From 21d358ae367058e7e8858dbbf6470220724c681c Mon Sep 17 00:00:00 2001 From: Michael Panchenko Date: Fri, 1 Mar 2024 17:49:40 +0100 Subject: [PATCH] Initial commit with pymetrius --- .github/workflows/lint_and_docs.yaml | 52 + .github/workflows/publish.yaml | 27 + .github/workflows/pytest.yml | 45 + .github/workflows/windows_mac_test.yml | 40 + .gitignore | 138 + .pre-commit-config.yaml | 52 + CHANGELOG.md | 10 + README.md | 8 + config.json | 10 + config.py | 45 + data/.gitignore | 2 + data/raw/hello.txt | 2 + docs/.gitignore | 5 + docs/01_tutorials/00_example.rst | 11 + docs/01_tutorials/index.rst | 2 + docs/02_notebooks/00_intro.md | 4 + docs/02_notebooks/01_library_example.ipynb | 128 + docs/02_notebooks/02_config_example.ipynb | 97 + docs/04_contributing/04_contributing.rst | 91 + docs/_config.yml | 143 + docs/_static/css/style.css | 138 + docs/_static/js/require.min.js | 5 + docs/autogen_rst.py | 151 + docs/bibtex.json | 10 + docs/create_toc.py | 8 + docs/index.rst | 15 + docs/nbstripout.py | 10 + docs/refs.bib | 21 + docs/spelling_wordlist.txt | 20 + poetry.lock | 4212 +++++++++++++++++ public/.gitignore | 0 pyproject.toml | 157 + scripts/run_sample.py | 5 + src/__init__.py | 1 + src/armscan_env/__init__.py | 1 + src/armscan_env/sample_module.py | 25 + src/armscan_env/sample_package/__init__.py | 0 .../sample_package/sample_module.py | 6 + test/armscan_env/conftest.py | 11 + .../test_lazy_fixture_demonstration.py | 17 + test/armscan_env/test_sample_class.py | 8 + 41 files changed, 5733 insertions(+) create mode 100644 .github/workflows/lint_and_docs.yaml create mode 100644 .github/workflows/publish.yaml create mode 100644 .github/workflows/pytest.yml create mode 100644 .github/workflows/windows_mac_test.yml create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 CHANGELOG.md create mode 100644 README.md create mode 100644 config.json create mode 100644 config.py create mode 100644 data/.gitignore create mode 100644 data/raw/hello.txt create mode 100644 docs/.gitignore create mode 100644 docs/01_tutorials/00_example.rst create mode 100644 docs/01_tutorials/index.rst create mode 100644 docs/02_notebooks/00_intro.md create mode 100644 docs/02_notebooks/01_library_example.ipynb create mode 100644 docs/02_notebooks/02_config_example.ipynb create mode 100644 docs/04_contributing/04_contributing.rst create mode 100644 docs/_config.yml create mode 100644 docs/_static/css/style.css create mode 100644 docs/_static/js/require.min.js create mode 100644 docs/autogen_rst.py create mode 100644 docs/bibtex.json create mode 100644 docs/create_toc.py create mode 100644 docs/index.rst create mode 100644 docs/nbstripout.py create mode 100644 docs/refs.bib create mode 100644 docs/spelling_wordlist.txt create mode 100644 poetry.lock create mode 100644 public/.gitignore create mode 100644 pyproject.toml create mode 100644 scripts/run_sample.py create mode 100644 src/__init__.py create mode 100644 src/armscan_env/__init__.py create mode 100644 src/armscan_env/sample_module.py create mode 100644 src/armscan_env/sample_package/__init__.py create mode 100644 src/armscan_env/sample_package/sample_module.py create mode 100644 test/armscan_env/conftest.py create mode 100644 test/armscan_env/test_lazy_fixture_demonstration.py create mode 100644 test/armscan_env/test_sample_class.py diff --git a/.github/workflows/lint_and_docs.yaml b/.github/workflows/lint_and_docs.yaml new file mode 100644 index 0000000..12d5f97 --- /dev/null +++ b/.github/workflows/lint_and_docs.yaml @@ -0,0 +1,52 @@ +name: PEP8, Types and Docs Check + +on: [push, pull_request] + +jobs: + check: + runs-on: ubuntu-latest + steps: + - name: Cancel previous run + uses: styfle/cancel-workflow-action@0.11.0 + with: + access_token: ${{ github.token }} + - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: 3.11 + # use poetry and cache installed packages, see https://github.com/marketplace/actions/python-poetry-action + - name: Install poetry + uses: abatilo/actions-poetry@v2 + - name: Setup a local virtual environment (if no poetry.toml file) + run: | + poetry config virtualenvs.create true --local + poetry config virtualenvs.in-project true --local + - uses: actions/cache@v3 + name: Define a cache for the virtual environment based on the dependencies lock file + with: + path: ./.venv + key: venv-${{ hashFiles('poetry.lock') }} + - name: Install the project dependencies + run: | + poetry install --with dev + - name: Lint + run: poetry run poe lint + - name: Types + run: poetry run poe type-check + - name: Docs + run: poetry run poe doc-build + - name: Prepare Pages + if: github.ref == 'refs/heads/main' + run: | + mv docs/_build/* public/ + - name: Deploy Pages + uses: JamesIves/github-pages-deploy-action@3.7.1 + if: github.ref == 'refs/heads/main' + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + BRANCH: gh-pages + FOLDER: public + TARGET_FOLDER: . + CLEAN: true + SINGLE_COMMIT: true \ No newline at end of file diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml new file mode 100644 index 0000000..74586aa --- /dev/null +++ b/.github/workflows/publish.yaml @@ -0,0 +1,27 @@ +name: Upload Python Package + +on: + release: + types: [created] + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v1 + with: + python-version: 3.11 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install setuptools wheel twine + - name: Build and publish + env: + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} + run: | + if [ -z "${PYPI_TOKEN}" ]; then echo "Set the PYPI_TOKEN variable in your repository secrets"; exit 1; fi + poetry config pypi-token.pypi $PYPI_TOKEN + poetry config repositories.pypi https://pypi.org/legacy + poetry publish --build --repository pypi diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 0000000..a5239a0 --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,45 @@ +name: Ubuntu + +on: [push, pull_request] + +jobs: + cpu: + runs-on: ubuntu-latest + if: "!contains(github.event.head_commit.message, 'ci skip')" + strategy: + matrix: + python-version: [3.11] + steps: + - name: Cancel