Merge branch 'develop'

bumping to v2.3.2
removing old docs, adding requirements
2025-12-22 13:05:45 +00:00 · 2021-11-14 09:12:31 +00:00 · 2021-11-14 09:12:26 +00:00 · 2021-11-14 08:53:11 +00:00 · 2021-11-14 08:33:29 +00:00 · 2021-11-14 08:33:22 +00:00
53 changed files with 840 additions and 1511 deletions
--- a/.DS_Store
+++ b/.DS_Store
--- a/.coveragerc
+++ b/.coveragerc
@@ -0,0 +1,7 @@
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise NotImplementedError
--- a/.gitignore
+++ b/.gitignore
@@ -127,3 +127,6 @@ dmypy.json

 # Pyre type checker
 .pyre/
+
+# custom
+.DS_Store
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -4,5 +4,20 @@
    "python.linting.enabled": true,
    "python.pythonPath": ".venv/bin/python",
    "restructuredtext.confPath": "${workspaceFolder}/docs/source",
-    "peacock.color": "#307E6A"
+    "peacock.color": "#307E6A",
+    "workbench.colorCustomizations": {
+        "editorGroup.border": "#3ea389",
+        "panel.border": "#3ea389",
+        "sash.hoverBorder": "#3ea389",
+        "sideBar.border": "#3ea389",
+        "statusBar.background": "#307e6a",
+        "statusBar.foreground": "#e7e7e7",
+        "statusBarItem.hoverBackground": "#3ea389",
+        "statusBarItem.remoteBackground": "#307e6a",
+        "statusBarItem.remoteForeground": "#e7e7e7",
+        "titleBar.activeBackground": "#307e6a",
+        "titleBar.activeForeground": "#e7e7e7",
+        "titleBar.inactiveBackground": "#307e6a99",
+        "titleBar.inactiveForeground": "#e7e7e799"
+    }
 }
--- a/README.md
+++ b/README.md
@@ -0,0 +1,81 @@
+# Panaetius
+
+This package provides:
+
+- Functionality to read user variables from a `config.yml` or environment variables.
+- A convenient default logging formatter printing `json` that can save to disk and rotate.
+- Utility functions.
+
+## Config
+
+### options
+
+#### skip_header_init
+
+If `skip_header_init=True` then the `config_path` will not use the `header_variable` as the
+sub-directory in the `config_path`.
+
+E.g
+
+`CONFIG = panaetius.Config("tembo", "~/tembo/.config", skip_header_init=True)`
+
+Will look in `~/tembo/config/config.yml`.
+
+If `skip_header_init=False` then would look in `~/tembo/config/tembo/config.yml`.
+
+### Module
+
+Convenient to place in a package/sub-package `__init__.py`.
+
+See Tembo for an example: <https://github.com/tembo-pages/tembo-core/blob/main/tembo/cli/__init__.py>
+
+Example snippet to use in a module:
+
+```python
+import os
+
+import panaetius
+from panaetius.exceptions import LoggingDirectoryDoesNotExistException
+
+
+if (config_path := os.environ.get("TEMBO_CONFIG")) is not None:
+    CONFIG = panaetius.Config("tembo", config_path, skip_header_init=True)
+else:
+    CONFIG = panaetius.Config("tembo", "~/tembo/.config", skip_header_init=True)
+
+
+panaetius.set_config(CONFIG, "base_path", "~/tembo")
+panaetius.set_config(CONFIG, "template_path", "~/tembo/.templates")
+panaetius.set_config(CONFIG, "scopes", {})
+panaetius.set_config(CONFIG, "logging.level", "DEBUG")
+panaetius.set_config(CONFIG, "logging.path")
+
+try:
+    logger = panaetius.set_logger(
+        CONFIG, panaetius.SimpleLogger(logging_level=CONFIG.logging_level)
+    )
+except LoggingDirectoryDoesNotExistException:
+    _LOGGING_PATH = CONFIG.logging_path
+    CONFIG.logging_path = ""
+    logger = panaetius.set_logger(
+        CONFIG, panaetius.SimpleLogger(logging_level=CONFIG.logging_level)
+    )
+    logger.warning("Logging directory %s does not exist", _LOGGING_PATH)
+
+```
+
+This means in `./tembo/cli/cli.py` you can
+
+```python
+import tembo.cli
+
+# access the CONFIG instance + variables from the config.yml
+tembo.cli.CONFIG
+```
+
+
+## Utility Functions
+
+### Squasher
+
+Squashes a json object or Python dictionary into a single level dictionary.
--- a/README.md.old
+++ b/README.md.old
@@ -1,33 +0,0 @@
-# Author
-
-Daniel Tomlinson (dtomlinson@panaetius.co.uk)
-
-# Requires
-
-`>= python3.7`
-
-# Python requirements
-
- toml = "^0.10.0"
- pylite = "^0.1.0"
-
-# Documentation
-
-_soon_
-
-# Installation
-
-_soon_
-
-# Easy Way
-
-## Python
-
-### From pip
-
-### From local wheel
-
-### From source
-
-# Example Usage
-
--- a/README.rst
+++ b/README.rst
@@ -1,62 +0,0 @@
-Author
-=======
-
-Daniel Tomlinson (dtomlinson@panaetius.co.uk)
-
-Requires
-=========
-
-`>= python3.7`
-
-Python requirements
-====================
-
- toml = "^0.10.0"
- pylite = "^0.1.0"
-
-Documentation
-==============
-
-Read the documentation on `read the docs`_.
-
-.. _read the docs: https://panaetius.readthedocs.io/en/latest/introduction.html
-
-Installation
-==============
-
-You can install ``panaetius`` the following ways:
-
-Python
-------
-
-.. Attention:: You should install in a python virtual environment
-
-From pypi using pip
-~~~~~~~~~~~~~~~~~~~~
-
-.. code-block:: bash
-
-    pip install panaetius
-
-From local wheel
-~~~~~~~~~~~~~~~~~
-
-Download the latest verion from the `releases`_ page.
-
-.. _releases: https://github.com/dtomlinson91/panaetius/releases
-
-Install with pip:
-
-.. code-block:: bash
-
-    pip install -U panaetius-1.0.2-py3-none-any.whl
-
-
-From source
-~~~~~~~~~~~~
-
-Clone the repo and install using ``setup.py``:
-
-.. code-block:: bash
-
-    python setup.py
--- a/3
+++ b/3
@@ -1,3 +0,0 @@
-
-Todo:
-  ☐ Item
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
--- a/docs/make.bat
+++ b/docs/make.bat
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
--- a/docs/source/_static/custom.css
+++ b/docs/source/_static/custom.css
@@ -1,87 +0,0 @@
-@import url("css/theme.css");
-
-.modname {
-    font-size: 0.8em;
-    opacity: 0.4;
-}
-.modname::before {
-    content: '- ';
-}
-.title {
-    font-weight: bold;
-    font-size: 1.2em;
-    background-color: #eee;
-    display: block;
-    padding: 1px 5px;
-    border-left: 2px solid #ddd;
-}
-
-/*colour of the text in the toc*/
-.wy-menu-vertical header, .wy-menu-vertical p.caption{
-    color: #b26d46;;
-}
-
-/*colour of the top left header*/
-.wy-side-nav-search{
-    background-color: #31465a;
-}
-
-/*colours of the class definitions*/
-.rst-content dl:not(.docutils) dt{
-    background: #e2d7d1;
-    color: #0b2852;
-    border-top: solid 3px #31465a;
-}
-
-/*colour of the link in the class defintions*/
-.rst-content .viewcode-link, .rst-content .viewcode-back{
-    color: #4b674a;
-}
-
-/*colour of the function definitions*/
-.rst-content dl:not(.docutils) dl dt{
-    border-left: solid 3px #31465a;
-    background: #e2d7d1;
-    color: #0b2852;
-}
-
-/*colour of the link in the function definitions*/
-.rst-content .viewcode-link, .rst-content .viewcode-back{
-    color: #4b674a;
-}
-
-/*edit the width of the body*/
-.wy-nav-content{
-    max-width: 1200px;
-}
-
-/*code example blocks*/
-.rst-content pre.literal-block, .rst-content div[class^="highlight"] pre, .rst-content .linenodiv pre{
-    background: #b4bec8;
-    color: black;
-    /*border-style: solid;*/
-    /*border-width: thin;*/
-}
-
-/*colour of inline code blocks using ``*/
-.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal{
-    color: #b26d46;
-}
-
-/* Change code blocks font and bump up font size slightly (normally 12px)*/
-.rst-content pre.literal-block, .rst-content div[class^="highlight"] pre, .rst-content .linenodiv pre {
-    font-family: 'Inconsolata', monospace !important;
-    font-size: 14px !important;
-    white-space: pre-wrap;
-}
-
-/* Change code descriptions and literal blocks (inline code via ``) to match the normal font size being used in the sphinx_RTD_theme text  (normally 14px)*/
-.rst-content dl:not(.docutils) tt.descname,.rst-content dl:not(.docutils) tt.descclassname,.rst-content dl:not(.docutils) tt.descname,.rst-content dl:not(.docutils) code.descname,.rst-content dl:not(.docutils) tt.descclassname,.rst-content dl:not(.docutils) code.descclassname, code.docutils {
-    font-family: 'Inconsolata', monospace !important;
-    font-size: 14px !important;
-}
-
-/*variables text*/
-dl.class > dd > table.docutils.field-list tbody tr.field-odd.field th.field-name::before{
-    content: '(Class Attributes) ';
-}
--- a/docs/source/changelog.rst
+++ b/docs/source/changelog.rst
@@ -1,17 +0,0 @@
-Version history
-================
-
-1.1
----
-
- Adding overwrite to ``__header__`` functionality. See the Configuration documentation page on how to configure.
-
-1.0.2
------
-
- Minor fixes and documentation updates.
-
-1.0
--------
-
- Initial release.
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -1,95 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-import panaetius
-from panaetius.__version__ import __version__ as version
-import sphinx_rtd_theme
-
-# -- Project information -----------------------------------------------------
-
-project = 'panaetius'
-copyright = '2019, Daniel Tomlinson'
-author = 'Daniel Tomlinson'
-
-# The full version, including alpha/beta/rc tags
-release = version
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.todo',
-]
-
-# -- Napoleon Settings -----------------------------------------------------
-napoleon_google_docstring = False
-napoleon_numpy_docstring = True
-napoleon_include_init_with_doc = True
-napoleon_include_private_with_doc = False
-napoleon_include_special_with_doc = False
-napoleon_use_admonition_for_examples = False
-napoleon_use_admonition_for_notes = False
-napoleon_use_admonition_for_references = False
-napoleon_use_ivar = True
-napoleon_use_param = True
-napoleon_use_rtype = True
-napoleon_use_keyword = True
-autodoc_member_order = 'bysource'
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The master toctree document.
-master_doc = 'index'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
-
-# -- 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 = "sphinx_rtd_theme"
-
-# 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_theme = "sphinx_rtd_theme"
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-html_static_path = ['_static']
-html_context = {'css_files': ['_static/custom.css']}
-html_theme_options = {
-    'collapse_navigation': True,
-    'display_version': True,
-    'prev_next_buttons_location': 'both',
-    #'navigation_depth': 3,
-}
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# Enable todo
-todo_include_todos = True
--- a/docs/source/configuration.rst
+++ b/docs/source/configuration.rst
@@ -1,68 +0,0 @@
-Configuration
-=============
-
-panaetius is fairly easy to configure. There are just a couple of options to be aware of.
-
-Manual configuration of ``Config`` instance
--------------------------------------------
-
-Configuring with a ``__header__.py`` is deprecated. Manually set this value.
-
-Use the following snippet to configure (in ``__init__.py``):
-
-.. code-block:: python
-
-    import panaetius
-    from panaetius.config import Config
-
-    CONFIG = Config(path="~/.config/island-code-extractor", header="island-code-extractor")
-
-    panaetius.set_config(CONFIG, "reddit.secret")
-
-Access this in your code by importing the ``CONFIG`` instance from your module:
-
-.. code-block:: python
-
-    from island_code_extractor import CONFIG
-    from island_code_extractor import panaetius
-
-    CONFIG.reddit_output_path
-    panaetius.logger.info("Using logger")
-
-__header__.py
-------------
-
-You should set a ``__header__.py`` next to your script or module.
-
-This ``__header__.py`` should contain a ``__header__`` variable that sets the name of your project/script.
-
-E.g a ``__header__.py`` for the module ``plex_posters`` would look like:
-
-.. code-block:: python
-
-    __header__ = 'plex_posters' 
-
-Your config file can then be created at ``~/.config/__header__/config.toml``. 
-
-Your environment variables can be created with:
-
-.. code-block:: bash
-
-    HEADER_FOO = "bar"
-    HEADER_SUBSECTION_FOO = "bar"
-
-The headers of the toml file would look like:
-
-.. code-block:: toml
-
-    [__header__]
-    foo = bar
-
-    [__header__.subsection]
-    foo = bar
-
-If you are writing a script, simply place this ``__header__.py`` along side your script. Panaetius will pick this up when the script is ran.
-
