Upgrade Codecov action v4 → v5

.github/workflows/gitlab_ci.yml

@@ -0,0 +1,222 @@
+---
+
+name: Mirror to Gitlab to trigger CI
+
+on:
+  push:
+  pull_request_target:
+    types: [opened, synchronize, reopened, labeled]
+  schedule:
+    - cron: '2 5 * * 1'
+
+jobs:
+  check_permission:
+    runs-on: ubuntu-latest
+    if: >-
+        (github.repository_owner == 'Parallel-in-Time') &&
+        ((github.event_name == 'push') ||
+         (github.event_name == 'schedule') ||
+         ((github.event_name == 'pull_request_target') &&
+          (contains(github.event.pull_request.labels.*.name, 'gitlab-mirror'))
+         )
+        )
+    steps:
+      - name: Query permissions of triggering actor
+        id: query_permission_triggering_actor
+        if: github.event_name == 'pull_request_target'
+        uses: actions-cool/check-user-permission@v2
+        with:
+          username: ${{ github.triggering_actor }}
+          require: 'write'
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Interpret the queried result
+        if: github.event_name == 'pull_request_target'
+        run: |
+          echo "Current permission level is ${{ steps.query_permission_triggering_actor.outputs.user-permission }}"
+          echo "Job originally triggered by ${{ github.actor }}"
+          echo "Checking permission returned ${{ steps.query_permission_triggering_actor.outputs.require-result }}"
+          if ${{ steps.query_permission_triggering_actor.outputs.require-result }}
+            then
+              echo 'Permissions granted'
+              exit 0
+            else
+              echo 'Not enough permissions. Please ask a member of Parallel-in-Time to rerun the job.'
+              exit 1
+          fi
+      - name: Pass if workflow from push or schedule
+        if: >-
+          (github.event_name == 'push') ||
+          (github.event_name == 'schedule')
+        run: exit 0
+      # - name: Fail for other triggers
+      #   if: >-
+      #     (github.event_name != 'push') &&
+      #     (github.event_name != 'schedule') &&
+      #     (github.event_name != 'pull_request_target')
+      #   run: exit 1
+
+  mirror_to_gitlab:
+    runs-on: ubuntu-latest
+    if: >-
+        (github.repository_owner == 'Parallel-in-Time') &&
+        ((github.event_name == 'push') ||
+         (github.event_name == 'schedule') ||
+         ((github.event_name == 'pull_request_target') &&
+          (contains(github.event.pull_request.labels.*.name, 'gitlab-mirror'))
+         )
+        )
+    needs:
+      - check_permission
+    steps:
+      - name: set proper sha
+        run: |
+          echo "${{ github.event_name }}"
+          if [ "${{ github.event_name }}" == 'push' ] || [ "${{ github.event_name }}" == 'schedule' ]
+          then
+            echo "USED_SHA=${{ github.sha }}" >> "$GITHUB_ENV"
+          fi
+          if [ "${{ github.event_name }}" == 'pull_request_target' ]
+          then
+            echo "USED_SHA=${{ github.event.pull_request.head.sha }}" >> "$GITHUB_ENV"
+          fi
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: "${{ env.USED_SHA }}"
+          persist-credentials: false
+      - name: check if merge is possible (merge is used for testing)
+        if: github.event_name == 'pull_request_target'
+        run: |
+          if $(git rev-parse --is-shallow-repository); then
+            git fetch --unshallow
+          else
+            git fetch
+          fi
+          echo "Checkout of ${{ github.base_ref }}"
+          git checkout "${{ github.base_ref }}"
+          echo "Git pull"
+          git pull
+          MIRROR_BRANCH="TEMPORARY_MERGE_PR_${{ github.event.number }}"
+          echo MIRROR_BRANCH="$MIRROR_BRANCH" >> $GITHUB_ENV
+          echo "Create new branch $MIRROR_BRANCH and check it out"
+          git checkout -b "$MIRROR_BRANCH"
+          echo "Setting git committer info, so that merge-commit can be created"
+          git config user.email "unused@example.com"
+          git config user.name "Sync bot"
+          echo "Merge the two parts of the Merge-Request to test the resulting version"
+          git merge "${{ github.event.pull_request.head.sha }}"
+      - name: Mirror and wait for Gitlab-CI
+        uses: jakob-fritz/github2lab_action@v0.8.1
+        env:
+          MODE: 'all'  # Either 'mirror', 'get_status', 'get_artifact', or 'all'
+          GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET }}
+          FORCE_PUSH: "true"
+          GITLAB_HOSTNAME: "gitlab.jsc.fz-juelich.de"
+          GITLAB_PROJECT_ID: "6029"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          MIRROR_BRANCH: ${{ env.MIRROR_BRANCH }}
+      - name: Unzip downloaded artifacts
+        run: |
+          pwd
+          ls -lah
+          cd artifacts
+          find . -name "*.zip" -type f -exec unzip -o {} \;
+          ls -lah
+          rm *.zip
+          cd ..
+          ls -lah
+      - name: Uploading artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: Gitlab-Action_artifacts
+          path: |
+            ./artifacts/*
+
+  get_artifacts_from_other_workflow:
+    runs-on: ubuntu-latest
+    needs:
+      - mirror_to_gitlab
+    steps:
+      - name: Download artifacts from this workflow
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+          path: ./github_ci_artifacts
+      - name: Set env-var
+        id: get_id
+        uses: actions/github-script@v7
+        env:
+          workflow_filename: 'ci_pipeline.yml'
+        with:
+          script: |
+            if (context.eventName == "pull_request_target") {
+              var used_sha = context.payload.pull_request.head.sha;
+              var used_event = "pull_request";
+            } else {
+              var used_sha = context.sha;
+              var used_event = context.eventName;
+            }
+            const result = await github.request('GET /repos/{owner}/{repo}/actions/workflows/{workflow_id}/runs', {
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              workflow_id: process.env.workflow_filename,
+              headers: {
+                'X-GitHub-Api-Version': '2022-11-28',
+                'accept': 'application/vnd.github+json'
+              },
+              head_sha: used_sha,
+              event: used_event
+            })
+            console.log("SHA of commit " + used_sha);
+            console.log("Found runs of workflow: " + result.data.total_count);
+            if (result.data.total_count == 1) {
+              console.log("Found workflow has id: " + result.data.workflow_runs[0].id);
+              return result.data.workflow_runs[0].id
+            } else {
+              console.log("Logging all found workflow ids:");
+              for (var i = 0; i < result.data.workflow_runs.length; i++) {
+                console.log(result.data.workflow_runs[i].id);
+              }
+              console.log("Returned workflow id is: " + result.data.workflow_runs[0].id);
+              return result.data.workflow_runs[0].id
+            }
+      - name: Wait for other workflow to finish
+        env:
+          RUN_ID: ${{ steps.get_id.outputs.result }}
+          POLL_TIMEOUT: 10
+        run: |
+          ci_conclusion="pending"
+          echo "Querying status of workflow $RUN_ID for repo $GITHUB_REPOSITORY"
+          until [ "$ci_conclusion" != "pending" ] && [ "$ci_conclusion" != "in_progress" ] && [ "$ci_conclusion" != "null" ]
+          do
+            # Wait some seconds
+            sleep "$POLL_TIMEOUT"
+            # Get the current state of the pipeline and the url of the website
+            run_reply=$(curl --header "'X-GitHub-Api-Version': '2022-11-28', 'accept': 'application/vnd.github+json'" --silent "https://api.github.com/repos/$GITHUB_REPOSITORY/actions/runs/$RUN_ID")
+            ci_conclusion=$(jq -n "$run_reply" | jq -r .conclusion)
+            echo "Current pipeline status: ${ci_conclusion}"
+            http_status=$(jq -n "$run_reply" | jq -r .status)
+            if [ "$http_status" != 200 ] && [[ "$http_status" =~ ^[0-9]+$ ]]; then
+              echo "Request returned status: ${http_status}"
+              exit 1
+            fi
+          done
+          # Set exit code for success or failure  (everything non-success)
+          if [ "$ci_conclusion" = "success" ]; then
+            exit 0
+          else
+            exit 1
+          fi
+      - name: Download artifacts from other workflow
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+          run-id: ${{ steps.get_id.outputs.result }}
+          github-token: ${{ secrets.ACTION_READ_TOKEN }}
+          path: ./github_ci_artifacts
+      - name: Uploading artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: Github_CI_artifacts
+          path: |
+            ./github_ci_artifacts/*

