Merge branch 'cathy/setup_repo'

.gitignore

@@ -0,0 +1,92 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# emacs autosave
+*~

Makefile

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+SHELL               := /bin/bash
+
+# see git describe documentation for a descption
+# the version as set in meta.yaml
+RELEASE_VERSION     = $(shell cat VERSION)
+PROJECT_NAME        = $(shell grep -Eo "name: .*" conda-build/meta.yaml | cut -f 2 -d ' ')
+
+GIT_URL             = $(shell git config --get remote.origin.url)
+GIT_REV             = $(shell git rev-parse --short HEAD)
+DEV_VERSION         = $(RELEASE_VERSION)_dev$(GIT_REV)
+
+# conda-build 2.1.12 started breaking our builds.
+#  2.1.10 was the last version we know works so let's lock to this and more carefully update.
+CONDA_BUILD_VERSION = 2.1.10
+
+CONDA_OUTPUT_FOLDER ?= /opt/releases/driver/
+# where to put the build objects. We can't use the default because
+# there is a known bug by which conda can't build on encrypted drives
+CONDA_BUILD_FOLDER  = /tmp/$(PROJECT_NAME)_$(DEV_VERSION)_$(shell whoami)
+# EXPORT_ALL_VARIABLES: will cause conflict with conda specific ENV variables.
+# this is required to satisfy our dependencies
+PYTHON_VERSION      = 3.5
+
+DRIVER_CONDA_CHANNELS = -c conda -c driver
+
+export GIT_LFS_SKIP_SMUDGE=1
+
+.EXPORT_ALL_VARIABLES:
+
+####################################################################################################
+# Development commands
+#
+
+develop: install-deps-in-current-env
+	VERSION=$(DEV_VERSION) DRIVER_BUILD_GIT_URL=$(GIT_URL) DRIVER_BUILD_GIT_REV=$(GIT_REV) \
+	    python .package_install_steps.py develop
+
+# builds a conda package from the meta.yaml file and places it into the local repo
+build-in-current-env: verify-conda-build-installed
+	-mkdir -p $(CONDA_OUTPUT_FOLDER) && test -w $(CONDA_OUTPUT_FOLDER)
+	conda config --set anaconda_upload no
+	VERSION=$(DEV_VERSION) DRIVER_BUILD_GIT_URL=$(GIT_URL) DRIVER_BUILD_GIT_REV=$(GIT_REV) \
+	    conda-build conda-build/meta.yaml \
+		$(DRIVER_CONDA_CHANNELS) \
+		--croot $(CONDA_BUILD_FOLDER) \
+		--output-folder $(CONDA_OUTPUT_FOLDER) \
+		--python $(PYTHON_VERSION)
+
+# Install package into the current environment
+install-in-current-env: build-in-current-env
+	conda install --yes $(DRIVER_CONDA_CHANNELS) -c file://$(CONDA_OUTPUT_FOLDER) $(PROJECT_NAME)=$(DEV_VERSION)
+
+uninstall-from-current-env: # develop uninstall  # install uninstall
+	-conda uninstall --yes $(PROJECT_NAME) || pip uninstall --yes $(PROJECT_NAME)
+
+install-deps-in-current-env: install-in-current-env uninstall-from-current-env
+
+####################################################################################################
+# Conda environment commands
+#
+
+# run the test scripts in a clean conda environment
+setup-clean-env:
+	-conda create --yes --name test_env_$(PROJECT_NAME)_$(DEV_VERSION) python=$(PYTHON_VERSION)
+
+teardown-clean-env:
+	conda remove --name test_env_$(PROJECT_NAME)_$(DEV_VERSION) --all --yes
+
+####################################################################################################
+# Release commands
+#
+
+git-tag:
+	git pull --tags
+	git tag -a v$(RELEASE_VERSION) -m "v$(RELEASE_VERSION)"
+	git push origin v$(RELEASE_VERSION)
+
+build-release-and-upload: verify-conda-build-installed
+	conda config --set anaconda_upload yes
+	# Create the package if it does not already exist and set the permission to
+	# private (to driver).
+	-anaconda package driver/$(PROJECT_NAME) --create --private
+	VERSION=$(RELEASE_VERSION) DRIVER_BUILD_GIT_URL=$(GIT_URL) DRIVER_BUILD_GIT_REV=$(GIT_REV) \
+	    conda-build conda-build/meta.yaml \
+		$(DRIVER_CONDA_CHANNELS) \
+		--croot $(CONDA_BUILD_FOLDER) \
+		--python $(PYTHON_VERSION) \
+		--channel driver
+
+release: test-in-clean-env git-tag build-release-and-upload
+
+####################################################################################################
+# test commands
+#
+
+test-in-clean-env: verify-conda-build-installed
+	$(MAKE) setup-clean-env
+	source activate test_env_$(PROJECT_NAME)_$(DEV_VERSION) && \
+	$(MAKE) install-in-current-env && \
+	$(MAKE) test-in-current-env && \
+	source deactivate test_env_$(PROJECT_NAME)_$(DEV_VERSION)
+	$(MAKE) teardown-clean-env
+
+# run tests in the current environment
+test-in-current-env:
+	git lfs fetch
+	echo TEST
+
+####################################################################################################
+# helper commands
+#
+
+# make sure that we don't have uncommited changes, we'll want to check for un-added files in the future
+verify-changes-commited:
+	git diff-index --quiet HEAD --
+
+verify-conda-build-installed:
+	-source deactivate && conda install conda-build=$(CONDA_BUILD_VERSION) --yes

