Release process updates and sourmash 3.0 release notes (sourmash-bio#776

)

* update release notes
* fix links
* add 3.0 release notes

doc/release-notes/sourmash-3.0.md

@@ -0,0 +1,34 @@
+# sourmash v3.0 release notes
+
+We are pleased to announce release 3.0 of sourmash!  This release includes internal changes like the new Rust backend (replacing C++) and lays the groundwork for future improvements.
+
+The full documentation for this version is available at
+https://sourmash.readthedocs.io/en/v3.0.0/. Documentation for the latest
+released version is at http://sourmash.readthedocs.io/en/stable/.
+
+**This release is compatible with sourmash 2.0: the sourmash
+Python API, command-line, signature and databases file formats are all the same.** We are releasing 3.0 to indicate the build system and internal implementation changed.
+
+Please post questions about migrating to sourmash 3.0
+in the [sourmash issue tracker](https://github.com/dib-lab/sourmash/issues/new).
+
+## Highlighted changes since 2.0
+
+This is a list of substantial new features and functionality since sourmash 2.0. For more details check the [releases page on GitHub](https://github.com/dib-lab/sourmash/releases).
+
+Features:
+
+- Replacing C++ with Rust ([#424](https://github.com/dib-lab/sourmash/pull/424))
+- Create an `Index` abstract base class ([#556](https://github.com/dib-lab/sourmash/pull/556))
+- Dayhoff and HP encoding for proteins ([#689](https://github.com/dib-lab/sourmash/pull/689)) ([#758](https://github.com/dib-lab/sourmash/pull/758))
+- Add `sourmash signature filter` to do abundance filtering. ([#748](https://github.com/dib-lab/sourmash/pull/748))
+- Parallelized compare function with multiprocessing ([#709](https://github.com/dib-lab/sourmash/pull/709))
+- add compute signatures for 10x bam file ([#713](https://github.com/dib-lab/sourmash/pull/713))
+
+Improvements:
+
+- improve error handling in `sourmash lca index`. ([#798](https://github.com/dib-lab/sourmash/pull/798))
+- Include more base deps: numpy, scipy and matplotlib ([#770](https://github.com/dib-lab/sourmash/pull/770))
+- use `bam2fasta` package to simplify `sourmash compute` ([#768](https://github.com/dib-lab/sourmash/pull/768))
+- add a `--abundances-from` flag to sourmash signature intersect, to preserve abundances ([#747](https://github.com/dib-lab/sourmash/pull/747))
+- Compare outputs can be saved to an output dir ([#715](https://github.com/dib-lab/sourmash/pull/715))

doc/release.md

@@ -42,16 +42,17 @@ cd testenv1
 source bin/activate
 git clone --depth 1 --branch v${new_version}${rc} https://github.com/dib-lab/sourmash.git
 cd sourmash
-pip install -r requirements.txt
+python -m pip install -U setuptools pip
+python -m pip install -r requirements.txt
 make test
 
 # Secondly we test via pip
 
 cd ../../testenv2
 deactivate
 source bin/activate
-pip install -U setuptools
-pip install -e git+https://github.com/dib-lab/sourmash.git@v${new_version}${rc}#egg=sourmash[test]
+python -m pip install -U setuptools pip
+python -m pip install -e git+https://github.com/dib-lab/sourmash.git@v${new_version}${rc}#egg=sourmash[test]
 cd src/sourmash
 make test
 make dist
@@ -63,14 +64,14 @@ cp dist/sourmash*tar.gz ../../../testenv3/
 cd ../../../testenv3/
 deactivate
 source bin/activate
-pip install -U setuptools
-pip install sourmash*tar.gz
-pip install pytest
+python -m pip install -U setuptools pip
+python -m pip install sourmash*tar.gz
+python -m pip install pytest
 tar xzf sourmash-${new_version}${rc}.tar.gz
 cd sourmash-${new_version}${rc}
-pip install -r requirements.txt
+python -m pip install -r requirements.txt
 make dist
-make test  ## Currently failing, we don't have all the test data...
+#make test  ## Currently failing, we don't have all the test data...
 ```
 
 4\. Publish the new release on the testing PyPI server.  You will need
@@ -88,9 +89,9 @@ twine upload --repository-url https://test.pypi.org/legacy/ dist/sourmash-${new_
 cd ../../testenv4
 deactivate
 source bin/activate
-pip install -U setuptools
+pip install -U setuptools pip
 # install as much as possible from non-test server!
-pip install screed pytest numpy matplotlib scipy khmer "ijson<2.5"
+pip install screed pytest numpy matplotlib scipy khmer ijson bam2fasta
 pip install -i https://test.pypi.org/simple --pre sourmash
 sourmash info  # should print "sourmash version ${new_version}${rc}"
 ```
@@ -137,16 +138,19 @@ twine upload *.whl
 The BiocondaBot has an `autobump` feature that should pick up new releases from PyPI, and open a PR in Bioconda. Review any changes
 (especially dependency versions, since these don't get picked up).
 
-This is an example PR (for `2.1.0`): https://github.com/bioconda/bioconda-recipes/pull/17113
+An example PR for [`2.1.0`](https://github.com/bioconda/bioconda-recipes/pull/17113).
 
 ## Announce it!
 
 If a bioinformatics software is released and no one tweets, is it really released?
 
 Examples:
-2.0.0 https://twitter.com/luizirber/status/1108846466502520832
-2.0.1 https://twitter.com/luizirber/status/1136786447518711808
-2.1.0 https://twitter.com/luizirber/status/1166910335120314369
+
+- [2.3.0](https://twitter.com/luizirber/status/1198027116396171264)
+- [2.2.0](https://twitter.com/luizirber/status/1179126660911661057)
+- [2.1.0](https://twitter.com/luizirber/status/1166910335120314369)
+- [2.0.1](https://twitter.com/luizirber/status/1136786447518711808)
+- [2.0.0](https://twitter.com/luizirber/status/1108846466502520832)
 
 ## To test on a blank Ubuntu system