luigibonati · luigibonati · Apr 27, 2023 · Feb 17, 2023 · Feb 17, 2023 · Feb 17, 2023
diff --git a/.gitattributes b/.gitattributes
@@ -1 +1 @@
-mlcvs/_version.py export-subst
+mlcolvar/_version.py export-subst
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into this mlcvs. 
+describes how to merge code changes into this mlcolvar. 
 
 ## Getting Started
 
@@ -19,7 +19,7 @@ describes how to merge code changes into this mlcvs.
   [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
   with the branch name relating to the feature you are going to add.
 * When you are ready for others to examine and comment on your new feature,
-  navigate to your fork of mlcvs on GitHub and open a [pull
+  navigate to your fork of mlcolvar on GitHub and open a [pull
   request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
   after you launch a PR from one of your fork's branches, all
   subsequent commits to that branch will be added to the open pull request
@@ -29,7 +29,7 @@ describes how to merge code changes into this mlcvs.
 * If you're providing a new feature, you must add test cases and documentation.
 * When the code is ready to go, make sure you run the test suite using pytest.
 * When you're ready to be considered for merging, check the "Ready to go"
-  box on the PR page to let the mlcvs devs know that the changes are complete.
+  box on the PR page to let the mlcolvar devs know that the changes are complete.
   The code will not be merged until this box is checked, the continuous
   integration returns checkmarks,
   and multiple core developers give "Approved" reviews.

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -2,16 +2,15 @@ name: CI
 
 on:
   # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
+  # The cookiecutter uses the "--initial-branch" flag when it runs git-init
   push:
     branches:
-      - "master"
       - "main"
+      - "lightning"
   pull_request:
     branches:
-      - "master"
       - "main"
+      - "lightning"
   schedule:
     # Weekly tests run on main by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
@@ -25,52 +24,44 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, "3.10"]
 
     steps:
-    - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
 
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
 
+      # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: test
+          channels: conda-forge,defaults
+          extra-specs: |
+            python=${{ matrix.python-version }}
 
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install . --no-deps
+          micromamba list
 
-        channels: conda-forge,defaults
+      - name: Run tests
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          pytest -v --cov=mlcolvar --cov-report=xml --color=yes mlcolvar/tests/
+          pytest --nbmake docs/notebooks/ --ignore=docs/notebooks/data/
 
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-
-    - name: Install package
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-
-
-    - name: Run tests
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-
-      run: |
-        pytest -v --cov=mlcvs --cov-report=xml --color=yes mlcvs/tests/
-
-    - name: CodeCov
-      uses: codecov/codecov-action@v1
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+      - name: CodeCov
+        uses: codecov/codecov-action@v3
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -2,9 +2,9 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "main", "lighting" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "main", "lighting"   ]
   schedule:
     - cron: "33 10 * * 1"
 

diff --git a/.gitignore b/.gitignore
@@ -106,4 +106,9 @@ ENV/
 # There are reports this comes from LLVM profiling, but also Xcode 9.
 *profraw
 
-*/_version.py
+*/_version.py
+
+old_code/
+.vscode/
+test_notebooks/
+lightning_logs/
diff --git a/.lgtm.yml b/.lgtm.yml
@@ -9,4 +9,4 @@ path_classifiers:
     - versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
     - devtools/*
   generated:
-    - mlcvs/_version.py
+    - mlcolvar/_version.py
diff --git a/LICENSE b/LICENSE
@@ -1,5 +1,5 @@
 
-Copyright 2021 Luigi Bonati
+Copyright (c) 2023 Luigi Bonati, Enrico Trizio and Andrea Rizzi
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
 following conditions are met:

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -2,5 +2,5 @@ include LICENSE
 include MANIFEST.in
 include CODE_OF_CONDUCT.md
 
-graft mlcvs
+graft mlcolvar
 global-exclude *.py[cod] __pycache__ *.so
diff --git a/README.md b/README.md
@@ -1,19 +1,25 @@
-mlcvs: Machine learning collective variables
-==============================
+mlcolvar: Machine learning collective variables
+===============================================
 [//]: # (Badges)
 ![status](https://img.shields.io/badge/status-development-orange)
-[![license](https://img.shields.io/github/license/luigibonati/mlcvs)](https://github.com/luigibonati/mlcvs/blob/main/LICENSE)
+[![license](https://img.shields.io/github/license/luigibonati/mlcolvar)](https://github.com/luigibonati/mlcolvar/blob/main/LICENSE)
 
