obsForge

Forging next generation of observation processing leveraging JEDI

Clone and Build

git clone --recursive --jobs 2 https://github.com/NOAA-EMC/obsForge.git
cd obsForge
./build.sh

Testing

This section provides instructions for running all tests in the main obsForge repository (excluding submodule tests). The testing includes both C++ tests managed by CTest and Python tests using pytest.

Prerequisites

1. Build the project (if not already done):

   ./build.sh

2. Load modules (on supported HPC systems):

   module use modulefiles
   module load obsforge/{hpc}.{compiler}

3. Set up Python environment for pytest:

   python3 -m venv obsforge_test_env
   source obsforge_test_env/bin/activate
   pip install -r requirements.txt

   Note: This virtual environment setup is essential when using JCSDA docker containers and recommended for local development to avoid dependency conflicts. It may not be necessary if you've already loaded appropriate modules on HPC systems, but it's still recommended for isolation.

Running C++ Tests (CTest)

All CTest commands should be run from the build directory. Note: These commands run only obsForge-specific tests, excluding submodule tests (OOPS, IODA, etc.).

cd build

Important for HPC Users:

• Some tests use MPI and cannot run on login nodes
• Start an interactive compute node session before running tests:

  # Example for SLURM systems
  salloc -N 1 --ntasks-per-node=4 --time=1:00:00
  # or
  srun --pty -N 1 --ntasks-per-node=4 --time=1:00:00 /bin/bash

Run obsForge-specific tests:

# Run obsforge-utils tests only
cd obsforge-utils
ctest --output-on-failure

Run tests in parallel (faster execution):

cd obsforge-utils
ctest -j$(nproc) --output-on-failure

Run specific test categories:

• BUFR to IODA converter tests:

  cd obsforge-utils
  ctest -R test_b2i --output-on-failure

• Non-BUFR to IODA converter tests (utility tests):

  cd obsforge-utils
  ctest -R test_obsforge_util --output-on-failure

Note: Some tests may require specific data files that are only available on certain HPC systems (WCOSS2, Hera, etc.). If tests fail due to missing data, they may need to be run on the appropriate HPC environment.

Running Python Tests (pytest)

Activate Python environment (if not already activated):

source obsforge_test_env/bin/activate

Run pytest tests:

# Test the pyobsforge module
pytest ush/python/pyobsforge/tests/ --disable-warnings -v

# Test the scripts (Note: may require HPC-specific data)
pytest scripts/tests/ --disable-warnings -v

Important: The scripts/tests/ tests may require specific data files that are only staged on certain HPC systems. If these tests fail due to missing data, they should be run on the appropriate HPC environment where the data is available.

Run tests with style checking:

# Install flake8 if not already installed
pip install flake8

# Check code style
flake8 ush/python/pyobsforge
flake8 ush/*.py
flake8 scripts/*.py

# Run pytest tests
pytest ush/python/pyobsforge/tests/ --disable-warnings -v
pytest scripts/tests/ --disable-warnings -v

Running All Tests (Combined)

To run both CTest and pytest tests in sequence:

# From the repository root
cd build/obsforge-utils
ctest --output-on-failure -j$(nproc)
cd ../..
source obsforge_test_env/bin/activate
pytest ush/python/pyobsforge/tests/ --disable-warnings -v
# Only run scripts tests if on HPC with required data
# pytest scripts/tests/ --disable-warnings -v

Notes

• Submodule tests are excluded from these instructions - they have their own testing procedures
• HPC considerations:
  • Some tests use MPI and cannot run on login nodes
  • Use interactive compute node sessions (salloc or srun) when on HPC systems
  • Some tests require data files only available on specific HPC systems (WCOSS2, Hera, etc.)
• Use ctest --output-on-failure to see detailed error messages when tests fail
• Parallel execution with -j$(nproc) can significantly speed up test runs
• The Python virtual environment setup is essential for JCSDA docker containers and recommended for local development to avoid dependency conflicts
• Focus on obsforge-utils directory for C++ tests to avoid running all submodule tests

Workflow Usage

source ush/of_setup.sh
setup_xml.py --config config.yaml  --template obsforge_rocoto_template.xml.j2 --output obsforge.xml

Note:

To load rocoto on WCOSS2:

module use /apps/ops/test/nco/modulefiles/core
module load rocoto