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Deprecate waterdynamics and replace with waterdynamics mdakit #4404

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merged 12 commits into from
Jan 11, 2024
Merged

Deprecate waterdynamics and replace with waterdynamics mdakit #4404

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4484a50
Add waterdynamics dep
IAlibay Dec 29, 2023
18c2222
Add deprecation docstring notice and see also
IAlibay Dec 29, 2023
3e3e33f
remove docstring
IAlibay Dec 29, 2023
a8918fe
remove local code
IAlibay Dec 29, 2023
6f49b3a
Add imports from waterdynamics
IAlibay Dec 29, 2023
e6679e9
fix import
IAlibay Dec 29, 2023
24c210e
Add deprecation warning
IAlibay Dec 29, 2023
e966944
Add deprecationwarning test
IAlibay Dec 29, 2023
3b2e85f
remove unit tests
IAlibay Dec 29, 2023
754c62c
update changelog
IAlibay Dec 29, 2023
755856a
Add removal version in changelog
IAlibay Dec 29, 2023
37a59d5
Merge branch 'develop' into deprecate-waterdynamics
IAlibay Jan 11, 2024
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3 changes: 3 additions & 0 deletions .github/actions/setup-deps/action.yaml
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Expand Up @@ -51,6 +51,8 @@ inputs:
default: 'threadpoolctl'
tqdm:
default: 'tqdm>=4.43.0'
waterdynamics:
default: 'waterdynamics'
# conda-installed optional dependencies
biopython:
default: 'biopython>=1.80'
Expand Down Expand Up @@ -124,6 +126,7 @@ runs:
${{ inputs.scipy }}
${{ inputs.threadpoolctl }}
${{ inputs.tqdm }}
${{ inputs.waterdynamics }}
CONDA_OPT_DEPS: |
${{ inputs.biopython }}
${{ inputs.chemfiles-python }}
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2 changes: 2 additions & 0 deletions package/CHANGELOG
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Expand Up @@ -29,6 +29,8 @@ Changes
is used from python 3.9 to 3.11 (Issue #4401, PR #4402)

Deprecations
* The MDAnalysis.analysis.waterdynamics module has been deprecated in favour
of the waterdynamics MDAKit and will be removed in version 3.0.0 (PR #4404)
* The MDAnalysis.analysis.psa module has been deprecated in favour of
the PathSimAnalysis MDAKit and will be removed in version 3.0.0
(PR #4403)
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