675 scipy integrate cumtrapz update #676

jpolton · 2025-03-04T21:03:51Z

Pull request checklist

Please check if your PR fulfills the following requirements:

Tests for the changes have been added (for bug fixes / features)
Docs have been reviewed and added / updated if needed (for bug fixes / features)
- Some docs updates need to be made in the COAsT-site repo, in a separate PR. See contributing to documentation for details.
Build (./build.sh) was run locally and no errors reported. NB not sure about this requirement: GitActions test this
Lint (pylint .) has passed locally and any fixes were made for failures. NB not sure about this requirement: GitActions test this with black

Pull request type

Please check the type of change your PR introduces:

What is the current behavior?

Issue URL: #675

What is the new behavior?

Checklist

Code compiles correctly
Created tests which fail without the change (if possible)
All tests passing (pip install . && pytest unit_testing/unit_test.py -s)
Extended the README / documentation, if necessary
Added myself / the copyright holder to the AUTHORS file

Does this introduce a breaking change?

Yes
No

Other information

jpolton · 2025-03-04T21:14:12Z

WIP. Segmentation fault during:

pytest unit_testing/test_gridded_initialisation.py -s

Fails during the test for loading multiple files.

jpolton · 2025-03-14T21:31:00Z

The following build works, using the setup.py file, where I have heavily specified packages to use the last "old" scipy==1.14 but also made changes to use the new cumulative_trapezoid functions

cd COAsT
conda create -n coast-15mar10 python==3.10 pip
conda activate coast-15mar10
pip install -e .
pip install cartopy #(got 0.24.1)
pip install 'pandas<=1.5.2'  # compatibility issue with old xr.resample() otherwise 

pytest unit_testing/unit_test.py

Works! With the last old scipy=1.14 but new scipy commands
@chrispeq

jpolton · 2025-03-17T09:42:51Z

Code passes tests on my local machine.
Next steps:
. investigate failing git Actions
. release as bug fix COAsT==3.3.1

Then investigate dependency package updates...

…channel

Install packages using conda command and environment.yml file

Remove python version 3.8 and swap pip install command by conda install command to download/install packages using environment.yml file

Add conda commands to create environment, install dependencies and then activate environment

Add conda init command

Swap conda commands order

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch and fix typo to step name

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch

Update specific version to dask and requests dependencies

Update specific version of dask dependency

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch and fix typo to step name

Update setup config to require python 3.9 and 3.10

Update specific version of dask dependencies

Update step to checkout current branch

Update versions of some dependencies so environment.yml and setup.py have same dependencies versions

Format file setup.py

Update script to set conda log's verbosity to level 3

Update workflow to set conda log's verbosity to level 3

…com/British-Oceanographic-Data-Centre/COAsT into 675_scipy_integrate_cumtrapz_update

Set conda log's verbosity to level 3

Add conda command to remove unused packages and caches

Remove conda command which removes unused packages and caches

Update version of scipy dependency

Add python 3.10 as dependency to setup.py. Update version to scikit-image dependency to both config files

Remove python dependency from install_requires section

Update version for pydap dependency in setup.py and environment.yml

Update version for cartopy dependency

Update version for zarr dependency

Remove conda command to set log verbosity to level 3

Jeffrey Polton and others added 3 commits March 4, 2025 19:24

cumtrapz --> cumulative_trapezoid

a03ae51

update to permit small tolerance

9e086cd

update dependencies

685ef9e

jpolton linked an issue Mar 4, 2025 that may be closed by this pull request

coast.transect: scipy.integrate.cumtrapz deprecated #675

Closed

1 task

jpolton removed a link to an issue Mar 4, 2025

coast.transect: scipy.integrate.cumtrapz deprecated #675

Closed

1 task

jpolton linked an issue Mar 4, 2025 that may be closed by this pull request

coast.transect: scipy.integrate.cumtrapz deprecated #675

Closed

1 task

Apply Black formatting to Python code.

25e3456

jpolton self-assigned this Mar 4, 2025

jpolton and others added 2 commits March 14, 2025 21:27

fixing packages that work

d264f20

Apply Black formatting to Python code.

