Improve thermochemistry

Update roadmaps and projects

Change some accepted symbols in reactions

Improve docs and some functions private

Employ energy corrections

Do tests on heat capacity

Add command-line interface

Calculate free volume

Create temporary ORCA parser

Add utilities for handling Hessian matrices

Create high level API

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+include = overreact/*
+[report]
+sort = Miss
+fail_under = 90
+show_missing = True
+skip_covered = True

.flake8

@@ -1,8 +1,9 @@
 [flake8]
 max-line-length = 88
-max-complexity = 22
+max-doc-length = 88
 enable-extensions = H106,H203,H204,H205,H210,H904
 extend-ignore = E203
+max-complexity = 17
 doctests = True
 docstring-convention = numpy
 include-in-doctest = "*.rst"

.github/workflows/pythonpackage.yml

@@ -23,9 +23,10 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install package and dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install .
         pip install -r requirements.txt
     - name: Lint with flake8
       run: |
@@ -34,7 +35,8 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings.
         flake8 . --count --exit-zero --statistics
-    - name: Test with pytest
+    - name: Test with pytest and coverage
       run: |
-        pip install pytest
-        pytest
+        pip install pytest coverage
+        coverage run -m pytest
+        coverage report

.gitignore

@@ -64,7 +64,9 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+docsrc/_build/
+docs/.buildinfo
+docs/.doctrees
 
 # PyBuilder
 target/

AUTHORS.rst

@@ -0,0 +1,4 @@
+Authors
+=======
+
+- Felipe S. S. Schneider

CHANGELOG.rst

@@ -0,0 +1,9 @@
+Changelog
+=========
+
+Version 1.0
+-----------
+
+Released 2020-06-14.
+
+- First public preview release.

CONTRIBUTING.rst

@@ -0,0 +1,42 @@
+Contributing
+============
+
+Thank you for considering contributing to overreact!
+
+Support questions
+-----------------
+
+Please don't use the issue tracker for asking questions.
+Use the `mailing list <https://groups.google.com/d/forum/overreact>`__ for
+questions about your own code or the use of overreact.
+
+You can also send me an e-mail. I'm more than happy to answer any personal or
+in-depth questions about overreact. Feel free to email [email protected].
+
+Reporting issues
+----------------
+
+The easiest way to get help with the project is to `open an issue on Github
+<http://github.com/schneiderfelipe/overreact/issues>`__:
+
+- Describe what you expected to happen.
+- If possible, include a `minimal reproducible example <https://stackoverflow.com/help/minimal-reproducible-example>`__
+  to help us identify the issue.
+  This also helps check that the issue is not with your own code.
+- Describe what actually happened. Include the full traceback if there was an
+  exception.
+- List your Python version, as well as other packages.
+  If possible, check if this issue is not already fixed in the repository.
+
+Submitting patches
+------------------
+
+- Use `Black <https://black.readthedocs.io/>`__ to autoformat your code.
+- Use `Numpydoc docstrings <https://numpydoc.readthedocs.io/en/latest/format.html>`__
+  to document your code.
+- Include tests if your patch is supposed to solve a bug, and explain clearly
+  under which circumstances the bug happens.
+  Make sure the test fails without your patch.
+- Include a string like “Fixes #123” in your commit message (where 123 is the
+  issue you fixed).
+  See `Closing issues using keywords <https://help.github.com/articles/creating-a-pull-request/>`__.

FAQ.rst

@@ -0,0 +1,2 @@
+Frequently asked questions
+==========================

INSTALL.rst

@@ -0,0 +1,24 @@
+Installation
+============
+
+overreact depends on:
+
+- `cclib <https://github.com/cclib/cclib/>`_ (parser for computational
+  chemistry logfiles).
+- `SciPy <https://github.com/scipy/scipy/>`_ (numerical integration,
+  optimization, unit conversion and others).
+
+The package, together with the above dependencies, can be installed from
+`PyPI <https://pypi.org/project/overreact/>`_, using
+`pip <https://pypi.org/project/pip/>`_, with the following command::
+
+   pip install overreact
+
+Optionally, extra functionality is provided by
+`thermo <https://github.com/CalebBell/thermo>`_::
+
+    pip install 'overreact[thermo]'
+
+This last line installs thermo  as well. thermo is used to calculate the
+dynamic viscosity of solvents in the context of the
+:doc:`tutorials/collins-kimball` for diffusion-limited reactions.