first stab at some files for pip

.gitignore

@@ -1,3 +1,8 @@
 .venv/
 modules/__pycache__/
 runs/
+*.swp
+.ipynb_checkpoints/
+build/
+dist/
+karoo_gp_kstaats.egg-info/

README-pip.md

@@ -0,0 +1,7 @@
+Set up `setup.py`.
+
+```
+python3 -m pip install --user --upgrade setuptools wheel
+python3 setup.py sdist bdist_wheel
+```
+

README.md

@@ -19,7 +19,7 @@ Learn more at <a href="http://kstaats.github.io/karoo_gp/">kstaats.github.io/kar
 
 # Debian Install
 
-To install on Debian (Buster, Stable, 10):
+To install on Debian (Buster/Stable/10):
 
 ```
 # Install Dependencies:
@@ -42,3 +42,147 @@ pip3 install numpy==1.16.4 sympy==1.4 tensorflow==1.13.1 scikit-learn==0.21.2
 python3 karoo_gp.py
 ```
 
+# Tensorflow 2 Install
+Using karoo_gp with Tensorflow 2 on Debian (Buster/Stable/10).
+
+```
+# Install Dependencies:
+sudo apt install python3 python3-pip python3-venv
+
+# Clone repo (choose this one or upstream):
+# git clone https://github.com/kstaats/karoo_gp
+git clone https://spacecruft.org/spacecruft/karoo_gp
+
+# Setup
+cd karoo_gp
+python3 -m venv .venv
+source .venv/bin/activate
+
+pip3 install --upgrade pip
+pip3 install --upgrade setuptools
+
+# Install python dependencies
+pip3 install wheel
+pip3 install sklearn sympy
+# This will install Tensorflow 2.1:
+pip3 install tensorflow
+
+# Run application
+python3 karoo_gp.py
+```
+
+# Jupyter
+Jupyter is a cute interface to python.
+
+## Jupyter Install
+To install everything for jupyter, not in virt env... Thusly:
+
+```
+# Install Dependencies:
+sudo apt install python3 python3-pip
+
+# Clone repo (choose this one or upstream):
+git clone https://spacecruft.org/spacecruft/karoo_gp
+
+# Setup
+cd karoo_gp
+git checkout jupyter
+
+pip3 install --user --upgrade pip
+pip3 install --user --upgrade setuptools
+
+# Install python dependencies
+pip3 install --user wheel
+pip3 install --user sklearn sympy
+# This will install Tensorflow 2.1:
+pip3 install --user tensorflow
+```
+
+## Run Jupyter
+Copy the `foo` to an appropriate place. Run similar to this:
+
+```
+jupyter-lab 								\
+	--config=/home/jebba/.jupyter/jupyter_karoo_gp_config.py	\
+	--debug								\
+	--notebook-dir=/home/jebba/devel/spacecruft/karoo_gp		\
+	--app-dir=/home/jebba/.local/share/jupyter/lab			\
+	1>>/home/jebba/log/karoo.log 2>>/home/jebba/log/karoo.err &
+```
+
+
+# Voila
+Voila can take Jupyter notebooks and turn them into websites.
+Example site below:
+
+* https://karoo.spacecruft.org/
+
+## Install Voila
+See other docs, maybe in satnogs-wut.
+
+
+```
+# Install Dependencies:
+sudo apt install python3 python3-pip python3-venv
+
+# Clone repo:
+git clone https://spacecruft.org/spacecruft/karoo_gp
+
+# Setup
+cd karoo_gp
+git checkout jupyter
+
+pip3 install --user --upgrade pip
+pip3 install --user --upgrade setuptools
+
+# Install python dependencies
+pip3 install --user wheel
+pip3 install --user sklearn sympy
+# This will install Tensorflow 2.1:
+pip3 install --user tensorflow
+```
+
+## Voila Apache
+Snippet of apache code to set up proxy using Certbot.
+
+```
+<VirtualHost karoo.spacecruft.org:443>
+ServerAdmin webmaster@localhost
+DocumentRoot /var/www/html
+ErrorLog ${APACHE_LOG_DIR}/error.log
+CustomLog ${APACHE_LOG_DIR}/access.log combined
+RewriteEngine on
+#LoadModule proxy_module modules/mod_proxy.so
+#LoadModule proxy_http_module modules/mod_proxy_http.so
+RequestHeader set X-Forwarded-Proto 'https'env=HTTPS
+RewriteCond %{HTTP:UPGRADE} ^WebSocket$ [NC]
+RewriteCond %{HTTP:CONNECTION} Upgrade$ [NC]
+RewriteRule /(.*) ws://127.0.0.1:8221/$1 [P]
+<Location />
+        ProxyPass http://127.0.0.1:8221/
+</Location>
+ProxyVia On
+ProxyPreserveHost On
+Include /etc/letsencrypt/options-ssl-apache.conf
+ServerName karoo.spacecruft.org
+SSLCertificateFile /etc/letsencrypt/live/wut.spacecruft.org/fullchain.pem
+SSLCertificateKeyFile /etc/letsencrypt/live/wut.spacecruft.org/privkey.pem
+</VirtualHost>
+```
+
+## Voila Start
+Start with `voila` something like this:
+
+```
+voila									\
+	--ExecutePreprocessor.timeout=600				\
+	--no-browser							\
+	--port=8221							\
+	--theme=dark							\
+	--autoreload=True						\
+	--template=default						\
+	--Voila.ip=localhost						\
+	--VoilaConfiguration.enable_nbextensions=False			\
+	karoo_gp.ipynb
+```
+

