Merge pull request #14 from CDCgov/mv_code_add_workflow

add container workflow, rm previous model code

Author: Emily-Po

.github/workflows/pkgdown.yaml

@@ -4,6 +4,7 @@
 archive/
 data/surveys
 data/*.rds
+poetry.lock
 
 # Exceptions
 !networks/networks_files/*

.github/workflows/testing.yaml

@@ -0,0 +1,9 @@
+FROM docker.io/rocker/r-ver:4.4.0
+
+RUN echo 'options(repos = c(P3M = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", \
+                            CRAN = "https://cloud.r-project.org"))' >>"${R_HOME}/etc/Rprofile.site"
+
+RUN install2.r remotes
+RUN installGithub.r statnet/tergmLite statnet/EpiModelHPC
+COPY epimodelcfa_*.tar.gz .
+RUN R CMD INSTALL epimodelcfa_*.tar.gz --dependencies=TRUE

.gitignore

@@ -0,0 +1,39 @@
+ifndef ENGINE
+ENGINE := podman
+endif
+
+ifndef IMAGE
+IMAGE := cfa-uw-modeling
+endif
+
+lib_path := /home/RUU7/r_libs
+
+help:
+	@echo "Makefile for the $(IMAGE) project."
+	@echo ""
+	@echo "Usage: make [target]"
+	@echo ""
+	@echo "Available targets:"
+	@echo "  help                : Displays this message."
+	@echo "  container_build     : Builds the container using the Dockerfile."
+	@echo "  container_run       : Runs the container mounting the current folder. Primarily used for testing container prior to running sims on Azure Batch."
+	@echo "  epimodelcfa_build   : Builds epimodelcfa package and adds to project repo, should be run prior to container_build if package recently updated."
+	@echo "  epimodelcfa_install : Builds and installs the epimodelcfa package into the R library, primarily used for development or local project activities."
+	@echo ""
+
+container_build:
+	$(ENGINE) build -t $(IMAGE) -f Dockerfile .
+
+container_run:
+	$(ENGINE) run --mount type=bind,source=$(PWD),target=/$(IMAGE) \
+                -it --rm -w /$(IMAGE) $(IMAGE) bash
+
+epimodelcfa_install:
+	epimodelcfa_build
+	R CMD INSTALL --preclean --clean --library=$(lib_path) epimodelcfa_*.tar.gz --dependencies=TRUE
+	rm -f epimodelcfa_*tar.gz
+
+epimodelcfa_build:
+	R CMD build /home/RUU7/repos/cfa-epimodel
+
+.PHONY: container_build container_run epimodelcfa_build epimodelcfa_install