From f23f6a39038276cb442d655abca6ca01c866b6ce Mon Sep 17 00:00:00 2001
From: Trevor James Smith <10819524+Zeitsperre@users.noreply.github.com>
Date: Thu, 14 Mar 2024 17:05:55 -0400
Subject: [PATCH 01/18] pre-commit adjustments

---
 .pre-commit-config.yaml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7ed941d..9877520 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     rev: v3.15.1
     hooks:
       - id: pyupgrade
-        args: ['--py39-plus']
+        args: [ '--py39-plus' ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
@@ -19,11 +19,6 @@ repos:
     hooks:
       - id: nbstripout
         files: '.ipynb'
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        args: [ '--config=setup.cfg' ]
   - repo: https://github.com/psf/black
     rev: 24.2.0
     hooks:
@@ -34,15 +29,20 @@ repos:
     hooks:
     - id: isort
       args: [ '--profile=black' ]
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: [ '--config=setup.cfg' ]
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.8.4
     hooks:
-      - id: nbqa-black
-        args: [ '--target-version=py37' ]
-        additional_dependencies: [ 'black==24.2.0' ]
       - id: nbqa-pyupgrade
-        args: [ '--py37-plus' ]
+        args: [ '--py39-plus' ]
         additional_dependencies: [ 'pyupgrade==v3.15.1' ]
+      - id: nbqa-black
+        args: [ '--target-version=py39' ]
+        additional_dependencies: [ 'black==24.2.0' ]
       - id: nbqa-isort
         args: [ '--profile=black' ]
         additional_dependencies: [ 'isort==5.13.2' ]

From ae2f903a04037e5814468ba9078c018d98a2de9b Mon Sep 17 00:00:00 2001
From: Trevor James Smith <10819524+Zeitsperre@users.noreply.github.com>
Date: Thu, 14 Mar 2024 17:07:29 -0400
Subject: [PATCH 02/18] use sphinx-autodoc, sphinx-codeautolink,
 sphinx-copybutton, address documentation warnings, add automodule
 documentation

---
 .gitignore               |  1 +
 Makefile                 | 12 ++++++++++--
 birdy/client/__init__.py |  2 +-
 birdy/utils.py           |  5 ++---
 docs/source/api.rst      |  2 ++
 docs/source/conf.py      | 21 +++++++++++++++++++--
 docs/source/index.rst    |  7 +++++++
 environment-docs.yml     |  4 +++-
 requirements_dev.txt     | 23 ++++++++++++-----------
 9 files changed, 57 insertions(+), 20 deletions(-)

diff --git a/.gitignore b/.gitignore
index 29f0c60..79b3660 100644
--- a/.gitignore
+++ b/.gitignore
@@ -65,6 +65,7 @@ docs/make.bat
 docs/doctrees/
 docs/html/
 docs/build/
+docs/source/apidoc
 
 # External Sources
 #src/external
diff --git a/Makefile b/Makefile
index 0170f7f..b75973d 100644
--- a/Makefile
+++ b/Makefile
@@ -38,6 +38,11 @@ clean-build: ## remove build artifacts
 	find . -name '*.egg-info' -exec rm -fr {} +
 	find . -name '*.egg' -exec rm -f {} +
 
+clean-docs: ## remove docs artifacts
+	rm -f docs/apidoc/birdy*.rst
+	rm -f docs/apidoc/modules.rst
+	$(MAKE) -C docs clean
+
 clean-pyc: ## remove Python file artifacts
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
@@ -72,8 +77,11 @@ coverage: ## check code coverage quickly with the default Python
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
-docs: ## generate Sphinx HTML documentation, including API docs
-	$(MAKE) -C docs clean
+autodoc: clean-docs ## create sphinx-apidoc files
+	mkdir -p docs/source/apidoc/
+	sphinx-apidoc -o docs/source/apidoc/ --private --module-first birdy
+
+docs: autodoc ## generate Sphinx HTML documentation, including API docs
 	$(MAKE) -C docs html
 
 servedocs: docs ## compile the docs watching for changes
diff --git a/birdy/client/__init__.py b/birdy/client/__init__.py
index 3458a74..c6e0004 100644
--- a/birdy/client/__init__.py
+++ b/birdy/client/__init__.py
@@ -87,7 +87,7 @@
 Birdy's own defaults.
 
