search

jason-neal / companion_simulations

Simulating combined host+companion spectra, and fitting to observed crires spectra.
MIT License
2 stars 0 forks source link

Scheduled monthly dependency update for October #58

Closed pyup-bot closed 5 years ago

pyup-bot commented 5 years ago

Update matplotlib from 2.2.3 to 3.0.0.

Changelog
Links - PyPI: https://pypi.org/project/matplotlib - Changelog: https://pyup.io/changelogs/matplotlib/ - Homepage: http://matplotlib.org

Update joblib from 0.12.3 to 0.12.5.

Changelog ### 0.12.5 ``` -------------- Thomas Moreau, Olivier Grisel Include loky 2.3.1 with better error reporting when a worker is abruptly terminated. Also fixes spurious debug output. Pierre Glaser Include cloudpickle 0.5.6. Fix a bug with the handling of global variables by locally defined functions. ``` ### 0.12.4 ``` -------------- Thomas Moreau, Pierre Glaser, Olivier Grisel Include loky 2.3.0 with many bugfixes, notably w.r.t. when setting non-default multiprocessing contexts. Also include improvement on memory management of long running worker processes and fixed issues when using the loky backend under PyPy. Maxime Weyl Loading a corrupted cached file with mmap mode enabled would recompute the results and return them without memmory mapping. ```
Links - PyPI: https://pypi.org/project/joblib - Changelog: https://pyup.io/changelogs/joblib/ - Docs: https://joblib.readthedocs.io

Update numba from 0.39.0 to 0.40.0.

