Splitting FCCAnalysisRun (#335)

* Splitting FCCAnalysisRun

* Check for HTCondor commands

* Improved batch submition

* Using with context for ROOT files

* Adding type hints

* Updated man pages

.github/scripts/man2html.sh

@@ -3,9 +3,9 @@
 mkdir -p ./man/html
 cd ./man/man1
 for MANFILE in *; do
-  mandoc -Thtml -Ostyle=/css/mandoc.css "${MANFILE}" > "../html/${MANFILE::-1}html"
+  mandoc -Thtml -Ostyle=../../css/mandoc.css "${MANFILE}" > "../html/${MANFILE::-1}html"
 done
 cd ../man7
 for MANFILE in *; do
-  mandoc -Thtml -Ostyle=/css/mandoc.css "${MANFILE}" > "../html/${MANFILE::-1}html"
+  mandoc -Thtml -Ostyle=../../css/mandoc.css "${MANFILE}" > "../html/${MANFILE::-1}html"
 done

bin/fccanalysis

@@ -1,8 +1,20 @@
 #!/usr/bin/env python3
+'''
+Starting point (executable) for fccanalysis command
+'''
 
 import argparse
 import logging
 
+from parsers import setup_subparsers
+from init_analysis import init_analysis
+from build_analysis import build_analysis
+from test_fccanalyses import test_fccanalyses
+from pin_analysis import PinAnalysis
+from run_analysis import run
+from run_final_analysis import run_final
+from do_plots import do_plots
+
 
 class MultiLineFormatter(logging.Formatter):
     '''
@@ -30,9 +42,12 @@ class MultiLineFormatter(logging.Formatter):
 
 
 def main():
+    '''
+    Starting point for fccanalysis command
+    '''
     parser = argparse.ArgumentParser(description='FCCAnalyses v0.8.0')
 
-    # Verbosity settings
+    # Verbosity arguments
     verbosity_argument_group = parser.add_mutually_exclusive_group()
     verbosity_argument_group.add_argument('-v', '--verbose',
                                           action='store_true',
@@ -42,42 +57,16 @@ def main():
                                           help='make output more verbose')
     verbosity_argument_group.add_argument('-vvv', '--most-verbose',
                                           action='store_true',
-                                          help='make output most verbose')
-
-    # Create sub-parsers
-    subparsers = parser.add_subparsers(help='types of running modes',
-                                       dest='command')
-    parser_init = subparsers.add_parser(
-        'init',
-        help="generate a RDataFrame based FCC analysis")
-    parser_build = subparsers.add_parser(
-        'build',
-        help='build and install local analysis')
-    parser_test = subparsers.add_parser(
-        'test',
-        help='test whole or a part of the analysis framework')
-    parser_pin = subparsers.add_parser(
-        'pin',
-        help='pin fccanalyses to the current version of Key4hep stack')
-    parser_run = subparsers.add_parser(
-        'run',
-        help="run a RDataFrame based FCC analysis")
-    parser_run_final = subparsers.add_parser(
-        'final',
-        help="run a RDataFrame based FCC analysis final configuration")
-    parser_run_plots = subparsers.add_parser(
-        'plots',
-        help="run a RDataFrame based FCC analysis plot configuration")
-
-    # Setup sub-parsers
-    import Parsers as fccpars
-    fccpars.setup_init_parser(parser_init)
-    fccpars.setup_build_parser(parser_build)
-    fccpars.setup_test_parser(parser_test)
-    fccpars.setup_pin_parser(parser_pin)
-    fccpars.setup_run_parser(parser_run)
-    fccpars.setup_run_parser_final(parser_run_final)
-    fccpars.setup_run_parser_plots(parser_run_plots)
+                                          help='make output even more verbose')
+
+    # Sub-parsers
+    subparsers = parser.add_subparsers(
+        title='sub-commands',
+        metavar='sub-command',
+        dest='command',
+        help='one of the available sub-commands')
+
+    setup_subparsers(subparsers)
 
     args = parser.parse_args()
 
@@ -94,19 +83,18 @@ def main():
     logger.addHandler(stream_handler)
 
     if args.command == 'init':
-        from FCCAnalysisSetup import setup
-        setup(parser)
+        init_analysis(parser)
     elif args.command == 'build':
-        from build_analysis import build_analysis
         build_analysis(parser)
     elif args.command == 'test':
-        from test import test_fccanalyses
         test_fccanalyses(parser)
     elif args.command == 'pin':
-        from pin_analysis import PinAnalysis
         PinAnalysis(parser)
+    elif args.command == 'final':
+        run_final(parser)
+    elif args.command == 'plots':
+        do_plots(parser)
     else:
-        from FCCAnalysisRun import run
         run(parser)
 