 However, it's possible to customize the output of a process. Each process has an input
-named ``output_formats`, that takes a dictionary as a parameter::
+named ``output_formats``, that takes a dictionary as a parameter::
 
     # example format = {
     #     'output_identifier': {
diff --git a/birdy/utils.py b/birdy/utils.py
index 06dde6f..1369b95 100644
--- a/birdy/utils.py
+++ b/birdy/utils.py
@@ -44,12 +44,11 @@ def is_url(url):
 
 
 def is_opendap_url(url):
-    """
-    Check if a provided url is an OpenDAP url.
+    """Check if a provided url is an OpenDAP url.
 
     The DAP Standard specifies that a specific tag must be included in the
     Content-Description header of every request. This tag is one of:
-        "dods-dds" | "dods-das" | "dods-data" | "dods-error"
+    "dods-dds" | "dods-das" | "dods-data" | "dods-error"
 
     So we can check if the header starts with `dods`.
 
diff --git a/docs/source/api.rst b/docs/source/api.rst
index 7a44b6c..0de3349 100644
--- a/docs/source/api.rst
+++ b/docs/source/api.rst
@@ -12,8 +12,10 @@ Using the command line
 ======================
 
 .. automodule:: birdy.cli
+    :noindex:
 
 Using the Python library
 ========================
 
 .. automodule:: birdy.client
+    :noindex:
diff --git a/docs/source/conf.py b/docs/source/conf.py
index e5c2736..329183a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -32,6 +32,11 @@
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx_codeautolink",
+    "sphinx_copybutton",
 ]
 
 autoapi_type = "python"
@@ -39,6 +44,9 @@
 autoapi_file_pattern = "*.py"
 autoapi_options = ["members", "undoc-members", "private-members"]
 
+autosectionlabel_prefix_document = True
+autosectionlabel_maxdepth = 2
+
 # To avoid having to install these and burst memory limit on ReadTheDocs.
 autodoc_mock_imports = [
     "click",
@@ -86,7 +94,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -96,7 +104,16 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "owslib-esgfwps.ipynb",
+    # Undocumented notebooks
+    "rook-demo.ipynb",
+    "twitcher-c3s-magic-demo.ipynb",
+    "twitcher-magic-cexp-demo.ipynb",
+]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 11cbd64..c5026cb 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -8,3 +8,10 @@
    development
    api
    changes
+
+Modules
+
+.. toctree::
+   :maxdepth: 1
+
+   apidoc/modules
diff --git a/environment-docs.yml b/environment-docs.yml
index 420dbfc..a328507 100644
--- a/environment-docs.yml
+++ b/environment-docs.yml
@@ -6,4 +6,6 @@ channels:
 dependencies:
   - ipython
   - nbsphinx
-  - sphinx
+  - sphinx >=7.0.0
+  - sphinx-codeautolink >=0.15.0
+  - sphinx-copybutton >=0.5.2
diff --git a/requirements_dev.txt b/requirements_dev.txt
index 96b9c67..d745ee4 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,18 +1,19 @@
-black>=20.8b1
+black>=24.2.0
+build>=1.0.0
 bumpversion>=0.5.3
 coverage>=4.5.1
-flake8>=3.8.4
+flake8>=7.0
 ipykernel
 nbconvert
-nbsphinx>=0.7.0
-nbval>=0.9.6
+nbsphinx >=0.7.0
+nbval >=0.9.6
 pandoc
-pip>=20.0
-pre-commit>=2.7.1
+pip >=23.3.0
+pre-commit>=3.6.2
 pytest-runner>=4.2
 pytest>=3.8.2
-sphinx>=1.8.1
-tox>=3.5.2
-twine>=1.12.1
-watchdog>=0.9.0
-wheel>=0.32.1
+sphinx-codeautolink>=0.15.0
+sphinx-copybutton>=0.5.2
+sphinx>=7.0.0
+twine>=4.0.0
+watchdog>=3.0.0