-If you are writing a module, you can either place the ``__header__.py`` alongside the script that uses your module. If this is not possible, panaetius will set the default ``__header__`` variable to the name of the virtualenv that the script is activated from.
-
-If neither of the above aren't possible (say your script is running in a lambda on AWS), then ``__header__`` will be set to the default of ``panaetius``.
--- a/docs/source/global.rst
+++ b/docs/source/global.rst
@@ -1,5 +0,0 @@
-.. role:: modname
-   :class: modname
-
-.. role:: title
-   :class: title
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -1,3 +0,0 @@
-Table of Contents
-=================
-.. include:: toc.rst
--- a/docs/source/introduction.rst
+++ b/docs/source/introduction.rst
@@ -1,154 +0,0 @@
-Introduction
-=============
-
-.. image:: https://img.shields.io/readthedocs/panaetius?style=for-the-badge   :target: https://panaetius.readthedocs.io/en/latest/?badge=latest
-   :alt: Documentation Status
-
-.. image:: https://img.shields.io/github/v/tag/dtomlinson91/panaetius?style=for-the-badge   :alt: GitHub tag (latest by date)
-
-.. image:: https://img.shields.io/github/commit-activity/m/dtomlinson91/panaetius?style=for-the-badge   :alt: GitHub commit activity
-
-.. image:: https://img.shields.io/github/issues/dtomlinson91/panaetius?style=for-the-badge   :alt: GitHub issues
-
-.. image:: https://img.shields.io/github/license/dtomlinson91/panaetius?style=for-the-badge   :alt: GitHubtbc
-
-Python module to gracefully handle a .config file/environment variables for scripts, with built in masking for sensitive options. Provides a Splunk friendly formatted logger instance.
-
-Usage
------
-
-Setting a config file
-~~~~~~~~~~~~~~~~~~~~~~
-
-The main functionality of ``panaetius`` is using a config file to store variables.
-
-Your ``config.toml`` can be created and found in ``~/.config/__header__/config.toml`` where ``__header__`` is equal to the variable configured/set. `See how to configure`_ this variable in the configuration section of panaetius.
-
-.. _See how to configure: https://panaetius.readthedocs.io/en/latest/configuration.html#header-py
-
-Setting values in a config.toml/environment variables
-#######################################################
-
-A ``config.toml`` can be created in the default folder for the module. In this example this would be found in ``~/.config/example_module/config.toml``. 
-
-An example ``config.toml`` could look like:
-
-.. code-block:: toml
-
-    [example_module]
-    test = "a6cbf36649b029f3618a0cc1"
-
-    [example_module.logging]
-    path = "~/.config/example_module"
-    level = "DEBUG"
-
-    [example_module.foo]
-    bar = "6b3b96815218960ceaf7cceb"
-
-These are equivalent to the environment variables:
-
-.. code-block:: bash
-
-    EXAMPLE_MODULE_TEST
-    EXAMPLE_MODULE_LOGGING_PATH
-    EXAMPLE_MODULE_LOGGING_LEVEL
-    EXAMPLE_MODULE_FOO_BAR
-
-
-.. Attention:: 
-    Environment variables take precedent over the ``config.toml``. If both are set then the environment variable will be used.
-
-You can overwrite the ``config.toml`` location by setting the environment variable:
-
-.. code-block:: bash
-
-    DEFAULT_CONFIG_PATH = "~/path/to/config"
-
-
-Setting values in your code
-############################
-
-Values in a ``config.toml`` or from an environment variable need to be set in your work in order for you to use them. You can do this easily by
-
- importing panaetius.
- using the :func:`~panaetius.library.set_config` function.
-  
-E.g your script could contain:
-
-.. code-block:: python
-
-    import panaetius
-    panaetius.set_config(panaetius.CONFIG, 'logging.path')
-
-.. Note::
-
-    The ``key`` attribute in :func:`~panaetius.library.set_config` is specified as a string, with the hirearchy in the config file split with a ``.``
-
-.. Important::
-
-    The default value for a variable defined using :func:`~panaetius.library.set_config` is ``None``. See the documentation of this function to see all the options available.
-
-
-Accessing values
-#################
-
-You can then access the result of this variable later in your code:
-
-.. code-block:: python
-
-    panaetius.CONFIG.logging_path
-
-
-Logging
-~~~~~~~~
-
-In order to save to disk, you need to specify a path for the log file in the config file/environment variable. There is no need to register this with :func:`~panaetius.library.set_config` as ``panaetius`` will do this automatically.
-
-There are other options available for you to configure a logger. These are (including the default values which can be overwritten):
-
-.. code-block:: toml
-
-    [example_module.logging]
-    backup_count = 3
-    format = "{\n\t"time": "%(asctime)s",\n\t"file_name": "%(filename)s",'
-    '\n\t"module": "%(module)s",\n\t"function":"%(funcName)s",\n\t'
-    '"line_number": "%(lineno)s",\n\t"logging_level":'
-    '"%(levelname)s",\n\t"message": "%(message)s"\n}"
-    level = "INFO" # Level should be in CAPS
-    rotate_bytes = 512000
-
-You can use the logger in your code by:
-
-.. code-block:: python
-
-    panaetius.logger.info('some log message')
-
-which gives an output of:
-
-.. code-block:: json
-
-    {
-        "time": "2020-01-13 23:07:17,913",
-        "file_name": "test.py",
-        "module": "test",
-        "function":"<module>",
-        "line_number": "33",
-        "logging_level":"INFO",
-        "message": "some logging message"
-    }
-
-
-Importing and using the api
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-See `panaetius api page`_ on how to use and import the module.
-
-.. _panaetius api page: https://panaetius.readthedocs.io/en/latest/modules/panaetius.html
-
-
-Configuration
---------------
-
-See `configuration page`_ on how to configure ``panaetius``.
-
-.. _configuration page: https://panaetius.readthedocs.io/en/latest/configuration.html
--- a/docs/source/modules/panaetius.config.rst
+++ b/docs/source/modules/panaetius.config.rst
@@ -1,9 +0,0 @@
-.. include:: ../global.rst
-
-panaetius.config :modname:`panaetius.config`
---------------------------------------------
-
-.. automodule:: panaetius.config
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/docs/source/modules/panaetius.config_inst.rst
+++ b/docs/source/modules/panaetius.config_inst.rst
@@ -1,9 +0,0 @@
-.. include:: ../global.rst
-
-panaetius.config_inst :modname:`panaetius.config_inst`
--------------------------------------------------------
-
-.. automodule:: panaetius.config_inst
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/docs/source/modules/panaetius.db.rst
+++ b/docs/source/modules/panaetius.db.rst
@@ -1,9 +0,0 @@
-.. include:: ../global.rst
-
-panaetius.db :modname:`panaetius.db`
-------------------------------------
-
-.. automodule:: panaetius.db
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/docs/source/modules/panaetius.header.rst
+++ b/docs/source/modules/panaetius.header.rst
@@ -1,9 +0,0 @@
-.. include:: ../global.rst
-
-panaetius.header :modname:`panaetius.header`
---------------------------------------------
-
-.. automodule:: panaetius.header
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/docs/source/modules/panaetius.library.rst
+++ b/docs/source/modules/panaetius.library.rst
@@ -1,9 +0,0 @@
-.. include:: ../global.rst
-
-panaetius.library :modname:`panaetius.library`
------------------------------------------------
-
-.. automodule:: panaetius.library
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/docs/source/modules/panaetius.logging.rst
+++ b/docs/source/modules/panaetius.logging.rst
@@ -1,9 +0,0 @@
-.. include:: ../global.rst
-
-panaetius.logging :modname:`panaetius.logging`
----------------------------------------------
-
-.. automodule:: panaetius.logging
-   :members:
-   :undoc-members:
-   :show-inheritance:
--- a/docs/source/modules/panaetius.rst
+++ b/docs/source/modules/panaetius.rst
@@ -1,66 +0,0 @@
-.. include:: ../global.rst
-
-*********
-panaetius
-*********
-
-API
-===
-
-The following is availble by importing the module:
-
-.. code-block:: python
-
-    import panaetius
-
-
-panaetius.CONFIG
----------------
-
-:obj:`panaetius.CONFIG` provides an instance of :class:`panaetius.config.Config`
-
-
-panaetius.set_config()
-----------------------
-
-Conveniently provides :func:`panaetius.library.set_config` 
-
-Use in your module/script with:
-
-.. code-block:: python
-
-    panaetius.set_config(panaetius.CONFIG, 'aws.secret_key', str, mask=True)    
-
-
-panaetius.CONFIG.aws_secret_key
-------------------------------
-
-Conveniently provides access to all attributes that have been declared with :func:`panaetius.library.set_config`:
-
-.. code-block:: python
-
-    my_secret_key = panaetius.CONFIG.aws_secret_key
-
-
-panaetius.logger
-----------------
-
-:obj:`panaetius.logger` provides a logger instance already formatted with a nice json output.
-
-.. code-block:: python
-
-    panaetius.logger.info('some logging message')
-
-This gives a logger output of:
-
-.. code-block:: json
-
-    {
-        "time": "2020-01-13 23:07:17,913",
-        "file_name": "test.py",
-        "module": "test",
-        "function":"<module>",
-        "line_number": "33",
-        "logging_level":"INFO",
-        "message": "some logging message"
-    }
--- a/docs/source/toc.rst
+++ b/docs/source/toc.rst
@@ -1,27 +0,0 @@
-.. toctree::
-   :maxdepth: 1
-   :caption: Overview
-   :titlesonly:
-
-   introduction
-   configuration
-   changelog
-
-.. toctree::
-   :maxdepth: 4
-   :caption: Modules
-   :titlesonly:
-
-   modules/panaetius.rst
-
-.. toctree::
-   :maxdepth: 4
-   :caption: Submodules
-   :titlesonly:
-
-   modules/panaetius.config.rst
-   modules/panaetius.config_inst.rst
-   modules/panaetius.db.rst
-   modules/panaetius.header.rst
-   modules/panaetius.library.rst
-   modules/panaetius.logging.rst
--- a/duties.py
+++ b/duties.py
@@ -0,0 +1,175 @@
+from __future__ import annotations
+
+import os
+import pathlib
+import re
+import shutil
+
+from duty import duty
+
+
+PACKAGE_NAME = "panaetius"
+
+
+@duty
+def update_deps(ctx, dry: bool = False):
+    """
+    Update the dependencies using Poetry.
+
+    Example:
+        `duty update_deps dry=False`
+    """
+    dry_run = "--dry-run" if dry else ""
+    ctx.run(
+        ["poetry", "update", dry_run],
+        title=f"Updating poetry deps {dry_run}",
+    )
+
+
+@duty
+def test(ctx):
+    """Run tests using pytest"""
+    pytest_results = ctx.run(["pytest", "-v"])
+    print(pytest_results)
+
+
+@duty
+def coverage(ctx):
+    """
+    Generate a coverage HTML report.
+
+    Example:
+        `duty coverage`
+    """
+    ctx.run(["coverage", "run", "--source", PACKAGE_NAME, "-m", "pytest"])
+    ctx.run(["coverage", "html"])
+
+
+@duty
+def version(ctx, bump: str = "patch"):
+    """
+    Bump the version using Poetry and update _version.py.
+
+    Args:
+        bump (str, optional) = poetry version flag. Available options are:
+            patch, minor, major, prepatch, preminor, premajor, prerelease.
+            Defaults to patch.
+
+    Example:
+        `duty version bump=major`
+    """
+
+    # bump with poetry
+    result = ctx.run(["poetry", "version", bump])
+    new_version = re.search(r"(?:.*)(?:\s)(\d+\.\d+\.\d+)$", result)
+    print(new_version.group(0))
+
+    # update _version.py
+    version_file = pathlib.Path(PACKAGE_NAME) / "_version.py"
+    with version_file.open("w", encoding="utf-8") as version_file:
+        version_file.write(
+            f'"""Module containing the version of {PACKAGE_NAME}."""\n\n'
+            + f'__version__ = "{new_version.group(1)}"\n'
+        )
+    print(f"Bumped _version.py to {new_version.group(1)}")
+
+
+@duty
+def build(ctx):
+    """
+    Build with poetry and extract the `setup.py` and copy to project root.
+
+    Example:
+        `duty build`
+    """
+
+    repo_root = pathlib.Path(".")
+
+    # build with poetry
+    result = ctx.run(["poetry", "build"])
+    print(result)
+
+    # extract the setup.py from the tar
+    extracted_tar = re.search(r"(?:.*)(?:Built\s)(.*)", result)
+    tar_file = pathlib.Path(f"./dist/{extracted_tar.group(1)}")
+    shutil.unpack_archive(tar_file, tar_file.parents[0])
+
