Run plates 3 and 3prime #10
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| @@ -77,6 +80,38 @@ | |||
| output_dir=output_dir, | |||
| metadata_dir=metadata_dir, | |||
| figshare_url=figshare_url, | |||
| unzip_files=unzip_files, | |||
| unzip_download="True", | |||
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consider adding an if statement for if the files are zipped or not to make this not break and reusable
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@MikeLippincott Can you explain what you mean a bit more here? Are you saying in the download_figshare function to create an if state to stop the function if the individual puts unzip download when the files being extracted are not zipped?
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@MikeLippincott, When you have a chance, can you please re-review this PR? Thank you! |
| @@ -12,7 +12,9 @@ To calculate and apply an IC function on each channel, run the [nf1_ic.ipynb](nf | |||
| # move to the 1.cellprofiler_ic directory to access the `sh` script | |||
| cd 1.cellprofiler_ic | |||
| # run the notebook as a python script | |||
| bash nf1_ic.sh | |||
| source nf1_ic.sh | |||
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There could be issues but I don't feel concerned in this instance. There are a lot of different ways one can configure their terminal environment; using source into the current shell could mean one runs into personal terminal / development issues (environment variables, settings, other system configurations, etc).
To get around permission issues specifically, you could issue chmod +x <filename>, which may allow you to execute the file without specifying the shell type or sourcing it into the current shell. This seems like it might allow for the script to run on MacOS (zsh) and other bash-based OS's terminals. It's also possible to install and use bash through brew on Macs.
Generally, if executing shell script as part of the project, I'd wonder what environment the shell should execute in (what OS, which shell, etc). This gets into more challenging spaces for reproducibility and I only bring this up to provoke thoughts.
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| image_query = f"select * from {image_table_name}" | ||
| image_df = pd.read_sql(sql=image_query, con=conn) | ||
| image_df = pd.read_sql_table(image_table_name, f'sqlite:///{sqlite_file_path}') |
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@d33bs Thank you for that quick rereview! I will now merge these changes! |
In this PR, we:
All intermediate file from processing CellProfiler features have been uploaded to GitHub.