search

jepegit / cellpy

extract and tweak data from electrochemical tests of cells
MIT License
81 stars 27 forks source link

Running example scripts (installation issues) #301

Closed MaximevdHeijden closed 3 months ago

MaximevdHeijden commented 3 months ago

Dear cellpy team,

I still encounter problems when running an example script (01_loading_data). I get the following error: "NoSuchModuleError: Can't load plugin: sqlalchemy.dialects:access.pyodbc", which is related to the odbc driver installation. I checked your documentation again and you do refer to this (for Windows users) by provinding a link to the website to install the driver. However the weblink does not work.

The example also does not work with Linux as I get the following error: InterfaceError: (pyodbc.InterfaceError) ('IM002', '[IM002] [Microsoft][ODBC Driver Manager] Data source name not found and no default driver specified (0) (SQLDriverConnect)') (Background on this error at: https://sqlalche.me/e/20/rvf5)"". I did install the mbdtools as referred to in the documentation and I should have the correct version of sqlalchemy as I installed the requirements.txt file.

Can you please fix this and try to install cellpy and run it on another machine? Thanks!

Can you also still add jupyter notebook to the requirements.txt file (and refer to it in the installation)?

This issue is related to https://github.com/openjournals/joss-reviews/issues/6236

MaximevdHeijden commented 3 months ago

I realized that my python and drives dont have the same bit on that PC so I tried the installation on another PC as well (Windows). There it seemed to run the script after specifically installing the requirements.txt file. Can you add this to the installation please?

MaximevdHeijden commented 3 months ago

Regarding the same example script, "tables" needs to have a specific version (at least 3.7). please add this to the requirements.txt

MaximevdHeijden commented 3 months ago

03_capacity_vs_voltage: required the installation of the kaleido package (pip install -U kaleido)

MaximevdHeijden commented 3 months ago

02_Initial_data_inspection: somehow it does not recognize the .summary_plot function for me, although its in the plotutils script.

MaximevdHeijden commented 3 months ago

04_incremental_capacity_analysis: the ica.dqdv(c) does not run, I get the following error: "TypeError: dqdv() missing 1 required positional argument: 'capacity'"

MaximevdHeijden commented 3 months ago

Please fix the above issuesand rerun all examples scripts. Once you have addressed the issues, the software is ready to use as far as I'm concerned!

juliawind commented 3 months ago

link to access drivers fixed and reference to requirements.txt added in installation notes. (issue with dqdv is fixed the master branch)

jepegit commented 3 months ago

Dear cellpy team,

I still encounter problems when running an example script (01_loading_data). I get the following error: "NoSuchModuleError: Can't load plugin: sqlalchemy.dialects:access.pyodbc", which is related to the odbc driver installation. I checked your documentation again and you do refer to this (for Windows users) by provinding a link to the website to install the driver. However the weblink does not work.

Updated the link :-)

The example also does not work with Linux as I get the following error: InterfaceError: (pyodbc.InterfaceError) ('IM002', '[IM002] [Microsoft][ODBC Driver Manager] Data source name not found and no default driver specified (0) (SQLDriverConnect)') (Background on this error at: https://sqlalche.me/e/20/rvf5)"". I did install the mbdtools as referred to in the documentation and I should have the correct version of sqlalchemy as I installed the requirements.txt file.

I forgot to make a conda package of the latest cellpy version. Now it is made. Tried it on several linux distros (ubuntu and RHEL) without being able to reproduce the error. The intended behavior of cellpy is to check if it is on windows or posix first by itself and then only use sqlalchemyand pyodbc if it is on windows, while using mdbtools and pandas.read_csv, when not on windows. Could be that the error was fixed "unintentionally" while fixing another error so that it works on the newest version while not on the older one...

Can you please fix this and try to install cellpy and run it on another machine? Thanks!

So, not sure if I have fixed it, but at least it runs on the ubuntu and RHEL linux distros I have access to.

Can you also still add jupyter notebook to the requirements.txt file (and refer to it in the installation)?

Yes, added jupyterlab and jupyter notebook to requirements.txt

This issue is related to openjournals/joss-reviews#6236

jepegit commented 3 months ago

04_incremental_capacity_analysis: the ica.dqdv(c) does not run, I get the following error: "TypeError: dqdv() missing 1 required positional argument: 'capacity'"

This should now have been fixed in v1.0.1b5 for both pip and conda

jepegit commented 3 months ago

Regarding the same example script, "tables" needs to have a specific version (at least 3.7). please add this to the requirements.txt

Added to requirements.txt

jepegit commented 3 months ago

I realized that my python and drives dont have the same bit on that PC so I tried the installation on another PC as well (Windows). There it seemed to run the script after specifically installing the requirements.txt file. Can you add this to the installation please?

Added "hint" about installing requirements using the "requirements.txt" file. Added link to note about need of same bit on driver and python there as well.

jepegit commented 3 months ago

02_Initial_data_inspection: somehow it does not recognize the .summary_plot function for me, although its in the plotutils script.

Runs well now

jepegit commented 3 months ago

03_capacity_vs_voltage: required the installation of the kaleido package (pip install -U kaleido)

Now a part of the conda package as well and referenced in the "installation guide" (under "Dependencies")

jepegit commented 3 months ago

Please fix the above issuesand rerun all examples scripts. Once you have addressed the issues, the software is ready to use as far as I'm concerned!

All fixed and all examples scripts were rerun also on linux without crashing :-)