+    # copy setup.py to repo root
+    extracted_path = tar_file.parents[0] / os.path.splitext(tar_file.stem)[0]
+    setup_py = extracted_path / "setup.py"
+    shutil.copyfile(setup_py, (repo_root / "setup.py"))
+
+    # cleanup
+    shutil.rmtree(extracted_path)
+
+
+@duty
+def export(ctx):
+    """
+    Export the dependencies to a requirements.txt file.
+
+    Example:
+        `duty export`
+    """
+    requirements_content = ctx.run(
+        [
+            "poetry",
+            "export",
+            "-f",
+            "requirements.txt",
+            "--without-hashes",
+        ]
+    )
+    requirements_dev_content = ctx.run(
+        [
+            "poetry",
+            "export",
+            "-f",
+            "requirements.txt",
+            "--without-hashes",
+            "--dev",
+        ]
+    )
+
+    requirements = pathlib.Path(".") / "requirements.txt"
+    requirements_dev = pathlib.Path(".") / "requirements_dev.txt"
+
+    with requirements.open("w", encoding="utf-8") as req:
+        req.write(requirements_content)
+
+    with requirements_dev.open("w", encoding="utf-8") as req:
+        req.write(requirements_dev_content)
+
+
+@duty
+def publish(ctx, password:str):
+    """
+    Publish the package to pypi.org.
+
+    Args:
+        password (str): pypi.org password.
+
+    Example:
+        `duty publish password=$my_password`
+    """
+    dist_dir = pathlib.Path(".") / "dist"
+    rm_result = rm_tree(dist_dir)
+    print(rm_result)
+
+    publish_result = ctx.run(["poetry", "publish", "-u", "dtomlinson", "-p", password, "--build"])
+    print(publish_result)
+
+
+def rm_tree(directory: pathlib.Path):
+    """
+    Recursively delete a directory and all its contents.
+
+    Args:
+        directory (pathlib.Path): The directory to delete.
+    """
+    for child in directory.glob('*'):
+        if child.is_file():
+            child.unlink()
+        else:
+            rm_tree(child)
+    directory.rmdir()
--- a/old_src/panaetius/init.py
+++ b/old_src/panaetius/init.py
@@ -1,6 +0,0 @@
-from panaetius.config_inst import CONFIG
-from .config import Config
-from .library import set_config
-from panaetius.header import __header__
-import panaetius.logging
-from panaetius.logging import logger as logger
--- a/old_src/panaetius/version.py
+++ b/old_src/panaetius/version.py
@@ -1 +0,0 @@
-__version__ = '1.0.2'
--- a/old_src/panaetius/config.py
+++ b/old_src/panaetius/config.py
@@ -1,178 +0,0 @@
-from typing import Callable, Union
-import os
-import toml
-
-from panaetius.library import export
-from panaetius.header import __header__
-from panaetius.db import Mask
-
-# __all__ = ['Config']
-
-
-class Config:
-
-    """Handles the config options for the module and stores config variables
-    to be shared.
-
-    Attributes
-    ----------
-    config_file : dict
-        Contains the config options. See
-        :meth:`~panaetius.config.Config.read_config`
-        for the data structure.
-    deferred_messages : list
-        A list containing the messages to be logged once the logger has been
-        instantiated.
-    Mask : panaetius.db.Mask
-        Class to mask values in a config file.
-    module_name : str
-        A string representing the module name. This is added in front of all
-        envrionment variables and is the title of the `config.toml`.
-    path : str
-        Path to config file
-
-    Parameters
-    ----------
-    path : str
-        Path to config file
-    """
-
-    def __init__(self, path: str, header: str = __header__) -> None:
-        """
-        See :class:`~panaetius.config.Config` for parameters.
-        """
-        self.path = os.path.expanduser(path)
-        self.header = header
-        self.deferred_messages = []
-        self.config_file = self.read_config(path)
-        self.module_name = self.header.lower()
-        self.Mask = Mask
-
-    def read_config(self, path: str, write: bool = False) -> Union[dict, None]:
-        """Reads the toml config file from `path` if it exists.
-
-        """
-
-        path += 'config.toml' if path[-1] == '/' else '/config.toml'
-        path = os.path.expanduser(path)
-        if not write:
-            try:
-                with open(path, 'r+') as config_file:
-                    config_file = toml.load(config_file)
-                self.defer_log(f'Config file found at {path}')
-                return config_file
-            except FileNotFoundError:
-                self.defer_log(f'Config file not found at {path}')
-        else:
-            try:
-                with open(path, 'w+') as config_file:
-                    config_file = toml.load(config_file)
-                self.defer_log(f'Config file found at {path}')
-                return config_file
-            except FileNotFoundError:
-                self.defer_log(f'Config file not found at {path}')
-
-    def get(
-        self,
-        key: str,
-        default: str = None,
-        cast: Callable = None,
-        mask: bool = False,
-    ) -> Union[str, None]:
-        """Retrives the config variable from either the `config.toml` or an
-        environment variable. Will default to the default value if nothing
-        is found
-
-        Parameters
-        ----------
-        key : str
-            Key to the configuration variable. Should be in the form
-            `panaetius.variable` or `panaetius.header.variable`.
-            When loaded, it will be accessable at
-            `Config.panaetius_variable` or
-            `Config.panaetius_header_variable`.
-        default : str, optional
-            The default value if nothing is found. Defaults to `None`.
-        cast : Callable, optional
-            The type of the variable. E.g `int` or `float`. Should reference
-            the type object and not as string. Defaults to `None`.
-
-        Returns
-        -------
-        Any
-            Will return the config variable if found, or the default.
-        """
-        env_key = f"{self.header.upper()}_{key.upper().replace('.', '_')}"
-
-        try:
-            # look in the config.toml
-            if len(key.split('.')) == 2:
-                # look for subsections
-                # print(mask)
-                if mask:
-                    # print('mask', key)
-                    value = self.Mask(
-                        self.path, self.config_file, key
-                    ).get_value()
-                else:
-                    # print('no-mask')
-                    section, name = key.lower().split('.')
-                    value = self.config_file[self.module_name][section][name]
-                    self.defer_log(f'{env_key} found in config.toml')
-            else:
-                # print('valueerror')
-                # look under top level module self.header
-                # key = f'{self.module_name}.key'
-                if mask:
-                    # key = f'{self.header}.{key}'
-                    # print(f'mask key={key}')
-                    value = self.Mask(
-                        self.path, self.config_file, key
-                    ).get_value()
-                else:
-                    name = key.lower()
-                    value = self.config_file[self.module_name][name]
-                    self.defer_log(f'{env_key} found in config.toml')
-            # finally:
-            try:
-                # return if found in config.toml
-                return cast(value) if cast else value
-            except UnboundLocalError:
-                # pass if nothing was found
-                # print('unbound error')
-                pass
-        except KeyError:
-            # print('key error')
-            self.defer_log(f'{env_key} not found in config.toml')
-        except TypeError:
-            # print('type error')
-            self.defer_log(f'{env_key} not found in config.toml')
-
-        # look for an environment variable
-        value = os.environ.get(env_key.replace("-", "_"))
-
-        if value is not None:
-            self.defer_log(f'{env_key} found in an environment variable')
-        else:
-            # fall back to default
-            self.defer_log(f'{env_key} not found in an environment variable.')
-            value = default
-            self.defer_log(f'{env_key} set to default {default}')
-        return cast(value) if cast else value
-
-    def defer_log(self, msg: str) -> None:
-        """Populates a list `Config.deferred_messages` with all the events to
-        be passed to the logger later if required.
-
-        Parameters
-        ----------
-        msg : str
-            The message to be logged.
-        """
-        self.deferred_messages.append(msg)
-
-    def reset_log(self) -> None:
-        """Empties the list `Config.deferred_messages`.
-        """
-        del self.deferred_messages
-        self.deferred_messages = []
--- a/old_src/panaetius/config_inst.py
+++ b/old_src/panaetius/config_inst.py
@@ -1,9 +0,0 @@
-import os
-
-from panaetius.header import __header__
-from panaetius.config import Config
-
-
-DEFAULT_CONFIG_PATH = f"~/.config/{__header__.lower()}"
-CONFIG_PATH = os.environ.get(f"{__header__.upper()}_CONFIG_PATH", DEFAULT_CONFIG_PATH)
-CONFIG = Config(CONFIG_PATH)
--- a/old_src/panaetius/db.py
+++ b/old_src/panaetius/db.py
@@ -1,256 +0,0 @@
-from os import path, urandom
-import hashlib
-from typing import Tuple
-import toml
-import io
-
-from pylite.simplite import Pylite
-
-from panaetius.header import __header__ as __header__
-import panaetius
-
-
-class Mask:
-
-    """Class to handle masking sensitive values in a config file
-
-    Attributes
-    ----------
-    config_contents : dict
-        A dict containing the contents of the config file.
-    config_path : str
-        The path to the config file.
-    config_var : str
-        The key corresponding to the config entry.
-    database : Pylite
-        A Pylite instance for the datbase.
-    entry : str
-        The result from the config file. Could either be a hash or the raw
-        value.
-    header : str
-        The __header__ which denotes where the config file is stored.
-    name : str
-        The key of the entry in the config file.
-    result : str
-        The value of the entry in the config file.
-    table_name : str
-        The sqlite table name. Defaults to the __header__ value.
-    """
-
-    @property
-    def hash(self):
-        """Property to determine the hash of a config entry.
-
-        Returns
-        -------
-        bytes
-            The hash as a bytes object.
-        """
-        try:
-            if not self._hash_exists:
-                pass
-        except AttributeError:
-            self._hash = hashlib.pbkdf2_hmac(
-                'sha256',
-                self.entry[self.name].encode('utf-8'),
-                self.salt,
-                100000,
-                dklen=12,
-            )
-            self._hash_exists = True
-        finally:
-            return self._hash
-
-    @property
-    def salt(self):
-        """Property to detemine a random salt to use in creation of the hash.
-
-        Returns
-        -------
-        bytes
-            The salt as a bytes object.
-        """
-        self._salt = urandom(32)
-        return self._salt
-
-    @staticmethod
-    def as_string(obj: bytes) -> str:
-        """Static method to return a string from a bytes object.
-
-        Parameters
-        ----------
-        obj : bytes
-            Bytes object to be converted to a string.
-
-        Returns
-        -------
-        str
-            The bytes object as a string.
-        """
-        return bytes.hex(obj)
-
-    @staticmethod
-    def fromhex(obj: str) -> bytes:
-        """Static method to create a bytes object from a string.
-
-        Parameters
-        ----------
-        obj : str
-            String object to be converted to bytes.
-
-        Returns
-        -------
-        bytes
-            The string object as bytes.
-        """
-        return bytes.fromhex(obj)
-
-    @staticmethod
-    def _from_key(config_var) -> Tuple[str, str]:
-        try:
