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Add a file to keep track of deprecated features #1371

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Dec 20, 2023
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Add a file to keep track of deprecated features #1371

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f08a7e2
Add a file to keep track of deprecated features
victorlin Dec 11, 2023
ce39767
Add deprecation entry for augur export v1
victorlin Dec 20, 2023
02f7618
docs: Replace "breaking changes" with DEPRECATED
victorlin Dec 20, 2023
8862cfe
Update changelog
victorlin Dec 20, 2023
171986e
DEV_DOCS: Add section on feature removal
victorlin Dec 20, 2023
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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -9,6 +9,7 @@

### Features

* Added a new file [DEPRECATED.md](./DEPRECATED.md) to document timelines and progress of deprecated features in the Augur CLI and Python API. [#1371][] (@victorlin)
* ancestral, translate: A range of improvements to how we parse GFF and GenBank reference files. [#1351][] (@jameshadfield)
* translate will now always export a 'nuc' annotation in the output JSON, allowing it to pass validation
* Gene/CDS names of 'nuc' are now forbidden.
Expand All @@ -35,6 +36,7 @@
[#1351]: https://github.com/nextstrain/augur/pull/1351
[#1349]: https://github.com/nextstrain/augur/issues/1349
[#1367]: https://github.com/nextstrain/augur/pull/1367
[#1371]: https://github.com/nextstrain/augur/pull/1371

## 23.1.1 (7 November 2023)

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21 changes: 21 additions & 0 deletions DEPRECATED.md
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# Deprecated

These features are deprecated, which means they are no longer maintained and
will go away in a future major version of Augur. They are currently still
available for backwards compatibility, but should not be used in new code.

## `augur export v1`

*Deprecated in version 22.2.0 (July 2023). Planned for [removal](https://github.com/nextstrain/augur/issues/1266)
January 2024 or after.*

`augur export v2` was introduced in Augur version 6.0.0. Migrate by following
the [official guide](https://docs.nextstrain.org/projects/augur/page/releases/migrating-v5-v6.html).

## `augur ancestral --output`

*Deprecated in version 5.2.0 (December 2019). Removed in version 7.0.0 (April
2020).*

`--output` was been replaced by `--output-node-data` to accommodate the addition
of `--output-sequences`.
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3 changes: 3 additions & 0 deletions docs/contribute/DEV_DOCS.md
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Expand Up @@ -172,6 +172,9 @@ Versions for this project, Augur, from 3.0.0 onwards aim to follow the
```
2. Define a new version number `X.X.X` based on changes and Semantic Versioning rules.

> [!NOTE]
> If releasing a major version, consider removing a [deprecated feature](../../DEPRECATED.md).

##### 2. Curate [CHANGES.md](../../CHANGES.md)

1. Go through each PR and note the PRs that didn't provide an update to [CHANGES.md](../../CHANGES.md).
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1 change: 1 addition & 0 deletions docs/releases/DEPRECATED.md
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../../DEPRECATED.md
38 changes: 0 additions & 38 deletions docs/releases/breaking.md
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2 changes: 1 addition & 1 deletion docs/releases/releases.rst
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Expand Up @@ -15,7 +15,7 @@ and learning what you need to change should be as pain-free as possible.
:glob:

Changelog <changelog>
Deprecated features <DEPRECATED>
v6
migrating-v5-v6
breaking
auspice-compatibility
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