feat: Add wrapper for ROOT hadd (#2785)

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Adds a wrapper for the ``hadd`` utility in the ROOT software package
used primarily in High Energy Physics. Since this is the first physics
wrapper, the top-level category ``phys`` is also added here.

### 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: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

phys/root/hadd/environment.yaml

@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - ROOT >6.24.0

phys/root/hadd/meta.yaml

@@ -0,0 +1,12 @@
+name: "hadd"
+description: Combine ntuples using the ROOT hadd command line tool
+url: https://root.cern/doc/master/hadd_8cxx.html
+authors:
+  - Jamie Gooding
+input:
+  - ROOT files to be combined.
+output:
+  - >
+    single ROOT file containing contents of input files.
+params:
+  - extra: extra parameters to `hadd` (see ROOT documentation, e.g. `-f[0-9]` for compression levels)

phys/root/hadd/test/Snakefile

@@ -0,0 +1,12 @@
+rule hadd:
+    input:
+        expand("ntuple{n}.root", n=range(3)),
+    log:
+        "logs/hadd/hadd.log",
+    params:
+        extra="-f5",
+    threads: 2
+    output:
+        "ntuple.root",
+    wrapper:
+        "master/phys/root/hadd"

phys/root/hadd/wrapper.py

@@ -0,0 +1,12 @@
+__author__ = "Jamie Gooding"
+__copyright__ = "Copyright 2024, Jamie Gooding"
+__email__ = "jamie.gooding@cern.ch"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell()
+
+shell("hadd -j {snakemake.threads} {extra} {snakemake.output} {snakemake.input} {log}")

test.py

@@ -6439,3 +6439,10 @@ def test_tmb_pytmb():
         "bio/tmb/pytmb",
         ["snakemake", "--cores", "1", "--use-conda", "-F"],
     )
+
+@skip_if_not_modified
+def test_root_hadd():
+    run(
+        "phys/root/hadd",
+        ["snakemake", "--cores", "2", "--use-conda", "-F"],
+    )