From b0b63d21c97b83debab48af0f35ef3bd58d8b00c Mon Sep 17 00:00:00 2001 From: Jamie Gooding Date: Tue, 17 Sep 2024 14:07:21 +0200 Subject: [PATCH 1/6] Add 'rootcp' ROOT CLI tool --- phys/root/rootcp/environment.linux-64.pin.txt | 274 ++++++++++++++++++ phys/root/rootcp/environment.yaml | 4 + phys/root/rootcp/meta.yaml | 12 + phys/root/rootcp/test/Snakefile | 12 + phys/root/rootcp/test/ntuple0.root | Bin 0 -> 9906 bytes phys/root/rootcp/wrapper.py | 12 + 6 files changed, 314 insertions(+) create mode 100644 phys/root/rootcp/environment.linux-64.pin.txt create mode 100644 phys/root/rootcp/environment.yaml create mode 100644 phys/root/rootcp/meta.yaml create mode 100644 phys/root/rootcp/test/Snakefile create mode 100644 phys/root/rootcp/test/ntuple0.root create mode 100644 phys/root/rootcp/wrapper.py diff --git a/phys/root/rootcp/environment.linux-64.pin.txt b/phys/root/rootcp/environment.linux-64.pin.txt new file mode 100644 index 0000000000..3953674f8d --- /dev/null +++ b/phys/root/rootcp/environment.linux-64.pin.txt @@ -0,0 +1,274 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23 +https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2024.3.11-h06a4308_0.conda#08529eb3504712baabcbda266a19feb7 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb 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b/phys/root/rootcp/environment.yaml new file mode 100644 index 0000000000..93f6ab8825 --- /dev/null +++ b/phys/root/rootcp/environment.yaml @@ -0,0 +1,4 @@ +channels: + - conda-forge +dependencies: + - ROOT >6.24.0 diff --git a/phys/root/rootcp/meta.yaml b/phys/root/rootcp/meta.yaml new file mode 100644 index 0000000000..5c60e90b8a --- /dev/null +++ b/phys/root/rootcp/meta.yaml @@ -0,0 +1,12 @@ +name: "rootcp" +description: Copy ROOT using the ROOT rootcp command line tool +url: https://github.com/root-project/root/blob/master/main/python/rootcp.py +authors: + - Jamie Gooding +input: + - ROOT file/object(s) target (to be copied) and destination. +output: + - > + single ROOT file containing copied target object(s). +params: + - extra: extra parameters to `rootcp` (see ROOT documentation, e.g. `-c` for compression levels) \ No newline at end of file diff --git a/phys/root/rootcp/test/Snakefile b/phys/root/rootcp/test/Snakefile new file mode 100644 index 0000000000..722f1dec45 --- 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z{lps8?=)>9r*me7aJoynZY42c;Gw|^`YD%XRQ2&k&X47GrCY||57-ZO507WFNtC0NZD)mj z9a;87*}`m>hlttBJXE_$!c)dw!1YuyA>i#X60s99i(UYqBEZjv<~49-u%vx|H+cI@ zoU?;0JF|&Gmhv*SWJQM8meOqNlYpjN7%TK$*p)iHUpmylvaE}WM=>f)-tFh7FfR-E znYUMB^nzc$0|jOc4UJI5PP-LLQM)fijEbW#1stbRXAFdPbA{}kZqKwlahypn<^iBD zyWKP2>w`28lC1feZ+=!SYZEnQEU6h>jwnpT7jOb(c=sZ zyY#t_QItyyfFxz6RT2~pSYpaA|bL+d*bghQL$EYW=tR8Jh5kp_glXuVh zboHrzFDjvQ&Jb>>a?!&OT?pOq$SB>GFtM$$kJ+>Re)HPYi3OC;nPmXTak6um}jYUv1m ztw`Ecq&hKIqXtq;&}#TSU;82s;=Fl<)MC_#Uxp4LP5~E(%-2;>{U35o4siafUoSJ> zhz1|@7EH!1pVMKcax~IQ^RMZPBin0C;S@}keOj+Ty4l$5k0jS%k7JrItKmH??YluE zIGjzaA^#8G>7RekUOl1z#CLjijOgmT Ic~e0D4KVa9y#N3J literal 0 HcmV?d00001 diff --git a/phys/root/rootcp/wrapper.py b/phys/root/rootcp/wrapper.py new file mode 100644 index 0000000000..770f543654 --- /dev/null +++ b/phys/root/rootcp/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("rootcp {extra} {snakemake.input} {snakemake.output} {log}") From 666b943a4fdc26e0947762ca992126b21cb15911 Mon Sep 17 00:00:00 2001 From: Jamie Gooding Date: Tue, 17 Sep 2024 14:12:08 +0200 Subject: [PATCH 2/6] Register 'rootcp' test in 'test.py' --- test.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/test.py b/test.py index 3ba1b9c4ea..e524482d5f 100644 --- a/test.py +++ b/test.py @@ -6852,6 +6852,14 @@ def test_root_filter_dict(): ) +@skip_if_not_modified +def test_root_rootcp(): + run( + "phys/root/rootcp", + ["snakemake", "--cores", "2", "--use-conda", "-F"], + ) + + @skip_if_not_modified def test_emu_abundance(): run( From cb16aeda9e65382b5832d44ee839a5ac00288756 Mon Sep 17 00:00:00 2001 From: Jamie Gooding Date: Tue, 17 Sep 2024 14:28:46 +0200 Subject: [PATCH 3/6] Add object input/output parameters --- phys/root/rootcp/meta.yaml | 6 ++++-- phys/root/rootcp/test/Snakefile | 1 + phys/root/rootcp/wrapper.py | 10 +++++++++- 