Add MegaLinter (AliceO2Group#679)

* Add MegaLinter

* Fix YAML

* Fix formatting

* Add Flake8 config file

* Check only modified files

* Allow formatting commits on push events

* Integrate alisw/pull-request

* Comments by Timo

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 120
+extend-ignore = E203

.github/workflows/mega-linter.yml

@@ -0,0 +1,82 @@
+---
+# MegaLinter GitHub Action configuration file
+# More info at https://megalinter.github.io
+name: MegaLinter
+
+'on': [pull_request_target]
+
+env: # Comment env block if you do not want to apply fixes
+  # Apply linter fixes configuration
+  APPLY_FIXES: all # When active, APPLY_FIXES must also be defined as environment variable (in github/workflows/mega-linter.yml or other CI tool)
+  PR_NUMBER: ${{ github.event.pull_request.number }}
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: MegaLinter
+    runs-on: ubuntu-latest
+    steps:
+      # Git Checkout
+      - name: Checkout Code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      # MegaLinter
+      - name: MegaLinter
+        id: ml
+        # You can override MegaLinter flavor used to have faster performances
+        # More info at https://megalinter.github.io/flavors/
+        uses: megalinter/megalinter@v5
+        env:
+          # All available variables are described in documentation
+          # https://megalinter.github.io/configuration/
+          VALIDATE_ALL_CODEBASE: false # ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }} # Validates all source when push on master, else just the git diff with master. Override with true if you always want to lint all sources
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # ADD YOUR CUSTOM ENV VARIABLES HERE OR DEFINE THEM IN A FILE .mega-linter.yml AT THE ROOT OF YOUR REPOSITORY
+          # DISABLE: COPYPASTE,SPELL # Uncomment to disable copy-paste and spell checks
+
+      # Create or delete the cleanup branch
+      - name: Update cleanup branch
+        if: ${{ github.event.repository.owner.login == 'AliceO2Group' }}
+        env:
+          REMOTE_URL: "https://alibuild:${{ secrets.ALIBUILD_GITHUB_TOKEN }}@\
+            github.com/alibuild/${{ github.event.repository.name }}"
+        run: |
+          # An empty CLEANUP_COMMIT means delete the branch.
+          CLEANUP_COMMIT=""
+          if [ "${{ steps.ml.outputs.has_updated_sources }}" = 1 ]
+          then
+            CLEANUP_COMMIT="HEAD"
+            git commit -am "MegaLinter fixes"
+          fi
+          git push -f "$REMOTE_URL" "$CLEANUP_COMMIT:refs/heads/alibot-cleanup-ml-$PR_NUMBER"
+
+      - name: Create pull request with applied fixes
+        uses: alisw/pull-request@v2
+        if: steps.ml.outputs.has_updated_sources == 1 && ${{ github.event.repository.owner.login == 'AliceO2Group' }}
+        with:
+          source_branch: 'alibuild:alibot-cleanup-ml-${{ env.PR_NUMBER }}'
+          destination_branch: '${{ github.event.pull_request.head.label }}'
+          github_token: ${{ secrets.ALIBUILD_GITHUB_TOKEN }}
+          pr_title: >-
+            [MegaLinter] Apply linters automatic fixes to
+            #${{ env.PR_NUMBER }}
+          pr_body: >-
+            Your PR ${{ github.event.repository.full_name }}#${{ env.PR_NUMBER }}
+            cannot be merged as is. You should either run MegaLinter
+            yourself and update the pull request, or merge this PR in yours.
+
+            You can find how to run MegaLinter locally at
+            <https://megalinter.github.io/latest/mega-linter-runner/>.
+        continue-on-error: true  # We do not create PRs if the branch is not there.
+
+      - name: Exit with error if the PR is not clean
+        run: |
+          case "${{ steps.ml.outputs.has_updated_sources }}" in
+            0) echo 'PR clean' ; exit 0 ;;
+            1) echo 'PR not clean' ; exit 1 ;;
+          esac

.github/workflows/stale.yml

@@ -1,16 +1,17 @@
+---
 name: "Close stale PRs"
 on:
   schedule:
-  - cron: "0 0 * * *"
+    - cron: "0 0 * * *"
 
 jobs:
   stale:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/stale@v1
-      with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-pr-message: 'This PR has not been updated in the last 30 days. Is it still needed? Unless further action is taken, it will be closed in 5 days.'
-        stale-pr-label: stale
-        days-before-stale: 30
-        days-before-close: 5
+      - uses: actions/stale@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          stale-pr-message: 'This PR has not been updated in the last 30 days. Is it still needed? Unless further action is taken, it will be closed in 5 days.'
+          stale-pr-label: stale
+          days-before-stale: 30
+          days-before-close: 5

