Use a single branch (#89)

* Set build action to run on main and dev repositories

* Drop official support for PyPy3 (#53)

Co-authored-by: Felipe S. S. Schneider <[email protected]>

* Invert small imaginary frequencies (#50)

* Use Rich library in the CLI (#47)

* Use Rich library in the CLI

* Improve reporting capabilities

Co-authored-by: Felipe S. S. Schneider <[email protected]>

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

* Create dependabot.yml (#54)

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

Co-authored-by: Felipe S. S. Schneider <[email protected]>

* Run tests on macOS as well (#45)

* Run all essential tests on macOS as well

* Test only on the oldest supported and latest Python versions

Co-authored-by: Felipe S. S. Schneider <[email protected]>

* Do not test on macOS anymore, only on Ubuntu/Linux (#57)

Co-authored-by: Felipe S. S. Schneider <[email protected]>

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

* Simple justification of text in the output

* Show initial and final concentrations in the output

Co-authored-by: Felipe S. S. Schneider <[email protected]>

* Automatically use reaction symmetry when necessary (#62)

* Create a function for calculating reaction symmetries

* 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)

* Use bias in the CLI

* 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

Co-authored-by: Felipe S. S. Schneider <[email protected]>

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

* Test more liquid viscosities

* Check and manage some TODOs and docs

* 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

Co-authored-by: Felipe S. S. Schneider <[email protected]>

* 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 testing eyring

* Improve get_k and its tests and docs

* Change 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

* Add a get_bias function for fitting experimental/reference kinetic data (#79)

* Make flake8 be more strict on function complexity

* Make CLI receive only biases in kcal/mol

* Optimize biases from experiments using get_bias

* Bump actions/setup-python from 1 to 2.2.2 (#85)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 1 to 2.2.2.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v1...v2.2.2)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* 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

* Update docs & README.md (#87)

* Move docs to https://geem-lab.github.io/overreact-docs/

* Update README.md

Co-authored-by: Felipe S. S. Schneider <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.github/workflows/pythonpackage.yml

@@ -21,29 +21,29 @@ jobs:
 
         runs-on: ${{ matrix.os }}
 
-        steps:
-            - uses: actions/checkout@v2
-              with:
-                  token: ${{ secrets.INTEGRATIVE_KEY }}
-                  submodules: true
-            - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v1
-              with:
-                  python-version: ${{ matrix.python-version }}
-            - name: Install package and dependencies
-              run: |
-                  python -m pip install --upgrade pip
-                  pip install .
-                  pip install -r requirements.txt
-            - name: Lint with flake8
-              run: |
-                  pip install flake8
-                  # stop the build if there are Python syntax errors or undefined names
-                  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 and coverage
-              run: |
-                  pip install pytest coverage
-                  coverage run -m pytest
-                  coverage report
+    steps:
+        - uses: actions/checkout@v2
+          with:
+              token: ${{ secrets.INTEGRATIVE_KEY }}
+              submodules: true
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v2.2.2
+          with:
+              python-version: ${{ matrix.python-version }}
+        - name: Install package and dependencies
+          run: |
+              python -m pip install --upgrade pip
+              pip install .
+              pip install -r requirements.txt
+        - name: Lint with flake8
+          run: |
+              pip install flake8
+              # stop the build if there are Python syntax errors or undefined names
+              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 and coverage
+          run: |
+              pip install pytest coverage
+              coverage run -m pytest
+              coverage report