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deprecate scvi #1703

Merged
merged 5 commits into from
Mar 9, 2021
Merged

deprecate scvi #1703

merged 5 commits into from
Mar 9, 2021

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mjayasur
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@mjayasur mjayasur commented Mar 2, 2021

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@adamgayoso
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Hi @ivirshup we were hoping to completely remove scvi from external. Users received notice about it's deprecation in the 1.7.X releases. I suppose this can wait until 1.8

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ivirshup commented Mar 2, 2021

Sounds good! I was wondering if that's what this is about.

We're trying to be good about semantic versioning, but it should be fine to merge this with the master branch once it's done (all 1.7.x stuff gets back ported to the 1.7.x branch, so we just won't backport this).

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We're trying to be good about semantic versioning, but it should be fine to merge this with the master branch once it's done (all 1.7.x stuff gets back ported to the 1.7.x branch, so we just won't backport this).

Great! I'm not sure why it's failing though. Thanks!

ivirshup
ivirshup reviewed Mar 5, 2021
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It looks like the docs are failing since there are still links to scvi in the release notes. If you just change remove the :func: part from the references to this.

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adamgayoso approved these changes Mar 8, 2021
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LGTM

@ivirshup ivirshup merged commit 27761ef into scverse:master Mar 9, 2021
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ivirshup commented Mar 9, 2021

Thanks for fixing that up!

Zethson pushed a commit that referenced this pull request Mar 15, 2021
@mjayasur @ivirshup @Zethson
deprecate scvi (#1703)
1e814cb 
* deprecate scvi

* Update .azure-pipelines.yml

Co-authored-by: Isaac Virshup <[email protected]>

* remove :func: links to scvi in release notes

* remove tildes in front of scvi in release notes

* Update docs/release-notes/1.5.0.rst

Co-authored-by: Michael Jayasuriya <[email protected]>
Co-authored-by: Isaac Virshup <[email protected]>
ivirshup added a commit that referenced this pull request Mar 18, 2021
@Zethson @flying-sheep
@Koncopd @ivirshup @pinin4fjords @mjayasur @alexmascension @gokceneraslan
add flake8 pre-commit (#1689)
1eafe3d 
* add flake8 pre-commit

Signed-off-by: Zethson <[email protected]>

* fix pre-commit

Signed-off-by: Zethson <[email protected]>

* add E402 to flake8 ignore

Signed-off-by: Zethson <[email protected]>

* revert neighbors

Signed-off-by: Zethson <[email protected]>

* fix flake8

Signed-off-by: Zethson <[email protected]>

* address review

Signed-off-by: Zethson <[email protected]>

* fix comment character in .flake8

Signed-off-by: Zethson <[email protected]>

* fix test

Signed-off-by: Zethson <[email protected]>

* black

Signed-off-by: Zethson <[email protected]>

* review round 2

Signed-off-by: Zethson <[email protected]>

* review round 3

Signed-off-by: Zethson <[email protected]>

* readded double comments

Signed-off-by: Zethson <[email protected]>

* Ignoring E262 & reverted comment

Signed-off-by: Zethson <[email protected]>

* using self for obs_tidy

Signed-off-by: Zethson <[email protected]>

* Restore setup.py

* rm call of black test (#1690)

* Fix print_versions for python<3.8 (#1691)

* add codecov so we can have a badge to point to (#1693)

* Attempt server-side search (#1672)

* Fix paga_path (#1047)

Fix paga_path

Co-authored-by: Isaac Virshup <[email protected]>

* Switch to flit

This reverts commit d645790

* add setup.py while leaving it ignored

* Update install instructions

* Circumvent new pip check (see pypa/pip#9628)

* Go back to regular pip (#1702)

* Go back to regular flit

Co-authored-by: Isaac Virshup <[email protected]>

* codecov comment (#1704)

* Use joblib for parallelism in regress_out (#1695)

* Use joblib for parallism in regress_out

* release note

* fix link in release notes

* Add todo for resource test

* Add sparsificiation step before sparse-dependent Scrublet calls (#1707)

* Add sparsificiation step before sparse-dependent Scrublet calls

* Apply sparsification suggestion

Co-authored-by: Isaac Virshup <[email protected]>

* Fix imports

Co-authored-by: Isaac Virshup <[email protected]>

* Fix version on Travis (#1713)

By default, Travis does `git clone --depth=50` which means the version can’t be detected from the git tag.

* `sc.metrics` module (add confusion matrix & Geary's C methods) (#915)

* Add `sc.metrics` with `gearys_c`

Add a module for computing useful metrics. Started off with Geary's C since I'm using it and finding it useful. I've also got a fairly fast way to calculate it worked out.

Unfortunatly my implementation runs into some issues with some global configs set by umap (see lmcinnes/umap#306), so I'm going to see if that can be resolved before changing it.

* Add sc.metrics.confusion_matrix

* Better tests and output for confusion_matrix

* Workaround umap<0.4 and increase numerical stability of gearys_c

* Work around lmcinnes/umap#306 by not
  calling out to kernel function. That code has been kept, but commented
  out.
* Increase numerical stability by casting data to system width. Tests
  were failing due to instability.

