Make documentation awesome 🎉 (#83)

* Set build action to run on central and dev repositories

* Drop official support for PyPy3 (#53)

* Invert minor imaginary frequencies (#50)

* Use Rich library in the CLI (#47)

* Improve reporting capabilities

* Make get_y return a function and use a clever default for t_span (#48)

* Create dependabot.yml (#54)

* Solve a standard error due to randomness (#55)

* Test only on the oldest supported and latest Python versions

* Show initial and final concentrations in the output (#56)

* Simple justification of text in the output

* Automatically use reaction symmetry when necessary (#62)

* Automatically introduce reaction symmetry when it exists

* Add tests for get_reaction_entropies

* Ensure standard state corrections are correct (#64)

* Use bias in the CLI and make model objects immutable (#66)

* Make model objects immutable and improve dotdict

* Improve numerical stability when integrating the ODE system (#69)

* Use the default integrator in general

* Optionally use JAX for speed

* Use an exact Jacobian using JAX

* Use rtol and atol with solve_ivp

* Improve reaction rate constants for equilibria

* Allow the user to choose among ODE solvers

* Allow the user to choose a simulation time

* Improve CLI, plots, and some tests (#73)

* Enlarge the default max simulation time

* Base max. time and plot on active species

* Select plot points according to simulation profile

* Allow selection of tunneling correction in the CLI

* Use an integrated keyword for --plot

* Improve CLI help page

* Refactor and allow fixing concentrations of selected compounds (#74)

* Allow fixing concentrations of certain compounds

* Improve testing convert_rate_constant

* Improve tests and docs on equilibrium_constant

* Improve get_k and its tests and docs

* Change the default behavior of convert_rate_constant

* Always use rate constants as a vector

* Correct bug about equilibria adjustments

* Correct and improve regressions

* Reproduce some literature data as graphs

* Match results from the literature and simplify API

* Make flake8 more strict on function complexity

* Make CLI receive only biases in kcal/mol

* Optimize biases from experiments using get_bias

* Update documentation

* Update links (fix #82)

* Make it future-proof and compatible with RTDs

* Update docs with a new theme

* Use MIT license

* Make the program display a (better) startup notice

* Inform we use semantic versioning

Author: schneiderfelipe

.flake8

@@ -3,7 +3,7 @@ max-line-length = 88
 max-doc-length = 88
 enable-extensions = H106,H203,H204,H205,H210,H904
 extend-ignore = E203
-max-complexity = 17
+max-complexity = 10
 doctests = True
 docstring-convention = numpy
 include-in-doctest = "*.rst"

.github/dependabot.yml

@@ -0,0 +1,25 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+    # Raise pull requests for version updates
+    # against the `dev` branch
+    target-branch: "dev"
+
+  # Maintain dependencies for pip
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+    # Raise pull requests for version updates
+    # against the `dev` branch
+    target-branch: "dev"

.github/workflows/pythonpackage.yml

@@ -5,17 +5,21 @@ name: build
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main, dev ]
   pull_request:
-    branches: [ master ]
+    branches: [ main, dev ]
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, '3.x', 'pypy3']
+        os:
+          - ubuntu-latest
+          # - windows-latest
+          # - macos-latest
+        python-version: [ 3.6, '3.x' ]
+
+    runs-on: ${{ matrix.os }}
 
     steps:
     - uses: actions/checkout@v2

CONTRIBUTING.rst

@@ -17,7 +17,7 @@ Reporting issues
 ----------------
 
 The easiest way to get help with the project is to `open an issue on Github
-<http://github.com/schneiderfelipe/overreact/issues>`__:
+<http://github.com/geem-lab/overreact/issues>`__:
 
 - Describe what you expected to happen.
 - If possible, include a `minimal reproducible example <https://stackoverflow.com/help/minimal-reproducible-example>`__
@@ -40,3 +40,4 @@ Submitting patches
 - 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/>`__.
+- Use `semantic versioning <https://semver.org/>`__.

COPYING

@@ -14,11 +14,15 @@ The package, together with the above dependencies, can be installed from
 
    pip install overreact
 
-Optionally, extra functionality is provided by
-`thermo <https://github.com/CalebBell/thermo>`_::
+Optionally, extra functionality is provided such as a command-line interface
+and solvent properties::
 
-    pip install 'overreact[thermo]'
+    pip install 'overreact[cli,fast,solvents]'
 
-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.
+This last line installs `Rich <https://github.com/willmcgugan/rich>`_,
+`JAX <https://jax.readthedocs.io/en/latest/index.html>`_ and
+`thermo <https://github.com/CalebBell/thermo>`_ as well.
+Rich is used in the command-line interface, JAX helps speedup calculations,
+and thermo is used to calculate the dynamic viscosity of solvents in the
+context of the :doc:`tutorials/collins-kimball` for diffusion-limited
+reactions.

INSTALL.rst

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Felipe Silveira de Souza Schneider
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

LICENSE

@@ -1,7 +1,7 @@
 |build|_
 
-.. |build| image:: https://github.com/schneiderfelipe/overreact/workflows/build/badge.svg
-.. _build: https://github.com/schneiderfelipe/overreact/actions?query=workflow:build
+.. |build| image:: https://github.com/geem-lab/overreact/workflows/build/badge.svg
+.. _build: https://github.com/geem-lab/overreact/actions?query=workflow:build
 
 overreact
 =========
@@ -13,7 +13,7 @@ overreact
 >>> from overreact import api
 >>> api.get_k("S -> E‡ -> S", {"S": "data/ethane/B97-3c/staggered.out",
 ...                            "E‡": "data/ethane/B97-3c/eclipsed.out"})
-array([8.15810511e+10])
+array([8.16e+10])
 
 The two lines above calculate the rate of methyl rotation in ethane at
 `B97-3c <https://doi.org/10.1063/1.5012601>`__.
@@ -23,5 +23,5 @@ The two lines above calculate the rate of methyl rotation in ethane at
 overreact uses precise thermochemical partition funtions and tunneling
 corrections.
 See the
-`installation instructions <https://schneiderfelipe.github.io/overreact/installation.html>`__
-and a `short introduction <https://schneiderfelipe.github.io/overreact/quickstart.html>`__.
+`installation instructions <https://geem-lab.github.io/overreact/installation.html>`__
+and a `short introduction <https://geem-lab.github.io/overreact/quickstart.html>`__.