-            header, name = config_var.split('.')
-        except ValueError:
-            header = ''
-            name = config_var
-        return (header, name)
-
-    def __init__(
-        self, config_path: str, config_contents: dict, config_var: str
-    ):
-        """Summary
-        See :class:`~Mask` for parameters.
-        """
-        self.table: str = __header__
-        self.config_path = config_path
-        self.config_contents = config_contents
-        self.config_var = config_var.replace('.', '_')
-        self.header = self._from_key(config_var)[0]
-        self.name = self._from_key(config_var)[1]
-        try:
-            # If value is under a subsection
-            self.entry = self.config_contents[self.table][self.header]
-        except KeyError:
-            # If value is under the main header
-            self.entry = self.config_contents[self.table]
-
-    def _get_database_file(self):
-        self.database = self.config_path
-        self.database += (
-            f'.{self.table}.db'
-            if self.config_path[-1] == '/'
-            else f'/.{self.table}.db'
-        )
-        self.database = path.expanduser(self.database)
-        return self
-
-    def _open_database(self):
-        self.database = Pylite(self.database)
-
-    def _get_table(self):
-        tables = [i[0] for i in self.database.get_tables()]
-        if self.table not in tables:
-            # panaetius.logger.debug(
-            #     'Table not present in the database;'
-            #     f'creating the table {self.table} now'
-            # )
-            self.database.add_table(
-                f'{self.table}',
-                Name='text',
-                Hash='text',
-                Salt='text',
-                Value='text',
-            )
-        else:
-            # panaetius.logger.debug('Table already exists in the database')
-            pass
-        self.table_name = self.table
-
-    def _check_entries(self):
-        var = self.database.get_items(self.table, f'Name="{self.config_var}"')
-        if len(var) == 0:
-            return False
-        else:
-            return True
-
-    def _insert_entries(self):
-        self.database.insert(
-            self.table,
-            self.config_var,
-            self.as_string(self.hash),
-            self.as_string(self.salt),
-            self.entry[self.name],
-        )
-
-    def _update_entries_in_db(self):
-        self.database.remove(self.table, f'Name="{self.config_var}"')
-        self._insert_entries()
-
-    def _run_query(self, query: str):
-        cur = self.database.db.cursor()
-        cur.execute(query)
-        self.database.db.commit()
-        self.result = cur.fetchall()
-        return self
-
-    def _get_all_items(self, where_clause: str = None):
-        if where_clause is not None:
-            self.result = self.database.get_items(self.table, where_clause)
-        else:
-            self.result = self.database.get_items(self.table)
-        return self
-
-    def _process(self):
-        if not self._check_entries():
-            # panaetius.logger.debug('does not exist')
-            self._insert_entries()
-            self._update_entries_in_config()
-            self._get_all_items()
-            # panaetius.logger.debug(f'returning: {self.result[0][3]}')
-            return self.entry[self.name]
-        else:
-            self._get_all_items(f'Name="{self.config_var}"')
-            if self.result[0][1] == self.entry[self.name]:
-                # panaetius.logger.debug('exists and hash matches')
-                # panaetius.logger.debug(f'returning: {self.result[0][3]}')
-                return self.result
-            else:
-                # panaetius.logger.debug('exists and hash doesnt match')
-                # panaetius.logger.debug(
-                #     f'file_hash={self.entry[self.name]}, {self.result[0][1]}'
-                # )
-                self._update_entries_in_db()
-                self._update_entries_in_config()
-                self._get_all_items(f'Name="{self.config_var}"')
-                # panaetius.logger.debug(f'returning: {self.result[0][3]}')
-                return self.entry[self.name]
-
-    def _open_config_file(self) -> io.TextIOWrapper:
-        self.config_path += (
-            '/config.toml' if self.config_path[-1] != '/' else 'config.toml'
-        )
-        c = open(path.expanduser(self.config_path), 'w')
-        return c
-
-    def _update_entries_in_config(self):
-        self.entry.update({self.name: self.as_string(self.hash)})
-        # panaetius.logger.debug(self.config_contents)
-        # panaetius.logger.debug(self.entry)
-        c = self._open_config_file()
-        toml.dump(self.config_contents, c)
-        c.close()
-
-    def get_value(self):
-        """Get the true value from the database if it exists, create if it'
-        ' doesn't exist or update if the hash has changed.
-
-        Returns
-        -------
-        str
-            The result from the database.
-        """
-        # print(f'key in db {self.config_var}')
-        self._get_database_file()
-        self._open_database()
-        self._get_table()
-        self._process()
-        return self.result[0][3]
--- a/old_src/panaetius/header.py
+++ b/old_src/panaetius/header.py
@@ -1,26 +0,0 @@
-import os
-from importlib import util
-
-__path = os.getcwd()
-
-try:
-    __spec = util.spec_from_file_location(
-        '__header__', f'{os.getcwd()}/__header__.py'
-    )
-    __header__ = util.module_from_spec(__spec)
-    __spec.loader.exec_module(__header__)
-    __header__ = __header__.__header__
-except FileNotFoundError:
-    try:
-        venv = os.environ.get('VIRTUAL_ENV').split('/')[-1]
-        __header__ = venv
-    except AttributeError:
-        print(
-            f'Cannot find a __header__.py file in {os.getcwd()} containing the'
-            ' __header__ value of your project name and you are not working'
-            ' from a virtual environment. Either make sure this file '
-            'exists and the value is set or create and work from a virtual '
-            'environment and try again. \n The __header__ value has been '
-            'set to the default of panaetius.'
-        )
-        __header__ = 'panaetius'
--- a/old_src/panaetius/library.py
+++ b/old_src/panaetius/library.py
@@ -1,112 +0,0 @@
-from __future__ import annotations
-import sys
-from typing import Any, TypeVar, Type, TYPE_CHECKING, Union, List
-import ast
-
-
-if TYPE_CHECKING:
-    import logging
-
-
-config_inst_t = TypeVar('config_inst_t', bound='panaetius.config.Config')
-
-
-def export(fn: callable) -> callable:
-    mod = sys.modules[fn.__module__]
-    if hasattr(mod, '__all__'):
-        mod.__all__.append(fn.__name__)
-    else:
-        mod.__all__ = [fn.__name__]
-    return fn
-
-
-def set_config(
-    config_inst: Type[config_inst_t],
-    key: str,
-    default: str = None,
-    cast: Any = None,
-    check: Union[None, List] = None,
-    mask: bool = False,
-) -> None:
-    """Sets the config variable on the instance of a class.
-
-    Parameters
-    ----------
-    config_inst : Type[config_inst_t]
-        Instance of the :class:`~panaetius.config.Config` class.
-    key : str
-        The key referencing the config variable.
-    default : str, optional
-        The default value.
-    mask : bool, optional
-        Boolean to indiciate if a value in the `config.toml` should be masked.
-        If this is set to True then the first time the variable is read from
-        the config file the value will be replaced with a hash. Any time that
-        value is then read the hash will be compared to the one stored and if
-        they match the true value will be returned. This is stored in a sqlite
-        `.db` next to the config file and is hidden by default. If the hash
-        provided doesn't match the default behaviour is to update the `.db`
-        with the new value and hash the value again. If you delete the
-        database file then you will need to set the value again in the
-        `config.toml`.
-    cast : Any, optional
-        The type of the variable.
-    check : Union[None, List], optional
-        Type of object to check against. This is useful if you want to use TOML
-        to define a list, but want to make sure that a string representation
-        of a list will be loaded properly if it set as an environment variable.
-
-        Example:
-
-        *config.toml* has the following attribute set::
-
-            [package.users]
-            auth = ['user1', 'user2']
-
-        If set as an environment variable you can pass this list as a string
-        and set :code:`check=list`::
-
-            Environment variable:
-            PACKAGE_USERS_AUTH = "['user1', 'user2']"
-
-        Usage in code::
-
-            set_config(CONFIG, 'users.auth', check=list)
-    """
-    config_var = key.lower().replace('.', '_')
-    if check is None:
-        setattr(
-            config_inst, config_var, config_inst.get(key, default, cast, mask)
-        )
-    else:
-        if type(config_inst.get(key, default, cast, mask)) is not check:
-            if check is list:
-                var = ast.literal_eval(
-                    config_inst.get(key, default, cast, mask)
-                )
-                setattr(config_inst, config_var, var)
-        else:
-            setattr(
-                config_inst,
-                config_var,
-                config_inst.get(key, default, cast, mask),
-            )
-
-
-# Create function to print cached logged messages and reset
-def process_cached_logs(
-    config_inst: Type[config_inst_t], logger: logging.Logger
-):
-    """Prints the cached messages from :class:`~panaetius.config.Config`
-    and resets the cache.
-
-    Parameters
-    ----------
-    config_inst : Type[config_inst_t]
-        Instance of :class:`~panaetius.config.Config`.
-    logger : logging.Logger
-        Instance of the logger.
-    """
-    for msg in config_inst.deferred_messages:
-        logger.info(msg)
-    config_inst.reset_log()
--- a/old_src/panaetius/logging.py
+++ b/old_src/panaetius/logging.py
@@ -1,54 +0,0 @@
-import logging
-from logging.handlers import RotatingFileHandler
-import os
-import sys
-
-import panaetius
-from panaetius import CONFIG as CONFIG
-from panaetius import __header__ as __header__
-from panaetius import set_config as set_config
-
-
-panaetius.set_config(CONFIG, 'logging.path')
-panaetius.set_config(
-    CONFIG,
-    'logging.format',
-    '{\n\t"time": "%(asctime)s",\n\t"file_name": "%(filename)s",'
-    '\n\t"module": "%(module)s",\n\t"function":"%(funcName)s",\n\t'
-    '"line_number": "%(lineno)s",\n\t"logging_level":'
-    '"%(levelname)s",\n\t"message": "%(message)s"\n}',
-    cast=str,
-)
-set_config(CONFIG, 'logging.level', 'INFO')
-
-# Logging Configuration
-logger = logging.getLogger(__header__)
-loghandler_sys = logging.StreamHandler(sys.stdout)
-
-# Checking if log path is set
-if CONFIG.logging_path:
-    CONFIG.logging_path += (
-        f'{__header__}.log'
-        if CONFIG.logging_path[-1] == '/'
-        else f'/{__header__}.log'
-    )
-    # Set default log file options
-    set_config(CONFIG, 'logging.backup_count', 3, int)
-    set_config(CONFIG, 'logging.rotate_bytes', 512000, int)
-
-    # Configure file handler
-    loghandler_file = RotatingFileHandler(
-        os.path.expanduser(CONFIG.logging_path),
-        'a',
-        CONFIG.logging_rotate_bytes,
-        CONFIG.logging_backup_count,
-    )
-
-    # Add to file formatter
-    loghandler_file.setFormatter(logging.Formatter(CONFIG.logging_format))
-    logger.addHandler(loghandler_file)
-
-# Configure and add to stdout formatter
-loghandler_sys.setFormatter(logging.Formatter(CONFIG.logging_format))
-logger.addHandler(loghandler_sys)
-logger.setLevel(CONFIG.logging_level)
--- a/panaetius/init.py
+++ b/panaetius/init.py
@@ -1,5 +1,7 @@
 """
-panaetius - a utility library to read variables and provide convenient logging.
+Panaetius package.
+
+A utility library to read variables and provide convenient logging.

