Implemented the building of congruent and embedded meshes from netCDF input data

.clang-format

@@ -70,5 +70,7 @@ SpacesInParentheses: 'false'
 SpacesInSquareBrackets: 'false'
 TabWidth: '2'
 UseTab: Never
+LineEnding: LF
+InsertNewlineAtEOF: 'true'
 
 ...

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,48 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# Bug report
+
+**Describe the bug**
+A clear and concise description of what the bug/unexpected behaviour is.
+
+**To Reproduce**
+Which command did you run/which function did you call?
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Log files**
+- If possible, add any output and error messages that you got
+- Please upload the `config.log` file (when building with autotools)
+- For failing tests, please upload the `test-suite.log` file (when building with autotools)
+- When building with CMake please upload
+  - `CMakeCache.txt`
+  - `CMakeFiles/CMakeError.log`
+  - `CMakeFiles/CMakeOutput.log`
+  - `Testing/Temporary/FailedTest.log` (for failing tests)
+  - `Testing/Temporary/LastTestsFailed.log` (for failing tests)
+
+**Environment (please complete the following information):**
+ - OS: [e.g. Ubuntu 22.04, Windows 11]
+ - Compiler: [e.g., gcc, icc, mpicc]
+ - Compiler version: [e.g. the output of 'gcc --version']
+ - MPI version (if MPI is used): [The output of 'mpirun --version' or 'mpiexec --version']
+
+**Estimated priority**
+Which of these is most applicable (remove the others):
+
+"Priority: high"  Should be solved as soon as possible 
+
+"Priority: medium"  Should be solved within half a year 
+
+"Priority: low" Should be solved eventually
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# Feature request
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution or feature you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Estimated priority**
+Which of these is most applicable (remove the others):
+
+"Priority: high"  Should be solved as soon as possible 
+
+"Priority: medium"  Should be solved within half a year 
+
+"Priority: low" Should be solved eventually
+
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,12 @@
+---
+name: Question
+about: I have a question about t8code
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# Question
+
+Please post any questions about t8code or the usage of t8code.

.github/workflows/add_release_documentation.yml

@@ -56,12 +56,17 @@ jobs:
 #
 # Setup and bootstrap
 #
+
+    - name: Update packages
+      run: sudo apt-get update && sudo apt-get upgrade -y
+    # This step is necessary to get the newest package data
     - name: checkout
       if: ${{ env.MINOR_RELEASE == 'true' }}
       uses: actions/checkout@v4
       with:
         path: t8code
-
+        fetch-tags: true
+        fetch-depth: 0
     - name: Install dependencies
       if: ${{ env.MINOR_RELEASE == 'true' }}
       run: sudo apt-get install libz-dev doxygen-latex
@@ -114,7 +119,6 @@ jobs:
       uses: actions/checkout@v4
       with:
         ref: ${{ github.head_ref }}
-        fetch-depth: 0
         repository: DLR-AMR/t8code-website
         path: t8code-website
         token: ${{ secrets.T8DDY_TOKEN }}
@@ -142,7 +146,7 @@ jobs:
         ./generate_redirections.sh $GITHUB_REF_NAME
     - name: Create Pull Request at DLR-AMR/t8code-website
       if: ${{ env.MINOR_RELEASE == 'true' }}
-      uses: peter-evans/create-pull-request@v6
+      uses: peter-evans/create-pull-request@v7
       with:
         path: t8code-website
         title: Add documentation for t8code ${{ github.ref_name }}

.github/workflows/check_indentation.yml

@@ -52,6 +52,17 @@ jobs:
     timeout-minutes: 10
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-tags: true # required to get version tags
+        fetch-depth: 0    # required to get all history, especially the version tags      
+    # Deactivated the install sudo because it failed.
+    #- name: install sudo
+    #  run: apt update && apt install sudo
+    # On the github Ubuntu 20.04, sudo is not available by default
+    # we need it, however, to update/upgrade our packages.
+    - name: Update packages
+      run: sudo apt-get update && sudo apt-get upgrade -y
+    # This step is necessary to get the newest package data
     - name: Install indent
       run: pip install clang-format==17.0.1
     - name: Indentation check

.github/workflows/ci_playground.yml

@@ -78,7 +78,15 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0
+          fetch-tags: true # required to get version tags
+          fetch-depth: 0    # required to get all history, especially the version tags      
+      - name: install sudo
+        run: apt update && apt install sudo
+      # On the github Ubuntu 20.04, sudo is not available by default
+      # we need it, however, to update/upgrade our packages.      
+      - name: Update packages
+        run: sudo apt-get update && sudo apt-get upgrade -y
+      # This step is necessary to get the newest package data
       - name: define sc var
         run: hash=`git rev-parse HEAD:sc` && echo sc_commit=$hash >> $GITHUB_ENV
       - name: define p4est var

