├── .gitignore ├── LICENSE ├── README.md ├── docs └── pypi-publish.md ├── scripts └── calc ├── setup.cfg ├── setup.py ├── src └── pkg_example │ ├── __init__.py │ └── calculator_module.py └── tests └── test_calculator_module.py /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | pip-wheel-metadata/ 24 | share/python-wheels/ 25 | *.egg-info/ 26 | .installed.cfg 27 | *.egg 28 | MANIFEST 29 | 30 | # PyInstaller 31 | # Usually these files are written by a python script from a template 32 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 33 | *.manifest 34 | *.spec 35 | 36 | # Installer logs 37 | pip-log.txt 38 | pip-delete-this-directory.txt 39 | 40 | # Unit test / coverage reports 41 | htmlcov/ 42 | .tox/ 43 | .nox/ 44 | .coverage 45 | .coverage.* 46 | .cache 47 | nosetests.xml 48 | coverage.xml 49 | *.cover 50 | *.py,cover 51 | .hypothesis/ 52 | .pytest_cache/ 53 | 54 | # Translations 55 | *.mo 56 | *.pot 57 | 58 | # Django stuff: 59 | *.log 60 | local_settings.py 61 | db.sqlite3 62 | db.sqlite3-journal 63 | 64 | # Flask stuff: 65 | instance/ 66 | .webassets-cache 67 | 68 | # Scrapy stuff: 69 | .scrapy 70 | 71 | # Sphinx documentation 72 | docs/_build/ 73 | 74 | # PyBuilder 75 | target/ 76 | 77 | # Jupyter Notebook 78 | .ipynb_checkpoints 79 | 80 | # IPython 81 | profile_default/ 82 | ipython_config.py 83 | 84 | # pyenv 85 | .python-version 86 | 87 | # pipenv 88 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 89 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 90 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 91 | # install all needed dependencies. 92 | #Pipfile.lock 93 | 94 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 95 | __pypackages__/ 96 | 97 | # Celery stuff 98 | celerybeat-schedule 99 | celerybeat.pid 100 | 101 | # SageMath parsed files 102 | *.sage.py 103 | 104 | # Environments 105 | .env 106 | .venv 107 | env/ 108 | venv/ 109 | ENV/ 110 | env.bak/ 111 | venv.bak/ 112 | 113 | # Spyder project settings 114 | .spyderproject 115 | .spyproject 116 | 117 | # Rope project settings 118 | .ropeproject 119 | 120 | # mkdocs documentation 121 | /site 122 | 123 | # mypy 124 | .mypy_cache/ 125 | .dmypy.json 126 | dmypy.json 127 | 128 | # Pyre type checker 129 | .pyre/ 130 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 CDT Data Science 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # pkg-example 2 | An example python package as a starter for good research code. 3 | 4 | 5 | ## Installation 6 | Create and activate a virtual environment (venv), then pip install the package. 7 | For example, with conda: 8 | 9 | ```python 10 | conda create -n pex python=3 11 | conda activate pex 12 | ``` 13 | 14 | Then to install the package, change directory to the root of the package and: 15 | ```python 16 | cd /where/the/package/lives/pkg-example 17 | pip install . 18 | # alternatively simply: pip install /where/the/package/lives/pkg-example 19 | ``` 20 | 21 | ### Developer mode 22 | 23 | If you would like to edit the code and for changes to be reflected without the 24 | need to reinstall the package, use pip's `-e` flag: 25 | ```python 26 | pip install -e . 27 | ``` 28 | 29 | -------- 30 | 31 | :point_up: You'd write install instructions like the above in the `README.md` of 32 | every package you create. If your package required system installations (e.g. 33 | a c++ library), you'd list instructions for that install here too. For an 34 | example, see the install instructions for a package like 35 | [soundfile](https://pysoundfile.readthedocs.io/en/latest/#installation). 36 | 37 | -------- 38 | 39 | 40 | ## So...what's happened?! 41 | 42 | ### The python package 43 | Your package, i.e. the code in `./src/pkg_example`, is available for use! Try 44 | it! 45 | ```bash 46 | # Check you're using the python of your venv 47 | which python 48 | # Spin it up! 49 | python 50 | >>> import pkg_example 51 | >>> # Handy tip - where is this installed package on your system?! 52 | >>> pkg_example.__file__ 53 | ``` 54 | 55 | How? You listed it as a package to install in `setup.cfg`. Relevant lines: 56 | ``` 57 | packages = find: 58 | package_dir = 59 | =src 60 | ``` 61 | Any folder inside `./src` with an `__init__.py` inside will have been picked up 62 | as a package to install. 