Bump version to 0.4.0

README.rst

@@ -1,3 +1,6 @@
+.. role:: raw-html-m2r(raw)
+   :format: html
+
 
 Summit
 ======
@@ -7,37 +10,64 @@ Summit is a set of tools for optimizing chemical processes.
 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>`_.
+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 Jupyterhub `here <https://github.com/sustainable-processes/server/blob/master/notes/session_1.md>`_.
 
 To install locally:
 
-``pip install git+https://github.com/sustainable-processes/summit.git@0.2.2#egg=summit``
+``pip install git+https://github.com/sustainable-processes/summit_private.git@0.3.0#egg=summit``
 
 You might need to enter your username and password for Github. 
 
 Documentation
 -------------
 
 The documentation for summit can be found on the `wiki <https://github.com/sustainable-processes/summit/wiki>`_.
+:raw-html-m2r:`<!-- It would be great to add a "Quick Start" here.-->`
 
-Case Studies
-------------
-
-In addition to the documentation, we are prepareing several case studies.  These contain jupyter notebooks with practical examples to follow. 
+Development
+-----------
 
+Downloading the code
+^^^^^^^^^^^^^^^^^^^^
 
-* `Formulation <case_studies/formulation>`_
-* `Nanosilica <case_studies/nanosilica>`_
-* `Photo Amination <case_studies/photoamination/>`_
-* `Borrowing Hydrogen <case_studies/borrowing_hydrogen>`_
 
-Develpment
-----------
+#. Clone the repository:
+   ``git clone https://github.com/sustainable-processes/summit_private.git``
+#. Intall poetry by following the instructions `here <https://python-poetry.org/docs/#installation>`_. We use poetry for dependency management.
+#. Install all dependencies:
+   ``poetry install``
+#. To run tests:
+   ``poetry run pytest --doctest-modules --ignore=case_studies``
 
-Build a release
+Commit Worfklow
 ^^^^^^^^^^^^^^^
 
-Below is the old process.
+
+* Use the `project board <https://github.com/orgs/sustainable-processes/projects/1>`_ to keep track of issues. Issues will automatically be moved along in the board when they are closed in Github.
+* Write tests in the tests/ folder
+* Documentation follows the `numpy docstring format <https://numpydoc.readthedocs.io/en/latest/format.html#documenting-class-instances>`_
+
+  * Please include examples when possible that can be tested using `doctest <https://docs.python.org/3/library/doctest.html>`_
+  * All publicly available classes and methods should have a docstring
+
+* Commit to a branch off master and submit pull requests to merge. 
+
+  * To create a branch locally and push it:
+    .. code-block:: bash
+
+       $ git checkout -b BRANCH_NAME
+       # Once you've made some changes
+       $ git commit -am "commit message"
+       $ git push -u origin BRANCH_NAME
+       #Now if you come back to Github, your branch should exist
+
+  * All pull requests need one review.
+  * Tests will be run automatically when a pull request is created, and all tests need to pass before the pull request is merged. 
+
+Releases
+^^^^^^^^
+
+Below is the old process for building a release. In the future, we will have this automated using Github actions.
 
 
 #. Install `s3pypi <https://github.com/novemberfiveco/s3pypi>`_ and `dephell <https://dephell.org/docs/installation.html>`_

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "summit"
-version = "0.3.0"
+version = "0.4.0"
 description = "Tools for optimizing chemical processes"
 authors = ["Kobi Felton <kobi.c.f@gmail.com>"]
 license = ""

setup.py

@@ -21,7 +21,7 @@
 setup(
     long_description=readme,
     name='summit',
-    version='0.3.0',
+    version='0.4.0',
     description='Tools for optimizing chemical processes',
     python_requires='==3.*,>=3.6.0',
     project_urls={
@@ -35,22 +35,14 @@
     ],
     package_data={},
     install_requires=[
-        'gpy==1.*,>=1.9.0', 'matplotlib==3.*,>=3.0.0', 'numpy==1.16.0',
-        'pandas==0.*,>=0.24.1', 'platypus-opt==1.*,>=1.0.0',
-        'sklearn==0.*,>=0.0.0'
+        'gpy==1.*,>=1.9.0', 'gpyopt==1.*,>=1.2.6', 'numpy==1.16.0',
+        'pandas==0.25.3', 'platypus-opt==1.*,>=1.0.0', 'sklearn==0.*,>=0.0.0',
+        'sqsnobfit==0.*,>=0.4.3'
     ],
     extras_require={
         'dev': [
-            'anvil-uplink==0.*,>=0.3.22', 'black==18.*,>=18.3.0',
-            'cheminventory==0.*,>=0.2.1', 'inspyred==1.*,>=1.0.0',
-            'ipdb==0.*,>=0.12.0', 'ipywidgets==7.*,>=7.5.0',
-            'jupyter==1.*,>=1.0.0', 'jupyterlab==1.*,>=1.1.3',
-            'lxml==4.*,>=4.3.0', 'notify-run==0.*,>=0.0.11',
-            'panel==0.*,>=0.6.2', 'papermill==1.*,>=1.0.0',
-            'plotly==4.*,>=4.1.0', 'pubchempy==1.*,>=1.0.0',
-            'pytest==3.*,>=3.0.0', 'pytest-mock==1.*,>=1.10.0',
-            'python-dotenv==0.*,>=0.10.1', 'statsmodels==0.*,>=0.9.0',
-            'tqdm==4.*,>=4.31.0', 'voila==0.*,>=0.1.10', 'xlrd==1.*,>=1.2.0'
+            'ipdb==0.*,>=0.13.2', 'jupyterlab==2.*,>=2.1.1',
+            'pytest==3.*,>=3.0.0'
         ]
     },
 )