Update doc

README.md

@@ -49,14 +49,11 @@ Run the following command and follow the instructions
 To utilize SimNotify you will need to create a notify channel so that your phone (or device)  can be linked to where the notifications will be sent.  
 Go to https://notify.run/ and click `create a channel`  
 Scan the QR code and subscribe/enable notifications (you may need to check your system settings to ensure these are turned on)  
-Copy the link generated, and set the config files on your machine to this link by running:  
-```notify-run configure <paste-link-here>```
-
-Now you should be able to run the python script:
+Copy the link generated, and you should be able to run the python script:
 ```
 from SimLogger import SimNotify
 endpoint = "<paste-link-here>"
-SimNotify.sendNotification("Hello World", endpoint=endpoint)
+SimNotify.sendNotification("Hello World", endpoint)
 ```
 
 ## Development  

docs/source/FigLogger.rst

@@ -0,0 +1,59 @@
+SimLogger.FigLogger module
+==========================
+
+The FigLogger is designed to solve the problem of not being able to easily
+view detailed graphs through a command line interface with remote computing
+systems. To solve this, an integration between the SimLogger for data archiving
+and kachery were combined to give remote access to data through a web interface.
+
+Installation
+------------
+
+After following the initial installation steps for the SimLogger package.
+Ensure the machine is setup to access the kachery cloud
+
+``kachery-cloud-init``
+
+and follow the steps to setup the connection.
+
+With that you can now generate your own graphs, and then remotely view them.
+The graphs are also saved to file using the SimLogger so you can always
+simply load up the pickled version of the graph and show it again on a local
+machine if desired.
+
+The simplest method is to let FigLogger generate the plot for you. This is
+great for when you want a simple scatter or line plot without much specifics.
+
+.. code-block:: python
+    from SimLogger import FigLogger
+
+    simTag = "testSim"
+    objTag = "samplePlot"
+
+    epoch = [0,1,2,3,4]
+    loss = [3.0, 2.7, 2.6, 2.5, 2.45]
+
+    plotType = "line"
+    title = "Sample Plot"
+    labels={"x":"Epoch","y":"Loss"}
+
+    FigLogger.createPlot(simTag, 
+                            objTag, 
+                            epoch, 
+                            loss,
+                            plotType=plotType, 
+                            title=title, 
+                            labels=labels)
+
+
+Which will automatically generate a line plot with the data given, and will
+give a link to the graph in the log file.
+
+SimLogger.FigLogger functions
+-----------------------------
+
+.. automodule:: SimLogger.FigLogger
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/SimLogger.rst

@@ -1,26 +1,63 @@
-SimLogger package
-=================
-
 SimLogger.SimLogger module
---------------------------
+==========================
 
-.. automodule:: SimLogger.SimLogger
-   :members:
-   :undoc-members:
-   :show-inheritance:
+The SimLogger module is the fundamental piece of the SimLogger package.
 
-SimLogger.FigLogger module
---------------------------
+The SimLogger functions on the key principal that everything in a simulation
+can be uniquely identified with the following:
+1. simTag - uniquely identifies a particular simulation configuration. 
+    This is changed for every single test run. Everytime the parameters
+    are changed (and you re-run your simulation) you should update your
+    simTag accordingly.  
+2. objTag - uniquely identifies a particular object within a simulation.
+    This is the same across simulations, but should be a unique name for the 
+    object within the simulation.
+3. date-time string - all pickled files have an additional date-time string
+    appended to the file name to avoid any accidental overwriting of data.
 
-.. automodule:: SimLogger.FigLogger
-   :members:
-   :undoc-members:
-   :show-inheritance:
+With that, all data can be uniquely named and pickled to file. Pickling provides
+an easy way to store and load files in python, and is the compression method
+used in the SimLogger.  
 
-SimLogger.SimNotify module
---------------------------
+This could be an example script
 
-.. automodule:: SimLogger.SimNotify
+.. code-block:: python
+    from SimLogger import SimLogger
+    simTag = 'sampleSimulation'
+    objTag = 'sampleArray'
+    sampleArray = [1,2,3,4]
+    SimLogger.saveObj(simTag, objTag, sampleArray, makeNote=True)
+
+    # Outputs
+    # 2024-06-25 10:44:44,063 [INFO ] Logger Loaded
+    # 2024-06-25 10:44:44,064 [INFO ] OBJECT,sampleSimulation,sampleArray,data/obj/sampleSimulation_sampleArray_2024-06-25_10-44-44.pkl
+    #
+    # additionally a file is saved: data/obj/sampleSimulation_sampleArray_2024-06-25_10-44-44.pkl
+
+Which lays out the simTag for the simualtion, then defines an object we are going to save,
+with the objTag and then stores it with the SimLogger. 
+This also generates an example.log file so that you can always refer somewhere to know exactly where the data has been stored.
+
+In future analysis, the data can be loaded as needed using the following
+To reference the object you will need the unique id of the object, which is simTag_objTag
+
+.. code-block:: python
+    from SimLogger import SimLogger
+    sampleArrayLoaded = SimLogger.getObjectFromuniqueId('sampleSimulation_sampleArray')
+    print(sampleArrayLoaded)
+
+    # Ouptuts
+    # [1, 2, 3, 4]
+
+Within this framework, various configurations can be changed:
+- log file name
+- folder where the pickled files get saved
+
+SimLogger.SimLogger Functions
+-----------------------------
+
+.. automodule:: SimLogger.SimLogger
    :members:
    :undoc-members:
    :show-inheritance:
+

docs/source/SimNotify.rst

@@ -0,0 +1,41 @@
+SimLogger.SimNotify module
+==========================
+
+Often when simulations are running for an extended period of time on a cluster machine,
+not to mention the time spent waiting for available resource, it is useful to get remote
+updates to know how well a simulation is performing. This module seeks to solve that
+problem while being integrated into the SimLogger system. Additionally, this uses
+an openly and freely available system for remote web notifications notify-run
+
+In this package we don't reference the python interface for notify-run since configuration
+can be finicky. Instead, we will directly send post requests to simplify the process.
+
+Installation
+------------
+
+Nofity runs on channels, that you can then easily subscribe to through the web interface.
+To do this, go to https://notify.run/ and create a new channel. Copy the link that it
+generates. This link will be the URL to go to and see any notifications.
+
+Using that link you can then send notifications:
+
+.. code-block:: python
+
+    from SimLogger import SimNotify
+    endpoint = "paste-link-here"
+    SimNotify.sendNotification("Hello World", endpoint)
+
+
+Which will post a Hello World message on the channel.
+
+Additionally, the notification, endpoint, and response code from the server are all
+listed in the log file.
+
+SimLogger.FigLogger functions
+-----------------------------
+
+.. automodule:: SimLogger.SimNotify
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/index.rst

@@ -9,20 +9,23 @@ Welcome to SimLogger's documentation!
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
-
+   
    SimLogger
-
-
+   FigLogger
+   SimNotify
 
 A simplified method for logging and saving information in scientific computing.
 
 SimLogger seeks to simplify the process of saving and archiving data for
 scientific computing by handling all the file naming a storing for you.
 
 Archive your python objects simply and easiy, and never worry about overwriting files.
-All data is defined with 3 key components  
+All data is defined with 3 key components
+
 ``simTag`` - tag unique for each simulation (like naming the experiment)  
+
 ``objTag`` - tag unique for each object (like the variable within the experiments)  
+
 ``date-time`` - this is automatically added by SimLogger to help ensure unqiueness of files  
 
 With that you can save your data easily!  
@@ -75,7 +78,7 @@ Development
 ===========
 install all dependencies (including linting and testing) with:  
 
-``pip install -e '.[lint,test]``
+``pip install -e '.[lint,test,doc]``
 
 run tests with: