Merge branch '14-setup-bokeh-server' into 'main'

Resolve "Setup bokeh server"

Closes #14

See merge request pjm363/why-senior-project!4

README.md

 # WHY Senior Project
 
+## Installing WHY
+
+There are two way in which the `WHY` package can be installed.
+First, follow the [prerequisite](#prerequisites) instructions.
+IF you do not need to rebuild documentation or make modifications to the library, follow the instructions under [User Installation](#user-installation).
+Otherwise, follow the instructions under [Developer Installation](#developer-installation).
+
+### Prerequisites
+
+The `WHY` requires at least `python3.8` and makes use of a number of third-party libraries. The bare minimum packages are automatically installed when you install `WHY` using `pip`. Additional dependencies for developers are contained in `requirements.txt` file. See the
+
+It's recommended that you use `WHY` within a python virtual environment. 
+Virtual environments are now included natively with Python 3 using `venv`. Instructions to create a virtual environment can be found [here](https://docs.python.org/3/library/venv.html).  
+
+API documentation requires the use of `sphinx` which will require installing `Cmake`.  Installation instructions can be found [here](https://cmake.org/install/).
+
+### User Installation
+
+First you must clone the repository using the following bash command.
+```bash
+pip clone git@gitlab.cci.drexel.edu:pjm363/why-senior-project.git
+```
+
+From the root path of the repository (the folder where `setup.py` is located) `WHY` can be installed using `pip` using the following command. 
+
+```bash
+pip install .
+```
+
+### Developer Installation
+Developers need an additional tool, `clang-format` in order to run the precommit script. 
+
+Install via Ubuntu.
+```bash 
+apt-get install clang-format
+```
+Install via MacOSX with homebrew.
+```bash
+brew install clang-format
+```
+Install via [installer](https://llvm.org/builds/) or using chocolatey via.
+```bash
+choco install llvm
+```
+
+## Building API Documentation
+
+To build the API Documentation in HTML format for local browsing, execute the following from the root of the repository.
+```
+cd docs/
+make html
+```
+
+This will also cause any examples contained in `examples` to be generated in the example gallery.  
+All documentation is also built automatically when the `./precommit.sh` script is run.

docs/Makefile

+# 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)

docs/source/conf.py

+# 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('../../'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'WHY'
+copyright = '2022, Philip Monaco'
+author = 'Philip Monaco'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.0'
+
+try:
+    import re
+    import WHY 
+    
+    reg = re.compile("([0-9]+\.[0-9]+\.[a-zA-Z0-9\+.]+)")
+    full_vers = WHY.__version__
+    partial_vers = reg.mathc(full_vers)[0]
+except:
+    full_vers = "dev"
+    partial_vers = "dev"
+    
+version = partial_vers
+release = full_vers
+# -- 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.todo",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "m2r2"
+]
+
+autoclass_content = "both"
+autosummary_generate = True
+
+source_suffix = [".rst", ".md"]
+
+master_doc = "index"
+
+language =  None
+
+pygments_style = "sphinx"
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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'
+
+htmlhelp_basename = "WHYdoc"
+
+html_theme_options = {
+    "canonical_url":"",
+    "logo_only": False,
+    "display_version": True,
+    "prev_next_buttons_location":"bottom",
+    "collapse_navigation":True,
+    "sticky_navigation": True,
+    "navigation_depth":4,
+}
+
+html_logo = ""
+
+man_pages = [(master_doc, "WHY", "WHY Documentation", [author], 1)]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+todo_include_todos = True
\ No newline at end of file

docs/source/index.rst

+.. WHY documentation master file, created by
+   sphinx-quickstart on Mon Feb 14 16:44:55 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to WHY's documentation!
+===============================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/introduction.rst