previous run + uses: styfle/cancel-workflow-action@0.11.0 + with: + access_token: ${{ github.token }} + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + # use poetry and cache installed packages, see https://github.com/marketplace/actions/python-poetry-action + - name: Install poetry + uses: abatilo/actions-poetry@v2 + - name: Setup a local virtual environment (if no poetry.toml file) + run: | + poetry config virtualenvs.create true --local + poetry config virtualenvs.in-project true --local + - uses: actions/cache@v3 + name: Define a cache for the virtual environment based on the dependencies lock file + with: + path: ./.venv + key: venv-${{ hashFiles('poetry.lock') }} + - name: Install the project dependencies + run: poetry install --with dev + - name: Test with pytest + run: poetry run poe test + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v1 + with: + token: ${{ secrets.CODECOV }} + file: ./coverage.xml + flags: unittests + name: codecov-umbrella + fail_ci_if_error: false diff --git a/.github/workflows/windows_mac_test.yml b/.github/workflows/windows_mac_test.yml new file mode 100644 index 0000000..00ad107 --- /dev/null +++ b/.github/workflows/windows_mac_test.yml @@ -0,0 +1,40 @@ +name: Windows/MacOS + +on: [push, pull_request] + +jobs: + cpu-extra: + runs-on: ${{ matrix.os }} + if: "!contains(github.event.head_commit.message, 'ci skip')" + strategy: + matrix: + os: [macos-latest, windows-latest] + python-version: [3.11] + steps: + - name: Cancel previous run + uses: styfle/cancel-workflow-action@0.11.0 + with: + access_token: ${{ github.token }} + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + # use poetry and cache installed packages, see https://github.com/marketplace/actions/python-poetry-action + - name: Install poetry + uses: abatilo/actions-poetry@v2 + - name: Setup a local virtual environment (if no poetry.toml file) + run: | + poetry config virtualenvs.create true --local + poetry config virtualenvs.in-project true --local + - uses: actions/cache@v3 + name: Define a cache for the virtual environment based on the dependencies lock file + with: + path: ./.venv + key: venv-${{ hashFiles('poetry.lock') }} + - name: Install the project dependencies + # ugly as hell, but well... + # see https://github.com/python-poetry/poetry/issues/7611 + run: poetry install --with dev || poetry install --with dev || poetry install --with dev + - name: Test with pytest + run: poetry run poe test-subset diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9dc8fd6 --- /dev/null +++ b/.gitignore @@ -0,0 +1,138 @@ +# +.idea +config_local.json +temp + +# 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/ + +# reports +pylint.html +.pylint.d diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..32f3350 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,52 @@ +default_install_hook_types: [commit-msg, pre-commit] +default_stages: [commit, manual] +fail_fast: false +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-added-large-files + - repo: local + hooks: + - id: ruff + name: ruff + entry: poetry run ruff + require_serial: true + language: system + types: [python] + - id: ruff-nb + name: ruff-nb + entry: poetry run nbqa ruff . + require_serial: true + language: system + pass_filenames: false + types: [python] + - id: black + name: black + entry: poetry run black + require_serial: true + language: system + types: [python] + - id: poetry-check + name: poetry check + entry: poetry check + language: system + files: pyproject.toml + pass_filenames: false + - id: poetry-lock-check + name: poetry lock check + entry: poetry check + args: [--lock] + language: system + pass_filenames: false + - id: mypy + name: mypy + entry: poetry run mypy src + # filenames should not be passed as they would collide with the config in pyproject.toml + pass_filenames: false + files: '^src(/[^/]*)*/[^/]*\.py$' + language: system + - id: mypy-nb + name: mypy-nb + entry: poetry run nbqa mypy + language: system diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..69e2e4f --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,10 @@ +# Changelog + +## 0.1.0 - Initial Release + +### Features: + +### Development: + +- Initial setup by python-library-template + diff --git a/README.md b/README.md new file mode 100644 index 0000000..cc13f61 --- /dev/null +++ b/README.md @@ -0,0 +1,8 @@ +# armscan_env + +Welcome to the armscan_env library! + + +## Contributing +Please open new issues for bugs, feature requests and extensions. See more details about the structure and +workflow in the [contributing page](CONTRIBUTING.md). \ No newline at end of file diff --git a/config.json b/config.json new file mode 100644 index 0000000..824fa0f --- /dev/null +++ b/config.json @@ -0,0 +1,10 @@ +{ + "data_raw": "./data/raw", + "data_cleaned": "./data/cleaned", + "data_processed": "./data/processed", + "data_ground_truth": "./data/ground_truth", + "visualizations": "./data/visualizations", + "artifacts": "./data/artifacts", + "temp": "./temp", + "data": "./data" +} diff --git a/config.py b/config.py new file mode 100644 index 0000000..15e6df0 --- /dev/null +++ b/config.py @@ -0,0 +1,45 @@ +"""Contains configuration utils. In its current, default form, configuration will be read from config.json and +the git-ignored file config_local.json (you have to create it yourself if you need it) and merged. The config_local.json +is a good place to keep access keys and other secrets. + +The configuration relies on runtime usage of generics, which might be unfamiliar to some python users. If you don't +fully understand what is going on here, you don't need to worry too much about it (although in that case it would be +useful to read the source code docu in accsr). In essence: + + 1. The `__Configuration` class is where you put your custom configuration getters. Since here it inherits from + `DefaultDataConfiguration`, you already have some default getter methods like `data_raw`, `data_processed` + and so on. You will probably want to extend this + class with more getters for your config needs. + A