jupyter_karoo_gp_config.py

@@ -0,0 +1,964 @@
+# Configuration file for jupyter-notebook.
+
+#------------------------------------------------------------------------------
+# Application(SingletonConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## This is an application.
+
+## The date format used by logging formatters for %(asctime)s
+#c.Application.log_datefmt = '%Y-%m-%d %H:%M:%S'
+
+## The Logging format template
+#c.Application.log_format = '[%(name)s]%(highlevel)s %(message)s'
+
+## Set the log level by value or name.
+#c.Application.log_level = 30
+
+#------------------------------------------------------------------------------
+# JupyterApp(Application) configuration
+#------------------------------------------------------------------------------
+
+## Base class for Jupyter applications
+
+## Answer yes to any prompts.
+#c.JupyterApp.answer_yes = False
+
+## Full path of a config file.
+#c.JupyterApp.config_file = '/home/jebba/.jupyter/jupyter_notebook_config.py'
+
+## Specify a config file to load.
+#c.JupyterApp.config_file_name = '/home/jebba/.jupyter/jupyter_notebook_config.py'
+
+## Generate default config file.
+#c.JupyterApp.generate_config = False
+
+#------------------------------------------------------------------------------
+# NotebookApp(JupyterApp) configuration
+#------------------------------------------------------------------------------
+
+## Set the Access-Control-Allow-Credentials: true header
+#c.NotebookApp.allow_credentials = False
+
+## Set the Access-Control-Allow-Origin header
+#  
+#  Use '*' to allow any origin to access your server.
+#  
+#  Takes precedence over allow_origin_pat.
+# XXX XXX XXX
+c.NotebookApp.allow_origin = '*'
+
+## Use a regular expression for the Access-Control-Allow-Origin header
+#  
+#  Requests from an origin matching the expression will get replies with:
+#  
+#      Access-Control-Allow-Origin: origin
+#  
+#  where `origin` is the origin of the request.
+#  
+#  Ignored if allow_origin is set.
+# XXX
+#c.NotebookApp.allow_origin_pat = ''
+
+## Allow password to be changed at login for the notebook server.
+#  
+#  While loggin in with a token, the notebook server UI will give the opportunity
+#  to the user to enter a new password at the same time that will replace the
+#  token login mechanism.
+#  
+#  This can be set to false to prevent changing password from the UI/API.
+# XXX
+#c.NotebookApp.allow_password_change = True
+
+## Allow requests where the Host header doesn't point to a local server
+#  
+#  By default, requests get a 403 forbidden response if the 'Host' header shows
+#  that the browser thinks it's on a non-local domain. Setting this option to
+#  True disables this check.
+#  
+#  This protects against 'DNS rebinding' attacks, where a remote web server
+#  serves you a page and then changes its DNS to send later requests to a local
+#  IP, bypassing same-origin checks.
+#  
+#  Local IP addresses (such as 127.0.0.1 and ::1) are allowed as local, along
+#  with hostnames configured in local_hostnames.
+# XXX
+c.NotebookApp.allow_remote_access = True
+
+## Whether to allow the user to run the notebook as root.
+c.NotebookApp.allow_root = False
+
+## DEPRECATED use base_url
+#c.NotebookApp.base_project_url = '/'
+
+## The base URL for the notebook server.
+#  
+#  Leading and trailing slashes can be omitted, and will automatically be added.
+# XXX
+c.NotebookApp.base_url = 'jupyter'
+
+## Specify what command to use to invoke a web browser when opening the notebook.
+#  If not specified, the default browser will be determined by the `webbrowser`
+#  standard library module, which allows setting of the BROWSER environment
+#  variable to override it.
+#c.NotebookApp.browser = ''
+
+## The full path to an SSL/TLS certificate file.
+#c.NotebookApp.certfile = ''
+
+## The full path to a certificate authority certificate for SSL/TLS client
+#  authentication.
+#c.NotebookApp.client_ca = ''
+
+## The config manager class to use
+#c.NotebookApp.config_manager_class = 'notebook.services.config.manager.ConfigManager'
+
+## The notebook manager class to use.
+#c.NotebookApp.contents_manager_class = 'notebook.services.contents.largefilemanager.LargeFileManager'
+
+## Extra keyword arguments to pass to `set_secure_cookie`. See tornado's
+#  set_secure_cookie docs for details.
+#c.NotebookApp.cookie_options = {}
+
+## The random bytes used to secure cookies. By default this is a new random
+#  number every time you start the Notebook. Set it to a value in a config file
+#  to enable logins to persist across server sessions.
+#  
+#  Note: Cookie secrets should be kept private, do not share config files with
+#  cookie_secret stored in plaintext (you can read the value from a file).
+#c.NotebookApp.cookie_secret = b''
+
+## The file where the cookie secret is stored.
+#c.NotebookApp.cookie_secret_file = ''
+
+## Override URL shown to users.
+#  
+#  Replace actual URL, including protocol, address, port and base URL, with the
+#  given value when displaying URL to the users. Do not change the actual
+#  connection URL. If authentication token is enabled, the token is added to the
+#  custom URL automatically.
+#  
+#  This option is intended to be used when the URL to display to the user cannot
+#  be determined reliably by the Jupyter notebook server (proxified or
+#  containerized setups for example).
+c.NotebookApp.custom_display_url = 'https://ml.spacecruft.org/jupyter'
+
+## The default URL to redirect to from `/`
+# XXX
+#c.NotebookApp.default_url = 'jupyter'
+
+## Disable cross-site-request-forgery protection
+#  
+#  Jupyter notebook 4.3.1 introduces protection from cross-site request
+#  forgeries, requiring API requests to either:
+#  
+#  - originate from pages served by this server (validated with XSRF cookie and
+#  token), or - authenticate with a token
+#  
+#  Some anonymous compute resources still desire the ability to run code,
+#  completely without authentication. These services can disable all
+#  authentication and security checks, with the full knowledge of what that
+#  implies.
+# XXX
+c.NotebookApp.disable_check_xsrf = False
+# XXX
+
+## Whether to enable MathJax for typesetting math/TeX
+#  
+#  MathJax is the javascript library Jupyter uses to render math/LaTeX. It is
+#  very large, so you may want to disable it if you have a slow internet
+#  connection, or for offline use of the notebook.
+#  
+#  When disabled, equations etc. will appear as their untransformed TeX source.
+#c.NotebookApp.enable_mathjax = True
+
+## extra paths to look for Javascript notebook extensions
+#c.NotebookApp.extra_nbextensions_path = []
+
+## handlers that should be loaded at higher priority than the default services
+#c.NotebookApp.extra_services = []
+
+## Extra paths to search for serving static files.
+#  
+#  This allows adding javascript/css to be available from the notebook server
+#  machine, or overriding individual files in the IPython
+# XXX
+#c.NotebookApp.extra_static_paths = []
+
+## Extra paths to search for serving jinja templates.
+#  
+#  Can be used to override templates from notebook.templates.
+#c.NotebookApp.extra_template_paths = []
+
+## 
+# XXX
+#c.NotebookApp.file_to_run = ''
+
+## Extra keyword arguments to pass to `get_secure_cookie`. See tornado's
+#  get_secure_cookie docs for details.
+#c.NotebookApp.get_secure_cookie_kwargs = {}
+
+## Deprecated: Use minified JS file or not, mainly use during dev to avoid JS
+#  recompilation
+#c.NotebookApp.ignore_minified_js = False
+
+## (bytes/sec) Maximum rate at which stream output can be sent on iopub before
+#  they are limited.
+#c.NotebookApp.iopub_data_rate_limit = 1000000
+
+## (msgs/sec) Maximum rate at which messages can be sent on iopub before they are
+#  limited.
+#c.NotebookApp.iopub_msg_rate_limit = 1000
+
+## The IP address the notebook server will listen on.
+c.NotebookApp.ip = '127.0.0.1'
+
+## Supply extra arguments that will be passed to Jinja environment.
+#c.NotebookApp.jinja_environment_options = {}
+
+## Extra variables to supply to jinja templates when rendering.
+#c.NotebookApp.jinja_template_vars = {}
+
+## The kernel manager class to use.
+#c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.MappingKernelManager'
+
+## The kernel spec manager class to use. Should be a subclass of
+#  `jupyter_client.kernelspec.KernelSpecManager`.
+#  
+#  The Api of KernelSpecManager is provisional and might change without warning
+#  between this version of Jupyter and the next stable one.
+#c.NotebookApp.kernel_spec_manager_class = 'jupyter_client.kernelspec.KernelSpecManager'
+
+## The full path to a private key file for usage with SSL/TLS.
+#c.NotebookApp.keyfile = ''
+
+## Hostnames to allow as local when allow_remote_access is False.
+#  
+#  Local IP addresses (such as 127.0.0.1 and ::1) are automatically accepted as
+#  local as well.
+#c.NotebookApp.local_hostnames = ['localhost']
+c.NotebookApp.local_hostnames = ['127.0.0.1', '185.165.171.164', 'ml.spacecruft.org']
+
+## The login handler class to use.
+#c.NotebookApp.login_handler_class = 'notebook.auth.login.LoginHandler'
+
+## The logout handler class to use.
+#c.NotebookApp.logout_handler_class = 'notebook.auth.logout.LogoutHandler'
+
+## The MathJax.js configuration file that is to be used.
+#c.NotebookApp.mathjax_config = 'TeX-AMS-MML_HTMLorMML-full,Safe'