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/phys/root/rootcp/meta.yaml b/phys/root/rootcp/meta.yaml index 5c60e90b8a..5674be6bba 100644 --- a/phys/root/rootcp/meta.yaml +++ b/phys/root/rootcp/meta.yaml @@ -1,5 +1,5 @@ name: "rootcp" -description: Copy ROOT using the ROOT rootcp command line tool +description: Copy ROOT file/object(s) using the ROOT rootcp command line tool url: https://github.com/root-project/root/blob/master/main/python/rootcp.py authors: - Jamie Gooding @@ -9,4 +9,6 @@ output: - > single ROOT file containing copied target object(s). params: - - extra: extra parameters to `rootcp` (see ROOT documentation, e.g. `-c` for compression levels) \ No newline at end of file + - extra: extra parameters to `rootcp` (see ROOT documentation, e.g. `-c` for compression levels) + - input_object_name: (optional) object in ROOT file to be copied. + - output_object_name: (optional) name of destination object to be copied to. \ No newline at end of file diff --git a/phys/root/rootcp/test/Snakefile b/phys/root/rootcp/test/Snakefile index 722f1dec45..b85cb054eb 100644 --- a/phys/root/rootcp/test/Snakefile +++ b/phys/root/rootcp/test/Snakefile @@ -4,6 +4,7 @@ rule rootcp: log: "logs/rootcp/rootcp.log", params: + input_object_name="TestTree", extra="--recreate", threads: 1 output: diff --git a/phys/root/rootcp/wrapper.py b/phys/root/rootcp/wrapper.py index 770f543654..b921d10dc9 100644 --- a/phys/root/rootcp/wrapper.py +++ b/phys/root/rootcp/wrapper.py @@ -9,4 +9,12 @@ extra = snakemake.params.get("extra", "") log = snakemake.log_fmt_shell() -shell("rootcp {extra} {snakemake.input} {snakemake.output} {log}") +object_in = snakemake.params.get("input_object_name", "") +if object_in: + object_in = ":" + object_in + +object_out = snakemake.params.get("output_object_name", "") +if object_out: + object_out = ":" + object_out + +shell("rootcp {extra} {snakemake.input}{object_in} {snakemake.output}{object_out} {log}") From 8442395e27cc010d00c4434cf311977561b4d2eb Mon Sep 17 00:00:00 2001 From: Jamie Gooding Date: Tue, 17 Sep 2024 14:31:45 +0200 Subject: [PATCH 4/6] Fixed formatting --- phys/root/rootcp/wrapper.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/phys/root/rootcp/wrapper.py b/phys/root/rootcp/wrapper.py index b921d10dc9..fc4f8335e8 100644 --- a/phys/root/rootcp/wrapper.py +++ b/phys/root/rootcp/wrapper.py @@ -17,4 +17,6 @@ if object_out: object_out = ":" + object_out -shell("rootcp {extra} {snakemake.input}{object_in} {snakemake.output}{object_out} {log}") +shell( + "rootcp {extra} {snakemake.input}{object_in} {snakemake.output}{object_out} {log}" +) From 8144a54764bd692386d77ea14176ce8f3d564aaf Mon Sep 17 00:00:00 2001 From: Jamie Gooding <74370983+GoodingJamie@users.noreply.github.com> Date: Tue, 17 Sep 2024 14:32:16 +0200 Subject: [PATCH 5/6] Update ROOT version in dependencies Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> --- phys/root/rootcp/environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/phys/root/rootcp/environment.yaml b/phys/root/rootcp/environment.yaml index 93f6ab8825..bfaef55f97 100644 --- a/phys/root/rootcp/environment.yaml +++ b/phys/root/rootcp/environment.yaml @@ -1,4 +1,4 @@ channels: - conda-forge dependencies: - - ROOT >6.24.0 + - ROOT =6.30.4 From 0a14defe533b6956c28150457180f78a2a171600 Mon Sep 17 00:00:00 2001 From: Jamie Gooding Date: Tue, 17 Sep 2024 15:05:59 +0200 Subject: [PATCH 6/6] Tidy up according to review --- phys/root/rootcp/wrapper.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/phys/root/rootcp/wrapper.py b/phys/root/rootcp/wrapper.py index fc4f8335e8..e0186ce4ef 100644 --- a/phys/root/rootcp/wrapper.py +++ b/phys/root/rootcp/wrapper.py @@ -7,15 +7,15 @@ from snakemake.shell import shell extra = snakemake.params.get("extra", "") -log = snakemake.log_fmt_shell() +log = snakemake.log_fmt_shell(stdout=True, stderr=True) object_in = snakemake.params.get("input_object_name", "") if object_in: - object_in = ":" + object_in + object_in = f":{object_in}" object_out = snakemake.params.get("output_object_name", "") if object_out: - object_out = ":" + object_out + object_out = f":{object_out}" shell( "rootcp {extra} {snakemake.input}{object_in} {snakemake.output}{object_out} {log}"