-[![Documentation Status](https://readthedocs.org/projects/mlcvs/badge/?version=latest)](https://mlcvs.readthedocs.io/en/latest/?badge=latest)
-[![GitHub Actions Build Status](https://github.com/luigibonati/mlcvs/workflows/CI/badge.svg)](https://github.com/luigibonati/mlcvs/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/luigibonati/mlcvs/branch/main/graph/badge.svg?token=H01H68KNNG)](https://codecov.io/gh/luigibonati/mlcvs)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/luigibonati/mlcvs.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/luigibonati/mlcvs/context:python)
+[![Documentation Status](https://readthedocs.org/projects/mlcolvar/badge/?version=latest)](https://mlcolvar.readthedocs.io/en/latest/?badge=latest)
+[![GitHub Actions Build Status](https://github.com/luigibonati/mlcolvar/workflows/CI/badge.svg)](https://github.com/luigibonati/mlcolvar/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/luigibonati/mlcolvar/branch/main/graph/badge.svg?token=H01H68KNNG)](https://codecov.io/gh/luigibonati/mlcolvar)
 
-### Copyright
+`mlcolvar`, short for Machine Learning COLlective VARiables, is a Python library aimed to help design data-driven collective-variables (CVs) for enhanced sampling simulations.
+The guiding principles of `mlcolvar` are twofold:
 
-Copyright (c) 2022, Luigi Bonati
+1. A unified framework to help test and utilize (some of) the CVs proposed in the literature. 
+2. A modular interface that simplifies the development of new approaches and the contamination between them.
 
-#### Acknowledgements
-
-Project based on the 
+The library is built upon the [PyTorch](https://pytorch.org/) ML library as well as the [Lightning](https://lightning.ai/) high-level framework. 
+
+The workflow for training CVs is illustrated in the figure below. The resulting CVs can be then deployed for enhancing sampling with the [PLUMED](https://www.plumed.org/) package via the [pytorch](https://www.plumed.org/doc-master/user-doc/html/_p_y_t_o_r_c_h__m_o_d_e_l.html>`_) interface. 
+
+<center><img src="docs/notebooks/images/graphical_overview_mlcvs.png" width="800" /></center> 
+
+
+Copyright (c) 2023 Luigi Bonati, Enrico Trizio and Andrea Rizzi. Project based on the 
 [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.6.
diff --git a/devtools/README.md b/devtools/README.md
@@ -59,5 +59,5 @@ is installed by looking at the `git` tags and how many commits ahead this versio
 \d+.\d+.\d+(?\+\d+-[a-z0-9]+)
 ```
 If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, 
-e.g. `mlcvs-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+e.g. `mlcolvar-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
 ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash.
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -19,11 +19,11 @@ dependencies:
   - numpy
   - pandas
   - pytorch
+  - lightning
   - matplotlib
-  - scikit-learn
 
     # Pip-only installs
   - pip:
     - KDEpy
-  #  - codecov
+    - nbmake
 
diff --git a/docs/Makefile b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = mlcvs
+SPHINXPROJ    = mlcolvar
 SOURCEDIR     = .
 BUILDDIR      = _build
 

diff --git a/docs/README.md b/docs/README.md
@@ -1,14 +1,14 @@
-# Compiling mlcvs's Documentation
+# Compiling mlcolvar's Documentation
 
 The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/).
 To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed.
 
 
 ```bash
 conda install sphinx sphinx_rtd_theme 
+pip install sphinx-copybutton furo nbsphinx
 ```
 
-
 Once installed, you can use the `Makefile` in this directory to compile static HTML pages by
 ```bash
 make html

diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst
@@ -5,7 +5,7 @@
 .. autoclass:: {{ objname }}
    :members:                                   
    :show-inheritance:                           
-   :inherited-members: Module                       
+   :inherited-members: Module,LightningModule                       
 
    {% block methods %}
    .. automethod:: __init__