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CDR at 25km #146

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Nov 5, 2024
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25701a1
Split amsr2 platform start date into its own config
trey-stafford Sep 12, 2024
11aa26b
Move current daily and monthly outputs to intermeidate dir
trey-stafford Sep 12, 2024
7b1c0ef
Init code for publishing finalized nc files with prototype group
trey-stafford Sep 12, 2024
63bcf3d
Rename `qa_of_cdr_seaice_conc` -> `cdr_qa_seaice_conc`
trey-stafford Sep 12, 2024
4d2d411
Rename `spatial_interpolation_flag` -> `cdr_spatial_interpolation_flag`
trey-stafford Sep 12, 2024
6f3dbc7
Rename `temporal_interpolation_flag` -> `cdr_temporal_interpolation_f…
trey-stafford Sep 12, 2024
66a1f54
Fixup qa var name in validation code
trey-stafford Sep 12, 2024
e81049f
Rename `stdev_of_cdr_seaice_conc` -> `cdr_stdev_seaice_conc`
trey-stafford Sep 12, 2024
433c7d3
Rename subgroup variables to indicate they are from amsr2
trey-stafford Sep 12, 2024
8ffaf9b
fix use of platform.id
Sep 13, 2024
e2abd8e
Rename `melt_onset_day_cdr_seaice_conc` -> `cdr_melt_onset_day`
trey-stafford Sep 13, 2024
d74e139
Group supplementary fields
trey-stafford Sep 13, 2024
07e5859
Rename nc subgroup `amsr2_prototype` -> `prototype_amsr2`
trey-stafford Sep 13, 2024
dc3c59a
abstract is_pre_AMSR() function
Sep 13, 2024
39ed8f7
remove debug output file
Sep 13, 2024
5f33c18
fix platform.id typo
Sep 13, 2024
80b0795
Revert "Revert "Update pm_icecon dep""
trey-stafford Sep 13, 2024
963cfb2
Merge branch 'revert-143-revert-142-update-pm_icecon' into combine-am…
trey-stafford Sep 13, 2024
858e7ec
Rename ancillary variables in prototype subgroup to match new names
trey-stafford Sep 13, 2024
d64bd4a
Filter prototype subgroup attrs to source, sensor, platform
trey-stafford Sep 13, 2024
329a1bb
Remove group attrs from cdr_supplementary
trey-stafford Sep 13, 2024
9aab1f2
Exclude the `missing_tb_mask` from non-verbose daily files
trey-stafford Sep 13, 2024
2ceb5e5
use CDRv4 dailyclim for SMMR, despite its errors
Sep 14, 2024
e967425
correct F17 start date if not using AMSR2
Sep 16, 2024
3f04d90
Mypy: ignore datatree
trey-stafford Sep 16, 2024
b121e9e
Fix global attrs referencing hard-coded 12.5km resolution
trey-stafford Sep 16, 2024
0468f48
Merge branch 'fix-attrs-12km-hardcode' into combine-amsr2-prototype-f…
trey-stafford Sep 16, 2024
10ad49f
Merge pull request #147 from nsidc/fix-attrs-12km-hardcode
trey-stafford Sep 16, 2024
87271ec
Merge pull request #141 from nsidc/ecdr-at-25km-ssmatchCDRv4
trey-stafford Sep 16, 2024
189883a
Add CHANGELOG and dev doc note about `match-cdrv4`
trey-stafford Sep 16, 2024
9e7bfdd
Merge pull request #148 from nsidc/match-ecdrv4-doc
trey-stafford Sep 16, 2024
60b1792
Adjust start date for AMSR2 to 2013-01-1
trey-stafford Sep 16, 2024
e6847c3
Tweaks to final daily output
trey-stafford Sep 16, 2024
8b886eb
Update nc summary attr text
trey-stafford Sep 16, 2024
ecf3033
Rename `cdr_spatial_interpolation_flag` -> `cdr_seaice_conc_interp_sp…
trey-stafford Sep 16, 2024
a45c8d6
Rename `cdr_temporal_interpolation_flag` -> `cdr_seaice_conc_interp_t…
trey-stafford Sep 16, 2024
727fd40
Rename `cdr_qa_seaice_conc` -> `cdr_seaice_conc_qa`
trey-stafford Sep 16, 2024
10c7acc
Rename `cdr_stdev_seaice_conc` -> `cdr_seaice_conc_stdev`
trey-stafford Sep 16, 2024
24fc0b7
Extract logic adding `coordinates` attr to func
trey-stafford Sep 16, 2024
b03d12c
Extract hopefully temporary logic into helper functions
trey-stafford Sep 16, 2024
76f75db
Add simple integration test for daily publication files
trey-stafford Sep 16, 2024
264d530
Rename `complete_daily_ecdr` module -> `intermediate_daily`
