{
    "info": {
        "author": "Kirill Smelkov",
        "author_email": "kirr@nexedi.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Framework :: ZODB",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: Implementation :: CPython",
            "Topic :: Software Development :: Libraries :: Python Modules"
        ],
        "description": "==========================================\n Wendelin.core - Out-of-core NumPy arrays\n==========================================\n\nWendelin.core allows you to work with arrays bigger than RAM and local disk.\nBigarrays are persisted to storage, and can be changed in transactional manner.\n\nIn other words bigarrays are something like `numpy.memmap`_ for numpy.ndarray\nand OS files, but support transactions and files bigger than disk. The whole\nbigarray cannot generally be used as a drop-in replacement for numpy arrays,\nbut bigarray *slices* are real ndarrays and can be used everywhere ndarray can\nbe used, including in C/Cython/Fortran code. Slice size is limited by\nvirtual address-space size, which is ~ max 127TB on Linux/amd64.\n\nThe main class to work with is `ZBigArray` and is used like `ndarray` from\n`NumPy`_:\n\n1. create array::\n\n    from wendelin.bigarray.array_zodb import ZBigArray\n    import transaction\n\n    # root is connected to opened database\n    root['A'] = A = ZBigArray(shape=..., dtype=...)\n    transaction.commit()\n\n2. view array as a real ndarray::\n\n    a = A[:]        # view which covers all array, if it fits into address-space\n    b = A[10:100]\n\n   data for views will be loaded lazily on memory access.\n\n3. work with views, including using C/Cython/Fortran functions from NumPy\n   and other libraries to read/modify data::\n\n    a[2] = 1\n    a[10:20] = numpy.arange(10)\n    numpy.mean(a)\n\n   | the amount of modifications in one transaction should be less than available RAM.\n   | the amount of data read is limited only by virtual address-space size.\n\n4. data can be appended to array in O(\u03b4) time::\n\n    values                  # ndarray to append of shape  (\u03b4,)\n    A.append(values)\n\n   and array itself can be resized in O(1) time::\n\n    A.resize(newshape)\n\n5. changes to array data can be either discarded or saved back to DB::\n\n    transaction.abort()     # discard all made changes\n    transaction.commit()    # atomically save all changes\n\n\n\nWhen using NEO_ or ZEO_ as a database, bigarrays can be simultaneously used by\nseveral nodes in a cluster.\n\n\nPlease see `demo/demo_zbigarray.py`__ for a complete example.\n\n__ demo/demo_zbigarray.py\n\n\nCurrent state and Roadmap\n=========================\n\nWendelin.core works in real life for workloads Nexedi_ is using in production,\nincluding 24/7 projects. We are, however, aware of the following\nlimitations and things that need to be improved:\n\n- wendelin.core is currently not very fast\n- there are big - proportional to input in size - temporary array allocations\n  in third-party libraries (NumPy_, `scikit-learn`_, ...) which might practically\n  prevent processing out-of-core arrays depending on the functionality used.\n\nThus\n\n- we are currently working on improved wendelin.core design and implementation,\n  which will use kernel virtual memory manager (instead of one implemented__ in__\n  userspace__) with arrays backend presented to kernel via FUSE as virtual\n  filesystem implemented in Go.\n\n__  https://lab.nexedi.com/nexedi/wendelin.core/blob/master/include/wendelin/bigfile/virtmem.h\n__  https://lab.nexedi.com/nexedi/wendelin.core/blob/master/bigfile/virtmem.c\n__  https://lab.nexedi.com/nexedi/wendelin.core/blob/master/bigfile/pagefault.c\n\nIn parallel we will also:\n\n- try wendelin.core 1.0 on large data sets\n- identify and incrementally fix big-temporaries allocation issues in NumPy and\n  scikit-learn\n\nWe are open to community help with the above.\n\n\nAdditional materials\n====================\n\n- Wendelin.core tutorial__\n- Slides__ (pdf__) from presentation about wendelin.core in PyData Paris 2015\n\n__  https://www.nexedi.com/wendelin-Core.Tutorial.2016\n__  http://www.wendelin.io/NXD-Wendelin.Core.Non.Secret/asEntireHTML\n__  http://www.wendelin.io/NXD-Wendelin.Core.Non.Secret?format=pdf\n\n\n.. _NumPy:          http://www.numpy.org/\n.. _scikit-learn:   http://scikit-learn.org/\n.. _numpy.memmap:   http://docs.scipy.org/doc/numpy/reference/generated/numpy.memmap.html\n.. _NEO:            http://www.neoppod.org/\n.. _ZEO:            https://pypi.python.org/pypi/ZEO\n.. _Nexedi:         https://www.nexedi.com/\n\n----\n\nWendelin.core change history\n============================\n\n0.13 (2019-06-18)\n-----------------\n\n- Add support for Python 3.7 (commit__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/bca5f79e6f\n\n- Add `RAMArray` class which is compatible to `ZBigArray` in API and semantic,\n  but stores its data in RAM only (`commit 1`__, 2__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/7365979b9d\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/fc9b69d8e1\n\n- Add `lib.xnumpy.structured` - utility to create structured view of an array (`commit 1`__, 2__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/6a5dfefaf8\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/32ca80e2d5\n\n- Fix logic to keep `ZBigFileH` in sync with ZODB connection (commit__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/d9d6adec1b\n\n- Fix crash on PyVMA deallocation (commit__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/d97641d2ba\n\n- Move `py.bench` to pygolang__ so that it can be used not only in\n  Wendelin.core (commit__).\n\n  __ https://pypi.org/project/pygolang/\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/318efce0bf\n\n- Enhance `t/qemu-runlinux` - utility that is used to work on combined\n  kernel/user-space workloads (`commit 1`__, 2__, 3__, 4__, 5__, 6__).