+
+## A custom url for MathJax.js. Should be in the form of a case-sensitive url to
+#  MathJax, for example:  /static/components/MathJax/MathJax.js
+#c.NotebookApp.mathjax_url = ''
+
+## Sets the maximum allowed size of the client request body, specified in  the
+#  Content-Length request header field. If the size in a request  exceeds the
+#  configured value, a malformed HTTP message is returned to the client.
+#  
+#  Note: max_body_size is applied even in streaming mode.
+#c.NotebookApp.max_body_size = 536870912
+
+# XXX Default is 512 Megabytes: 536870912 bytes
+# Perhaps do 4x more?
+## Gets or sets the maximum amount of memory, in bytes, that is allocated  for
+#  use by the buffer manager.
+#c.NotebookApp.max_buffer_size = 536870912
+c.NotebookApp.max_buffer_size = 2147483648
+
+# XXX Number of open files.
+## Gets or sets a lower bound on the open file handles process resource limit.
+#  This may need to be increased if you run into an OSError: [Errno 24] Too many
+#  open files. This is not applicable when running on Windows.
+#c.NotebookApp.min_open_files_limit = 4096
+c.NotebookApp.min_open_files_limit = 16384
+
+## Dict of Python modules to load as notebook server extensions.Entry values can
+#  be used to enable and disable the loading ofthe extensions. The extensions
+#  will be loaded in alphabetical order.
+#c.NotebookApp.nbserver_extensions = {}
+
+## The directory to use for notebooks and kernels.
+# XXX
+#c.NotebookApp.notebook_dir = ''
+
+## Whether to open in a browser after starting. The specific browser used is
+#  platform dependent and determined by the python standard library `webbrowser`
+#  module, unless it is overridden using the --browser (NotebookApp.browser)
+#  configuration option.
+c.NotebookApp.open_browser = False
+
+## Hashed password to use for web authentication.
+#  
+#  To generate, type in a python/IPython shell:
+#  
+#    from notebook.auth import passwd; passwd()
+#  
+#  The string should be of the form type:salt:hashed-password.
+# XXX
+#c.NotebookApp.password = ''
+
+## Forces users to use a password for the Notebook server. This is useful in a
+#  multi user environment, for instance when everybody in the LAN can access each
+#  other's machine through ssh.
+#  
+#  In such a case, server the notebook server on localhost is not secure since
+#  any user can connect to the notebook server via ssh.
+# XXX
+#c.NotebookApp.password_required = False
+
+## The port the notebook server will listen on.
+c.NotebookApp.port = 9999
+
+## The number of additional ports to try if the specified port is not available.
+c.NotebookApp.port_retries = 0
+
+## DISABLED: use %pylab or %matplotlib in the notebook to enable matplotlib.
+#c.NotebookApp.pylab = 'disabled'
+
+## If True, display a button in the dashboard to quit (shutdown the notebook
+#  server).
+#c.NotebookApp.quit_button = True
+
+## (sec) Time window used to  check the message and data rate limits.
+#c.NotebookApp.rate_limit_window = 3
+
+## Reraise exceptions encountered loading server extensions?
+#c.NotebookApp.reraise_server_extension_failures = False
+
+## DEPRECATED use the nbserver_extensions dict instead
+#c.NotebookApp.server_extensions = []
+
+## The session manager class to use.
+#c.NotebookApp.session_manager_class = 'notebook.services.sessions.sessionmanager.SessionManager'
+
+## Shut down the server after N seconds with no kernels or terminals running and
+#  no activity. This can be used together with culling idle kernels
+#  (MappingKernelManager.cull_idle_timeout) to shutdown the notebook server when
+#  it's not in use. This is not precisely timed: it may shut down up to a minute
+#  later. 0 (the default) disables this automatic shutdown.
+#c.NotebookApp.shutdown_no_activity_timeout = 0
+
+## Supply SSL options for the tornado HTTPServer. See the tornado docs for
+#  details.
+#c.NotebookApp.ssl_options = {}
+
+## Supply overrides for terminado. Currently only supports "shell_command".
+#c.NotebookApp.terminado_settings = {}
+
+## Set to False to disable terminals.
+#  
+#  This does *not* make the notebook server more secure by itself. Anything the
+#  user can in a terminal, they can also do in a notebook.
+#  
+#  Terminals may also be automatically disabled if the terminado package is not
+#  available.
+#c.NotebookApp.terminals_enabled = True
+
+## Token used for authenticating first-time connections to the server.
+#  
+#  When no password is enabled, the default is to generate a new, random token.
+#  
+#  Setting to an empty string disables authentication altogether, which is NOT
+#  RECOMMENDED.
+#c.NotebookApp.token = '<generated>'
+
+## Supply overrides for the tornado.web.Application that the Jupyter notebook
+#  uses.
+#c.NotebookApp.tornado_settings = {}
+
+## Whether to trust or not X-Scheme/X-Forwarded-Proto and X-Real-Ip/X-Forwarded-
+#  For headerssent by the upstream reverse proxy. Necessary if the proxy handles
+#  SSL
+c.NotebookApp.trust_xheaders = True
+
+## Disable launching browser by redirect file
+#  
+#  For versions of notebook > 5.7.2, a security feature measure was added that
+#  prevented the authentication token used to launch the browser from being
+#  visible. This feature makes it difficult for other users on a multi-user
+#  system from running code in your Jupyter session as you.
+#  
+#  However, some environments (like Windows Subsystem for Linux (WSL) and
+#  Chromebooks), launching a browser using a redirect file can lead the browser
+#  failing to load.  This is because of the difference in file structures/paths
+#  between the runtime and  the browser.
+#  
+#  Disabling this setting to False will disable this behavior, allowing the
+#  browser  to launch by using a URL and visible token (as before).
+#c.NotebookApp.use_redirect_file = True
+
+## DEPRECATED, use tornado_settings
+#c.NotebookApp.webapp_settings = {}
+
+## Specify Where to open the notebook on startup. This is the `new` argument
+#  passed to the standard library method `webbrowser.open`. The behaviour is not
+#  guaranteed, but depends on browser support. Valid values are:
+#  
+#   - 2 opens a new tab,
+#   - 1 opens a new window,
+#   - 0 opens in an existing window.
+#  
+#  See the `webbrowser.open` documentation for details.
+#c.NotebookApp.webbrowser_open_new = 2
+
+## Set the tornado compression options for websocket connections.
+#  
+#  This value will be returned from
+#  :meth:`WebSocketHandler.get_compression_options`. None (default) will disable
+#  compression. A dict (even an empty one) will enable compression.
+#  
+#  See the tornado docs for WebSocketHandler.get_compression_options for details.
+#c.NotebookApp.websocket_compression_options = None
+
+## The base URL for websockets, if it differs from the HTTP server (hint: it
+#  almost certainly doesn't).
+#  
+#  Should be in the form of an HTTP origin: ws[s]://hostname[:port]
+# XXX
+#c.NotebookApp.websocket_url = ''
+
+#------------------------------------------------------------------------------
+# LabApp(NotebookApp) configuration
+#------------------------------------------------------------------------------
+
+## The app directory to launch JupyterLab from.
+c.LabApp.app_dir = '/home/jebba/.local/share/jupyter/lab'
+
+## Whether to start the app in core mode. In this mode, JupyterLab will run using
+#  the JavaScript assets that are within the installed JupyterLab Python package.
+#  In core mode, third party extensions are disabled. The `--dev-mode` flag is an
+#  alias to this to be used when the Python package itself is installed in
+#  development mode (`pip install -e .`).
+#c.LabApp.core_mode = False
+
+## The default URL to redirect to from `/`
+# XXX XXX
+c.LabApp.default_url = '/jupyter/lab'
+
+## Whether to start the app in dev mode. Uses the unpublished local JavaScript
+#  packages in the `dev_mode` folder.  In this case JupyterLab will show a red
+#  stripe at the top of the page.  It can only be used if JupyterLab is installed
+#  as `pip install -e .`.
+#c.LabApp.dev_mode = False
+
+## The override url for static lab assets, typically a CDN.
+#c.LabApp.override_static_url = ''
+# XXX
+#c.LabApp.override_static_url = '/static'
+
+## The override url for static lab theme assets, typically a CDN.
+# XXX
+#c.LabApp.override_theme_url = 'https://ml.spacecruft.org/jupyter'
+
+## The directory for user settings.
+# XXX
+#c.LabApp.user_settings_dir = '/home/jebba/.jupyter/lab/user-settings'
+
+## Whether to serve the app in watch mode
+# XXX
+#c.LabApp.watch = False
+
+## The directory for workspaces
+# XXX
+#c.LabApp.workspaces_dir = '/home/jebba/.jupyter/lab/workspaces'
+
+#------------------------------------------------------------------------------
+# ConnectionFileMixin(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## Mixin for configurable classes that work with connection files
+
+## JSON file in which to store connection info [default: kernel-<pid>.json]
+#  
+#  This file will contain the IP, ports, and authentication key needed to connect
+#  clients to this kernel. By default, this file will be created in the security
+#  dir of the current profile, but can be specified by absolute path.
+#c.ConnectionFileMixin.connection_file = ''
+
+## set the control (ROUTER) port [default: random]
+#c.ConnectionFileMixin.control_port = 0
+