typical example that is often used at appliedAI is to include a remote storage config + (for which there is also support in accsr), with + .. code-block:: python + @property + def remote_storage(self): + return RemoteStorageConfig(**self._get_non_empty_entry("remote_storage_config")) + + but you can include anything you want. + 2. The `ConfigProvider` related things are there to provides instances of `__Configuration` without having to + reload it from disc, unless specifically desired. Essentially, it is a singleton provider. Most likely you + will not need to adjust it and just use the `get_config` function to retrieve your config. +""" + + +from accsr.config import ConfigProviderBase, DefaultDataConfiguration + + +class __Configuration(DefaultDataConfiguration): + pass + + +class ConfigProvider(ConfigProviderBase[__Configuration]): + pass + + +_config_provider = ConfigProvider() + + +def get_config(reload: bool = False) -> __Configuration: + """:param reload: if True, the configuration will be reloaded from the json files + :return: the configuration instance + """ + return _config_provider.get_config(reload=reload) diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 0000000..d90d927 --- /dev/null +++ b/data/.gitignore @@ -0,0 +1,2 @@ + * + !.gitignore \ No newline at end of file diff --git a/data/raw/hello.txt b/data/raw/hello.txt new file mode 100644 index 0000000..92160a7 --- /dev/null +++ b/data/raw/hello.txt @@ -0,0 +1,2 @@ +Place your real and sample data in the proposed directory structure. Access the files from anywhere in your +code through the corresponding configuration methods \ No newline at end of file diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..75bda11 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,5 @@ +/03_api/* +jupyter_execute +_toc.yml +.jupyter_cache +conf.py diff --git a/docs/01_tutorials/00_example.rst b/docs/01_tutorials/00_example.rst new file mode 100644 index 0000000..88ddbae --- /dev/null +++ b/docs/01_tutorials/00_example.rst @@ -0,0 +1,11 @@ +Example +======= +This is a placeholder for the example. + +Citation example +---------------- +It contains an example of citation :cite:`TURING.1950`. + +.. bibliography:: /refs.bib + :style: unsrtalpha + :filter: docname in docnames diff --git a/docs/01_tutorials/index.rst b/docs/01_tutorials/index.rst new file mode 100644 index 0000000..f08b66f --- /dev/null +++ b/docs/01_tutorials/index.rst @@ -0,0 +1,2 @@ +Tutorials +========= \ No newline at end of file diff --git a/docs/02_notebooks/00_intro.md b/docs/02_notebooks/00_intro.md new file mode 100644 index 0000000..0b8b6d3 --- /dev/null +++ b/docs/02_notebooks/00_intro.md @@ -0,0 +1,4 @@ +# Notebook Tutorials + +Here is a collection of executable tutorials for armscan_env. +You can run them directly in colab, or download them and run them locally. diff --git a/docs/02_notebooks/01_library_example.ipynb b/docs/02_notebooks/01_library_example.ipynb new file mode 100644 index 0000000..c25188a --- /dev/null +++ b/docs/02_notebooks/01_library_example.ipynb @@ -0,0 +1,128 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# The role of notebooks\n", + "\n", + "Notebooks are great for illustrations and examples that at the same time serve as integration tests.\n", + "In this library template, notebooks will be executed with pytest (thus on every\n", + "commit in your CI/CD pipeline). The results of the executions will be saved to the docs directory and converted to\n", + "static websites through nbconvert. The static websites are then added to the documentation under the\n", + "_Guides and Tutorials_ section. These websites will be deployed to Github pages on push to develop." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Before running the notebook\n", + "\n", + "Install the library and its dependencies with, if you haven't done so already\n", + "```\n", + "poetry install\n", + "```\n", + "from the root directory. You can also execute this command directly in the notebook but will need to reload the\n", + "kernel afterwards" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "pycharm": { + "name": "#%%\n" + } + }, + "outputs": [], + "source": [ + "# Here an illustration of your library\n", + "from armscan_env.sample_package.sample_module import hello_stranger\n", + "\n", + "hello_stranger()" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "pycharm": { + "name": "#%% md\n" + } + }, + "source": [ + "## Interactive Documentation\n", + "\n", + "Note that since notebooks are rendered to html+javascript, you can embed interactive components like maps, videos and\n", + "widgets into your documentation, as long as the interaction does not require re-execution of cells.\n", + "Below an example of an interactive map created with plotly {cite}`PlotlyMaps`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "pycharm": { + "name": "#%%\n" + } + }, + "outputs": [], + "source": [ + "# slightly adjusted example from https://plotly.com/python/mapbox-layers/\n", + "import pandas as pd\n", + "import plotly.express as px\n", + "\n", + "us_cities = pd.read_csv(\n", + " \"https://raw.githubusercontent.com/plotly/datasets/master/us-cities-top-1k.csv\",\n", + ")\n", + "\n", + "fig = px.scatter_mapbox(\n", + " us_cities,\n", + " lat=\"lat\",\n", + " lon=\"lon\",\n", + " hover_name=\"City\",\n", + " hover_data=[\"State\", \"Population\"],\n", + " color_discrete_sequence=[\"fuchsia\"],\n", + " zoom=3,\n", + " height=300,\n", + ")\n", + "\n", + "fig.update_layout(mapbox_style=\"open-street-map\", margin={\"r\": 0, \"t\": 0, \"l\": 0, \"b\": 0})\n", + "fig.show()" + ] + }, + { + "cell_type": "markdown", + "source": [ + "```{bibliography}\n", + ":style: unsrtalpha\n", + ":filter: docname in docnames\n", + "```" + ], + "metadata": { + "collapsed": false + } + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 0 +} diff --git a/docs/02_notebooks/02_config_example.ipynb b/docs/02_notebooks/02_config_example.ipynb new file mode 100644 index 0000000..2a31bc0 --- /dev/null +++ b/docs/02_notebooks/02_config_example.ipynb @@ -0,0 +1,97 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "pycharm": { + "name": "#%% md\n" + } + }, + "source": [ + "# The configuration utils\n", + "\n", + "You decided to opt in to use appliedAI's [accsr](https://github.com/appliedAI-Initiative/accsr) package to manage\n", + "configuration for you project - great choice :) In this template, you see a minimal usage of the `config.py`" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "pycharm": { + "name": "#%%\n" + } + }, + "outputs": [], + "source": [ + "# Note - this cell should be executed only once per session\n", + "\n", + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "import os\n", + "import sys\n", + "\n", + "# in order to get the config (it is not part of the library) and sane paths to data\n", + "if os.path.basename(os.getcwd()) != \"02_notebooks\":\n", + " raise Exception(\"Wrong directory. Did you execute this cell twice?