develop to stable - originally created for updates landcover code and notebooks #1345

GL-S · 2025-05-15T04:40:09Z

Merging develop into stable so that the knowledge hub documentation reflects the most recent updates to the landcover code and notebooks

* add WIT app files desired from lauren_WIT_app * Grammatical edits to markdown cells * edit licence section to add ccby info and removed witapp link from pubs * updates from review comments --------- Co-authored-by: Claire Phillips <[email protected]> Co-authored-by: BexDunn <[email protected]>

* update-LC-planetary-NB * removed unused Python package * formatting

…ion() * new notebook and function * changed area and added viz * consistent colours * formatting * mask with vector * fixed output table * fixed text * consitency figures size method * same colours of LC * last fixes * more robust code * Update Land_cover_export_data.ipynb * edits to markdown text for lc export notebook * small typos * Update Land_cover_pixel_drill.ipynb * adjusted order markdown cells * Update README.rst new notebook * move analysis params to top, load based on polygon * refine and simplify * rename * small typos fixed * applied formatting style --------- Co-authored-by: Jenna Guffogg <[email protected]> Co-authored-by: cbur24 <[email protected]>

…cs-token Documented a personal access token as a code comment (minor change)

* first attempt at continental-scale animation notebook * testing notebook can execute in small sandbox. Minor fixes to markdown text. * test and reduce years to speed up processing * Minor formatting and code updates --------- Co-authored-by: Jenna Guffogg <[email protected]> Co-authored-by: robbibt <[email protected]>

* first attempt at a new climate notebook * add era5 * refactor markdown cell order * refine markdown * fixes to climate notebook * alternative * remove 2nd nb and refine chunks and params of era5 --------- Co-authored-by: GL-S <[email protected]>

review-notebook-app · 2025-05-15T04:40:15Z

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* Update USAGE.rst Add recent citation from DE-Africa * sort --------- Co-authored-by: Gianluca S. <[email protected]>

* make copy tidal and pull image optional for reusing db connection provisioning * specify input type * suppress chattering messages * explicit on condition * use strings in condition * always typos --------- Co-authored-by: James Miller <[email protected]> Co-authored-by: ClaireP <[email protected]> Co-authored-by: Emma Ai <[email protected]>

Update rst to include WIT app so it will appear in interactive apps.

Add WIT app to README.rst

* begin retesting ML notebooks * continue ML updates * clean up remaining ML nbs * add missing import

* Update packaging to use uv, hatch * Remove ciso8601 * Pin odc-algo, remove pyTMD, add odc-stac to STAC * Remove setup.py, update deptry * Add additional notebook dependencies * Set ruff linting fix to false for safety * Simplify jupyter * Fix test install * Pin old PyTMD, remove eo-tides * Update readme * Updates from review * Wording * Update README_tools.md * Remove warp sub-dependency

* Simplify package publication using uv * Simplify environment creation * Upgrade dask-ml * Test Python 3.10 * Try to pin numba * Fix deptry, test publish * Switch to Python 3.11 * Run full repo tests on changes to pyproject.toml * Simplify action

…talled (#1354) * Raise error if datacube not installed * Updates to relative package imports * Update spatial and temporal * Update maps.py, dask.py, wit_app.py

* Apply Ruff formatting * Apply Ruff linting to fix code issues * Revert relative imports * Fix type formatting

* Apply Ruff formatting * Apply Ruff linting to fix code issues * Revert relative imports * Fix type formatting * Update repo to use eo-tides, temporarily delete HLTC notebook

* update WIT app tools files and name * Update rst to new WIT app name update name of WIT interactive app

…ncy (#1360) * update create_local_dask_cluster to work without datacube * fix cluster creation in nb * fix docstrings * remove doc string reference to /scripts, and ad kwargs * update doc string with kwargs arg * rm int from kwargs arg * Make configure_rio a param * add default memory limit to client * add more info to docstring * constrain memory limit by number of workers * docstrings --------- Co-authored-by: Robbi Bishop-Taylor <[email protected]>

