Merge pull request #42 from Phelimb/dev

v0.3

.conda/bigsi/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+$PYTHON -m pip install . --no-deps --ignore-installed -vvv 
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

.conda/bigsi/conda_build_config.yaml

@@ -0,0 +1,2 @@
+python:
+    - 3.6

.conda/bigsi/meta.yaml

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+{% set name = "bigsi" %}
+{% set version = "0.3.1" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+# source:
+#   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+#   sha256: 33487a8b81a9cc10f68417a81695f7451321dd2ece4ded7e4e4b23561bca57a7
+source:
+   path: ../../
+
+build:
+  number: 0
+  entry_points:
+    - bigsi = bigsi.__main__:main
+
+requirements:
+  build:
+      - python {{ python }}  
+  host:
+    - mmh3    
+#    - mccortex
+    - biopython
+    - bitarray
+    - cython
+    - hug
+    - humanfriendly
+    - numpy
+    - pip
+    - python
+    - pyyaml
+    - redis
+    - redis-py 
+    - rocksdb 
+    - libdb
+    - python-rocksdb
+    - bsddb3
+  run:
+    - mmh3    
+#    - mccortex
+    - biopython
+    - bitarray
+    - cython
+    - hug
+    - humanfriendly
+    - numpy
+    - python
+    - pyyaml
+    - redis
+    - redis-py 
+    - mmh3    
+    - rocksdb 
+    - libdb
+    - python-rocksdb
+    - bsddb3
+
+# test:
+#   imports:
+#     - bigsi
+#     - bigsi.bloom
+#     - bigsi.cmds
+#     - bigsi.graph
+#     - bigsi.matrix
+#     - bigsi.scoring
+#     - bigsi.storage
+#     - bigsi.utils
+#     - bigsi.tests
+#   requires:
+#     - pytest    
+#   commands:
+#     - py.test --pyargs bigsi
+
+about:
+  home: http://github.com/phelimb/bigsi
+  license: MIT
+  license_family: MIT
+  license_file: 
+  summary: BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data
+  doc_url: 
+  dev_url: 
+
+extra:
+  recipe-maintainers:
+    - phelimb