trey-stafford Sep 16, 2024
788e763
CLI for publish_daily
trey-stafford Sep 16, 2024
e58c08e
Add `stage-for-publication` step to `make_25km_ecdr.sh`
trey-stafford Sep 17, 2024
b91c752
Rename `multiprocess_daily` -> `multiprocess_intermediate_daily`
trey-stafford Sep 17, 2024
6cf10f2
CLI for daily complete files ready for staging to publication
trey-stafford Sep 17, 2024
05fdaf5
Publication-ready daily generation produces checksum files
trey-stafford Sep 17, 2024
8a0ff93
Delete OBE `make_25km_cdr.py`
trey-stafford Sep 17, 2024
1001c61
Merge branch 'ecdr-at-25km' into combine-amsr2-prototype-fields
trey-stafford Sep 17, 2024
1c6d87c
Update `make_25km_ecdr.sh` script
trey-stafford Sep 17, 2024
f4a87b7
Update TODOs and improve visibility on hard-coded AMSR2 startdate
trey-stafford Sep 17, 2024
647e3b7
Update CHANGELOG for next release
trey-stafford Sep 17, 2024
3ac991a
Update conda-lock
trey-stafford Sep 17, 2024
852922b
Add TODO about interp range in multiprocess daily
trey-stafford Sep 17, 2024
3ffabb0
Update code around how # cores is set for multiprocessing
trey-stafford Sep 17, 2024
6da45a3
TODO
trey-stafford Sep 17, 2024
d3c7919
Merge pull request #140 from nsidc/combine-amsr2-prototype-fields
trey-stafford Sep 17, 2024
38a2193
Remove unused kwarg
trey-stafford Sep 17, 2024
c6b951f
Fixup `make_25km_ecdr.sh`
trey-stafford Sep 17, 2024
d55be27
update daily aggregation code to support groups in daily files
trey-stafford Sep 18, 2024
2e36092
Upate cli/entrypoint w/ comments about CLIs that ops will use
trey-stafford Sep 18, 2024
20e5f69
Fixup `cdr_seaice_conc_stdev` long name
trey-stafford Sep 18, 2024
2926fa0
Rename `prototype_amsr2` -> `prototype_am2`
trey-stafford Sep 18, 2024
e31b4fc
Merge pull request #151 from nsidc/daily-aggregate-update-for-nc-groups
trey-stafford Sep 18, 2024
0e4b9d2
Merge pull request #152 from nsidc/update-prototype-group-name
trey-stafford Sep 18, 2024
ec8b62f
Reset ECDR Product version for initial release
trey-stafford Sep 18, 2024
c5aa6fe
Update docstring refs to `cdr_product_version` -> `ECDR_PRODUCT_VERSION`
trey-stafford Sep 18, 2024
6bd81ce
Merge pull request #153 from nsidc/reset-version-string
trey-stafford Sep 18, 2024
0f8a220
Add `--no-multiprocesing` option to `daily` CLI
trey-stafford Sep 18, 2024
4b20866
Merge pull request #154 from nsidc/multiproc-switch
trey-stafford Sep 18, 2024
62e8b49
Rename `monthly` module and functions to indicate intermediate status
trey-stafford Sep 18, 2024
557030a
Add util func for finding monthly files on disk
trey-stafford Sep 18, 2024
96ccd77
Init monthly code support for groups in datasets
trey-stafford Sep 19, 2024
8955933
Fixup monthly stdev variable name
trey-stafford Sep 19, 2024
974d395
Add monthly cli for preparing final monthly files for publication
trey-stafford Sep 19, 2024
740a5dc
Rename `cdr_seaice_conc_qa_monthly` -> `cdr_seaice_conc_monthly_qa`
trey-stafford Sep 19, 2024
eaa7cac
Rename `cdr_seaice_conc_stdev_monthly` -> `cdr_seaice_conc_monthly_st…
trey-stafford Sep 19, 2024
43d36fc
add combined bt and nt2 spillover
Sep 19, 2024
3326841
Merge pull request #155 from nsidc/monthly-update-for-prototype-groups
trey-stafford Sep 19, 2024
35f742f
Use `find_standard_monthly_netcdf_files` in `monthly_aggregate`
trey-stafford Sep 19, 2024
7b383a4
remove BT_NT2 (keep NT2_BT) land spillover
Sep 19, 2024
00dbabe
Monthly aggregate code supports groups in final nc files
trey-stafford Sep 19, 2024
1cdebfe
Make daily agg CLI use 25km resolution by default
trey-stafford Sep 19, 2024
df14407
Update entrypoint to place monthly agg CLI w/ others for ops
trey-stafford Sep 19, 2024
c790f82
remove unused kwargs; fix typo
Sep 19, 2024
13a3947
Merge pull request #157 from nsidc/ecdr-at-25km-ss