\")\n", + "os.chdir(\"../..\")\n", + "sys.path.append(os.path.abspath(\".\"))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "pycharm": { + "name": "#%%\n" + } + }, + "outputs": [], + "source": [ + "from config import get_config\n", + "\n", + "c = get_config(reload=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "pycharm": { + "name": "#%%\n" + } + }, + "outputs": [], + "source": [ + "# Here an example for using the config for finding and loading files\n", + "\n", + "sample_file = c.datafile_path(\"hello.txt\", stage=c.RAW)\n", + "\n", + "with open(sample_file) as file:\n", + " print(file.read())" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 0 +} diff --git a/docs/04_contributing/04_contributing.rst b/docs/04_contributing/04_contributing.rst new file mode 100644 index 0000000..535b989 --- /dev/null +++ b/docs/04_contributing/04_contributing.rst @@ -0,0 +1,91 @@ +Contributing to armscan_env +=========================== + + +Install Develop Version +----------------------- + +armscan_env is built and managed by `poetry `_. For example, +to install all relevant requirements in editable mode you can simply call + +.. code-block:: bash + + $ poetry install --with dev + + +PEP8 Code Style Check and Formatting +---------------------------------------- + +Please set up pre-commit by running + +.. code-block:: bash + + $ pre-commit install + +in the main directory. This should make sure that your contribution is properly +formatted before every commit. + +The code is inspected and formatted by `black` and `ruff`. They are executed as +pre-commit hooks. In addition, `poe the poet` tasks are configured. +Simply run `poe` to see the available tasks. +E.g, to format and check the linting manually you can run: + +.. code-block:: bash + + $ poe format + $ poe lint + + +Type Check +---------- + +We use `mypy `_ to check the type annotations. To check, in the main directory, run: + +.. code-block:: bash + + $ poe type-check + + +Test Locally +------------ + +This command will run automatic tests in the main directory + +.. code-block:: bash + + $ poe test + + +Documentation +------------- + +Documentations are written under the ``docs/`` directory as ReStructuredText (``.rst``) files. ``index.rst`` is the main page. A Tutorial on ReStructuredText can be found `here `_. + +API References are automatically generated by `Sphinx `_ according to the outlines under ``docs/api/`` and should be modified when any code changes. + +To compile documentation into webpage, run + +.. code-block:: bash + + $ poe doc-build + +The generated webpage is in ``docs/_build`` and can be viewed with browser (http://0.0.0.0:8000/). + + +Documentation Generation Test +----------------------------- + +We have the following three documentation tests: + +1. pydocstyle (as part of ruff): test all docstring under ``armscan_env/``; + +2. doc8 (as part of ruff): test ReStructuredText format; + +3. sphinx spelling and test: test if there is any error/warning when generating front-end html documentation. + +To check, in the main directory, run: + +.. code-block:: bash + + $ poe lint + $ poe doc-build diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000..8a98a58 --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,143 @@ +# Book settings +# Learn more at https://jupyterbook.org/customize/config.html + +####################################################################################### +# A default configuration that will be loaded for all jupyter books +# Users are expected to override these values in their own `_config.yml` file. +# This is also the "master list" of all allowed keys and values. + +####################################################################################### +# Book settings +title : armscan_env Documentation # The title of the book. Will be placed in the left navbar. +author : armscan_env contributors # The author of the book +copyright : "" # Copyright year to be placed in the footer +logo : "" # A path to the book logo +# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb") +exclude_patterns : ['**.ipynb_checkpoints', '.DS_Store', 'Thumbs.db', '_build', 'jupyter_execute', '.jupyter_cache', '.pytest_cache', 'docs/autogen_rst.py', 'docs/create_toc.py'] +# Auto-exclude files not in the toc +only_build_toc_files : false + +####################################################################################### +# Execution settings +execute: + execute_notebooks : cache # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off") + cache : "" # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/` + exclude_patterns : [] # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time) + timeout : -1 # The maximum time (in seconds) each notebook cell is allowed to run. + run_in_temp : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd), + # otherwise the notebook's parent directory will be the cwd. + allow_errors : false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run. + stderr_output : show # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe' + +####################################################################################### +# Parse and render settings +parse: + myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html + - amsmath + - colon_fence + # - deflist + - dollarmath + # - html_admonition + # - html_image + - linkify + # - replacements + # - smartquotes + - substitution + - tasklist + myst_url_schemes: [ mailto, http, https ] # URI schemes that will be recognised as external URLs in Markdown links + myst_dmath_double_inline: true # Allow display math ($$) within an inline context + +####################################################################################### +# HTML-specific settings +html: + favicon : "" # A path to a favicon image + use_edit_page_button : false # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in + use_repository_button : false # Whether to add a link to your repository button + use_issues_button : false # Whether to add an "open an issue" button + use_multitoc_numbering : true # Continuous numbering across parts/chapters + extra_footer : "" + google_analytics_id : "" # A GA id that can be used to track book views. + home_page_in_navbar : true # Whether to include your home page in the left Navigation Bar + baseurl : "https://github.com/appliedAI-Initiative/armscan_env" + analytics: + + comments: + hypothesis : false + utterances : false + announcement : "" # A banner announcement at the top of the site. + +####################################################################################### +# LaTeX-specific settings +latex: + latex_engine : pdflatex # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex' + use_jupyterbook_latex : true # use sphinx-jupyterbook-latex for pdf builds as default + targetname : book.tex +# Add a bibtex file so that we can create citations +bibtex_bibfiles: + - refs.bib + +####################################################################################### +# Launch button settings +launch_buttons: + notebook_interface : classic # The interface interactive links will activate ["classic", "jupyterlab"] + binderhub_url : "" # The URL of the BinderHub (e.g., https://mybinder.org) + jupyterhub_url : "" # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu) + thebe : false # Add a thebe button to pages (requires the repository to run on Binder) + colab_url : "https://colab.research.google.com" + +repository: + url : https://github.com/appliedAI-Initiative/armscan_env # The URL to your book's repository + path_to_book : docs # A path to your book's folder, relative to the repository root. + branch : main # Which branch of the repository should be used when creating links + +####################################################################################### +# Advanced and power-user settings +sphinx: + extra_extensions : + - sphinx.ext.autodoc + - sphinx.ext.viewcode + - sphinx_toolbox.more_autodoc.sourcelink + - sphinxcontrib.spelling + local_extensions : # A list of local extensions to load by sphinx specified by "name: path" items + recursive_update : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update (false) + config : # key-value pairs to directly over-ride the Sphinx configuration + autodoc_typehints_format: "short" + suppress_warnings: ["mystnb.unknown_mime_type"] # needed for plotly rendering + autodoc_show_sourcelink: True + add_module_names: False + github_username: Carlo Cagnetta} + github_repository: armscan_env + python_use_unqualified_type_names: True + nb_mime_priority_overrides: [ + [ 'html', 'application/vnd.jupyter.widget-view+json', 10 ], + [ 'html', 'application/javascript', 20 ], + [ 'html', 'text/html', 30 ], + [ 'html', 'text/latex', 40 ], + [ 'html', 'image/svg+xml', 50 ], + [ 'html', 'image/png', 60 ], + [ 'html', 'image/jpeg', 70 ], + [ 'html', 'text/markdown', 80 ], + [ 'html', 'text/plain', 90 ], + [ 'spelling', 'application/vnd.jupyter.widget-view+json', 10 ], + [ 'spelling', 'application/javascript', 20 ], + [ 'spelling', 'text/html', 30 ], + [ 'spelling', 'text/latex', 40 ], + [ 'spelling', 'image/svg+xml', 50 ], + [ 'spelling', 'image/png', 60 ], + [ 'spelling', 'image/jpeg', 70 ], + [ 'spelling', 'text/markdown', 80 ], + [ 'spelling', 'text/plain', 90 ], + ] + mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js + mathjax3_config: + loader: { load: [ '[tex]/configmacros' ] } + tex: + packages: { '[+]': [ 'configmacros' ] } + macros: + vect: ["{\\mathbf{\\boldsymbol{#1}} }", 1] + E: "{\\mathbb{E}}" + P: "{\\mathbb{P}}" + R: "{\\mathbb{R}}" + abs: ["{\\left| #1 \\right|}", 1] + simpl: ["{\\Delta^{#1} }", 1] + amax: "{\\text{argmax}}" \ No newline at end of file diff --git a/docs/_static/css/style.css b/docs/_static/css/style.css new file mode 100644 index 0000000..e929c46 --- /dev/null +++ b/docs/_static/css/style.css @@ -0,0 +1,138 @@ +body { + font-family: "Lato","proxima-nova","Helvetica Neue",Arial,sans-serif; +} + +/* Default header fonts are ugly */ +h1, h2, .rst-content .toctree-wrapper p.caption, h3, h4, h5, h6, legend, p.caption { + font-family: "Lato","proxima-nova","Helvetica Neue",Arial,sans-serif; +} + +/* Use white for docs background */ +.wy-side-nav-search { + background-color: #fff; +} + +.wy-nav-content { + max-width: 1200px !important; +} + +.wy-nav-content-wrap, .wy-menu li.current > a { + background-color: #fff; +} + +.wy-side-nav-search>a img.logo { + width: 80%; + margin-top: 10px; +} + +@media screen and (min-width: 1400px) { + .wy-nav-content-wrap { + background-color: #fff; + } + + .wy-nav-content { + background-color: #fff; + } +} + +/* Fixes for mobile */ +.wy-nav-top { + background-color: #fff; + background-repeat: no-repeat; + background-position: center; + padding: 0; + margin: 0.4045em 0.809em; + color: #333; +} + +.wy-nav-top > a { + display: none; +} + +@media screen and (max-width: 768px) { + .wy-side-nav-search>a img.logo { + height: 60px; + } +} + +/* This is needed to ensure that logo above search scales properly */ +.wy-side-nav-search a { + display: block; +} + +/* This ensures that multiple constructors will remain in separate lines. */ +.rst-content dl:not(.docutils) dt { + display: table; +} + +/* Use our red for literals (it's very similar to