Merge pull request #97 from rest-for-physics/lobis-pre-commit

Implement pre-commit checks and format files
rest-for-physics · Feb 10, 2023 · f403fce · f403fce
2 parents 4ab6c30 + 716528b
commit f403fce
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Showing 25 changed files with 302 additions and 271 deletions.
diff --git a/.cmake-format.yaml b/.cmake-format.yaml
@@ -0,0 +1,6 @@
+# https://cmake-format.readthedocs.io/en/latest/configuration.html
+
+format:
+  tab_size: 4
+  separate_ctrl_name_with_space: true
+  separate_fn_name_with_space: false
diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -21,7 +21,7 @@ defaults:
 jobs:
   framework-validation:
     uses: rest-for-physics/framework/.github/workflows/validation.yml@master
-  
+
   libCheck:
     name: Validate library
     runs-on: ubuntu-latest
@@ -43,6 +43,10 @@ jobs:
         with:
           cmake-flags: "-DCMAKE_INSTALL_PREFIX=${{ env.REST_PATH }} -DCMAKE_BUILD_TYPE=${{ env.CMAKE_BUILD_TYPE }} -DREST_WELCOME=ON -DRESTLIB_RAW=ON"
           branch: ${{ env.BRANCH_NAME }}
+      - name: Verify pre-commit config files match
+        run: |
+          cd $GITHUB_WORKSPACE
+          curl https://raw.githubusercontent.com/rest-for-physics/framework/master/scripts/validatePreCommitConfig.py | python
       - name: Cache framework installation
         id: rawlib-install-cache
         uses: actions/cache@v3

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-xml
+      - id: requirements-txt-fixer
+      - id: end-of-file-fixer
+        exclude: external/.*$
+      - id: mixed-line-ending
+        exclude: external/.*$
+      - id: trailing-whitespace
+        exclude: external/.*$
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v15.0.6
+    hooks:
+      - id: clang-format
+        exclude: external/.*$
+
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+        additional_dependencies: [ pyyaml ]
+      # - id: cmake-lint
+
+  - repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+      - id: black
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -11,12 +11,12 @@ if (NOT ${RESTLIB_DETECTOR} MATCHES "ON")
     list(REMOVE_ITEM deps detector)
 endif ()
 
-COMPILELIB(deps)
+compilelib(deps)
 
 file(GLOB_RECURSE MAC "${CMAKE_CURRENT_SOURCE_DIR}/macros/*")
-INSTALL(FILES ${MAC} DESTINATION ./macros/raw)
+install(FILES ${MAC} DESTINATION ./macros/raw)
 
 file(GLOB_RECURSE MAC "${CMAKE_CURRENT_SOURCE_DIR}/examples/*")
-INSTALL(FILES ${MAC} DESTINATION ./examples/raw)
+install(FILES ${MAC} DESTINATION ./examples/raw)
 