 Author: Daniel Tomlinson (dtomlinson@panaetius.co.uk)
 """
--- a/panaetius/_version.py
+++ b/panaetius/_version.py
@@ -0,0 +1,3 @@
+"""Module containing the version of panaetius."""
+
+__version__ = "2.3.2"
--- a/panaetius/config.py
+++ b/panaetius/config.py
@@ -1,8 +1,8 @@
 """
-Access variables from a config file or an environment variable.
+Config module to access variables from a config file or an environment variable.

 This module defines the `Config` class to interact and read variables from either a
-`config.toml` or an environment variable.
+`config.yml` or an environment variable.
 """

 from __future__ import annotations
@@ -12,33 +12,53 @@ import os
 import pathlib
 from typing import Any

-import toml
+# import toml
+import yaml

-from panaetius.exceptions import KeyErrorTooDeepException, InvalidPythonException
+from panaetius.exceptions import KeyErrorTooDeepException


 class Config:
-    """The configuration class to access variables."""
+    """
+    A configuration class to access user variables.

-    def __init__(self, header_variable: str, config_path: str = "") -> None:
+    Args:
+        header_variable (str): the `header` variable.
+        config_path (str|None=None): the path where the header directory is stored.
+        skip_header_init (bool=False): if True will not use a header subdirectory in the
+            `config_path`.
+
+    """
+
+    def __init__(
+        self,
+        header_variable: str,
+        config_path: str | None = None,
+        skip_header_init: bool = False,
+    ) -> None:
        """
        Create a Config object to set and access variables.

        Args:
            header_variable (str): Your header variable name.
            config_path (str, optional): The path where the header directory is stored.
-                Defaults to `~/.config`.
+                Defaults to None on initialisation.
+            skip_header_init (bool, optional): If True will not use a header
+                subdirectory in the `config_path`. Defaults to False.
+
+        Examples:
+            `config_path` defaults to None on initialisation but will be set to `~/.config`.

-        Example:
            A header of `data_analysis` with a config_path of `~/myapps` will define
-                a config file in `~/myapps/data_analysis/config.toml`.
+                a config file in `~/myapps/data_analysis/config.yml`.
        """
        self.header_variable = header_variable
        self.config_path = (
-            pathlib.Path(config_path)
-            if config_path
+            pathlib.Path(config_path).expanduser()
+            if config_path is not None
            else pathlib.Path.home() / ".config"
        )
+        self.skip_header_init = skip_header_init
        self._missing_config = self._check_config_file_exists()

        # default logging options
@@ -49,15 +69,23 @@ class Config:
    @property
    def config(self) -> dict:
        """
-        Return the contents of the config file. If missing returns an empty dictionary.
+        Return the contents of the config file.
+
+        If no config file is specified then this returns an empty dictionary.

        Returns:
-            dict: The contents of the `.toml` loaded as a python dictionary.
+            dict: The contents of the config `.yml` loaded as a python dictionary.
        """
-        config_file_location = self.config_path / self.header_variable / "config.toml"
+        if self.skip_header_init:
+            config_file_location = self.config_path / "config.yml"
+        else:
+            config_file_location = (
+                self.config_path / self.header_variable / "config.yml"
+            )
        try:
            with open(config_file_location, "r", encoding="utf-8") as config_file:
-                return dict(toml.load(config_file))
+                # return dict(toml.load(config_file))
+                return dict(yaml.load(stream=config_file, Loader=yaml.SafeLoader))
        except FileNotFoundError:
            return {}

@@ -67,8 +95,8 @@ class Config:

        The key can either be one (`value`) or two (`data.value`) levels deep.

-        A key of (`value`) (with a header of `data_analysis`) would refer to a
-        `config.toml` of:
+        A key of `value` (with a header of `data_analysis`) would refer to a
+        `config.yml` of:

        ```
        [data_analysis]
@@ -77,7 +105,7 @@ class Config:

        or an environment variable of `DATA_ANALYSIS_VALUE="'some value'"`.

-        A key of (`data.value`) would refer to a `config.toml` of:
+        A key of `data.value` would refer to a `config.yml` of:
        ```
        [data_analysis.data]
        value = "some value"
@@ -101,7 +129,10 @@ class Config:
        return self._get_env_value(env_key, default)

    def _check_config_file_exists(self) -> bool:
-        config_file_location = self.config_path / self.header_variable / "config.toml"
+        if self.skip_header_init is False:
+            config_file_location = self.config_path / self.header_variable / "config.yml"
+        else:
+            config_file_location = self.config_path / "config.yml"
        try:
            with open(config_file_location, "r", encoding="utf-8"):
                return False
@@ -163,7 +194,8 @@ class Config:
        try:
            return ast.literal_eval(value)
        except (ValueError, SyntaxError):
-            raise InvalidPythonException(f"{value} is not valid Python.")  # noqa
+            # string without spaces: ValueError, with spaces; SyntaxError
+            return value

    def __load_default_value(self, default: Any) -> Any:  # noqa
        return default
--- a/panaetius/exceptions.py
+++ b/panaetius/exceptions.py
@@ -1,13 +1,13 @@
-"""Exceptions for the module."""
+"""Module that defines custom exceptions for Panetius."""


 class KeyErrorTooDeepException(Exception):
-    pass
+    """Raised if the keys in the config.yml are nested too deeply."""


 class LoggingDirectoryDoesNotExistException(Exception):
-    pass
+    """Raised if the logging directory does not exist."""


 class InvalidPythonException(Exception):
-    pass
+    """Raised if the environement variable Python type is invalid."""
--- a/panaetius/logging.py
+++ b/panaetius/logging.py
@@ -63,11 +63,17 @@ def set_logger(config_inst: Config, logging_format_inst: LoggingData) -> logging

    # configure file handler
    if config_inst.logging_path is not None:
+        if not config_inst.skip_header_init:
            logging_file = (
                pathlib.Path(config_inst.logging_path)
                / config_inst.header_variable
                / f"{config_inst.header_variable}.log"
            ).expanduser()
+        else:
+            logging_file = (
+                pathlib.Path(config_inst.logging_path)
+                / f"{config_inst.header_variable}.log"
+            ).expanduser()

        if not logging_file.parents[0].exists():
            raise LoggingDirectoryDoesNotExistException()
@@ -98,11 +104,11 @@ class LoggingData(metaclass=ABCMeta):
    @property
    @abstractmethod
    def format(self) -> str:
-        pass
+        raise NotImplementedError

