Merge pull request #74 from LCSB-BioCore/sew-truncate-memote-test-output

Truncate memote test output

README.md

@@ -77,25 +77,27 @@ FBCModelTests.Memote.run_tests("e_coli_core.json", GLPK.Optimizer; workers=worke
 Any optimizer supported by [JuMP](https://jump.dev/) can be used. The output of
 `run_tests` is the standard Julia unit testing scheme. However, in the repl the
 full output is usually truncated, and only a summary is shown. If you want more
-details about where/why your model failed certain tests, it is best to capture the
-output, and save it to a file. A convenient way to do this is with
-[ansi2html](https://github.com/agnoster/ansi2html).
+details about where/why your model failed certain tests, it is best to capture
+the output, and save it to a file. A convenient way to do this is with
+[ansi2html](https://github.com/agnoster/ansi2html). Additionally, to make the
+output more display friendly, we recommend `run_tests_toplevel` is used instead
+of `run_tests`.
 
 An example workflow entails using the scripts located in `bin/`:
 ```
-fbcmt-memote-run --color=yes -s GLPK -w 6 e_coli_core.xml > e_coli_core.test.out
+julia --color=yes fbcmt-memote-run -s GLPK -w 6 e_coli_core.xml > e_coli_core.test.out
 ansi2html < e_coli_core.test.out > e_coli_core.test.html
 ```
 The resultant `html` can be inspected in any browser.
 
 See the function documentation for additional test configuration information.
 Note, the tests implemented here are significantly more conservative than in the
-original Memote. In particular, no heuristics are used to guess reactions types,
-e.g. biomass, atp maintenance, transporters, exchanges, etc. Only [SBO
+original Memote. In particular, no heuristics are used to guess reaction types,
+e.g. biomass, atp maintenance, transporter, exchange, etc. Only [SBO
 annotations](https://github.com/EBI-BioModels/SBO/blob/master/SBO_OBO.obo) are
 used for this purpose, because only these are actually standardized.
 Consequently, all tests that rely on properly annotated reactions will fail if
-this is not incorporated in a model.
+this is not incorporated into the model being tested.
 
 The implementation in FBCModelTests.jl is mostly authored by
 St. Elmo Wilken ([@stelmo](https://github.com/stelmo))

bin/fbcmt-memote-run

@@ -16,6 +16,7 @@ while optind <= length(ARGS)
         global nworkers = ARGS[optind]    
     elseif ARGS[optind] == "-h"
         global help = true
+        break
     else
         push!(freeargs, ARGS[optind])
     end
@@ -26,14 +27,14 @@ if help
     println(
         """Usage: fbcmt-memote-run [-s|--solver <GLPK>] [-h|--help] [-w|--nworkers <1>] <model>""",
     )
-    exit(1)
+    exit(0)
 end
 
 if length(freeargs) == 1
-    global model_file = first(freeargs)
+    global model_file = last(freeargs)
 else
-    @error "Expected precisely 1 non-keyword argument: the model location."
-    exit(1)
+    @error "Expected only one argument, the model location, got $(length(freeargs)) instead."
+    exit(1) 
 end
 
 if !isfile(model_file)
@@ -49,7 +50,7 @@ using FBCModelTests, FBCModelTests.Memote
 import Distributed
 
 if nw > 1
-    Distributed.addprocs(nw)
+    Distributed.addprocs(nw, exeflags=`--project=$(Base.active_project())`) # necessary due to issue #48217 in julialang
     Distributed.@everywhere using FBCModelTests, FBCModelTests.Memote
     Distributed.@everywhere @eval using $solver
 end
@@ -59,4 +60,6 @@ optimizer = @eval $solver.Optimizer
 @info "Initialization done, starting MEMOTE..." model_file optimizer nworkers
 
 # run the Memote
-Memote.run_tests(model_file, optimizer; workers=Distributed.workers())
+Memote.run_tests_toplevel(model_file, optimizer; workers=Distributed.workers())
+exit(0)
+

src/memote.jl

@@ -14,6 +14,7 @@ using Test
 using JuMP
 using Distributed
 
+include(joinpath("common.jl")) # quiet tests
 include(joinpath("memote", "utils.jl")) # memote utils
 include(joinpath("memote", "config.jl")) # memote test parameters
 include.(