What’s New
Contents
What’s New¶
v0.1.10 (4 Mar. 2022)¶
Internals
Update and clean up requirements. Remove upper bound on all dependencies (#182) by R. Abernathey.
v0.1.9 (19 Jan. 2022)¶
Features and front-end API
New method to preprocess data for OWC software. This method can preprocessed Argo data and possibly create float_source/<WMO>.mat files to be used as inputs for OWC implementations in Matlab and Python. See the Salinity calibration documentation page for more. (#142) by G. Maze.
from argopy import DataFetcher as ArgoDataFetcher
ds = ArgoDataFetcher(mode='expert').float(6902766).load().data
ds.argo.create_float_source("float_source")
ds.argo.create_float_source("float_source", force='raw')
ds_source = ds.argo.create_float_source()
This new method comes with others methods and improvements:
A new
Dataset.argo.filter_scalib_pres()
method to filter variables according to OWC salinity calibration software requirements,A new
Dataset.argo.groupby_pressure_bins()
method to subsample a dataset down to one value by pressure bins (a perfect alternative to interpolation on standard depth levels to precisely avoid interpolation…), see Pressure levels: Group-by bins for more help,An improved
Dataset.argo.filter_qc()
method to select which fields to consider (new optionQC_fields
),Add conductivity (
CNDC
) to the possible output of theTEOS10
method.
New dataset properties accessible from the argo xarray accessor:
N_POINTS
,N_LEVELS
,N_PROF
. Note that depending on the format of the dataset (a collection of points or of profiles) these values do or do not take into account NaN. These information are also visible by a simple print of the accessor. (#142) by G. Maze.
from argopy import DataFetcher as ArgoDataFetcher
ds = ArgoDataFetcher(mode='expert').float(6902766).load().data
ds.argo.N_POINTS
ds.argo.N_LEVELS
ds.argo.N_PROF
ds.argo
New plotter function
argopy.plotters.open_sat_altim_report()
to insert the CLS Satellite Altimeter Report figure in a notebook cell. (#159) by G. Maze.
from argopy.plotters import open_sat_altim_report
open_sat_altim_report(6902766)
open_sat_altim_report([6902766, 6902772, 6902914])
open_sat_altim_report([6902766, 6902772, 6902914], embed='dropdown') # Default
open_sat_altim_report([6902766, 6902772, 6902914], embed='slide')
open_sat_altim_report([6902766, 6902772, 6902914], embed='list')
open_sat_altim_report([6902766, 6902772, 6902914], embed=None)
from argopy import DataFetcher
from argopy import IndexFetcher
DataFetcher().float([6902745, 6902746]).plot('qc_altimetry')
IndexFetcher().float([6902745, 6902746]).plot('qc_altimetry')
New utility method to retrieve topography. The
argopy.TopoFetcher
will load the GEBCO topography for a given region. (#150) by G. Maze.
from argopy import TopoFetcher
box = [-75, -45, 20, 30]
ds = TopoFetcher(box).to_xarray()
ds = TopoFetcher(box, ds='gebco', stride=[10, 10], cache=True).to_xarray()
For convenience we also added a new property to the data fetcher that return the domain covered by the dataset.
loader = ArgoDataFetcher().float(2901623)
loader.domain # Returns [89.093, 96.036, -0.278, 4.16, 15.0, 2026.0, numpy.datetime64('2010-05-14T03:35:00.000000000'), numpy.datetime64('2013-01-01T01:45:00.000000000')]
Update the documentation with a new section about Data quality control.
Internals
Uses a new API endpoint for the
argovis
data source when fetching aregion
. More on this issue here. (#158) by G. Maze.Update documentation theme, and pages now use the xarray accessor sphinx extension. (#104) by G. Maze.
Update Binder links to work without the deprecated Pangeo-Binder service. (#164) by G. Maze.
v0.1.8 (2 Nov. 2021)¶
Features and front-end API
Improve plotting functions. All functions are now available for both the index and data fetchers. See the Data visualisation page for more details. Reduced plotting dependencies to Matplotlib only. Argopy will use Seaborn and/or Cartopy if available. (#56) by G. Maze.
from argopy import IndexFetcher as ArgoIndexFetcher
from argopy import DataFetcher as ArgoDataFetcher
obj = ArgoIndexFetcher().float([6902766, 6902772, 6902914, 6902746])
# OR
obj = ArgoDataFetcher().float([6902766, 6902772, 6902914, 6902746])
fig, ax = obj.plot()
fig, ax = obj.plot('trajectory')
fig, ax = obj.plot('trajectory', style='white', palette='Set1', figsize=(10,6))
fig, ax = obj.plot('dac')
fig, ax = obj.plot('institution')
fig, ax = obj.plot('profiler')
New methods and properties for data and index fetchers. (#56) by G. Maze. The
argopy.DataFetcher.load()
andargopy.IndexFetcher.load()
methods internally call on the to_xarray() methods and store results in the fetcher instance. Theargopy.DataFetcher.to_xarray()
will trigger a fetch on every call, while theargopy.DataFetcher.load()
will not.
from argopy import DataFetcher as ArgoDataFetcher
loader = ArgoDataFetcher().float([6902766, 6902772, 6902914, 6902746])
loader.load()
loader.data
loader.index
loader.to_index()
from argopy import IndexFetcher as ArgoIndexFetcher
indexer = ArgoIndexFetcher().float([6902766, 6902772])
indexer.load()
indexer.index
Add optional speed of sound computation to xarray accessor teos10 method. (#90) by G. Maze.
