feat: Add wrapper for defining columns in TTree in ROOT (#2898)

Adds a wrapper for defining columns in TTree in [the ROOT software
package](https://root.cern.ch/). The ntuple ROOT files in the test are
from the test of the `hadd` wrapper.

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### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Anfeng Li <anfeng.li@cern.ch>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

phys/root/define_columns/environment.yaml

@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - ROOT=6.30.4

phys/root/define_columns/meta.yaml

@@ -0,0 +1,15 @@
+name: "define_columns"
+description: Define columns in a TTree using RDataFrame
+url: https://root.cern/doc/master/classROOT_1_1RDataFrame.html
+authors:
+  - Anfeng Li
+input:
+  - TTree ROOT file
+output:
+  - TTree ROOT file
+params:
+  - input_tree_name: name of the input TTree
+  - output_tree_name: name of the output TTree
+  - branches: branches to be defined, specified in the format of [["branch_name1", "definition_expression1"], ["branch_name2", "definition_expression2"]]. If not specified, no branch will be defined, i.e. just save the TTree.  (optional)
+  - redefine: list of branch names to be redefined. It must be defined in `params.branch` also. (optional)
+  - branches_to_save: list of branch names to be saved. If not specified, all branches of the input TTree will be saved. (optional)

phys/root/define_columns/test/Snakefile

@@ -0,0 +1,18 @@
+rule define_columns:
+    input:
+        "ntuple0.root",
+    output:
+        "ntuple0_output.root",
+    log:
+        "logs/define_columns/define_columns.log",
+    params:
+        input_tree_name="TestTree",
+        output_tree_name="TestTree",
+        branches=[
+            ["p2", "px * px + py * py + pz * pz"],
+            ["pt", "sqrt(px * px + py * py)"],
+        ],
+        redefine=["pt"],
+    threads: 2
+    wrapper:
+        "master/phys/root/define_columns"

phys/root/define_columns/wrapper.py

@@ -0,0 +1,28 @@
+__author__ = "Anfeng Li"
+__copyright__ = "Copyright 2024, Anfeng Li"
+__email__ = "anfeng.li@cern.ch"
+__license__ = "MIT"
+
+
+import ROOT
+
+ROOT.EnableImplicitMT(snakemake.threads)
+
+redefine_list = snakemake.params.get("redefine", [])
+branches = snakemake.params.get("branches", [])
+branches_to_save = snakemake.params.get("branches_to_save", None)
+
+df = ROOT.RDataFrame(snakemake.params.input_tree_name, snakemake.input[0])
+for branch_name, branch_definition in branches:
+    if branch_name in redefine_list:
+        df = df.Redefine(branch_name, branch_definition)
+    else:
+        df = df.Define(branch_name, branch_definition)
+if branches_to_save is not None:
+    df.Snapshot(
+        snakemake.params.output_tree_name,
+        snakemake.output[0],
+        branches_to_save,
+    )
+else:
+    df.Snapshot(snakemake.params.output_tree_name, snakemake.output[0])

test.py

@@ -6484,6 +6484,14 @@ def test_root_hadd():
     )
 
 
+@skip_if_not_modified
+def test_root_define_columns():
+    run(
+        "phys/root/define_columns",
+        ["snakemake", "--cores", "2", "--use-conda", "-F"],
+    )
+
+
 @skip_if_not_modified
 def test_emu_abundance():
     run(