Makefile.j2

{% set types = ['simulations', 'hospitalization', 'importation', 'filter', 'reports'] %}
.PHONY: clean rerun {{ types | map('format_string', 'clean_{}') | join(' ') }} {{ types | map('format_string', 'rerun_{}') | join(' ') }}

NCOREPER={{ num_cores }}
RSCRIPT=Rscript
PYTHON=python3
PIPELINE=COVIDScenarioPipeline
CONFIG={{ config_path }}
OUTPUTBASE={{ output_base }}

report: {% for simulation_name in simulation_names %} .files/{{ num_sims }}_simulation_{{ simulation_name }} {% for death_rate_name in death_rate_names %} .files/{{ num_sims }}_hospitalization_{{ simulation_name }}_{{ death_rate_name }} {% endfor %} {% endfor %} 
	touch .files/{{ num_sims }}_report

.files/{{ num_sims }}_importation: 
	$(RSCRIPT) $(PIPELINE)/R/scripts/importation.R -c $(CONFIG) -j $(NCOREPER)
	touch .files/{{ num_sims }}_importation

.files/{{ num_sims }}_filter: .files/{{ num_sims }}_importation
	$(RSCRIPT) $(PIPELINE)/R/scripts/create_filter.R -c $(CONFIG)
	touch .files/{{ num_sims }}_filter

{% for simulation_name in simulation_names %}
.files/{{ num_sims }}_simulation_{{ simulation_name }}: .files/{{ num_sims }}_filter .files/{{ num_sims }}_importation
	$(PYTHON) $(PIPELINE)/simulate.py -c $(CONFIG) -s {{ simulation_name }} -n {{ num_sims }} -j $(NCOREPER)
	touch .files/{{ num_sims }}_simulation_{{ simulation_name }}
{% endfor %}

{% for simulation_name in simulation_names %}
  {% for death_rate_name in death_rate_names %}
.files/{{ num_sims }}_hospitalization_{{ simulation_name }}_{{ death_rate_name }}: .files/{{ num_sims }}_simulation_{{ simulation_name }}
	$(RSCRIPT) $(PIPELINE)/R/scripts/hosp_run.R -s {{ simulation_name }} -d {{ death_rate_name }} -j $(NCOREPER) -c $(CONFIG)
	touch .files/{{ num_sims }}_hospitalization_{{ simulation_name }}_{{ death_rate_name }}
  {% endfor %}
{% endfor %}

{# These occur at the bottom of every Makefile #}

clean: {{ types | map('format_string', 'clean_{}') | join(' ') }}

rerun: {{ types | map('format_string', 'rerun_{}') | join(' ') }}

{% for type in types %}
  {% if type in ['simulations', 'hospitalization'] %}
    {% set prefix = 'model_output' %}
  {% elif type in ['importation', 'reports'] %}
    {% set prefix = type %}
  {% else %}
    {% set prefix = 'data' %}
  {% endif %}

{{ type | format_string('clean_{}') }}:
	rm -rf {{ prefix }}/{{ type }}

{{ type | format_string('rerun_{}') }}: {{ type | format_string('clean_{}') }}
	rm -rf .files/*_{{ type }}
{% endfor %}