diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 04e9da2..1044c0a 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.9] # Allows testing multiple python versions. + python-version: ["3.10.6"] # Allows testing multiple python versions. steps: - uses: actions/checkout@v2 @@ -25,14 +25,15 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 mock pytest + pip install pre-commit + if [ -f pyproject.toml ]; then + pip install poetry + poetry install --with dev + fi if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Lint with flake8 + - name: Lint with pre-commit run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + poetry run pre-commit run --all-files - name: Test with pytest run: | pytest diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 434a113..c6e225f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -42,5 +42,3 @@ repos: rev: "v2.6.2" hooks: - id: prettier -default_language_version: - python: python3.9 diff --git a/.travis.yml b/.travis.yml index 7321b68..b4f7b6d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,8 +4,8 @@ sudo: false # Set the build language to Python. language: python -# Set the python version to 3.9. -python: 3.9 +# Set the python version +python: 3.10.6 # Install the codecov pip dependency. install: diff --git a/README.md b/README.md index 73ae779..f631c25 100644 --- a/README.md +++ b/README.md @@ -26,14 +26,33 @@ Integration tests, those which involve use of multiple modules, are placed in th We do not provide example end-to-end tests for this repo, but they would also have their own directory and would run in the context of a non-production service (_eg_ a _staging_ or _dev_ service). +### Install poetry + +Poetry is emerging as the de-facto standard tool for managing Python dependencies. There are many +options for using `poetry`, but examples here assume you'll use it to create and manage a virtual +environment (aka virtualenv) specific to your project. Virtual environments help prevent +conflicting Python dependencies interfering with one another, e.g. if you work on multiple projects +on the same computer. + +1. [Install poetry][https://python-poetry.org/docs/] +2. Install the [poetry-dynamic-versioning][https://github. + com/mtkennerly/poetry-dynamic-versioning] plugin +3. Create a virtualenv for this project (run from the repo base directory) + `poetry install --with dev` +4. Open a shell in the virtualenv + This enables you to use Python dependencies installed by poetry. + ``` + poetry shell # CRTL-D to exit when finished + ``` + ### Test Coverage -Install the test coverage tool: +Activate the poetry virtualenv to use the installed Python packages. -```pip install coverage``` +```poetry shell``` -This tool is called in the _run_all_tests.sh_ script. It will show you a text description of the -coverage if the tests all pass, and it will generate a directory of html that gives a more +The coverage tool is called in the _run_all_tests.sh_ script. It will show you a text description +of the coverage if the tests all pass, and it will generate a directory of html that gives a more detailed description of the coverage. You can access this by running: ```open htmlcov/index.html``` @@ -47,13 +66,16 @@ as a library module. We do _not_ test this code, which you can see when you insp ### Testing Notebooks DemoRepo contains two jupyter notebooks in */notebooks*. This directory also contains a script -to run the notebooks with *runipy*. To run this script, install runipy: +to run the notebooks with *runipy*. To run this script, first activate the poetry virtualenv: -```pip install runipy``` +```poetry shell``` You can then run the script: -```./run_notebook_tests.sh``` +``` +cd notebooks +./run_notebook_tests.sh +``` Note that these tests only ensure that the notebooks can execute; they do not test correctness of the notebook code. @@ -78,6 +100,8 @@ You can then install the pre-commit script in your local repo by running: If you have a _.pre-commit-config.yaml_ file in your repo, you will notice differences in your next commit. The tools specified in _.pre-commit-config.yaml_ will run and will block the commit if any errors are found. It may be helpful to run the tools directly when you are trying to fix these errors. +Pre-commit runs the same checks as the GitHub continuous integration, so running it at commit +time helps you to catch errors earlier in the process. ### Running Black and Flake8 @@ -96,7 +120,7 @@ may have to make fixes by hand. ### Advanced use -See [Advanced.md][Advanced.md] for examples that may be helpful for advanced use. +See [Advanced.md](Advanced.md) for examples that may be helpful for advanced use. ## Automated Documentation @@ -112,10 +136,12 @@ Follow the steps below to create a new repo using DemoRepo as a template: 4. Remove the images in */images/*. 5. Remove the python files in */demo_repo/* and */demo_repo/integration_tests/*. 6. Rename the */demo_repo/* source directory to the name of your repo. Update the directory name in *run_all_tests.sh*. -7. Modify *setup.py* as needed for your repo. -8. Go to [CodeCov repository page](https://codecov.io/gh/JBEI) and add your new repo. -9. Go to the *Settings* your repo in CodeCov and copy the *Repository Upload Token*. Edit the *codecov.yml* file in your local repo and replace the token with the one you copied. -10. Update the markdown README file for your repo. Note that you will want to get a new code coverage badge which is available in *Settings* under the *Badge* section (left-hand panel). For example, the link to the badge for the DemoRepo project is available [here](https://app.codecov.io/gh/JBEI/DemoRepo/settings/badge). -11. Double check set up instructions in the DemoRepo README to ensure that pre-commit is ready to go. - - +7. Modify *pyproject.toml* as needed for your repo. +8. Run `poetry lock` to lock Python dependencies based on *pyproject.toml* +9. Go to [CodeCov repository