the original color) */ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #4692BC; +} + +.rst-content tt.xref, a .rst-content tt, .rst-content tt.xref, +.rst-content code.xref, a .rst-content tt, a .rst-content code { + color: #404040; +} + +/* Change link colors (except for the menu) */ + +a { + color: #4692BC; +} + +a:hover { + color: #4692BC; +} + + +a:visited { + color: #4692BC; +} + +.wy-menu a { + color: #b3b3b3; +} + +.wy-menu a:hover { + color: #b3b3b3; +} + +/* Default footer text is quite big */ +footer { + font-size: 80%; +} + +footer .rst-footer-buttons { + font-size: 125%; /* revert footer settings - 1/80% = 125% */ +} + +footer p { + font-size: 100%; +} + +.ethical-rtd { + display: none; +} + +.ethical-fixedfooter { + display: none; +} + +.ethical-content { + display: none; +} + +/* For hidden headers that appear in TOC tree */ +/* see http://stackoverflow.com/a/32363545/3343043 */ +.rst-content .hidden-section { + display: none; +} + +nav .hidden-section { + display: inherit; +} + +.wy-side-nav-search>div.version { + color: #000; +} diff --git a/docs/_static/js/require.min.js b/docs/_static/js/require.min.js new file mode 100644 index 0000000..a4203f0 --- /dev/null +++ b/docs/_static/js/require.min.js @@ -0,0 +1,5 @@ +/** vim: et:ts=4:sw=4:sts=4 + * @license RequireJS 2.3.6 Copyright jQuery Foundation and other contributors. + * Released under MIT license, https://github.com/requirejs/requirejs/blob/master/LICENSE + */ +var requirejs,require,define;!function(global,setTimeout){var req,s,head,baseElement,dataMain,src,interactiveScript,currentlyAddingScript,mainScript,subPath,version="2.3.6",commentRegExp=/\/\*[\s\S]*?\*\/|([^:"'=]|^)\/\/.*$/gm,cjsRequireRegExp=/[^.]\s*require\s*\(\s*["']([^'"\s]+)["']\s*\)/g,jsSuffixRegExp=/\.js$/,currDirRegExp=/^\.\//,op=Object.prototype,ostring=op.toString,hasOwn=op.hasOwnProperty,isBrowser=!("undefined"==typeof window||"undefined"==typeof navigator||!window.document),isWebWorker=!isBrowser&&"undefined"!=typeof importScripts,readyRegExp=isBrowser&&"PLAYSTATION 3"===navigator.platform?/^complete$/:/^(complete|loaded)$/,defContextName="_",isOpera="undefined"!=typeof opera&&"[object Opera]"===opera.toString(),contexts={},cfg={},globalDefQueue=[],useInteractive=!1;function commentReplace(e,t){return t||""}function isFunction(e){return"[object Function]"===ostring.call(e)}function isArray(e){return"[object Array]"===ostring.call(e)}function each(e,t){var i;if(e)for(i=0;i" + :param clean: whether to completely clean the target directory beforehand, removing any existing .rst files + :param overwrite: whether to overwrite existing rst files. This should be used with caution as it will delete + all manual changes to documentation files + :package_prefix: a prefix to prepend to each module (for the case where the src_root is not the base package), + which, if not empty, should end with a "." + :return: + """ + rst_root = os.path.abspath(rst_root) + + if clean and os.path.isdir(rst_root): + shutil.rmtree(rst_root) + + base_package_name = package_prefix + os.path.basename(src_root) + + # TODO: reduce duplication with same logic for subpackages below + files_in_dir = os.listdir(src_root) + module_names = [f[:-3] for f in files_in_dir if f.endswith(".py") and not f.startswith("_")] + subdir_refs = [ + f"{f}/index" + for f in files_in_dir + if os.path.isdir(os.path.join(src_root, f)) and not f.startswith("_") + ] + package_index_rst_path = os.path.join( + rst_root, + "index.rst", + ) + log.info(f"Writing {package_index_rst_path}") + write_to_file( + index_template( + base_package_name, + doc_references=module_names + subdir_refs, + text_prefix=_SUBTITLE, + ), + package_index_rst_path, + ) + + for root, dirnames, filenames in os.walk(src_root): + if os.path.basename(root).startswith("_"): + continue + base_package_relpath = os.path.relpath(root, start=src_root) + base_package_qualname = package_prefix + os.path.relpath( + root, + start=os.path.dirname(src_root), + ).replace(os.path.sep, ".") + + for dirname in dirnames: + if dirname.startswith("_"): + log.debug(f"Skipping {dirname}") + continue + files_in_dir = os.listdir(os.path.join(root, dirname)) + module_names = [ + f[:-3] for f in files_in_dir if f.endswith(".py") and not f.startswith("_") + ] + subdir_refs = [ + f"{f}/index" + for f in files_in_dir + if os.path.isdir(os.path.join(root, dirname, f)) and not f.startswith("_") + ] + if not module_names: + log.debug(f"Skipping {dirname} as it does not contain any .py files") + continue + package_qualname = f"{base_package_qualname}.{dirname}" + package_index_rst_path = os.path.join( + rst_root, + base_package_relpath, + dirname, + "index.rst", + ) + log.info(f"Writing {package_index_rst_path}") + write_to_file( + index_template(package_qualname, doc_references=module_names + subdir_refs), + package_index_rst_path, + ) + + for filename in filenames: + base_name, ext = os.path.splitext(filename) + if ext == ".py" and not filename.startswith("_"): + module_qualname = f"{base_package_qualname}.{filename[:-3]}" + + module_rst_path = os.path.join(rst_root, base_package_relpath, f"{base_name}.rst") + if os.path.exists(module_rst_path) and not overwrite: + log.debug(f"{module_rst_path} already exists, skipping it") + + log.info(f"Writing module documentation to {module_rst_path}") + write_to_file(module_template(module_qualname), module_rst_path) + + +if __name__ == "__main__": + logging.basicConfig(level=logging.INFO) + docs_root = Path(__file__).parent + make_rst( + docs_root / ".." / "src" / "armscan_env", + docs_root / "03_api", + clean=True, + ) diff --git a/docs/bibtex.json b/docs/bibtex.json new file mode 100644 index 0000000..175e65e --- /dev/null +++ b/docs/bibtex.json @@ -0,0 +1,10 @@ +{ + "cited": { + "01_tutorials/00_example": [ + "TURING.1950" + ], + "02_notebooks/00_example": [ + "PlotlyMaps" + ] + } +} \ No newline at end of file diff --git a/docs/create_toc.py b/docs/create_toc.py new file mode 100644 index 0000000..3e1779c --- /dev/null +++ b/docs/create_toc.py @@ -0,0 +1,8 @@ +import os +from pathlib import