Introduce dev container Makefile (#139)

* Added a makefile with what we think is reasonable

* remove test thingy

* Better singularity url

* Update makefile to non-privileged run

* Add docs building functionality and default target

* Fix building docs

* Remove userid things

* Comments, help and very explicit login

* Just a bit .PHONY

* Enhance Makefile (#156)

* Enhance Makefile

* Add review changes

* Move quotation mark

Author: joasode

Makefile

@@ -0,0 +1,75 @@
+CONTAINER_RUN=docker
+
+TESTFLAGS=
+CONTAINER_TEST_COMMAND=cd /home/ubuntu/code && uv sync --group=tests && uv run pytest
+CONTAINER_DOC_COMMAND=cd /home/ubuntu/code/doc && uv sync --group docs && uv run make apidoc && uv run make relnotes && uv run make html
+
+
+CONTAINER_ENTRYPOINT=--entrypoint bash
+CONTAINER_INTERNAL_PYTHON_VENV=--tmpfs=/venv:exec
+CONTAINER_ENVIRONMENT=--env UV_PROJECT_ENVIRONMENT=/venv
+CONTAINER_VOLUME_MOUNT=-v ${PWD}:/home/ubuntu/code
+CONTAINER_USER_ID=1000
+CONTAINER_SECURITY_OPTIONS=--security-opt label=disable --security-opt systempaths=unconfined --security-opt seccomp=unconfined --security-opt apparmor=unconfined
+CONTAINER_OPTIONS=--rm -it --user=$(CONTAINER_USER_ID) $(CONTAINER_SECURITY_OPTIONS) $(CONTAINER_ENTRYPOINT) $(CONTAINER_INTERNAL_PYTHON_VENV) $(CONTAINER_ENVIRONMENT) $(CONTAINER_VOLUME_MOUNT) $(OPTIONAL)
+
+APPTAINER_URL=ghcr.io/deic-hpc/cotainr-dev_env-apptainer-1.3.6:main
+SINGULARITY_URL=ghcr.io/deic-hpc/cotainr-dev_env-singularity-ce-4.3.0:main
+
+CONTAINER_URL=$(APPTAINER_URL)
+
+HELP_OUTPUT=" Welcome to the cotainr makefile\n\
+This is to help you easily test cotainr\n\
+\n\
+The default way of running cotainr is by using 'make test'\n\
+We have a list of different goals defined to help out:\n\
+\n\
+help: prints this output\n\
+login: helps you login to the container registry\n\
+\n\
+Execution goals that are executed in the container\n\
+test: executes the cotainr test-suite in a container\n\
+docs: build the cotainr documentation in a container\n\
+\n\
+Environments goals that are defined before the execution goal to setup the environment\n\
+podman: changes the cotainer runner from docker to podman\n\
+singularity: changes the container to one containing singularity\n\
+apptainer: changes the container to one containing apptainer (default)\n\
+\n\
+Runtime environment flags can be provided in any order\n\
+TESTFLAGS: string that is parsed to pytest, e.g. TESTFLAGS='-k test_info.py'\n\
+"
+
+.PHONY:default help podman login singularity apptainer test docs
+default: test
+
+help:
+	@echo $(HELP_OUTPUT)
+
+podman:
+	$(eval OPTIONAL=--userns=keep-id)
+	$(eval CONTAINER_RUN=podman)
+
+login:
+	@echo "For more details on how to login to the github container registry see: https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry";\
+	read -p "Enter Github username:" USERNAME;\
+	echo "Username: "$$USERNAME;\
+	read -p "Enter Github token:" CR_PAT;\
+	read -p "Enter Github password:" -s PASS;\
+	echo $$CR_PAT | $(CONTAINER_RUN) login ghcr.io -u $$USERNAME -p $$PASS
+
+singularity:
+	$(eval CONTAINER_URL=$(SINGULARITY_URL))
+
+apptainer:
+	$(eval CONTAINER_URL=$(APPTAINER_URL))
+
+test:
+	$(eval CONTAINER_COMMAND="$(CONTAINER_TEST_COMMAND) $(TESTFLAGS)")
+	$(call execute)
+
+docs:
+	$(eval CONTAINER_COMMAND="$(CONTAINER_DOC_COMMAND)")
+	$(call execute)
+
+execute = $(CONTAINER_RUN) run $(CONTAINER_OPTIONS) $(CONTAINER_URL) -c $(CONTAINER_COMMAND)