initial commit of skeleton files

.circleci/config.yml

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+
+version: 2
+jobs:
+  build:
+    working_directory: /root/project
+    docker:
+
+      - image: karrlab/wc_env_dependencies:latest
+
+    steps:
+      # Clone repository
+      - checkout
+
+      # Load packages from cache
+      - restore_cache:
+          keys:
+            - v1-{{ arch }}-{{ .Branch }}-{{ checksum "/etc/docker-image-tag" }}-{{ checksum "requirements.txt" }}
+
+      # Python 3 installation tasks      
+      - run:
+          name: Install pkg_utils (Python 3)
+          command: pip3 install -U git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
+      - run:
+          name: Install karr_lab_build_utils (Python 3)
+          command: |
+            pip3 install -U git+https://github.com/KarrLab/log.git#egg=log
+            pip3 install -U git+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git#egg=sphinxcontrib_googleanalytics
+            pip3 install -U git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]
+            pip3 install -U git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils[all]
+      - run:
+          name: Install package configuration files including credentials
+          command: karr_lab_build_utils3 download-install-package-config-files
+      - run:
+          name: Setup Python environment
+          command: |
+            if [[ -f .circleci/requirements.txt ]]; then
+              while IFS="" read -r line || [ -n "$line" ]; do
+                if [[ ! -z "$line" ]] && [[ ! "$line" =~ ^# ]]; then
+                  pip3 install -U "$line"
+                fi
+              done < .circleci/requirements.txt
+            fi
+      - run:
+          name: Install package (Python 3)
+          command: pip3 install -U -e .[all]
+
+      # Save packages to cache
+      - save_cache:
+          key: v1-{{ arch }}-{{ .Branch }}-{{ checksum "/etc/docker-image-tag" }}-{{ checksum "requirements.txt" }}
+          paths:
+            - /usr/local/lib/python3.6/site-packages
+
+      # Test code
+      - run:
+          name: Test code
+          command: |
+            set +e
+
+            karr_lab_build_utils3 run-tests --with-xunit --with-coverage
+            TEST_EXIT_CODE_PY3=$?
+
+            # Calculate exit code and save to file for reading by the next step
+            if [[ $TEST_EXIT_CODE_PY3 -eq 0 ]]; then
+              echo "0" > TEST_EXIT_CODE
+              exit 0
+            else
+              echo "0" > TEST_EXIT_CODE
+              exit 1
+            fi
+
+      # Generate reports, archive results, and send notifications
+      - run:
+          name: Generate reports, archive results, and send notifications
+          when: always
+          command: |
+            if [[ -f TEST_EXIT_CODE ]]; then
+              INSTALLATION_EXIT_CODE=0
+              TEST_EXIT_CODE=$(<TEST_EXIT_CODE)
+            else
+              INSTALLATION_EXIT_CODE=1
+              TEST_EXIT_CODE=1
+            fi
+
+            karr_lab_build_utils3 do-post-test-tasks $INSTALLATION_EXIT_CODE $TEST_EXIT_CODE
+
+      - store_test_results:
+          path: /root/project/tests/reports
+      - store_artifacts:
+          path: /root/project/tests/reports
+          destination: reports
+      - store_artifacts:
+          path: /root/.wc/log
+          destination: log
+      - store_artifacts:
+          path: /root/project/docs/_build/html
+          destination: docs
+
+
+# workflows:
+#  version: 2
+#  build:
+#    jobs:
+#      - build:
+#          context: karr_lab

.circleci/requirements.txt

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+# Karr Lab packages
+git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
+git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils

.gitignore

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+# compiled files
+*.pyc
+
+# python cache
+__pycache__/
+
+#distribution files
+/build/
+/dist/
+/sdists/
+*.egg-info
+
+# test reports
+tests/reports
+
+# coverage file
+.coverage*
+htmlcov/
+.tox/
+
+# profiling data
+prof/
+
+# .rst-formatted README
+README.rst
+
+# compiled documentation
+docs/source
+docs/_build
+docs/.doctrees/
+
+# pytest .cache directory
+.cache/
+.pytest_cache/
+
+# passwords
+tests/fixtures/secret/
+
+# IDE configuration
+.idea/
+.spyderproject
+.ropeproject
+
+# temporary files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+.~lock.*
+Thumbs.db
+~$*.xlsx
+~$*.xls
+.~*.xlsx

.karr_lab_build_utils.yml

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+static_analyses:
+  ignore_files: []
+downstream_dependencies: []
+email_notifications: []

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2019 Karr Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

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+# description
+README.rst
+
+# version
+include bcforms/VERSION
+
+# license
+include LICENSE
+
+# requirements
+include requirements.txt
+include requirements.optional.txt