+## set the heartbeat port [default: random]
+#c.ConnectionFileMixin.hb_port = 0
+
+## set the iopub (PUB) port [default: random]
+#c.ConnectionFileMixin.iopub_port = 0
+
+## Set the kernel's IP address [default localhost]. If the IP address is
+#  something other than localhost, then Consoles on other machines will be able
+#  to connect to the Kernel, so be careful!
+c.ConnectionFileMixin.ip = '127.0.0.1'
+
+## set the shell (ROUTER) port [default: random]
+#c.ConnectionFileMixin.shell_port = 0
+
+## set the stdin (ROUTER) port [default: random]
+#c.ConnectionFileMixin.stdin_port = 0
+
+## 
+#c.ConnectionFileMixin.transport = 'tcp'
+
+#------------------------------------------------------------------------------
+# KernelManager(ConnectionFileMixin) configuration
+#------------------------------------------------------------------------------
+
+## Manages a single kernel in a subprocess on this host.
+#  
+#  This version starts kernels with Popen.
+
+# XXX
+## Should we autorestart the kernel if it dies.
+#c.KernelManager.autorestart = True
+c.KernelManager.autorestart = False
+
+## DEPRECATED: Use kernel_name instead.
+#  
+#  The Popen Command to launch the kernel. Override this if you have a custom
+#  kernel. If kernel_cmd is specified in a configuration file, Jupyter does not
+#  pass any arguments to the kernel, because it cannot make any assumptions about
+#  the arguments that the kernel understands. In particular, this means that the
+#  kernel does not receive the option --debug if it given on the Jupyter command
+#  line.
+#c.KernelManager.kernel_cmd = []
+
+# XXX
+## Time to wait for a kernel to terminate before killing it, in seconds.
+#c.KernelManager.shutdown_wait_time = 5.0
+
+#------------------------------------------------------------------------------
+# Session(Configurable) configuration
+#------------------------------------------------------------------------------
+
+## Object for handling serialization and sending of messages.
+#  
+#  The Session object handles building messages and sending them with ZMQ sockets
+#  or ZMQStream objects.  Objects can communicate with each other over the
+#  network via Session objects, and only need to work with the dict-based IPython
+#  message spec. The Session will handle serialization/deserialization, security,
+#  and metadata.
+#  
+#  Sessions support configurable serialization via packer/unpacker traits, and
+#  signing with HMAC digests via the key/keyfile traits.
+#  
+#  Parameters ----------
+#  
+#  debug : bool
+#      whether to trigger extra debugging statements
+#  packer/unpacker : str : 'json', 'pickle' or import_string
+#      importstrings for methods to serialize message parts.  If just
+#      'json' or 'pickle', predefined JSON and pickle packers will be used.
+#      Otherwise, the entire importstring must be used.
+#  
+#      The functions must accept at least valid JSON input, and output *bytes*.
+#  
+#      For example, to use msgpack:
+#      packer = 'msgpack.packb', unpacker='msgpack.unpackb'
+#  pack/unpack : callables
+#      You can also set the pack/unpack callables for serialization directly.
+#  session : bytes
+#      the ID of this Session object.  The default is to generate a new UUID.
+#  username : unicode
+#      username added to message headers.  The default is to ask the OS.
+#  key : bytes
+#      The key used to initialize an HMAC signature.  If unset, messages
+#      will not be signed or checked.
+#  keyfile : filepath
+#      The file containing a key.  If this is set, `key` will be initialized
+#      to the contents of the file.
+
+## Threshold (in bytes) beyond which an object's buffer should be extracted to
+#  avoid pickling.
+#c.Session.buffer_threshold = 1024
+
+## Whether to check PID to protect against calls after fork.
+#  
+#  This check can be disabled if fork-safety is handled elsewhere.
+#c.Session.check_pid = True
+
+# XXX
+## Threshold (in bytes) beyond which a buffer should be sent without copying.
+#c.Session.copy_threshold = 65536
+
+## Debug output in the Session
+#c.Session.debug = False
+
+## The maximum number of digests to remember.
+#  
+#  The digest history will be culled when it exceeds this value.
+#c.Session.digest_history_size = 65536
+
+## The maximum number of items for a container to be introspected for custom
+#  serialization. Containers larger than this are pickled outright.
+#c.Session.item_threshold = 64
+
+## execution key, for signing messages.
+#c.Session.key = b''
+
+## path to file containing execution key.
+#c.Session.keyfile = ''
+
+## Metadata dictionary, which serves as the default top-level metadata dict for
+#  each message.
+#c.Session.metadata = {}
+
+## The name of the packer for serializing messages. Should be one of 'json',
+#  'pickle', or an import name for a custom callable serializer.
+#c.Session.packer = 'json'
+
+## The UUID identifying this session.
+#c.Session.session = ''
+
+## The digest scheme used to construct the message signatures. Must have the form
+#  'hmac-HASH'.
+#c.Session.signature_scheme = 'hmac-sha256'
+
+## The name of the unpacker for unserializing messages. Only used with custom
+#  functions for `packer`.
+#c.Session.unpacker = 'json'
+
+## Username for the Session. Default is your system username.
+# XXX
+#c.Session.username = 'jebba'
+
+#------------------------------------------------------------------------------
+# MultiKernelManager(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## A class for managing multiple kernels.
+
+## The name of the default kernel to start
+#c.MultiKernelManager.default_kernel_name = 'python3'
+
+## The kernel manager class.  This is configurable to allow subclassing of the
+#  KernelManager for customized behavior.
+#c.MultiKernelManager.kernel_manager_class = 'jupyter_client.ioloop.IOLoopKernelManager'
+
+#------------------------------------------------------------------------------
+# MappingKernelManager(MultiKernelManager) configuration
+#------------------------------------------------------------------------------
+
+## A KernelManager that handles notebook mapping and HTTP error handling
+
+## White list of allowed kernel message types. When the list is empty, all
+#  message types are allowed.
+#c.MappingKernelManager.allowed_message_types = []
+
+## Whether messages from kernels whose frontends have disconnected should be
+#  buffered in-memory.
+#  
+#  When True (default), messages are buffered and replayed on reconnect, avoiding
+#  lost messages due to interrupted connectivity.
+#  
+# XXX
+#  Disable if long-running kernels will produce too much output while no
+#  frontends are connected.
+#c.MappingKernelManager.buffer_offline_messages = True
+
+# XXX
+## Whether to consider culling kernels which are busy. Only effective if
+#  cull_idle_timeout > 0.
+#c.MappingKernelManager.cull_busy = False
+
+# XXX
+## Whether to consider culling kernels which have one or more connections. Only
+#  effective if cull_idle_timeout > 0.
+#c.MappingKernelManager.cull_connected = False
+
+## Timeout (in seconds) after which a kernel is considered idle and ready to be
+#  culled. Values of 0 or lower disable culling. Very short timeouts may result
+#  in kernels being culled for users with poor network connections.
+#c.MappingKernelManager.cull_idle_timeout = 0
+
+# XXX
+## The interval (in seconds) on which to check for idle kernels exceeding the
+#  cull timeout value.
+#c.MappingKernelManager.cull_interval = 300
+
+# XXX
+## Timeout for giving up on a kernel (in seconds).
+#  
+#  On starting and restarting kernels, we check whether the kernel is running and
+#  responsive by sending kernel_info_requests. This sets the timeout in seconds
+#  for how long the kernel can take before being presumed dead. This affects the
+#  MappingKernelManager (which handles kernel restarts) and the
+#  ZMQChannelsHandler (which handles the startup).
+#c.MappingKernelManager.kernel_info_timeout = 60
+c.MappingKernelManager.kernel_info_timeout = 480
+
+## 
+#c.MappingKernelManager.root_dir = ''
+
+#------------------------------------------------------------------------------
+# KernelSpecManager(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## If there is no Python kernelspec registered and the IPython kernel is
+#  available, ensure it is added to the spec list.
+#c.KernelSpecManager.ensure_native_kernel = True
+
+## The kernel spec class.  This is configurable to allow subclassing of the
+#  KernelSpecManager for customized behavior.
+#c.KernelSpecManager.kernel_spec_class = 'jupyter_client.kernelspec.KernelSpec'
+
+## Whitelist of allowed kernel names.
+#  
+#  By default, all installed kernels are allowed.
+#c.KernelSpecManager.whitelist = set()
+
+#------------------------------------------------------------------------------
+# ContentsManager(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## Base class for serving files and directories.
+#  
+#  This serves any text or binary file, as well as directories, with special
+#  handling for JSON notebook documents.
+#  
+#  Most APIs take a path argument, which is always an API-style unicode path, and
+#  always refers to a directory.
+#  
+#  - unicode, not url-escaped
+#  - '/'-separated
+#  - leading and trailing '/' will be stripped
+#  - if unspecified, path defaults to '',
+#    indicating the root path.
+