Changelog ### 0.40.0 ``` -------------- This release adds a number of major features: * A new GPU backend: kernels for AMD GPUs can now be compiled using the ROCm driver on Linux. * The thread pool implementation used by Numba for automatic multithreading is configurable to use TBB, OpenMP, or the old "workqueue" implementation. (TBB is likely to become the preferred default in a future release.) * New documentation on thread and fork-safety with Numba, along with overall improvements in thread-safety. * Experimental support for executing a block of code inside a nopython mode function in object mode. * Parallel loops now allow arrays as reduction variables * CUDA improvements: FMA, faster float64 atomics on supporting hardware, records in const memory, and improved datatime dtype support * More NumPy functions: vander, tri, triu, tril, fill_diagonal General Enhancements: * PR 3017: Add facility to support with-contexts * PR 3033: Add support for multidimensional CFFI arrays * PR 3122: Add inliner to object mode pipeline * PR 3127: Support for reductions on arrays. * PR 3145: Support for np.fill_diagonal * PR 3151: Keep a queue of references to last N deserialized functions. Fixes 3026 * PR 3154: Support use of list() if typeable. * PR 3166: Objmode with-block * PR 3179: Updates for llvmlite 0.25 * PR 3181: Support function extension in alias analysis * PR 3189: Support literal constants in typing of object methods * PR 3190: Support passing closures as literal values in typing * PR 3199: Support inferring stencil index as constant in simple unary expressions * PR 3202: Threading layer backend refactor/rewrite/reinvention! * PR 3209: Support for np.tri, np.tril and np.triu * PR 3211: Handle unpacking in building tuple (BUILD_TUPLE_UNPACK opcode) * PR 3212: Support for np.vander * PR 3227: Add NumPy 1.15 support * PR 3272: Add MemInfo_data to runtime._nrt_python.c_helpers * PR 3273: Refactor. Removing thread-local-storage based context nesting. * PR 3278: compiler threadsafety lockdown * PR 3291: Add CPU count and CFS restrictions info to numba -s. CUDA Enhancements: * PR 3152: Use cuda driver api to get best blocksize for best occupancy * PR 3165: Add FMA intrinsic support * PR 3172: Use float64 add Atomics, Where Available * PR 3186: Support Records in CUDA Const Memory * PR 3191: CUDA: fix log size * PR 3198: Fix GPU datetime timedelta types usage * PR 3221: Support datetime/timedelta scalar argument to a CUDA kernel. * PR 3259: Add DeviceNDArray.view method to reinterpret data as a different type. * PR 3310: Fix IPC handling of sliced cuda array. ROCm Enhancements: * PR 3023: Support for AMDGCN/ROCm. * PR 3108: Add ROC info to `numba -s` output. * PR 3176: Move ROC vectorize init to npyufunc * PR 3177: Add auto_synchronize support to ROC stream * PR 3178: Update ROC target documentation. * PR 3294: Add compiler lock to ROC compilation path. * PR 3280: Add wavebits property to the HSA Agent. * PR 3281: Fix ds_permute types and add tests Continuous Integration / Testing: * PR 3091: Remove old recipes, switch to test config based on env var. * PR 3094: Add higher ULP tolerance for products in complex space. * PR 3096: Set exit on error in incremental scripts * PR 3109: Add skip to test needing jinja2 if no jinja2. * PR 3125: Skip cudasim only tests * PR 3126: add slack, drop flowdock * PR 3147: Improve error message for arg type unsupported during typing. * PR 3128: Fix recipe/build for jetson tx2/ARM * PR 3167: In build script activate env before installing. * PR 3180: Add skip to broken test. * PR 3216: Fix libcuda.so loading in some container setup * PR 3224: Switch to new Gitter notification webhook URL and encrypt it * PR 3235: Add 32bit Travis CI jobs * PR 3257: This adds scipy/ipython back into windows conda test phase. Fixes: * PR 3038: Fix random integer generation to match results from NumPy. * PR 3045: Fix 3027 - Numba reassigns sys.stdout * PR 3059: Handler for known LoweringErrors. * PR 3060: Adjust attribute error for NumPy functions. * PR 3067: Abort simulator threads on exception in thread block. * PR 3079: Implement +/-(types.boolean) Fix 2624 * PR 3080: Compute np.var and np.std correctly for complex types. * PR 3088: Fix 3066 (array.dtype.type in prange) * PR 3089: Fix invalid ParallelAccelerator hoisting issue. * PR 3136: Fix 3135 (lowering error) * PR 3137: Fix for issue3103 (race condition detection) * PR 3142: Fix Issue 3139 (parfors reuse of reduction variable across prange blocks) * PR 3148: Remove dead array equal infer code * PR 3153: Fix canonicalize_array_math typing for calls with kw args * PR 3156: Fixes issue with missing pygments in testing and adds guards. * PR 3168: Py37 bytes output fix. * PR 3171: Fix 3146. Fix CFUNCTYPE void* return-type handling * PR 3193: Fix setitem/getitem resolvers * PR 3222: Fix 3214. Mishandling of POP_BLOCK in while True loop. * PR 3230: Fixes liveness analysis issue in looplifting * PR 3233: Fix return type difference for 32bit ctypes.c_void_p * PR 3234: Fix types and layout for `np.where`. * PR 3237: Fix DeprecationWarning about imp module * PR 3241: Fix 3225. Normalize 0nd array to scalar in typing of indexing code. * PR 3256: Fix 3251: Move imports of ABCs to collections.abc for Python >= 3.3 * PR 3292: Fix issue3279. * PR 3302: Fix error due to mismatching dtype Documentation Updates: * PR 3104: Workaround for 3098 (test_optional_unpack Heisenbug) * PR 3132: Adds an ~5 minute guide to Numba. * PR 3194: Fix docs RE: np.random generator fork/thread safety * PR 3242: Page with Numba talks and tutorial links * PR 3258: Allow users to choose the type of issue they are reporting. * PR 3260: Fixed broken link * PR 3266: Fix cuda pointer ownership problem with user/externally allocated pointer * PR 3269: Tweak typography with CSS * PR 3270: Update FAQ for functions passed as arguments * PR 3274: Update installation instructions * PR 3275: Note pyobject and voidptr are types in docs * PR 3288: Do not need to call parallel optimizations "experimental" anymore * PR 3318: Tweak spacing to avoid search box wrapping onto second line Contributors: * Alex Ford * Anthony Bisulco * Ehsan Totoni (core dev) * Leonard Lausen * Matthew Petroff * Nick White * Ray Donnelly * rjenc29 * Siu Kwan Lam (core dev) * Stan Seibert (core dev) * Stuart Archibald (core dev) * Stuart Reynolds * Todd A. Anderson (core dev) ```
Links - PyPI: https://pypi.org/project/numba - Changelog: https://pyup.io/changelogs/numba/ - Repo: http://numba.github.com

Update numpy from 1.15.1 to 1.15.2.