10cf0fe

jpolton and others added 7 commits March 17, 2025 08:57

restore test for xr.open_mfdataset

fa718b1

restore test_tide_gauge_method test. Added note

d751dc9

Apply Black formatting to Python code.

4b0eb4e

black formatting

c095ee4

remove editting error

1811382

set version of coast=3.3.1 for pip build

a82f585

restore edits that I did not use

4e6f643

jpolton and others added 10 commits March 17, 2025 14:58

remove references to untested python=3.11

b7a5a51

clear depreciation warnings

2b9299d

Apply Black formatting to Python code.

eec3807

update environment.yml file to download some dependencies from conda …

4e39800

…channel

update verify_package.yml

06c1e30

Update verify_package.yml

6244298

Install packages using conda command and environment.yml file

Update build_package.yml

301d03b

Remove python version 3.8 and swap pip install command by conda install command to download/install packages using environment.yml file

Update build_package.yml

a640244

Add conda commands to create environment, install dependencies and then activate environment

Update build_package.yml

be5fbe7

Add conda init command

Update build_package.yml

5be1be1

Swap conda commands order

MagdaJuarez and others added 29 commits June 6, 2025 10:49

Update markdown-tidegauge.yml

acc53a7

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch and fix typo to step name

Update markdown-gridded.yml

170071b

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch and fix typo to step name

Update markdown-general.yml

e20ce58

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch

Update setup.py

e2861f9

Update specific version to dask and requests dependencies

Update setup.py

a973b41

Update specific version of dask dependency

Update markdown-profile.yml

c3c2bce

Swap develop branch for 675_scipy_integrate_cumtrapz_update branch and fix typo to step name

Update setup.py

51aad1d

Update setup config to require python 3.9 and 3.10

Update setup.py

f91d96b

Update specific version of dask dependencies

Update markdown-altimetry.yml

c6a16f5

Update step to checkout current branch

Update markdown workflows

92d83d2

Update step to checkout current branch

Update environment.yml and setup.py

f4b4410

Update versions of some dependencies so environment.yml and setup.py have same dependencies versions

Apply Black formatting to Python code.

bf4c8fc

Format setup.py

83b0e7f

Format file setup.py

Update setup_environment.sh

0c5dc60

Update script to set conda log's verbosity to level 3

Update verify_package.yml

cb9563c

Update workflow to set conda log's verbosity to level 3

Merge branch '675_scipy_integrate_cumtrapz_update' of https://github.…

683a945

…com/British-Oceanographic-Data-Centre/COAsT into 675_scipy_integrate_cumtrapz_update

Update setup_environment.sh

01d185c

Set conda log's verbosity to level 3

Update verify_package.yml

216f9b3

Set conda log's verbosity to level 3

Update verify_package.yml

4d638ef

Add conda command to remove unused packages and caches

Update setup_environment.sh

d966efe

Add conda command to remove unused packages and caches

Update verify_package.yml

89b001c

Remove conda command which removes unused packages and caches

Update setup_environment.sh

867b1c7

Remove conda command which removes unused packages and caches

Update environment.yml and setup.py

f2310fb

Update version of scipy dependency

Update environment.yml and setup.py

9c91fba

Add python 3.10 as dependency to setup.py. Update version to scikit-image dependency to both config files

Update setup.py

83db956

Remove python dependency from install_requires section

Updated setup.py and environment.yml

2922cf7

Update version for pydap dependency in setup.py and environment.yml

Update setup.py and environment.yml

45bf52f

Update version for cartopy dependency

Update setup.py and environment.yml

f8ae02c

Update version for zarr dependency

Update setup_environment.sh and verify_package.yml

4d81d83

Remove conda command to set log verbosity to level 3

MagdaJuarez merged commit decba75 into develop Jun 17, 2025
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675 scipy integrate cumtrapz update #676

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675 scipy integrate cumtrapz update #676

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Pull request checklist

Pull request type

What is the current behavior?

What is the new behavior?

Checklist

Does this introduce a breaking change?

Other information

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