From 7026481e37d7663aac50820045aae5d1b1d2c28f Mon Sep 17 00:00:00 2001
From: Trevor James Smith <10819524+Zeitsperre@users.noreply.github.com>
Date: Thu, 14 Mar 2024 17:07:58 -0400
Subject: [PATCH 03/18] WIP - Update MANIFEST.in to add files missing from
 packaged sources

---
 MANIFEST.in | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 8a614f4..ced7b4f 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -7,3 +7,5 @@ include LICENSE.txt
 include requirements.txt
 include requirements_dev.txt
 include requirements_extra.txt
+
+recursive-include birdy *.py

From 11418ec93c598f9525c68c5d70838c5271601b30 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:46:01 -0400
Subject: [PATCH 04/18] move templates to top-level

---
 {birdy/templates => templates}/cmd.py.j2 | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {birdy/templates => templates}/cmd.py.j2 (100%)

diff --git a/birdy/templates/cmd.py.j2 b/templates/cmd.py.j2
similarity index 100%
rename from birdy/templates/cmd.py.j2
rename to templates/cmd.py.j2

From 146987e67be267fd8ad57d9750a8ae9814e73827 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:49:56 -0400
Subject: [PATCH 05/18] update module docstrings

---
 birdy/cli/__init__.py           |  4 +++
 birdy/client/__init__.py        | 55 ++++++++++++++-------------------
 birdy/dependencies.py           |  6 +++-
 birdy/ipyleafletwfs/__init__.py | 31 ++++++++++++++++++-
 4 files changed, 62 insertions(+), 34 deletions(-)

diff --git a/birdy/cli/__init__.py b/birdy/cli/__init__.py
index 4f026b2..39384f2 100644
--- a/birdy/cli/__init__.py
+++ b/birdy/cli/__init__.py
@@ -1,4 +1,8 @@
+# noqa: D205, D400
 """
+Birdy CLI module
+================
+
 Birdy has a command line interface to interact with a Web Processing Service.
 
 Example
diff --git a/birdy/client/__init__.py b/birdy/client/__init__.py
index c6e0004..959485e 100644
--- a/birdy/client/__init__.py
+++ b/birdy/client/__init__.py
@@ -1,29 +1,25 @@
-"""WPSClient Class.
+# noqa: D205, D400
+"""
+WPSClient Class
+===============
 
-The :class:`WPSClient` class aims to make working with WPS servers easy,
-even without any prior knowledge of WPS.
+The :class:`WPSClient` class aims to make working with WPS servers easy, even without any prior knowledge of WPS.
 
-Calling the :class:`WPSClient` class creates an instance whose methods call
-WPS processes. These methods are generated at runtime based on the
-process description provided by the WPS server. Calling a function sends
-an `execute` request to the server. The server response is parsed and
-returned as a :class:`WPSExecution` instance, which includes information
-about the job status, the progress percentage, the starting time, etc. The
-actual output from the process are obtained by calling the `get` method.
+Calling the :class:`WPSClient` class creates an instance whose methods call WPS processes.
+These methods are generated at runtime based on the process description provided by the WPS server.
+Calling a function sends an `execute` request to the server. The server response is parsed and
+returned as a :class:`WPSExecution` instance, which includes information about the job status, the progress percentage,
+the starting time, etc. The actual output from the process are obtained by calling the `get` method.
 
 The output is parsed to convert the outputs in native Python whenever possible.
-`LiteralOutput` objects (string, float, integer, boolean) are automatically
-converted to their native format. For `ComplexOutput`, the module can either
-return a link to the output files stored on the server, or try to
-convert the outputs to a Python object based on their mime type. This conversion
-will occur with `get(asobj=True)`. So for example, if the mime type is
-'application/json', the output would be a `dict`.
-
-Inputs to processes can be native Python types (string, float, int, date, datetime),
-http links or local files. Local files can be transferred to a remote server by
-including their content into the WPS request. Simply set the input to a valid path
-or file object and the client will take care of reading and converting the file.
+`LiteralOutput` objects (string, float, integer, boolean) are automatically converted to their native format.
+For `ComplexOutput`, the module can either return a link to the output files stored on the server,
+or try to convert the outputs to a Python object based on their mime type. This conversion will occur with
+`get(asobj=True)`. So for example, if the mime type is 'application/json', the output would be a `dict`.
 
