time units and DPI

Dockerfile

@@ -0,0 +1,11 @@
+FROM jupyter/base-notebook
+
+RUN mkdir /tmp/build
+COPY README.md meta.yaml setup.py /tmp/build/
+COPY metadynminer/ /tmp/build/metadynminer/
+
+RUN pip3 install /tmp/build
+
+COPY python_metadynminer.ipynb /home/jan8be
+
+RUN mamba install --yes ipywidgets ipympl 

README.md

@@ -1,16 +1,32 @@
 # metadynminer.py
 
+
+
 [![Build](https://github.com/Jan8be/metadynminer.py/actions/workflows/ci.yml/badge.svg)](https://github.com/Jan8be/metadynminer.py/actions/workflows/ci.yml)
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/metadynminer?label=PyPI%20downloads&color=green&link=https%3A%2F%2Fpypi.org%2Fproject%2Fmetadynminer%2F)](https://pypi.org/project/metadynminer/)
 [![conda downloads](https://img.shields.io/conda/d/Jan8be/metadynminer?label=Conda%20total%20downloads&color=green&link=https%3A%2F%2Fanaconda.org%2FJan8be%2Fmetadynminer)](https://anaconda.org/Jan8be/metadynminer)
 
+
 Metadynminer is a package designed to help you analyse output HILLS files from PLUMED metadynamics simulations. 
 
 It is inspired by existing Metadynminer package for R. It supports HILLS files with one, two or three collective variables. 
 
 All built-in functions can be customized with many parameters. You can learn more about that in the documentation. There are also other predefined functions allowing you to for example to enhance your presentation with animations of your 3D FES or remove a CV from existing FES. 
 
-Installation:
+## Quickstart: run in Binder
+
+Click the icon bellow and wait (couple of minutes) for the container to build and started on public [MyBinder](http://mybinder.org/).
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jan8be/metadynminer.py/main)
+
+Alternatively, for [Metacentrum](https://metacentrum.cz/) users, somewhat better resources are available:
+
+[![Binder](https://binderhub.cloud.e-infra.cz/badge_logo.svg)](https://binderhub.cloud.e-infra.cz/v2/gh/jan8be/metadynminer.py/main?urlpath=lab)
+
+Once in the Jupyterlab environment, upload your ```HILLS``` file and start the ```python_metadynminer.ipynb``` notebook.
+
+## Installation:
+
 ```bash
 pip install metadynminer
 ```
@@ -19,7 +35,12 @@ or
 conda install -c jan8be metadynminer
 ```
 
-Sample code:
+## Sample code:
+
+Load metadynminer:
+```python
+import metadynminer
+```
 
 Load your HILLS file: 
 ```python
@@ -37,7 +58,12 @@ with the option original=True. This algorithm was checked and it gives the same
 fes2 = metadynminer.Fes(hillsfile, original=True)
 ```
 
-Visualize the free energy surface and save the picture to a file:
+Visualize the free energy surface:
+```python
+fes.plot()
+```
+
+Visualize and save the picture to a file:
 ```python
 fes.plot(png_name="fes.png")
 ```
@@ -46,13 +72,13 @@ Find local minima on the FES, print them and save FES with minima as a picture:
 ```python
 minima = metadynminer.Minima(fes)
 print(minima.minima)
-minima.plot(png_name="fes_with_minima.png")
+minima.plot()
 ```
 
 You can also plot free energy profile to see, how the differences between each minima were evolving 
 during the simulation. Convergence in the free energy profile suggests that the resulting free energy surface converged to correct values.
 ```python
 fep = metadynminer.FEProfile(minima, hillsfile)
-fep.plot(png_name="FEProfile.png")
+fep.plot()
 ```
 

python_metadynminer.ipynb

@@ -178,7 +178,7 @@
    "id": "f1c0752e-86ca-41c2-9caa-21c7bbf80fbd",
    "metadata": {},
    "source": [
-    "<img src=\"flooding.gif\" width=\"750\" align=\"center\">"
+    "<img src=\"flooding.gif\" width=\"750\" align=\"center\"/>"
    ]
   }
  ],