trey-stafford Sep 19, 2024
5799392
Merge pull request #159 from nsidc/monthly-aggregate-update-for-groups
trey-stafford Sep 19, 2024
aab81e6
Rename `cdr_seaice_conc_interp_spatial` -> `cdr_seaice_conc_interp_sp…
trey-stafford Sep 19, 2024
9faf184
Remove breakpoint
trey-stafford Sep 19, 2024
9087d9e
Rename `cdr_seaice_conc_qa` -> `cdr_seaice_conc_qa_flag`
trey-stafford Sep 19, 2024
d75802c
`cdr_seaice_conc_interp_temporal` -> `cdr_seaice_conc_interp_temporal…
trey-stafford Sep 19, 2024
e6e050d
Another pass on qa flag
trey-stafford Sep 19, 2024
6a067eb
minor tweaks to validation CLI
trey-stafford Sep 19, 2024
98b338c
Merge pull request #160 from nsidc/rename-flag-vars
trey-stafford Sep 19, 2024
60a7ca2
Merge pull request #161 from nsidc/update-validation-script-for-groups
trey-stafford Sep 19, 2024
f3b5f43
Default output dir is calculated from environment
trey-stafford Sep 19, 2024
d082ae3
Environment-specific logs dir
trey-stafford Sep 23, 2024
a4f3c2d
Update GHA to create expected share dir
trey-stafford Sep 23, 2024
ff19054
Merge pull request #162 from nsidc/operationalize-for-prod
trey-stafford Sep 23, 2024
3ef8458
Init work to support NRT using NSIDC-0080 F18 as input
trey-stafford Sep 23, 2024
e3f4120
Update NRT code to write publication-ready output files
trey-stafford Sep 23, 2024
ee18544
Cleanup now-unused constant
trey-stafford Sep 23, 2024
eaddc21
Update doc & help strings
trey-stafford Sep 23, 2024
e23be68
Fixup output filename for publication-ready nrt files
trey-stafford Sep 23, 2024
c823437
Write checksums for nrt files
trey-stafford Sep 23, 2024
6185a9d
Simplify handling of nrt temporal interp range
trey-stafford Sep 23, 2024
c34a269
Write NRT outputs to G10016 v3 dir and update fn w/ new version
trey-stafford Sep 24, 2024
d04df9a
Update land spillover alg for NRT data to use NT2_BT
trey-stafford Sep 24, 2024
ec2fa41
Update NRT NetCDF attrs for publication to G10016
trey-stafford Sep 24, 2024
a32cf41
Update summary text in nrt files
trey-stafford Sep 24, 2024
0770d10
NRT: Use null grid for missing dates of data
trey-stafford Sep 24, 2024
1c0635a
Add TODO about ancillary data location
trey-stafford Sep 24, 2024
6a818f4
Wrap NRT CLI so that nrt platform start date config is used
trey-stafford Sep 24, 2024
83dc0ea
Add note/TODO
trey-stafford Sep 24, 2024
4b8f92d
Use the F17 polemask for F18
trey-stafford Sep 24, 2024
fbd379c
Use nsidc-0001 F18 BT params for nsidc-0080 F18 NRT
trey-stafford Sep 25, 2024
f7241bb
Pin GHA micromamba version to the release before v2
trey-stafford Sep 25, 2024
87e0228
Pin `pm_tb_data` and `pm_icecon` to new versions for G10016
trey-stafford Sep 25, 2024
46c7f04
Add `platform_id` kwarg to function call in test module
trey-stafford Sep 26, 2024
01ab4e4
Cleanup TODO.
trey-stafford Sep 26, 2024
3b6bd6a
Merge pull request #163 from nsidc/nrt-like-v4
trey-stafford Sep 26, 2024
66b94e4
Use F17 instead of F18 for NRT
trey-stafford Sep 26, 2024
73a30a8
Make error handling around missing data issues more generic
trey-stafford Sep 26, 2024
4fd8ce6
fix F17 start date
Sep 26, 2024
194f743
Fixup platform start date for F17
trey-stafford Sep 26, 2024
3c6aa6e
Merge pull request #164 from nsidc/use-f17-nrt
trey-stafford Sep 26, 2024
b77d0b3
Add `--latest-n-days` option to NRT CLI
trey-stafford Sep 26, 2024
edf1921
Merge branch 'ecdr-at-25km' into ecdr-at-25km-towards-cdrv5
Sep 26, 2024
c4b341b
Update NRT CLI to support both running both hemispheres at once
trey-stafford Sep 26, 2024
04522f0
Remove nrt-specific output dir code
trey-stafford Sep 26, 2024
b987eda
Fixup output checksum file location for NRT
trey-stafford Sep 26, 2024
ccb56a6
remove specific code to support BT_NT land spillover algorithm
Sep 27, 2024
9235dcf