+Inputs to processes can be native Python types (string, float, int, date, datetime), http links or local files.
+Local files can be transferred to a remote server by including their content into the WPS request.
+Simply set the input to a valid path or file object and the client will take care of reading and converting the file.
 
 Example
 -------
@@ -55,10 +51,8 @@
 
 Authentication
 --------------
-If you want to connect to a server that requires authentication, the
-:class:`WPSClient` class accepts an `auth` argument that
-behaves exactly like in the popular `requests` module
-(see `requests Authentication`_)
+If you want to connect to a server that requires authentication, the :class:`WPSClient` class accepts
+an `auth` argument that behaves exactly like in the popular `requests` module (see `requests Authentication`_)
 
 The simplest form of authentication is HTTP Basic Auth. Although
 wps processes are not commonly protected by this authentication method,
@@ -69,11 +63,10 @@
     >>> auth = HTTPBasicAuth('user', 'pass')
     >>> wps = WPSClient('http://www.example.com/wps', auth=auth)
 
-Because any `requests`-compatible class is accepted, custom
-authentication methods are implemented the same way as in `requests`.
+Because any `requests`-compatible class is accepted, custom authentication methods are implemented
+the same way as in `requests`.
 
-For example, to connect to a magpie_ protected wps, you can use the
-requests-magpie_ module::
+For example, to connect to a magpie_ protected wps, you can use the requests-magpie_ module::
 
     >>> from birdy import WPSClient
     >>> from requests_magpie import MagpieAuth
@@ -83,8 +76,7 @@
 Output format
 -------------
 
-Birdy automatically manages process output to reflect it's default values or
-Birdy's own defaults.
+Birdy automatically manages process output to reflect its default values or Birdy's own defaults.
 
 However, it's possible to customize the output of a process. Each process has an input
 named ``output_formats``, that takes a dictionary as a parameter::
@@ -122,7 +114,6 @@
 .. _requests Authentication: https://2.python-requests.org/en/master/user/authentication/
 .. _magpie: https://github.com/ouranosinc/magpie
 .. _requests-magpie: https://github.com/ouranosinc/requests-magpie
-
 """
 
 from birdy.client.notebook import gui  # noqa: F401
diff --git a/birdy/dependencies.py b/birdy/dependencies.py
index 78c517a..0dd6d00 100644
--- a/birdy/dependencies.py
+++ b/birdy/dependencies.py
@@ -1,9 +1,13 @@
+# noqa: D205,D400
 """
+Dependencies Module
+===================
+
 Module for managing optional dependencies.
 
 Example usage::
 
-    from birdy.dependencies import ipywidgets as widgets
+    >>> from birdy.dependencies import ipywidgets as widgets
 """
 
 import warnings
diff --git a/birdy/ipyleafletwfs/__init__.py b/birdy/ipyleafletwfs/__init__.py
index 9fbfe55..66ffc2d 100644
--- a/birdy/ipyleafletwfs/__init__.py
+++ b/birdy/ipyleafletwfs/__init__.py
@@ -1,3 +1,32 @@
-# noqa: D104
+# noqa: D205,D400
+"""
+IpyleafletWFS Module
+====================
+
+This module facilitates the use of a WFS service through the ipyleaflet module in jupyter notebooks.
+It uses owslib to get a geojson out of a WFS service, and then creates an ipyleaflet GeoJSON layer with it.
+
+Dependencies
+------------
+
+Ipyleaflet and Ipywidgets dependencies are included in the requirements_extra.txt, at the root of this repository.
+To install::
+
+    $ pip install -r requirements_extra.txt
+
+Use
+---
+
+This module is to be used inside a jupyter notebook, either with a standard server or through vscode/pycharm.
+There are notebook examples which show how to use this module and what can be done with it.
+
+The WFS request is filtered by the extent of the visible map, to make large layers easier to work with.
+Using the on-map 'Refresh WFS layer' button will make a new request for the current extent.
+
+.. warning::
+    WFS requests and GeoJSON layers are costly operations to process and render.
+    Trying to load lake layers at the nationwide extent may take a long time and probably crash.
+    The more dense and complex the layer, the more zoomed-in the map extent should be.
+"""
 