Code spell fixes (#89) by K. Schwehr.
Internals
Check validity of access points options (WMO and box) in the facade, no checks at the fetcher level. (#92) by G. Maze.
More general options. Fix #91. (#102) by G. Maze.
trust_env
to allow for local environment variables to be used by fsspec to connect to the internet. Useful for those using a proxy.
Documentation on Read The Docs now uses a pip environment and get rid of memory eager conda. (#103) by G. Maze.
xarray.Dataset
argopy accessorargo
has a clean documentation.
Breaking changes with previous versions
Drop support for python 3.6 and older. Lock range of dependencies version support.
In the plotters module, the
plot_dac
andplot_profilerType
functions have been replaced bybar_plot
. (#56) by G. Maze.
Internals
Internal logging available and upgrade dependencies version support (#56) by G. Maze. To see internal logs, you can set-up your application like this:
import logging
DEBUGFORMATTER = '%(asctime)s [%(levelname)s] [%(name)s] %(filename)s:%(lineno)d: %(message)s'
logging.basicConfig(
level=logging.DEBUG,
format=DEBUGFORMATTER,
datefmt='%m/%d/%Y %I:%M:%S %p',
handlers=[logging.FileHandler("argopy.log", mode='w')]
)
v0.1.7 (4 Jan. 2021)¶
Long due release !
Features and front-end API
Live monitor for the status (availability) of data sources. See documentation page on Status of sources. (#36) by G. Maze.
import argopy
argopy.status()
# or
argopy.status(refresh=15)
Optimise large data fetching with parallelization, for all data fetchers (erddap, localftp and argovis). See documentation page on Parallel data fetching. Two parallel methods are available: multi-threading or multi-processing. (#28) by G. Maze.
from argopy import DataFetcher as ArgoDataFetcher
loader = ArgoDataFetcher(parallel=True)
loader.float([6902766, 6902772, 6902914, 6902746]).to_xarray()
loader.region([-85,-45,10.,20.,0,1000.,'2012-01','2012-02']).to_xarray()
Breaking changes with previous versions
In the teos10 xarray accessor, the
standard_name
attribute will now be populated using values from the CF Standard Name table if one exists. The previous values ofstandard_name
have been moved to thelong_name
attribute. (#74) by A. Barna.The unique resource identifier property is now named
uri
for all data fetchers, it is always a list of strings.
Internals
New
open_mfdataset
andopen_mfjson
methods in Argo stores. These can be used to open, pre-process and concatenate a collection of paths both in sequential or parallel order. (#28) by G. Maze.Unit testing is now done on a controlled conda environment. This allows to more easily identify errors coming from development vs errors due to dependencies update. (#65) by G. Maze.
v0.1.6 (31 Aug. 2020)¶
JOSS paper published. You can now cite argopy with a clean reference. (#30) by G. Maze and K. Balem.
Maze G. and Balem K. (2020). argopy: A Python library for Argo ocean data analysis. Journal of Open Source Software, 5(52), 2425 doi: 10.21105/joss.02425.
v0.1.5 (10 July 2020)¶
Features and front-end API
A new data source with the argovis data fetcher, all access points available (#24). By T. Tucker and G. Maze.
from argopy import DataFetcher as ArgoDataFetcher
loader = ArgoDataFetcher(src='argovis')
loader.float(6902746).to_xarray()
loader.profile(6902746, 12).to_xarray()
loader.region([-85,-45,10.,20.,0,1000.,'2012-01','2012-02']).to_xarray()
Easily compute TEOS-10 variables with new argo accessor function teos10. This needs gsw to be installed. (#37) By G. Maze.
from argopy import DataFetcher as ArgoDataFetcher
ds = ArgoDataFetcher().region([-85,-45,10.,20.,0,1000.,'2012-01','2012-02']).to_xarray()
ds = ds.argo.teos10()
ds = ds.argo.teos10(['PV'])
ds_teos10 = ds.argo.teos10(['SA', 'CT'], inplace=False)
argopy can now be installed with conda (#29, #31, #32). By F. Fernandes.
conda install -c conda-forge argopy
Breaking changes with previous versions
The
local_ftp
option of thelocalftp
data source must now points to the folder where thedac
directory is found. This breaks compatibility with rsynced local FTP copy because rsync does not give adac
folder (e.g. #33). An instructive error message is raised to notify users if any of the DAC name is found at the n-1 path level. (#34).