.mega-linter.yml

@@ -0,0 +1,24 @@
+---
+# Configuration file for Mega-Linter
+# See all available variables at https://megalinter.github.io/configuration/ and in linters documentation
+
+APPLY_FIXES: all # all, none, or list of linter keys
+DEFAULT_BRANCH: master # Usually master or main
+# ENABLE: # If you use ENABLE variable, all other languages/formats/tooling-formats will be disabled by default
+# ENABLE_LINTERS: # If you use ENABLE_LINTERS variable, all other linters will be disabled by default
+DISABLE:
+  - C
+  - COPYPASTE # abusive copy-pastes
+  - SPELL # spelling mistakes
+DISABLE_LINTERS:
+  - CPP_CPPLINT
+  - BASH_EXEC
+  - BASH_SHFMT
+  - JSON_PRETTIER
+  - YAML_V8R
+  - YAML_PRETTIER
+SHOW_ELAPSED_TIME: true
+FILEIO_REPORTER: false
+GITHUB_COMMENT_REPORTER: false
+UPDATED_SOURCES_REPORTER: false
+PRINT_ALPACA: false # Don't print ASCII alpaca in the log

EventFiltering/PWGUD/README.md

@@ -4,14 +4,14 @@ Checks for diffractive events and fills table `DiffractionFilters`. The table is
 
 The diffractive event filter is contained in the following set of files:
 
-### cutHolder.cxx, cutHolder.h
+## cutHolder.cxx, cutHolder.h
 `cutHolder` is a buffer for the various cut parameters. Is used to create a configurable which values can be set by command line options.
 
-### diffHelpers.h
+## diffHelpers.h
 Contains helper functions for the diffractive event selection and the actual filter logics for the various types of events. Currently implemented are:
 
 - DGSelector: a filter for Double Gap (DG) events
 
-### diffractionFilter.cxx
+## diffractionFilter.cxx
 Contains the actual filter tasks. Currently implemented are:
 - DGFilterRun3: filter task for DG events in Run 3 data

README.md

@@ -1,3 +1,5 @@
+# O2Physics
+
 Documentation for the ALICE Analysis framework is available at:
 
-https://aliceo2group.github.io/analysis-framework/
+<https://aliceo2group.github.io/analysis-framework/>

Scripts/update_ccdb.py

@@ -22,27 +22,35 @@
 TODO add support for 3 files update
 """
 
+import argparse
 import subprocess
 from datetime import datetime
+
 import matplotlib.pyplot as plt
-import argparse
 
 
 def convert_timestamp(ts):
     """
     Converts the timestamp in milliseconds in human readable format
     """
-    return datetime.utcfromtimestamp(ts/1000).strftime('%Y-%m-%d %H:%M:%S')
+    return datetime.utcfromtimestamp(ts / 1000).strftime("%Y-%m-%d %H:%M:%S")
 
 
 def get_ccdb_obj(path, timestamp, dest="/tmp/", verbose=0):
     """
     Gets the ccdb object from 'path' and 'timestamp' and downloads it into 'dest'
     """
     if verbose:
-        print("Getting obj", path, "with timestamp",
-              timestamp, convert_timestamp(timestamp))
-    cmd = f"o2-ccdb-downloadccdbfile --path {path} --dest {dest} --timestamp {timestamp}"
+        print(
+            "Getting obj",
+            path,
+            "with timestamp",
+            timestamp,
+            convert_timestamp(timestamp),
+        )
+    cmd = (
+        f"o2-ccdb-downloadccdbfile --path {path} --dest {dest} --timestamp {timestamp}"
+    )
     subprocess.run(cmd.split())
 
 
@@ -61,7 +69,7 @@ def get_ccdb_obj_validity(path, dest="/tmp/", verbose=0):
         print(*output, "\n")
         print("err:")
         print(error)
-    result = list(filter(lambda x: x.startswith('Valid-'), output))
+    result = list(filter(lambda x: x.startswith("Valid-"), output))
     ValidFrom = result[0].split()
     ValidUntil = result[1].split()
     return [int(ValidFrom[-1]), int(ValidUntil[-1])]
@@ -71,12 +79,18 @@ def upload_ccdb_obj(path, timestamp_from, timestamp_until, dest="/tmp/", meta=""
     """
     Uploads a new object to CCDB in the 'path' using the validity timestamp specified
     """
-    print("Uploading obj", path, "with timestamp", [timestamp_from, timestamp_until],
-          convert_timestamp(timestamp_from), convert_timestamp(timestamp_until))
+    print(
+        "Uploading obj",
+        path,
+        "with timestamp",
+        [timestamp_from, timestamp_until],
+        convert_timestamp(timestamp_from),
+        convert_timestamp(timestamp_until),
+    )
     key = path.split("/")[-1]
     cmd = f"o2-ccdb-upload -f {dest}{path}/snapshot.root "
     cmd += f"--key {key} --path {path} "
-    cmd += f"--starttimestamp {timestamp_from} --endtimestamp {timestamp_until} --meta \"{meta}\""
+    cmd += f'--starttimestamp {timestamp_from} --endtimestamp {timestamp_until} --meta "{meta}"'
     subprocess.run(cmd.split())
 