 from .base import IpyleafletWFS  # noqa: F401

From faaf7971204eb2bc83d76c617ed50fce897f5b95 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:50:48 -0400
Subject: [PATCH 06/18] documentation structure adjustment, raise minimum
 sphinx to v7.0

---
 docs/source/conf.py   | 10 +++++-----
 docs/source/index.rst |  4 +---
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 329183a..4946379 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -22,7 +22,7 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = "1.8"
+needs_sphinx = "7.0"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -108,11 +108,11 @@
     "_build",
     "Thumbs.db",
     ".DS_Store",
-    "owslib-esgfwps.ipynb",
     # Undocumented notebooks
-    "rook-demo.ipynb",
-    "twitcher-c3s-magic-demo.ipynb",
-    "twitcher-magic-cexp-demo.ipynb",
+    "notebooks/examples/owslib-esgfwps.ipynb",
+    "notebooks/examples/rook-demo.ipynb",
+    "notebooks/examples/twitcher-c3s-magic-demo.ipynb",
+    "notebooks/examples/twitcher-magic-cexp-demo.ipynb",
 ]
 
 # The reST default role (used for this markup: `text`) to use for all
diff --git a/docs/source/index.rst b/docs/source/index.rst
index c5026cb..7790f13 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -9,9 +9,7 @@
    api
    changes
 
-Modules
-
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 3
 
    apidoc/modules

From c6072c00922fa2cfe46ccab59fc0a52e4da97852 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:51:59 -0400
Subject: [PATCH 07/18] tests and docs should not be installed as sub-packages
 as wheel but should be fully available in source distribution

---
 MANIFEST.in       | 17 ++++++++++++-----
 setup.py          | 10 +++++++---
 tests/__init__.py |  1 -
 3 files changed, 19 insertions(+), 9 deletions(-)
 delete mode 100644 tests/__init__.py

diff --git a/MANIFEST.in b/MANIFEST.in
index ced7b4f..bb4fe79 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,11 +1,18 @@
-include *.rst
-graft birdy
-global-exclude __pycache__
-global-exclude *.py[co]
+graph birdy
 
+include *.rst
 include LICENSE.txt
 include requirements.txt
 include requirements_dev.txt
 include requirements_extra.txt
+include setup.cfg
+include docs Makefile make.bat
+
+recursive-include docs/source Makefile make.bat *.rst *.py *.ipynb *.svg *.ico *.txt *.yml *.cfg *.md
+recursive-include tests *.py *.nc *.tif *.geojson *.xml
 
-recursive-include birdy *.py
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * *.ipynb_checkpoints
+recursive-exclude docs/build *
+recursive-exclude docs/source/apidoc *.rst
diff --git a/setup.py b/setup.py
index 6b76cc5..2b0cffb 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 import re
 from pathlib import Path
 
-from setuptools import find_packages, setup
+from setuptools import find_namespace_packages, setup
 
 
 def parse_reqs(file):
@@ -62,12 +62,16 @@ def parse_reqs(file):
     license="Apache License v2.0",
     # This qualifier can be used to selectively exclude Python versions -
     # in this case early Python 2 and 3 releases
-    python_requires=">=3.6.0",
-    packages=find_packages(),
+    python_requires=">=3.9.0",
+    packages=find_namespace_packages(exclude=["docs", "docs.*", "tests", "tests.*"]),
     include_package_data=True,
+    package_data={
+        "birdy": ["ipyleafletwps/examples/*.ipynb"],
+    },
     install_requires=requirements,
     extras_require={
         "dev": dev_requirements,  # pip install ".[dev]"
     },
     entry_points={"console_scripts": ["birdy=birdy.cli.run:cli"]},
+    zip_safe=False,
 )
diff --git a/tests/__init__.py b/tests/__init__.py
deleted file mode 100644
index 6e03199..0000000
--- a/tests/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-# noqa: D104