Changelog ### 1.15.2 ``` ========================== This is a bugfix release for bugs and regressions reported following the 1.15.1 release. * The matrix PendingDeprecationWarning is now suppressed in pytest 3.8. * The new cached allocations machinery has been fixed to be thread safe. * The boolean indexing of subclasses now works correctly. * A small memory leak in PyArray_AdaptFlexibleDType has been fixed. The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg problems reported for NumPy 1.14. Compatibility Note ================== The NumPy 1.15.x OS X wheels released on PyPI no longer contain 32-bit binaries. That will also be the case in future releases. See `11625 <https://github.com/numpy/numpy/issues/11625>`__ for the related discussion. Those needing 32-bit support should look elsewhere or build from source. Contributors ============ A total of 4 people contributed to this release. People with a "+" by their names contributed a patch for the first time. * Charles Harris * Julian Taylor * Marten van Kerkwijk * Matti Picus Pull requests merged ==================== A total of 4 pull requests were merged for this release. * `11902 <https://github.com/numpy/numpy/pull/11902>`__: BUG: Fix matrix PendingDeprecationWarning suppression for pytest... * `11981 <https://github.com/numpy/numpy/pull/11981>`__: BUG: fix cached allocations without the GIL for 1.15.x * `11982 <https://github.com/numpy/numpy/pull/11982>`__: BUG: fix refcount leak in PyArray_AdaptFlexibleDType * `11992 <https://github.com/numpy/numpy/pull/11992>`__: BUG: Ensure boolean indexing of subclasses sets base correctly. ========================== ```
Links - PyPI: https://pypi.org/project/numpy - Changelog: https://pyup.io/changelogs/numpy/ - Homepage: http://www.numpy.org

Update sqlalchemy from 1.2.11 to 1.2.12.