+## Allow access to hidden files
+c.ContentsManager.allow_hidden = False
+
+## 
+#c.ContentsManager.checkpoints = None
+
+## 
+#c.ContentsManager.checkpoints_class = 'notebook.services.contents.checkpoints.Checkpoints'
+
+## 
+#c.ContentsManager.checkpoints_kwargs = {}
+
+## handler class to use when serving raw file requests.
+#  
+#  Default is a fallback that talks to the ContentsManager API, which may be
+#  inefficient, especially for large files.
+#  
+#  Local files-based ContentsManagers can use a StaticFileHandler subclass, which
+#  will be much more efficient.
+#  
+#  Access to these files should be Authenticated.
+#c.ContentsManager.files_handler_class = 'notebook.files.handlers.FilesHandler'
+
+## Extra parameters to pass to files_handler_class.
+#  
+#  For example, StaticFileHandlers generally expect a `path` argument specifying
+#  the root directory from which to serve files.
+#c.ContentsManager.files_handler_params = {}
+
+## Glob patterns to hide in file and directory listings.
+#c.ContentsManager.hide_globs = ['__pycache__', '*.pyc', '*.pyo', '.DS_Store', '*.so', '*.dylib', '*~']
+
+## Python callable or importstring thereof
+#  
+#  To be called on a contents model prior to save.
+#  
+#  This can be used to process the structure, such as removing notebook outputs
+#  or other side effects that should not be saved.
+#  
+#  It will be called as (all arguments passed by keyword)::
+#  
+#      hook(path=path, model=model, contents_manager=self)
+#  
+#  - model: the model to be saved. Includes file contents.
+#    Modifying this dict will affect the file that is stored.
+#  - path: the API path of the save destination
+#  - contents_manager: this ContentsManager instance
+#c.ContentsManager.pre_save_hook = None
+
+## 
+# XXX
+#c.ContentsManager.root_dir = '/'
+
+## The base name used when creating untitled directories.
+c.ContentsManager.untitled_directory = 'untitled_folder'
+
+## The base name used when creating untitled files.
+c.ContentsManager.untitled_file = 'untitled'
+
+## The base name used when creating untitled notebooks.
+c.ContentsManager.untitled_notebook = 'notebook'
+
+#------------------------------------------------------------------------------
+# FileManagerMixin(Configurable) configuration
+#------------------------------------------------------------------------------
+
+## Mixin for ContentsAPI classes that interact with the filesystem.
+#  
+#  Provides facilities for reading, writing, and copying both notebooks and
+#  generic files.
+#  
+#  Shared by FileContentsManager and FileCheckpoints.
+#  
+#  Note ---- Classes using this mixin must provide the following attributes:
+#  
+#  root_dir : unicode
+#      A directory against against which API-style paths are to be resolved.
+#  
+#  log : logging.Logger
+
+## By default notebooks are saved on disk on a temporary file and then if
+#  successfully written, it replaces the old ones. This procedure, namely
+#  'atomic_writing', causes some bugs on file system without operation order
+#  enforcement (like some networked fs). If set to False, the new notebook is
+#  written directly on the old one which could fail (eg: full filesystem or quota
+#  )
+#c.FileManagerMixin.use_atomic_writing = True
+
+#------------------------------------------------------------------------------
+# FileContentsManager(FileManagerMixin,ContentsManager) configuration
+#------------------------------------------------------------------------------
+
+## If True (default), deleting files will send them to the platform's
+#  trash/recycle bin, where they can be recovered. If False, deleting files
+#  really deletes them.
+c.FileContentsManager.delete_to_trash = False
+
+## Python callable or importstring thereof
+#  
+#  to be called on the path of a file just saved.
+#  
+#  This can be used to process the file on disk, such as converting the notebook
+#  to a script or HTML via nbconvert.
+#  
+#  It will be called as (all arguments passed by keyword)::
+#  
+#      hook(os_path=os_path, model=model, contents_manager=instance)
+#  
+#  - path: the filesystem path to the file just written - model: the model
+#  representing the file - contents_manager: this ContentsManager instance
+#c.FileContentsManager.post_save_hook = None
+
+## 
+# XXX
+#c.FileContentsManager.root_dir = ''
+
+## DEPRECATED, use post_save_hook. Will be removed in Notebook 5.0
+#c.FileContentsManager.save_script = False
+
+#------------------------------------------------------------------------------
+# NotebookNotary(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## A class for computing and verifying notebook signatures.
+
+## The hashing algorithm used to sign notebooks.
+#c.NotebookNotary.algorithm = 'sha256'
+c.NotebookNotary.algorithm = 'sha512'
+
+## The sqlite file in which to store notebook signatures. By default, this will
+#  be in your Jupyter data directory. You can set it to ':memory:' to disable
+#  sqlite writing to the filesystem.
+# XXX
+#c.NotebookNotary.db_file = ''
+
+## The secret key with which notebooks are signed.
+# XXX
+#c.NotebookNotary.secret = b''
+
+## The file where the secret key is stored.
+# XXX
+#c.NotebookNotary.secret_file = ''
+
+## A callable returning the storage backend for notebook signatures. The default
+#  uses an SQLite database.
+# XXX
+#c.NotebookNotary.store_factory = traitlets.Undefined
+
+#------------------------------------------------------------------------------
+# GatewayKernelManager(MappingKernelManager) configuration
+#------------------------------------------------------------------------------
+
+## Kernel manager that supports remote kernels hosted by Jupyter Kernel or
+#  Enterprise Gateway.
+
+#------------------------------------------------------------------------------
+# GatewayKernelSpecManager(KernelSpecManager) configuration
+#------------------------------------------------------------------------------
+
+#------------------------------------------------------------------------------
+# GatewayClient(SingletonConfigurable) configuration
+#------------------------------------------------------------------------------
+
+## This class manages the configuration.  It's its own singleton class so that we
+#  can share these values across all objects.  It also contains some helper methods
+#   to build request arguments out of the various config options.
+
+## The authorization token used in the HTTP headers.  (JUPYTER_GATEWAY_AUTH_TOKEN
+#  env var)
+#c.GatewayClient.auth_token = None
+
+## The filename of CA certificates or None to use defaults.
+#  (JUPYTER_GATEWAY_CA_CERTS env var)
+#c.GatewayClient.ca_certs = None
+
+## The filename for client SSL certificate, if any.  (JUPYTER_GATEWAY_CLIENT_CERT
+#  env var)
+#c.GatewayClient.client_cert = None
+
+## The filename for client SSL key, if any.  (JUPYTER_GATEWAY_CLIENT_KEY env var)
+#c.GatewayClient.client_key = None
+
+## The time allowed for HTTP connection establishment with the Gateway server.
+#  (JUPYTER_GATEWAY_CONNECT_TIMEOUT env var)
+#c.GatewayClient.connect_timeout = 60.0
+
+## A comma-separated list of environment variable names that will be included,
+#  along with their values, in the kernel startup request.  The corresponding
+#  `env_whitelist` configuration value must also be set on the Gateway server -
+#  since that configuration value indicates which environmental values to make
+#  available to the kernel. (JUPYTER_GATEWAY_ENV_WHITELIST env var)
+#c.GatewayClient.env_whitelist = ''
+
+## Additional HTTP headers to pass on the request.  This value will be converted
+#  to a dict. (JUPYTER_GATEWAY_HEADERS env var)
+#c.GatewayClient.headers = '{}'
+
+## The password for HTTP authentication.  (JUPYTER_GATEWAY_HTTP_PWD env var)
+#c.GatewayClient.http_pwd = None
+
+## The username for HTTP authentication. (JUPYTER_GATEWAY_HTTP_USER env var)
+#c.GatewayClient.http_user = None
+
+## The gateway API endpoint for accessing kernel resources
+#  (JUPYTER_GATEWAY_KERNELS_ENDPOINT env var)
+# XXX
+#c.GatewayClient.kernels_endpoint = '/jupyter/api/kernels'
+
+## The gateway API endpoint for accessing kernelspecs
+#  (JUPYTER_GATEWAY_KERNELSPECS_ENDPOINT env var)
+# XXX
+#c.GatewayClient.kernelspecs_endpoint = '/jupyter/api/kernelspecs'
+
+## The gateway endpoint for accessing kernelspecs resources
+#  (JUPYTER_GATEWAY_KERNELSPECS_RESOURCE_ENDPOINT env var)
+# XXX
+#c.GatewayClient.kernelspecs_resource_endpoint = '/jupyter/kernelspecs'
+
+## The time allowed for HTTP request completion. (JUPYTER_GATEWAY_REQUEST_TIMEOUT
+#  env var)
+#c.GatewayClient.request_timeout = 60.0
+
+## The url of the Kernel or Enterprise Gateway server where kernel specifications
+#  are defined and kernel management takes place. If defined, this Notebook
+#  server acts as a proxy for all kernel management and kernel specification
+#  retrieval.  (JUPYTER_GATEWAY_URL env var)
+# XXX
+#c.GatewayClient.url = None
+
+## For HTTPS requests, determines if server's certificate should be validated or
+#  not. (JUPYTER_GATEWAY_VALIDATE_CERT env var)
+#c.GatewayClient.validate_cert = True
+
+## The websocket url of the Kernel or Enterprise Gateway server.  If not
+#  provided, this value will correspond to the value of the Gateway url with 'ws'
+#  in place of 'http'.  (JUPYTER_GATEWAY_WS_URL env var)
+# XXX
+#c.GatewayClient.ws_url = None

karoo_gp.ipynb

@@ -0,0 +1,291 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Karoo GP (desktop + server combined)\n",
+    "# Use Genetic Programming for Classification and Symbolic Regression\n",
+    "# by Kai Staats, MSc with TensorFlow support provided by Iurii Milovanov; see LICENSE.md\n",
+    "# version 2.3 for Python 3.6\n",
+    "\n",
+    "'''\n",
+    "A word to the newbie, expert, and brave--\n",
+    "Even if you are highly experienced in Genetic Programming, it is recommended that you review the 'Karoo User Guide' \n",
+    "before running this application. While your computer will not burst into flames nor will the sun collapse into a black \n",
+    "hole if you do not, you will likely find more enjoyment of this particular flavour of GP with a little understanding \n",
+    "of its intent and design.\n",
+    "\n",
+    "Without any command line arguments, Karoo GP relies upon user settings and the datasets located in karoo_gp/files/.\n",
+    "\n",
+    "\t$ python karoo_gp_main.py\n",
+    "\t\n",
+    "\n",
+    "If you include the path to an external dataset, it will auto-load at launch:\n",
+    "\n",
+    "\t$ python karoo_gp_main.py /[path]/[to_your]/[filename].csv\n",
+    "\t\n",
+    "\n",
+    "If you include one or more additional arguments, they will override the default values, as follows:\n",
+    "\n",
+    "\t-ker [r,c,m]\t\t\tfitness function: (r)egression, (c)lassification, or (m)atching\n",
+    "\t-typ [f,g,r]\t\t\tTree type: (f)ull, (g)row, or (r)amped half/half\n",
+    "\t-bas [3...10]\t\t\tmaximum Tree depth for initial population\n",
+    "\t-max [3...10]\t\t\tmaximum Tree depth for entire run\n",
+    "\t-min [3 to 2^(bas +1) - 1]\tminimum number of nodes\n",
+    "\t-pop [10...1000]\t\tnumber of trees in each generational population\n",
+    "\t-gen [1...100]\t\t\tnumber of generations\n",
+    "\t-tor [7 per 100]\t\tnumber of trees selected for tournament\n",
+    "\t-evr [0.0...1.0]  \t\tdecimal percent of pop generated through Reproduction\n",
+    "\t-evp [0.0...1.0]  \t\tdecimal percent of pop generated through Point Mutation\n",
+    "\t-evb [0.0...1.0]  \t\tdecimal percent of pop generated through Branch Mutation\n",
+    "\t-evc [0.0...1.0]  \t\tdecimal percent of pop generated through Crossover\n",
+    "\t\n",
+    "If you include any of the above flags, then you *must* also include a flag to load an external dataset.\n",
+    "\n",
+    "\t-fil [path]/[to]/[data].csv\tan external dataset\n",
+    "\n",
+    "\n",
+    "An example is given, as follows:\n",
+    "\n",
+    "\t$ python karoo_gp_server.py -ker c -typ r -bas 4 -fil [path]/[to]/[data].csv\n",
+    "\n",
+    "'''\n",
+    "\n",
+    "import os\n",
+    "import sys; sys.path.append('modules/') # add directory 'modules' to the current path\n",
+    "import argparse\n",
+    "import karoo_gp_base_class; gp = karoo_gp_base_class.Base_GP()\n",
+    "\n",
+    "os.system('clear')\n",
+    "print ('\\n\\033[36m\\033[1m')\n",
+    "print ('\\t **   **   ******    *****    ******    ******       ******    ******')\n",
+    "print ('\\t **  **   **    **  **   **  **    **  **    **     **        **    **')\n",
+    "print ('\\t ** **    **    **  **   **  **    **  **    **     **        **    **')\n",
+    "print ('\\t ****     ********  ******   **    **  **    **     **   ***  *******')\n",
+    "print ('\\t ** **    **    **  ** **    **    **  **    **     **    **  **')\n",
+    "print ('\\t **  **   **    **  **  **   **    **  **    **     **    **  **')\n",
+    "print ('\\t **   **  **    **  **   **  **    **  **    **     **    **  **')\n",
+    "print ('\\t **    ** **    **  **    **  ******    ******       ******   **')\n",
+    "print ('\\033[0;0m')\n",
+    "print ('\\t\\033[36m Genetic Programming in Python with TensorFlow - by Kai Staats, version 2.3\\033[0;0m')\n",
+    "print ('')\n",
+    "\n",
+    "\n",
+    "#++++++++++++++++++++++++++++++++++++++++++\n",
+    "#   User Interface for Configuation       |\n",
+    "#++++++++++++++++++++++++++++++++++++++++++\n",
+    "\n",
+    "if len(sys.argv) < 3: # either no command line argument, or only a filename is provided\n",
+    "\n",
+    "\twhile True:\n",
+    "\t\ttry:\n",
+    "\t\t\tquery = input('\\t Select (c)lassification, (r)egression, (m)atching, or (p)lay (default m): ')\n",
+    "\t\t\tif query in ['c','r','m','p','']: kernel = query or 'm'; break\n",
+    "\t\t\telse: raise ValueError()\n",
+    "\t\texcept ValueError: print ('\\t\\033[32m Select from the options given. Try again ...\\n\\033[0;0m')\n",
+    "\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\n",
+    "\tif kernel == 'p': # play mode\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Select (f)ull or (g)row (default g): ')\n",
+    "\t\t\t\tif query in ['f','g','']: tree_type = query or 'f'; break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Select from the options given. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Enter the depth of the Tree (default 1): ')\n",
+    "\t\t\t\tif query == '': tree_depth_base = 1; break\n",
+    "\t\t\t\telif int(query) in list(range(1,11)): tree_depth_base = int(query); break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Enter a number from 1 including 10. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\ttree_depth_max = tree_depth_base\n",
+    "\t\ttree_depth_min = 3\n",
+    "\t\ttree_pop_max = 1\n",
+    "\t\tgen_max = 1\n",
+    "\t\ttourn_size = 0\n",
+    "\t\tdisplay = 'm'\n",
+    "\t\t#\tevolve_repro, evolve_point, evolve_branch, evolve_cross, tourn_size, precision, filename are not required\n",
+    "\t\n",
+    "\telse: # if any other kernel is selected\n",
+    "\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Select (f)ull, (g)row, or (r)amped 50/50 method (default r): ')\n",
+    "\t\t\t\tif query in ['f','g','r','']: tree_type = query or 'r'; break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Select from the options given. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Enter depth of the \\033[3minitial\\033[0;0m population of Trees (default 3): ')\n",
+    "\t\t\t\tif query == '': tree_depth_base = 3; break\n",
+    "\t\t\t\telif int(query) in list(range(1,11)): tree_depth_base = int(query); break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Enter a number from 1 including 10. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Enter maximum Tree depth (default %s): ' %str(tree_depth_base))\n",
+    "\t\t\t\tif query == '': tree_depth_max = tree_depth_base; break\n",
+    "\t\t\t\telif int(query) in list(range(tree_depth_base,11)): tree_depth_max = int(query); break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Enter a number from %s including 10. Try again ...\\n\\033[0;0m' %str(tree_depth_base))\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\tmax_nodes = 2**(tree_depth_base+1)-1 # calc the max number of nodes for the given depth\n",
+    "\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Enter minimum number of nodes for any given Tree (default 3; max %s): ' %str(max_nodes))\n",
+    "\t\t\t\tif query == '': tree_depth_min = 3; break\n",
+    "\t\t\t\telif int(query) in list(range(3,max_nodes + 1)): tree_depth_min = int(query); break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Enter a number from 3 including %s. Try again ...\\n\\033[0;0m' %str(max_nodes))\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\t#while True:\n",
+    "\t\t\t#try:\n",
+    "\t\t\t\t#query = input('\\t Select (p)artial or (f)ull operator inclusion (default p): ')\n",
+    "\t\t\t\t#if query == '': swim = 'p'; break\n",
+    "\t\t\t\t#elif query in ['p','f']: swim = query; break\n",
+    "\t\t\t\t#else: raise ValueError()\n",
+    "\t\t\t#except ValueError: print ('\\t\\033[32m Select from the options given. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\t#except KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Enter number of Trees in each population (default 100): ')\n",
+    "\t\t\t\tif query == '': tree_pop_max = 100; break\n",
+    "\t\t\t\telif int(query) in list(range(1,1001)): tree_pop_max = int(query); break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Enter a number from 1 including 1000. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\t# calculate the tournament size\n",
+    "\t\ttourn_size = int(tree_pop_max * 0.07) # default 7% can be changed by selecting (g)eneration and then 'ts'\n",
+    "\t\tif tourn_size < 2: tourn_size = 2 # forces some diversity for small populations\n",
+    "\t\tif tree_pop_max == 1: tourn_size = 1 # in theory, supports the evolution of a single Tree - NEED TO FIX 2018 04/19\n",
+    "\t\t\n",
+    "\t\twhile True:\n",
+    "\t\t\ttry:\n",
+    "\t\t\t\tquery = input('\\t Enter max number of generations (default 10): ')\n",
+    "\t\t\t\tif query == '': gen_max = 10; break\n",
+    "\t\t\t\telif int(query) in list(range(1,101)): gen_max = int(query); break\n",
+    "\t\t\t\telse: raise ValueError()\n",
+    "\t\t\texcept ValueError: print ('\\t\\033[32m Enter a number from 1 including 100. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\n",
+    "\t\tif gen_max > 1:\n",
+    "\t\t\twhile True:\n",
+    "\t\t\t\ttry:\n",
+    "\t\t\t\t\tquery = input('\\t Display (i)nteractive, (g)eneration, (m)iminal, (s)ilent, or (d)e(b)ug (default m): ')\n",
+    "\t\t\t\t\tif query in ['i','g','m','s','db','']: display = query or 'm'; break\n",
+    "\t\t\t\t\telse: raise ValueError()\n",
+    "\t\t\t\texcept ValueError: print ('\\t\\033[32m Select from the options given. Try again ...\\n\\033[0;0m')\n",
+    "\t\t\t\texcept KeyboardInterrupt: sys.exit()\n",
+    "\t\t\t\t\n",
+    "\t\telse: display = 's' # display mode is not used, but a value must be passed\n",
+    "\t\t\t\t\n",
+    "\t### additional configuration parameters ###\n",
+    "\t\n",
+    "\tevolve_repro = int(0.1 * tree_pop_max) # quantity of a population generated through Reproduction\n",
+    "\tevolve_point = int(0.0 * tree_pop_max) # quantity of a population generated through Point Mutation\n",
+    "\tevolve_branch = int(0.2 * tree_pop_max) # quantity of a population generated through Branch Mutation\n",
+    "\tevolve_cross = int(0.7 * tree_pop_max) # quantity of a population generated through Crossover\n",
+    "\tfilename = '' # not required unless an external file is referenced\n",
+    "\tprecision = 6 # number of floating points for the round function in 'fx_fitness_eval'\n",
+    "\tswim = 'p' # require (p)artial or (f)ull set of features (operators) for each Tree entering the gene_pool\n",
+    "\tmode = 'd' # pause at the (d)esktop when complete, awaiting further user interaction; or terminate in (s)erver mode\n",
+    "\t\n",
+    "\n",
+    "#++++++++++++++++++++++++++++++++++++++++++\n",
+    "#   Command Line for Configuation         |\n",
+    "#++++++++++++++++++++++++++++++++++++++++++\n",
+    "\n",
+    "else: # 2 or more command line arguments are provided\n",
+    "\n",
+    "\tap = argparse.ArgumentParser(description = 'Karoo GP Server')\n",
+    "\tap.add_argument('-ker', action = 'store', dest = 'kernel', default = 'c', help = '[c,r,m] fitness function: (r)egression, (c)lassification, or (m)atching')\n",
+    "\tap.add_argument('-typ', action = 'store', dest = 'type', default = 'r', help = '[f,g,r] Tree type: (f)ull, (g)row, or (r)amped half/half')\n",
+    "\tap.add_argument('-bas', action = 'store', dest = 'depth_base', default = 4, help = '[3...10] maximum Tree depth for the initial population')\n",
+    "\tap.add_argument('-max', action = 'store', dest = 'depth_max', default = 4, help = '[3...10] maximum Tree depth for the entire run')\n",
+    "\tap.add_argument('-min', action = 'store', dest = 'depth_min', default = 3, help = 'minimum nodes, from 3 to 2^(base_depth +1) - 1')\n",
+    "\tap.add_argument('-pop', action = 'store', dest = 'pop_max', default = 100, help = '[10...1000] number of trees per generation')\n",
+    "\tap.add_argument('-gen', action = 'store', dest = 'gen_max', default = 10, help = '[1...100] number of generations')\n",
+    "\tap.add_argument('-tor', action = 'store', dest = 'tor_size', default = 7, help = '[7 for each 100] recommended tournament size')\n",
+    "\tap.add_argument('-evr', action = 'store', dest = 'evo_r', default = 0.1, help = '[0.0-1.0] decimal percent of pop generated through Reproduction')\n",
+    "\tap.add_argument('-evp', action = 'store', dest = 'evo_p', default = 0.0, help = '[0.0-1.0] decimal percent of pop generated through Point Mutation')\n",
+    "\tap.add_argument('-evb', action = 'store', dest = 'evo_b', default = 0.2, help = '[0.0-1.0] decimal percent of pop generated through Branch Mutation')\n",
+    "\tap.add_argument('-evc', action = 'store', dest = 'evo_c', default = 0.7, help = '[0.0-1.0] decimal percent of pop generated through Crossover')\n",
+    "\tap.add_argument('-fil', action = 'store', dest = 'filename', default = '', help = '/path/to_your/[data].csv')\n",
+    "\t\n",
+    "\targs = ap.parse_args()\n",
+    "\n",
+    "\t# pass the argparse defaults and/or user inputs to the required variables\n",
+    "\tkernel = str(args.kernel)\n",
+    "\ttree_type = str(args.type)\n",
+    "\ttree_depth_base = int(args.depth_base)\n",
+    "\ttree_depth_max = int(args.depth_max)\n",
+    "\ttree_depth_min = int(args.depth_min)\n",
+    "\ttree_pop_max = int(args.pop_max)\n",
+    "\tgen_max = int(args.gen_max)\n",
+    "\ttourn_size = int(args.tor_size)\n",
+    "\tevolve_repro = int(float(args.evo_r) * tree_pop_max)\n",
+    "\tevolve_point = int(float(args.evo_p) * tree_pop_max)\n",
+    "\tevolve_branch = int(float(args.evo_b) * tree_pop_max)\n",
+    "\tevolve_cross = int(float(args.evo_c) * tree_pop_max)\n",
+    "\t#filename = str(args.filename)\n",
+    "\tfilename='files/data_MATCH.csv'\n",
+    "\tdisplay = 's' # display mode is set to (s)ilent\n",
+    "\tprecision = 6 # number of floating points for the round function in 'fx_fitness_eval'\n",
+    "\tswim = 'p' # require (p)artial or (f)ull set of features (operators) for each Tree entering the gene_pool\n",
+    "\tmode = 's' # pause at the (d)esktop when complete, awaiting further user interaction; or terminate in (s)erver mode\n",
+    "\t"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#++++++++++++++++++++++++++++++++++++++++++\n",
+    "#   Conduct the GP run                    |\n",
+    "#++++++++++++++++++++++++++++++++++++++++++\n",
+    "\n",
+    "gp.fx_karoo_gp(kernel, tree_type, tree_depth_base, tree_depth_max, tree_depth_min, tree_pop_max, gen_max, tourn_size, filename, evolve_repro, evolve_point, evolve_branch, evolve_cross, display, precision, swim, mode)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

modules/karoo_gp_base_class.py

@@ -56,8 +56,8 @@ operators = {ast.Add: tf.add, # e.g., a + b
 	'square': tf.square, # e.g., square(a)
 	'sqrt': tf.sqrt, # e.g., sqrt(a)
 	'pow': tf.pow, # e.g., pow(a, b)
-	'log': tf.log, # e.g., log(a)
-	'log1p': tf.log1p, # e.g., log1p(a)
+	'log': tf.math.log, # e.g., log(a)
+	'log1p': tf.math.log1p, # e.g., log1p(a)
 	'cos': tf.cos, # e.g., cos(a)
 	'sin': tf.sin, # e.g., sin(a)
 	'tan': tf.tan, # e.g., tan(a)
@@ -174,12 +174,12 @@ class Base_GP(object):
 		if self.kernel == 'p': # terminate here for Play mode
 			self.fx_display_tree(self.tree) # print the current Tree
 			self.fx_data_tree_write(self.population_a, 'a') # save this one Tree to disk
-			sys.exit()
+			#sys.exit()
 
 		elif self.gen_max == 1: # terminate here if constructing just one generation
 			self.fx_data_tree_write(self.population_a, 'a') # save this single population to disk
 			print ('\n We have constructed a single, stochastic population of', self.tree_pop_max,'Trees, and saved to disk')
-			sys.exit()
+			#sys.exit()
 			
 		else: print ('\n We have constructed the first, stochastic population of', self.tree_pop_max,'Trees')
 		
@@ -342,7 +342,7 @@ class Base_GP(object):
 		print ('\n\033[3m "It is not the strongest of the species that survive, nor the most intelligent,\033[0;0m')
 		print ('\033[3m  but the one most responsive to change."\033[0;0m --Charles Darwin\n')
 		print ('\033[3m Congrats!\033[0;0m Your Karoo GP run is complete.\n')
-		sys.exit()
+		#sys.exit()
 		
 		return
 		
@@ -1228,11 +1228,11 @@ class Base_GP(object):
 		'''
 		
 		# Initialize TensorFlow session
-		tf.reset_default_graph() # Reset TF internal state and cache (after previous processing)
-		config = tf.ConfigProto(log_device_placement=self.tf_device_log, allow_soft_placement=True)
+		tf.compat.v1.reset_default_graph() # Reset TF internal state and cache (after previous processing)
+		config = tf.compat.v1.ConfigProto(log_device_placement=self.tf_device_log, allow_soft_placement=True)
 		config.gpu_options.allow_growth = True
 		
-		with tf.Session(config=config) as sess:
+		with tf.compat.v1.Session(config=config) as sess:
 			with sess.graph.device(self.tf_device):
 			
 				# 1 - Load data into TF vectors
@@ -1314,7 +1314,7 @@ class Base_GP(object):
 					
 				else: raise Exception('Kernel type is wrong or missing. You entered {}'.format(self.kernel))
 				
-				fitness = tf.reduce_sum(pairwise_fitness)
+				fitness = tf.reduce_sum(input_tensor=pairwise_fitness)
 				
 				# Process TF graph and collect the results
 				result, pred_labels, solution, fitness, pairwise_fitness = sess.run([result, pred_labels, solution, fitness, pairwise_fitness])
@@ -1433,9 +1433,9 @@ class Base_GP(object):
 		
 		for class_label in range(self.class_labels - 2, 0, -1):
 			cond = (class_label - 1 - skew < result) & (result <= class_label - skew)
-			label_rules[class_label] = tf.cond(cond, lambda: (tf.constant(class_label), tf.constant(' <= {}'.format(class_label - skew))), lambda: label_rules[class_label + 1])
+			label_rules[class_label] = tf.cond(pred=cond, true_fn=lambda: (tf.constant(class_label), tf.constant(' <= {}'.format(class_label - skew))), false_fn=lambda: label_rules[class_label + 1])
 			
-		pred_label = tf.cond(result <= 0 - skew, lambda: (tf.constant(0), tf.constant(' <= {}'.format(0 - skew))), lambda: label_rules[1])
+		pred_label = tf.cond(pred=result <= 0 - skew, true_fn=lambda: (tf.constant(0), tf.constant(' <= {}'.format(0 - skew))), false_fn=lambda: label_rules[1])
 			
 		return pred_label
 		

requirements.txt

@@ -0,0 +1,4 @@
+wheel
+sklearn
+sympy
+tensorflow

setup.py

@@ -0,0 +1,24 @@
+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="karoo_gp-kstaats", # Replace with your own username
+    version="2.3",
+    author="Kai Staats",
+    author_email="pip@overthesun.com",
+    description="evolutionary algorithm, genetic programming suite",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/kstaats/karoo_gp",
+    packages={''},
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.6',
+)
+
+#    packages=setuptools.find_packages(),