Initial commit

README.md

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+**Note: Do not attempt to use this directly unless you
+know what you are doing. The happy path is to let `roadie` interact with this
+template for you.**
+
+This is a template repository. It will be used by `roadie` to instantiate
+instances. We will make an initial commit on those repos with this boilerplate,
+so there is traceability as to the version of this template the repo was created
+with. This could be useful in figuring out later upgrades necessary to keep
+a repo up-to-date with compliance standards.

cookiecutter.json

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+{
+    "repo_name": "Repository name (use hyphens)",
+    "description": "Project summary description",
+    "package": "package? (y/n)",
+    "type": "dash/package/service/task",
+    "yapf": "yapf configuration",
+    "flake8": "flake8 configuration",
+    "cli": "cli? (y/n)",
+    "python_name": "{{cookiecutter.repo_name|replace('-', '_')|lower}}"
+  }

hooks/post_gen_project.py

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+import os
+import shutil
+
+
+def move_files(files_to_move):
+    for f in files_to_move:
+        shutil.move(f['src'], f['dest'])
+
+
+def main():
+    have_cli = {{cookiecutter.cli == 'y'}}
+    python_name = '{{cookiecutter.python_name}}'
+
+
+    files_to_delete = set()
+    dirs_to_delete = set()
+
+    if not have_cli:
+        files_to_delete = files_to_delete.union({f'{python_name}/cli.py'})
+
+    for f in files_to_delete:
+        os.remove(f)
+
+    for d in dirs_to_delete:
+        shutil.rmtree(d)
+
+
+main()

template-tests/.gitignore

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+test-package/*

template-tests/requirements.txt

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+--index-url https://${PYPI_DOWNLOAD_USERNAME}:${PYPI_DOWNLOAD_PASSWORD}@nexus.rxrx.io/repository/pypi-all/simple
+bandit
+cookiecutter
+flake8
+mypy
+roadie[cli]>=2.3.9
+safety
+yapf

template-tests/test.sh

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+#!/bin/bash
+
+set -e
+set -x
+
+python3.9 -m pip install -r requirements.txt
+
+################################################################################
+#### Test Case: Package With CLI
+rm -rf test-package || true
+python3.9 test_generate.py y
+
+pushd test-package
+
+python3.9 -m roadie.cli.main yapf dump -o ./style.yapf
+python3.9 -m roadie.cli.main lock -u ${PYPI_DOWNLOAD_USERNAME} -p ${PYPI_DOWNLOAD_PASSWORD} --all
+python3.9 -m roadie.cli.main venv -u ${PYPI_DOWNLOAD_USERNAME} -p ${PYPI_DOWNLOAD_PASSWORD} --use-venv
+source venv/bin/activate
+
+flake8
+yapf --style ./style.yapf --parallel --diff -r .
+mypy
+bandit -r . -x /tests/,/venv/
+safety check $(ls requirements/*.txt | xargs -i echo -n ' -r {}')
+CONFIGOME_ENV=test pytest
+pip install --upgrade tox
+tox --parallel
+
+popd
+
+################################################################################
+#### Test Case: Package Without a CLI
+rm -rf test-package || true
+python3.9 test_generate.py n
+
+pushd test-package
+
+python3.9 -m roadie.cli.main yapf dump -o ./style.yapf
+python3.9 -m roadie.cli.main lock -u ${PYPI_DOWNLOAD_USERNAME} -p ${PYPI_DOWNLOAD_PASSWORD} --all
+python3.9 -m roadie.cli.main venv -u ${PYPI_DOWNLOAD_USERNAME} -p ${PYPI_DOWNLOAD_PASSWORD} --use-venv
+source venv/bin/activate
+
+flake8
+yapf --style ./style.yapf --parallel --diff -r .
+mypy
+bandit -r . -x /tests/,/venv/
+safety check $(ls requirements/*.txt | xargs -i echo -n ' -r {}')
+CONFIGOME_ENV=test pytest
+pip install --upgrade tox
+tox --parallel
+
+popd

template-tests/test_generate.py

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+from cookiecutter.main import cookiecutter
+from roadie.constants import FLAKE8_STYLE, YAPF_STYLE
+import sys
+
+
+def main():
+
+    yapf_configuration = ''
+    for k, v in YAPF_STYLE.items():
+        yapf_configuration += f'{k.lower()} = {str(v).lower()}\n'
+    flake8_configuration = ''
+    for k, v in FLAKE8_STYLE.items():
+        flake8_configuration += f'{k.lower()} = {str(v).lower()}\n'
+
+    cookiecutter_context = {
+        'repo_name': "test-package",
+        'description': "words go here",
+        'type': 'package',
+        'yapf': yapf_configuration,
+        'flake8': flake8_configuration,
+        'cli': sys.argv[1],
+    }
+    cookiecutter('..', no_input=True, extra_context=cookiecutter_context)
+
+
+main()