VERSION

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+0.0.1

beliefs/models/DirectedGraph.py

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+import networkx as nx
+
+
+class DirectedGraph(nx.DiGraph):
+    """
+    Base class for all directed graphical models.
+    """
+    def __init__(self, edges, node_labels):
+        """
+        Input:
+            edges: an edge list, e.g. [(parent1, child1), (parent1, child2)]
+            node_labels: a list of strings of node labels
+        """
+        super().__init__()
+        if edges is not None:
+            self.add_edges_from(edges)
+        if node_labels is not None:
+            self.add_nodes_from(node_labels)
+
+    def get_leaves(self):
+        """
+        Returns a list of leaves of the graph.
+        """
+        return [node for node, out_degree in self.out_degree_iter() if
+                out_degree == 0]
+
+    def get_roots(self):
+        """
+        Returns a list of roots of the graph.
+        """
+        return [node for node, in_degree in self.in_degree().items() if
+                in_degree == 0]
+
+    def get_topologically_sorted_nodes(self, reverse=False):
+        return nx.topological_sort(self, reverse=reverse)

conda-build/.package_install_steps.py

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+import os
+from setuptools import setup, find_packages
+from yaml import load
+import jinja2
+
+
+def load_meta_data(fname):
+    with open(fname) as input_fp:
+        # note that EDITABLE_FLAG is not required because we getting it from environ
+        template = jinja2.Template(input_fp.read(), undefined=jinja2.StrictUndefined)
+        return load(template.render(**os.environ))
+
+
+def main():
+    meta_data = load_meta_data('conda-build/meta.yaml')
+    setup(
+        name=meta_data['package']['name'],
+        version=meta_data['package']['version'],
+        include_package_data=True,
+        zip_safe=False,
+        entry_points={
+            'console_scripts': meta_data['build'].get('entry_points', [])
+        },
+        packages=find_packages()
+    )
+
+
+if __name__ == '__main__':
+    main()

conda-build/meta.yaml

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+package:
+  name: beliefs
+  version: {{ VERSION }}
+
+source:
+  git_url: ..
+
+build:
+  script: python .package_install_steps.py install
+  script_env:
+    - VERSION
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - jinja2
+    - pyyaml
+
+  run:
+    - python
+    - jinja2
+    - pyyaml
+    - pytest
+    - numpy
+    - networkx >=1.11
+
+anaconda_upload: True
+
+about:
+  home: https://github.com/drivergroup/beliefs/