-ADD_LIBRARY_TEST()
+add_library_test()
diff --git a/examples/tdsAQS.rml b/examples/tdsAQS.rml
@@ -1,34 +1,25 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
-
-<TRestManager name="TDS" title="Reading TDS rawdata" verboseLevel="info" >
-
-	<TRestRun name="TDSRun" title="Reading a TDS Scope file" verboseLevel="silent">
-		<parameter name="experimentName" value="GEMMM"/>
-		<parameter name="runNumber" value="preserve"/>
-		<parameter name="runTag" value="preserve"/>
-		<parameter name="runType" value="TDS"/>
-		<parameter name="runDescription" value=""/>
-		<parameter name="user" value="${USER}"/>
-		<parameter name="verboseLevel" value="0"/>
-		<parameter name="overwrite" value="on" />
-		<parameter name="outputFileName" value="R[fRunNumber]_[fRunType]_[fParentRunNumber].root" />
-		<parameter name="readOnly" value="false" />
-		<parameter name="inputFormat" value="GEMMM[fRunNumber].raw.[fParentRunNumber]" />
-	</TRestRun>
-
-	<TRestProcessRunner name="Processor" verboseLevel="info">
-		<parameter name="eventsToProcess" value="0" />
-		<parameter name="threadNumber" value="1"/>
-
-		<parameter name="inputAnalysisStorage" value="on"/>
-		<parameter name="inputEventStorage" value="on"/>
-		<parameter name="outputEventStorage" value="on"/>
-
-		<addProcess type="TRestRawTDSToSignalProcess" name="tdsRaw" value="ON" electronics="TDS"/>
-
-	</TRestProcessRunner>
-
-	<addTask command="Processor->RunProcess()" value="ON"/>
-
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<TRestManager name="TDS" title="Reading TDS rawdata" verboseLevel="info">
+    <TRestRun name="TDSRun" title="Reading a TDS Scope file" verboseLevel="silent">
+        <parameter name="experimentName" value="GEMMM"/>
+        <parameter name="runNumber" value="preserve"/>
+        <parameter name="runTag" value="preserve"/>
+        <parameter name="runType" value="TDS"/>
+        <parameter name="runDescription" value=""/>
+        <parameter name="user" value="${USER}"/>
+        <parameter name="verboseLevel" value="0"/>
+        <parameter name="overwrite" value="on"/>
+        <parameter name="outputFileName" value="R[fRunNumber]_[fRunType]_[fParentRunNumber].root"/>
+        <parameter name="readOnly" value="false"/>
+        <parameter name="inputFormat" value="GEMMM[fRunNumber].raw.[fParentRunNumber]"/>
+    </TRestRun>
+    <TRestProcessRunner name="Processor" verboseLevel="info">
+        <parameter name="eventsToProcess" value="0"/>
+        <parameter name="threadNumber" value="1"/>
+        <parameter name="inputAnalysisStorage" value="on"/>
+        <parameter name="inputEventStorage" value="on"/>
+        <parameter name="outputEventStorage" value="on"/>
+        <addProcess type="TRestRawTDSToSignalProcess" name="tdsRaw" value="ON" electronics="TDS"/>
+    </TRestProcessRunner>
+    <addTask command="Processor-&gt;RunProcess()" value="ON"/>
 </TRestManager>
-
diff --git a/inc/TRestRawBaseLineCorrectionProcess.h b/inc/TRestRawBaseLineCorrectionProcess.h
@@ -57,7 +57,8 @@ class TRestRawBaseLineCorrectionProcess : public TRestEventProcess {
         BeginPrintProcess();
 
         RESTMetadata << "Smoothing window size: " << fSmoothingWindow << RESTendl;
-        RESTMetadata << "Baseline correction applied to signals with IDs in range (" << fSignalsRange.X() << "," << fSignalsRange.Y() << ")" << RESTendl;
+        RESTMetadata << "Baseline correction applied to signals with IDs in range (" << fSignalsRange.X()
+                     << "," << fSignalsRange.Y() << ")" << RESTendl;
 
         EndPrintProcess();
     }

diff --git a/inc/TRestRawFEUDreamToSignalProcess.h b/inc/TRestRawFEUDreamToSignalProcess.h
@@ -73,7 +73,7 @@ class TRestRawFEUDreamToSignalProcess : public TRestRawToSignalProcess {
         bool get_zs_mode() const { return (((data)&0x400) >> 10); }
         int get_Feu_ID() const { return (((data)&0xFF)); }
         long int get_finetstp() const { return (((data)&0x0007)); }
-        //#define GET_FINETSTP(word)      (word & 0x0007)
+        // #define GET_FINETSTP(word)      (word & 0x0007)
         int get_sample_ID() const { return (((data)&0xFF8) >> 3); }
         int get_channel_ID() const { return (((data)&0x3F)); }
         int get_dream_ID() const { return (((data)&0xE00) >> 9); }     // non-zS mode

diff --git a/inc/TRestRawSignalAnalysisProcess.h b/inc/TRestRawSignalAnalysisProcess.h
@@ -70,9 +70,9 @@ class TRestRawSignalAnalysisProcess : public TRestEventProcess {
         BeginPrintProcess();
 
