Taskfile.yml

version: '3'

tasks:

  install-pixelator-r:
      desc: Install the PixelatorR R package into a specific environment
      summary: |-
        Install PixelatorR into an environment.

        Variables:
          DEPS: Whether to install pixelatorR dependencies. Default is false.

        Example:
        task install-pixelator-r ENV_NAME=my_env

      vars:
        DEPS: '{{ .DEPS | default "false" }}'
      cmds:
        - |
          set -euo pipefail

          # Determine the environment to use, handle unbound variable
          ENV_TO_USE="{{.ENV_NAME}}"
          if [ -z "$ENV_TO_USE" ]; then
            ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
          fi

          # Check if the environment exists, otherwise quit
          micromamba env list | grep -q "$ENV_TO_USE" || {
            echo "Environment $ENV_TO_USE does not exist. Please create it first."
            exit 1
          }

          echo "Installing pixelatorR in environment $ENV_TO_USE"

          micromamba run -n $ENV_TO_USE Rscript -e '
            local({r <- getOption("repos")
              r["CRAN"] <- "https://cran.r-project.org"
              options(repos=r)
            })
            remotes::install_github(
              "PixelgenTechnologies/pixelatorR",
              upgrade="never",
              deps={{ .DEPS | upper }}
            )
          '
      silent: true

  setup-env-bare:
    desc: Create a micromamba environment with R installed
    summary: |-
      Create a micromamba environment with R installed
      --------------------------------------------------------------

      The environment name can be set using the ENV_NAME environment variable.
      By default, the environment will be named r-pixelator.

      Example:
      task setup-env ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Default environment name
        ENV_NAME=${ENV_NAME:-r-pixelator}

        # Check if micromamba is installed
        if ! command -v micromamba &> /dev/null; then
          echo "micromamba is not installed. Please install it first."
          exit 1
        fi

        # Create the environment
        if micromamba create -n '{{.ENV_NAME}}' -y -c conda-forge conda-forge::r-base; then
          echo "Environment '{{.ENV_NAME}}' created successfully."
        else
          echo "Failed to create environment '{{.ENV_NAME}}'."
          exit 1
        fi
    vars:
      ENV_NAME: '{{.ENV_NAME | default "r-pixelator"}}'
    silent: true

  setup-env-pixelatorR:
    desc: Create a micromamba environment with pixelatorR
    summary: |-
      Create a micromamba environment with pixelatorR
      --------------------------------------------------------------

      The environment name can be set using the ENV_NAME environment variable.
      By default, the environment will be named r-pixelator.

      Examples:
      task setup-env-pixelatorR ENV_NAME=my_env
      task setup-env-pixelatorR ENV_NAME=my_env MICROMAMBA_ARGS="--platform osx-64"

    vars:
      MICROMAMBA_ARGS: '{{ .MICROMAMBA_ARGS | default "" }}'
      ENV_NAME: '{{.ENV_NAME | default "r-pixelator"}}'

    cmds:
      - |
        set -euo pipefail

        # Check if micromamba is installed
        if ! command -v micromamba &> /dev/null; then
          echo "micromamba is not installed. Please install it first."
          exit 1
        fi

        echo "Creating environment '{{.ENV_NAME}}'."

        # Create the environment
        if micromamba env create -y -n {{.ENV_NAME}} -f environment.yml {{ .MICROMAMBA_ARGS }}; then
          echo "Environment '{{.ENV_NAME}}' created successfully."
        else
          echo "Failed to create environment '{{.ENV_NAME}}'."
          exit 1
        fi

        task install-pixelator-r ENV_NAME={{.ENV_NAME}}

    silent: true

  install-pixelatorR-with-pak:
    desc: Install package dependencies
    summary: |-
      Install package dependencies
      --------------------------------------------------------------

      The ENV_NAME environment environment determines the micromamba
      environment to use.

      Example:
      task install-with-pak ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Determine the environment to use, handle unbound variable
        ENV_TO_USE="{{.ENV_NAME}}"
        if [ -z "$ENV_TO_USE" ]; then
          ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
        fi

        # Check if micromamba is installed
        if ! command -v micromamba &> /dev/null; then
          echo "micromamba is not installed. Please install it first."
          exit 1
        fi

        # Check if the environment exists
        micromamba env list | grep -q "$ENV_TO_USE" || {
            echo "Environment $ENV_TO_USE does not exist. Please create it first."
            exit 1
          }

        echo "Installing R packages in environment '$ENV_TO_USE'."