 

examples/FCCee/higgs/mH-recoil/mumu/analysis_final.py

@@ -22,6 +22,8 @@
 #produces ROOT TTrees, default is False
 doTree = False
 
+saveTabular = True
+
 ###Dictionnay of the list of cuts. The key is the name of the selection that will be added to the output file
 cutList = {"sel0":"Zcand_q == 0",
             "sel1":"Zcand_q == -1 || Zcand_q == 1",

man/man1/fccanalysis-build.1

@@ -0,0 +1,60 @@
+.\" Manpage for fccanalysis-build
+.\" Contact [email protected] to correct errors or typos.
+.TH FCCANALYSIS\-BUILD 1 "17 Jan 2024" "0.8.0" "fccanalysis-build man page"
+.SH NAME
+\fBfccanalysis\-build\fR \(en helper to build FCCAnalyses framework locally
+.SH SYNOPSIS
+.B fccanalysis build
+[\fB\-h\fR | \fB\-\-help\fR]
+[\fB\-c\fR]
+[\fB\-j\fR \fIBUILD_THREADS\fR]
+.SH DESCRIPTION
+.B fccanalysis\-build
+will build the whole FCCAnalyses framework\&.
+
+This sub-command is not intended as a replacement for the CMake build procedure,
+it just makes this task a little easier\&. The helper will build the framework in
+the directory: build and install it into the directory: install\&.
+.SH OPTIONS
+.TP
+.BR \-h ", " \-\-help
+Prints short help message and exits\&.
+.TP
+.BR \-c ", " \-\-clean\-build
+Completely clean build directory before compilation\&.
+.TP
+\fB\-j\fR \fIBUILD_THREADS\fR, \fB\-\-build\-threads\fR \fIBUILD_THREADS\fR
+Specify number of threads used when compiling (equivalent to `make -j`)
+.SH SEE ALSO
+fccanalysis(1), fccanalysis\-test(7), cmake(1)
+.SH BUGS
+Many
+.SH AUTHORS
+There are many contributors to the FCCAnalyses framework, but the principal
+authors are:
+.in +4
+Clement Helsens
+.br
+Valentin Volk
+.br
+Gerardo Ganis
+.SH FCCANALYSES
+Part of the FCCAnalyses framework\&.
+.SH LINKS
+.PP
+.UR https://hep-fcc\&.github\&.io/FCCAnalyses/
+FCCAnalyses webpage
+.UE
+.PP
+.UR https://github\&.com/HEP\-FCC/FCCAnalyses/
+FCCAnalysises GitHub repository
+.UE
+.PP
+.UR https://fccsw\-forum\&.web\&.cern\&.ch/
+FCCSW Forum
+.UE
+.SH CONTACT
+.pp
+.MT [email protected]
+FCC-PED-SoftwareAndComputing-Analysis
+.ME

