Improved output file names

[MBartkowiakSTFC]

Description of work
Introduces sensible suggestions of output file names. Prevents from writing into a file that it already open (which would fail anyway).

This PR does NOT prevent overwriting existing files, since users could have valid reasons to do so. The initial filename suggested by the GUI will prevent overwriting, and the file dialog will issue a warning when overwriting. Once a job has started, the output filename becomes protected, preventing from running another job with the same output filename. However, after the job has ended, it will be possible to overwrite the file ONLY after removing the output file from the GUI (e.g. from the plot creator of from the trajectory viewer).

closes #599
closes #608

Fixes

• improved communication between widgets and session settings,
• created a list of protected filenames in the session object,
• added filename suggestions to the output file widgets.

To test
Please run at least two trajectory converters. See if the output trajectory widget suggests a valid path and filename. It should be impossible to run the same analysis twice without changing the output filename.
Try running an analysis. Check if the suggested output filename is valid.
Load an analysis result into the plotter. Check if you can run an analysis that overwrites the file. It should be impossible to overwrite as long as the file is on the list of open files in the plot creator.

[ChiCheng45]

Looks good just a few suggestions.

Can we update the trajectory converter widget so that the full path of the suggested trajectory is written out? I think it might not be obvious to a new user that ".\DL-POLY_trajectory1" will be the place where they ran mdanse_gui.

In the analysis job output file suggestion it uses a mix forward and back slash on windows e.g. E:/MDANSE-Examples-main/Data/Trajectories/DFTB\DensityOfStates_result2. Can you update it so on windows it only uses the forward or back slash?

[ChiCheng45]

I still find #608 occurring for a few cases.

This can occur when the path of the trajectory loaded is the absolute path and the input is a relative path. For example, I can load a trajectory which has the path "D:/Users/chi-y/DFTB_trajectory1.mdt" and I used a relative path in the converter tab ".\DFTB_trajectory1". Running the job causes the conversion to fail and the file to be cleared.

I'm also still able overwrite MDA files that are loaded in the plotter. Could this be some issue with window paths?

[MBartkowiakSTFC]

Looks good just a few suggestions.

Can we update the trajectory converter widget so that the full path of the suggested trajectory is written out? I think it might not be obvious to a new user that ".\DL-POLY_trajectory1" will be the place where they ran mdanse_gui.

In the analysis job output file suggestion it uses a mix forward and back slash on windows e.g. E:/MDANSE-Examples-main/Data/Trajectories/DFTB\DensityOfStates_result2. Can you update it so on windows it only uses the forward or back slash?

Normally, the full path should appear once you have selected one of the input files. Has this happened at all?

[MBartkowiakSTFC]

I still find #608 occurring for a few cases.

This can occur when the path of the trajectory loaded is the absolute path and the input is a relative path. For example, I can load a trajectory which has the path "D:/Users/chi-y/DFTB_trajectory1.mdt" and I used a relative path in the converter tab ".\DFTB_trajectory1". Running the job causes the conversion to fail and the file to be cleared.

I'm also still able overwrite MDA files that are loaded in the plotter. Could this be some issue with window paths?

Thanks for pointing this out. I will change the way paths are handled.