allow raw BT and NT conc of 0 to 200%
Sep 27, 2024
57cc450
fix QA flag values
Sep 27, 2024
2dcc36b
fix ncattr typos
Sep 27, 2024
d345373
comment out rounding statements used to match v4 results
Sep 27, 2024
c711455
seaice_ecdr/temporal_composite_daily.py
Sep 27, 2024
07433e8
comment out CDRv4 spatial interpolation method
Sep 27, 2024
885625e
fix daily melt onset fields
Sep 27, 2024
cbc46d4
Merge pull request #166 from nsidc/nrt-improvement-for-ops
trey-stafford Sep 27, 2024
686febd
Merge pull request #167 from nsidc/update-paths-for-nrt
trey-stafford Sep 27, 2024
e3b59f3
Init operations doc for ops
trey-stafford Sep 26, 2024
e2dbc82
for monthly stdev field, use np.std() instead of xr.DataArray.std() t…
Sep 27, 2024
7a934df
Monthly NRT code
trey-stafford Sep 26, 2024
86a51c3
Tweak comment
trey-stafford Sep 27, 2024
d25212d
update comments and valid range for melt onset fields
Sep 27, 2024
51d4eca
useful refactor of monthly publication code
trey-stafford Sep 27, 2024
e96300f
Override attrs in monthly nrt files to be G10016-specific.
trey-stafford Sep 27, 2024
23cfab1
Improve formatting of func call
trey-stafford Sep 27, 2024
014fa50
Add assertion to check NRT platform ID is in the summary
trey-stafford Sep 27, 2024
616d6b2
use axis identification of 'time' axis to do monthly stdev calculation
Sep 28, 2024
ccd3bf0
clamp lower bound of monthly cdr_seaice_conc to 10%
Sep 28, 2024
18a22a0
clean up comments
Sep 30, 2024
7675d69
Merge pull request #169 from nsidc/monthly-nrt-override-attrs
trey-stafford Sep 30, 2024
37d8da4
Merge pull request #168 from nsidc/monthly-nrt
trey-stafford Sep 30, 2024
36e382e
tweaks per PR review
Oct 2, 2024
97f52a7
set default log levels to SUCCESS for both dev and <other> users
Oct 2, 2024
6b63eaf
ensure no siconc between 0 and 10% after temporal interpolation
Oct 2, 2024
4cc4a6c
Merge pull request #165 from nsidc/ecdr-at-25km-towards-cdrv5
sc0tts Oct 3, 2024
f16f644
test smmr-era masks for CDRv4 and CDRv5
Oct 6, 2024
f9e413a
re-include temporal composite test
Oct 6, 2024
decc1f0
remove validation integration test skip
Oct 6, 2024
90db08a
use CDRv5 without dynamic BT tiepoints
Oct 6, 2024
881852f
implement dynamic tiepoints for BT
Oct 6, 2024
932864f
only warn of high NT conc values over ocean
Oct 6, 2024
011bc91
change print to logger statement
Oct 6, 2024
67a54b8
explicitly create empty idecdr files
Oct 6, 2024
826a02c
remove breakpoint from test
Oct 6, 2024
e6e80c1
use info instead of warning if making empty idecdr file
Oct 6, 2024
187052f
enforce consistent time units
Oct 9, 2024
bf2bc1d
add tests for determining dates with missing tbs or fields
Oct 9, 2024
cc1e3bd
move read and read/write of tiecdr to proper source file
Oct 9, 2024
1ed99b5
move read and read/write idecdr to correct source file
Oct 9, 2024
27ecd86
commit WIP to refactor TB dataarray assignment
Oct 11, 2024
56019b9
set cdr_seaice_conc fields to missing for days with known bad data
Oct 11, 2024
ddcffb0
add explicit setting of null TBs; eg for am2 on 12/16/2018
Oct 11, 2024
5fd78cb
add script to fix CDRv5 ancillary adj123 and land90 masks
Oct 13, 2024
46e568e
update for CDRv5 ancillary
Oct 13, 2024
7e29e86
cause stdev to be consistently named
Oct 13, 2024
7998d18
improve stdev calculation
Oct 15, 2024
26fc120
handle xarray empty-but-3d index-selection of pre-SMMR fields
Oct 15, 2024
d796bf8
ensure units of meters are set in ancillary file
Oct 15, 2024
3e671eb
remove overwrite-with-NaNs F17 for Mar 24-25, 2008
Oct 15, 2024
da49a48
change out-of-range to logger error rather than exception
Oct 16, 2024
12aab26
test that all-missing does not crash stdev calculation
Oct 16, 2024
ca668ac
add 'coordinates' attr to prototype_am2 group vars so that they plot …