 
@@ -87,9 +101,9 @@ def main(path, timestamp_from, timestamp_until, verbose=0, show=False):
     Gets the object from CCDB specified in 'path' and for 'timestamp_until+1'
     If required plots the situation before and after the update
     """
-    get_ccdb_obj(path, timestamp_from-1)
+    get_ccdb_obj(path, timestamp_from - 1)
     val_before = get_ccdb_obj_validity(path, verbose=verbose)
-    get_ccdb_obj(path, timestamp_until+1)
+    get_ccdb_obj(path, timestamp_until + 1)
     val_after = get_ccdb_obj_validity(path, verbose=verbose)
     overlap_before = val_before[1] > timestamp_from
     overlap_after = val_after[0] < timestamp_until
@@ -98,48 +112,67 @@ def main(path, timestamp_from, timestamp_until, verbose=0, show=False):
             print("Previous objects overalps")
         if overlap_after:
             print("Next objects overalps")
-    trimmed_before = val_before if not overlap_before else [
-        val_before[0], timestamp_from - 1]
-    trimmed_after = val_after if not overlap_after else [
-        timestamp_until+1, val_after[1]]
+    trimmed_before = (
+        val_before if not overlap_before else [val_before[0], timestamp_from - 1]
+    )
+    trimmed_after = (
+        val_after if not overlap_after else [timestamp_until + 1, val_after[1]]
+    )
     if show:
         fig, ax = plt.subplots()
         fig
 
         def bef_af(v, y):
             return [v[0] - 1] + v + [v[1] + 1], [0, y, y, 0]
+
         if True:
-            ax.plot(*bef_af(val_before, 0.95), label='before')
-            ax.plot(*bef_af(val_after, 1.05), label='after')
+            ax.plot(*bef_af(val_before, 0.95), label="before")
+            ax.plot(*bef_af(val_after, 1.05), label="after")
         if False:
-            ax.plot(*bef_af(trimmed_before, 0.9), label='trimmed before')
-            ax.plot(*bef_af(trimmed_after, 1.1), label='trimmed after')
-        ax.plot(*bef_af([timestamp_from, timestamp_until], 1), label='object')
+            ax.plot(*bef_af(trimmed_before, 0.9), label="trimmed before")
+            ax.plot(*bef_af(trimmed_after, 1.1), label="trimmed after")
+        ax.plot(*bef_af([timestamp_from, timestamp_until], 1), label="object")
         xlim = 10000000
-        plt.xlim([timestamp_from-xlim, timestamp_until+xlim])
+        plt.xlim([timestamp_from - xlim, timestamp_until + xlim])
         plt.ylim(0, 2)
-        plt.xlabel('Timestamp')
-        plt.ylabel('Validity')
+        plt.xlabel("Timestamp")
+        plt.ylabel("Validity")
         plt.legend()
         plt.show()
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
-        description="Uploads timestamp non overlapping objects to CCDB."
-        "Basic example: `./update_ccdb.py qc/TOF/TOFTaskCompressed/hDiagnostic 1588956517161 1588986517161 --show --verbose`")
-    parser.add_argument('path', metavar='path_to_object', type=str,
-                        help='Path of the object in the CCDB repository')
-    parser.add_argument('timestamp_from', metavar='from_timestamp', type=int,
-                        help='Timestamp of start for the new object to use')
-    parser.add_argument('timestamp_until', metavar='until_timestamp', type=int,
-                        help='Timestamp of stop for the new object to use')
-    parser.add_argument('--verbose', '-v', action='count', default=0)
-    parser.add_argument('--show', '-s', action='count', default=0)
+        description="Uploads timestamp non overlapping objects to CCDB. "
+        "Basic example: `./update_ccdb.py qc/TOF/TOFTaskCompressed/hDiagnostic "
+        "1588956517161 1588986517161 --show --verbose`"
+    )
+    parser.add_argument(
+        "path",
+        metavar="path_to_object",
+        type=str,
+        help="Path of the object in the CCDB repository",
+    )
+    parser.add_argument(
+        "timestamp_from",
+        metavar="from_timestamp",
+        type=int,
+        help="Timestamp of start for the new object to use",
+    )
+    parser.add_argument(
+        "timestamp_until",
+        metavar="until_timestamp",
+        type=int,
+        help="Timestamp of stop for the new object to use",
+    )
+    parser.add_argument("--verbose", "-v", action="count", default=0)
+    parser.add_argument("--show", "-s", action="count", default=0)
 
     args = parser.parse_args()
-    main(path=args.path,
-         timestamp_from=args.timestamp_from,
-         timestamp_until=args.timestamp_until,
-         verbose=args.verbose,
-         show=args.show)
+    main(
+        path=args.path,
+        timestamp_from=args.timestamp_from,
+        timestamp_until=args.timestamp_until,
+        verbose=args.verbose,
+        show=args.show,
+    )