Initial commit after new repo setup

variables:

  GIT_STRATEGY: clone

  CONTAINER_IMAGE_URL: "${ASRP_CONTAINER_IMAGE_REPOSITORY}"

# This import is for the func_rse_docker_* functions

before_script:

  - curl https://code.ornl.gov/rse-deployment/rse-sharables/raw/master/rse-bash-modules.sh -O

  - docker login -u ${ASRP_CONTAINER_IMAGE_USER} -p ${ASRP_CONTAINER_IMAGE_PASSWORD} ${ASRP_CONTAINER_IMAGE_REPOSITORY}

  - source rse-bash-modules.sh

  - func_rse_docker_cleanup

after_script:

  - curl https://code.ornl.gov/rse-deployment/rse-sharables/raw/master/rse-bash-modules.sh -O

  - source rse-bash-modules.sh

  - func_rse_docker_cleanup

  - sudo chown -R gitlab-runner .

.test_docker_job:

  stage: test

  variables:

    PROJECT: project

    NAME: name

    TEST_COMMAND: test # must be a single value string ("pytest"), not multi-values in single string ("pytest --cov=.")

  script:

    - cd ${PROJECT}/${NAME}

    - docker build -f Dockerfile -t image .

    - docker run --entrypoint=${TEST_COMMAND} image

  tags:

    - rse-multi-builder

.build_docker_job:

  stage: build

  variables:

    PROJECT: project

    NAME: name

    TAG: "0.1"

    FORCE_TAGS: "false"

  when: manual

  script:

    - cd ${PROJECT}/${NAME}

    - docker build -f Dockerfile --target devel -t image_devel . || true

    - docker build -f Dockerfile -t image .

    - IMAGE_NAME=${CONTAINER_IMAGE_URL}/${PROJECT}/${NAME}

    - docker tag image ${IMAGE_NAME}:$CI_COMMIT_SHORT_SHA

    - docker push ${IMAGE_NAME}:$CI_COMMIT_SHORT_SHA

    - >

      if [ "$CI_COMMIT_BRANCH" == "$CI_DEFAULT_BRANCH" ] || [ "$FORCE_TAGS" == "true" ]; then

        docker tag image ${IMAGE_NAME}:latest

        docker push ${IMAGE_NAME}:latest

        docker pull ${IMAGE_NAME}:${TAG} || docker tag image ${IMAGE_NAME}:${TAG} &&  docker push ${IMAGE_NAME}:${TAG}

      fi

  tags:

    - rse-multi-builder

test-asrp-gsas2-refinement:

  extends: .test_docker_job

  variables:

    PROJECT: asrp

    NAME: gsas2_refinement

    TEST_COMMAND: pytest

build-asrp-gsas2-refinement:

  extends: .build_docker_job

  needs: [test-asrp-gsas2-refinement]

  variables:

    PROJECT: asrp

    NAME: gsas2_refinement

    TAG: "0.8"

ARG GSAS2_VERSION=v5.5.2

FROM savannah.ornl.gov/rse/gsas2:${GSAS2_VERSION} AS base

#WORKDIR /app

#--------------------------#

FROM base AS production

COPY . .

RUN pixi run python -m pip install .

# Creates input (./inputs) and output (./portal) directories accessible by all

RUN mkdir -p ./portal \

    && mkdir -p ./inputs \

    && chmod -R 777 ./portal ./inputs

CMD [ "pixi", "run", "python", "-m", "gsas2_refinement.gsas2_refinement" ]

# ASRP's GSAS2 Refinement Tool

ASRP repo: https://code.ornl.gov/neutrons/asrp

# Developers

### Using Docker

This uses the RSE shared docker image for GSAS2 found in [this repo][rse_gsas2_image]

Build the image

```

docker login code.ornl.gov:4567

docker build -t asrp-gsas2-refinement .

```

# Usage

Test:

```

docker run --entrypoint="" asrp-gsas2-refinement pytest

```

To run (use your parameters):

```

docker run \

    -v /path/to/input/structure:/refinement/input.cif \

    -v /path/to/input/gsas_file:/refinement/input.gsa \

    -v /path/to/input/instrument_parametes:/refinement/input.instprm \

    -v /path/to/output/folder:/app/portal \

    asrp-gsas2-refinement \

        --cif-filename /refinement/input.cif \

        --gsas-filename /refinement/input.gsa \

        --instrument-params-filename /refinement/input.instprm \

        --scatter-type N \

        --bank-id 5 \

        --xmin 5000.0 \

        --xmax 15000.0

```

[rse_gsas2_image]: https://code.ornl.gov/rse/images/gsas2

[project]

name = "gsas2-refinement"

version = "0.1.0"

description = "GSAS2 Refinement Application for ASRP"

authors = [

  { name="Marshall McDonnell", email="mcdonnellmt@ornl.gov" },

]

[tool.pytest.ini_options]

pythonpath = [

  "src", "src/gsas2_refinement"

]