.conda/mmh3/meta.yaml

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+{% set name = "mmh3" %}
+{% set version = "2.5.1" %}
+{% set file_ext = "tar.gz" %}
+{% set hash_type = "sha256" %}
+{% set hash_value = "185209a217c52afe43e079e5b232d0ef0f3a262601eaaf4371326ab6dcbec508" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  fn: '{{ name }}-{{ version }}.{{ file_ext }}'
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }}
+  '{{ hash_type }}': '{{ hash_value }}'
+
+build:
+  number: 0
+  script: python setup.py install --single-version-externally-managed --record=record.txt
+
+requirements:
+  host:
+    - python
+    - setuptools
+  run:
+    - python
+
+about:
+  home: http://packages.python.org/mmh3
+  license: 'License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication'
+  license_family: CC
+  license_file: ''
+  summary: Python wrapper for MurmurHash (MurmurHash3), a set of fast and robust hash functions.
+  description: "mmh3\n====\n\n.. image:: https://img.shields.io/travis/hajimes/mmh3.svg?branch=master\n   :target: https://travis-ci.org/hajimes/mmh3\n\n.. image:: https://ci.appveyor.com/api/projects/status/github/hajimes/mmh3?branch=master&svg=true\n\
+    \   :target: https://ci.appveyor.com/project/hajimes/mmh3\n\nPython wrapper for MurmurHash (MurmurHash3), a set of fast and robust hash functions.\n\nmmh3 2.5.1 supports Python 2.7, Python 3.3 and higher.\n\
+    \nUsage\n-----\n\nSample Usage::\n\n    >>> import mmh3\n    >>> mmh3.hash('foo') # 32 bit signed int\n    -156908512\n    >>> mmh3.hash('foo', 42) # uses 42 for its seed\n    -1322301282\n    >>> mmh3.hash('foo',\
+    \ signed=False) # 32 bit unsigned int (since Version 2.5)\n    4138058784\n\nOther functions::\n\n    >>> mmh3.hash64('foo') # two 64 bit signed ints (by using the 128-bit algorithm as its backend)\n\
+    \    (-2129773440516405919, 9128664383759220103)\n    >>> mmh3.hash64('foo',signed =False) #  two 64 bit unsigned ints\n    (16316970633193145697, 9128664383759220103)\n    >>> mmh3.hash128('foo', 42)\
+    \ # 128 bit unsigned int\n    215966891540331383248189432718888555506\n    >>> mmh3.hash128('foo', 42, signed = True) # 128 bit signed int\n    -124315475380607080215185174712879655950\n    >>> mmh3.hash_bytes('foo')\
+    \ # 128 bit value as bytes\n    'aE\\xf5\\x01W\\x86q\\xe2\\x87}\\xba+\\xe4\\x87\\xaf~'\n\n``hash64``, ``hash128``, and ``hash_bytes`` have the third argument for architecture optimization. Use True\
+    \ for x64 and False for x86 (default: True).::\n\n    >>> mmh3.hash64('foo', 42, True) \n    (-840311307571801102, -6739155424061121879)\n\nVersion 2.5 added ``hash_from_buffer``, which hashes byte-likes\
+    \ without memory copying. The method is suitable when you hash a large memory-view such as ``numpy.ndarray``.\n\n    >>> mmh3.hash_from_buffer(numpy.random.rand(100))\n    -2137204694\n    >>> mmh3.hash_from_buffer(numpy.random.rand(100),\
+    \ signed = False)\n    3812874078\n\nBeware that ``hash64`` returns **two** values, because it uses the 128-bit version of MurmurHash3 as its backend.\n\nVersion 2.4 added support for 64-bit data.\n\
+    \n    >>> import numpy as np\n    >>> a = np.zeros(2**32, dtype=np.int8)\n    >>> mmh3.hash_bytes(a)\n    b'V\\x8f}\\xad\\x8eNM\\xa84\\x07FU\\x9c\\xc4\\xcc\\x8e'\n\nVersion 2.4 also changed the type\
+    \ of seeds from signed 32-bit int to unsigned 32-bit int. (**The resulting values with signed seeds still remain the same as before, as long as they are 32-bit**)\n\n    >>> mmh3.hash('aaaa', -1756908916)\
+    \ # signed rep. for 0x9747b28c\n    1519878282\n    >>> mmh3.hash('aaaa', 2538058380) # unsigned rep. for 0x9747b28c\n    1519878282\n\nBe careful so that these seeds do not exceed 32-bit. Unexpected\
+    \ results may happen with invalid values.\n\n    >>> mmh3.hash('foo', 2 ** 33)\n    -156908512\n    >>> mmh3.hash('foo', 2 ** 34)\n    -156908512\n\n\nChanges\n=======\n2.5.1 (2017-10-31)\n------------------\n\
+    * Bug fix for ``hash_bytes``. Thanks `doozr <https://github.com/doozr>`_!\n\n2.5 (2017-10-28)\n------------------\n* Add ``hash_from_buffer``. Thanks `Dimitri Vorona <https://github.com/alendit>`_!\n\
+    * Add a keyword argument ``signed``.\n\n2.4 (2017-05-27)\n------------------\n* Support seeds with 32-bit unsigned integers; thanks `Alexander Maznev <https://github.com/pik>`_!\n* Support 64-bit data\