README.md

@@ -1,2 +1,34 @@
+[//]: # ( [![PyPI package](https://img.shields.io/pypi/v/bcforms.svg)](https://pypi.python.org/pypi/bcforms) )
+[![Documentation](https://readthedocs.org/projects/bcforms/badge/?version=latest)](https://docs.karrlab.org/bcforms)
+[![Test results](https://circleci.com/gh/KarrLab/bcforms.svg?style=shield)](https://circleci.com/gh/KarrLab/bcforms)
+[![Test coverage](https://coveralls.io/repos/github/KarrLab/bcforms/badge.svg)](https://coveralls.io/github/KarrLab/bcforms)
+[![Code analysis](https://api.codeclimate.com/v1/badges/c8f15ac1e50c27ca44cc/maintainability)](https://codeclimate.com/github/KarrLab/bcforms)
+[![License](https://img.shields.io/github/license/KarrLab/bcforms.svg)](LICENSE)
+![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/bcforms/README.md?pixel)
+
 # bcforms
-Toolkit for concretely describing macromolecular complexes
+
+Write an overview
+
+## Installation
+1. Install dependencies
+2. Install the latest release from PyPI
+  ```
+  pip install bcforms.git[all]
+  ```
+3. Install the latest revision from GitHub
+  ```
+  pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[all]
+  ```
+
+## Documentation
+Please see the [API documentation](https://docs.karrlab.org/bcforms).
+
+## License
+The package is released under the [MIT license](LICENSE).
+
+## Development team
+This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, USA.
+
+## Questions and comments
+Please contact the [Karr Lab](https://www.karrlab.org) with any questions or comments.

bcforms/VERSION

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+0.0.1

bcforms/__init__.py

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+import pkg_resources
+
+# read version
+with open(pkg_resources.resource_filename('bcforms', 'VERSION'), 'r') as file:
+    __version__ = file.read().strip()

bcforms/__main__.py

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+""" bcforms command line interface
+
+:Author: Name <email>
+:Date: 2019-6-25
+:Copyright: 2019, Karr Lab
+:License: MIT
+"""
+
+import cement
+import bcforms
+import bcforms.core
+
+
+class BaseController(cement.Controller):
+    """ Base controller for command line application """
+
+    class Meta:
+        label = 'base'
+        description = "bcforms"
+        arguments = [
+            (['-v', '--version'], dict(action='version', version=bcforms.__version__)),
+        ]
+
+    @cement.ex(help='command_1 description')
+    def cmd1(self):
+        """ command_1 description """
+        print('command_1 output')
+
+    @cement.ex(help='command_2 description')
+    def cmd2(self):
+        """ command_2 description """
+        print('command_2 output')
+
+    @cement.ex(hide=True)
+    def _default(self):
+        self._parser.print_help()
+
+
+class Command3WithArgumentsController(cement.Controller):
+    """ Command3 description """
+
+    class Meta:
+        label = 'command-3'
+        description = 'Command3 description'
+        stacked_on = 'base'
+        stacked_type = 'nested'
+        arguments = [
+            (['arg_1'], dict(
+                type=str, help='Description of arg_1')),
+            (['arg_2'], dict(
+                type=str, help='Description of arg_2')),
+            (['--opt-arg-3'], dict(
+                type=str, default='default value of opt-arg-1', help='Description of opt-arg-3')),
+            (['--opt-arg-4'], dict(
+                type=float, default=float('nan'), help='Description of opt-arg-4')),
+        ]
+
+    @cement.ex(hide=True)
+    def _default(self):
+        args = self.app.pargs
+        args.arg_1
+        args.arg_2
+        args.opt_arg_3
+        args.opt_arg_4
+
+
+class App(cement.App):
+    """ Command line application """
+    class Meta:
+        label = 'bcforms'
+        base_controller = 'base'
+        handlers = [
+            BaseController,
+            Command3WithArgumentsController,
+        ]
+
+def main():
+    with App() as app:
+        app.run()

bcforms/core.py

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+""" bcforms
+
+:Author: Name <email>
+:Date: 2019-6-25
+:Copyright: 2019, Karr Lab
+:License: MIT
+"""
+
+
+class ExampleClass(object):
+    """ Descipton of ExampleClass
+
+    Attributes:
+        attr_1 (:obj:`type of attr_1`): description of attr_1
+        attr_2 (:obj:`type of attr_2`): description of attr_2
+        ...
+    """
+
+    def __init__(self, arg_1, arg_2, kwarg_1=None, kwarg_2=None):
+        """
+        Args:
+            arg_1 (:obj:`type of arg_1`): description of arg_1
+            arg_2 (:obj:`type of arg_2`): description of arg_2
+            kwarg_1 (:obj:`type of kwarg_1`, optional): description of kwarg_1
+            kwarg_2 (:obj:`type of kwarg_2`, optional): description of kwarg_2
+            ...
+        """
+        self.attr_1 = arg_1
+        self.attr_2 = arg_2
+
+    def method_1(self, arg_1, arg_2, kwarg_1=None, kwarg_2=None):
+        """ Description of method_1
+
+        Args:
+            arg_1 (:obj:`type of arg_1`): description of arg_1
+            arg_2 (:obj:`type of arg_2`): description of arg_2
+            kwarg_1 (:obj:`type of kwarg_1`, optional): description of kwarg_1
+            kwarg_2 (:obj:`type of kwarg_2`, optional): description of kwarg_2
+            ...
+
+        Returns:
+            :obj:`type of return value`: description of return value
+
+        Raises:
+            :obj:`type of raised exception(s)`: description of raised exceptions
+        """
+        pass