and cellID of the 1st of the 5, and no hits will be merged
along eta.

The previous behavior of the algorithm can be recovered by simply
specifying the index to be mapped onto. For example:
```
app->Add(new JOmniFactoryGeneratorT<CalorimeterHitsMerger_factory>(
  "HcalEndcapNMergedHits", {"HcalEndcapNRecHits"}, {"HcalEndcapNMergedHits"},
  {
    .readout = "HcalEndcapNHits",
    .fieldTransformations = {"layer:4", "slice:0"}
  },
  app   // TODO: Remove me once fixed
));
```

An example script of to change a transformation (and how to update the
adjacency matrix accordingly) from the command-line is provided in the
snippets repo
[here](https://github.com/eic/snippets/blob/main/Calorimetery/CaloDebugTools/UtilityScripts/RunEICReconWithTileMerging.rb).

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [x] New feature (issue #1669 )
- [ ] Documentation update
- [ ] Other: __

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [x] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?

No.

### Does this PR change default behavior?

No.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Dmitry Kalinkin <[email protected]>

feat(ci): runs-on: ubuntu-latest -> ubuntu-22.04 (#1687)

### Briefly, what does this PR introduce?
This PR updates the target operating system for CI jobs, from
ubuntu-latest to a more explicit ubuntu-22.04. This is in part to avoid
the automatic update of implicit ubuntu-latest that will break
everything (#1686), and in part
because it makes sense to be explicit about the target operating system.

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [x] New feature (issue
actions/runner-images#10636)
- [ ] Documentation update
- [ ] Other: __

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [ ] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?
No.

### Does this PR change default behavior?
No.

Update of the BIC sampling fractions (#1664)

### Briefly, what does this PR introduce?
Sampling fractions of the BIC ScFi and imaging layers have been updated
using 5 GeV electrons generated at eta = 0. Only the constant sampling
fractions are provided this time. The energy- and eta-dependent ones
will be provided next time referring to the comments on the last BIC
sampling fraction PR.

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [x] New feature (issue #__)
- [ ] Documentation update
- [ ] Other: __

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [x] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?
No

### Does this PR change default behavior?
No

[Backport v1.18] Fix RP reco bug in p_y (#1636)

# Description
Backport of #1634 to `v1.18`.

Co-authored-by: Alex Jentsch <[email protected]>

Fix JANA2-related deprecation warnings and TODOs (#1622)

### Briefly, what does this PR introduce?

This cleans up the EICrecon compilation output by fixing some
deprecation warnings coming from JANA2. It also removes some
JANA2-related TODO comments. It updates a test case to no longer use a
template method that hasn't been deprecated, but is about to be.

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [ ] New feature (issue #__)
- [ ] Documentation update
- [x] Other: Fixes deprecation warnings

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [ ] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?
No

### Does this PR change default behavior?
No

added PrimaryVertices factory (subCollection of CentralTrackVertices) (…

…#1609)

### Briefly, what does this PR introduce?


### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [X] New feature (issue #__)
- [ ] Documentation update
- [ ] Other: __

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [ ] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?

### Does this PR change default behavior?

---------

Co-authored-by: Xin Dong <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Xin Dong <[email protected]>
Co-authored-by: Dmitry Kalinkin <[email protected]>

lowered the amount of distance neighbor hits in topoclustering in the…

… ZDC (#1532)

### Briefly, what does this PR introduce?
Redefines neighboring subcell hits in the ZDC (in the context of topo
clustering) to be the nearest neighbors only for hits in the same layer,
and the same position for hits in adjacent layers. This change reduces
the cases where showers from different particles are merged into a
single cluster

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [ ] New feature (issue #__)
- [ ] Documentation update
- [X] Other: parameter tweak

### Please check if this PR fulfills the following:
- [X] Tests for the changes have been added
- [X] Documentation has been added / updated
- [X] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?
no.  
### Does this PR change default behavior?
yes.  Changes the default behavior of the topo clustering in the ZDC

---------

Co-authored-by: Dmitry Kalinkin <[email protected]>
Co-authored-by: Derek M Anderson <[email protected]>

Add one-to-one relation with raw tracker/calorimeter hit for reconstr…

…ucted tracker/calorimeter hit (#1535)

### Briefly, what does this PR introduce?
Add one-to-one relation with raw tracker/calorimeter hit for
reconstructed tracker/calorimeter hit. Contingent on
eic/EDM4eic#86.

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [ ] New feature (issue #__)
- [ ] Documentation update
- [ ] Other: __

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [ ] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?

### Does this PR change default behavior?

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Dmitry Kalinkin <[email protected]>
Co-authored-by: Wouter Deconinck <[email protected]>

treewide: add missing AlgorithmsInit_service for particleSvc (#1524)

More of changes like #1522.
Closes: #1523