Path + +# This script provides a platform-independent way of making the jupyter-book call (used in pyproject.toml) +toc_file = Path(__file__).parent / "_toc.yml" +cmd = f"jupyter-book toc from-project docs -e .rst -e .md -e .ipynb >{toc_file}" +print(cmd) +os.system(cmd) diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..8b7f4a3 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,15 @@ +Welcome to armscan_env! +========================================= + +Welcome to the armscan_env library. +See the project's repository_ for more information. + +.. _repository: https://github.com/appliedAI-Initiative/armscan_env + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/nbstripout.py b/docs/nbstripout.py new file mode 100644 index 0000000..95d4193 --- /dev/null +++ b/docs/nbstripout.py @@ -0,0 +1,10 @@ +"""Implements a platform-independent way of calling nbstripout (used in pyproject.toml).""" +import glob +import os +from pathlib import Path + +if __name__ == "__main__": + docs_dir = Path(__file__).parent + for path in glob.glob(str(docs_dir / "02_notebooks" / "*.ipynb")): + cmd = f"nbstripout {path}" + os.system(cmd) diff --git a/docs/refs.bib b/docs/refs.bib new file mode 100644 index 0000000..98c79a2 --- /dev/null +++ b/docs/refs.bib @@ -0,0 +1,21 @@ +@article{TURING.1950, + author = {TURING, A. M.}, + year = {1950}, + title = {I.---COMPUTING MACHINERY AND INTELLIGENCE}, + pages = {433--460}, + volume = {LIX}, + number = {236}, + issn = {0026-4423}, + journal = {Mind}, + doi = {10.1093/mind/LIX.236.433}, + file = {ICOMPUTING MACHINERY AND INTELLIGENCE:Attachments/ICOMPUTING MACHINERY AND INTELLIGENCE.pdf:application/pdf} +} + + +@misc{PlotlyMaps, + abstract = {Plotly's}, + year = {2/16/2024}, + title = {Maps}, + url = {https://plotly.com/python/maps/}, + urldate = {2/28/2024} +} \ No newline at end of file diff --git a/docs/spelling_wordlist.txt b/docs/spelling_wordlist.txt new file mode 100644 index 0000000..1936276 --- /dev/null +++ b/docs/spelling_wordlist.txt @@ -0,0 +1,20 @@ +armscan_env +armscan_env +Carlo Cagnetta + +appliedAI +autogenerated +colab +docstring +docstrings +Github +html +init +javascript +pre +pycharm +pydocstyle +submodules +subpackages +utils +webpage \ No newline at end of file diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..0a000ef --- /dev/null +++ b/poetry.lock @@ -0,0 +1,4212 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "accessible-pygments" +version = "0.0.4" +description = "A collection of accessible pygments styles" +optional = false +python-versions = "*" +files = [ + {file = "accessible-pygments-0.0.4.tar.gz", hash = "sha256:e7b57a9b15958e9601c7e9eb07a440c813283545a20973f2574a5f453d0e953e"}, + {file = "accessible_pygments-0.0.4-py2.py3-none-any.whl", hash = "sha256:416c6d8c1ea1c5ad8701903a20fcedf953c6e720d64f33dc47bfb2d3f2fa4e8d"}, +] + +[package.dependencies] +pygments = ">=1.5" + +[[package]] +name = "accsr" +version = "0.4.6" +description = "Utils for accessing data from anywhere" +optional = false +python-versions = ">=3.8" +files = [ + {file = "accsr-0.4.6-py3-none-any.whl", hash = "sha256:7de4ca0a89924ddfa27c67b4b36561f4638c1fffddace883927bcb876d787e3f"}, + {file = "accsr-0.4.6.tar.gz", hash = "sha256:59d27b3e9ccdb26712381adc8ffe4228f2518661b3ecf4446af9c3e1d7989db5"}, +] + +[package.dependencies] +apache-libcloud = "3.7.0" +numpy = ">1" +pyyaml = "6.0.1" +tqdm = ">=4.48.2" + +[package.extras] +docs = ["Sphinx (==3.2.1)", "ipython", "nbsphinx", "sphinx-rtd-theme", "sphinxcontrib-websupport (==1.2.4)"] +test = ["pytest"] + +[[package]] +name = "alabaster" +version = "0.7.16" +description = "A light, configurable Sphinx theme" +optional = false +python-versions = ">=3.9" +files = [ + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, +] + +[[package]] +name = "anyio" +version = "4.3.0" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +optional = false +python-versions = ">=3.8" +files = [ + {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, + {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, +] + +[package.dependencies] +idna = ">=2.8" +sniffio = ">=1.1" + +[package.extras] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] + +[[package]] +name = "apache-libcloud" +version = "3.7.0" +description = "A standard Python library that abstracts away differences among multiple cloud provider APIs. 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b/pyproject.toml new file mode 100644 index 0000000..6400cbe --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,157 @@ +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + +[tool.poetry] +name = "armscan_env" +version = "0.1.0" +description = "" +authors = ["Carlo Cagnetta ", "Michael Panchenko "] +license = "MIT" +readme = "README.md" +homepage = "https://github.com/appliedAI-Initiative/armscan_env" +classifiers = [ + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3.11", +] +exclude = ["test/*", "examples/*", "docs/*"] + +[tool.poetry.dependencies] +python = "^3.11" +accsr = "^0.4.6" +pandas = "^2.2.1" +plotly = "^5.19.0" +pytest = "^8.0.2" +pytest-lazy-fixtures = "^1.0.5" + +[tool.poetry.group.dev] +optional = true +[tool.poetry.group.dev.dependencies] +black = { version = "^23.7.0", extras = ["jupyter"] } +docutils = "0.20.1" +jinja2 = "*" +jupyter = "^1.0.0" +jupyter-book = "^1.0.0" +mypy = "^1.4.1" +nbqa = 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+[tool.nbqa.exclude] +ruff = "\\.jupyter_cache|jupyter_execute" +mypy = "\\.jupyter_cache|jupyter_execute" + +[tool.ruff] +select = [ + "ASYNC", "B", "C4", "C90", "COM", "D", "DTZ", "E", "F", "FLY", "G", "I", "ISC", "PIE", "PLC", "PLE", "PLW", "RET", "RUF", "RSE", "SIM", "TID", "UP", "W", "YTT", +] +ignore = [ + "E501", # line too long. black does a good enough job + "E741", # variable names like "l". this isn't a huge problem + "B008", # do not perform function calls in argument defaults. we do this sometimes + "B011", # assert false. we don't use python -O + "B028", # we don't need explicit stacklevel for warnings + "D100", "D101", "D102", "D104", "D105", "D107", "D203", "D213", "D401", "D402", # docstring