Scottgigante/bugfix/alra import #1
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Testing Sagemaker Example Images
Update 3.8 kernel
…agemaker-basic Sagemaker basic
This reverts commit 33cba34.
…blems/singlecellopenproblems into docker-jupyter-kernels
* use cmake==3.18.4 for multicoretsne build * install cli>=3.1.0 * install ellipsis 0.3.2 * update rlang to 1.0.1 * pre-commit * update lifecycle to 1.0.1 * rewuire Rcpp==1.0.7 * fix gpg server * use keyserver.ubuntu.com * port 80 * new key * r 4.1 to sources.list * apparently we're on bullseye now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
…ante-immunai/openproblems into scottgigante/bugfix/alra_import
* convert normalizers to return anndata * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* add test kwarg to methods * pre-commit * bugfix * allow overriding of test parameters * pre-commit * pre-commit * Convert top_genes to a test parameter * pre-commit * bump version due to breaking change * No longer need patch_anndata Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <[email protected]>
Co-authored-by: SingleCellOpenProblems <[email protected]>
* update black 22.3.0 per psf/black#2964 * pre-commit * require specific black version Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* ignore coverage for non-test parameter setting * ignore coverage for NJIT code * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
…o#339) * remove unused line in trustworthiness * assert embedding is not infinite * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* more tests for the CLI * set do_print=False * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* store adata.X in adata.layers['counts'] * document * Don't add `adata.layers['counts']` if already exists * assert that X is equal to layers['counts'] * document adata.layers functionality * Update CONTRIBUTING.md add option for task dataset function normalization as implemented in batch integration PR. Co-authored-by: MalteDLuecken <[email protected]>
* add gh-actions container * fix repo name * new rlang * Remove sagemaker boilerplate
* pull run_tests image from ECR * pre-commit * use ecr for pre-commit too * run ecr password at least once * temp remove schedule * simpler still * break it down more * update * this branch * try doing this on the fly * use outputs * test * store the password * back to regular testing * fix typo * use a different image * get password inside tests * fix typo * unnecessary install * don't need any of this stuff * region * run as root * remove setup * fix path * typo * run tests on docker * ubuntu latest * fix cache * install docker * install some stuff * update * manually install docker * debian * install -y * run in /opt for clean mount * try again * path * copy source to /tmp * already in /usr/src * different basedir * print * ignore benchmark * mount /tmp * remove mount * codecov in setup.py * un-exclude benchmark * fix coverage * just pull from dockerhub, duh: * fix tag * mount /_w * __w * __w is already mounted * need to mount * use gh actions image * don't need to install docker anymore * only install when necessary * pre-commit * fix lintr styler conflict * need to update version to prevent rebuilds * cancel previous runs * remove print * revert to old coverage code * refresh should use install_renv * fix dockerignore * mount to the same basedir for coverage Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* only test modified tasks * make sure we fetch the base repo to compare against * exclude markdown and website * exclude individual tasks explicitly, not the whole tasks folder * test everything on base/main HEAD * run all tests in PRs * use relpath
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@scottgigante-immunai Here is my attempt to merge your branch into my method-alra branch from the old scOP. |
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