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orbeckst committed Nov 25, 2024
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20 changes: 10 additions & 10 deletions _posts/2024-11-22-release-2.8.0.md
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Expand Up @@ -176,7 +176,7 @@ For a full list of changes, bugfixes and deprecations see the [CHANGELOG][].
* Deprecations of old guessing functionality (in favor of the new
Guesser API)
* `MDAnalysis.topology.guessers` is deprecated in favour of the new
Guessers API and will be removed in version 3.0 (PR #4752)
Guessers API and will be removed in version 3.0 (PR #4752)
* The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound`
kwargs are deprecated for bond guessing during Universe
creation. Instead, pass `("bonds", "angles", "dihedrals")` into
Expand All @@ -187,12 +187,12 @@ For a full list of changes, bugfixes and deprecations see the [CHANGELOG][].
`Universe.guess_TopologyAttrs`, they will override the previous
values of those kwargs. (Issue #4756, PR #4757)
* `MDAnalysis.topology.tables` is deprecated in favour of
`MDAnalysis.guesser.tables` and will be removed in version 3.0 (PR #4752)
`MDAnalysis.guesser.tables` and will be removed in version 3.0 (PR #4752)
* Element guessing in the `ITPParser` is deprecated and will be removed in version 3.0
(Issue #4698)
(Issue #4698)
* **Unknown masses are still set to 0.0 for current version**, this
will be changed **in version 3.0.0 and replaced by
`Masses` "no_value_label" attribute (`np.nan`)** (PR #3753)
will be changed **in version 3.0.0 and replaced by
`Masses` "no_value_label" attribute (`np.nan`)** (PR #3753)
* A number of analysis modules have been moved into their own
[MDAKits][], following the [3.0 roadmap towards a trimmed down core
library][roadmap]. Until release 3.0, these modules are still
Expand All @@ -202,13 +202,13 @@ For a full list of changes, bugfixes and deprecations see the [CHANGELOG][].
install the MDAKit explicitly and then import it by themselves.

* The `MDAnalysis.analysis.encore` module has been deprecated in
favour of the [mdaencore]() MDAKit and will be removed in version
3.0.0 (PR #4737)
favour of the [mdaencore]() MDAKit and will be removed in version
3.0.0 (PR #4737)
* 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)
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)
the [PathSimAnalysis][] MDAKit and will be removed in version 3.0.0
(PR #4403)
* The MMTF Reader is deprecated and will be removed in version 3.0 as
the MMTF format is no longer supported (Issue #4634).

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