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Refactor-odf-parser #106

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Refactor-odf-parser #106

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JessyBarrette
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Refactor ODF parser and apply the following changes:

  • Change some of the attributes from mission_* to cruise_ and
  • Reduce the differences betweent he original ODF terms and the netcdf equivalent.

JessyBarrette and others added 30 commits December 7, 2022 08:19
@JessyBarrette
replace Pad value by np.nan in to_xarray ouput
87fb2e7
@JessyBarrette
rename observation_time variable time
72d6eb4
@JessyBarrette
swap dimension if time exist and set coordinates available
447c3c1
@JessyBarrette
improve write_ios_ncfiles method and add console inputs
b0f3011
@JessyBarrette
add default config and drifter one
3d37206
@JessyBarrette
drop netcf4-python folder
f0a5d69
@JessyBarrette
add another drifter test file
ed9d616
@JessyBarrette
fix time variable and drop of index coordinate if time exist
b496580
@JessyBarrette
fix logic for vocabulary mapping
bf70414
@JessyBarrette
add time:utc variable as time
d22641c
@JessyBarrette
ignore white spaces in dates
2db1dbd
@JessyBarrette
fix time:utc
5b7142b
@JessyBarrette
drop index coords if time is available as coordinate
ed1c2e9
@JessyBarrette
refactor date handling
c33f8de
@JessyBarrette
Merge branch 'dev' into ios-parser-extra-vocabulary
9a451bd
@JessyBarrette
drop duplicated rows in vocab
8857e30
@JessyBarrette
add some vocabulary corrections from IOS
4c06346
@JessyBarrette
update IOS vocabulary
deb5028
@JessyBarrette
add few fixes to ios vocabulary from me
71aff49
@JessyBarrette
clean up vocabulary
2b4ecf3
@JessyBarrette
remove unused columns
6e4bd4e
@JessyBarrette
add file type column to vocabulary
afdb51c
@JessyBarrette
add local to gitignore
02ed987
@JessyBarrette
move print commands in IosObsFile to logging calls
36ce7c9
@JessyBarrette
fix write_ios_ncfiles
1bad217
@JessyBarrette
add history section and deployment|recovery logic
abd1b90
@JessyBarrette
update log file name
e20c12a
@JessyBarrette
drop few columns from vocabulary
c0fd20a
@JessyBarrette
fix vocabulary logic and compatibility with netcdf
ab5d87f
@JessyBarrette
add option to generate sub variables and use rename attribute
e5430f5
@JessyBarrette
add another mapping to ITS-90
059452b
@JessyBarrette
include "/a" for record_number
73b4e07
@JessyBarrette
vocab fix record_number
cb4d656
@JessyBarrette
convert salinity ppt to psu
fe069ad
@JessyBarrette
add missing chlorophyll terms
56774fd
@JessyBarrette
drop duplicated salinity
93b8eeb
@JessyBarrette
improve dissolved oxygen variables attribues
6e7d929
@JessyBarrette
fix more vocab
7b4f7e7
@JessyBarrette
streamline temperature variables to CTD and bottle only
3d875a1
@JessyBarrette
fix some vocabulary issues
a344171
@JessyBarrette
Update setup.py
869b680
@JessyBarrette
Create __init__.py in odf_transform
91ed074
@JessyBarrette
make vocabulary for UNKN more specific
f64ca6a
@JessyBarrette
fix odf instrument attributes
0d91e06
@JessyBarrette
split odf_to_xarray and odf_to_netcdf
a9749e2
@JessyBarrette
drop rpy2 which isn't used anymore
e7cf633
@JessyBarrette
black .
ce7aaf1
@JessyBarrette
make odf files pytest file specific
63714af
@JessyBarrette
update reference files
305e967
@JessyBarrette
run all pytests
e3d444a
@JessyBarrette
black .
bbfd5c0
@JessyBarrette
add init in odf
dfb9e8e
@JessyBarrette
add utils import to odf_transform.__init__
3c1f2b4
@JessyBarrette
make shapely package optional dependency
441c517
@JessyBarrette
make gsw dependency gsw>=3.4.0
ba52e67
@JessyBarrette
add to vocabulary
16a57dd
@JessyBarrette
fix seabird when instrument attrs is None
040320f
@JessyBarrette
significantely refactor odf conversion
d690c45
@JessyBarrette
increase version number
4d165fb
@JessyBarrette JessyBarrette changed the base branch from master to dev July 5, 2023 16:39
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@JessyBarrette