+## Installing WHY
+
+There are two way in which the `WHY` package can be installed.
+First, follow the [prerequisite](#prerequisites) instructions.
+IF you do not need to rebuild documentation or make modifications to the library, follow the instructions under [User Installation](#user-installation).
+Otherwise, follow the instructions under [Developer Installation](#developer-installation).
+
+### Prerequisites
+
+The `WHY` requires at least `python3.8` and makes use of a number of third-party libraries. The bare minimum packages are automatically installed when you install `WHY` using `pip`. Additional dependencies for developers are contained in `requirements.txt` file. See the
+
+It's recommended that you use `WHY` within a python virtual environment. 
+Virtual environments are now included natively with Python 3 using `venv`. Instructions to create a virtual environment can be found [here](https://docs.python.org/3/library/venv.html).  
+
+API documentation requires the use of `sphinx` which will require installing `Cmake`.  Installation instructions can be found [here](https://cmake.org/install/).
+
+### User Installation
+
+First you must clone the repository using the following bash command.
+```bash
+pip clone git@gitlab.cci.drexel.edu:pjm363/why-senior-project.git
+```
+
+From the root path of the repository (the folder where `setup.py` is located) `WHY` can be installed using `pip` using the following command. 
+
+```bash
+pip install .
+```
+
+### Developer Installation
+Developers need an additional tool, `clang-format` in order to run the precommit script. 
+
+Install via Ubuntu.
+```bash 
+apt-get install clang-format
+```
+Install via MacOSX with homebrew.
+```bash
+brew install clang-format
+```
+Install via [installer](https://llvm.org/builds/) or using chocolatey via.
+```bash
+choco install llvm
+```
+
+## Building API Documentation
+
+To build the API Documentation in HTML format for local browsing, execute the following from the root of the repository.
+```
+cd docs/
+make html
+```
+
+This will also cause any examples contained in `examples` to be generated in the example gallery.  
+All documentation is also built automatically when the `./precommit.sh` script is run.
\ No newline at end of file

setup.py

 import os
 import subprocess
+from io import open
 
 from setuptools import find_packages, setup
 
@@ -25,8 +26,6 @@ core_requires = [
     "scikit-learn>=1.0.2"
 ]
 
-all_requires += core_requires
-
 lint_requires = [
     "black==21.12b0",
     "isort==5.10.1",
@@ -34,8 +33,6 @@ lint_requires = [
     "mypy"
 ]
 
-all_requires += lint_requires
-
 docs_requires = [
     "Sphinx",
     "sphinx-gallery",
@@ -43,7 +40,17 @@ docs_requires = [
     "m2r2"
 ]
 
-all_requires += docs_requires
+all_requires = [
+    *core_requires,
+    *lint_requires,
+    docs_requires,
+]
+
+requires_map={
+    "lint": lint_requires,
+    "docs": docs_requires,
+    "all": all_requires,
+}
 
 def _minimal_ext_cmd(cmd):
     env = {}
@@ -57,3 +64,57 @@ def _minimal_ext_cmd(cmd):
     out = subprocess.check_output(cmd, stderr=subprocess.STDOUT, env=env)
     return out
 
+def get_git_hash():
+    try:
+        out = _minimal_ext_cmd(["git", "rev-parse", "HEAD"])
+        git_rev = out.strip().decode("ascii")
+    except (subprocess.SUbprocessError, OSError):
+        git_rev = "Unknown"
+        
+    if not git_rev:
+        git_rev = "Unknown"
+        
+    return git_rev
+
+def is_tagged_released():
+    try:
+        out = _minimal_ext_cmd(["git", "describe", "--exact-match", "--tags", "HEAD"])
+        tag_name = out.strip().decode("ascii")
+        
+        is_tagged_release = tag_name.startswith(SEMVER_STRING)
+    except (subprocess.SubprocessError, OSError):
+        is_tagged_release = False
+        
+    return is_tagged_release
+
+def render_version_string():
+    version_string = SEMVER_STRING
+    if os.path.exists(".git") and not is_tagged_released():
+        version_string += ".dev0+" + get_git_hash()[:7]
+        
+    return version_string
+
+here = os.path.abspath(os.path.split(__file__)[0])
+
+with open(os.path.join(here, "README.md"), encoding="utf-8") as f:
+    long_description = f.read()
+    
+setup(
+    name=PROJECT_NAME,
+    version=render_version_string(),
+    author=AUTHOR_NAME,
+    url=PROJECT_URL,
+    description=PROJECT_DESCRIPTION,
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    license="LICENSE.md",
+    packages=find_packages(where="src"),
+    package_dir={"":"src"},
+    python_requires=">=3.8",
+    install_requires=core_requires,
+    extras_require=requires_map,
+    include_package_data=True,
+    zip_safe=False,
+    package_data={"WHY": ["py.typed"]},
+    entry_points={},
+)
\ No newline at end of file