MSNoise 2 branch

[ThomasLecocq]

Big changes from now on so pushing to a branch for now, as this BREAKS the previous CLI cron jobs etc.

Changes already done in the master, or here, should fit (or be added to) #213

[ThomasLecocq]

current command line interface now looks like this architecture/hierarchy, with:

• project initialisation & configuration: at the root level
• data & station plot: root level
• cc workflow as a group
• dvv workflow as a group inside the cc group
• qc workflow as a group
• smaller codes in utils

(ms2) λ msnoise tree
cli
├── tree
├── admin
├── db
│   ├── init
│   ├── update_loc_chan
│   ├── execute
│   ├── upgrade
│   ├── clean_duplicates
│   ├── dump
│   └── import
├── info
├── config
│   ├── sync
│   ├── set
│   └── get
├── reset
├── populate
├── scan_archive
├── plot
│   ├── data_availability
│   └── station_map
├── new_jobs
├── cc
│   ├── compute_cc
│   ├── compute_cc_rot
│   ├── stack
│   ├── stack2
│   ├── plot
│   │   ├── distance
│   │   ├── interferogram
│   │   ├── ccftime
│   │   └── spectime
│   └── dvv
│       ├── compute_mwcs
│       ├── compute_mwcs2
│       ├── compute_stretching
│       ├── compute_dtt
│       ├── compute_dtt2
│       └── plot
│           ├── mwcs
│           ├── dvv
│           ├── dtt
│           └── timing
├── qc
│   ├── compute_psd
│   ├── psd_to_hdf
│   ├── plot_psd
│   ├── hdf_to_rms
│   ├── export_rms
│   └── optimize
├── plugin
└── utils
    ├── bugreport
    ├── test
    └── jupyter

this means: for a standard project, with changes highlighted in bold:

msnoise db init --tech 1
msnoise config set data_folder=/archive
msnoise populate
msnoise db update_loc_chan
msnoise new_jobs --init
msnoise db execute "insert into filters (ref, low, mwcs_low, high, mwcs_high, rms_threshold, mwcs_wlen, mwcs_step, used) values (1, 0.1, 0.1, 1.0, 1.0, 0.0, 12.0, 4.0, 1)"
msnoise cc compute_cc
msnoise cc plot ccftime NET.STA.LOC NET2.STA2.LOC2
msnoise cc stack -r
msnoise cc plot distance
msnoise cc stack -m
msnoise cc dvv compute_mwcs
msnoise cc dvv compute_dtt
msnoise cc dvv plot dvv

[codecov]

Codecov Report

Base: 64.42% // Head: 5.56% // Decreases project coverage by -58.86% ⚠️

Coverage data is based on head (45d7657) compared to base (87bd771).
Patch coverage: 0.74% of modified lines in pull request are covered.

❗ Current head 45d7657 differs from pull request most recent head 0911593. Consider uploading reports for the commit 0911593 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #227       +/-   ##
==========================================
- Coverage   64.42%   5.56%   -58.86%     
==========================================
  Files          24       5       -19     
  Lines        4528    1726     -2802     
==========================================
- Hits         2917      96     -2821     
- Misses       1611    1630       +19     

Impacted Files	Coverage Δ
msnoise/test/tests.py	3.07% <0.00%> (-91.78%)	⬇️
msnoise/api.py	2.67% <0.95%> (-58.36%)	⬇️
msnoise/s01scan_archive.py	5.36% <0.00%> (-64.37%)	⬇️
msnoise/default.py
msnoise/plots/ccftime.py
msnoise/plots/data_availability.py
msnoise/plots/distance.py
msnoise/plots/interferogram.py
... and 14 more

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[ThomasLecocq]

the 🟢 tests are for the "default workflow steps", currently using the classic "many files" option.

TODO: add the new workflow steps, making use of xarray 2D tables (currently named stack2, compute_mwcs2, compute_dtt2)