+    \ (under 64-bit environments)\n* Fix compile errors for Python 3.6 under Windows systems.\n* Add unit testing and continuous integration with Travis CI and AppVeyor.\n\n2.3.2 (2017-05-26)\n------------------\n\
+    * Relicensed from public domain to `CC0-1.0 <./LICENSE>`_.\n\n2.3.1 (2015-06-07)\n------------------\n* Fix compile errors for gcc >=5.\n\n2.3 (2013-12-08)\n----------------\n* Add ``hash128``, which\
+    \ returns a 128-bit signed integer.\n* Fix a misplaced operator which could cause memory leak in a rare condition.\n* Fix a malformed value to a Python/C API function which may cause runtime errors\
+    \ in recent Python 3.x versions.\n\nThe first two commits are from `Derek Wilson <https://github.com/underrun>`_. Thanks!\n\n2.2 (2013-03-03)\n----------------\n* Improve portability to support systems\
+    \ with old gcc (version < 4.4) such as CentOS/RHEL 5.x. (Commit from `Micha Gorelick <https://github.com/mynameisfiber>`_. Thanks!)\n\n2.1 (2013-02-25)\n----------------\n\n* Add `__version__` constant.\
+    \ Check if it exists when the following revision matters for your application.\n* Incorporate the revision r147, which includes robustness improvement and minor tweaks.\n\nBeware that due to this revision,\
+    \ **the result of 32-bit version of 2.1 is NOT the same as that of 2.0**. E.g.,::\n\n    >>> mmh3.hash('foo') # in mmh3 2.0\n    -292180858\n    >>> mmh3.hash('foo') # in mmh3 2.1\n    -156908512\n\n\
+    The results of hash64 and hash_bytes remain unchanged. Austin Appleby, the author of Murmurhash, ensured this revision was the final modification to MurmurHash3's results and any future changes would\
+    \ be to improve performance only.\n\nLicense\n=======\n\n`CC0-1.0 <./LICENSE>`_.\n\nFAQ\n===\n\nHow can I use this module? Any tutorials?\n-----------------------------------------\n\nThe following\
+    \ textbooks and tutorials are great sources to learn how to use mmh3 (and other hash algorithms in general) for high-performance computing.\n\n* Chapter 11: Using Less Ram in Micha Gorelick and Ian\
+    \ Ozsvald. 2014. *High Performance Python: Practical Performant Programming for Humans*. O'Reilly Media. `ISBN: 978-1-4493-6159-4 <https://www.amazon.com/dp/1449361595>`_.\n* Duke University. `Efficient\
+    \ storage of data in memeory <http://people.duke.edu/~ccc14/sta-663-2016/20B_Big_Data_Structures.html>`_.\n* Max Burstein. `Creating a Simple Bloom Filter <http://www.maxburstein.com/blog/creating-a-simple-bloom-filter/>`_.\n\
+    * Bugra Akyildiz. `A Gentle Introduction to Bloom Filter <https://bugra.github.io/work/notes/2016-06-05/a-gentle-introduction-to-bloom-filter/>`_.\n\nSome results are different from other MurmurHash3-based\
+    \ libraries.\n------------------------------------------------------------------\n\nBy default, mmh3 returns **signed** values for 32-bit and 64-bit versions and **unsigned** values for ```hash128```,\
+    \ due to historical reasons. Please use the keyword argument ``signed`` to obtain a desired result.\n\nFor compatibility with Google Guava (Java), see https://stackoverflow.com/questions/29932956/murmur3-hash-different-result-between-python-and-java-implementation\n\
+    \n\nI want to report errors/ask questions/send requests.\n----------------------------------------------------\n\nThank you for helping me to improve the library. Please make sure to post them *through\
+    \ the issue tracking system of GitHub*. Issues sent directly to my email account may go unnoticed.\n\nAuthors\n=======\n\nMurmurHash3 was originally developed by Austin Appleby and distributed under\
+    \ public domain.\n\n* http://code.google.com/p/smhasher/\n\nPorted and modified for Python by Hajime Senuma.\n\n* http://pypi.python.org/pypi/mmh3\n* http://github.com/hajimes/mmh3\n\nSee also\n========\n\
+    \n* https://github.com/wc-duck/pymmh3: mmh3 in pure python (Fredrik Kihlander and Swapnil Gusani)\n* https://github.com/escherba/python-cityhash: Python bindings for CityHash (Eugene Scherba)\n* https://github.com/veelion/python-farmhash:\
+    \ Python bindigs for FarmHash (Veelion Chong)\n* https://github.com/escherba/python-metrohash: Python bindings for MetroHash (Eugene Scherba)"
+  doc_url: ''
+  dev_url: ''
+
+extra:
+  recipe-maintainers: ''