* Final tidy up before DEA Tools 0.4.0 release * Fix docstring formatting * Try fixing package level * Update * Fix typo * Try settting target wheel * Move readme, alphabetise imports, add sunriset * Update readme * Add stac dependency * Minor formatting * Remove STAC optional dep, make tests only run once * Update readmes * Update code owners * Fix code owners * Add odc.io * add Ipython warning (#1361) --------- Co-authored-by: Chad Burton <[email protected]>

Forecasting/modelling notebook

* first commit of random sampling tools * more efficient algo working * write nb and docs for func * rename nb * add section on sapling large rasters * remove unused libraries * add tags * update tags * remove large-scale testing * refine description * typos * update readme.rst * add tests for random_samples_xr * tidy up function and make more consistent * test nb again * Use spatial_dims, minor formatting * Docstring * Rename * Update validation.py --------- Co-authored-by: robbibt <[email protected]>

* more-flexible-inputs * first-draft-notebook * fixed-doc-functions * read-me-file * index-updated * finished-notebook * first-draft-testing * test_notebooks * improved-test * test-script * finalised-test-script * changed-description-delete-output * screenshot-example * functions-can-work-with-cli * fixed-funct-names-test * update-readme * Updates to continental mosaics PR (#1364) * Updates to COG mosaic and VRT code * Fix formatting * typo * Improve logging * Update tests, fix commented out lines * Update with beter logging, URLs * Revert path change * naming-and-structure * revert-accidental-changes * Implement temporary workaround for S3 access issue * Temporarily ignore notebook * Update test_notebooks_pullrequest.yml * Fix formatting * extra-details_update-names --------- Co-authored-by: Robbi Bishop-Taylor <[email protected]>

…for VRTs (#1368) * colour-schemes-in-deatools-package * udpated-tests

GL-S · 2025-08-07T06:58:51Z

I was wondering if we could do a merge from develop to stable. Currently, the default notebooks in the Sandbox still use old versions of landcover functions, which do not work with LC 2.0.
Of course, it's not a too big issue, because one can just clone the develop branch and everything works as expected.

BexDunn · 2025-08-11T00:19:02Z

.github/CODEOWNERS

@GL-S can you check the codeowners are correct? Github is flagging that it can't find some of the users? Unknown owner on line 5: make sure @margaret-dea exists and has write access to the repository

I am not sure how to do that. Considering this PR is a bit old, is it worth it to just delete this and start a new one?
Maybe it will fix the issue

Yeah, sounds like a plan :) Maybe rather than deleting it just close it with a comment and start again?

BexDunn

Hi @GL-S thanks for doing this. Can you please check that you've got the most up-to-date version of develop in this PR so that any new changes are captured, and that any missing files from this PR are intentional. I'm sure it's the case, however it's a really big PR and I don't want to upset stable! I note there are a few files removed, including a licence one and a number of notebooks and tools packages. I'd love a few more eyes on it as it seems like a lot of deletions. Probably because we haven't pushed to stable in a while :) thanks!

BexDunn · 2025-08-11T00:20:58Z

DEA_products/README.rst

Did we mean to remove the high and low tide imagery notebook here?

BexDunn · 2025-08-11T00:21:29Z

How_to_guides/External_data_ERA5_Climate.ipynb

Is this one supposed to be removed @cbur24 ?

BexDunn · 2025-08-11T00:21:49Z

DEA_products/DEA_High_and_Low_Tide_Imagery.ipynb

did we mean to remove this one @erialC-P @GL-S

BexDunn · 2025-08-11T00:23:32Z

Tools/LICENSE

did this file mean to be removed? @GL-S

BexDunn · 2025-08-11T00:26:16Z

Tools/dea_tools/climate.py

BexDunn · 2025-08-11T00:26:31Z

Tools/dea_tools/coastal.py

@robbibt @erialC-P is this intended?

