Merge pull request #19 from camillescott/rename

Rename Repo

.gitignore

@@ -113,13 +113,13 @@ cython_debug/
 Debug/
 
 *.o
-**boink.pc
-**libboink.*
+**goetia.pc
+**libgoetia.*
 **a.out
 _libbuild/
-src/boink/test_assembly
-src/boink/benchmark_boink_consume
-src/boink/benchmark_oxli_consume
+src/goetia/test_assembly
+src/goetia/benchmark_goetia_consume
+src/goetia/benchmark_oxli_consume
 *.pyx.pxi
 *.pxd.pxi
 

.vscode/c_cpp_properties.json

@@ -0,0 +1,19 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${workspaceFolder}/include/**",
+                "${workspaceFolder}/include"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/lib/ccache/g++-7",
+            "cStandard": "c11",
+            "cppStandard": "c++17",
+            "intelliSenseMode": "gcc-x64",
+            "compileCommands": "${workspaceFolder}/Debug/compile_commands.json"
+        }
+    ],
+    "version": 4
+}

.vscode/settings.json

@@ -0,0 +1,14 @@
+{
+    "python.pythonPath": "/home/camille/miniconda/envs/boink-sourmash/bin/python",
+    "python.linting.pylintPath": "/home/camille/miniconda/envs/boink/bin/pylint",
+    "cmake.configureOnOpen": false,
+    "files.watcherExclude": {
+        "**/.git/objects/**": true,
+        "**/.git/subtree-cache/**": true,
+        "**/node_modules/*/**": true,
+        "**/tox_build/*/**": true,
+        "**/.tox/*/**": true
+    }
+
+
+}

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.9)
 cmake_policy(SET CMP0063 NEW)
 
 #
-# libboink
+# libgoetia
 #
 
 if(DEFINED ENV{BOINK_VERSION})
@@ -20,11 +20,11 @@ else()
 endif()
 message(STATUS "version: ${python_pkg_version}")
 
-project(boink
+project(goetia
         LANGUAGES CXX  C
         VERSION ${sharedlib_version}
         DESCRIPTION "streaming cDBG and dBG sketching algorithms"
-        HOMEPAGE_URL "https://github.com/camillescott/boink"
+        HOMEPAGE_URL "https://github.com/camillescott/goetia"
         )
 
 if(DEFINED ENV{CONDA_PREFIX})
@@ -79,93 +79,93 @@ set(CMAKE_CXX_FLAGS_RELEASE "-O2")
 set(CMAKE_CXX_FLAGS_DEBUG "-O0")
 
 #
-# The boink shared library needs all the source files, the direct object
+# The goetia shared library needs all the source files, the direct object
 # targets, and the gfakluge static library.
 #
-add_library(boink SHARED
+add_library(goetia SHARED
             ${LIB_SOURCES}
 )
-set_target_properties(boink PROPERTIES LINKER_LANGUAGE CXX)
-set_target_properties(boink PROPERTIES CXX_VISIBILITY_PRESET default)
-set_property(TARGET boink PROPERTY LINK_WHAT_YOU_USE TRUE)
-set_property(TARGET boink PROPERTY VISIBILITY_INLINES_HIDDEN 0)
-set_target_properties(boink PROPERTIES
+set_target_properties(goetia PROPERTIES LINKER_LANGUAGE CXX)
+set_target_properties(goetia PROPERTIES CXX_VISIBILITY_PRESET default)
+set_property(TARGET goetia PROPERTY LINK_WHAT_YOU_USE TRUE)
+set_property(TARGET goetia PROPERTY VISIBILITY_INLINES_HIDDEN 0)
+set_target_properties(goetia PROPERTIES
                       VERSION ${PROJECT_VERSION}
                       SOVERSION 1
 )
 
-#set_target_properties(boink PROPERTIES PUBLIC_HEADER ${LIB_HEADERS})
-target_include_directories(boink
+#set_target_properties(goetia PROPERTIES PUBLIC_HEADER ${LIB_HEADERS})
+target_include_directories(goetia
                            PUBLIC
                            ${CMAKE_SOURCE_DIR}/include
 )
-target_include_directories(boink PRIVATE ${ZLIB_INCLUDE_DIRS})
-target_link_libraries(boink
+target_include_directories(goetia PRIVATE ${ZLIB_INCLUDE_DIRS})
+target_link_libraries(goetia
                       Threads::Threads
                       ${ZLIB_LIBRARIES} 
                       ${LIBSOURMASH}
 )
 