.conda/python-rocksdb/bld.bat

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+"%PYTHON%" setup.py install 
+if errorlevel 1 exit 1
+
+:: Add more build steps here, if they are necessary.
+
+:: See
+:: http://docs.continuum.io/conda/build.html
+:: for a list of environment variables that are set during the build process.

.conda/python-rocksdb/build.sh

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+#!/bin/bash
+
+export CPLUS_INCLUDE_PATH=${CPLUS_INCLUDE_PATH}:$PREFIX/include
+#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$PREFIX/lib
+export LIBRARY_PATH=${LIBRARY_PATH}:$PREFIX/lib
+$PYTHON setup.py install 
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

.conda/python-rocksdb/conda_build_config.yaml

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+c_compiler: gcc
+cpu_optimization_target: nocona
+cxx_compiler: gxx
+fortran_compiler: gfortran
+ignore_build_only_deps: [python]
+lua: '5'
+numpy: '1.11'
+perl: 5.26.0
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python: '3.5'
+r_base: '3.4'
+target_platform: linux-64

.conda/python-rocksdb/meta.yaml

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+# This file created by conda-build 3.0.30
+# meta.yaml template originally from:
+# /home/vagrant/projects/ags_conda_recipes/python-rocksdb-0.6.7, last modified Tue Nov 28 17:56:42 2017
+# ------------------------------------------------
+
+package:
+    name: python-rocksdb
+    version: 0.6.7
+source:
+    fn: python-rocksdb-0.6.7.tar.gz
+    md5: f5ae12586f706f3b5bbba120da7814d4
+    url: https://pypi.python.org/packages/a2/99/382b48731aa307e5550a6bee706c13e5df73638f4188ae4fc2a455e3d26b/python-rocksdb-0.6.7.tar.gz
+build:
+    preserve_egg_dir: 'True'
+    string: py35h226b7d0_0
+requirements:
+    build:
+        - bzip2 1.0.6 h6d464ef_2
+        - ca-certificates 2017.08.26 h1d4fec5_0
+        - certifi 2017.11.5 py35h9749603_0
+        - cython 0.26.1 py35h636ebcb_0
+        - libedit 3.1 heed3624_0
+        - libffi 3.2.1 hd88cf55_4
+        - libgcc-ng 7.2.0 h7cc24e2_2
+        - libstdcxx-ng 7.2.0 h7a57d05_2
+        - ncurses 6.0 h9df7e31_2
+        - openssl 1.0.2m h26d622b_1
+        - pip 9.0.1 py35h7e7da9d_4
+        - pytest-runner 3.0 py35_0
+        - python 3.5.4 h417fded_24
+        - readline 7.0 ha6073c6_4
+        - rocksdb 5.3.6 0
+        - setuptools 36.5.0 py35ha8c1747_0
+        - setuptools_scm 1.15.6 py35_0
+        - snappy 1.1.7 0
+        - sqlite 3.20.1 hb898158_2
+        - tk 8.6.7 hc745277_3
+        - wheel 0.30.0 py35hd3883cf_1
+        - xz 5.2.3 h55aa19d_2
+        - zlib 1.2.11 ha838bed_2
+    run:
+        - bzip2
+        - bzip2 >=1.0.6,<2.0a0
+        - python >=3.5,<3.6.0a0
+        - rocksdb
+        - setuptools
+        - zlib
+        - zlib >=1.2.11,<1.3.0a0
+test:
+    imports:
+        - rocksdb
+        - rocksdb.tests
+    requires:
+        - pytest
+about:
+    home: https://github.com/twmht/python-rocksdb
+    license: BSD License
+    license_family: BSD
+    summary: Python bindings for RocksDB
+extra:
+    copy_test_source_files: true
+    final: true

.conda/python-rocksdb/meta.yaml.template

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+package:
+  name: python-rocksdb
+  version: "0.6.7"
+
+source:
+  fn: python-rocksdb-0.6.7.tar.gz
+  url: https://pypi.python.org/packages/a2/99/382b48731aa307e5550a6bee706c13e5df73638f4188ae4fc2a455e3d26b/python-rocksdb-0.6.7.tar.gz
+  md5: f5ae12586f706f3b5bbba120da7814d4
+#  patches:
+   # List any patch files here
+   # - fix.patch
+
+build:
+  # noarch: python
+  preserve_egg_dir: True
+  # entry_points:
+    # Put any entry points (scripts to be generated automatically) here. The
+    # syntax is module:function.  For example
+    #
+    # - python-rocksdb = python-rocksdb:main
+    #
+    # Would create an entry point called python-rocksdb that calls python-rocksdb.main()
+
+
+  # If this is a new build for the same version, increment the build
+  # number. If you do not include this key, it defaults to 0.
+  # number: 1
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - pytest-runner
+    - rocksdb
+    - bzip2
+    - cython
+    - zlib
+
+  run:
+    - python
+    - setuptools
+    - rocksdb
+    - bzip2
+    - zlib
+
+test:
+  # Python imports
+  imports:
+    - rocksdb
+    - rocksdb.tests
+
+  # commands:
+    # You can put test commands to be run here.  Use this to test that the
+    # entry points work.
+
+
+  # You can also put a file called run_test.py in the recipe that will be run
+  # at test time.
+
+  requires:
+    - pytest
+    # Put any additional test requirements here.  For example
+    # - nose
+
+about:
+  home: https://github.com/twmht/python-rocksdb
+  license: BSD License
+  summary: 'Python bindings for RocksDB'
+  license_family: BSD
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml

.conda/rocksdb/build.sh

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+#!/bin/bash
+
+INSTALL_PATH=$PREFIX make shared_lib

.conda/rocksdb/meta.yaml

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+# This file created by conda-build 2.1.17
+
+
+package:
+    name: rocksdb
+    version: 5.2.1
+source:
+    fn: v5.2.1.tar.gz
+    url: https://github.com/facebook/rocksdb/archive/v5.2.1.tar.gz
+build:
+    noarch: ''
+    noarch_python: false
+    number: '0'
+    string: '0'
+requirements:
+    build:
+        - gflags 2.1.2 0
+        - libgcc-ng 
+        - zlib 
+        - cmake 3.2.3 0
+        - snappy 1.1.7 0
+        - bzip2 
+    run:
+        - snappy
+        - zlib
+        - bzip2
+about:
+    home: https://github.com/facebook/rocksdb
+    license: BSD
+extra:
+    final: true