.github/workflows/postprocess.yml

@@ -39,9 +39,11 @@ jobs:
         run: |
           genbadge coverage -i coverage.xml -o htmlcov/coverage-badge.svg
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV }}
+          fail_ci_if_error: true
+          verbose: true
 
 #      - name: Generate benchmark report
 #        uses: pancetta/github-action-benchmark@v1

README.md

@@ -33,7 +33,12 @@ implemented.
     [PETSc](http://www.mcs.anl.gov/petsc/) (through
     [petsc4py](https://bitbucket.org/petsc/petsc4py))
 -   Continuous integration via [GitHub
+<<<<<<< HEAD
+    Actions](https://github.com/Parallel-in-Time/pySDC/actions) and
+    [Gitlab CI](https://gitlab.hzdr.de/r.speck/pysdc/-/pipelines) (through the [GitHub2Gitlab Action](https://github.com/jakob-fritz/github2lab_action))
+=======
     Actions](https://github.com/Parallel-in-Time/pySDC/actions)
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 -   Fully compatible with Python 3.10 - 3.13, runs at least on Ubuntu
 
 ## Getting started

docs/contrib/02_continuous_integration.md

@@ -112,8 +112,11 @@ pytest -v pySDC/tests
 
 ## Running CI on HPC from pull requests
 
+<<<<<<< HEAD
+=======
 > :warning: **Note:** The GitLab mirror integration is currently disabled due to technical issues. This section describes functionality that is temporarily unavailable.
 
