Smetana addConstr() error while using gurobi solver

[BananaJumper96]

This is my smetana command:

rule smetana:
    input:
        gatherbinmodels
    output:
        detailed_tsv = os.path.join(outpath, "SMETANA", "{binID}_detailed.tsv")
    params:
        smetana_media = "M8",  # Replace with your media
        smetana_solver = "gurobi",    # Replace with your solver
        smetana_flavor = "fbc2",
        media_db = os.path.join(databasesDir, "media_db.tsv"),
        binID = lambda wildcards: wildcards.binID  # Extract bin ID from the input filename
    conda:
        os.path.join(envDir, "env_gurobi.yaml")
    log:
        os.path.join(outpath, "logs", "{binID}_smetana.log")
    shell:
        """
        tmpdir=$(mktemp -d)
        trap "rm -rf $tmpdir" EXIT

        mkdir -p "$(dirname "{output.detailed_tsv}")"

        echo -e "\\nRunning SMETANA for sample {wildcards.binID} ... " >> "{log}"

        cp "{params.media_db}" "$tmpdir/" >> "{log}" 2>&1
        cp {input:q} "$tmpdir/" >> "{log}" 2>&1

        cd "$tmpdir"
        smetana -o "{wildcards.binID}" \
            --flavor "{params.smetana_flavor}" \
            --mediadb "$(basename "{params.media_db}")" \
            -m "{params.smetana_media}" \
            --detailed \
            --solver "{params.smetana_solver}" \
            -v *.xml >> "{log}" 2>&1

        cp "{wildcards.binID}_detailed.tsv" "{output.detailed_tsv}" >> "{log}" 2>&1

        echo "SMETANA analysis for sample {wildcards.binID} completed." >> "{log}"
        """
        

    It is running a snakemake file. However when using the gurobi solver, I get the following error:

Running SMETANA for sample bin.122 ... 
Loading community: all
Running SCS for community all on medium M8...
Restricted license - for non-production use only - expires 2026-11-23
Traceback (most recent call last):
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/bin/smetana", line 89, in <module>
    main(
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/smetana/interface.py", line 345, in main
    entries = run_detailed(comm_id, community, medium_id, excluded_mets, env, verbose, min_mol_weight,
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/smetana/interface.py", line 174, in run_detailed
    scs = sc_score(community, environment=env, verbose=verbose)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/smetana/smetana.py", line 38, in sc_score
    solver = solver_instance(community.merged)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/reframed/solvers/__init__.py", line 104, in solver_instance
    return solvers[solver](model)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/reframed/solvers/gurobi_solver.py", line 57, in __init__
    self.build_problem(model)
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/reframed/solvers/solver.py", line 99, in build_problem
    self.update()
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/reframed/solvers/solver.py", line 80, in update
    self.add_constraints(self._cached_constrs)
  File "/mnt/lscratch/users/rparise/Thesis/Envs/ece8ca1e4744f5192f12549dd720d25d_/lib/python3.11/site-packages/reframed/solvers/gurobi_solver.py", line 72, in add_constraints
    self.problem.addConstr(expr, sense_mapping[sense], rhs, constr_id)
  File "src/gurobipy/_model.pyx", line 3894, in gurobipy._model.Model.addConstr
TypeError: addConstr() takes at most 3 positional arguments (5 given)

Could you help me find out what is causing this error and how I can fix that addConstr() error? Thank you

[dingxia97]

I have the same problem.

This is my smetana command:
smetana --flavor fbc2 --mediadb media_db.tsv -m M1,M2,M3,M4,M5,M7,M8,M9,M10,M11,M13,M14,M15A,M15B,M16 --detailed --solver gurobi -v *.xml

Loading community: all
Running SCS for community all on medium M1...
Set parameter LicenseID to value 2590555
Traceback (most recent call last):
  File "/Users/dingxia/mambaforge/envs/metagem/bin/smetana", line 89, in <module>
    main(
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/smetana/interface.py", line 345, in main
    entries = run_detailed(comm_id, community, medium_id, excluded_mets, env, verbose, min_mol_weight,
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/smetana/interface.py", line 174, in run_detailed
    scs = sc_score(community, environment=env, verbose=verbose)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/smetana/smetana.py", line 38, in sc_score
    solver = solver_instance(community.merged)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/reframed/solvers/__init__.py", line 104, in solver_instance
    return solvers[solver](model)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/reframed/solvers/gurobi_solver.py", line 57, in __init__
    self.build_problem(model)
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/reframed/solvers/solver.py", line 99, in build_problem
    self.update()
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/reframed/solvers/solver.py", line 80, in update
    self.add_constraints(self._cached_constrs)
  File "/Users/dingxia/mambaforge/envs/metagem/lib/python3.12/site-packages/reframed/solvers/gurobi_solver.py", line 72, in add_constraints
    self.problem.addConstr(expr, sense_mapping[sense], rhs, constr_id)
  File "src/gurobipy/_model.pyx", line 3894, in gurobipy._model.Model.addConstr
TypeError: addConstr() takes at most 3 positional arguments (5 given)

---

When I run the example in the gurobi installation directory examples/python/mip1.py successfully, it's work:

base$ python /Library/gurobi1200/macos_universal2/examples/python/mip1.py
Set parameter LicenseID to value 2590555
Gurobi Optimizer version 12.0.0 build v12.0.0rc1 (mac64[arm] - Darwin 22.6.0 22G74)

CPU model: Apple M1
Thread count: 8 physical cores, 8 logical processors, using up to 8 threads

Optimize a model with 2 rows, 3 columns and 5 nonzeros
Model fingerprint: 0x98886187
Variable types: 0 continuous, 3 integer (3 binary)
Coefficient statistics:
  Matrix range     [1e+00, 3e+00]
  Objective range  [1e+00, 2e+00]
  Bounds range     [1e+00, 1e+00]
  RHS range        [1e+00, 4e+00]
Found heuristic solution: objective 2.0000000
Presolve removed 2 rows and 3 columns
Presolve time: 0.00s
Presolve: All rows and columns removed

Explored 0 nodes (0 simplex iterations) in 0.00 seconds (0.00 work units)
Thread count was 1 (of 8 available processors)

Solution count 2: 3 2 

Optimal solution found (tolerance 1.00e-04)
Best objective 3.000000000000e+00, best bound 3.000000000000e+00, gap 0.0000%
x 1
y 0
z 1
Obj: 3

my python version is 3.12, gurobi v12.0.0, smetana v1.2.0.
I tried different versions of gurobi, but the result is always the same.
Could you help me find out what is causing this error and how I can fix that addConstr() error? Thank you