Ingested the introduction to NICER analysis notebook from SciServer cookbooks#116

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DavidT3 wants to merge 29 commits intomainfrom

notebook/ingestNICERDemoNotebookSciServer

Commits on Oct 20, 2025

Commits on Oct 21, 2025

Added more commentary to the model fitting and plotting steps, also made the major tick formatter of the spectrum x-axis the same as the minor formatter. Also also fixed a stupid mistake where I tr…
DavidT3
committed
Added more commentary to data-analysis-nicer.md, and improved the light curve figure(s). This may move issue #115 to review, after testing
DavidT3
committed
Removed blank space from source name in NICER notebook. Also added NICER timing guide to additional resources. For issue #115
DavidT3
committed
The NICER notebook added for issue #115 and now in PR #116, does not run on CircleCI (though does on Fornax proper). I think this is because of the lack of some XSPEC model files. The CircleCI conf…
DavidT3
committed
Actually closed the if statement in the getting XSPEC model step of config.yml for CircleCI. For PR #116
DavidT3
committed
Made sure an unzip installation doesn't ask the user for input in the CircleCI config yml. For PR #116
DavidT3
committed
Screwed up the micromamba command to install unzip, put the -y flag in the wrong place. For PR #116
DavidT3
committed
Really trying to make unzip be installed into a conda environment in CircleCI so I can deal with these XSPEC model files I'm downloading. For PR #116
DavidT3
committed
Continued to screw up the unzip install command in every possible way. For PR #116
DavidT3
committed
Unzip now installs but because I switched the environment it was being installed in the next step (actually running it) fails... For issue #116
DavidT3
committed
Mistyped the path to the XSPEC model data directory. For PR #116
DavidT3
committed
The NICER notebook (#115) is still failing to execute on CircleCI when it does work on Fornax proper. Added some debug ls-es to try and see whether the xspec data are set up properly
DavidT3
committed
Really trying to understand what is causing the issue with the NICER notebook on CircleCI. For PR #116. Upped the chatter of the failing task to get some more info.
DavidT3
committed
Added some stupid debugging steps to figure out what is going on in CircleCI
DavidT3
committed
[pre-commit.ci] auto fixes from pre-commit.com hooks
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Ingested the introduction to NICER analysis notebook from SciServer cookbooks#116

Ingested the introduction to NICER analysis notebook from SciServer cookbooks#116
DavidT3 wants to merge 29 commits intomainfrom
notebook/ingestNICERDemoNotebookSciServer

Commits on Oct 20, 2025

Added a nicer directory/index file, and pointed to it in the top level index.md - for issue #115

Finished the first ingestion of the SciServer NICER notebook. For issue #115

Added something to catch something that I believe is a bug in nicerl2 pipeline. For issue #115

The notebook now for sure runs on Fornax, so it should be able to pass CI/CD checks. Now to add more commentary and do some editing. For issue #115

Made some minor code changes (added a new tick formatter to a spectrum plot), but made a fair few changes to the commentary around all the code cells. For issue #115

Commits on Oct 21, 2025

Added more commentary to the model fitting and plotting steps, also made the major tick formatter of the spectrum x-axis the same as the minor formatter. Also also fixed a stupid mistake where I tr…

Added more commentary to data-analysis-nicer.md, and improved the light curve figure(s). This may move issue #115 to review, after testing

Removed blank space from source name in NICER notebook. Also added NICER timing guide to additional resources. For issue #115

The NICER notebook added for issue #115 and now in PR #116, does not run on CircleCI (though does on Fornax proper). I think this is because of the lack of some XSPEC model files. The CircleCI conf…

Actually closed the if statement in the getting XSPEC model step of config.yml for CircleCI. For PR #116

Made sure an unzip installation doesn't ask the user for input in the CircleCI config yml. For PR #116

Screwed up the micromamba command to install unzip, put the -y flag in the wrong place. For PR #116

Really trying to make unzip be installed into a conda environment in CircleCI so I can deal with these XSPEC model files I'm downloading. For PR #116

Continued to screw up the unzip install command in every possible way. For PR #116

Unzip now installs but because I switched the environment it was being installed in the next step (actually running it) fails... For issue #116

Mistyped the path to the XSPEC model data directory. For PR #116

The NICER notebook (#115) is still failing to execute on CircleCI when it does work on Fornax proper. Added some debug ls-es to try and see whether the xspec data are set up properly

Really trying to understand what is causing the issue with the NICER notebook on CircleCI. For PR #116. Upped the chatter of the failing task to get some more info.

Added some stupid debugging steps to figure out what is going on in CircleCI

[pre-commit.ci] auto fixes from pre-commit.com hooks

Commits on Oct 22, 2025

Added some stupid debugging steps to figure out what is going on in CircleCI

Added some stupid debugging steps to figure out what is going on in CircleCI (now read and print the XSPEC log file).

May have found the cause of my continued issues with the NICER notebook on CircleCI - the method I have for determining the version of model files to download was being run in the wrong environment…

In a fit of optimism I have restored the original contents of the spectral generation cell in the NICER notebook. For issue #115, PR #116

Added a way of manually specifying the XSPEC data version acquired by CircleCI. Should help solve the problems I'm seeing with PR #116

Added a way of manually specifying the XSPEC data version acquired by CircleCI. Should help solve the problems I'm seeing with PR #116

My manual override for XSPEC data version is not working - trying to diagnose why.

Removed some extra comments/echos that were in the CircleCI config.yml, now I've finally gotten it working for PR #116.

Captured the output from nigeodown. Neatens the configuration cell in the NICER notebook. For issue #115 and PR #116