63 | 64 | Importantly, this means you don't need to mess around with relative imports 65 | **within** your package (e.g. `from .calculator_module import Calculator`), just 66 | reference it like a normal package e.g. 67 | `from pkg_example.calculator_module import Calculator`. 68 | 69 | > A gotcha to note - you cant have a `-` in your package name for python, only 70 | underscores. The minus sign is a reserved character. I used a minus sign for the 71 | top level folder name to make it clear that this folder is *not* the python 72 | package; the folder `./src/pkg_example` is the folder containing the python 73 | package code. 74 | 75 | ### Scripts 76 | The script `./scripts/calc` is also available on your path: 77 | ```bash 78 | # calc is in the bin of your venv 79 | which calc 80 | # note that the venv bin folder is on your path 81 | echo $PATH 82 | ``` 83 | It will be in the `bin` folder of your venv, which will have been added 84 | to your [`$PATH`](http://www.linfo.org/path_env_var.html), so, wherever you are 85 | located on your system, if the venv is activated, you can just type calc to 86 | use your package. Neat. 87 | 88 | How? Again, you listed this script as something to install in `setup.cfg`. 89 | Relevant lines: 90 | ``` 91 | scripts = 92 | scripts/calc 93 | ``` 94 | 95 | ### The virtual environment 96 | In addition, your venv has all the packages installed that your package 97 | requires. Relevant lines in `setup.cfg`: 98 | 99 | ``` 100 | install_requires = 101 | black 102 | fire 103 | ipython 104 | pylint 105 | pytest 106 | ... 107 | [options.extras_require] 108 | dev = 109 | twine 110 | ``` 111 | 112 | That `options.extras_require` is fancy: as a developer, you'll likely want to 113 | install packages which wont be necessary for the general user. This is an 114 | optional flag you can use on the pip install, e.g. 115 | ```bash 116 | pip install -e /where/the/package/lives/pkg-example[dev] 117 | ``` 118 | will install the package in development mode (`-e`), install all the 119 | `install_requires` packages, *and* the `dev` option package(s), just `twine` 120 | here. 121 | 122 | 123 | ## What next? 124 | You can upload your package to PyPI! See [docs/pypi-publish.md](docs/pypi-publish.md) 125 | for more information. Once you do that, everyone in the world can mash 126 | 127 | ```bash 128 | pip install your_package_name 129 | ``` 130 | 131 | into their console, and just crack on. Neat huh?! 132 | 133 | ## Linting & Testing 134 | You will have installed `pytest`, `black`, and `pylint` as part of the installation. 135 | 136 | * Running `pytest` from the root directory will run all the tests in `./test`. 137 | * Running `black .` will reformat your code to fit with a specific standard (e.g. 138 | line lengths etc.) 139 | * Running `pylint pkg_example` will check the package conforms to pep8 standards. 140 | 141 | Motivation for testing and linting: 142 | 143 | * Python is permissive and not precompiled 144 | * If your code doesn't need to 'go there' it wont 145 | * ...so it wont error till you're 28 hours into the job 146 | * you know, the very important job due for yesterday? 147 | 148 | So imagine the scenario: 149 | * You renamed a variable 150 | * Your code is much more understandable, great job! 151 | * ...oops you missed one (your `ctrl` + `f` regex didn't account for bracket first) 152 | * What would have saved your ass: 153 | * having written a test that runs that part of the code 154 | * simply running pylint - `unused-variable (W0612)` 155 | * YOU LITERALLY JUST SAVED 24-26 HOURS (You spent 2-4 writing better code - 156 | this gets significantly faster with practice) 157 | 158 | A pylint tip - you can exclude some of the warnings using the `--disable` flag. Given that 159 | `black` doesn't actually conform to PEP8 (:grimacing:), you may want to call pylint as below 160 | to remove some guff: 161 | ``` 162 | pylint --disable=C0330 pkg_example 163 | ``` 164 | 165 | 166 | ## References 167 | 168 | * [The (crappy) slides from the talk][1] 169 | * [A great blog post on pacakging your python project][2] 170 | * [The Python Fire Project - super easy CLIs][3] 171 | * [Comments & docstrings a la the **Google Style Guide**][4] 172 | * [...but combine the above with **type hinting** and you're golden][5] 173 | * [More on setup.cfg][6] 174 | 175 | 176 | [1]: https://docs.google.com/presentation/d/1dZXcjCLKMEpq_HbjI0L4A_ZVMjBmEVN3mbOytily-78/edit?usp=sharing "Slides from the talk" 177 | [2]: https://realpython.com/pypi-publish-python-package/ "Packaging your python project" 178 | [3]: https://github.com/google/python-fire "python fire" 179 | [4]: http://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings "Google code styleguide - conmments and docstrings" 180 | [5]: https://docs.python.org/3/library/typing.html "Type hints" 181 | [6]: https://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files "setup.cfg" 182 | -------------------------------------------------------------------------------- /docs/pypi-publish.md: -------------------------------------------------------------------------------- 1 | **This doc is a work in progress! SORRY! For now, follow this great blog post** 2 | 3 | Nice tutorial: 4 | 5 | And for more detail, read the official docs (pretty concise actually): 6 | 1. 7 | 2. 8 | 9 | The below will be a practical adaptation of the above links for this project: 10 | 11 | # How to publish your package on PyPI 12 | 13 | 1. make your python package 14 | 2. test it locally 15 | 3. create a 'source archive' for distribution 16 | 4. test *that* 17 | 5. publish on pypi test 18 | 6. publish 4 realz 19 | 20 | ## Creating an sdist 21 | 22 | ## Testing your sdist 23 | tar tzf realpython-reader-1.0.0.tar.gz 24 | 25 | ## Publishing to test pypi 26 | 27 | ## Publishing to public pypi 28 | 29 | 30 | ## See also 31 | 32 | bdist_wheel 33 | -------------------------------------------------------------------------------- /scripts/calc: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import fire 3 | 4 | from pkg_example.calculator_module import Calculator 5 | 6 | if __name__ == '__main__': 7 | fire.Fire(Calculator) 8 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | name = pkg-example 3 | version = 0.1b1 4 | license = MIT 5 | license_files = LICENSE 6 | url = https://github.com/cdt-data-science/pkg-example 7 | author = James Owers 8 | author_email = james.f.owers@gmail.com 9 | keywords = template python-packaging best-practice 10 | description = An example python package as a starter for good research code. 11 | long_description = file: README.md 12 | long_description_content_type = text/markdown 13 | classifiers = 14 | License :: MIT 15 | Programming Language :: Python :: 3 16 | 17 | [options] 18 | zip_safe = False 19 | include_package_data = True 20 | install_requires = 21 | black 22 | fire 23 | ipython 24 | pylint 25 | pytest 26 | setup_requires = 27 | pytest-runner 28 | tests_require = 29 | pytest 30 | packages = find: 31 | package_dir = 32 | =src 33 | scripts = 34 | scripts/calc 35 | 36 | [options.extras_require] 37 | dev = 38 | twine 39 | 40 | [options.packages.find] 41 | where = src 42 | 43 | [bdist_wheel] 44 | universal = 0 45 | 46 | [aliases] 47 | test = pytest 48 | 49 | [tool:pytest] 50 | testpaths = tests 51 | pythonfiles = test_*.py 52 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """Packaging setup script. 2 | 3 | This file is required by setuptools. All configuration data is in the setup.cfg file. 4 | """ 5 | 6 | from setuptools import setup 7 | 8 | setup() 9 | -------------------------------------------------------------------------------- /src/pkg_example/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cdt-data-science/pkg-example/a78724acd33346d7955ad0029eec72b134f7c578/src/pkg_example/__init__.py -------------------------------------------------------------------------------- /src/pkg_example/calculator_module.py: -------------------------------------------------------------------------------- 1 | """Calculator class and friends""" 2 | 3 | class Calculator: 4 | """A simple calculator class.""" 5 | 6 | def double(self, number): 7 | """Doubles the input number.""" 8 | return 2 * number 9 | -------------------------------------------------------------------------------- /tests/test_calculator_module.py: -------------------------------------------------------------------------------- 1 | from pkg_example.calculator_module import Calculator 2 | 3 | def test_double(): 4 | calc = Calculator() 5 | assert calc.double(3) == 6 6 | assert calc.double(3.0) == 6.0 7 | --------------------------------------------------------------------------------