Automatic data model update

.github/FUNDING.yml

@@ -1 +1 @@
-custom: ["https://git.io/JJAW8"]
+

.github/workflows/mega-linter.yml

@@ -1,29 +1,34 @@
 ---
 # MegaLinter GitHub Action configuration file
-# More info at https://oxsecurity.github.io/megalinter
+# More info at https://megalinter.io
 name: MegaLinter
 
 'on': [pull_request_target]
 
+permissions: {}
+
 env:
   # Apply linter fixes configuration
   APPLY_FIXES: all
   PR_NUMBER: ${{ github.event.pull_request.number }}
 
 concurrency:
-  group: ${{ github.ref }}-${{ github.workflow }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.run_id }}
   cancel-in-progress: true
 
 jobs:
-  build:
+  megalinter:
     name: MegaLinter
     runs-on: ubuntu-latest
     steps:
       # Git Checkout
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
+          # Checkout the HEAD of the PR instead of the merge commit.
           ref: ${{ github.event.pull_request.head.sha }}
+          # Checkout the merge commit. (If a fixing PR is made, it will include also missing commits from upstream.)
+          # ref: refs/pull/${{ github.event.number }}/merge
           fetch-depth: 0
           # So we can use secrets.ALIBUILD_GITHUB_TOKEN to push later.
           persist-credentials: false
@@ -32,11 +37,11 @@ jobs:
       - name: MegaLinter
         id: ml
         # You can override MegaLinter flavor used to have faster performances
-        # More info at https://oxsecurity.github.io/megalinter/flavors/
-        uses: oxsecurity/megalinter@v6
+        # More info at https://megalinter.io/flavors/
+        uses: oxsecurity/megalinter@v7
         env:
           # All available variables are described in documentation:
-          # https://oxsecurity.github.io/megalinter/configuration/
+          # https://megalinter.io/configuration/
           # Validates all source when push on master, else just the diff with
           # master. Override with true if you always want to lint all sources.
           VALIDATE_ALL_CODEBASE: false
@@ -77,7 +82,7 @@ jobs:
             yourself and update the pull request, or merge this PR in yours.
 
             You can find how to run MegaLinter locally at
-            <https://oxsecurity.github.io/megalinter/latest/mega-linter-runner/>.
+            <https://megalinter.io/latest/mega-linter-runner/>.
         # We do not create PRs if the branch is not there.
         continue-on-error: true
 

.mega-linter.yml

@@ -24,7 +24,7 @@ MARKDOWN_MARKDOWNLINT_DISABLE_ERRORS: false
 SHOW_ELAPSED_TIME: true
 FILEIO_REPORTER: false
 GITHUB_COMMENT_REPORTER: false
-UPDATED_SOURCES_REPORTER: false
+UPDATED_SOURCES_REPORTER: true
 PRINT_ALPACA: false # Don't print ASCII alpaca in the log
 PRINT_ALL_FILES: true # Print all processed files
 FLAVOR_SUGGESTIONS: false # Don't show suggestions about different MegaLinter flavors

CPPLINT.cfg

@@ -1 +1 @@
-filter=-build/namespaces,-readability/todo,-runtime/references,-whitespace/blank_line,-whitespace/braces,-whitespace/comments,-whitespace/line_length,-whitespace/semicolon,-whitespace/todo
+filter=-build/c++11,-build/namespaces,-readability/fn_size,-readability/todo,-runtime/references,-whitespace/blank_line,-whitespace/braces,-whitespace/comments,-whitespace/line_length,-whitespace/semicolon,-whitespace/todo

_includes/templates/breadcrumbs.liquid

@@ -38,5 +38,5 @@
 Feel like information is missing? Please send your suggestions for updates and improvements to <a href = "mailto:
 [email protected]">docadmin</a>. If you wish to contribute, you're very welcome! Please follow
 the instructions <a
-href="https://aliceo2group.github.io/analysis-framework/docs/gettingstarted/contributingtocode.html">here</a>.
+href="https://aliceo2group.github.io/analysis-framework/docs/gettingstarted/contributingtodocs.html">here</a>.
 </div>

docs/advanced-specifics/eventMixing.md

@@ -1,5 +1,5 @@
 ---
-sort: 1
+sort: 2
 title: Event Mixing
 ---
 
@@ -17,23 +17,23 @@ o2::soa::combinations (CombinationIndexPolicy(tracks1, tracks2, ...))
 
 which returns tuples of tracks (one track from each table of tracks).
 
-There are several *CombinationIndexPolicies* available which are explained [here](../framework/framework.md#getting-combinations-pairs-triplets-). It is recommended that you will get first well acquainted with combinations before moving on to mixing.
+There are several *CombinationIndexPolicies* available which are explained [here](../basics-tasks/CombiningData.md). It is recommended that you will get first well acquainted with combinations before moving on to mixing.
 