        # Run installation in the environment
        micromamba run -n $ENV_TO_USE bash -c '
          micromamba install -y conda-forge::hdf5 &&
          Rscript inst/dev/install-deps.R
        '
    silent: true

  document:
    desc: Generate documentation using roxygen2
    summary: |-
      Generate documentation using roxygen2
      --------------------------------------------------------------

      The ENV_NAME environment environment variable sets the
      micromamba environment to use.

      Example:
      task document ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Determine the environment to use, handle unbound variable
        ENV_TO_USE="{{.ENV_NAME}}"
        if [ -z "$ENV_TO_USE" ]; then
          ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
        fi

        # Check if the environment exists
        if ! micromamba env list | grep -q "$ENV_TO_USE"; then
          echo "Environment '$ENV_TO_USE' does not exist"
          exit 1
        else
          echo "Using environment '$ENV_TO_USE'"
          micromamba run -n $ENV_TO_USE bash -c '
            Rscript -e "devtools::document()"
          '
        fi
    silent: true

  style-staged-files:
    desc: Style staged files using styler
    summary: |-
      Style staged files using styler
      --------------------------------------------------------------

      The ENV_NAME environment environment variable sets the
      micromamba environment to use.

      Example:
      task style-staged-files ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Determine the environment to use, handle unbound variable
        ENV_TO_USE="{{.ENV_NAME}}"
        if [ -z "$ENV_TO_USE" ]; then
          ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
        fi

        # Check if the environment exists
        if ! micromamba env list | grep -q "$ENV_TO_USE"; then
          echo "Environment '$ENV_TO_USE' does not exist"
          exit 1
        else
          echo "Using environment '$ENV_TO_USE'"
          micromamba run -n $ENV_TO_USE bash -c '
            Rscript inst/dev/style-staged.R
          '
        fi
    silent: true

  test-staged-files:
    desc: Run tests on staged files using testthat
    summary: |-
      Run tests on staged files using testthat
      --------------------------------------------------------------

      The ENV_NAME environment environment variable sets the
      micromamba environment to use.

      Example:
      task test-staged-files ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Determine the environment to use, handle unbound variable
        ENV_TO_USE="{{.ENV_NAME}}"
        if [ -z "$ENV_TO_USE" ]; then
          ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
        fi

        echo $ENV_TO_USE

        # Check if the environment exists
        if ! micromamba env list | grep -q "$ENV_TO_USE"; then
          echo "Environment '$ENV_TO_USE' does not exist"
          exit 1
        else
          echo "Using environment '$ENV_TO_USE'"
          micromamba run -n $ENV_TO_USE bash -c '
            Rscript inst/dev/test-staged.R
          '
        fi
    silent: true

  test-all:
    desc: Run all tests using testthat
    summary: |-
      Run all tests using testthat
      --------------------------------------------------------------

      The ENV_NAME environment environment variable sets the
      micromamba environment to use.

      Example:
      task test-all ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Determine the environment to use, handle unbound variable
        ENV_TO_USE="{{.ENV_NAME}}"
        if [ -z "$ENV_TO_USE" ]; then
          ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
        fi

        # Check if the environment exists
        if ! micromamba env list | grep -q "$ENV_TO_USE"; then
          echo "Environment '$ENV_TO_USE' does not exist"
          exit 1
        else
          echo "Using environment '$ENV_TO_USE'"
          micromamba run -n $ENV_TO_USE bash -c '
            Rscript -e "devtools::test()"
          '
        fi

        find tests/testthat -maxdepth 1 -type f -name "*.pdf" -delete
    silent: true

  test-examples:
    desc: Run examples in pixelatorR
    summary: |-
      Run examples in pixelatorR
      --------------------------------------------------------------

      The ENV_NAME environment environment variable sets the
      micromamba environment to use.

      Example:
      task test-examples ENV_NAME=my_env
    cmds:
      - |
        set -euo pipefail

        # Determine the environment to use, handle unbound variable
        ENV_TO_USE="{{.ENV_NAME}}"
        if [ -z "$ENV_TO_USE" ]; then
          ENV_TO_USE=$(basename $CONDA_DEFAULT_ENV)
        fi

        # Check if the environment exists
        if ! micromamba env list | grep -q "$ENV_TO_USE"; then
          echo "Environment '$ENV_TO_USE' does not exist"
          exit 1
        else
          echo "Using environment '$ENV_TO_USE'"
          micromamba run -n $ENV_TO_USE bash -c '
            Rscript -e "devtools::run_examples()"
          '
        fi

        find . -maxdepth 1 -type f -name "*.pdf" -delete
    silent: true