Merge pull request #11 from KrisThielemans/prd2PETSIRD

Changes prd to PETSIRD and update module/CI

Author: KrisThielemans

.devcontainer/Dockerfile

@@ -29,7 +29,7 @@ ARG USERNAME="vscode"
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 ARG CONDA_GID=900
-ARG CONDA_ENVIRONMENT_NAME=prd
+ARG CONDA_ENVIRONMENT_NAME=petsird
 
 RUN apt-get update && apt-get install -y \
     libc6-dbg \
@@ -83,7 +83,7 @@ ENV CMAKE_GENERATOR=Ninja
 
 # Create a kits file for the VSCode CMake Tools extension, so you are not prompted for which kit to select whenever you open VSCode
 RUN mkdir -p /home/vscode/.local/share/CMakeTools \
-    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
+    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/petsird/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/petsird/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
     && chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json
 
 # Install the yardl tool

.devcontainer/devcontainer.bashrc

@@ -2,7 +2,7 @@
 # shellcheck source=/dev/null
 
 source /opt/conda/etc/profile.d/conda.sh
-conda activate prd
+conda activate petsird
 source <(yardl completion bash)
 
 if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 // For format details, see https://aka.ms/devcontainer.json.
 {
-  "name": "prd",
+  "name": "petsird",
   "build": {
     "dockerfile": "Dockerfile",
     "context": ".."
@@ -47,7 +47,7 @@
         "cmake.buildDirectory": "${workspaceFolder}/cpp/build",
         "cmake.configureOnOpen": false,
 
-        "python.defaultInterpreterPath": "/opt/conda/envs/prd/bin/python",
+        "python.defaultInterpreterPath": "/opt/conda/envs/petsird/bin/python",
         "python.analysis.typeCheckingMode": "strict",
         "python.analysis.diagnosticMode": "workspace",
         "python.analysis.diagnosticSeverityOverrides": {
@@ -87,7 +87,7 @@
           "gitlens.showWhatsNewAfterUpgrades": false
         },
 
-        "gcovViewer.gcovBinary": "/opt/conda/envs/prd/bin/x86_64-conda-linux-gnu-gcov",
+        "gcovViewer.gcovBinary": "/opt/conda/envs/petsird/bin/x86_64-conda-linux-gnu-gcov",
         "gcovViewer.buildDirectories": ["${workspaceFolder}/cpp/build"],
 
         "search.useIgnoreFiles": false,

.github/actions/configure-environment/action.yml

@@ -23,23 +23,25 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with: {submodules: recursive}
+      - name: strip environment.yml
+        run: |
+          cat environment.yml | grep -v "#.*\<\local\>" > temp-ci-environment.yml
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          submodules: recursive
-
-      - name: Configure environment
-        uses: ./.github/actions/configure-environment
-
+          activate-environment: yardl
+          environment-file: temp-ci-environment.yml
       - name: Install yardl
         run: |
+          rm temp-ci-environment.yml
           YARDL_DIR=${{github.workspace}}/yardl
           mkdir ${YARDL_DIR}
-          cd ${YARDL_DIR}
-          echo "${{github.workspace}}/yardl" >> $GITHUB_PATH
-          YARDL_VERSION=0.3.2
+          YARDL_VERSION=0.6.2
           wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
-          tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+          tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" -C "${YARDL_DIR}"
           rm "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+          echo "${YARDL_DIR}" >> $GITHUB_PATH
 
       - name: Build model
         run: |

.github/workflows/ci.yml

@@ -1,3 +1,4 @@
 [submodule "PETSIRD"]
 	path = PETSIRD
-	url = https://github.com/ETSInitiative/PRDdefinition
+	url = https://github.com/ETSInitiative/PETSIRD
+        branch=main

.gitmodules

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12.0) # older would work, but could give warnings on policy CMP0074
-project(PETSIRDUseCaseTemplate VERSION 0.1.0)
+project(PETSIRDUseCaseTemplate VERSION 0.2.0)
 
 set(CMAKE_CXX_STANDARD 17)
 
@@ -11,7 +11,7 @@ endif()
 
 # Example lines for a new executable
 # add_executable(my_prog my_prog.cpp)
-# target_link_libraries(my_prog PUBLIC prd_generated)
+# target_link_libraries(my_prog PUBLIC petsird_generated)
 # install(TARGETS my_prog DESTINATION bin)
 
 add_subdirectory(../PETSIRD/cpp/generated PETSIRD_generated)

PETSIRD

@@ -1,4 +1,4 @@
-name: prd
+name: petsird
 channels:
   - conda-forge
   - defaults

cpp/CMakeLists.txt

@@ -1,5 +1,5 @@
 import sys
 # Currently hard-wire location of generated files. This will need to change!
 sys.path.append('../PETSIRD/python/')
-import prd
+import petsird