-## Event mixing
+## Mixing generator
 
 `GroupedCombinationsGenerator` which generates mixed event pairs is a generalization of block combination policies. Therefore, it accepts the same parameters:
 
 - binning policy
 - outsider
 - category neighbours (equivalent to the number of other collisions to mix with)
 
-You can consult a detailed description of these parameters in the [block combinations section](../framework/framework.md#block--binned-combination-policies).
+You can consult a detailed description of these parameters in the [block combinations section](../basics-tasks/CombiningData.md#block--binned-combination-policies).
 
 The `GroupedCombinationsGenerator` general constructor is defined as:
 
 ```cpp
 template <typename T1, typename GroupingPolicy, typename BP, typename G, typename... As>
-GroupedCombinationsGenerator(const BP& binningPolicy, int catNeighbours, const T1& outsider, G& grouping, std::tuple<T2s...>& associated)
+GroupedCombinationsGenerator(const BP& binningPolicy, int catNeighbours, const T1& outsider, G& grouping, std::tuple<T2s...>& associated, SliceCache* cache)
 ```
 
 This is a more general functionality which potentially could be used for other applications beyond event mixing. However, to simplify this tutorial, let's assume our `grouping` table is the table of collisions, and the `associated` are tables of structures like tracks and V0s.
@@ -43,7 +43,8 @@ This is a more general functionality which potentially could be used for other a
 - `T1`: type of an outsider value as well as the value itself as a parameter,
 - `GroupingPolicy`: type of a *BlockCombinationIndexPolicies* which specifies how collision pairs will be generated (strictly upper, upper or full block combinations)i,
 - `BP`: type of a binning policy applied to the block combinations of collisions as well as the policy instance,
-- input grouping (collisions) and associated (tracks, V0s) tables and their types.
+- input grouping (collisions) and associated (tracks, V0s) tables and their types
+- a pointer to the `SliceCache` which is used implicitly for efficient slicing of associated tables
 
 To simplify the code, there are helper shortcuts defined for the most common use cases:
 

docs/advanced-specifics/machineLearning.md

@@ -1,5 +1,5 @@
 ---
-sort: 2
+sort: 3
 title: Machine Learning
 ---
 

docs/advanced-specifics/pwgcf.md

@@ -1,5 +1,5 @@
 ---
-sort: 3
+sort: 4
 title: PWG-CF
 ---
 

docs/advanced-specifics/pwgdq.md

@@ -1,17 +1,17 @@
 ---
-sort: 4
+sort: 5
 title: PWG-DQ
 ---
 
 ## Get started
 
-[link to indico page of the Hands-On session :]
+In the past, some hands-on sessions have been organised within the PWG-DQ. A list of the corresponding indico events is down below:
 
-1. O2 DQ (7/12/21)(<https://indico.cern.ch/event/1098200/>)
-2. O2 DQ (April 2022) <https://indico.cern.ch/event/1150382/>
-3. O2 tutorial (Oct 2022) <https://indico.cern.ch/event/1200252/timetable/?view=standard>
-
-[ZOOM recordings of the first part of the session](https://indico.cern.ch/event/1098200/sessions/419561/attachments/2362418/4033057/videoPlenarySession.mp4)
+**most recent:**
+1. O2 DQ hands-on session (7 Dec 21) [indico event](https://indico.cern.ch/event/1098200/) , [ZOOM recordings of the first part of the session](https://indico.cern.ch/event/1098200/sessions/419561/attachments/2362418/4033057/videoPlenarySession.mp4)
+2. O2 DQ hands-on session (April 2022) [indico event](https://indico.cern.ch/event/1150382/)
+3. O2 Analysis tutorial (Oct 2022) [indico event](https://indico.cern.ch/event/1200252/timetable/?view=standard)
+4. O2 DQ hands-on session (13 Dec 22) [indico event](https://indico.cern.ch/event/1220887/), [ZOOM recordings, DQ User Interfce](https://indico.cern.ch/event/1220887/contributions/5168779/attachments/2568116/4427919/afternoon_session.mp4)
 