         RESTMetadata << "Baseline range : ( " << fBaseLineRange.X() << " , " << fBaseLineRange.Y() << " ) "
-                 << RESTendl;
+                     << RESTendl;
         RESTMetadata << "Integral range : ( " << fIntegralRange.X() << " , " << fIntegralRange.Y() << " ) "
-                 << RESTendl;
+                     << RESTendl;
         RESTMetadata << "Point Threshold : " << fPointThreshold << " sigmas" << RESTendl;
         RESTMetadata << "Signal threshold : " << fSignalThreshold << " sigmas" << RESTendl;
         RESTMetadata << "Number of points over threshold : " << fPointsOverThreshold << RESTendl;

diff --git a/inc/TRestRawUSTCToSignalProcess.h b/inc/TRestRawUSTCToSignalProcess.h
@@ -27,9 +27,9 @@
 
 #include "TRestRawToSignalProcess.h"
 
-//#define V3_Readout_Format_Long
+// #define V3_Readout_Format_Long
 #define V4_Readout_Format
-//#define Incoherent_Event_Generation
+// #define Incoherent_Event_Generation
 
 #ifdef V3_Readout_Format_Long
 #define DATA_SIZE 1048

diff --git a/pipeline/clang-format/clang-format.sh b/pipeline/clang-format/clang-format.sh
@@ -106,4 +106,3 @@ if [ "-" = "$1" ] ; then
 																																																																																																		  }"' '"${file}"'
 																																																																																																	  done
 																																																																																																  fi
-
diff --git a/pipeline/clang-format/clangformattest.sh b/pipeline/clang-format/clangformattest.sh
@@ -52,4 +52,3 @@ fi
 git reset HEAD --hard
 
 exit 1
-
diff --git a/pipeline/processes/analysis/globals.xml b/pipeline/processes/analysis/globals.xml
@@ -2,13 +2,13 @@
     <parameter name="mainDataPath" value="." />
     <parameter name="verboseLevel" value="silent" /> %options are : silent, warning, info, silent
 
-    <variable name="BL_MIN" value="20" overwrite="false" /> 
-    <variable name="BL_MAX" value="150" overwrite="false" /> 
+    <variable name="BL_MIN" value="20" overwrite="false" />
+    <variable name="BL_MAX" value="150" overwrite="false" />
 
-    <variable name="INT_MIN" value="150" overwrite="false" /> 
-    <variable name="INT_MAX" value="450" overwrite="false" /> 
+    <variable name="INT_MIN" value="150" overwrite="false" />
+    <variable name="INT_MAX" value="450" overwrite="false" />
 
-    <variable name="NPOINTS" value="7" overwrite="false" /> 
-    <variable name="POINT_TH" value="3.5" overwrite="false" /> 
-    <variable name="SGNL_TH" value="3.5" overwrite="false" /> 
+    <variable name="NPOINTS" value="7" overwrite="false" />
+    <variable name="POINT_TH" value="3.5" overwrite="false" />
+    <variable name="SGNL_TH" value="3.5" overwrite="false" />
 </globals>
diff --git a/pipeline/processes/analysis/veto.rml b/pipeline/processes/analysis/veto.rml
@@ -18,7 +18,7 @@
 	<parameter name="user" value="${USER}"/>
 	<parameter name="verboseLevel" value="0"/>
 	<parameter name="overwrite" value="off" />
-	
+
 	<parameter name="inputFormat" value="R[fRunNumber]_[fRunTag]-[fParentRunNumber].aqs"/>
 	<parameter name="outputFileName" value="R[fRunNumber]_output.root" />
 
@@ -56,15 +56,15 @@
 			pointThreshold="${POINT_TH}" pointsOverThreshold="${NPOINTS}" signalThreshold="${SGNL_TH}"
 			verboseLevel="silent" >
             // We define all observables except MinValue because is not yet on validation.root
-                <observable name="NumberOfSignals" type="int" value="ON" />                         
-                <observable name="NumberOfGoodSignals" type="int" value="ON" />                     
-                <observable name="ThresholdIntegral" type="double" value="ON" />                       
-                <observable name="TripleMaxIntegral" type="double" value="ON" />                        
-                <observable name="AmplitudeRatio" type="double" value="ON" />                           
-                <observable name="MaxPeakTime" type="double" value="ON" />                              
-                <observable name="MinPeakTime" type="double" value="ON" />                             
-                <observable name="MaxPeakTimeDelay" type="double" value="ON" />                        
-                <observable name="AveragePeakTime" type="double" value="ON" />                         
+                <observable name="NumberOfSignals" type="int" value="ON" />
+                <observable name="NumberOfGoodSignals" type="int" value="ON" />
+                <observable name="ThresholdIntegral" type="double" value="ON" />
+                <observable name="TripleMaxIntegral" type="double" value="ON" />
+                <observable name="AmplitudeRatio" type="double" value="ON" />
+                <observable name="MaxPeakTime" type="double" value="ON" />
+                <observable name="MinPeakTime" type="double" value="ON" />
+                <observable name="MaxPeakTimeDelay" type="double" value="ON" />
+                <observable name="AveragePeakTime" type="double" value="ON" />
 