From f5b99ec2b9ccaa06387689ab28bbfcf669fd684d Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:52:31 -0400
Subject: [PATCH 08/18] documentation fixes

---
 Makefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index b75973d..dc86307 100644
--- a/Makefile
+++ b/Makefile
@@ -39,8 +39,8 @@ clean-build: ## remove build artifacts
 	find . -name '*.egg' -exec rm -f {} +
 
 clean-docs: ## remove docs artifacts
-	rm -f docs/apidoc/birdy*.rst
-	rm -f docs/apidoc/modules.rst
+	rm -f docs/source/apidoc/birdy*.rst
+	rm -f docs/source/apidoc/modules.rst
 	$(MAKE) -C docs clean
 
 clean-pyc: ## remove Python file artifacts
@@ -79,7 +79,7 @@ coverage: ## check code coverage quickly with the default Python
 
 autodoc: clean-docs ## create sphinx-apidoc files
 	mkdir -p docs/source/apidoc/
-	sphinx-apidoc -o docs/source/apidoc/ --private --module-first birdy
+	sphinx-apidoc -o docs/source/apidoc/ --private --module-first --separate birdy
 
 docs: autodoc ## generate Sphinx HTML documentation, including API docs
 	$(MAKE) -C docs html

From 81fe03227e5a663691cefe8e1a9fada81c7deeea Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:57:23 -0400
Subject: [PATCH 09/18] add install steps to GitHub workflows

---
 .github/workflows/main.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6578150..d4d7b0b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -52,6 +52,13 @@ jobs:
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
           if [ -f requirements_extra.txt ]; then pip install -r requirements_extra.txt; fi
+      - name: Install Birdy 🐦
+        run: |
+          python pip install --editable .
+      - name: Check dependencies
+        run: |
+          python -m pip list
+          python -m pip check
       - name: Build docs 🏗️
         run: |
           make docs
@@ -80,6 +87,13 @@ jobs:
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
           if [ -f requirements_extra.txt ]; then pip install -r requirements_extra.txt; fi
+      - name: Install Birdy 🐦
+        run: |
+          python pip install --editable .
+      - name: Check dependencies
+        run: |
+          python -m pip list
+          python -m pip check
       - name: Test with pytest ⚙️
         run: |
           make test

From 4fbbe4e18f2d8f3fbbf515a63c7358292f070ad1 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 11:59:04 -0400
Subject: [PATCH 10/18] -m

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d4d7b0b..c4c3bc5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -54,7 +54,7 @@ jobs:
           if [ -f requirements_extra.txt ]; then pip install -r requirements_extra.txt; fi
       - name: Install Birdy 🐦
         run: |
-          python pip install --editable .
+          python -m pip install --editable .
       - name: Check dependencies
         run: |
           python -m pip list
@@ -89,7 +89,7 @@ jobs:
           if [ -f requirements_extra.txt ]; then pip install -r requirements_extra.txt; fi
       - name: Install Birdy 🐦
         run: |
-          python pip install --editable .
+          python -m pip install --editable .
       - name: Check dependencies
         run: |
           python -m pip list

From 6a17a3d38acac117bc13a63c5739eaef4af044ea Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:08:24 -0400
Subject: [PATCH 11/18] remove obsolete python pandoc package

---
 requirements_dev.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/requirements_dev.txt b/requirements_dev.txt
index d745ee4..8718c74 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -7,7 +7,6 @@ ipykernel
 nbconvert
 nbsphinx >=0.7.0
 nbval >=0.9.6
-pandoc
 pip >=23.3.0
 pre-commit>=3.6.2
 pytest-runner>=4.2

From 6db4b7610a76423dc1f7cdd3c60c349daa754e91 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:08:44 -0400
Subject: [PATCH 12/18] undo move of templates outside of package

---
 {templates => birdy/templates}/cmd.py.j2 | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {templates => birdy/templates}/cmd.py.j2 (100%)

diff --git a/templates/cmd.py.j2 b/birdy/templates/cmd.py.j2
similarity index 100%
rename from templates/cmd.py.j2
rename to birdy/templates/cmd.py.j2