stuff + "DTZ005", # we don't need that + # remaining rules from https://github.com/psf/black/blob/main/.flake8 (except W503) + # this is a simplified version of config, making vscode plugin happy + "E402", "E501", "E701", "E731", "C408", "E203", + # Logging statement uses f-string warning + "G004", + # Unnecessary `elif` after `return` statement + "RET505", + "D106", # undocumented public nested class + "D205", # blank line after summary (prevents summary-only docstrings, which makes no sense) +] +unfixable = [ + +] +extend-fixable = [ + "F401", # unused import + "B905", # bugbear +] + +target-version = "py311" + +[tool.ruff.mccabe] +max-complexity = 20 + +[tool.ruff.per-file-ignores] +"test/**" = ["D103"] +"docs/**" = ["D103"] +"examples/**" = ["D103"] + +[tool.poetry_bumpversion.file."armscan_env/__init__.py"] + +[tool.poetry-sort] +move-optionals-to-bottom = true + +[tool.poe.env] +PYDEVD_DISABLE_FILE_VALIDATION="1" +# keep relevant parts in sync with pre-commit +[tool.poe.tasks] # https://github.com/nat-n/poethepoet +test = "pytest test --cov=armscan_env --cov-report=xml --cov-report=term-missing --durations=0 -v --color=yes" +# Adjust to a smaller set of tests if appropriate +test-subset = "pytest test --color=yes" +_black_check = "black --check ." +_ruff_check = "ruff check ." +_ruff_check_nb = "nbqa ruff docs" +_black_format = "black ." +_ruff_format = "ruff --fix ." +_ruff_format_nb = "nbqa ruff --fix docs" +lint = ["_black_check", "_ruff_check", "_ruff_check_nb"] +_poetry_install_sort_plugin = "poetry self add poetry-plugin-sort" +_poetry_sort = "poetry sort" +clean-nbs = "python docs/nbstripout.py" +format = ["_black_format", "_ruff_format", "_ruff_format_nb", "_poetry_install_sort_plugin", "_poetry_sort"] +_autogen_rst = "python docs/autogen_rst.py" +_sphinx_build = "sphinx-build -W -b html docs docs/_build" +_jb_generate_toc = "python docs/create_toc.py" +_jb_generate_config = "jupyter-book config sphinx docs/" +doc-clean = "rm -rf docs/_build" +doc-generate-files = ["_autogen_rst", "_jb_generate_toc", "_jb_generate_config"] +doc-spellcheck = "sphinx-build -W -b spelling docs docs/_build" +doc-build = ["doc-generate-files", "doc-spellcheck", "_sphinx_build"] +_mypy = "mypy src" +_mypy_nb = "nbqa mypy docs" +type-check = ["_mypy", "_mypy_nb"] diff --git a/scripts/run_sample.py b/scripts/run_sample.py new file mode 100644 index 0000000..4913810 --- /dev/null +++ b/scripts/run_sample.py @@ -0,0 +1,5 @@ +from armscan_env.sample_module import SampleClass + +if __name__ == "__main__": + print(SampleClass().sample_method("Carlo Cagnetta")) + print("Your new library project armscan_env is waiting for you!") diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..9792e10 --- /dev/null +++ b/src/__init__.py @@ -0,0 +1 @@ +__version__ = "0.1.0.dev1" diff --git a/src/armscan_env/__init__.py b/src/armscan_env/__init__.py new file mode 100644 index 0000000..f1acdf7 --- /dev/null +++ b/src/armscan_env/__init__.py @@ -0,0 +1 @@ +__version__ = "0.1.0-dev1" diff --git a/src/armscan_env/sample_module.py b/src/armscan_env/sample_module.py new file mode 100644 index 0000000..b562663 --- /dev/null +++ b/src/armscan_env/sample_module.py @@ -0,0 +1,25 @@ +"""Top-level module.""" + + +class SampleClass: + """Sample docstring. Note that init docstrings should be underneath the class and not the init method itself + (this looks prettier in sphinx). They still will be rendered correctly in pycharm's quick documentation. + + :param param: some parameter + """ + + def __init__(self, param: str | None = None): + self.hello = "hello " + self.param = param + + def sample_method(self, name: str) -> str: + """>>> from armscan_env.sample_module import SampleClass + >>> + >>> greeter = SampleClass() + >>> greeter.sample_method("Carlo Cagnetta") + 'hello Carlo Cagnetta'. + + :param name: + :return: + """ + return self.hello + name diff --git a/src/armscan_env/sample_package/__init__.py b/src/armscan_env/sample_package/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/armscan_env/sample_package/sample_module.py b/src/armscan_env/sample_package/sample_module.py new file mode 100644 index 0000000..8902797 --- /dev/null +++ b/src/armscan_env/sample_package/sample_module.py @@ -0,0 +1,6 @@ +"""Module in a separate package.""" + + +def hello_stranger() -> None: + """Hello.""" + print("Hello from a separate package!") diff --git a/test/armscan_env/conftest.py b/test/armscan_env/conftest.py new file mode 100644 index 0000000..a2d2dfb --- /dev/null +++ b/test/armscan_env/conftest.py @@ -0,0 +1,11 @@ +import pytest + + +@pytest.fixture() +def fixture_1(): + return 1 + + +@pytest.fixture() +def fixture_2(): + return 2 diff --git a/test/armscan_env/test_lazy_fixture_demonstration.py b/test/armscan_env/test_lazy_fixture_demonstration.py new file mode 100644 index 0000000..7a32ae4 --- /dev/null +++ b/test/armscan_env/test_lazy_fixture_demonstration.py @@ -0,0 +1,17 @@ +# Here we demonstrate a convenient pytest plugin called lazy fixture. +# It allows to use fixtures within test parametrization, which is especially useful +# if you want to test the method on different input data. Unfortunately, this forces one to use string +# interfaces for fixture but this is a price one might be willing to pay. +import pytest +from pytest_lazy_fixtures import lf + + +@pytest.mark.parametrize( + "fixture, result", + [ + (lf("fixture_1"), 1), + (lf("fixture_2"), 2), + ], +) +def test_demonstrateLazyFixture(fixture, result): + assert fixture == result diff --git a/test/armscan_env/test_sample_class.py b/test/armscan_env/test_sample_class.py new file mode 100644 index 0000000..dc8a5bd --- /dev/null +++ b/test/armscan_env/test_sample_class.py @@ -0,0 +1,8 @@ +from armscan_env.sample_module import SampleClass + + +# the suggested naming convention for unit tests is test_method_name_testDescriptionInCamelCase +# this leads to a nicely readable output of pytest +def test_sample_class_attributes_greeterSaysHello(): + greeter = SampleClass() + assert greeter.hello == "hello "