Oct 18, 2024
43e24c2
add ncattr and default values to aggregation routines
Oct 22, 2024
09c414d
update ancillary field names
Oct 24, 2024
26a0999
allow computation of NH conc for Dec 26-27, 1990
Oct 28, 2024
c757671
fix various nc attributes
Oct 29, 2024
489b307
fix mis-identification of platform because of xarray data_stacking me…
Oct 29, 2024
b2436cd
further attribute fixes
Oct 29, 2024
0785d6b
fix integration test
Oct 30, 2024
e903f04
fix prototype attributes
Oct 30, 2024
ea82250
add empty months to config file
Oct 30, 2024
082cce8
warn if pole hole unfillable; fix nt_conc clamping
Oct 30, 2024
c359344
handle months with so little data that we set them to all-missing
Oct 30, 2024
f9ace4d
fix temporal interpolation flag to be 255 where land and everywhere i…
Oct 31, 2024
3ddf88d
x, y may not exist in xr (datatree) groups
Nov 4, 2024
29bea40
remove calls to NT spillover routines
Nov 4, 2024
231c5f1
add script to remove min_concentration field from ancillary file(s)
Nov 4, 2024
3a9672c
address requested PR changes part 1
Nov 4, 2024
55f868c
update test_monthly to use 25km rather than 12.5km
Nov 4, 2024
9633a82
address PR change reqests, part two
Nov 4, 2024
7108d5b
move test_monthly that requires anc file to integration tests
Nov 4, 2024
6c27ec9
Remove commented-out config that is now set by ancillary file
trey-stafford Nov 4, 2024
c26d2de
Add docstring/context for nc_util
trey-stafford Nov 4, 2024
d21a2cf
Merge pull request #170 from nsidc/ecdr-at-25km-use-CDRv5-ancillary
trey-stafford Nov 4, 2024
7f95922
Support both F17 and AM2 NRT processing
trey-stafford Nov 5, 2024
62b97cf
Override NRT "reference" attr in cdr variables
trey-stafford Nov 4, 2024
807d5ee
Fixup `publish_monthly` to assert NRT platform in nrt check
trey-stafford Nov 5, 2024
fa383fa
Rename NRT files to include `_icdr_` instead of `_P`.
trey-stafford Nov 5, 2024
039239a
In AM2 NRT files: rename `cdr_` vars -> `am2_`
trey-stafford Nov 5, 2024
ea6e4df
Remove choice to ues `am2` platform for monthly nrt data files
trey-stafford Nov 5, 2024
b5bead4
Update operation doc for nrt processing
trey-stafford Nov 5, 2024
5ce4238
Remove now-unnecessary flag from ops doc for monthly nrt cmd
trey-stafford Nov 5, 2024
e52dd2d
Update operation doc w/ latest info about structure of nrt files
trey-stafford Nov 5, 2024
3e0a431
Fixup hack to only drop cdr melt onset var if it exists
trey-stafford Nov 5, 2024
da8aa66
Monthly NRT CLI: support `--hemisphere both`
trey-stafford Nov 5, 2024
7c1c392
Cleanup OBE note
trey-stafford Nov 5, 2024
6ffcf0d
Use default constants to set resolution & anc. source for monthly nrt
trey-stafford Nov 5, 2024
fe6cb9e
Merge pull request #171 from nsidc/nrt-for-f17-and-am2
trey-stafford Nov 5, 2024
5988f6d
Support `--hemisphere both` for daily CLI
trey-stafford Nov 5, 2024
35ef15c
Update ops doc
trey-stafford Nov 5, 2024
d9b5c65
Support `--hemisphere both` for monthly CLI
trey-stafford Nov 5, 2024
f265b2d
Another update to the ops doc
trey-stafford Nov 5, 2024
c5c42d0
Merge pull request #172 from nsidc/support-both-hemis-ops-cli
trey-stafford Nov 5, 2024
91ea8da
CHANGELOG for v1
trey-stafford Nov 5, 2024
dd146a5
Bumpversion to v1.0.0
trey-stafford Nov 5, 2024
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8 changes: 8 additions & 0 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ jobs:
- name: "Install Conda environment"
uses: "mamba-org/setup-micromamba@v1"
with:
micromamba-version: '1.5.10-0' # any version from https://github.com/mamba-org/micromamba-releases
environment-file: "conda-lock.yml"
# When using a lock-file, we have to set an environment name.
environment-name: "seaice_ecdr-ci"
Expand All @@ -48,6 +49,13 @@ jobs:
ref: "main"
path: "pm_tb_data"

