WIP: add tree command

[bjarthur]

still a work in progress as i haven't tested all corner cases. please let me know if something doesn't work for you.

for example:

help?> tree
  tree(obj::Union{HDF5File,HDF5Group})

  Display the hierarchical structure of object obj, much like the bash tree command does for file
  system paths. Similar to h5dump on the linux command line but more concise as it omits the full
  contents of datasets.

julia> fid=h5open("plate_001/patch_attempt_0000_000/camera_clamp2_000/000/Clamp2.ma")

julia> tree(fid)
MetaArray: 2
data (80000, 3) Float64
└─ info
   ├─ _metaType_: list
   ├─ 0
   │  ├─ _metaType_: dict
   │  ├─ name: 'Channel'
   │  └─ cols
   │     ├─ _metaType_: list
   │     ├─ 0
   │     │  ├─ _metaType_: dict
   │     │  ├─ name: 'command'
   │     │  └─ units: 'V'
   │     ├─ 1
   │     │  ├─ _metaType_: dict
   │     │  ├─ name: 'primary'
   │     │  └─ units: 'A'
   │     └─ 2
   │        ├─ _metaType_: dict
   │        ├─ name: 'secondary'
   │        └─ units: 'V'
   ├─ 1
   │  ├─ _metaType_: dict
   │  ├─ name: 'Time'
   │  ├─ units: 's'
   │  └─ values (80000,) Float64
   └─ 2
      ├─ _metaType_: dict
      ├─ startTime: 1.5627830491764686e9
      ├─ ClampState
      │  ├─ LPFCutoff: 20000.0
      │  ├─ _metaType_: dict
      │  ├─ extCmdScale: 0.02
      │  ├─ holding: -0.07
      │  ├─ membraneCapacitance: 0.0
      │  ├─ mode: 'VC'
      │  ├─ primaryGain: 2.0
      │  ├─ primaryScaleFactor: 1.0e-9
      │  ├─ primarySignal: 'Membrane Current'
      │  ├─ primaryUnits: 'A'
      │  ├─ secondaryGain: 1.0
      │  ├─ secondaryScaleFactor: 0.1
      │  ├─ secondarySignal: 'Membrane Potential'
      │  ├─ secondaryUnits: 'V'
      │  └─ ClampParams
      │     ├─ BridgeBalEnable: 6004
      │     ├─ BridgeBalResist: 8.413395979806202e-42
      │     ├─ FastCompCap: 1.848093076142754e-12
      │     ├─ FastCompTau: 1.7999999499807018e-6
      │     ├─ Holding: -4.915825115858752e-7
      │     ├─ HoldingEnable: 0
      │     ├─ LeakSubEnable: 0
      │     ├─ LeakSubResist: 4.0950001664e10
      │     ├─ NeutralizationCap: 8.413395979806202e-42
      │     ├─ NeutralizationEnable: 6004
      │     ├─ OutputZeroAmplitude: 0.0
      │     ├─ OutputZeroEnable: 0
      │     ├─ PipetteOffset: 0.038417998701334
      │     ├─ PrimarySignalHPF: 0.0
      │     ├─ PrimarySignalLPF: 20000.0
      │     ├─ RsCompBandwidth: 2867.199951171875
      │     ├─ RsCompCorrection: 0.0
      │     ├─ RsCompEnable: 0
      │     ├─ SlowCompCap: 0.0
      │     ├─ SlowCompTau: 9.999999747378752e-6
      │     ├─ WholeCellCompCap: 2.7520702730599034e-11
      │     ├─ WholeCellCompEnable: 0
      │     ├─ WholeCellCompResist: 8.969545e6
      │     └─ _metaType_: dict
      ├─ DAQ
      │  ├─ _metaType_: dict
      │  ├─ command
      │  │  ├─ _metaType_: dict
      │  │  ├─ holding: -0.07
      │  │  ├─ numPts: 80000L
      │  │  ├─ rate: 40000.0
      │  │  ├─ startTime: 1.5627830491764686e9
      │  │  └─ type: 'ao'
      │  ├─ primary
      │  │  ├─ _metaType_: dict
      │  │  ├─ numPts: 80000L
      │  │  ├─ rate: 40000.0
      │  │  ├─ startTime: 1.5627830491764686e9
      │  │  └─ type: 'ai'
      │  └─ secondary
      │     ├─ _metaType_: dict
      │     ├─ numPts: 80000L
      │     ├─ rate: 40000.0
      │     ├─ startTime: 1.5627830491764686e9
      │     └─ type: 'ai'
      └─ Protocol
         ├─ _metaType_: dict
         ├─ mode: 'VC'
         ├─ primary: None
         ├─ recordState: 1
         └─ secondary: None

[musm]

I wonder if it makes sense to just wrap something like h5dump ?

[musm]

Should we try to get this in? It's pretty nice and we might want to use it for the default show method.

[jmert]

Should we modify this to duplicate the show style from JLD2?

[musm]

That would be a great idea.

[musm]

@bjarthur Any chance you have time to work on this PR?

[bjarthur]

not really, but i could try to find the time. can you give me an example of the show from JLD2.jl? better yet, does anyone have any ideas as to how we could make it possible to interactively collapse and expand the hierarchy in the REPL, much like one can do with dicts in Juno.jl?

[musm]

Here's what JLD2 does https://github.com/JuliaIO/JLD2.jl/blob/e84b06eb72b850048453df13fdd7f685ce213225/src/groups.jl#L417
I think it would be nice to use the same icons.

[jmert]

I took a stab at prototyping an implementation the other day:

julia> HDF5.show_tree(hid)
🗃️ HDF5 data file: /mnt/shared/a_file.h5
├─ 🔖 creator
├─ 🔖 description
├─ 📂 R
│  ├─ 🔖 description
│  ├─ 🔖 format
│  ├─ 🔖 shape
│  ├─ 🔢 data
│  ├─ 🔢 indices
│  └─ 🔢 indptr
├─ 🔢 fields
├─ 📂 pixels_left
│  ├─ 🔖 description
│  ├─ 🔢 dec
│  ├─ 🔢 order
│  ├─ 🔢 ra
│  └─ 🔢 type
└─ 📂 pixels_right
   ├─ 🔖 description
   ├─ 🔢 nside
   ├─ 🔢 pixels
   └─ 🔢 type

I guess icon choices need to be tweaked — on my terminal, the description fields' icons are little tags (my choice of icon for Attributes), but here the bookmark icon doesn't work so well. (Or maybe that just my browser's view?? At any rate, if I can't predict what the icon is going to look like, then it obviously needs to be chosen differently.)

Edit: Terminal view —

[musm]

better yet, does anyone have any ideas as to how we could make it possible to interactively collapse and expand the hierarchy in the REPL, much like one can do with dicts in Juno.jl?

https://github.com/pfitzseb/REPLTreeViews.jl maybe?

[bjarthur]

REPLTreeViews.jl is totally what i've been looking for! thanks for the link @musm . i've opened an issue over there asking how we could add support for HDF5.

[musm]

@bjarthur many thanks for this PR and starting this effort! I think we can explore further updates using TreeViews etc. to further improve the experience. For now I'll close this since it's implemented in #725