 # Dileptons-Quarkonia (DQ) analysis framework
 
@@ -29,7 +29,7 @@ Mattermost channel: [O2-DQ Analysis Framework Alpha](https://mattermost.web.cern
 [`VarManager.h`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Core/VarManager.h).
 * Class to define and fill histograms are defined in
 [`HistogramManager.h`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Core/HistogramManager.h).
-* Class to set of predefined selection cuts(either AnalysisCut or AnalysisCompositeCut) are defined in
+* Class to set predefined selection cuts (either AnalysisCut or AnalysisCompositeCut) are defined in
 [`CutsLibrary.h`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Core/CutsLibrary.h).
 * Class for analysis cuts applied on the variables defined in the VarManager is defined in
 [`AnalysisCut.h`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Core/AnalysisCut.h) class.
@@ -61,12 +61,22 @@ Mattermost channel: [O2-DQ Analysis Framework Alpha](https://mattermost.web.cern
 * [`dqEfficiency.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Tasks/dqEfficiency.cxx) Analysis task for processing O2::DQ MC skimmed AODs.
 * [`v0selector.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Tasks/v0selector.cxx) Select barrel tracks which belong to clean V0 and cascade topologies. This code loops over a V0Data table and produces some standard analysis output for select clean V0 sample.
 * [`dileptonMuMu.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Tasks/dileptonMuMu.cxx) It refers to The dimuon analysis task. It’s a derivative of the tableReader, but with muon only informations.  takes tracks flaged as « muon » and creates Pairs calculating mass, rapidity, pT.
-* [`dileptonEE.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Tasks/dileptonEE.cxx) It refers to The dielectron analysis task. It’s a derivative of the tableReader, but with electron only informations.  takes tracks flaged as « electron » and creates Pairs calculating mass, rapidity, pT.
+
+## Python Interface
+To simplify the handling and usage of the O2-DQ framework a [python interface](https://github.com/ctolon/PythonInterfaceOOP) has been developed and will be maintained for further user support.
+
+Its main features are:
+
+- run tasks with simple commands (all main workflows are included)
+- dependencies are selected and set with no need to specify them in the command line
+- auto completion for workflows, settings and configurables
+
+To get started, a [detailed introduction](https://github.com/ctolon/PythonInterfaceOOP#user-python-based-interface) has been written and an introduction was given in the [hands-on session](https://indico.cern.ch/event/1220887/) (Dec 22).
 
 ## AliHyperloop
 
 [JIRA tickets](https://alice.its.cern.ch/jira/browse/PWGDQ-57?jql=project%20%3D%20PWGDQ%20AND%20issuetype%20%3D%20Analysis)
-of the DQ analyses on [AliHyperloop](https://alimonitor.cern.ch/hyperloop/):
+of the DQ analyses on [AliHyperloop](https://alimonitor.cern.ch/hyperloop/).
 
 ## DQ Data Model
 

docs/advanced-specifics/pwgem.md

@@ -1,16 +1,42 @@
 ---
-sort: 5
+sort: 6
 title: PWG-EM
 ---
 
 # Electromagnetic probes (EM) analysis framework
 
 ## Get started
+In the past several O2 hands-on sessions have been taken placed. A list of the most recent ones in DQ, can be found [here](pwgdq.md#get-started).
 
 ## Contact
+Coordinators: Raphaelle Bailhache, Mike Sas
 
-## Code
+Mattermost channel: [EM LMEE O2](https://mattermost.web.cern.ch/alice/channels/em-lmee-o2)
 
-- The codebase can be found in the
+## Code
+  - The codebase can be found in the
 [`PWGEM`](https://github.com/AliceO2Group/O2Physics/tree/master/PWGEM) directory.
-.h).
+
+### Dileptons
+Due to a large overlap with the PWGDQ, the low mass dielectron tasks are using some tasks of the [framework from DQ](pwgdq.md#code).
+
+* [`TableMaker.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/TableProducer/tableMaker.cxx) Is used to produced skimmed data tables for EM analysis from central barrel and muon AODs based on selected event information, barrel track and muon track information.
+* [`TableReader.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGDQ/Tasks/tableReader.cxx) Analyze EM skimmed data tables. This workflow runs a few tasks: event selection, barrel track selection, muon track selection, same event pairing, event mixing, and dilepton hadron combinations.
+* [`dileptonEE.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGEM/Dilepton/Tasks/dileptonEE.cxx) It refers to The dielectron analysis task. It’s a derivative of the tableReader, but with electron only informations.  takes tracks flaged as « electron » and creates Pairs calculating mass, rapidity, pT.
+* [`emEfficiencyEE.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGEM/Dilepton/Tasks/emEfficiencyEE.cxx) Task to calculate the dielectron efficiency.
+* [`v0gammaQA.cxx`](https://github.com/AliceO2Group/O2Physics/blob/master/PWGEM/Dilepton/Tasks/v0gammaQA.cxx)
+
+### Neutral Meson and Photon
+
+```todo
+List all imporant tasks.
+```
+
+## AliHyperloop
+
+- [JIRA ticket](https://alice.its.cern.ch/jira/browse/PWGEM-2)
+of the EM dielectron analyses on [AliHyperloop](https://alimonitor.cern.ch/hyperloop/user#analysis-50501)
+- [JIRA ticket](https://alice.its.cern.ch/jira/browse/PWGEM-6)
+of the EM PCM and V0-finder analyses on [AliHyperloop](https://alimonitor.cern.ch/hyperloop/view-analysis/50539)
+- [JIRA ticket](https://alice.its.cern.ch/jira/browse/PWGEM-3)
+of the EM neutral meson analyses on [AliHyperloop](https://alimonitor.cern.ch/hyperloop/view-analysis/50508)