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 By syncing the GitHub repository to a certain Gitlab instance, CI-Jobs can be run on HPC machines. This can be helpful for benchmarks or when running on accelerators that are not available as GitHub runners.
 
 For security and accounting reasons, a few extra steps are needed in order to run the contents of a pull request on HPC:

pySDC/core/common.py

@@ -7,7 +7,10 @@
 Module containing utility classe(s) from which inherit some of the pySDC base
 classes.
 """
+<<<<<<< HEAD
+=======
 
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 from pySDC.core.errors import ReadOnlyError
 
 

pySDC/core/hooks.py

@@ -1,6 +1,10 @@
 import logging
 from collections import namedtuple
 
+<<<<<<< HEAD
+
+=======
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 # metadata with defaults
 meta_data = {
     'process': None,

pySDC/core/sweeper.py

@@ -6,6 +6,10 @@
 from pySDC.core.collocation import CollBase
 from pySDC.helpers.pysdc_helper import FrozenClass
 
+<<<<<<< HEAD
+
+=======
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 # Organize QDeltaGenerator class in dict[type(QDeltaGenerator),set(str)] to retrieve aliases
 QDELTA_GENERATORS_ALIASES = {v: set() for v in set(QDELTA_GENERATORS.values())}
 for k, v in QDELTA_GENERATORS.items():

pySDC/helpers/fieldsIO.py

@@ -47,7 +47,10 @@
 To use MPI collective writing, you need to call first the class methods :class:`Rectilinear.setupMPI` (cf their docstring).
 Also, `Rectilinear.setHeader` **must be given the global grids coordinates**, whether the code is run in parallel or not.
 """
+<<<<<<< HEAD
+=======
 
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 import os
 import numpy as np
 from typing import Type, TypeVar

pySDC/helpers/testing.py

@@ -5,7 +5,10 @@
 
 Helpers module for testing utilities
 """
+<<<<<<< HEAD
+=======
 
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 import os
 import json
 import warnings

pySDC/helpers/vtkIO.py

@@ -3,7 +3,10 @@
 """
 Helper functions for VTK files IO (to be used with Paraview or PyVista)
 """
+<<<<<<< HEAD
+=======
 
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 import os
 import vtk
 from vtkmodules.util import numpy_support

pySDC/implementations/convergence_controller_classes/estimate_embedded_error.py

@@ -114,8 +114,15 @@ def estimate_embedded_error_serial(self, L):
             else:
                 return comm.bcast(abs(L.uold[comm.rank + 1] - L.u[comm.rank + 1]), root=comm.size - 1)
         else:
+<<<<<<< HEAD
+            raise NotImplementedError(
+                f"Don't know how to estimate embedded error for sweeper type \
+\"{self.params.sweeper_type}\""
+            )
+=======
             raise NotImplementedError(f"Don't know how to estimate embedded error for sweeper type \
 \"{self.params.sweeper_type}\"")
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 
     def setup_status_variables(self, controller, **kwargs):
         """
@@ -207,8 +214,15 @@ def post_iteration_processing(self, controller, S, **kwargs):
             None
         """
         if len(S.levels) > 1 and len(controller.MS) > 1:
+<<<<<<< HEAD
+            raise NotImplementedError(
+                "Embedded error estimate only works for serial multi-level or parallel single \
+level"
+            )
+=======
             raise NotImplementedError("Embedded error estimate only works for serial multi-level or parallel single \
 level")
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 
         if S.status.iter > 0 or self.params.sweeper_type == "RK":
             if self.params.averaged:

pySDC/implementations/convergence_controller_classes/estimate_extrapolation_error.py

@@ -139,8 +139,15 @@ def store_values(self, S, **kwargs):
         elif type(f) == mesh:
             self.prev.f[oldest_val] = f
         else:
+<<<<<<< HEAD
+            raise DataError(
+                f"Unable to store f from datatype {type(f)}, extrapolation based error estimate only\
+ works with types imex_mesh and mesh"
+            )
+=======
             raise DataError(f"Unable to store f from datatype {type(f)}, extrapolation based error estimate only\
  works with types imex_mesh and mesh")
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 
         # store the rest of the values
         self.prev.u[oldest_val] = S.levels[0].u[-1]
@@ -479,8 +486,15 @@ def post_iteration_processing(self, controller, S, **kwargs):
         elif type(lvl.f[0]) == mesh:
             f = [lvl.f[i] if self.coeff.f[i] else 0.0 for i in range(len(lvl.f) - 1)]
         else:
+<<<<<<< HEAD
+            raise DataError(
+                f"Unable to store f from datatype {type(lvl.f[0])}, extrapolation based error estimate only\
+ works with types imex_mesh and mesh"
+            )
+=======
             raise DataError(f"Unable to store f from datatype {type(lvl.f[0])}, extrapolation based error estimate only\
  works with types imex_mesh and mesh")
+>>>>>>> d3e0bb943e63560d7b018cac8a624c1883aa0c7b
 
         # compute the error with the weighted sum
         if self.comm: