WIP: Code cleanup (#205)

* update get-diff shell script

* add badge

* remove unneeded imports

* shell script formatting

* code cleanup

* Update zenodo release

README.md

@@ -3,8 +3,9 @@
 
 <p align="left">
 <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+<a href="https://app.codacy.com/gh/KIT-CMS/CROWN/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade"><img src="https://app.codacy.com/project/badge/Grade/681a25523b544d788155696eb829e38b"/></a>
 <a href="https://crown.readthedocs.io/en/latest/?badge=latest"><img alt="Documentation Status" src="https://readthedocs.org/projects/crown/badge/?version=latest"></a>
-<a href="https://doi.org/10.5281/zenodo.7181926"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7181926.svg" alt="DOI"></a>
+<a href="https://doi.org/10.5281/zenodo.8325327"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.8325327.svg" alt="DOI"></a>
 </p>
 
 ---

analysis_configurations/unittest/generate.py

@@ -1,8 +1,6 @@
-from os import path, makedirs
+from os import path
 import importlib
 from code_generation.code_generation import CodeGenerator
-from code_generation.friend_trees import FriendTreeConfiguration
-import inspect
 
 
 def run(args):

analysis_configurations/unittest/generate_friends.py

@@ -1,8 +1,6 @@
-from os import path, makedirs
+from os import path
 import importlib
 from code_generation.code_generation import CodeGenerator
-from code_generation.friend_trees import FriendTreeConfiguration
-import inspect
 
 
 def run(args):

analysis_configurations/unittest/producers/muon_sf_friends.py

@@ -1,5 +1,4 @@
 from ..quantities import output as q
-from ..quantities import nanoAOD as nanoAOD
 from code_generation.producer import Producer
 
 

analysis_configurations/unittest/unittest_friends.py

@@ -3,8 +3,6 @@
 from typing import List, Union
 import os
 from .producers import muon_sf_friends as muon_sf_friends
-from .producers import pairquantities as pairquantities
-from .producers import scalefactors as scalefactors
 from .quantities import output as q
 
 # from code_generation.configuration import Cnofiguration

checks/cpp-formatting.sh

@@ -2,7 +2,7 @@
 
 for FILENAME in $(find . -name "*.[h,c]xx");
 do
-    clang-format -i $FILENAME
+    clang-format -i "$FILENAME"
 done
 
 DIFF=$(git --no-pager diff)

checks/get-diff.sh

@@ -10,31 +10,31 @@ if [ -z "$analysis" ] || [ -z "$base_path" ] || [ -z "$result_dir" ]; then
 fi
 # create the result folder if it does not exist
 if [ ! -d "$result_dir" ]; then
-    mkdir -p $result_dir
+    mkdir -p "$result_dir"
 fi
 # go to the base_path
-cd $base_path
+cd "$base_path"
 base_diff=$result_dir/base_diff.patch
 commit_hash=$result_dir/base_commit_hash.txt
-touch $base_diff
+touch "$base_diff"
 for next in $(git ls-files --others --exclude-standard); do
-    git --no-pager diff --no-index /dev/null $next >>$base_diff
+    git --no-pager diff --no-index /dev/null "$next" >>"$base_diff"
 done
-git rev-parse HEAD >$commit_hash
+git rev-parse HEAD >"$commit_hash"
 
 # cd into the analysis directory
 analysis_path=$base_path/analysis_configurations/$analysis
 if [ -d "$analysis_path" ]; then
-    cd $analysis_path
+    cd "$analysis_path"
     analysis_diff=$result_dir/analysis_diff.patch
     analysis_commit=$result_dir/analysis_commit_hash.txt
     analysis_name=$result_dir/analysis_name.txt
-    touch $analysis_diff
+    touch "$analysis_diff"
     for next in $(git ls-files --others --exclude-standard); do
-        git --no-pager diff --no-index /dev/null $next >>$analysis_diff
+        git --no-pager diff --no-index /dev/null "$next" >>"$analysis_diff"
     done
-    git rev-parse HEAD >$analysis_commit
-    echo $analysis >$analysis_name
+    git rev-parse HEAD >"$analysis_commit"
+    echo "$analysis" >"$analysis_name"
 else
-    analysiscommit="not_found"
+    echo "ERROR: analysis directory does not exist"
 fi

checks/git-status.sh

@@ -8,7 +8,7 @@ if [ -z "$analysis" ] || [ -z "$basepath" ]; then
     exit 1
 fi
 # go to the basepath
-cd $basepath
+cd "$basepath"
 # get the status of the git repo and store it in a variable
 if output=$(git status --porcelain) && [ -z "$output" ]; then
     crown_is_clean="true"
@@ -19,9 +19,9 @@ fi
 # get the current commit hash and store it in a variable
 maingitcommit=$(git rev-parse HEAD)
 # cd into the analysis directory
-analysispath=$basepath/analysis_configurations/$analysis
+analysispath="$basepath/analysis_configurations/$analysis"
 if [ -d "$analysispath" ]; then
-    cd $analysispath
+    cd "$analysispath"
     # get the status of the git repo and store it in a variable
     if output=$(git status --porcelain) && [ -z "$output" ]; then
         analysis_is_clean="true"

checks/python-formatting.sh

@@ -4,11 +4,11 @@ FOUND_ISSUE=0
 
 for FILENAME in $(find . -name "*.py");
 do
-    black --check $FILENAME
+    black --check "$FILENAME"
     RETURN_VALUE=$?
     if [ $RETURN_VALUE -ne 0 ]
     then
-        black --diff $FILENAME 2> /dev/null
+        black --diff "$FILENAME" 2> /dev/null
         FOUND_ISSUE=1
     fi
 done

checks/setup_from_tarball.sh

@@ -9,47 +9,47 @@ if [ -z "$tarball" ]; then
 fi
 # create the checkout location if it does not exist
 if [ ! -d "$checkout_location" ]; then
-    mkdir -p $checkout_location
+    mkdir -p "$checkout_location"
 fi
 
 if [ -d "$tarball" ]; then
     echo "Using tarball folder $tarball"
     mkdir temp
-    cp -r $tarball temp/
-    tarball=$(realpath temp/$tarball)
+    cp -r "$tarball" temp/
+    tarball=$(realpath "temp/$tarball")
 # if tarball is a file, unpack it here
 elif [ -f "$tarball" ]; then
     echo "Using tarball file $tarball"
     mkdir temp
-    tar -xzf $tarball -C temp/
+    tar -xzf "$tarball" -C temp/
     tarball=$(realpath temp)
 else
     echo "ERROR: tarball must be a file or a folder"
     exit 1
 fi
 # go to the checkout location
-cd $checkout_location
+cd "$checkout_location"
 echo "Using temporary tarball copy in $tarball"
 # read the commit hashes from the diff folder in the tarball
-base_commit=$(cat $tarball/diff/base_commit_hash.txt)
-analysis_commit=$(cat $tarball/diff/analysis_commit_hash.txt)
-analysis_name=$(cat $tarball/diff/analysis_name.txt)
+base_commit=$(cat "$tarball/diff/base_commit_hash.txt")
+analysis_commit=$(cat "$tarball/diff/analysis_commit_hash.txt")
+analysis_name=$(cat "$tarball/diff/analysis_name.txt")
 
 # checkout the base repository with the commit hash
 git clone --recursive [email protected]:KIT-CMS/CROWN
 cd CROWN
-git checkout $base_commit
+git checkout "$base_commit"
 # apply the base diff
-git apply $tarball/diff/base_diff.patch
+git apply "$tarball/diff/base_diff.patch"
 # setup the analysis with the init script
-bash init.sh $analysis_name
+bash init.sh "$analysis_name"
 # checkout the analysis repository with the commit hash
-cd analysis_configurations/$analysis_name
-git checkout $analysis_commit
+cd "analysis_configurations/$analysis_name"
+git checkout "$analysis_commit"
 # apply the analysis diff
-git apply $tarball/diff/analysis_diff.patch
+git apply "$tarball/diff/analysis_diff.patch"
 # cleanup the temporary tarball
-rm -rf $tarball
+rm -rf "$tarball"
 echo "**************************************************************"
 echo "*  Setup from tarball finished. You can now run the analysis *"
 echo "**************************************************************"

include/SVFit/FastMTT.hxx

@@ -1,6 +1,9 @@
 #ifndef FastMTT_FastMTT_H
 #define FastMTT_FastMTT_H
 
+#include "Math/LorentzVector.h"
+#include "TBenchmark.h"
+#include "TMatrixD.h"
 #include <bitset>
 #include <string>
 #include <tuple>
@@ -18,10 +21,6 @@ class Functor;
 } // namespace ROOT
 class TVector2;
 
-#include "Math/LorentzVector.h"
-#include "TBenchmark.h"
-#include "TMatrixD.h"
-
 typedef ROOT::Math::LorentzVector<ROOT::Math::PxPyPzE4D<double>> LorentzVector;
 
 namespace fastMTT {

init.sh

@@ -58,16 +58,15 @@ if [ -z "$1" ]; then
 else
     if [[ "$1" == "tau" && ! -d "${SCRIPT_DIR}/analysis_configurations/tau" ]]; then
         echo "Cloning analysis tau into ${SCRIPT_DIR}/analysis_configurations/tau"
-        git clone [email protected]:KIT-CMS/TauAnalysis-CROWN.git ${SCRIPT_DIR}/analysis_configurations/tau
+        git clone [email protected]:KIT-CMS/TauAnalysis-CROWN.git "${SCRIPT_DIR}/analysis_configurations/tau"
     elif [[ "$1" == "earlyrun3" && ! -d "${SCRIPT_DIR}/analysis_configurations/earlyrun3" ]]; then
         echo "Cloning analysis earlyrun3 into ${SCRIPT_DIR}/analysis_configurations/earlyrun3"
-        git clone https://github.com/khaosmos93/CROWN-config-earlyRun3.git ${SCRIPT_DIR}/analysis_configurations/earlyrun3
+        git clone https://github.com/khaosmos93/CROWN-config-earlyRun3.git "${SCRIPT_DIR}/analysis_configurations/earlyrun3"
     elif [[ "$1" == "whtautau" && ! -d "${SCRIPT_DIR}/analysis_configurations/whtautau" ]]; then
         echo "Cloning analysis whtautau into ${SCRIPT_DIR}/analysis_configurations/whtautau"
-        git clone [email protected]:KIT-CMS/WHTauTauAnalysis-CROWN.git ${SCRIPT_DIR}/analysis_configurations/whtautau
-    elif [[ "$1" == "s" && ! -d "${SCRIPT_DIR}/analysis_configurations/s" ]]
-    then
+        git clone [email protected]:KIT-CMS/WHTauTauAnalysis-CROWN.git "${SCRIPT_DIR}/analysis_configurations/whtautau"
+    elif [[ "$1" == "s" && ! -d "${SCRIPT_DIR}/analysis_configurations/s" ]]; then
         echo "Cloning analysis s-channel into ${SCRIPT_DIR}/analysis_configurations/s"
-        git clone [email protected]:nfaltermann/CROWNs.git ${SCRIPT_DIR}/analysis_configurations/s
+        git clone [email protected]:nfaltermann/CROWNs.git "${SCRIPT_DIR}/analysis_configurations/s"
     fi
 fi