    @abstractmethod
    def __init__(self, logging_level: str):
-        self.logging_level = logging_level
+        raise NotImplementedError


 class SimpleLogger(LoggingData):
--- a/panaetius/utilities/init.py
+++ b/panaetius/utilities/init.py
@@ -0,0 +1,3 @@
+"""Sub-package which defines general utility functions."""
+
+from panaetius.utilities.squasher import Squash
--- a/panaetius/utilities/squasher.py
+++ b/panaetius/utilities/squasher.py
@@ -0,0 +1,64 @@
+"""Sub-module that defines squashing json objects into a single json object."""
+
+from __future__ import annotations
+
+from copy import deepcopy
+import itertools
+from typing import Iterator, Tuple
+
+
+class Squash:
+    """Squash a json object or Python dictionary into a single level dictionary."""
+
+    def __init__(self, data: dict) -> None:
+        """
+        Create a Squash object to squash data into a single level dictionary.
+
+        Args:
+            data (dict): [description]
+
+        Example:
+            squashed_data = Squash(my_data)
+
+            squashed_data.as_dict
+        """
+        self.data = data
+
+    @property
+    def as_dict(self) -> dict:
+        """
+        Return the squashed data as a dictionary.
+
+        Returns:
+            dict: The original data squashed as a dict.
+        """
+        return self._squash()
+
+    @staticmethod
+    def _unpack_dict(
+        key: str, value: dict | list | str
+    ) -> Iterator[Tuple[str, dict | list | str]]:
+        if isinstance(value, dict):
+            for sub_key, sub_value in value.items():
+                temporary_key = f"{key}_{sub_key}"
+                yield temporary_key, sub_value
+        elif isinstance(value, list):
+            for index, sub_value in enumerate(value):
+                temporary_key = f"{key}_{index}"
+                yield temporary_key, sub_value
+        else:
+            yield key, value
+
+    def _squash(self) -> dict:
+        result = deepcopy(self.data)
+        while True:
+            result = dict(
+                itertools.chain.from_iterable(
+                    itertools.starmap(self._unpack_dict, result.items())
+                )
+            )
+            if not any(
+                isinstance(value, dict) for value in result.values()
+            ) and not any(isinstance(value, list) for value in result.values()):
+                break
+        return result
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,3 +1,18 @@
+[[package]]
+name = "ansimarkup"
+version = "1.5.0"
+description = "Produce colored terminal text with an xml-like markup"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+colorama = "*"
+
+[package.extras]
+devel = ["bumpversion (>=0.5.2)", "check-manifest (>=0.35)", "readme-renderer (>=16.0)", "flake8", "pep8-naming"]
+tests = ["tox (>=2.6.0)", "pytest (>=3.0.3)", "pytest-cov (>=2.3.1)"]
+
 [[package]]
 name = "astroid"
 version = "2.8.2"
@@ -49,6 +64,14 @@ PyYAML = ">=5.3.1"
 six = ">=1.10.0"
 stevedore = ">=1.20.0"

+[[package]]
+name = "cached-property"
+version = "1.5.2"
+description = "A decorator for caching properties in classes."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "colorama"
 version = "0.4.4"
@@ -76,6 +99,18 @@ category = "dev"
 optional = false
 python-versions = "*"

+[[package]]
+name = "duty"
+version = "0.7.0"
+description = "A simple task runner."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cached-property = {version = ">=1.5,<2.0", markers = "python_version < \"3.8\""}
+failprint = ">=0.8,<1.0"
+
 [[package]]
 name = "execnet"
 version = "1.9.0"
@@ -87,6 +122,19 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 [package.extras]
 testing = ["pre-commit"]

+[[package]]
+name = "failprint"
+version = "0.8.0"
+description = "Run a command, print its output only if it fails."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+ansimarkup = ">=1.4,<2.0"
+jinja2 = ">=2.11,<4"
+ptyprocess = {version = ">=0.6,<1.0", markers = "sys_platform != \"win32\""}
+
 [[package]]
 name = "flake8"
 version = "2.3.0"
@@ -173,6 +221,20 @@ requirements_deprecated_finder = ["pipreqs", "pip-api"]
 colors = ["colorama (>=0.4.3,<0.5.0)"]
 plugins = ["setuptools"]

+[[package]]
+name = "jinja2"
+version = "3.0.3"
+description = "A very fast and expressive template engine."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
 [[package]]
 name = "lazy-object-proxy"
 version = "1.6.0"
@@ -181,6 +243,14 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"

+[[package]]
+name = "markupsafe"
+version = "2.0.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "mccabe"
 version = "0.6.1"
@@ -315,6 +385,14 @@ with_mypy = ["mypy (>=0.600)"]
 with_pyroma = ["pyroma (>=2.4)"]
 with_vulture = ["vulture (>=1.5)"]

+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "py"
 version = "1.10.0"
@@ -421,14 +499,6 @@ python-versions = "*"
 [package.dependencies]
 pylint = ">=1.7"

-[[package]]
-name = "pylite"
-version = "0.1.0"
-description = "Intract with sqlite3 in python as simple as it can be."
-category = "main"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "pyparsing"
 version = "2.4.7"
@@ -504,7 +574,7 @@ testing = ["filelock"]
 name = "pyyaml"
 version = "6.0"
 description = "YAML parser and emitter for Python"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"

@@ -621,9 +691,13 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytes
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7"
-content-hash = "468d1aa5e0c440262f6041ad859358a84ef32462941aa6f3ba71838a52cc1ced"
+content-hash = "dcca7e2e7b6854ab40c11f6e3385b08fffb34b874981f1079205855badd7caea"

 [metadata.files]
+ansimarkup = [
+    {file = "ansimarkup-1.5.0-py2.py3-none-any.whl", hash = "sha256:3146ca74af5f69e48a9c3d41b31085c0d6378f803edeb364856d37c11a684acf"},
+    {file = "ansimarkup-1.5.0.tar.gz", hash = "sha256:96c65d75bbed07d3dcbda8dbede8c2252c984f90d0ca07434b88a6bbf345fad3"},
+]
 astroid = [
    {file = "astroid-2.8.2-py3-none-any.whl", hash = "sha256:9eaeaf92b3e21b70bec1a262e7eb118d2e96294892a5de595c92a12adc80dfc2"},
    {file = "astroid-2.8.2.tar.gz", hash = "sha256:304e99c129794f2cfda584a12b71fde85205da950e2f330f4be09150525ae949"},
@@ -640,6 +714,10 @@ bandit = [
    {file = "bandit-1.7.0-py3-none-any.whl", hash = "sha256:216be4d044209fa06cf2a3e51b319769a51be8318140659719aa7a115c35ed07"},
    {file = "bandit-1.7.0.tar.gz", hash = "sha256:8a4c7415254d75df8ff3c3b15cfe9042ecee628a1e40b44c15a98890fbfc2608"},
 ]
+cached-property = [
+    {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"},
+    {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"},
+]
 colorama = [
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 py = [
    {file = "py-1.10.0-py2.py3-none-any.whl", hash = "sha256:3b80836aa6d1feeaa108e046da6423ab8f6ceda6468545ae8d02d9d58d18818a"},
    {file = "py-1.10.0.tar.gz", hash = "sha256:21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3"},
@@ -834,10 +999,6 @@ pylint-plugin-utils = [
    {file = "pylint-plugin-utils-0.6.tar.gz", hash = "sha256:57625dcca20140f43731311cd8fd879318bf45a8b0fd17020717a8781714a25a"},
    {file = "pylint_plugin_utils-0.6-py3-none-any.whl", hash = "sha256:2f30510e1c46edf268d3a195b2849bd98a1b9433229bb2ba63b8d776e1fc4d0a"},
 ]
-pylite = [
-    {file = "pylite-0.1.0-py3-none-any.whl", hash = "sha256:eb46f5beb1f2102672fd4355c013ac2feebc0df284d65f7711f2041a0a410141"},
-    {file = "pylite-0.1.0.tar.gz", hash = "sha256:e338d20d3f8f72dd84d1e58f2fd6dba008d593e0cfacfb5fbdd5a297b830628e"},
-]
 pyparsing = [
    {file = "pyparsing-2.4.7-py2.py3-none-any.whl", hash = "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"},
    {file = "pyparsing-2.4.7.tar.gz", hash = "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1"},
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,10 +1,10 @@
 [tool.poetry]
 name = "panaetius"
-version = "1.1"
+version = "2.3.2"
 description = "Python module to gracefully handle a .config file/environment variables for scripts, with built in masking for sensitive options. Provides a Splunk friendly formatted logger instance."
 license = "MIT"
 authors = ["dtomlinson <dtomlinson@panaetius.co.uk>"]
-readme = "./README.rst"
+readme = "./README.md"
 homepage = "https://github.com/dtomlinson91/panaetius"
 repository = "https://github.com/dtomlinson91/panaetius"
 documentation = "https://panaetius.readthedocs.io/en/latest/introduction.html"
@@ -25,7 +25,7 @@ classifiers = [
 [tool.poetry.dependencies]
 python = "^3.7"
 toml = "^0.10.0"
-pylite = "^0.1.0"
+PyYAML = "^6.0"

 [tool.poetry.dev-dependencies]
 prospector = {extras = ["with_bandit", "with_mypy"], version = "^1.5.1"}
@@ -34,6 +34,7 @@ pytest = "^6.2.5"
 pytest-datadir = "^1.3.1"
 pytest-xdist = "^2.4.0"
 coverage = "^6.0.2"
+duty = "^0.7.0"

