Upstream 107 #257
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Upstream 107 #257
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* [batch] Quiet down MJC and MJS logging exceptions * address comment * delint
) Bumps [aiohttp-session](https://github.com/aio-libs/aiohttp_session) from 2.7.0 to 2.12.0. - [Release notes](https://github.com/aio-libs/aiohttp_session/releases) - [Changelog](https://github.com/aio-libs/aiohttp-session/blob/master/CHANGES.txt) - [Commits](aio-libs/aiohttp-session@v2.7.0...v2.12.0) --- updated-dependencies: - dependency-name: aiohttp-session dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [botocore](https://github.com/boto/botocore) from 1.29.13 to 1.29.16. - [Release notes](https://github.com/boto/botocore/releases) - [Changelog](https://github.com/boto/botocore/blob/develop/CHANGELOG.rst) - [Commits](boto/botocore@1.29.13...1.29.16) --- updated-dependencies: - dependency-name: botocore dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.12 to 1.26.13. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@1.26.12...1.26.13) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [query] Add `compute_charr` * fix lints * fix lint Co-authored-by: Dan King <daniel.zidan.king@gmail.com>
* [batch] Expose region variable to users * address comments * fix * fixes * fixes * address comments * fix test * revert env check * fix test * fix test * fix * fix
…is#12514) Bumps [googleapis-common-protos](https://github.com/googleapis/python-api-common-protos) from 1.56.4 to 1.57.0. - [Release notes](https://github.com/googleapis/python-api-common-protos/releases) - [Changelog](https://github.com/googleapis/python-api-common-protos/blob/main/CHANGELOG.md) - [Commits](googleapis/python-api-common-protos@v1.56.4...v1.57.0) --- updated-dependencies: - dependency-name: googleapis-common-protos dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [batch] Automatic resource price updates for GCP * add reference to Job.regions in docs * revert types change * Revert "revert types change" This reverts commit 123ccedb97e20a8ab9e7c7d351a802d0157517c3. * fixes * requires valid credentials and not anonymous credentials * update pinned requirements * update pinned requirements * fix * fixes * fix missing persistent ssd regions * delint
* [query] persist=checkpoint in all backends * fix circular import * add test * let aggregate_entries return missing * test fixes
* Bump pycodestyle from 2.8.0 to 2.9.1 in /hail/python/dev Bumps [pycodestyle](https://github.com/PyCQA/pycodestyle) from 2.8.0 to 2.9.1. - [Release notes](https://github.com/PyCQA/pycodestyle/releases) - [Changelog](https://github.com/PyCQA/pycodestyle/blob/main/CHANGES.txt) - [Commits](PyCQA/pycodestyle@2.8.0...2.9.1) --- updated-dependencies: - dependency-name: pycodestyle dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * update pins Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Dan King <dking@broadinstitute.org>
…#12396) * [test] hail-run image should depend on base not service base * [gear] Move cache test out of hailtop * lint * install hailtop in hail-run image * add hail_version * undo
* [hailctl] Add hailctl batch submit * make name an option not an argument * lint' * use relative file paths for files * add basic test * use the current hailgenetics/hail image not the dockerhub one * get quiet mode working to fully test hailctl batch submit * fix * cleanup * submit sets HAIL_QUERY_BACKEND to batch * fix * fixes * lint * name the batch that the submitted job spawns
…2497) CHANGELOG: Added support for `scales`, `nrow`, and `ncol` arguments, as well as grouped legends, to `hail.ggplot.facet_wrap`. This change brings the `facet_wrap` interface more in line with [the `ggplot2` implementation](https://ggplot2-book.org/facet.html#facet-wrap) by defaulting to show axes (with tick marks) for all facets, as well as providing `scales`, `nrow` and `ncol` arguments that the user can use to specify whether the scales should be the same across facets and how many rows or columns to use. It also updates the faceting code to avoid duplicating legend entries when [grouped legends](hail-is#12254) are used, and to disable interactivity accordingly.
* Bump protobuf from 3.20.2 to 4.21.9 in /docker Bumps [protobuf](https://github.com/protocolbuffers/protobuf) from 3.20.2 to 4.21.9. - [Release notes](https://github.com/protocolbuffers/protobuf/releases) - [Changelog](https://github.com/protocolbuffers/protobuf/blob/main/generate_changelog.py) - [Commits](https://github.com/protocolbuffers/protobuf/commits) --- updated-dependencies: - dependency-name: protobuf dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * update google cloud profiler to support new protobufs Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Dan King <dking@broadinstitute.org>
* add stream expressions * enable new rng * delete global seed management * fixes * persist = checkpoint * fixes * wip * fixup stream randomness handling * fixes * set global seed in test setup * try to catch who’s making a HailContext * start to update doctests * init hunt take 2 * refactor hail context management in tests * fixes * update random.rst * typo * fixes * fix docs * add dev doc * fix _seeded_func seed handling * address comments * delete ‘startTestHailContext’ in new python fs tests * fix bad doctest from merge * remove unittest to try to get pytest fixture used Co-authored-by: Dan King <daniel.zidan.king@gmail.com>
1. If the user has not specified a configuration for disable_progress_bar, then only disable it if we are noninteractive. 2. Change @fails_service_backend to @Skip... for a `to_spark` test. 3. Pass the path collision test by using `Validate`. 4. Fix a test which was trying to write to a local file.
The environment variables should be affecting `pytest`, not `cd`. `test_import_bed` just needs to use an `open` that can speak `gs://`.
hail-is#12512) * [query] Expose `hl.keyed_intersection` and `hl.keyed_union` in Python. * linting * fix lint * fix docs
The FS tests were accidentally disabled because pytest-asyncio was never included in dev/requirements.txt (as it should have been). As a result, all the `async def` tests were (silently) ignored by pytest.
…il-is#12525) * [hailctl] allow passing arguments to hailctl batch submit scripts * Update build.yaml
…2371) * [ci] Narrow what parts of repo some steps need to localize * fix * Update build.yaml * fix pip installed images * dont need anything from the repo for the hail-build image * give build_hail steps the whole repo back * fix hail-build * more fixes * fix get_pip_versioned_docs Co-authored-by: Dan King <daniel.zidan.king@gmail.com>
* [hailtop] safely use chunks If we hit an exception and exit the iterator early, then we are no longer iterating. We need to record that fact so that we can retry transient errors. * add missing import
* [batch] Quiet warning log messages * address comments * address comments * fix
hail-is#12327) * [batch] Mitigation for case insensitive billing projects and usernames * fix migration * fixes * add indices and fix test * fixes * fix test * fix test * fix extra new lines * fix * fixes * fix
hail-is#12541) * [batch] Remove disk usage monitoring that was added for debugging purposes only * delint
…12416) * add a type and an op * remove bitwidth parameter from hail int * add example ir * reorganize source structure * push missed cpp files * folding and canonicalization for I32Plus * make naming more consistent with mlir conventions * setup infrastructure for lowering passes * add bool type, bool lit & compare ops * Fix up includes * more includes * add canonicalize pass back to hail-opt * partially implement sandbox lowering * support comparison op * polymorphic constant op * lower print * finish lowering pass * add .clang-format, format current sources * add LowerToLLVM pass and hailc jit runner tool * basic array support * more array stuff working * array lowering working * delete accidental cmake change * add dialects to hailc * add dialects and passes to hail-opt * add hail-mlir-lsp-server tool * wip missingness * set cmake policy to silence warnings * add missingness dialect and analysis * add cps dialect * tidy build system to simplify adding dialects * reworks docs to use devbin scripts and adds editor setup instructions * adds filecheck tests * add CPSToCF pass * CPS tidying * add Option dialect * lower option to CPS pass * flesh out option dialect * improve ergonomics of op interfaces * fix include path * Add simple RUN lines to all tests * start adding tests * add some diagnostics tests * wip adding clang-tidy * enable clang-tidy * format everything * tweak to appease clang-tidy * add missing library dependencies * hail prefix in include paths, import common symbols into hail namespace * fix ‘test/option.mlir’ * Attempt to find clang-tidy rather than erroring at build time * install clang-tidy and clang-format in query build image * Install lit into build image through pip * Add newlines to end of files * fix clang-tidy config, apply to codebase * clang-tidy fixes * remove superfluous build.yaml line * remove unused includes * Add HAIL_USE_CLANG_TIDY cmake variable for toggling clang-tidy Testing -j1 builds shows an increase in build time from around 30 seconds to nearly 20 minutes. This will only get worse as the project grows. Co-authored-by: Tim Poterba <tpoterba@gmail.com> Co-authored-by: Iris Rademacher <irademac@broadinstitute.org> Co-authored-by: Chris Vittal <cvittal@broadinstitute.org>
Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.9.24 to 2022.12.7. - [Release notes](https://github.com/certifi/python-certifi/releases) - [Commits](certifi/python-certifi@2022.09.24...2022.12.07) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.9.24 to 2022.12.7. - [Release notes](https://github.com/certifi/python-certifi/releases) - [Commits](certifi/python-certifi@2022.09.24...2022.12.07) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ail-is#12510) * [hailctl] Fix dependency installation for hailctl dataproc clusters * make the pinned requirements files actual targets * strip the spaces from each dependency * fix hailctl dataproc package installation * require the user regenerate pinned-requirements for install-on-cluster if out of date * install pip-tools * pip installing pip-tools puts it in the user local bin which is not on path in dataproc * fix #s * just have the user sudo * add permission again * fix requirements parsing before installation * put lockfile generation into a separate file * fix for dataproc * remove dependency from deploy.yaml * remove targets but ensure compatibility * undo requirements test change * fix requirements * fix' * add file to build.yaml * add more inputs in build.yaml * make singular
* Upstream azure changes * FIX: minor improvements * FIX: formatting changes * FIX: letsencrypt docs * FIX: azure docs * FIX: certs stuff * FIX: small cleanup * COMMENTS: address some name change and refactor comments * COMMENTS: use query args and add to README.md * FIX: quick bug fix for no rows returned admin/user check in create_database.py * remove lints * blacken Co-authored-by: Sabrina <9669990+violetbrina@users.noreply.github.com>
* [release] update changelog for 0.2.106 * Update change_log.md Co-authored-by: Dan King <daniel.zidan.king@gmail.com>
…2554) * [batch] Omit setup progress bars on small batch submission * add test that two small jobs still trigger create fast
lgruen
approved these changes
Dec 14, 2022
…l-is#12543) * [vds] Fix local_to_global to support non-ascending local alleles Fixes hail-is#12534 * remove reindex * fix linting
…-is#12544) * [service-base] fix libsass by downgrading google-cloud-profiler * downgrade protobuf * remove unnecessary pip installs
Bumps [pycares](https://github.com/saghul/pycares) from 4.2.2 to 4.3.0. - [Release notes](https://github.com/saghul/pycares/releases) - [Changelog](https://github.com/saghul/pycares/blob/master/ChangeLog) - [Commits](saghul/pycares@pycares-4.2.2...pycares-4.3.0) --- updated-dependencies: - dependency-name: pycares dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Hey @lgruen, I have merged 107 into this branch now :) |
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Conflicts:
batch/batch/cloud/gcp/driver/create_instance.pyci/create_database.pyhail/Makefile