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SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
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feat: update GH Action workflow #468

Closed mihai-sysbio closed 1 year ago

mihai-sysbio commented 1 year ago

Main improvements in this PR:

This PR aimed to update the GH Action dependencies and formatting. While doing so, a bug was spotted that highlighted that the latest RAVEN was actually not used, since the GH Action was relying on the system-provided RAVEN.

This PR also adds a corresponding badge in the Readme.

I hereby confirm that I have:

github-actions[bot] commented 1 year ago

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
 > Checking RAVEN release               DEVELOPMENT
 > Checking MATLAB release              2020b
 > Checking system architecture         glnxa64
 > Set RAVEN in MATLAB path             Pass
 > Save MATLAB path                     Pass
   > Make binaries executable           Pass

 > Add Java paths for Excel format      Pass
 > Checking libSBML version             5.19.0
 > Checking model import and export
   > Import Excel format                Pass
   > Export Excel format                Pass
   > Import SBML format                 Pass
   > Export SBML format                 Pass

 > Checking for LP solvers
   > glpk                               Pass
   > gurobi                             Pass
   > soplex                             [Fail]
   > cobra                              Pass
 > Set RAVEN solver                     gurobi

 > Checking BLAST+                      Pass
 > Checking DIAMOND                     Pass
 > Checking HMMER                       Pass

 > Checking function uniqueness         Fail
   Duplicate functions in /home/m/crap/Human-GEM/code/GPRs
     getGenesFromGrRules.m
   Resolve conflicting functions to ensure RAVEN functionality

*** checkInstallation complete ***

Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
PASS: [Gen e[s] from a[s]] Gen e[s] from a[s]
FAIL: [Gen e[s] from a[s]] Gen e[s] from a[s]
.
Done checkTasksTests

Running diamondTests
.
Done diamondTests

Running fillGapsLargeTests
..
Done fillGapsLargeTests

Running fillGapsSmallTests
...
Done fillGapsSmallTests

Running hmmerTests
.
Done hmmerTests

Running importExportTests
....
Done importExportTests

Running mafftTests
.
Done mafftTests

Running miriamTests
.
Done miriamTests

Running modelAbilitiesTests
......Getting minimal and maximal fluxes...   0%25 complete 10%25 completeCOMPLETE
..
Done modelAbilitiesTests

Running modelConversionTests
.
Done modelConversionTests

Running modelCurationTests
.......... ........
Done modelCurationTests

Running modelSortingTests
..
Done modelSortingTests

Running solverTests
..
Error occurred in solverTests/testSoplex and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testSoplex (line 79)
    SoPlex not installed or cannot be found, test skipped
..
Done solverTests

Running tinitTests
.Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 20%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 20%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
.Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
PASS: [Gen e[s] from a[s]] Gen e[s] from a[s]
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 25%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
[Gen e[s] from a[s]] Gen e[s] from a[s]: Added 0 reaction(s), 0 reactions added in total
.WARNING: "[Gen e[s] from a[s]] Gen e[s] from a[s]" could not be performed for any set of reactions


.
New genes added to the model:
G10
G11
G5
G6
G7
G8
G9
No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001"
...Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 20%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 20%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.

New genes added to the model:
G11
G12
G13
G14
No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001"
Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 11%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 11%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
.Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete 20%25 completeCOMPLETE
Step 5: Final work
.Step 1: Gene rules
Step 2: First simplification
Step 3: Check tasks (~10 min)
Step 4: Second simplification (~1 hour)
Getting minimal and maximal fluxes...   0%25 complete  3%25 complete100%25 completeCOMPLETE
Step 5: Final work
ftINIT: Running step 1
MILP detected.
ftINIT: Running step 2
MILP detected.
ftINIT: Running step 1
MILP detected.
.
Done tinitTests

Failure Summary:

     Name                    Failed  Incomplete  Reason(s)
    =======================================================
     solverTests/testSoplex    X         X       Errored.

Note: In the case of multiple test runs, this post will be edited.

edkerk commented 1 year ago

Actually, maybe it is okay to leave out line 318 in checkInstallation completely? Missings files are also caught by status~=0 in line 319.

mihai-sysbio commented 1 year ago

It seems there is progress. The reported missing files are:

-           fullfile(binDir,'GLPKmex','glpkcc');
-           fullfile(binDir,'libSBML','TranslateSBML');
-           fullfile(binDir,'libSBML','OutputSBML');

And this is accurate, since these file names are missing their extensions.

mihai-sysbio commented 1 year ago

This PR is ready for review. Notes: soplex is installed, but not available due to dependencies, so all soplex tests will continue to fail for some time; the code now marks as executable also .exe dependencies.

mihai-sysbio commented 1 year ago

@edkerk if you'd prefer a slightly better solution, this could be a nice syntax to leverage:

chmod +x glpkcc.(mexa64|mexglx|mexmaci64)

While it doesn't guarantee the existence of the right file for the platform, it avoids e.g. marking as executable the files for the Windows platform.

mihai-sysbio commented 1 year ago

Looking again at the diff now - it looks weird and it should not be merged yet.