tests with TAP

[lightning-auriga]

add tests of the C++ component of the repository. please add more as desired

Big Book o' Tests:

• [x] preflight: pytest and snakemake available in run environment
• [x] single rule
• [x] multiple rules
• [x] automatically remove cooked in all rule
• [x] allow user specification of all synonym [in exclude_rules]
• [x] restrict tested rules to those present in -l logfile
• [x] remove simple comments
• [x] handle comments correctly
• [x] preserve string literals
• [x] keep general python content
• [x] keep string literals assigned to variables
• [x] detect rules buried in python blocks
• [x] resolve rules with identical names but different implementations under python logic
• [x] top-level snakefile doesn't have to be in workflow/
• [x] snakemake directives
  • [x] include directives
  • [x] include files from simple strings
  • [x] include files from python variables
  • [x] include directives buried in conditional statements
  • [x] include within standard included files (in same directory)
  • [x] include within conditionally included files (in same directory)
  • [x] include within standard included files (under rules/ or other subdir)
  • [x] include within conditionally included files (under rules/ or other subdir)
  • [x] wildcard_constraints directives
  • [x] recognize and exclude from python interpretation global "wildcard_constraints"
  • [x] configfile directives (note that these are not handled any differently than regular python code at this point)
  • [x] recognize and inject python support code for configfile from simple string
  • [x] allow schema validation of configfile from simple string

Parameter detection:

• [x] detect config file (needs updating with new interface parameters)
• [x] allow override of config file with CLI -o
• [x] allow override of config file with CLI -l
• [x] allow override of config file with CLI -s
• [ ] allow override of config file with CLI -p
• [x] allow override of config file with CLI -i (in cppunit content)
• [x] allow addition to config file with CLI -e (in cppunit content)
• [x] allow addition to config file with CLI -f (in cppunit content)
• [x] allow addition to config file with CLI -d (in cppunit content)
• [ ] recognize CLI -v (in cppunit content)
• [ ] recognize CLI -h (in cppunit content)
• [ ] run without flags mimics -h (in cppunit content)
• [ ] update selectors (all in cppunit content)
  • [ ] --update-all (probably implied by other tests which require it)
  • [x] --update-snakefiles
  • [ ] --update-pytest
  • [ ] --update-added-content
  • [ ] --update-inputs
  • [ ] --update-outputs

[lightning-auriga]

I've added handlers for making individual tests SKIP if the available snakemake version does not meet a minimum level (see for example the test for default_targets in tests/test32.test)

[lightning-auriga]

this list is horrendously old and predates the cppunit content entirely; I keep debating just removing it but I feel like some version of this that's actually updated properly would be beneficial.