TypeError: add_variable() got an unexpected keyword argument 'update'

[yyyuechen]

Dear developer,
I am trying to run smenata with this command:
smetana --flavor fbc2 -o test3 -v -d --molweight --solver cplex --zeros genome2.xml genome1.xml
but i received this error: TypeError: add_variable() got an unexpected keyword argument 'update'
so I removed the update argument in all relavent scripts, but then i received this error:
TypeError: solve() got an unexpected keyword argument 'pool_size'
Does anyone ever faced the same issue? I am running my program on a docker and the version i am using is:
carveme 1.6.2
cplex 22.1.1.0
memote 0.17.0
smetana 1.2.0
Python 3.9.20
and the same issue happened when i used gurobi

[shikidj16]

I'm facing the same problem! As you did , I removed the update argument.

From what I see, solve () no longer requires pool size as an argument. So I removed that argument for now. I don't get that error anymore, but I keep getting other errors such as AttributeError: 'GurobiSolver' object has no attribute 'remove_constraint'.

I've noticed that the arguments used in the functions differ from what is actually required. This issue has occurred with addVariable(), solve(), and now it is also affecting removeConstraints(). I'm not sure why this is happening, but I suspect it may be due to a recent update in the solver that hasn't been taken into account in the code.

[yyyuechen]

I'm facing the same problem! As you did , I removed the update argument.

From what I see, solve () no longer requires pool size as an argument. So I removed that argument for now. I don't get that error anymore, but I keep getting other errors such as AttributeError: 'GurobiSolver' object has no attribute 'remove_constraint'.

I've noticed that the arguments used in the functions differ from what is actually required. This issue has occurred with addVariable(), solve(), and now it is also affecting removeConstraints(). I'm not sure why this is happening, but I suspect it may be due to a recent update in the solver that hasn't been taken into account in the code.

Hi I think yes there is something incompatible between the code and the solver, have you tried to run the code with an older version solver? I will try to do this next week and let u know if it works! And also check this website if you still need to use smetana: https://inap.denglab.org.cn/

[cdanielmachado]

There were some changes in the latest version of *reframed (1.5.3). *You need to uninstall it and install an older version (1.5.2 should still work).

…

On Thu, Oct 24, 2024 at 1:19 PM Yuec ***@***.***> wrote: I'm facing the same problem! As you did , I removed the update argument. From what I see, solve () no longer requires pool size as an argument. So I removed that argument for now. I don't get that error anymore, but I keep getting other errors such as AttributeError: 'GurobiSolver' object has no attribute 'remove_constraint'. I've noticed that the arguments used in the functions differ from what is actually required. This issue has occurred with addVariable(), solve(), and now it is also affecting removeConstraints(). I'm not sure why this is happening, but I suspect it may be due to a recent update in the solver that hasn't been taken into account in the code. Hi I think yes there is something incompatible between the code and the solver, have you tried to run the code with an older version solver? I will try to do this next week and let u know if it works! And also check this website if you still need to use smetana: https://inap.denglab.org.cn/ — Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AATX4VPZPTWIGDVRF5VW4K3Z5DJVRAVCNFSM6AAAAABQJYUFUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZUHE4TSNJVGI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[yyyuechen]

Hi Daniel, Thank you for the reply!! This combination finally worked for me : CPLEX 12.10.0.0,smetana 1.2.0.python 3.6.15,reframed 1.5.1. On Thu, Oct 24, 2024 at 9:28 PM Daniel Machado ***@***.***> wrote:

…

There were some changes in the latest version of *reframed (1.5.3). *You need to uninstall it and install an older version (1.5.2 should still work). On Thu, Oct 24, 2024 at 1:19 PM Yuec ***@***.***> wrote: > I'm facing the same problem! As you did , I removed the update argument. > > From what I see, solve () no longer requires pool size as an argument. So > I removed that argument for now. I don't get that error anymore, but I keep > getting other errors such as AttributeError: 'GurobiSolver' object has no > attribute 'remove_constraint'. > > I've noticed that the arguments used in the functions differ from what is > actually required. This issue has occurred with addVariable(), solve(), > and now it is also affecting removeConstraints(). I'm not sure why this > is happening, but I suspect it may be due to a recent update in the solver > that hasn't been taken into account in the code. > > Hi I think yes there is something incompatible between the code and the > solver, have you tried to run the code with an older version solver? I will > try to do this next week and let u know if it works! And also check this > website if you still need to use smetana: https://inap.denglab.org.cn/ > > — > Reply to this email directly, view it on GitHub > < #50 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AATX4VPZPTWIGDVRF5VW4K3Z5DJVRAVCNFSM6AAAAABQJYUFUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZUHE4TSNJVGI> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BD2FYNXILLQRG5QXTHHFE4LZ5E33LAVCNFSM6AAAAABQJYUFUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZWGA3TGNJWGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[yyyuechen]

Thank you for all the help guys, This combination finally worked for me : CPLEX 12.10.0.0,smetana 1.2.0.python 3.6.15,reframed 1.5.1.

[16607020803]

感谢所有帮助，这个组合终于对我有用了：CPLEX 12.10.0.0，smetana 1.2.0.python 3.6.15，reframed 1.5.1。

Hi, I'm also experiencing this problem, but when I install it using the pip install refarmed command, I run into a problem: it says that the installation of python-libsbml via setup.py failed, resulting in refarmed not being installed successfully. How did you solve this and can you help me please?

[yyyuechen]

hi! Sadly I didn't have this issue when i installed reframed, can you check if you are in the correct python version? you can also check what is installed by running : pip --list

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On Thu, Nov 28, 2024 at 11:02 AM 16607020803 ***@***.***> wrote: 感谢所有帮助，这个组合终于对我有用了：CPLEX 12.10.0.0，smetana 1.2.0.python 3.6.15，reframed 1.5.1。 Hi, I'm also experiencing this problem, but when I install it using the pip install refarmed command, I run into a problem: it says that the installation of python-libsbml via setup.py failed, resulting in refarmed not being installed successfully. How did you solve this and can you help me please? — Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BD2FYNSJW3OA2MT2HQNXMW32C3E27AVCNFSM6AAAAABQJYUFUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBVGQ3TSMJSGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>