Internals
Implement a webAPI availability check in unit testing. This allows for more robust
erddap
andargovis
tests that are not only based on internet connectivity only. (@5a46a39).
v0.1.4 (24 June 2020)¶
Features and front-end API
ds = ArgoDataFetcher().region([-85,-45,10.,20.,0,1000.,'2012-01','2012-12']).to_xarray()
ds = ds.argo.point2profile()
ds_interp = ds.argo.interp_std_levels(np.arange(0,900,50))
Insert in a Jupyter notebook cell the Euro-Argo fleet monitoring dashboard page, possibly for a specific float (#20). By G. Maze.
import argopy
argopy.dashboard()
# or
argopy.dashboard(wmo=6902746)
The
localftp
index and data fetcher now have theregion
andprofile
access points available (#25). By G. Maze.
Breaking changes with previous versions
[None]
Internals
Now uses fsspec as file system for caching as well as accessing local and remote files (#19). This closes issues #12, #15 and #17. argopy fetchers must now use (or implement if necessary) one of the internal file systems available in the new module
argopy.stores
. By G. Maze.Erddap fetcher now uses netcdf format to retrieve data (#19).
v0.1.3 (15 May 2020)¶
Features and front-end API
from argopy import IndexFetcher as ArgoIndexFetcher
idx = ArgoIndexFetcher().float(6902746)
idx.to_dataframe()
idx.plot('trajectory')
The index
fetcher can manage caching and works with both Erddap and localftp data sources. It is basically the same as the data fetcher, but do not load measurements, only meta-data. This can be very useful when looking for regional sampling or trajectories.
Tip
Performance: we recommend to use the localftp
data source when working this index
fetcher because the erddap
data source currently suffers from poor performances. This is linked to #16 and is being addressed by Ifremer.
The index
fetcher comes with basic plotting functionalities with the argopy.IndexFetcher.plot()
method to rapidly visualise measurement distributions by DAC, latitude/longitude and floats type.
Warning
The design of plotting and visualisation features in argopy
is constantly evolving, so this may change in future releases.
The
argopy.DataFetcher
now has aargopy.DataFetcher.to_dataframe()
method to return apandas.DataFrame
.New utilities function:
argopy.utilities.open_etopo1()
,argopy.show_versions()
.
Breaking changes with previous versions
The
backend
option in data fetchers and the global optiondatasrc
have been renamed tosrc
. This makes the code more coherent (@ec6b32e).
Code management
v0.1.2 (15 May 2020)¶
We didn’t like this one this morning, so we move one to the next one !
v0.1.1 (3 Apr. 2020)¶
Features and front-end API
Added new data fetcher backend
localftp
in DataFetcher (@c5f7cb6):
from argopy import DataFetcher as ArgoDataFetcher
argo_loader = ArgoDataFetcher(backend='localftp', path_ftp='/data/Argo/ftp_copy')
argo_loader.float(6902746).to_xarray()
Introduced global
OPTIONS
to set values for: cache folder, dataset (eg:phy or bgc), local ftp path, data fetcher (erddap or localftp) and user level (standard or expert). Can be used in context with (@83ccfb5):
with argopy.set_options(mode='expert', datasrc='erddap'):
ds = argopy.DataFetcher().float(3901530).to_xarray()
Added a
argopy.tutorial
module to be able to load sample data for documentation and unit testing (@4af09b5):
ftproot, flist = argopy.tutorial.open_dataset('localftp')
txtfile = argopy.tutorial.open_dataset('weekly_index_prof')
Improved xarray argo accessor. Added methods for casting data types, to filter variables according to data mode, to filter variables according to quality flags. Useful methods to transform collection of points into collection of profiles, and vice versa (@14cda55):
ds = argopy.DataFetcher().float(3901530).to_xarray() # get a collection of points
dsprof = ds.argo.point2profile() # transform to profiles
ds = dsprof.argo.profile2point() # transform to points
Changed License from MIT to Apache (@25f90c9)
Internal machinery
Add
__all__
to controlfrom argopy import *
(@83ccfb5)All data fetchers inherit from class
ArgoDataFetcherProto
inproto.py
(@44f45a5)Data fetchers use default options from global OPTIONS
In Erddap fetcher: methods to cast data type, to filter by data mode and by QC flags are now delegated to the xarray argo accessor methods.
Data fetchers methods to filter variables according to user mode are using variable lists defined in utilities.
argopy.utilities
augmented with listing functions of: backends, standard variables and multiprofile files variables.Introduce custom errors in errors.py (@2563c9f)
Front-end API ArgoDataFetcher uses a more general way of auto-discovering fetcher backend and their access points. Turned of the
deployments
access point, waiting for the index fetcher to do that.Improved xarray argo accessor. More reliable
point2profile
and data type casting withcast_type
Code management
v0.1.0 (17 Mar. 2020)¶
Initial release.
Erddap data fetcher