Drop Python 3.7, tinker with devopsy stuff

- Relax a bunch of overly-zealous linter args - Ignore missing AssertionError in docstrings - Lock down bandit (see: tylerwince/flake8-bandit#21) - Disable strict optional - Ignore missing stubs from third-party libraries pandas,tqdm,sqlalchemy - Update lockfile - Remove unused module - Basic logging configuration (null handler) Notebooks: - Add formatting of notebooks - Add run-jupyter.sh convenience script (nosec) - Add PerfTestTemplate.ipynb
rsundqvist · Mar 11, 2022 · bec1096 · bec1096
1 parent f1d3197
commit bec1096
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -7,7 +7,7 @@ current_version = 0.1.0
 search = version = "{current_version}"
 replace = version = "{new_version}"
 
-[bumpversion:file:src/rics/__init__.py]
+[bumpversion:file:src/rics/__version__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 

diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,29 @@
+[paths]
+source = src
+
+[report]
+omit =
+    tests/*
+    src/rics/translation/fetching/*
+    src/rics/translation/dio/*
+    src/rics/_internal*
+    */exceptions.py
+
+fail_under = 99
+
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if self.debug
+    if settings.DEBUG:
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == __main__:
+    LOGGER.isEnabledFor
+    if not isinstance\(other
+
+show_missing = true
+
+[html]
+directory = htmlcov
diff --git a/.darglint b/.darglint
@@ -1,2 +1,3 @@
 [darglint]
 strictness = short
+ignore_raise=AssertionError
diff --git a/.github/workflows/pre-commit-autoupdate.yml b/.github/workflows/pre-commit-autoupdate.yml
@@ -12,10 +12,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2.3.4
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2.3.2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -11,10 +11,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2.3.4
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2.3.2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install system deps
         shell: bash

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -3,6 +3,7 @@ name: tests
 on:
   push:
     branches:
+     - master
   pull_request:
     branches:
 
@@ -13,10 +14,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2.3.4
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2.3.2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Linting
         run: |
@@ -30,7 +31,7 @@ jobs:
     strategy:
       matrix:
         os: [ Ubuntu, MacOS, Windows ]
-        python-version: [ '3.7', '3.8', '3.9', '3.10' ]
+        python-version: [ '3.8', '3.9', '3.10' ]
       fail-fast: true
     steps:
       - uses: actions/checkout@v2.3.4
@@ -72,10 +73,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2.3.4
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2.3.2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install system deps
         shell: bash

diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,12 @@
+codecov
+
+# Data
+*.pkl
+*.gz
+*.zip
+*.csv
+jupyterlab/data-cache/*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/.idea/runConfigurations/run_all_tests.xml b/.idea/runConfigurations/run_all_tests.xml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -35,6 +35,8 @@ repos:
           'flake8-bugbear~=21.9.2',
           'flake8-annotations~=2.6.2',
           'flake8-docstrings~=1.6.0',
-          'flake8-bandit~=2.1.2',
-          'darglint~=1.8.0'
+          'flake8-bandit==2.1.2',
+          'flake8-bandit==2.1.2',
+          'bandit==1.7.2',
+          'darglint~=1.8.0',
         ]
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: pip

diff --git a/.venv/!PLACEHOLDER.md b/.venv/!PLACEHOLDER.md
@@ -0,0 +1,7 @@
+# Placeholder
+
+Ensure that venv is installed locally. If Poetry doesn't respect this, run:
+
+```bash
+poetry config virtualenvs.in-project true
+```
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+- The `rics.utils` module for various common operations
+- The `rics.translation` package for translating IDs into human-readable labels
+- The `rics.mapping` package for linking elements in multiple directions
+- The `rics.cardinality` package; enum types for `1:1`, `1:N`, `N:1`, and `M:N`
+
+
 ## [0.1.0] - 2022-02-24
 ### Added
 - First release on PyPI.

diff --git a/README.md b/README.md
@@ -1,6 +1,4 @@
-
-# Rics
-
+# Readme
 
 <div align="center">
 
@@ -20,23 +18,63 @@
 
 My personal little ML engineering library.
 