man/man1/fccanalysis-run.1

@@ -1,125 +1,89 @@
-.\" Manpage for fccanalysis
-.\" Contact fcc-experiments-sw-dev@cern.ch to correct errors or typos.
-.TH FCCANALYSIS\-RUN 1 "24 May 2023" "0.8.0" "fccanalysis-run man page"
+.\" Manpage for fccanalysis-run
+.\" Contact FCC-PED-SoftwareAndComputing-Analysis@cern.ch to correct errors or typos.
+.TH FCCANALYSIS\-RUN 1 "17 Jan 2024" "0.8.0" "fccanalysis-run man page"
 .SH NAME
-fccanalysis\-run \- run FCC analysis
+\fBfccanalysis\-run\fR \- run FCC analysis
 .SH SYNOPSIS
-.sp
-.nf
-\fIfccanalysis run\fR [\-h | \-\-help] [\-\-files\-list FILES_LIST [FILES_LIST ...]]
-                [\-\-output OUTPUT] [\-\-nevents NEVENTS] [\-\-test] [\-\-bench]
-                [\-\-ncpus NCPUS] [\-\-preprocess] [\-\-validate] [\-\-rerunfailed]
-                [\-\-jobdir JOBDIR] <analysis-file>
-.fi
-.sp
+.B fccanalysis run
+[\fB\-h\fR | \fB\-\-help\fR]
+[\fB\-\-files\-list\fR \fIFILES_LIST\fR [\fIFILES_LIST\fR ...]]
+[\fB\-\-output\fR \fIOUTPUT\fR]
+[\fB\-\-nevents\fR \fINEVENTS\fR]
+[\fB\-\-test\fR]
+[\fB\-\-bench\fR]
+[\fB\-\-ncpus\fR \fINCPUS\fR]
+.I analysis-script
 .SH DESCRIPTION
-\fIfccanalysis-run\fR will run analysis provided in the analysis file\&. The
+.B fccanalysis-run
+will run analysis provided in the analysis file\&. The
 analysis itself can be divided into several stages if desired\&. For all those
 stages \fIfccanalysis-run\fR is used\&.
-.sp
-When using \fIfccanalysis-run\fR the analysis is running in the managed mode,
-where the RDataFrame provided is steered by the framework and users can control
-some aspects of the running with additional global attributes, see
-\fBfccanalysis-file\fR(8).
+
+When using \fBfccanalysis-run\fR the analysis is running in the managed mode,
+where the RDataFrame is steered by the framework and users can control some
+aspects of the running with additional global attributes, see
+\fIfccanalysis-script\fR(8).
 .SH OPTIONS
-.PP
-<analysis-file>
-.RS 4
-Path to analysis file\&.
-.RE
-.PP
-\-\-help
-.RS 4
+.TP
+.I analysis-script
+Path to analysis script\&.
+.TP
+.BR \-h ", " \-\-help
 Prints short help message and exits\&.
-.RE
-.PP
-\-\-files\-list FILES_LIST [FILES_LIST ...]
-.RS 4
+.TP
+\fB\-\-files\-list\fR \fIFILES_LIST\fR [\fIFILES_LIST\fR ...]
 Specify input file to bypass the processList\&.
-.RE
-.PP
-\-\-output OUTPUT
-.RS 4
+.TP
+\fB\-\-output\fR \fIOUTPUT\fR
 Specify output file name to bypass the processList and or outputList, default
 \fIoutput.root\fR\&.
-.RE
-.PP
-\-\-nevents NEVENTS
-.RS 4
+.TP
+\fB\-\-nevents\fR \fINEVENTS\fR
 Specify max number of events to process\&.
-.RE
-.PP
-\-\-test
-.RS 4
+.TP
+.B \-\-test
 Run over the test file\&.
-.RE
-.PP
-\-\-bench
-.RS 4
+.TP
+.B \-\-bench
 Output benchmark results to a JSON file\&.
-.RE
-.PP
-\-\-ncpus NCPUS
-.RS 4
+.TP
+\-\-ncpus \fINCPUS\fR
 Set number of threads\&.
-.RE
-.PP
-\-\-preprocess
-.RS 4
-Run preprocessing\&.
-.RE
-.PP
-\-\-validate
-.RS 4
-Validate a given production\&.
-.RE
-.PP
-\-\-rerunfailed
-.RS 4
-Rerun failed jobs\&.
-.RE
-.PP
-\-\-jobdir JOBDIR
-.RS 4
-Specify the batch job directory\&.
-.RE
 .SH ENVIRONMENT VARIABLES
-.PP
-\fBFCCDICTSDIR\fR
-.RS 4
+.TP
+.B FCCDICTSDIR
 Controls search path for the process dictionaries. The default value is
 \fI/cvmfs/fcc.cern.ch/FCCDicts/\fR\&.
-.RE
 .SH SEE ALSO
-fccanalysis(1), fccanalysis-file(7)
+fccanalysis(1), fccanalysis-script(7)
 .SH BUGS
 Many
 .SH AUTHORS
 There are many contributors to the FCCAnalyses framework, but the principal
 authors are:
-.br
-.RS 4
+.in +4
 Clement Helsens
 .br
 Valentin Volk
 .br
 Gerardo Ganis
-.RE
 .SH FCCANALYSES
 Part of the FCCAnalyses framework\&.
 .SH LINKS
 .PP
-1\&. FCCAnalyses webpage
-.RS 4
-https://hep-fcc\&.github\&.io/FCCAnalyses/
-.RE
-.PP
-2\&. FCCAnalysises GitHub repository
-.RS
-https://github\&.com/HEP\-FCC/FCCAnalyses/
-.RE
-.PP
-3\&. FCCSW Forum
-.RS
-https://fccsw\-forum\&.web\&.cern\&.ch/
-.RE
+.UR https://hep-fcc\&.github\&.io/FCCAnalyses/
+FCCAnalyses webpage
+.UE
+.PP
+.UR https://github\&.com/HEP\-FCC/FCCAnalyses/
+FCCAnalysises GitHub repository
+.UE
+.PP
+.UR https://fccsw\-forum\&.web\&.cern\&.ch/
+FCCSW Forum
+.UE
+.SH CONTACT
+.pp
+.MT [email protected]
+FCC-PED-SoftwareAndComputing-Analysis
+.ME