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Maintenance release to fix a few issues introduced in version 2.0

Maintenance release that fixes multiple issues introduced in version 2.0

> NOTE: although this is a beta release it mature enough to be used in your research.

- New: Added a new program called `sonicparanoid-get-profiles` to download the MMseqs-PFam profile DB files. This can be used if the [Profile DB could not be built locally](https://gitlab.com/salvo981/sonicparanoid2/-/issues/54).
- Maintenance: Upgrade cython code to use `dataclasses` [issue](https://gitlab.com/salvo981/sonicparanoid2/-/issues/68).
- Fix: [scikit-learn](https://gitlab.com/salvo981/sonicparanoid2/-/issues/55), and upgrade to 1.5.0
- Fix: [inclusion of hits with lower bitscores due to overwrite](https://gitlab.com/salvo981/sonicparanoid2/-/issues/63)
- Fix: in species-species ortholog [tables single relations were counted as 2](https://gitlab.com/salvo981/sonicparanoid2/-/issues/69)
- Fix: [slowdowns due to queue timeout](https://gitlab.com/salvo981/sonicparanoid2/-/issues/65) (only happened with thousands of proteomes and using slow storage)
- Python version: 3.9<=python<3.13 (this means that Python 3.8 is not supported anymore)
- Maintenance: update to support latest Cython release
- Maintenance: include early version of pyproject.toml (still use setup.py to compile Cython source files)

- Maintenance: Upgrade cython code to use `dataclasses` [issue](https://gitlab.com/salvo981/sonicparanoid2/-/issues/68).
- Fix: [inclusion of hits with lower bitscores due to overwrite](https://gitlab.com/salvo981/sonicparanoid2/-/issues/63)
- Fix: in species-species ortholog [tables single relations were counted as 2](https://gitlab.com/salvo981/sonicparanoid2/-/issues/69)
- Fix: [slowdowns due to queue timeout](https://gitlab.com/salvo981/sonicparanoid2/-/issues/65) (only happened with thousands of proteomes and using slow storage)
- Python version: 3.9<=python<=3.11 (this means that Python 3.8 is not supported anymore)
- Maintenance: update to support latest Cython release
- Maintenance: include ealy version of pyproject.toml (still use setup.py to compile Cython source files)

- Add support for latest Cython
- Update type hint annotations as of python3.9+

Minor maintenance update

Fixed issue related to scikit-learn 1.3.0

**First stable release of SonicParanoid2**

**First stable release of SonicParanoid2**

Release candidate 2. Use for testing.
Changes from 2.0.0rc1:
- Hot-fix: closed [issue #42](https://gitlab.com/salvo981/sonicparanoid2/-/issues/47), thanks to [Eric Chen](https://gitlab.com/Eric-CH-Chen)

Release candidate 1. Use for testing.
Some of the changes from 2.0.0b7 are:
- Core: minor changes to d2v.pyx
- Considerably reduced PyPI package size compressing binaries using `xz` instead of `zip`
- Enhancement: removed a lot legacy code

- CLI: commands now conform to SonicParanoid 2 presets
- CLI: added parameters `--mmseqs-sens`, `--diamond-sens` and `--blast`;
- CLI: removed parameter `--aln-tool`
- CLI: removed `most-sensitive` mode
- HTML page update

#### 2.0.0b5 (November 22, 2022)
- Fix: [issue 45](https://gitlab.com/salvo981/sonicparanoid2/-/issues/45)
- Partially updated web-page

`This is a beta-version, use it for testing`

#### 2.0.0 alpha 3
`Do not use it for any research/production purposes`