From 4bccaa9b4013b86fc7a60109b5600553307a5183 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:09:20 -0400
Subject: [PATCH 13/18] relative imports are now absolute imports in tests

---
 tests/test_cli.py        | 3 +--
 tests/test_client.py     | 6 +-----
 tests/test_converters.py | 3 +--
 tests/test_utils.py      | 5 ++---
 4 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/tests/test_cli.py b/tests/test_cli.py
index 55bf659..069264d 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -2,11 +2,10 @@
 
 import pytest
 from click.testing import CliRunner
+from common import EMU_CAPS_XML, URL_EMU
 
 import birdy.cli.run
 
-from .common import EMU_CAPS_XML, URL_EMU
-
 cli = birdy.cli.run.cli
 cli.url = URL_EMU
 cli.caps_xml = EMU_CAPS_XML
diff --git a/tests/test_client.py b/tests/test_client.py
index 6c958b6..e67df71 100644
--- a/tests/test_client.py
+++ b/tests/test_client.py
@@ -7,17 +7,13 @@
 
 import owslib.wps
 import pytest
+from common import EMU_CAPS_XML, EMU_DESC_XML, URL_EMU, resource_file
 
 from birdy import WPSClient
 from birdy.client import nb_form
 from birdy.client.base import sort_inputs_key
 from birdy.client.utils import is_embedded_in_request
 
-from .common import EMU_CAPS_XML, EMU_DESC_XML, URL_EMU, resource_file
-
-# from owslib import crs
-
-
 # 52 north WPS
 url_52n = "http://geoprocessing.demo.52north.org:8080/wps/WebProcessingService?service=WPS&version=1.0.0&request=GetCapabilities"  # noqa: E501
 
diff --git a/tests/test_converters.py b/tests/test_converters.py
index fd4c229..0acca1b 100644
--- a/tests/test_converters.py
+++ b/tests/test_converters.py
@@ -5,11 +5,10 @@
 import tempfile
 
 import pytest
+from common import resource_file
 
 from birdy.client import converters
 
-from .common import resource_file
-
 
 def test_all_subclasses():  # noqa: D103
     c = converters.all_subclasses(converters.BaseConverter)
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 312d681..2a6fc89 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,13 +1,12 @@
-# noqa
+# noqa: D100
 
 from pathlib import Path
 
 import pytest
+from common import resource_file
 
 from birdy import utils
 
-from .common import resource_file
-
 
 def test_is_url():  # noqa: D103
     assert utils.is_url("http://localhost:5000/wps")

From 74023d63dbffe927ee4d4cd7708ca9513d4282f7 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:14:34 -0400
Subject: [PATCH 14/18] add requirements_extra to pip installation method

---
 setup.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/setup.py b/setup.py
index 2b0cffb..6bb0fe8 100644
--- a/setup.py
+++ b/setup.py
@@ -33,6 +33,7 @@ def parse_reqs(file):
 
 requirements = parse_reqs("requirements.txt")
 dev_requirements = parse_reqs("requirements_dev.txt")
+extra_requirements = parse_reqs("requirements_extra.txt")
 
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -71,6 +72,7 @@ def parse_reqs(file):
     install_requires=requirements,
     extras_require={
         "dev": dev_requirements,  # pip install ".[dev]"
+        "extra": extra_requirements,  # pip install ".[extra]"
     },
     entry_points={"console_scripts": ["birdy=birdy.cli.run:cli"]},
     zip_safe=False,

From 5f7d93f8cbbd59219ffe2d00973eb276ba5415c1 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:28:38 -0400
Subject: [PATCH 15/18] run sphinx-apidoc on ReadTheDocs

---
 .readthedocs.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 5d2589c..c2f27db 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -6,15 +6,18 @@
 version: 2
 
 sphinx:
-    configuration: docs/source/conf.py
+  configuration: docs/source/conf.py
 
 build:
   os: ubuntu-22.04
   tools:
     python: "mambaforge-22.9"
+  jobs:
+    pre_build:
+      - sphinx-apidoc -o docs/source/apidoc/ --private --module-first --separate birdy
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
 conda:
-    environment: environment-docs.yml
+  environment: environment-docs.yml