 
 #
-# Add all the include directories. Includes that are only used in boink's
+# Add all the include directories. Includes that are only used in goetia's
 # source files are set private, so that they are not installed.
 #
-target_include_directories(boink PRIVATE third-party/)
-target_include_directories(boink PRIVATE include/)
+target_include_directories(goetia PRIVATE third-party/)
+target_include_directories(goetia PRIVATE include/)
 
 #
-# Configure the boink pc.
+# Configure the goetia pc.
 #
-configure_file(src/boink/boink.pc.in boink.pc @ONLY)
+configure_file(src/goetia/goetia.pc.in goetia.pc @ONLY)
 
 
 #
 # Benchmark exes
 #
-add_executable(do_bench_storage EXCLUDE_FROM_ALL ${CMAKE_SOURCE_DIR}/src/boink/benchmarks/do_bench_storage.cc)
-target_link_libraries(do_bench_storage boink)
+add_executable(do_bench_storage EXCLUDE_FROM_ALL ${CMAKE_SOURCE_DIR}/src/goetia/benchmarks/do_bench_storage.cc)
+target_link_libraries(do_bench_storage goetia)
 
-add_executable(test_hashing EXCLUDE_FROM_ALL ${CMAKE_SOURCE_DIR}/src/boink/benchmarks/benchmark_hashing.cc)
-target_link_libraries(test_hashing boink)
+add_executable(test_hashing EXCLUDE_FROM_ALL ${CMAKE_SOURCE_DIR}/src/goetia/benchmarks/benchmark_hashing.cc)
+target_link_libraries(test_hashing goetia)
 
 #
 # Set up the Cppyy bindings generation. This is a customized version defined
-# in boink's cmake/ dir; it uses genreflex rather than calling rootcling directly.
+# in goetia's cmake/ dir; it uses genreflex rather than calling rootcling directly.
 # I did this because I couldn't get rootcling to properly include/exclude classes
 # via the LinkDef header, and I wanted to be able to use the better syntax in
 # the genreflex selection XML anyhow. Also, I think this is now the recommended /
 # more modern way anyhow? Code was modified from the versions cppyy distributes.
 #
 cppyy_add_bindings(
-    "boink" ${python_pkg_version} "Camille Scott" "[email protected]"
+    "goetia" ${python_pkg_version} "Camille Scott" "[email protected]"
    LICENSE "MIT"
    LANGUAGE_STANDARD "17"
-   SELECTION_XML  ${CMAKE_SOURCE_DIR}/boink_select.xml
-   INTERFACE_FILE ${BOINK_INCLUDE_ROOT}/include/boink/interface.hh
-   PKG_SRC_DIR    ${CMAKE_SOURCE_DIR}/boink
+   SELECTION_XML  ${CMAKE_SOURCE_DIR}/goetia_select.xml
+   INTERFACE_FILE ${BOINK_INCLUDE_ROOT}/include/goetia/interface.hh
+   PKG_SRC_DIR    ${CMAKE_SOURCE_DIR}/goetia
    TESTS_DIR      ${CMAKE_SOURCE_DIR}/tests
    HEADERS        ${LIB_HEADERS}
    INCLUDE_DIRS   ${BOINK_INCLUDE_ROOT}/include
                   ${CMAKE_CURRENT_SOURCE_DIR}/third-party
                   ${ZLIB_INCLUDE_DIRS}
-   LINK_LIBRARIES boink
+   LINK_LIBRARIES goetia
 )
 
 #
-# libboink's install commands. Installs the libboink shared so,
+# libgoetia's install commands. Installs the libgoetia shared so,
 # its headers, the prometheus headers, and any other public includes.
 #
-install(TARGETS boink
+install(TARGETS goetia
         LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
         INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
 )
 
-#install(DIRECTORY include/boink/
-#        DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/boink
+#install(DIRECTORY include/goetia/
+#        DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/goetia
 #)
 
-install(FILES ${CMAKE_BINARY_DIR}/boink.pc
+install(FILES ${CMAKE_BINARY_DIR}/goetia.pc
         DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig
 )
 

INSTALL

@@ -1,6 +1,6 @@
 # Source and deps
 
-$ git clone https://github.com/camillescott/boink.git && cd boink
+$ git clone https://github.com/camillescott/goetia.git && cd goetia
 $ pip install numpy jinja2 doit pyyaml cython sh pandas
 $ git submodule update --init --remote --recursive 
 
