Merge pull request #17 from alvaradoo/main

prod and property graph arachne

.gitignore

@@ -1 +1,130 @@
 GraphServerModules.cfg.*
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

arachne/README.md

@@ -0,0 +1,48 @@
+# Arachne: Graph Analysis Extension to Arkouda
+
+## Overview
+The Arachne project provides an extension for graph analysis that works with Arkouda. Arachne mimics the NetworkX API while providing high-performance implementations of graph kernels in Chapel. 
+
+## Installation
+Installation is performed by running `module_configuration.py`. This file is copied from the `Bears-R-Us/arkouda-contrib` repository. When running `module_configuration.py`, the complete path to the location of the Arkouda repo must be specificed through the `ak_loc` flag along with the complete path to the Arkouda contrib repo. In our case, it would be the complete path to this directory housing Arachne. An example follows below:
+
+```
+python3 module_configuration.py --ak_loc=/complete/path/to/arkouda/ --pkg_path=/complete/path/to/arkouda-njit/arachne/
+```
+
+When the above command completes, the result will be a couple of commands along the lines of:
+```
+pip install -U /rhome/oaa9/Research/arkouda-njit/arachne/client
+cp /rhome/oaa9/Research/arkouda/ServerModules.cfg ~/TmpServerModules.cfg.1681487975
+ARKOUDA_SERVER_USER_MODULES=" /rhome/oaa9/Research/arkouda-njit/arachne/server/GraphMsg.chpl" ARKOUDA_CONFIG_FILE=~/TmpServerModules.cfg.1681487975 ARKOUDA_SKIP_CHECK_DEPS=true make -C /rhome/oaa9/Research/arkouda
+```
+
+The length of the last command is dependent on the number of modules you have listen inside of `arkouda-njit/arachne/server/ServerModules.cfg`. Within here you can comment in and out the lines of the modules you wish to compile and not compile. By default, all of them are left uncommented.
+
+Next, simply just copy and paste the outputted commands into terminal and your arkouda server should start to build with Arachne added onto it. 
+
+If you run into environment errors, you can run the commands below to ensure both Arachne and Arkouda have been pip installed into your environment. 
+```
+pip3 install -e /path/to/arachne/client/.
+pip3 install -e /path/to/arkouda/.
+```
+
+## Usage
+Functions currently available can be found in `client/README.md` with a benchmark file that can be used as a sample found in `benchmarks/bfs.py`. Sample executions of benchmark file follow.
+
+For benchmarking a single graph you can execute: 
+```
+python3 bfs.py node port -f /path/to/arkouda-njit/arachne/data/karate.mtx -t 10
+```
+
+For benchmarking a directory of graphs you can execute: 
+```
+python3 bfs.py node01 5554 -d /path/to/arkouda-njit/arachne/data -t 10
+```
+
+## Testing
+The Arachne tests are executed from the arkouda-njit/arachne directory as follows:
+```
+python3 -m pytest test/bfs_test.py test/reading_test.py test/class_test.py
+```
+**Note**: Errors when executing using pytest from arachne directory. 

arachne/base_test.py

@@ -0,0 +1,84 @@
+import unittest, os
+import arkouda as ak
+from server_util.test.server_test_util import get_arkouda_numlocales, start_arkouda_server, \
+    stop_arkouda_server, TestRunningMode
+import importlib
+
+'''
+ArkoudaTest defines the base Arkouda test logic for starting up the arkouda_server at the 
+launch of a unittest TestCase and shutting down the arkouda_server at the completion of
+the unittest TestCase.
+
+Note: each Arkouda TestCase class extends ArkoudaTest and encompasses 1..n test methods, the 
+names of which match the pattern 'test*' (e.g., ArkoudaTest.test_arkouda_server).
+'''
+
+
+class ArkoudaTest(unittest.TestCase):
+    verbose = True if os.getenv('ARKOUDA_VERBOSE') == 'True' else False
+    port = int(os.getenv('ARKOUDA_SERVER_PORT', 5555))
+    server = os.getenv('ARKOUDA_SERVER_HOST', 'localhost')
+    test_running_mode = TestRunningMode(os.getenv('ARKOUDA_RUNNING_MODE', 'GLOBAL_SERVER'))
+    timeout = int(os.getenv('ARKOUDA_CLIENT_TIMEOUT', 5))
+
+    @classmethod
+    def setUpClass(cls):
+        '''
+        If in full stack mode, configures and starts the arkouda_server process and sets the
+        ArkoudaTest.server class attribute, noop in client mode.
+
+        :return: None
+        :raise: EnvironmentError if 1..n required test libraries are missing, RuntimeError
+                if there is an error in configuring or starting arkouda_server
+        '''
+        if not importlib.util.find_spec('pytest') or not importlib.util.find_spec('pytest_env'):
+            raise EnvironmentError('pytest and pytest-env must be installed')
+        if TestRunningMode.CLASS_SERVER == ArkoudaTest.test_running_mode:
+            try:
+                nl = get_arkouda_numlocales()
+                ArkoudaTest.server, _, _ = start_arkouda_server(numlocales=nl, port=ArkoudaTest.port)
+                print('Started arkouda_server in TEST_CLASS mode with host: {} port: {} locales: {}'. \
+                      format(ArkoudaTest.server, ArkoudaTest.port, nl))
+            except Exception as e:
+                raise RuntimeError('in configuring or starting the arkouda_server: {}, check ' +
+                                   'environment and/or arkouda_server installation', e)
+        else:
+            print('in client stack test mode with host: {} port: {}'.format(ArkoudaTest.server, ArkoudaTest.port))
+
+    def setUp(self):
+        '''
+        Connects an Arkouda client for each test case
+
+        :return: None
+        :raise: ConnectionError if exception is raised in connecting to arkouda_server
+        '''
+        try:
+            ak.client.connect(server=ArkoudaTest.server, port=ArkoudaTest.port,
+                              timeout=ArkoudaTest.timeout)
+        except Exception as e:
+            raise ConnectionError(e)
+
+    def tearDown(self):
+        '''
+        Disconnects the client connection for each test case
+        :return: None
+        :raise: ConnectionError if exception is raised in connecting to arkouda_server
+        '''
+        try:
+            ak.client.disconnect()
+        except Exception as e:
+            raise ConnectionError(e)
+
+    @classmethod
+    def tearDownClass(cls):
+        '''
+        Shuts down the arkouda_server started in the setUpClass method if test is run
+        in full stack mode, noop if in client stack mode.
+
+        :return: None
+        '''
+        if TestRunningMode.CLASS_SERVER == ArkoudaTest.test_running_mode:
+            try:
+                stop_arkouda_server()
+            except Exception:
+                pass