From 7636fd3178100baefa4ea7f9334d2f0c68f2a4f3 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:50:29 -0400
Subject: [PATCH 16/18] add build documentation

---
 docs/source/development.rst | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/docs/source/development.rst b/docs/source/development.rst
index f952795..5a6f973 100644
--- a/docs/source/development.rst
+++ b/docs/source/development.rst
@@ -9,19 +9,19 @@ Get Started!
 
 Check out code from the birdy GitHub repo and start the installation::
 
-   $ git clone https://github.com/bird-house/birdy.git
-   $ cd birdy
-   $ conda env create -f environment.yml
-   $ pip install --editable .
+    $ git clone https://github.com/bird-house/birdy.git
+    $ cd birdy
+    $ conda env create -f environment.yml
+    $ pip install --editable .
 
 Install additional dependencies::
 
-  $ pip install -r requirements_dev.txt
+    $ pip install -r requirements_dev.txt
 
 When you're done making changes, check that your changes pass `black`, `flake8` and the tests::
 
-    $ black birdy tests
     $ flake8 birdy tests
+    $ black --check --target-version py39 birdy tests
     $ pytest -v tests
 
 Or use the Makefile::
@@ -46,7 +46,7 @@ Write Documentation
 You can find the documentation in the `docs/source` folder. To generate the Sphinx
 documentation locally you can use the `Makefile`::
 
-  $ make docs
+    $ make docs
 
 Bump a new version
 ===================
@@ -64,6 +64,19 @@ See the bumpversion_ documentation for details.
 
 .. _bumpversion: https://pypi.org/project/bumpversion/
 
+Build a source distribution and wheel
+=====================================
+
+To build a source distribution (`.sdist`) and wheel (`.whl`) locally, run the following command::
+
+    $ python -m build
+
+This will create a `dist` folder with the source distribution and wheel.
+
+See the `build`_ documentation for details.
+
+.. _build: https://build.pypa.io/en/latest/
+
 Release a new version
 =====================
 

From b2ed896c98836d5d98e03d933a98e9ef595410ad Mon Sep 17 00:00:00 2001
From: Trevor James Smith <10819524+Zeitsperre@users.noreply.github.com>
Date: Mon, 18 Mar 2024 10:42:52 -0400
Subject: [PATCH 17/18] Update MANIFEST.in

---
 MANIFEST.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index bb4fe79..2670216 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
-graph birdy
+graft birdy
 
 include *.rst
 include LICENSE.txt

From 518d1ce127eb4e31e367de2221b0a74f40159645 Mon Sep 17 00:00:00 2001
From: Zeitsperre <10819524+Zeitsperre@users.noreply.github.com>
Date: Mon, 18 Mar 2024 11:21:54 -0400
Subject: [PATCH 18/18] update CHANGES.rst

---
 CHANGES.rst | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/CHANGES.rst b/CHANGES.rst
index 74b1c3f..0334599 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,6 +1,21 @@
 Change History
 **************
 
+v0.8.6 (2024-xx-xx)
+===================
+
+Changes:
+
+* Restructure the package so that the wheel does not install the testing and docs as non-importable packages.
+* Ensure that data required to run tests and build docs is present in the source distribution (via `Manifest.in` changes).
+* Documentation now includes a `sphinx-apidoc`-based listing of all installed modules and functions
+* Add `sphinx-copybutton` and `sphinx-codeautolink` in order to increase the usefulness of code-blocks in the example documentation (copying of code blocks and ability to click on `birdy` objects and go straight to the documentation entry for the object).
+* All documentation build warnings have been addressed.
+* Add the `birdy[extra]` pip install recipe to be able to install all extras needed more directly.
+* Raise the minimum Python required to 3.9 in the setup block.
+* Remove the Python package for `pandoc` (unmaintained).
+* Add a documentation entry on using `build` to build the documentation.
+
 0.8.5 (2024-03-14)
 ==================