-
 * GitHub repo: <https://github.com/rsundqvist/rics.git>
 * Documentation: <https://rics.readthedocs.io>
 * Free software: MIT
 
-
 ## Features
 
 * TODO
 
-## Quickstart
-
-TODO
+## Quickstart for development
+
+### Notice
+This project uses groups for extras dependencies, which is currently a **PRERELEASE** feature (slated for `1.2`). Assuming
+poetry was installed the recommended way (see below), this can be done using:
+```bash
+url -sSL https://install.python-poetry.org/ | python -
+poetry upgrade self --prerelease --version="1.2.0a2"
+```
+
+### Setting up for local development
+Assumes a "modern" version of Ubuntu (guide written under `Ubuntu 20.04.2 LTS`) with basic dev dependencies installed.
+To get started, run the following commands:
+
+Installing the latest version of Poetry
+```bash
+curl -sSL https://install.python-poetry.org/ | python -
+```
+This is the way recommended by the Poetry project.
+
+```bash
+git clone git@github.com:rsundqvist/rics.git
+cd rics
+poetry install
+inv install-hooks
+```
+This project uses groups for extras dependencies. If installation fails, make sure that output from
+`poetry --version` is `1.2.0` or greater.
+
+### Registering the project on Codecov
+
+Probably only for forking?
+```bash
+curl -Os https://uploader.codecov.io/latest/linux/codecov
+chmod +x codecov
+```
+
+Visit https://app.codecov.io and log in, follow instructions to link the repo and get a token for private repos.
+```bash
+CODECOV_TOKEN="<from-the-website>"
+inv coverage --fmt=xml
+./codecov -t ${CODECOV_TOKEN}
+```
 
 ## Credits
 
-This package was created with [Cookiecutter][cookiecutter] and the [fedejaure/cookiecutter-modern-pypackage][cookiecutter-modern-pypackage] project template.
+This package was created with [Cookiecutter][cookiecutter] and
+the [fedejaure/cookiecutter-modern-pypackage][cookiecutter-modern-pypackage] project template.
 
 [cookiecutter]: https://github.com/cookiecutter/cookiecutter
+
 [cookiecutter-modern-pypackage]: https://github.com/fedejaure/cookiecutter-modern-pypackage
diff --git a/docs/conf.py b/docs/conf.py
@@ -13,12 +13,12 @@
 #
 import rics
 
-# -- Project information -----------------------------------------------------
+# -- Project information -------------------------------------------------------
 
 # General information about the project.
-project = "rics"
-copyright = "2022, Richard Sundqvist"  # noqa: A001
-author = "Richard Sundqvist"
+project = rics.__title__
+copyright = rics.__copyright__  # noqa: A001
+author = rics.__author__
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
 # the built documents.
@@ -28,7 +28,7 @@
 # The full version, including alpha/beta/rc tags.
 release = rics.__version__
 
-# -- General configuration ---------------------------------------------------
+# -- General configuration -----------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -37,6 +37,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
     "recommonmark",
 ]
 
@@ -48,25 +49,53 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-# -- Options for HTML output -------------------------------------------------
+# -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "alabaster"
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
+    "display_version": True,
+}
+
+# Used py sphinx_rtd_theme
+html_context = {
     "github_user": "rsundqvist",
-    "github_repo": "rics",
-    "github_banner": True,
-    "show_related": False,
-    "fixed_sidebar": True,
+    "display_github": True,  # Integrate GitHub
+    "github_version": "master",  # Version
+    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
+
+# -- Nitpicky configuration ----------------------------------------------------
+nitpicky = True
+nitpick_ignore = [("py:class", "re.Pattern")]
+nitpick_ignore_regex = []
+with open("nitpick-regex-exceptions") as f:
+    for line in map(str.rstrip, filter(lambda l: l.strip(), f.readlines())):
+        if line.startswith("#"):
+            continue
+        nitpick_ignore_regex.append(("py:.*", "rics.*" + line))
+
+# -- Autodoc configuration -----------------------------------------------------
+autodoc_typehints = "signature"
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "member-order": "bysource",
+}
+
+# -- Intersphinx configuration -------------------------------------------------
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "pandas": ("http://pandas.pydata.org/pandas-docs/stable/", None),
+}
diff --git a/docs/nitpick-regex-exceptions b/docs/nitpick-regex-exceptions
@@ -0,0 +1,19 @@
+# Regex exceptions for nitpick. There's an issue for any and all generics
+# and typevars of which there are a lot.
+
+\.types\..*
+
+# Online translation
+_fetch_instruction\.FetchInstruction
+_resolve\.DefaultTranslatable
+_ids_to_fetch\.IdsToFetch
+
+# Offline translation
+_placeholder_overrides\.T
+online\.PlaceholderOverrides
+
+# Mapping
+mapping\.BidirectionalMapping
+_directional_mapping\.(HL|HR)
+score_functions\.H
+_mapper\.(ValueType|CandidateType)