README.rst

@@ -1,7 +1,6 @@
 Initial code idea:
 
 y0 = [1.0, 0.0]
-t_span = [0.0, 100.0]
 freeenergies = [0.0, 20.0, -10.0]
 
 model = parse("A -> A‡ -> B")
@@ -13,8 +12,8 @@ model = parse("A -> A‡ -> B")
 k = eyring(model.B @ freeenergies)
 
 dydt = get_dydt(model, k)
-t, y, r = get_y(dydt, t_span, y0)
-y[:, -1]
+y, r = get_y(dydt, y0)
+y(y.t_max)
 
 In some advanced tutorial, I might show how to create a polymerization model
 (Pn + P -> Pn+1‡ -> Pn+1) using data extrapolated from data on small to
@@ -40,12 +39,6 @@ I use flake8 to ensure style. The following plugins are used:
 I use black to ensure formatting. flake8 configuration is such that it is
 minimally compatible with black.
 
-TODO
-----
-
-[ ] Ensure raises are correct and documented.
-[ ] Select which functions are exposed in the final API.
-
 Extras #1
 ---------
 
@@ -60,17 +53,6 @@ citation here).
   to 1000 times faster than the fastest reaction constant, but this might
   depend on a case-by-case basis, so the user should have some freedom here
 
-Extras #2
----------
-
-TODO: promote reproducible science and get citations at the same time:
-generate a state file (checkpoint? choose a pretty name) that has all the
-basic data to reproduce anything. Things can be remade, retested, shared, etc
-with it. Furthermore, it might be useful locally as well if, as we override
-it by doing a similar calculation (e.g. in the same folder), we first check
-if files have changed (by, say, a hash) and only reread what has changed
-(say, because it has been recalculated).
-
 The future CLI
 --------------
 
@@ -159,7 +141,7 @@ in the future.
 
     // All compound below will be read and the analysis will be made for all of
     // common temperatures in the logfiles. Logfiles are check for having the
-    // same level of theory if possible (here MP2/6-311G(3d,2p)).
+    // same level of theory if possible (here UMP2/6-311G(3d,2p)).
     $compounds
      [H3C·H·Cl]‡:
        logfile=ch4cl_ts_mp2_3d2p.out
@@ -247,69 +229,30 @@ collins-kimball for diffusion limit
 Marcus theory for electron transfer
 molar fractions for pH
 
-Roadmap
--------
-
-The following is what I think how overreact will soon be:
-
-io
-  # standard structure-energy data <- many sources
-  # read gibbs freeenergies and electronic energies, symmetry numbers, IRC potential energy surface, etc. from logfiles
-  # databases? this might be a very simple set of utilities if tutorials are well written
-rates:
-  def eyring(delta_freeenergy : np.ndarray, temperature : float) -> np.ndarray
-
 Things I which cclib could read from ORCA logfiles
 --------------------------------------------------
 - Absolute free and electronic energies
-- Symmetry numbers
 
 Approximations per paper
 ------------------------
 Items with an * are not necessary in our present approach, or are
 incorporated in chunks compatible with our methodology, but the effects are
 still taken in consideration.
 
-doi:10.1002/qua.25686 (EyringPy):
-- Partition function* (we read from logfiles)
-- Transition state theory (TST)
-- Gas to solution equilibrium constant correction
-- Gas to solution standard state correction
-- Reaction symmetry
-- Tunneling corrections:
-  - Wigner
-  - Eckart
-- Pre-reactive and product complexes* (we simulate kinetics)
+doi:10.1002/qua.25686:
 - Corrections for reactions in solution:
   - Diffusion effect through Collins-Kimball theory
   - Electron transfer through Marcus theory
-  - Effect of pH (maybe solved by simulation)
   - Some of the above are from QM-ORSA for reactions in solution*
 
 doi:10.1039/C5CP00628G:
-- Gas to solution standard state correction
-- Molecular symmetry numbers
-- Anharmonicity and low frequency modes
-- Conformations* (solved by simulation)
-- Molecular charge and pH
-- Solvation thermodynamics
-
-doi:10.1016/0301-0104(94)00069-7:
-- Transition state theory
-- Eckart tunneling correction
-
-doi:10.1021/acs.orglett.0c00367:
-- Sistematic adjustment of free energies
+- Anharmonicity
+- Molecular charge
 
 doi:10.1021/acs.jpca.8b06092:
-- High level calculation
 - Variational transition state theory
 - Small curvature tunneling
 
-doi:10.1021/jp8012464:
-- High level calculation
-- Wigner tunneling correction
-
 doi:10.1021/acscatal.7b00115:
 - Degree of rate control
 - Degree of selective control
@@ -319,7 +262,6 @@ doi:10.1021/acscatal.7b00115:
 - Use of degree of rate control for screening catalysts
 
 doi:10.1039/c8cs00398j (lots of interesting things, some highlighted below):
-- Microkinetic modeling
 - Apparent activation energy
 - Degree of rate control
 - Linear free energy relationships