Changelog ### 1.2.12 ``` :released: September 19, 2018 .. change:: :tags: bug, postgresql :tickets: 4325 Fixed bug in PostgreSQL dialect where compiler keyword arguments such as ``literal_binds=True`` were not being propagated to a DISTINCT ON expression. .. change:: :tags: bug, ext :tickets: 4328 Fixed issue where :class:`.BakedQuery` did not include the specific query class used by the :class:`.Session` as part of the cache key, leading to incompatibilities when using custom query classes, in particular the :class:`.ShardedQuery` which has some different argument signatures. .. change:: :tags: bug, postgresql :tickets: 4324 Fixed the :func:`.postgresql.array_agg` function, which is a slightly altered version of the usual :func:`.functions.array_agg` function, to also accept an incoming "type" argument without forcing an ARRAY around it, essentially the same thing that was fixed for the generic function in 1.1 in :ticket:`4107`. .. change:: :tags: bug, postgresql :tickets: 4323 Fixed bug in PostgreSQL ENUM reflection where a case-sensitive, quoted name would be reported by the query including quotes, which would not match a target column during table reflection as the quotes needed to be stripped off. .. change:: :tags: bug, orm Added a check within the weakref cleanup for the :class:`.InstanceState` object to check for the presence of the ``dict`` builtin, in an effort to reduce error messages generated when these cleanups occur during interpreter shutdown. Pull request courtesy Romuald Brunet. .. change:: :tags: bug, orm, declarative :tickets: 4326 Fixed bug where the declarative scan for attributes would receive the expression proxy delivered by a hybrid attribute at the class level, and not the hybrid attribute itself, when receiving the descriptor via the ``declared_attr`` callable on a subclass of an already-mapped class. This would lead to an attribute that did not report itself as a hybrid when viewed within :attr:`.Mapper.all_orm_descriptors`. .. change:: :tags: bug, orm :tickets: 4334 :versions: 1.3.0b1 Fixed bug where use of :class:`.Lateral` construct in conjunction with :meth:`.Query.join` as well as :meth:`.Query.select_entity_from` would not apply clause adaption to the right side of the join. "lateral" introduces the use case of the right side of a join being correlatable. Previously, adaptation of this clause wasn't considered. Note that in 1.2 only, a selectable introduced by :meth:`.Query.subquery` is still not adapted due to :ticket:`4304`; the selectable needs to be produced by the :func:`.select` function to be the right side of the "lateral" join. .. change:: :tags: bug, oracle :tickets: 4335 Fixed issue for cx_Oracle 7.0 where the behavior of Oracle param.getvalue() now returns a list, rather than a single scalar value, breaking autoincrement logic throughout the Core and ORM. The dml_ret_array_val compatibility flag is used for cx_Oracle 6.3 and 6.4 to establish compatible behavior with 7.0 and forward, for cx_Oracle 6.2.1 and prior a version number check falls back to the old logic. .. change:: :tags: bug, orm :tickets: 4327 Fixed 1.2 regression caused by :ticket:`3472` where the handling of an "updated_at" style column within the context of a post-update operation would also occur for a row that is to be deleted following the update, meaning both that a column with a Python-side value generator would show the now-deleted value that was emitted for the UPDATE before the DELETE (which was not the previous behavor), as well as that a SQL- emitted value generator would have the attribute expired, meaning the previous value would be unreachable due to the row having been deleted and the object detached from the session.The "postfetch" logic that was added as part of :ticket:`3472` is now skipped entirely for an object that ultimately is to be deleted. .. changelog:: ```
Links - PyPI: https://pypi.org/project/sqlalchemy - Changelog: https://pyup.io/changelogs/sqlalchemy/ - Homepage: http://www.sqlalchemy.org

Update hypothesis from 3.70.3 to 3.74.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/hypothesis - Repo: https://github.com/HypothesisWorks/hypothesis/tree/master/hypothesis-python

Update pytest from 3.7.4 to 3.8.1.