 [build-system]
 requires = ["poetry>=0.12"]
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,2 @@
-pylite==0.1.0 \
-    --hash=sha256:e338d20d3f8f72dd84d1e58f2fd6dba008d593e0cfacfb5fbdd5a297b830628e \
-    --hash=sha256:eb46f5beb1f2102672fd4355c013ac2feebc0df284d65f7711f2041a0a410141
-toml==0.10.0 \
-    --hash=sha256:229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c \
-    --hash=sha256:235682dd292d5899d361a811df37e04a8828a5b1da3115886b73cf81ebc9100e \
-    --hash=sha256:f1db651f9657708513243e61e6cc67d101a39bad662eaa9b5546f789338e07a3
+pyyaml==6.0; python_version >= "3.6"
+toml==0.10.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -0,0 +1,60 @@
+ansimarkup==1.5.0; python_version >= "3.6"
+astroid==2.8.2; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
+atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
+attrs==21.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+bandit==1.7.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.5"
+cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
+colorama==0.4.4; sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.6.1" and python_version < "4.0" and platform_system == "Windows" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
+coverage==6.0.2; python_version >= "3.6"
+dodgy==0.2.1; python_full_version >= "3.6.1" and python_version < "4.0"
+duty==0.7.0; python_version >= "3.6"
+execnet==1.9.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+failprint==0.8.0; python_version >= "3.6"
+flake8-polyfill==1.0.2; python_full_version >= "3.6.1" and python_version < "4.0"
+flake8==2.3.0; python_full_version >= "3.6.1" and python_version < "4.0"
+gitdb==4.0.7; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.7"
+gitpython==3.1.24; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.7"
+importlib-metadata==4.8.1; python_version < "3.8" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and python_full_version >= "3.6.1"
+iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+isort==5.9.3; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
+jinja2==3.0.3; python_version >= "3.6"
+lazy-object-proxy==1.6.0; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
+markupsafe==2.0.1; python_version >= "3.6"
+mccabe==0.6.1; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
+mypy-extensions==0.4.3; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.5"
+mypy==0.910; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.5"
+packaging==21.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+pbr==5.6.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
+pep8-naming==0.10.0; python_full_version >= "3.6.1" and python_version < "4.0"
+pep8==1.7.1; python_full_version >= "3.6.1" and python_version < "4.0"
+platformdirs==2.4.0; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
+pluggy==1.0.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+prospector==1.5.1; python_full_version >= "3.6.1" and python_version < "4.0"
+ptyprocess==0.7.0; sys_platform != "win32" and python_version >= "3.6"
+py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+pycodestyle==2.8.0; python_full_version >= "3.6.1" and python_version < "4.0"
+pydocstyle==6.1.1; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
+pyflakes==2.3.1; python_full_version >= "3.6.1" and python_version < "4.0"
+pylint-celery==0.3; python_full_version >= "3.6.1" and python_version < "4.0"
+pylint-django==2.4.4; python_full_version >= "3.6.1" and python_version < "4.0"
+pylint-flask==0.6; python_full_version >= "3.6.1" and python_version < "4.0"
+pylint-plugin-utils==0.6; python_full_version >= "3.6.1" and python_version < "4.0"
+pylint==2.11.1; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
+pyparsing==2.4.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
+pytest-datadir==1.3.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+pytest-forked==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+pytest-xdist==2.4.0; python_version >= "3.6"
+pytest==6.2.5; python_version >= "3.6"
+pyyaml==6.0; python_version >= "3.6"
+requirements-detector==0.7; python_full_version >= "3.6.1" and python_version < "4.0"
+setoptconf-tmp==0.3.1; python_full_version >= "3.6.1" and python_version < "4.0"
+six==1.16.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.5"
+smmap==4.0.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.7"
+snowballstemmer==2.1.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
+stevedore==3.4.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
+toml==0.10.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+typed-ast==1.4.3; python_full_version >= "3.6.1" and python_version < "3.8" and python_version >= "3.6" and implementation_name == "cpython"
+types-toml==0.10.1
+typing-extensions==3.10.0.2; python_full_version >= "3.6.1" and python_version < "3.8" and python_version >= "3.7"
+wrapt==1.12.1; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
+zipp==3.6.0; python_version < "3.8" and python_version >= "3.6"
--- a/rewrite.todo
+++ b/rewrite.todo
@@ -1,70 +0,0 @@
-Coding:
-    No Config File:
-        ✔ Handle if a bool is passed in as a default @done(21-10-16 05:25)
-        needs to be lower case in the toml, need a check for this
-
-    Config File:
-        ✔ Handle if a bool is passed in as a default @done(21-10-16 05:25)
-        needs to be lower case in the toml, need a check for this
-
-    Logging:
-        ✔ Create SimpleLogger, AdvancedLogger, CustomLogger classes @done(21-10-16 16:22)
-        should simply have the different logging strings to output
-        should both specify whether to save to file or not
-        ✔ Logging path should take by default the config path unless overwritten? @done(21-10-16 23:49)
-
-    Errors:
-        ✔ Check logging path + config path are valid, if not raise error. @done(21-10-18 00:04)
-            ✔ Add tests for these. @done(21-10-18 00:04)
-        ✔ Check for a key > 2 levels, raise custom error, write test @done(21-10-17 23:30)
-
-    Linting:
-        ✔ Check all functions and annotations. @done(21-10-18 01:07)
-
-    Docstrings:
-        ✔ Write the docstrings for public functions/methods. @done(21-10-18 02:29)
-
-    Functionality:
-        ✔ When both a config file and a env var is found, use the env var. @done(21-10-18 00:38)
-
-Documentation:
-    ☐ Rewrite documentation using `mkdocs` and using `.md`. @2h
-
-Misc:
-    ☐ Use the python runner to build the docs & run the tests (including coverage html)
-        coverage run -m pytest && coverage report && coverage html
-        ☐ document this in trilium
-
-Tests:
-    Bugfixes:
-        ✔ If loading from a default, don't covert to TOML @done(21-10-17 20:33)
-        ✔ Env Vars should be given as python objects @done(21-10-17 20:33)
-            The string or node provided may only consist of the following Python literal structures: strings, bytes, numbers, tuples, lists, dicts, sets, booleans, and None.
-            use ast.literal_eval()
-            https://docs.python.org/3/library/ast.html#ast.literal_eval
-
-    __init__:
-        ✔ Test default config path set to "~/.config" @done(21-10-17 17:25)
-        ✔ Test config path is set when passed in @done(21-10-17 17:25)
-
-    config property:
-        ✔ Check testing config file is returned as dict @done(21-10-17 17:25)
-        ✔ Check _self.missing_config and empty dict is returned @done(21-10-17 17:25)
-
-    get_value:
-        config_file:
-            ✔ Arrays & tables loaded correctly from config file @done(21-10-17 20:34)
-            ✔ test when key length is 1 the value is returned @done(21-10-17 18:55)
-            ✔ test when key length is 2 the value is returned @done(21-10-17 18:55)
-            ✔ test when key not found and no env var default is loaded @done(21-10-17 19:01)
-                ✔ test bool's are properly converted @done(21-10-17 19:01)
-            ✔ test when key not found and env var is set value is loaded @done(21-10-17 20:43)
-
-        env_var:
-            ✔ check if env key is missing the default is read in @done(21-10-17 20:55)
-            ✔ check if env key is present the values are read in @done(21-10-17 22:24)
-                ✔ parametrise a test to read in values form env vars and they're set correctly @done(21-10-17 22:24)
-            ✔ test that the env var is valid python @done(21-10-18 01:03)
-
-    library:
-        ✔ test set_config works @done(21-10-17 23:29)
--- a/setup.py
+++ b/setup.py
@@ -1,27 +1,25 @@
 # -*- coding: utf-8 -*-
-from distutils.core import setup
-
-package_dir = \
-{'': 'src'}
+from setuptools import setup

 packages = \
-['panaetius']
+['panaetius', 'panaetius.utilities']

 package_data = \
 {'': ['*']}

 install_requires = \
-['pylite>=0.1.0,<0.2.0', 'toml>=0.10.0,<0.11.0']
+['PyYAML>=6.0,<7.0', 'toml>=0.10.0,<0.11.0']

 setup_kwargs = {
    'name': 'panaetius',
-    'version': '1.0.2',
-    'description': 'Python module to gracefully handle a .config file/environment variables for scripts, with built in masking for sensitive options. Provides a Splunk friendly logger instance.',
-    'long_description': 'Author\n=======\n\nDaniel Tomlinson (dtomlinson@panaetius.co.uk)\n\nRequires\n=========\n\n`>= python3.7`\n\nPython requirements\n====================\n\n- toml = "^0.10.0"\n- pylite = "^0.1.0"\n\nDocumentation\n==============\n\nRead the documentation on `read the docs`_.\n\n.. _read the docs: https://panaetius.readthedocs.io/en/latest/introduction.html\n\nInstallation\n==============\n\nYou can install ..:obj:`panaetius`\n\nEasy Way\n=========\n\nPython\n-------\n\nFrom pip\n~~~~~~~~~\n\nFrom local wheel\n~~~~~~~~~~~~~~~~~\n\nFrom source\n~~~~~~~~~~~~\n\nExample Usage\n==============\n\n',
+    'version': '2.3.1',
+    'description': 'Python module to gracefully handle a .config file/environment variables for scripts, with built in masking for sensitive options. Provides a Splunk friendly formatted logger instance.',
+    'long_description': '# Panaetius\n\nThis package provides:\n\n- Functionality to read user variables from a `config.yml` or environment variables.\n- A convenient default logging formatter printing `json` that can save to disk and rotate.\n- Utility functions.\n\n## Config\n\n### options\n\n#### skip_header_init\n\nIf `skip_header_init=True` then the `config_path` will not use the `header_variable` as the\nsub-directory in the `config_path`.\n\nE.g\n\n`CONFIG = panaetius.Config("tembo", "~/tembo/.config", skip_header_init=True)`\n\nWill look in `~/tembo/config/config.yml`.\n\nIf `skip_header_init=False` then would look in `~/tembo/config/tembo/config.yml`.\n\n### Module\n\nConvenient to place in a package/sub-package `__init__.py`.\n\nSee Tembo for an example: <https://github.com/tembo-pages/tembo-core/blob/main/tembo/cli/__init__.py>\n\nExample snippet to use in a module:\n\n```python\nimport os\n\nimport panaetius\nfrom panaetius.exceptions import LoggingDirectoryDoesNotExistException\n\n\nif (config_path := os.environ.get("TEMBO_CONFIG")) is not None:\n    CONFIG = panaetius.Config("tembo", config_path, skip_header_init=True)\nelse:\n    CONFIG = panaetius.Config("tembo", "~/tembo/.config", skip_header_init=True)\n\n\npanaetius.set_config(CONFIG, "base_path", "~/tembo")\npanaetius.set_config(CONFIG, "template_path", "~/tembo/.templates")\npanaetius.set_config(CONFIG, "scopes", {})\npanaetius.set_config(CONFIG, "logging.level", "DEBUG")\npanaetius.set_config(CONFIG, "logging.path")\n\ntry:\n    logger = panaetius.set_logger(\n        CONFIG, panaetius.SimpleLogger(logging_level=CONFIG.logging_level)\n    )\nexcept LoggingDirectoryDoesNotExistException:\n    _LOGGING_PATH = CONFIG.logging_path\n    CONFIG.logging_path = ""\n    logger = panaetius.set_logger(\n        CONFIG, panaetius.SimpleLogger(logging_level=CONFIG.logging_level)\n    )\n    logger.warning("Logging directory %s does not exist", _LOGGING_PATH)\n\n```\n\nThis means in `./tembo/cli/cli.py` you can\n\n```python\nimport tembo.cli\n\n# access the CONFIG instance + variables from the config.yml\ntembo.cli.CONFIG\n```\n\n\n## Utility Functions\n\n### Squasher\n\nSquashes a json object or Python dictionary into a single level dictionary.\n',
    'author': 'dtomlinson',
    'author_email': 'dtomlinson@panaetius.co.uk',
+    'maintainer': None,
+    'maintainer_email': None,
    'url': 'https://github.com/dtomlinson91/panaetius',
-    'package_dir': package_dir,
    'packages': packages,
    'package_data': package_data,
    'install_requires': install_requires,
--- a/tests/data/without_header/config.yml
+++ b/tests/data/without_header/config.yml
@@ -0,0 +1,9 @@
+panaetius_testing:
+  some_top_string: some_top_value
+  second:
+    some_second_string: some_second_value
+    some_second_int: 1
+    some_second_float: 1.0
+    some_second_list: ["some", "second", "value"]
+    some_second_table: { "first": ["some", "first", "value"] }
+    some_second_table_bools: { "bool": [true, false] }
--- a/tests/data/without_logging/panaetius_testing/config.yml
+++ b/tests/data/without_logging/panaetius_testing/config.yml
@@ -0,0 +1,9 @@
+panaetius_testing:
+  some_top_string: some_top_value
+  second:
+    some_second_string: some_second_value
+    some_second_int: 1
+    some_second_float: 1.0
+    some_second_list: ["some", "second", "value"]
+    some_second_table: { "first": ["some", "first", "value"] }
+    some_second_table_bools: { "bool": [true, false] }
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -29,6 +29,17 @@ def test_user_config_path_set(header, shared_datadir):
    assert str(config.config_path) == config_path