@@ -24,4 +24,4 @@ $ pip install .
 $ pip install pytest-benchmark
 $ pip install git+https://github.com/camillescott/debruijnal-enhance-o-tron.git
 $ pip install git+https://github.com/dib-lab/khmer.git
-$ pytest boink
+$ pytest goetia

README.rst

@@ -1,10 +1,10 @@
-.. image:: https://travis-ci.org/camillescott/boink.svg?branch=master
-    :target: https://travis-ci.org/camillescott/boink
+.. image:: https://travis-ci.org/camillescott/goetia.svg?branch=master
+    :target: https://travis-ci.org/camillescott/goetia
 
 .. image:: https://mybinder.org/badge_logo.svg
-    :target: https://mybinder.org/v2/gh/camillescott/boink/master?filepath=examples%2FStreaming%20Sourmash%20Demo.ipynb
+    :target: https://mybinder.org/v2/gh/camillescott/goetia/master?filepath=examples%2FStreaming%20Sourmash%20Demo.ipynb
 
-boink
+goetia
 -----
 
 Installation
@@ -16,23 +16,23 @@ Conda
 We recommend using `conda <https://docs.conda.io/en/latest/miniconda.html>`_. Within a conda
 environment, install with::
 
-    conda install graph-boink
+    conda install graph-goetia
 
-This will install the boink python package, and install the `libboink` shared library
+This will install the goetia python package, and install the `libgoetia` shared library
 and its headers into your conda prefix.
 
 Building from Source
 ~~~~~~~~~~~~~~~~~~~~
 
 To build and install from source, first clone the repo::
 
-    git clone https://github.com/camillescott/boink && cd boink
+    git clone https://github.com/camillescott/goetia && cd goetia
     git submodule update --init --recursive
 
 Then create a conda environment::
 
-    conda create -y -n libboink -c conda-forge python=3 cppyy cmake cxx-compiler c-compiler clangdev libcxx libstdcxx-ng libgcc-ng pytest numpy scipy openmp python-clang screed blessings pytest-benchmark pyfiglet py-cpuinfo
-    conda activate libboink
+    conda create -y -n libgoetia -c conda-forge python=3 cppyy cmake cxx-compiler c-compiler clangdev libcxx libstdcxx-ng libgcc-ng pytest numpy scipy openmp python-clang screed blessings pytest-benchmark pyfiglet py-cpuinfo
+    conda activate libgoetia
 
 Then build and install with cmake::
 

environment.yml

@@ -1,4 +1,4 @@
-name: boink
+name: goetia
 channels:
     - bioconda
     - conda-forge
@@ -9,5 +9,5 @@ dependencies:
     - ficus
     - sourmash
     - screed
-    - graph-boink
+    - graph-goetia
     - numpy

examples/Streaming Sourmash Demo.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "## Streaming Sourmash\n",
     "\n",
-    "This notebook demonstrates how to use boink to perform a streaming analysis of sourmash minhash signatures. Boink includes the sourmash C++ header and exposes it with cpppy, and wraps it so it can be used with boink's sequence processors. This enables a simple way to perform fast streaming signature analysis in Python."
+    "This notebook demonstrates how to use goetia to perform a streaming analysis of sourmash minhash signatures. Goetia includes the sourmash C++ header and exposes it with cpppy, and wraps it so it can be used with goetia's sequence processors. This enables a simple way to perform fast streaming signature analysis in Python."
    ]
   },
   {
@@ -24,9 +24,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from boink import libboink\n",
-    "from boink.alphabets import DNAN_SIMPLE\n",
-    "from boink.signatures import SourmashSignature\n",
+    "from goetia import libgoetia\n",
+    "from goetia.alphabets import DNAN_SIMPLE\n",
+    "from goetia.signatures import SourmashSignature\n",
     "\n",
     "from sourmash import load_one_signature, MinHash\n",
     "import screed\n",
@@ -47,7 +47,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The boink `SourmashSignature.Signature` is derived from `sourmash::MinHash`, and so follows the same interface. This signature will contain 10000 hashes at a $K$ of 31."
+    "The goetia `SourmashSignature.Signature` is derived from `sourmash::MinHash`, and so follows the same interface. This signature will contain 10000 hashes at a $K$ of 31."
    ]
   },
   {