GL-S · 2025-08-11T00:36:07Z

Closing because this was opened months ago. Starting a new one

cbur24 and others added 26 commits March 31, 2022 05:39

working draft of forecasting notebook

e104909

typos

caf13e3

Merge branch 'develop' into forecasting

4ff5251

test forecasting nb works after sandbox image update

7afcd69

remove warning about statsmodel package

06f3f72

Merge branch 'develop' into forecasting

8f56a03

Merge develop

3c8dfb9

merge develop

bec9972

Updates to notebook to use new products, reduce load time

124f8d2

Update lc planetary nb (#1330)

9dd5d68

* update-LC-planetary-NB * removed unused Python package * formatting

fixed text (#1331)

b2f0579

merge develop

a93f891

retest forecasting and add exogenous variable

b07a1d9

remove exogenous variable and tidy up

5a9c789

Update README.rst (#1333)

a5d8c85

add verbose parameter to load_ard (#1338)

20e3bb0

Documented the token as a code comment

277f147

Merge pull request #1339 from GeoscienceAustralia/document-trigger-do…

45289a0

…cs-token Documented a personal access token as a code comment (minor change)

Fix contiguity masking by applying fuse function (#1341)

6e32714

markdown edits to landcover and Landsat notebooks (#1342)

491533a

New climate data notebook (#1335)

b75ef2b

* first attempt at a new climate notebook * add era5 * refactor markdown cell order * refine markdown * fixes to climate notebook * alternative * remove 2nd nb and refine chunks and params of era5 --------- Co-authored-by: GL-S <[email protected]>

typos (#1343)

f7795b0

descriptions-improvements (#1344)

46040a8

GL-S requested review from robbibt, BexDunn, erialC-P and uchchwhash as code owners May 15, 2025 04:40

GL-S requested review from Ariana-B, amanda2099, supermarkion and erin-telfer as code owners May 15, 2025 04:40

GL-S changed the title ~~updates landcover code and notebooks~~ updates landcover code and notebooks - and others May 15, 2025

cbur24 and others added 18 commits May 22, 2025 12:58

Update USAGE.rst (#1346)

39f8869

* Update USAGE.rst Add recent citation from DE-Africa * sort --------- Co-authored-by: Gianluca S. <[email protected]>

move dask client to fix loading issue (#1350)

50a1a52

Add WIT app to README.rst

3b5825f

Update rst to include WIT app so it will appear in interactive apps.

Merge pull request #1352 from GeoscienceAustralia/WIT_rst_update

34d91d5

Add WIT app to README.rst

Update classification tools and ML notebooks (#1351)

fd6db98

* begin retesting ML notebooks * continue ML updates * clean up remaining ML nbs * add missing import

DEA Tools cleanup to improve user experience when datacube is not ins…

4a22474

…talled (#1354) * Raise error if datacube not installed * Updates to relative package imports * Update spatial and temporal * Update maps.py, dask.py, wit_app.py

Apply Ruff code formatting and linting to entire DEA Tools (#1356)

bfa7bde

* Apply Ruff formatting * Apply Ruff linting to fix code issues * Revert relative imports * Fix type formatting

Refactor to use eo-tides tide modelling tools (#1357)

da365d4

* Apply Ruff formatting * Apply Ruff linting to fix code issues * Revert relative imports * Fix type formatting * Update repo to use eo-tides, temporarily delete HLTC notebook

Merge WIT_app.py into wetlands.py in DEA Tools (#1359)

50d35ad

* update WIT app tools files and name * Update rst to new WIT app name update name of WIT interactive app

Merge pull request #911 from GeoscienceAustralia/forecasting

de7bd17

Forecasting/modelling notebook

Modified continental COG mosaics submodule to contain colour schemes …

8b3dc66

…for VRTs (#1368) * colour-schemes-in-deatools-package * udpated-tests

GL-S changed the title ~~updates landcover code and notebooks - and others~~ develop to stable - originally created for updates landcover code and notebooks Aug 11, 2025

BexDunn reviewed Aug 11, 2025

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GL-S closed this Aug 11, 2025

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develop to stable - originally created for updates landcover code and notebooks #1345

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develop to stable - originally created for updates landcover code and notebooks #1345

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