+def test_user_config_path_without_header_dir_set(header, shared_datadir):
+    # arrange
+    config_path = str(shared_datadir / "without_header")
+
+    # act
+    config = panaetius.Config(header, config_path, skip_header_init=True)
+
+    # assert
+    assert str(config.config_path) == config_path
+
+
 # test config files


@@ -44,6 +55,18 @@ def test_config_file_exists(header, shared_datadir):
    assert config._missing_config is False


+def test_config_file_without_header_dir_exists(header, shared_datadir):
+    # arrange
+    config_path = str(shared_datadir / "without_header")
+
+    # act
+    config = panaetius.Config(header, config_path, skip_header_init=True)
+    _ = config.config
+
+    # assert
+    assert config._missing_config is False
+
+
 def test_config_file_contents_read_success(
    header, shared_datadir, testing_config_contents
 ):
@@ -106,7 +129,7 @@ def test_get_value_from_key(

 def test_get_value_environment_var_override(header, shared_datadir):
    # arrange
-    os.environ[f"{header.upper()}_SOME_TOP_STRING"] = '"some_overridden_value"'
+    os.environ[f"{header.upper()}_SOME_TOP_STRING"] = "some_overridden_value"
    config_path = str(shared_datadir / "without_logging")
    config = panaetius.Config(header, config_path)
    panaetius.set_config(config, "some_top_string")
@@ -158,7 +181,7 @@ def test_get_value_missing_key_from_default(header, shared_datadir):

 def test_get_value_missing_key_from_env(header, shared_datadir):
    # arrange
-    os.environ[f"{header.upper()}_MISSING_KEY"] = '"some missing key"'
+    os.environ[f"{header.upper()}_MISSING_KEY"] = "some missing key"

    config_path = str(shared_datadir / "without_logging")
    config = panaetius.Config(header, config_path)
@@ -205,7 +228,7 @@ def test_missing_config_read_from_default(header, shared_datadir):
@pytest.mark.parametrize(
    "env_value,expected_value",
    [
-        ('"a missing string"', "a missing string"),
+        ("a missing string", "a missing string"),
        ("1", 1),
        ("1.0", 1.0),
        ("True", True),
@@ -237,6 +260,7 @@ def test_missing_config_read_from_env_var(
    del os.environ[f"{header.upper()}_MISSING_KEY_READ_FROM_ENV_VAR"]


+@pytest.mark.skip(reason="No longer needed as strings are loaded without quotes")
 def test_missing_config_read_from_env_var_invalid_python(header):
    # arrange
    os.environ[f"{header.upper()}_INVALID_PYTHON"] = "a string without quotes"
--- a/tests/test_logging.py
+++ b/tests/test_logging.py
@@ -21,6 +21,7 @@ def test_logging_directory_does_not_exist(header, shared_datadir):
    assert str(logging_exception.value) == ""


+# TODO: change this test so it asserts the dir exists
 def test_logging_directory_does_exist(header, shared_datadir):
    # arrange
    config = Config(header)
@@ -32,3 +33,5 @@ def test_logging_directory_does_exist(header, shared_datadir):

    # assert
    assert isinstance(logger, logging.Logger)
+
+# TODO: add tests to check that SimpleLogger, AdvancedLogger, CustomLogger work as intended
--- a/tests/test_utilities/init.py
+++ b/tests/test_utilities/init.py
--- a/tests/test_utilities/test_squasher.py
+++ b/tests/test_utilities/test_squasher.py
@@ -0,0 +1,119 @@
+import pytest
+
+from panaetius import utilities
+
+
+def test_squashed_data(squashed_data, squashed_data_result):
+    # act
+    squashed_data_pre_squashed = utilities.squasher.Squash(squashed_data).as_dict
+
+    # assert
+    assert squashed_data_pre_squashed == squashed_data_result
+
+
+@pytest.fixture
+def squashed_data():
+    return {
+        "destination_addresses": [
+            "Washington, DC, USA",
+            "Philadelphia, PA, USA",
+            "Santa Barbara, CA, USA",
+            "Miami, FL, USA",
+            "Austin, TX, USA",
+            "Napa County, CA, USA",
+        ],
+        "origin_addresses": ["New York, NY, USA"],
+        "rows": [
+            {
+                "elements": [
+                    {
+                        "distance": {"text": "227 mi", "value": 365468},
+                        "duration": {
+                            "text": "3 hours 54 mins",
+                            "value": 14064,
+                        },
+                        "status": "OK",
+                    },
+                    {
+                        "distance": {"text": "94.6 mi", "value": 152193},
+                        "duration": {"text": "1 hour 44 mins", "value": 6227},
+                        "status": "OK",
+                    },
+                    {
+                        "distance": {"text": "2,878 mi", "value": 4632197},
+                        "duration": {
+                            "text": "1 day 18 hours",
+                            "value": 151772,
+                        },
+                        "status": "OK",
+                    },
+                    {
+                        "distance": {"text": "1,286 mi", "value": 2069031},
+                        "duration": {
+                            "text": "18 hours 43 mins",
+                            "value": 67405,
+                        },
+                        "status": "OK",
+                    },
+                    {
+                        "distance": {"text": "1,742 mi", "value": 2802972},
+                        "duration": {"text": "1 day 2 hours", "value": 93070},
+                        "status": "OK",
+                    },
+                    {
+                        "distance": {"text": "2,871 mi", "value": 4620514},
+                        "duration": {
+                            "text": "1 day 18 hours",
+                            "value": 152913,
+                        },
+                        "status": "OK",
+                    },
+                ]
+            }
+        ],
+        "status": "OK",
+    }
+
+
+@pytest.fixture
+def squashed_data_result():
+    return {
+        "destination_addresses_0": "Washington, DC, USA",
+        "destination_addresses_1": "Philadelphia, PA, USA",
+        "destination_addresses_2": "Santa Barbara, CA, USA",
+        "destination_addresses_3": "Miami, FL, USA",
+        "destination_addresses_4": "Austin, TX, USA",
+        "destination_addresses_5": "Napa County, CA, USA",
+        "origin_addresses_0": "New York, NY, USA",
+        "rows_0_elements_0_distance_text": "227 mi",
+        "rows_0_elements_0_distance_value": 365468,
+        "rows_0_elements_0_duration_text": "3 hours 54 mins",
+        "rows_0_elements_0_duration_value": 14064,
+        "rows_0_elements_0_status": "OK",
+        "rows_0_elements_1_distance_text": "94.6 mi",
+        "rows_0_elements_1_distance_value": 152193,
+        "rows_0_elements_1_duration_text": "1 hour 44 mins",
+        "rows_0_elements_1_duration_value": 6227,
+        "rows_0_elements_1_status": "OK",
+        "rows_0_elements_2_distance_text": "2,878 mi",
+        "rows_0_elements_2_distance_value": 4632197,
+        "rows_0_elements_2_duration_text": "1 day 18 hours",
+        "rows_0_elements_2_duration_value": 151772,
+        "rows_0_elements_2_status": "OK",
+        "rows_0_elements_3_distance_text": "1,286 mi",
+        "rows_0_elements_3_distance_value": 2069031,
+        "rows_0_elements_3_duration_text": "18 hours 43 mins",
+        "rows_0_elements_3_duration_value": 67405,
+        "rows_0_elements_3_status": "OK",
+        "rows_0_elements_4_distance_text": "1,742 mi",
+        "rows_0_elements_4_distance_value": 2802972,
+        "rows_0_elements_4_duration_text": "1 day 2 hours",
+        "rows_0_elements_4_duration_value": 93070,
+        "rows_0_elements_4_status": "OK",
+        "rows_0_elements_5_distance_text": "2,871 mi",
+        "rows_0_elements_5_distance_value": 4620514,
+        "rows_0_elements_5_duration_text": "1 day 18 hours",
+        "rows_0_elements_5_duration_value": 152913,
+        "rows_0_elements_5_status": "OK",
+        "status": "OK",
+    }
Author	SHA1	Message	Date
Daniel Tomlinson	bd1aa09b4c	Merge branch 'develop'	2021-11-14 09:12:31 +00:00
Daniel Tomlinson	b0d635eb04	bumping to v2.3.2	2021-11-14 09:12:26 +00:00
Daniel Tomlinson	1d72b976a4	removing old docs, adding requirements	2021-11-14 08:53:11 +00:00
Daniel Tomlinson	4f93519c41	Merge branch 'develop'	2021-11-14 08:33:29 +00:00
Daniel Tomlinson	3a2a8951a7	updating docstrings, adding duty, updating README	2021-11-14 08:33:22 +00:00
Daniel Tomlinson	89655d46ae	patching to 2.2.2	2021-10-23 21:10:11 +01:00
Daniel Tomlinson	bbc580424c	Merge branch 'develop'	2021-10-23 21:08:37 +01:00
Daniel Tomlinson	8add8aaefd	Merge branch 'feature/skip_header_in_config_init' into develop	2021-10-23 21:08:27 +01:00
Daniel Tomlinson	1af790f01a	updating tests	2021-10-23 21:08:16 +01:00
Daniel Tomlinson	485ab9ef09	change abc to raise NotImplementedError for tests	2021-10-23 21:08:07 +01:00
Daniel Tomlinson	844a2f6f3f	changing env var to use strings without extra quotes	2021-10-23 21:07:31 +01:00
Daniel Tomlinson	2092245dad	adding skip header directory option	2021-10-23 21:07:07 +01:00
Daniel Tomlinson	16f753fdf3	updating todo	2021-10-23 21:05:36 +01:00
Daniel Tomlinson	9f1caf79ff	patch - v2.2.1	2021-10-23 05:06:10 +01:00
Daniel Tomlinson	70911f98b0	add expand_user to Config	2021-10-23 05:05:46 +01:00
Daniel Tomlinson	441a26127f	remove DS_Store	2021-10-23 05:05:35 +01:00
Daniel Tomlinson	9cc6f2483d	bumping to 2.2.0	2021-10-22 22:45:13 +01:00
Daniel Tomlinson	6e24f9d70b	adding Squash to __init__.py	2021-10-22 22:44:50 +01:00
Daniel Tomlinson	8c18d01f05	bumping version to 2.1	2021-10-20 22:29:19 +01:00
Daniel Tomlinson	d7700c4863	adding squasher utility	2021-10-20 22:29:08 +01:00
Daniel Tomlinson	948bc65e76	removing old files	2021-10-20 22:26:46 +01:00
Daniel Tomlinson	a0627a0922	Merge branch 'feature/toml_to_yaml' into develop	2021-10-19 21:46:49 +01:00
Daniel Tomlinson	525107ad63	adding a config.yml instead of config.toml	2021-10-19 21:46:41 +01:00
Daniel Tomlinson	d604179cbf	updating todos	2021-10-18 02:36:27 +01:00
Daniel Tomlinson	31fe9b1afc	removing old source code	2021-10-18 02:32:15 +01:00
Daniel Tomlinson	78b86967e7	Merge branch 'feature/rewrite' into develop	2021-10-18 02:31:35 +01:00