* Split up gearys_c tests

* Improved unexpected error message

* gearys_c working again. Sadly, a bit slower

* One option for doc strings

* Simplify implementation to use single dispatch

* release notes

* Fix clipped images in docs (#1717)

* Cleanup normalize_total (#1667)

* Cleanup normalize_total

* Add modification tests and copy kwarg for normalize_total

* Test that 'layers' argument is deprecated

* Added more mutation checks for normalize_total

* release note

* Error message

* deprecate scvi (#1703)

* deprecate scvi

* Update .azure-pipelines.yml

Co-authored-by: Isaac Virshup <[email protected]>

* remove :func: links to scvi in release notes

* remove tildes in front of scvi in release notes

* Update docs/release-notes/1.5.0.rst

Co-authored-by: Michael Jayasuriya <[email protected]>
Co-authored-by: Isaac Virshup <[email protected]>

* updated ecosystem.rst to add triku (#1722)

* Minor addition to contributing docs (#1726)

* Preserve category order when groupby is a list (#1735)

Preserve category order when groupby is a list

* Asymmetrical diverging colormaps and vcenter (#1551)

Add vcenter and norm arguments to plotting functions

* add flake8 pre-commit

Signed-off-by: Zethson <[email protected]>

* add E402 to flake8 ignore

Signed-off-by: Zethson <[email protected]>

* revert neighbors

Signed-off-by: Zethson <[email protected]>

* address review

Signed-off-by: Zethson <[email protected]>

* black

Signed-off-by: Zethson <[email protected]>

* using self for obs_tidy

Signed-off-by: Zethson <[email protected]>

* rebased

Signed-off-by: Zethson <[email protected]>

* rebasing

Signed-off-by: Zethson <[email protected]>

* rebasing

Signed-off-by: Zethson <[email protected]>

* rebasing

Signed-off-by: Zethson <[email protected]>

* add flake8 to dev docs

Signed-off-by: Zethson <[email protected]>

* add autopep8 to pre-commits

Signed-off-by: Zethson <[email protected]>

* add flake8 ignore docs

Signed-off-by: Zethson <[email protected]>

* add exception todos

Signed-off-by: Zethson <[email protected]>

* add ignore directories

Signed-off-by: Zethson <[email protected]>

* reinstated lambdas

Signed-off-by: Zethson <[email protected]>

* fix tests

Signed-off-by: Zethson <[email protected]>

* fix tests

Signed-off-by: Zethson <[email protected]>

* fix tests

Signed-off-by: Zethson <[email protected]>

* fix tests

Signed-off-by: Zethson <[email protected]>

* fix tests

Signed-off-by: Zethson <[email protected]>

* Add E741 to allowed flake8 violations.

Co-authored-by: Isaac Virshup <[email protected]>

* Add F811 flake8 ignore for tests

Co-authored-by: Isaac Virshup <[email protected]>

* Fix mask comparison

Co-authored-by: Isaac Virshup <[email protected]>

* Fix mask comparison

Co-authored-by: Isaac Virshup <[email protected]>

* fix flake8 config file

Signed-off-by: Zethson <[email protected]>

* readded autopep8

Signed-off-by: Zethson <[email protected]>

* import Literal

Signed-off-by: Zethson <[email protected]>

* revert literal import

Signed-off-by: Zethson <[email protected]>

* fix scatterplot pca import

Signed-off-by: Zethson <[email protected]>

* false comparison & unused vars

Signed-off-by: Zethson <[email protected]>

* Add cleaner level determination

Co-authored-by: Isaac Virshup <[email protected]>

* Fix comment formatting

Co-authored-by: Isaac Virshup <[email protected]>

* Add smoother dev documentation

Co-authored-by: Isaac Virshup <[email protected]>

* fix flake8

Signed-off-by: Zethson <[email protected]>

* Readd long comment

Co-authored-by: Isaac Virshup <[email protected]>

* Assuming X as array like

Co-authored-by: Isaac Virshup <[email protected]>

* fix flake8

Signed-off-by: Zethson <[email protected]>

* fix flake8 config

Signed-off-by: Zethson <[email protected]>

* reverted rank_genes

Signed-off-by: Zethson <[email protected]>

* fix disp_mean_bin formatting

Co-authored-by: Isaac Virshup <[email protected]>

* fix formatting

Signed-off-by: Zethson <[email protected]>

* add final todos

Signed-off-by: Zethson <[email protected]>

* boolean checks with is

Signed-off-by: Zethson <[email protected]>

* _dpt formatting

Signed-off-by: Zethson <[email protected]>

* literal fixes

Signed-off-by: Zethson <[email protected]>

* links to leafs

Signed-off-by: Zethson <[email protected]>

* revert paga variable naming

Co-authored-by: Philipp A <[email protected]>
Co-authored-by: Sergei Rybakov <[email protected]>
Co-authored-by: Isaac Virshup <[email protected]>
Co-authored-by: Jonathan Manning <[email protected]>
Co-authored-by: mjayasur <[email protected]>
Co-authored-by: Michael Jayasuriya <[email protected]>
Co-authored-by: Alex M. Ascensión <[email protected]>
Co-authored-by: Gökçen Eraslan <[email protected]>
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@mjayasur @adamgayoso @ivirshup