                 <cut name="NumberOfGoodSignals" value="(1,1000)" />
 		</addProcess>

diff --git a/pipeline/processes/noise/addNoise.py b/pipeline/processes/noise/addNoise.py
@@ -9,22 +9,22 @@
 
 sgnl = ROOT.TRestRawSignal()
 
-for x in range(0,512):
+for x in range(0, 512):
     sgnl.AddPoint(0)
 
 rawEv.AddSignal(sgnl)
 
 addNoiseProcess = ROOT.TRestRawSignalAddNoiseProcess("metadata.rml")
 
-outEv = addNoiseProcess.ProcessEvent( rawEv )
+outEv = addNoiseProcess.ProcessEvent(rawEv)
 
-outEv.GetSignal(0).CalculateBaseLine(50,450)
+outEv.GetSignal(0).CalculateBaseLine(50, 450)
 baseLineSigma = outEv.GetSignal(0).GetBaseLineSigma()
 
-print ("\nEvaluating baseline sigma at the output event")
+print("\nEvaluating baseline sigma at the output event")
 if baseLineSigma < 15 or baseLineSigma > 25:
-    print ("\nEvaluation failed! Sigma is outside (15,25) range!" )
+    print("\nEvaluation failed! Sigma is outside (15,25) range!")
     exit(202)
-print ("[\033[92m OK \x1b[0m]")
+print("[\033[92m OK \x1b[0m]")
 