page](https://codecov.io/gh/JBEI) and add your new repo. +10. Go to the *Settings* your repo in CodeCov and copy the *Repository Upload Token*. Edit the + *codecov.yml* file in your local repo and replace the token with the one you copied. +11. Update the markdown README file for your repo. Note that you will want to get a new code + coverage badge which is available in *Settings* under the *Badge* section (left-hand panel). For example, the link to the badge for the DemoRepo project is available [here](https://app.codecov.io/gh/JBEI/DemoRepo/settings/badge). +12. Double check set up instructions in the DemoRepo README to ensure that pre-commit is ready + to go. diff --git a/demo_repo/__init__.py b/demo_repo/__init__.py index e69de29..b51a855 100644 --- a/demo_repo/__init__.py +++ b/demo_repo/__init__.py @@ -0,0 +1,3 @@ +# Expose version number so it's easily checked in client code (e.g. in Jupyter notebooks). +# "0.0.0" is a placeholder -- versions are actually controlled by Git tags. +__version__ = "0.0.0" diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..41d085c --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1386 @@ +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "asttokens" +version = "2.1.0" +description = "Annotate AST trees with source code positions" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +six = "*" + +[package.extras] +test = ["astroid (<=2.5.3)", "pytest"] + +[[package]] +name = "attrs" +version = "22.1.0" +description = "Classes Without Boilerplate" +category = "dev" +optional = false +python-versions = ">=3.5" + +[package.extras] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "beautifulsoup4" +version = "4.11.1" +description = "Screen-scraping library" +category = "dev" +optional = false +python-versions = ">=3.6.0" + +[package.dependencies] +soupsieve = ">1.2" + +[package.extras] +html5lib = ["html5lib"] +lxml = ["lxml"] + +[[package]] +name = "bleach" +version = "5.0.1" +description = "An easy safelist-based HTML-sanitizing tool." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +six = ">=1.9.0" +webencodings = "*" + +[package.extras] +css = ["tinycss2 (>=1.1.0,<1.2)"] +dev = ["Sphinx (==4.3.2)", "black (==22.3.0)", "build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "mypy (==0.961)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)"] + +[[package]] +name = "cffi" +version = "1.15.1" +description = "Foreign Function Interface for Python calling C code." +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +pycparser = "*" + +[[package]] +name = "colorama" +version = "0.4.6" +description = "Cross-platform colored terminal text." +category = "dev" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" + +[[package]] +name = "coverage" +version = "6.5.0" +description = "Code coverage measurement for Python" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +toml = ["tomli"] + +[[package]] +name = "debugpy" +version = "1.6.3" +description = "An implementation of the Debug Adapter Protocol for Python" +category = "dev" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +category = "dev" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "defusedxml" +version = "0.7.1" +description = "XML bomb protection for Python stdlib modules" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[[package]] +name = "entrypoints" +version = "0.4" +description = "Discover and load entry points from installed packages." +category = "dev" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "exceptiongroup" +version = "1.0.4" +description = "Backport of PEP 654 (exception groups)" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +test = ["pytest (>=6)"] + +[[package]] +name = "executing" +version = "1.2.0" +description = "Get the currently executing AST node of a frame, and other information" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +tests = ["asttokens", "littleutils", "pytest", "rich"] + +[[package]] +name = "fastjsonschema" +version = "2.16.2" +description = "Fastest Python implementation of JSON schema" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] + +[[package]] +name = "iniconfig" +version = "1.1.1" +description = "iniconfig: brain-dead simple config-ini parsing" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "ipykernel" +version = "6.17.1" +description = "IPython Kernel for Jupyter" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +appnope = {version = "*", markers = "platform_system == \"Darwin\""} +debugpy = ">=1.0" +ipython = ">=7.23.1" +jupyter-client = ">=6.1.12" +matplotlib-inline = ">=0.1" +nest-asyncio = "*" +packaging = "*" +psutil = "*" +pyzmq = ">=17" +tornado = ">=6.1" +traitlets = ">=5.1.0" + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-cov", "pytest-timeout"] + +[[package]] +name = "ipython" +version = "8.6.0" +description = "IPython: Productive Interactive Computing" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +appnope = {version = "*", markers = "sys_platform == \"darwin\""} +backcall = "*" +colorama = {version = "*", markers = "sys_platform == \"win32\""} +decorator = "*" +jedi = ">=0.16" +matplotlib-inline = "*" +pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} +pickleshare = "*" +prompt-toolkit = ">3.0.1,<3.1.0" +pygments = ">=2.4.0" +stack-data = "*" +traitlets = ">=5" + +[package.extras] +all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.20)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"] +black = ["black"] +doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"] +kernel = ["ipykernel"] +nbconvert = ["nbconvert"] +nbformat = ["nbformat"] +notebook = ["ipywidgets", "notebook"] +parallel = ["ipyparallel"] +qtconsole = ["qtconsole"] +test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] +test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.20)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] + +[[package]] +name = "jedi" +version = "0.18.1" +description = "An autocompletion tool for Python that can be used for text editors." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +parso = ">=0.8.0,<0.9.0" + +[package.extras] +qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] +testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"] + +[[package]] +name = "jinja2" +version = "3.1.2" +description = "A very fast and expressive template engine." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +MarkupSafe = ">=2.0" + +[package.extras] +i18n = ["Babel (>=2.7)"] + +[[package]] +name = "jsonschema" +version = "4.17.0" +description = "An implementation of JSON Schema validation for Python" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +attrs = ">=17.4.0" +pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" + +[package.extras] +format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] +format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] + +[[package]] +name = "jupyter-client" +version = "7.4.7" +description = "Jupyter protocol implementation and client libraries" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +entrypoints = "*" +jupyter-core = ">=4.9.2" +nest-asyncio = ">=1.5.4" +python-dateutil = ">=2.8.2" +pyzmq = ">=23.0" +tornado = ">=6.2" +traitlets = "*" + +[package.extras] +doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] +test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] + +[[package]] +name = "jupyter-core" +version = "5.0.0" +description = "Jupyter core package. A base package on which Jupyter projects rely." +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +platformdirs = "*" +pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} +traitlets = "*" + +[package.extras] +test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] + +[[package]] +name = "jupyterlab-pygments" +version = "0.2.2" +description = "Pygments theme using JupyterLab CSS variables" +category = "dev" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "markupsafe" +version = "2.1.1" +description = "Safely add untrusted strings to HTML/XML markup." +category = "dev" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "matplotlib-inline" +version = "0.1.6" +description = "Inline Matplotlib backend for Jupyter" +category = "dev" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +traitlets = "*" + +[[package]] +name = "mistune" +version = "2.0.4" +description = "A sane Markdown parser with useful plugins and renderers" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "mock" +version = "4.0.3" +description = "Rolling backport of unittest.mock for all Pythons" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +build = ["blurb", "twine", "wheel"] +docs = ["sphinx"] +test = ["pytest (<5.4)", "pytest-cov"] + +[[package]] +name = "mypy" +version = "0.991" +description = "Optional static typing for Python" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +mypy-extensions = ">=0.4.3" +tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} +typing-extensions = ">=3.10" + +[package.extras] +dmypy = ["psutil (>=4.0)"] +install-types = ["pip"] +python2 = ["typed-ast (>=1.4.0,<2)"] +reports = ["lxml"] + +[[package]] +name = "mypy-extensions" +version = "0.4.3" +description = "Experimental type system extensions for programs checked with the mypy typechecker." +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "nbclient" +version = "0.7.0" +description = "A client library for executing notebooks. 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tools for good code \ + health.""" +# https://pypi.org/classifiers/ +classifiers = [ + # start new projects at the pre-alpha level + "Development Status :: 3 - Pre-Alpha", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "Intended Audience :: Scientific Engineering", + "Intended Audience :: Application", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + "Topic :: Scientific/Engineering :: Bio-Informatics", + # Prevent upload to PyPi until license is determined + "Private :: Do Not Upload", +] +authors = ["Bret Peterson ", "Mark Forrer "] +maintainers = ["Mark Forrer ", "Hector Garcia Martin "] +readme = "README.md" +homepage = "" +repository="https://github.com/JBEI/DemoRemo" +# version: 0.0.0. is a placeholder. Git tags denote version numbers via +# the poetry-dynamic-versioning plugin configured below. +version = "0.0.0" +license = "Proprietary" + +# Production code dependencies (none beyond Python for this demo project). +[tool.poetry.dependencies] +python = "~3.10.6" + +# Development dependencies (only needed @ development time) +[tool.poetry.group.dev] +optional = true +[tool.poetry.group.dev.dependencies] +coverage = "*" +runipy = "*" +mock = "*" +mypy = "*" +pytest = "*" + +# Configure poetry-dynamic-versioning plugin. +# Derives release numbers from git tags. +[tool.poetry-dynamic-versioning] +enable = true +vcs = "git" +dirty = true # include "dirty" in the release name if there are uncommitted changes +strict = true # fail if there's no version tag + +[build-system] +requires = ["poetry-core>=1.2.2", "poetry-dynamic-versioning"] +build-backend = "poetry_dynamic_versioning.backend" diff --git a/setup.py b/setup.py deleted file mode 100755 index 6b0095f..0000000 --- a/setup.py +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env python - -import setuptools - -setuptools.setup( - name="DemoRepo", - version="0.1", - description="An example repository that describes how to set up basic tools" - " for good code health.", - author="Bret Peterson", - author_email="bretpeterson@lbl.gov", - url="https://github.com/JBEI/DemoRemo", - packages=setuptools.find_packages(), - install_requires=["ipython", "mock", "pytest"], - classifiers=[ - "Intended Audience :: Developers", - "Intended Audience :: Science/Research/Development", - "Intended Audience :: Scientific Engineering", - "Intended Audience :: Application", - "Natural Language :: English", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.8", - ], -)