Changelog ### 3.8.1 ``` ========================= Bug Fixes --------- - `3286 <https://github.com/pytest-dev/pytest/issues/3286>`_: ``.pytest_cache`` directory is now automatically ignored by Git. Users who would like to contribute a solution for other SCMs please consult/comment on this issue. - `3749 <https://github.com/pytest-dev/pytest/issues/3749>`_: Fix the following error during collection of tests inside packages:: TypeError: object of type 'Package' has no len() - `3941 <https://github.com/pytest-dev/pytest/issues/3941>`_: Fix bug where indirect parametrization would consider the scope of all fixtures used by the test function to determine the parametrization scope, and not only the scope of the fixtures being parametrized. - `3973 <https://github.com/pytest-dev/pytest/issues/3973>`_: Fix crash of the assertion rewriter if a test changed the current working directory without restoring it afterwards. - `3998 <https://github.com/pytest-dev/pytest/issues/3998>`_: Fix issue that prevented some caplog properties (for example ``record_tuples``) from being available when entering the debugger with ``--pdb``. - `3999 <https://github.com/pytest-dev/pytest/issues/3999>`_: Fix ``UnicodeDecodeError`` in python2.x when a class returns a non-ascii binary ``__repr__`` in an assertion which also contains non-ascii text. Improved Documentation ---------------------- - `3996 <https://github.com/pytest-dev/pytest/issues/3996>`_: New `Deprecations and Removals <https://docs.pytest.org/en/latest/deprecations.html>`_ page shows all currently deprecated features, the rationale to do so, and alternatives to update your code. It also list features removed from pytest in past major releases to help those with ancient pytest versions to upgrade. Trivial/Internal Changes ------------------------ - `3955 <https://github.com/pytest-dev/pytest/issues/3955>`_: Improve pre-commit detection for changelog filenames - `3975 <https://github.com/pytest-dev/pytest/issues/3975>`_: Remove legacy code around im_func as that was python2 only ``` ### 3.8.0 ``` ========================= Deprecations and Removals ------------------------- - `2452 <https://github.com/pytest-dev/pytest/issues/2452>`_: ``Config.warn`` and ``Node.warn`` have been deprecated, see `<https://docs.pytest.org/en/latest/deprecations.htmlconfig-warn-and-node-warn>`_ for rationale and examples. - `3936 <https://github.com/pytest-dev/pytest/issues/3936>`_: ``pytest.mark.filterwarnings`` second parameter is no longer regex-escaped, making it possible to actually use regular expressions to check the warning message. **Note**: regex-escaping the match string was an implementation oversight that might break test suites which depend on the old behavior. Features -------- - `2452 <https://github.com/pytest-dev/pytest/issues/2452>`_: Internal pytest warnings are now issued using the standard ``warnings`` module, making it possible to use the standard warnings filters to manage those warnings. This introduces ``PytestWarning``, ``PytestDeprecationWarning`` and ``RemovedInPytest4Warning`` warning types as part of the public API. Consult `the documentation <https://docs.pytest.org/en/latest/warnings.htmlinternal-pytest-warnings>`_ for more info. - `2908 <https://github.com/pytest-dev/pytest/issues/2908>`_: ``DeprecationWarning`` and ``PendingDeprecationWarning`` are now shown by default if no other warning filter is configured. This makes pytest more compliant with `PEP-0506 <https://www.python.org/dev/peps/pep-0565/recommended-filter-settings-for-test-runners>`_. See `the docs <https://docs.pytest.org/en/latest/warnings.htmldeprecationwarning-and-pendingdeprecationwarning>`_ for more info. - `3251 <https://github.com/pytest-dev/pytest/issues/3251>`_: Warnings are now captured and displayed during test collection. - `3784 <https://github.com/pytest-dev/pytest/issues/3784>`_: ``PYTEST_DISABLE_PLUGIN_AUTOLOAD`` environment variable disables plugin auto-loading when set. - `3829 <https://github.com/pytest-dev/pytest/issues/3829>`_: Added the ``count`` option to ``console_output_style`` to enable displaying the progress as a count instead of a percentage. - `3837 <https://github.com/pytest-dev/pytest/issues/3837>`_: Added support for 'xfailed' and 'xpassed' outcomes to the ``pytester.RunResult.assert_outcomes`` signature. Bug Fixes --------- - `3911 <https://github.com/pytest-dev/pytest/issues/3911>`_: Terminal writer now takes into account unicode character width when writing out progress. - `3913 <https://github.com/pytest-dev/pytest/issues/3913>`_: Pytest now returns with correct exit code (EXIT_USAGEERROR, 4) when called with unknown arguments. - `3918 <https://github.com/pytest-dev/pytest/issues/3918>`_: Improve performance of assertion rewriting. Improved Documentation ---------------------- - `3566 <https://github.com/pytest-dev/pytest/issues/3566>`_: Added a blurb in usage.rst for the usage of -r flag which is used to show an extra test summary info. - `3907 <https://github.com/pytest-dev/pytest/issues/3907>`_: Corrected type of the exceptions collection passed to ``xfail``: ``raises`` argument accepts a ``tuple`` instead of ``list``. Trivial/Internal Changes ------------------------ - `3853 <https://github.com/pytest-dev/pytest/issues/3853>`_: Removed ``"run all (no recorded failures)"`` message printed with ``--failed-first`` and ``--last-failed`` when there are no failed tests. ```
Links - PyPI: https://pypi.org/project/pytest - Changelog: https://pyup.io/changelogs/pytest/ - Homepage: https://docs.pytest.org/en/latest/
coveralls commented 5 years ago

Coverage Status

Coverage remained the same at 55.948% when pulling c59d5517073ec6e98a68a838e3a9fc6495963ce2 on pyup/scheduled-update-2018-10-01 into 24ad36ffaa0d51a6564ed46a41dfa1558acc3f90 on develop.