Circular import

[matthiasbirkich]

Dear developers,

thank you for your help and your work! I have following issue, when I am running the script(s).

partially initialized module 'cbsyst' has no attribute 'Bsys' (most likely due to a circular import)

Do you have any clou, how to solve that problem?

best regards, Matthias

[oscarbranson]

Thanks for raising this @matthiasbirkich.

Could you post the full error message, as well as some info on your python environment? Specifically, the versions of Python, numpy, scipy, pandas, uncertainties and tqdm that you have installed. In case you're unsure how to do this, open a terminal and run:

python --version
> [prints python version]
pip list | grep 'numpy\|scipy\|pandas\|tqdm\|uncertainties'
> [prints versions of installed packages]

[matthiasbirkich]

Dear Oscar,

thank you for your fast response. I did a mistake with the environment. I thought, your examples are executable Jupyter Notbooks, but it is a viewer. Sorry for the inconvenience! We are doing pH and TA measurements with the photometric methods. We are using purified mCP in HCl+NaCl for pH on the total scale and BPB for TA. The pH values are fitting good to the calculated pH of DIC, pCO2 and TA(titrimetric, VINDTA, SUNDANS). The photometrical determination of TA have an offset, because we are not bubbling at the moment. We are missing certified NIST pH standards (Tris in synthetic seawater). Do you have an idea, where we can order it for less money? For our biological studies we are using the algorithm of Bo Yang / Liu et. al. (2011) for photometric pH measurement and for TA a calibration with NaHCO3 and Dickson standard for correction. Whats your experience and your suggestion about TA and pH for calculating DIC and pCO2? Do you think, that the pH with glass electrodes on the NBS scale is also sufficient?

Thank you very much for your answers. I like your python repositories cbsyst and carbspec very much! Actually we are looking for a cooperation in ocean acidification studies in the tropics. We have an experimental wet lab (MAREE) and 25 years experience in biogeochemistry...

best regards and stay healthy Matthias

Oscar notifications@github.com schrieb am Mo. 27. Juli 2020 um 12:09:

Thanks for raising this @matthiasbirkich https://github.com/matthiasbirkich.

Could you post the full error message, as well as some info on your python environment? Specifically, the versions of Python, numpy, scipy, pandas, uncertainties and tqdm that you have installed. In case you're unsure how to do this, open a terminal and run:

python --version

[prints python version] pip list | grep 'numpy|scipy|pandas|tqdm|uncertainties' [prints versions of installed packages]

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oscarbranson/cbsyst/issues/22#issuecomment-664257652, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOH3QCEFRQS6ON35E3XXTRLR5VG5RANCNFSM4PH66EYQ .

--

Matthias Birkicht Georg-Seebeck-Straße 47 27570 Bremerhaven mobile: 01609 48 68 28 7 phone: +49 471 306608 work: +49 421 23 800 34 skype: matthias.birkicht www.oberton.info

[oscarbranson]

I'm glad you're enjoying the repositories, @matthiasbirkich!

For the Tris buffer, I recommend making it yourself! There's a protocol in SOP 6a of the 'Best Practices' guide by Dickson, Sabine and Christian.

It's best to avoid using pH electrodes with NBS buffers because of the difference in ionic strength in the solutions. If you have no other option, I recommend regularly checking your electrode against a seawater TRIS solution to ensure the offset is what it should be.

I would be interested to hear about your ocean acidification plans, if you're looking for geochemical collaborators do get in touch!

[oscarbranson]

Closing this now, as you say the issue was in your python environment

[matthiasbirkich]

Dear Oscar,

thank you very much for your answer. I agree with your opinion. I have to collect arguments against the potentiometric pH measurements. I was asking Andrew Dickson a couple of years ago for a small amount of his (uncertified) TRIS-buffer in synthetic seawater, because it is complicate for us to guarantee the pH of self made buffers. I met him in Southampton during a workshop for seawater analysis. The PTB in Germany is also going to collaborate with us to make the Norm for spectrophotometric pH measurement of seawater better. Also I was asking the french NIST for these buffers. They have not answered yet.

I am looking for Traceable Reference Standards for Seawater pH

best regards Matthias

Oscar notifications@github.com schrieb am Do. 6. Aug. 2020 um 16:36:

I'm glad you're enjoying the repositories, @matthiasbirkich https://github.com/matthiasbirkich!

For the Tris buffer, I recommend making it yourself! There's a protocol in SOP 6a of the 'Best Practices' guide by Dickson, Sabine and Christian https://www.nodc.noaa.gov/ocads/oceans/Handbook_2007.html.

It's best to avoid using pH electrodes with NBS buffers because of the difference in ionic strength in the solutions. If you have no other option, I recommend regularly checking your electrode against a seawater TRIS solution to ensure the offset is what it should be.

I would be interested to hear about your ocean acidification plans, if you're looking for geochemical collaborators do get in touch!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oscarbranson/cbsyst/issues/22#issuecomment-669966927, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOH3QCC6FWERRO4ROY4HN6LR7K5TJANCNFSM4PH66EYQ .

--

Matthias Birkicht Georg-Seebeck-Straße 47 27570 Bremerhaven mobile: 01609 48 68 28 7 phone: +49 471 306608 work: +49 421 23 800 34 skype: matthias.birkicht www.oberton.info