{{cookiecutter.repo_name}}/.gitignore

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+# 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/

{{cookiecutter.repo_name}}/.yapfignore

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+venv*/
+build/
+dist/
+.tox

{{cookiecutter.repo_name}}/Dockerfile.test

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+FROM gcr.io/eng-infrastructure/rxrx-pyenv as test
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+ENV CONFIGOME_ENV=test
+ENTRYPOINT [ "tox", "--parallel" ]

{{cookiecutter.repo_name}}/README.md

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+# {{cookiecutter.repo_name}}
+
+{{cookiecutter.description}}
+
+## Installation
+
+### PIP
+
+This package is installable via [Nexus](nexus.rxrx.io). You should configure your PIP using the instructions listed at
+[roadie: PIP Configuration](https://github.com/recursionpharma/roadie#pip-configuration). Then, execute the following:
+
+```bash
+pip install {{cookiecutter.python_name}}
+```
+
+### Conda
+
+You will need [anaconda cloud setup](https://github.com/recursionpharma/drug-discovery/wiki/Anaconda-Setup#setup-anaconda-cloud-locally)
+in order to access the Recursion conda packages. Once that is setup you can install this library like so:
+
+```
+conda config --add channels conda-forge
+conda config --add channels defaults
+conda config --add channels recursion
+conda install {{cookiecutter.python_name}}
+```
+
+## Developing
+
+Please refer to [Developing Python at Recursion](https://github.com/recursionpharma/roadie/blob/trunk/Developing.md)
+for all tasks related to development of this codebase.

{{cookiecutter.repo_name}}/VERSION

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+MAJOR="0"
+MINOR="0"

{{cookiecutter.repo_name}}/conda.recipe/meta.yaml

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+{# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
+{% raw -%}
+{% set data = load_setup_py_data() %}
+{%- endraw %}
+
+package:
+  name: {{cookiecutter.python_name}}
+  {# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
+  {% raw -%}
+  version: {{ data['version'] }}
+  {%- endraw %}
+
+source:
+  path: ..
+
+build:
+  # If the installation is complex, or different between Unix and Windows, use
+  # separate bld.bat and build.sh files instead of this key.  Add the line
+  # "skip: True  # [py<35]" (for example) to limit to Python 3.5 and newer, or
+  # "skip: True  # [not win]" to limit to Windows.
+  script: python setup.py install --single-version-externally-managed --record=record.txt
+  noarch: python
+  {%- if cookiecutter.cli == 'y' %}
+  entry_points:
+    - {{cookiecutter.python_name}} = {{cookiecutter.python_name}}.cli:cli
+  {%- endif %}
+
+requirements:
+  build:
+    - python>=3.6
+    - setuptools
+    - roadie
+  run:
+    - python>=3.6
+    {% raw -%}
+    # dependencies are defined in setup.py
+    {% for dep in data['install_requires'] %}
+    - {{ dep.lower() }}
+    {% endfor %}
+    {# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
+    {%- endraw %}
+
+test:
+  source_files:
+    - tests
+  requires:
+    - pytest
+  commands:
+    - pytest tests
+
+about:
+  home: https://github.com/recursionpharma/{{cookiecutter.repo_name}}
+  summary: {{cookiecutter.description}}

{{cookiecutter.repo_name}}/requirements/dev.in

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+# These are the minimum specifications required to set up a development
+# environment and includes things like  depedencies required for testing, tools
+# for ensuring security, formatting, and static checking compliance. Feel free
+# to add anything that improves your developer experience.
+#
+# Do you like to test things in a notebook? Then, add `notebook` here. Do you
+# find yourself inspecting objects a lot in the REPL? May I suggest `pdir2`. Do
+# you like lots of colors and formatting options in your REPL, then get `rich`.
+# Remember, it doesn't pay to be too specific here, roadie can be used to
+# resolve your environment and make it reproducible for others.
+
+-c main
+
+bandit
+flake8<4; python_version<'3.8'
+flake8; python_version>='3.8'
+mypy
+pytest
+pytest-cov
+roadie
+safety
+types-pkg_resources
+yapf