Merge pull request #26 from craabreu/update-docs

Updates documentation

.github/workflows/Anaconda.yaml

@@ -42,24 +42,13 @@ jobs:
         shell: bash -l {0}
         working-directory: ./devtools/conda-recipes/anaconda
         run: |
-          dir=$(mktemp -d)
+          echo "::group::Building ufedmm $UFEDMM_VERSION"
+          outdir=$(mktemp -d)
           export UFEDMM_VERSION=${{ github.ref_name }}
-          for version in 3.{8..11}; do
-            echo "::group::Building ufedmm $UFEDMM_VERSION for Python $version"
-            outdir=$dir/py$version
-            mkdir $outdir
-            export PYTHON_VERSION=$version
-            conda mambabuild . --no-anaconda-upload -c conda-forge --output-folder $outdir --python $version
-            PACKAGE=$(find $outdir -name *.tar.bz2 | head -1)
-            for platform in osx-64 linux-32 linux-64 win-32 win-64; do
-              echo "Converting package to platform $platform"
-              conda convert --platform $platform $PACKAGE -o $outdir
-            done
-            echo "::endgroup::"
-          done
+          conda mambabuild . --no-anaconda-upload -c conda-forge --output-folder $outdir
+          echo "::endgroup::"
+          echo "::group::Uploading package to craabreu conda channel"
+          PACKAGE=$(find $outdir -name *.tar.bz2 | head -1)
           export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
-          echo "::group::Uploading packages to craabreu conda channel"
-          for filename in $(find $dir -name *.tar.bz2); do
-            anaconda upload --user craabreu --force --label main $filename
-          done
+          anaconda upload --user craabreu --force --label main $PACKAGE
           echo "::endgroup::"

.github/workflows/Linux.yaml

@@ -17,12 +17,13 @@ on:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.9, "3.10"]
+        openmm-version: ["7.7", "8.0"]
 
     steps:
       - uses: actions/checkout@v3
@@ -42,6 +43,7 @@ jobs:
           channels: conda-forge
           extra-specs: |
             python=${{ matrix.python-version }}
+            openmm=${{ matrix.openmm-version }}
 
       - name: Install package
         # conda setup requires this special shell

.github/workflows/MacOS.yaml

@@ -17,12 +17,12 @@ on:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [macOS-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.9, "3.10"]
         openmm-version: ["8.0"]
 
     steps:

.github/workflows/Windows.yaml

@@ -17,12 +17,12 @@ on:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [windows-latest]
-        python-version: [3.8, 3.9]
+        python-version: [3.9, "3.10"]
         openmm-version: ["8.0"]
 
     steps:

README.md

@@ -9,6 +9,10 @@ Unified Free Energy Dynamics with OpenMM
 [![Coverage](https://craabreu.github.io/ufedmm/coverage/coverage.svg)](https://craabreu.github.io/ufedmm/coverage/)
 [![License](https://img.shields.io/badge/License-MIT-yellowgreen.svg?style=flat)](https://github.com/craabreu/ufedmm/blob/main/LICENSE.md)
 
+[![Conda ufedmm version](https://img.shields.io/conda/v/craabreu/ufedmm.svg)](https://anaconda.org/craabreu/ufedmm)
+[![Conda ufedmm platforms](https://img.shields.io/conda/pn/craabreu/ufedmm.svg)](https://anaconda.org/craabreu/ufedmm)
+[![Conda ufedmm downloads](https://img.shields.io/conda/dn/craabreu/ufedmm.svg)](https://anaconda.org/craabreu/ufedmm)
+
 UFEDMM extends [OpenMM's Python API] so that the user can easily run
 efficient simulations in extended phase spaces, perform enhanced sampling
 of systems with barriers and rare events, and compute accurate free-energy
@@ -17,9 +21,9 @@ surfaces for collective variables or reaction coordinates.
 #### Extended Phase-Space Dynamics
 
 The concept of extended phase space is a powerful tool in Molecular
-Dynamics. It consists in treating arbitrary variables as coordinates of
+Dynamics. It consists of treating arbitrary variables as coordinates of
 fictitious particles, assigning masses to these particles, and solving
-equations of motion which encode their interactions with the system
+equations of motion that encode their interactions with the system
 molecules. Differently from _collective variables_, which are functions
 of atomic coordinates, these _extra dynamical variables_ are independent
 ones. Together with their conjugate momenta, they add new dimensions to
@@ -32,7 +36,7 @@ relative likelihood of different states of a system. UFEDMM uses
 extended phase-space dynamics to facilitate the calculation of free
 energy as a function of extra dynamical variables. Under certain
 assumptions, this is a suitable approximation for the free energy as
-a function of collective variables, also known as potential of mean
+a function of collective variables, also known as the potential of mean
 force (PMF).
 
