Update docs & README.md (#87)

* Move docs to https://geem-lab.github.io/overreact-docs/ * Update README.md
geem-lab · Oct 13, 2021 · fe84975 · fe84975
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diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
@@ -4,46 +4,46 @@
 name: build
 
 on:
-  push:
-    branches: [ main, dev ]
-  pull_request:
-    branches: [ main, dev ]
+    push:
+        branches: [main, dev]
+    pull_request:
+        branches: [main, dev]
 
 jobs:
-  build:
-    strategy:
-      matrix:
-        os:
-          - ubuntu-latest
-          # - windows-latest
-          # - macos-latest
-        python-version: [ 3.6, '3.x' ]
+    build:
+        strategy:
+            matrix:
+                os:
+                    - ubuntu-latest
+                    # - windows-latest
+                    # - macos-latest
+                python-version: [3.6, "3.x"]
 
-    runs-on: ${{ matrix.os }}
+        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/[email protected]
-      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
+        - uses: actions/checkout@v2
+          with:
+              token: ${{ secrets.INTEGRATIVE_KEY }}
+              submodules: true
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/[email protected]
+          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
diff --git a/AUTHORS.rst b/AUTHORS.rst
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
diff --git a/FAQ.rst b/FAQ.rst
diff --git a/INSTALL.rst b/INSTALL.rst
diff --git a/README.md b/README.md
@@ -0,0 +1,66 @@
+# Welcome to **overreact**!
+
+<div style="text-align:center;">
+
+![overreact](https://raw.githubusercontent.com/geem-lab/overreact-docs/master/logo.png)
+
+</div>
+
+**overreact** is a _library_ and a _command-line tool_ for creating and
+analyzing [microkinetic models](https://geem-lab.github.io/overreact-docs/#microkinetic).
+Data is parsed directly from computational chemistry output files thanks to
+[`cclib`](https://cclib.github.io/) (see the [list of supported programs](https://cclib.github.io/#summary)).
+
+## Installation
+
+**overreact** is a Python package, so you can easily install it with `pip`.
+See the [installation instructions](https://geem-lab.github.io/overreact-docs/install.html).
+
+## License
+
+**overreact** is open-source, released under the permissive **MIT license**.
+See [our LICENSE file](https://github.com/geem-lab/overreact/blob/main/LICENSE).
+
+## Citing **overreact**
+
+If you use **overreact** in your research, please cite:
+
+> F. S. S. Schneider and G. F. Caramori. _**overreact**: a tool for creating and analyzing microkinetic models built from computational chemistry data_. **2021**.
+> Available at: <https://github.com/geem-lab/overreact>.
+
+Here's the reference in [BibTeX](http://www.bibtex.org/) format:
+
+<!-- @article{overreact,
+  title = \textbf{overreact}: a tool for creating and analyzing microkinetic models built from computational chemistry data},
+  author = {Schneider, F. S. S. and Caramori, G. F.},
+  journal={J. Chem. Phys.},
+  volume={155},
+  number={1},
+  pages={0},
+  year = {2021},
+  publisher={American Chemical Society (ACS)},
+  doi={10.1063/1.5058983},
+  url={https://doi.org/10.1063/1.5058983}
+} -->
+
+```bibtex
+@misc{overreact2021,
+  title        = {
+    \textbf{overreact}: a tool for creating and analyzing microkinetic models
+    built from computational chemistry data, ver. 1.0
+  },
+  author       = {Schneider, F. S. S. and Caramori, G. F.},
+  year         = 2021,
+  howpublished = {\url{https://github.com/geem-lab/overreact}}
+}
+```
+
+A paper describing **overreact** is currently being prepared.
+When it is published, the above BibTeX entry will be updated.
+
+## Funding
+
+This project was developed at the [GEEM lab](https://geem-ufsc.org/) ([Federal University of Santa
+Catarina](https://en.ufsc.br/), Brazil), and was partially funded by the
+[Brazilian National Council for Scientific and Technological Development (CNPq)](https://cnpq.br/),
+grant number 140485/2017-1.
diff --git a/README.rst b/README.rst
diff --git a/data b/data
diff --git a/overreact/cli.py b/overreact/cli.py
@@ -217,6 +217,11 @@ def _yield_compounds(self):
             point_group = coords.find_point_group(
                 atommasses=data.atommasses, atomcoords=data.atomcoords
             )
+
+            vibfreqs_text = Text(
+                ", ".join([f"{vibfreq:+7.1f}" for vibfreq in data.vibfreqs[:3]])
+            )
+            vibfreqs_text.highlight_regex(r"-\d+\.\d", "bright_yellow")
             compounds_table.add_row(
                 f"{i:d}",
                 name,
@@ -644,6 +649,15 @@ def _prepare_simulation(scheme, k, concentrations):
 
     return scheme, k, y0
 
+            if self.savepath is not None:
+                np.savetxt(
+                    self.savepath,
+                    np.block([t[:, np.newaxis], y(t).T]),
+                    header=f"t,{','.join(self.model.scheme.compounds)}",
+                    delimiter=",",
+                )
+                yield Markdown(f"Simulation data was saved to **{self.savepath}**")
+
 
 def main():
     """Command-line interface."""

diff --git a/overreact/simulate.py b/overreact/simulate.py
@@ -28,6 +28,14 @@
 
 logger = logging.getLogger(__name__)
 
+logger = logging.getLogger(__name__)
+
+_found_jax = _misc._find_package("jax")
+if _found_jax:
+    import jax.numpy as jnp
+    from jax import jacfwd
+    from jax import jit
+    from jax.config import config
 
 # TODO(schneiderfelipe): allow y0 to be a dict-like object.
 def get_y(