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Set numpy and scipy as direct dependencies #1120

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Jan 18, 2023
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2 changes: 2 additions & 0 deletions CHANGES.md
Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,12 @@
* filter: Standardize exit codes from internal error handling. [#931][] (@victorlin)
* tree: Suppress the `Cannot specify --substitution-model unless using IQTree` warning when `--substitution-model` is left at its default. [#1127][] (@tsibley)
* tree: Print the underlying error message when tree building fails. [#1127][] (@tsibley)
* Previously, `numpy` and `scipy` were installed as dependencies of dependencies. Mark them as direct dependencies since they are used directly within Augur. [#1120][] (@victorlin)

[#931]: https://github.com/nextstrain/augur/pull/931
[#1118]: https://github.com/nextstrain/augur/pull/1118
[#1119]: https://github.com/nextstrain/augur/pull/1119
[#1120]: https://github.com/nextstrain/augur/pull/1120
[#1127]: https://github.com/nextstrain/augur/pull/1127

## 19.2.0 (19 December 2022)
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2 changes: 2 additions & 0 deletions setup.py
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Expand Up @@ -57,10 +57,12 @@
"isodate ==0.6.*",
"jsonschema >=3.0.0, ==3.*",
"networkx >= 2.5, ==2.*",
"numpy ==1.*",
"packaging >=19.2",
"pandas >=1.0.0, ==1.*",
"phylo-treetime >=0.9.3, ==0.9.*",
"pyfastx >=0.8.4, ==0.8.*",
"scipy ==1.*",
"xopen[zstd] >=1.7.0, ==1.*"
],
extras_require = {
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