 #### Enhanced Sampling of Rare Events
@@ -51,17 +55,17 @@ enacted by adding, to the total potential energy of the system, a new
 term that depends both on the corresponding dynamical variable and at
 least one collective variable. With OpenMM's [CustomCVForce] class,
 adding such a term is as simple as writing down a mathematical expression.
-All the low-level coding and compilation takes place automatically in the
+All the low-level coding and compilation take place automatically in the
 background.
 
-UFEDMM build on the customization capability of OpenMM to enable efficient
-[UFED] simulations in GPU's and other parallel computation platforms. It
+UFEDMM builds on the customization capability of OpenMM to enable efficient
+[UFED] simulations in GPUs and other parallel computation platforms. It
 is efficient because it makes OpenMM treat extra dynamical variables like
 normal atomic coordinates, thus avoiding the computational overhead of
 dealing with [Context] parameters.
 
 [TAMD]/[d-AFED] is optionally enabled by assigning distinct temperatures
-to the molecules and to the extra dynamical variables. For this, UFEDMM
+to the molecules and the extra dynamical variables. For this, UFEDMM
 provides special [CustomIntegrator] subclasses, given that the intrinsic
 OpenMM integrators cannot handle multiple temperatures. Extended-space
 [Metadynamics] is enabled by explicitly defining the height and widths of
@@ -80,6 +84,28 @@ an external library of useful collective variables named
 [CVPack](https://cvpack.readthedocs.io/en/latest/). It can be accessed via
 the `ufedmm.cvpack` module.
 
+### Installation and Usage
+
+UFEDMM is available as a conda package installable from the
+[craabreu](https://anaconda.org/craabreu) channel.
+To install it, either run:
+
+```bash
+    conda install -c conda-forge -c craabreu ufedmm
+```
+
+Or:
+
+```bash
+    mamba install -c conda-forge -c craabreu ufedmm
+```
+
+To use UFEDMM in your own Python script or Jupyter notebook, import it as follows:
+
+```python
+    import ufedmm
+```
+
 ## Documentation
 
 https://craabreu.github.io/ufedmm/

docs/installation.rst

@@ -2,8 +2,22 @@
 Installation
 ============
 
-At the command line::
+UFEDMM is available as a conda package installable from the
+[craabreu](https://anaconda.org/craabreu) channel.
+To install it, either run:
 
-    git clone https://github.com/craabreu/ufedmm.git
-    cd ufedmm
-    python setup.py install
+.. code-block:: bash
+
+    conda install -c conda-forge -c craabreu ufedmm
+
+Or:
+
+.. code-block:: bash
+
+    mamba install -c conda-forge -c craabreu ufedmm
+
+To use UFEDMM in your own Python script or Jupyter notebook, import it as follows:
+
+.. code-block:: python
+
+    import ufedmm

docs/readme.rst

@@ -9,16 +9,35 @@ UFEDMM is an OpenMM extension for applying the Unified Free Energy Dynamics meth
 Installation
 ============
 
-::
+UFEDMM is available as a conda package installable from the
+[craabreu](https://anaconda.org/craabreu) channel.
+To install it, either run:
 
-    git clone https://github.com/craabreu/ufedmm.git
-    cd ufedmm
-    python setup.py install
+.. code-block:: bash
+
+    conda install -c conda-forge -c craabreu ufedmm
+
+Or:
+
+.. code-block:: bash
+
+    mamba install -c conda-forge -c craabreu ufedmm
+
+To use UFEDMM in your own Python script or Jupyter notebook, import it as follows:
+
+.. code-block:: python
+
+    import ufedmm
 
 Documentation
 =============
 
-https://ufedmm.readthedocs.io/
+https://craabreu.github.io/ufedmm/
+
+Contributing
+============
+
+Feedback, bug reports, and feature requests are welcome. They should be
+submitted to https://github.com/craabreu/ufedmm/issues.
 
-Development
-===========
+Pull requests are greatly appreciated!