\n  This was in particular useful to develop Linux kernel fixes that are needed\n  for Wendelin.core 2.0 (`kernel commit 1`__, 2__, 3__, 4__, 5__, 6__, 7__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/fe541453f8\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/ccca055cfe\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/6ab952207e\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/a568d6d999\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/208aca62ae\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/89fb89929a\n\n  __ https://git.kernel.org/linus/ad2ba64dd489\n  __ https://git.kernel.org/linus/10dce8af3422\n  __ https://git.kernel.org/linus/bbd84f33652f\n  __ https://git.kernel.org/linus/c5bf68fe0c86\n  __ https://git.kernel.org/linus/438ab720c675\n  __ https://git.kernel.org/linus/7640682e67b3\n  __ https://git.kernel.org/linus/d4b13963f217\n\n- Various bugfixes.\n\n0.12 (2018-04-16)\n-----------------\n\n- Update licensing to be in line with whole Nexedi stack (`commit`__). Please\n  see https://www.nexedi.com/licensing for details, rationale and options.\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/f11386a4\n\n- Add `ArrayRef` utility to find out for a NumPy array its top-level root\n  parent and how to recreate the array as some view of the root;\n  this builds the foundation for e.g. sending arrays as references without copy\n  in CMFActivity joblib backend\n  (`commit 1`__, 2__, 3__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/e9d61a89\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/d53371b6\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/450ad804\n\n\n- Don't crash if during `loadblk()` garbage collection was run twice at tricky\n  times (`commit 1`__, 2__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/4228d8b6\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/3804cc39\n\n- Don't crash on writeout if previously `storeblk()` resulted in error\n  (`commit`__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/87bf4908\n\n\n\n- Fix `py.bench` and rework it to produce output in Go benchmarking format\n  (`commit 1`__, 2__, 3__, 4__, 5__); add benchmarks for handling pagefaults\n  (`commit`__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/51f252d4\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/074ce24d\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/ed13c3f9\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/fc08766d\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/5a1ed45a\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/3cfc2728\n\n- Use zodbtools/zodburi, if available, to open database by URL\n  (`commit`__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/f785ac07\n\n- Start to make sure it works with ZODB5 too (`commit 1`__, 2__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/808b59b7\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/0dbf3c44\n\n- Various bugfixes.\n\n0.11 (2017-03-28)\n-----------------\n\n- Switch back to using ZBlk0 format by default (`commit`__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/0b68f178\n\n0.10 (2017-03-16)\n-----------------\n\n- Tell the world `dtype=object` is not supported (`commit`__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/e44bd761\n\n0.9 (2017-01-17)\n----------------\n\n- Avoid deadlocks via doing `storeblk()` calls with virtmem lock released\n  (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/8bb7f2f2\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/fb4bfb32\n\n- Don't crash if in `loadblk()` implementation an exception is internally\n  raised & caught\n  (`commit 1`__, 2__, 3__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/9aa6a5d7\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/61b18a40\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/024c246c\n\n0.8 (2016-09-28)\n----------------\n\n- Do not leak memory when loading data in ZBlk1 format (`commit`__).\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/542917d1\n\n0.7 (2016-07-14)\n------------------\n\n- Add support for Python 3.5 (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/20115391\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/e6beab19\n\n- Fix bug in pagemap code which could lead to crashes and other issues (`commit`__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/ee9bcd00\n\n- Various bugfixes\n\n0.6 (2016-06-13)\n----------------\n\n- Add support for FORTRAN ordering (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/ab9ca2df\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/2ca0f076\n\n\n- Avoid deadlocks via doing `loadblk()` calls with virtmem lock released\n  (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/f49c11a3\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/0231a65d\n\n- Various bugfixes\n\n0.5 (2015-10-02)\n----------------\n\n- Introduce another storage format, which is optimized for small changes, and\n  make it the default.\n  (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/13c0c17c\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/9ae42085\n\n- Various bugfixes and documentation improvements\n\n\n0.4 (2015-08-19)\n----------------\n\n- Add support for O(\u03b4) in-place BigArray.append() (commit__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/1245acc9\n\n- Implement proper multithreading support (commit__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/d53271b9\n\n- Implement proper RAM pages invalidation when backing ZODB objects are changed\n  from outside (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/cb779c7b\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/92bfd03e\n\n- Fix all kind of failures that could happen when ZODB connection changes\n  worker thread in-between handling requests (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/c7c01ce4\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/64d1f40b\n\n- Tox tests now cover usage with FileStorage, ZEO and NEO ZODB storages\n  (`commit 1`__, 2__)\n\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/010eeb35\n  __ https://lab.nexedi.com/nexedi/wendelin.core/commit/7fc4ec66\n\n- Various bugfixes\n\n\n\n0.3 (2015-06-12)\n----------------\n\n- Add support for automatic BigArray -> ndarray conversion, so that e.g. the\n  following::\n\n    A = BigArray(...)\n    numpy.mean(A)       # passing BigArray to plain NumPy function\n\n  either succeeds, or raises MemoryError if not enough address space is\n  available to cover whole A. 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