.github/workflows/mattermost_issue.yml

@@ -0,0 +1,76 @@
+#  This file is part of t8code.
+#  t8code is a C library to manage a collection (a forest) of multiple
+#  connected adaptive space-trees of general element types in parallel.
+#
+#  Copyright (C) 2024 the developers
+#
+#  t8code is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  t8code is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with t8code; if not, write to the Free Software Foundation, Inc.,
+#  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+# This is a workflow that posts messages in our Mattermost-Team concerning issues.
+# See https://docs.github.com/en/webhooks/webhook-events-and-payloads?actionType=closed#issues for
+# a documentation of the github issues event.
+
+name: Mattermost_message_issue
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pull request events on the feature-CI_mattermost_messages, develop or main branch
+  issues:
+    types: [ opened, closed, reopened]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+env:
+  message_build: 0
+
+jobs:
+  send_mm_message_issue:
+    if: github.repository == 'DLR-AMR/t8code'
+    runs-on: ubuntu-20.04
+    steps:
+      - name: debug_before_build
+        run: echo ${{ env.message_build}}
+      # build the message depending on different types of events and event actions. Message is written into mattermost.json
+      - name: dispatch_run
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          echo message_build=1 >> $GITHUB_ENV &&
+          echo message_content='User ${{github.actor}} triggered the workflow_dispatch' >> $GITHUB_ENV
+      - name: closed_message
+        if: github.event.action == 'closed'
+        run: |
+          echo message_build=1 >> $GITHUB_ENV &&
+          echo message_content='User ${{ github.actor }} closed issue ${{ github.event.issue.number }}. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
+      - name: opened_message
+        if: github.event.action == 'opened'
+        run: |
+          echo message_build=1 >> $GITHUB_ENV &&
+          echo message_content='User ${{ github.actor }} opened issue ${{ github.event.issue.number }}. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
+      - name: reopened_message
+        if: github.event.action == 'reopened'
+        run: |
+          echo message_build=1 >> $GITHUB_ENV &&
+          echo message_content='User ${{ github.actor }} reopened issue ${{ github.event.issue.number }}. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
+      - name: debug_after_build
+        run: echo ${{ env.message_build }}
+      # if a message has been written send the message to the mattermost-channel described in the secrets
+      - name: send_message
+        if: ${{ env.message_build == 1 }}
+        uses: mattermost/action-mattermost-notify@master
+        with:
+          MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
+          MATTERMOST_USERNAME: t8ddy
+          TEXT: ${{ env.message_content }}

.github/workflows/mattermost.yml → .github/workflows/mattermost_pull_request.yml

@@ -22,7 +22,7 @@
 # This is a workflow that posts messages in our Mattermost-Team concerning pull-requests and pushes
 # on the main, develop and feature-CI_mattermost_messages branch.
 
-name: Mattermost_message
+name: Mattermost_message_pull_request
 
 # Controls when the workflow will run
 on:
@@ -37,7 +37,7 @@ env:
   message_build: 0
 
 jobs:
-  send_mm_message:
+  send_mm_message_pr:
     if: github.repository == 'DLR-AMR/t8code'
     runs-on: ubuntu-20.04
     steps:
@@ -48,23 +48,24 @@ jobs:
         if: github.event.action == 'closed' && github.event.pull_request.merged == true
         run: |
           echo message_build=1 >> $GITHUB_ENV &&
-          echo "{\"text\":\"Pull request ${{ github.event.number }} has been merged. See ${{ github.event.pull_request.html_url }} for more details.\"}" > mattermost.json
+          echo message_content='Pull request ${{ github.event.number }} has been merged. See ${{ github.event.pull_request.html_url }} for more details.' >> $GITHUB_ENV
       - name: push_message
         if: github.event_name == 'push' && github.event.action != 'closed'
         run: |
           echo message_build=1 >> $GITHUB_ENV &&
-          echo "{\"text\":\"${{ github.event.pusher.name }} pushed into ${{ github.event.ref }}. See ${{ github.event.compare }} for more details.\"}" > mattermost.json
+          echo message_content='${{ github.event.pusher.name }} pushed into ${{ github.event.ref }}. See ${{ github.event.compare }} for more details.' >> $GITHUB_ENV
       - name: pull_request_message
         if: github.event_name == 'pull_request' && github.event.action != 'synchronize' && github.event.action != 'closed'
         run: |
           echo message_build=1 >> $GITHUB_ENV &&
-          echo "{\"text\":\"Pull request ${{ github.event.number }} has been ${{ github.event.action }}. See ${{ github.event.pull_request.html_url }} for more details.\"}" > mattermost.json
+          echo message_content='Pull request ${{ github.event.number }} has been ${{ github.event.action }}. See ${{ github.event.pull_request.html_url }} for more details.'  >> $GITHUB_ENV
       - name: debug_after_build
         run: echo ${{ env.message_build }}
       # if a message has been written send the message to the mattermost-channel described in the secrets
       - name: send_message
         if: ${{ env.message_build == 1 }}
         uses: mattermost/action-mattermost-notify@master
-        env:
+        with:
           MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
-          MATTERMOST_USERNAME: t8y
+          MATTERMOST_USERNAME: t8ddy
+          TEXT: ${{ env.message_content }}