Restructure repository (#13)

* Redo folder structure and start amending references

* Update setup.py using dephell to be able to install summit

* Set up tests for domains
The variables don't have __eq__ methods

* Update random strategy doctests

* Update lhs doc test code... might need to take this out if it is too brittle

* Bump version and output setup.py

* Make updates to tsemo

README.md

@@ -29,6 +29,8 @@ In addition to the documentation, we are prepareing several case studies.  These
 
 ### Build a release
 
+Below is the old process.
+
 1. Install [s3pypi](https://github.com/novemberfiveco/s3pypi) and [dephell](https://dephell.org/docs/installation.html)
 2. Install AWS credentials to upload pypi.rxns.io (Kobi is the one who controls this).
 3. Bump the version in pyproject.toml and then run:
@@ -38,30 +40,3 @@ In addition to the documentation, we are prepareing several case studies.  These
     ```s3pypi --bucket pypi.rxns.io```
 
 
-### Building Containers
-
-This is useful when you want to run summit on a remote server. 
-
-1. Download [habitus](https://www.habitus.io/). Habitus is used to insert ssh keys into containers safely, so you can pull from for private Github repositories. 
-
-2. If you are on mac, you need to install gnu-tar:
-
-    ```
-    brew install gnu-tar
-    echo "export PATH=/usr/local/opt/gnu-tar/libexec/gnubin:$PATH" >> ~./bash_profile
-    echo "aliast tar='gtar'" >> ~/.bash_profile
-    source ~/.bash_profile
-    ```
-
-3. Change line 10 of the build.yml to be the name of your [ssh key for github](https://help.github.com/en/articles/connecting-to-github-with-ssh) 
-
-4. Inside the main folder for summit (i.e., the same folder as this README), build the container:
-
-    ```
-    #On Mac
-    sudo habitus --build host=docker.for.mac.localhost --binding=127.0.0.1 --secrets=true
-
-    #This is what I think it will be on linux
-    sudo habitus --build host=gateway.docker.local --binding=127.0.0.1 --secrets=true
-    ```
-

README.rst

@@ -2,42 +2,48 @@
 Summit
 ======
 
-Summit is a set of tools for optimizing chemical reactions. 
+Summit is a set of tools for optimizing chemical processes. 
 
-Case Studies
+Installation
 ------------
 
+If you want to use summit immediately without installing python on your computer, go to our `Jupyterhub <hub.rxns.io>`_\ , which already has it installed. You can find a description of it `here <https://github.com/sustainable-processes/server/blob/master/notes/session_1.md>`_.
 
-* `Photo Amination <case_studies/photoamination/>`_
-* `Borrowing Hydrogen <case_studies/borrowing_hydrogen>`_
+To install locally:
 
-Building Containers
--------------------
+``pip install git+https://github.com/sustainable-processes/[email protected]#egg=summit``
 
+You might need to enter your username and password for Github. 
 
-#. 
-   Download `habitus <https://www.habitus.io/>`_. Habitus is used to insert ssh keys into containers safely, so you can pull from for private Github repositories. 
+Documentation
+-------------
 
-#. 
-   If you are on mac, you need to install gnu-tar:
+The documentation for summit can be found on the `wiki <https://github.com/sustainable-processes/summit/wiki>`_.
 
-   .. code-block::
+Case Studies
+------------
 
-       brew install gnu-tar
-       echo "export PATH=/usr/local/opt/gnu-tar/libexec/gnubin:$PATH" >> ~./bash_profile
-       echo "aliast tar='gtar'" >> ~/.bash_profile
-       source ~/.bash_profile
+In addition to the documentation, we are prepareing several case studies.  These contain jupyter notebooks with practical examples to follow. 
+
+
+* `Formulation <case_studies/formulation>`_
+* `Nanosilica <case_studies/nanosilica>`_
+* `Photo Amination <case_studies/photoamination/>`_
+* `Borrowing Hydrogen <case_studies/borrowing_hydrogen>`_
 
-#. 
-   Change line 10 of the build.yml to be the name of your `ssh key for github <https://help.github.com/en/articles/connecting-to-github-with-ssh>`_ 
+Develpment
+----------
 
-#. 
-   Inside the main folder for summit (i.e., the same folder as this README), build the container:
+Build a release
+^^^^^^^^^^^^^^^
 
-   .. code-block::
+Below is the old process.
 
-       #On Mac
-       sudo habitus --build host=docker.for.mac.localhost --binding=127.0.0.1 --secrets=true
 
-       #This is what I think it will be on linux
-       sudo habitus --build host=gateway.docker.local --binding=127.0.0.1 --secrets=true
+#. Install `s3pypi <https://github.com/novemberfiveco/s3pypi>`_ and `dephell <https://dephell.org/docs/installation.html>`_
+#. Install AWS credentials to upload pypi.rxns.io (Kobi is the one who controls this).
+#. Bump the version in pyproject.toml and then run:
+    ``dephell deps convert --from=pyproject.toml --to=setup.py``
+#. Go into setup.py and delete the lines for extras_install_requires
+#. Upload the package to the private pypi repository:
+    ``s3pypi --bucket pypi.rxns.io``