 exit(0)
diff --git a/pipeline/processes/veto/veto.rml b/pipeline/processes/veto/veto.rml
@@ -1,67 +1,49 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
-
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <TRestManager>
-
-<globals>
-	<parameter name="mainDataPath" value="." />
-
-</globals>
-
-
-<TRestRun name="VetoTest9Units" title="IAXO D0 Muon Veto Test" verboseLevel="silent">
-	<parameter name="experimentName" value="IAXOD0"/>
-	<parameter name="runNumber" value="preserve"/>
-	<parameter name="runTag" value="preserve"/>
-	<parameter name="runType" value="VetoValidation"/>
-	<parameter name="runDescription" value=""/>
-	<parameter name="user" value="${USER}"/>
-	<parameter name="verboseLevel" value="0"/>
-	<parameter name="overwrite" value="off" />
-
-	<parameter name="inputFormat" value="R[fRunNumber]_[fRunTag]-[fParentRunNumber].aqs"/>
-	<parameter name="outputFileName" value="R[fRunNumber]_output.root" />
-
-	<parameter name="readOnly" value="false" />
-
-</TRestRun>
-
-	<TRestProcessRunner name="RawSignals" title="Raw processing and analysis" verboseLevel="info">
-
-		<parameter name="firstEntry" value="0" />
-		<parameter name="lastEntry" value="0" />
-		<parameter name="eventsToProcess" value="50" />
-
-		<addProcess type="TRestRawMultiFEMINOSToSignalProcess" name="virtualDAQ" value="ON" verboseLevel="silent">
-			<parameter name="pedScript" value="ped"/>
-			<parameter name="runScript" value="run"/>
-			<parameter name="electronics" value="TCMFeminos"/>
-			<parameter name="fileFormat" value="SJTU" />
-		</addProcess>
-
-		<addProcess type="TRestRawVetoAnalysisProcess" name="veto" value="ON">
-			<parameter name="baseLineRange" value="(10,100)"/>
-			<parameter name="range" value="(10,500)"/>
-			<parameter name="observable" value="all"/>
-
-			<vetoGroup name="top" signalIDs="4688,4705,4728,4744"/>
-			<vetoGroup name="bottom" signalIDs="4647,4620,4637,4668"/>
-			<vetoGroup name="back" signalIDs="4676,4612,4672"/>
-			<vetoGroup name="right" signalIDs="4849,4620,4637,4668"/>
-		</addProcess>
-
-	</TRestProcessRunner>
-
-	<addTask type="processEvents" value="ON" />
-
-	<TRestRawVetoAnalysisProcess name="veto" value="ON">
-		<parameter name="baseLineRange" value="(10,100)"/>
-		<parameter name="range" value="(10,500)"/>
-		<parameter name="observable" value="all"/>
-
-		<vetoGroup name="top" signalIDs="4688,4705,4728,4744"/>
-		<vetoGroup name="bottom" signalIDs="4647,4620,4637,4668"/>
-		<vetoGroup name="back" signalIDs="4676,4612,4672"/>
-		<vetoGroup name="right" signalIDs="4849,4620,4637,4668"/>
-	</TRestRawVetoAnalysisProcess>
-
+    <globals>
+        <parameter name="mainDataPath" value="."/>
+    </globals>
+    <TRestRun name="VetoTest9Units" title="IAXO D0 Muon Veto Test" verboseLevel="silent">
+        <parameter name="experimentName" value="IAXOD0"/>
+        <parameter name="runNumber" value="preserve"/>
+        <parameter name="runTag" value="preserve"/>
+        <parameter name="runType" value="VetoValidation"/>
+        <parameter name="runDescription" value=""/>
+        <parameter name="user" value="${USER}"/>
+        <parameter name="verboseLevel" value="0"/>
+        <parameter name="overwrite" value="off"/>
+        <parameter name="inputFormat" value="R[fRunNumber]_[fRunTag]-[fParentRunNumber].aqs"/>
+        <parameter name="outputFileName" value="R[fRunNumber]_output.root"/>
+        <parameter name="readOnly" value="false"/>
+    </TRestRun>
+    <TRestProcessRunner name="RawSignals" title="Raw processing and analysis" verboseLevel="info">
+        <parameter name="firstEntry" value="0"/>
+        <parameter name="lastEntry" value="0"/>
+        <parameter name="eventsToProcess" value="50"/>
+        <addProcess type="TRestRawMultiFEMINOSToSignalProcess" name="virtualDAQ" value="ON" verboseLevel="silent">
+            <parameter name="pedScript" value="ped"/>
+            <parameter name="runScript" value="run"/>
+            <parameter name="electronics" value="TCMFeminos"/>
+            <parameter name="fileFormat" value="SJTU"/>
+        </addProcess>
+        <addProcess type="TRestRawVetoAnalysisProcess" name="veto" value="ON">
+            <parameter name="baseLineRange" value="(10,100)"/>
+            <parameter name="range" value="(10,500)"/>
+            <parameter name="observable" value="all"/>
+            <vetoGroup name="top" signalIDs="4688,4705,4728,4744"/>
+            <vetoGroup name="bottom" signalIDs="4647,4620,4637,4668"/>
+            <vetoGroup name="back" signalIDs="4676,4612,4672"/>
+            <vetoGroup name="right" signalIDs="4849,4620,4637,4668"/>
+        </addProcess>
+    </TRestProcessRunner>
+    <addTask type="processEvents" value="ON"/>
+    <TRestRawVetoAnalysisProcess name="veto" value="ON">
+        <parameter name="baseLineRange" value="(10,100)"/>
+        <parameter name="range" value="(10,500)"/>
+        <parameter name="observable" value="all"/>
+        <vetoGroup name="top" signalIDs="4688,4705,4728,4744"/>
+        <vetoGroup name="bottom" signalIDs="4647,4620,4637,4668"/>
+        <vetoGroup name="back" signalIDs="4676,4612,4672"/>
+        <vetoGroup name="right" signalIDs="4849,4620,4637,4668"/>
+    </TRestRawVetoAnalysisProcess>
 </TRestManager>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -106,4 +106,3 @@ if [ "-" = "$1" ] ; then
		}"' '"${file}"'
		done
		fi