# Our code expects `/share/apps/G02202_V5` to exist already, and raises an
# error if it does not. This would be a sign, on NSIDC infrastructure,
# that NFS mounts are not setup correctly. For CI, we can just create
# those dirs:
- name: "Make share dir"
run: "sudo mkdir -p /share/apps/G02202_V5 && sudo chown -R runner:runner /share/"

# Unit tests
- name: "Run typecheck and tests"
run: "PYTHONPATH=/home/runner/work/seaice_ecdr/seaice_ecdr/:/home/runner/work/seaice_ecdr/seaice_ecdr/pm_icecon/:/home/runner/work/seaice_ecdr/seaice_ecdr/pm_tb_data/ DISABLE_FILE_LOGGING=TRUE invoke test.ci"
28 changes: 28 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,31 @@
# v1.0.0

* First production release of 25km CDR

* Add new `daily` cli that produces daily NC files ready for publication. During
the AMSR2 period, a `prototype_am2` group is added to the final output files
with AMSR2-derived fields.

* Support daily and monthly NRT processing. Daily NRT processing supports
producing AMSR2 and F17 outputs. Monthly processing supports F17 output, but
not AMSR2.

* Removes much of the code required to match CDR v4.

# match-cdrv4 (commit 87271ec)

* `match-cdrv4` tag marks the commit at which this code supports replicating the
behavior of CDRv4 at 25km resolution. This is useful for comparison
purposes. Future commits will remove support for producing CDRv4 in favor of
the improvements and bugfixes provided by CDRv5.

# v0.2.0

* Produce 25km CDR instead of 12.5km.
* Refactor how platforms are handled to support overriding platform start dates
via yaml configuration files.


# v0.1.0

* Initial version of the ECDR.
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