Packaging and github actions updates

.github/workflows/tests.yml

@@ -21,11 +21,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install build packages
-        run: python -m pip install build wheel setuptools pytest
-
-      - name: Install dependencies
-        run: (cd MDANSE && python -m pip install -r requirements.txt)
+      - name: Install pytest
+        run: python -m pip install pytest
 
       - name: install MDANSE
         run: (cd MDANSE && python -m pip install .)

.github/workflows/wheels.yml

@@ -21,11 +21,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install build packages
-        run: python -m pip install build wheel setuptools
-
-      - name: Install dependencies
-        run: (cd MDANSE && python -m pip install -r requirements.txt)
+      - name: Install build
+        run: python -m pip install build
 
       - name: Build wheels
         run: (cd MDANSE && python -m build)
@@ -62,8 +59,8 @@ jobs:
         with:
           name: ${{ matrix.os }}_python${{ matrix.python-version }}_wheel
 
-      - name: Install build packages
-        run: python -m pip install build wheel setuptools
+      - name: Install build
+        run: python -m pip install build
 
       - name: Install MDANSE
         if: runner.os == 'Linux' || runner.os == 'macOS'
@@ -73,9 +70,6 @@ jobs:
         if: runner.os == 'Windows'
         run: foreach ($file in Get-ChildItem *.whl) {python -m pip install $file}
 
-      - name: Install dependencies
-        run: (cd MDANSE_GUI && python -m pip install -r requirements.txt)
-
       - name: Build wheels
         run: (cd MDANSE_GUI && python -m build)
         # to supply options, put them in 'env', like:

.gitignore

@@ -30,8 +30,5 @@ share/python-wheels/
 *.egg
 MANIFEST
 
-# extensions
-*.pyd
-
 # pycharm
 .idea

MDANSE/AUTHORS

@@ -5,12 +5,14 @@ MDANSE project has been created by:
 MDANSE source code is currently developed by
 
 * Eric Pellegrini
+* Maciej Bartkowiak
+* Chi Cheng
 * Sanghamitra Mukhopadhyay
-* Rastislav Turanyi
 
 MDANSE former contributors:
 
 * Bachir Aoun
 * Gael Goret
 * Remi Perenon
+* Rastislav Turanyi
 

MDANSE/MANIFEST.in

@@ -1,12 +1,11 @@
-include LICENCE
-include requirements.txt
+include LICENSE
 
 recursive-include Extensions/qhull_lib *.h *c *.pxd
 recursive-include Extensions/xtc *.h *c *.pxd
 recursive-include Src/MDANSE/Chemistry *.json
 recursive-include Src/MDANSE/Framework *.json
-recursive-include Tests/Data/*
 
-recursive-include Doc *
+graft Tests/UnitTests/Data
+graft Doc
 
 recursive-include Tests *.py

MDANSE/README.md

@@ -1,46 +1,79 @@
 # MDANSE 
 
+## MDANSE Python Module
+
+This is the module containing the command-line utilities and libraries of the
+Molecular Dynamics Analysis for Neutron Scattering Experiments (MDANSE) software package.
+
+If you would like to use a graphical user interface, you will need to install also the MDANSE_GUI package.
+
 ## Molecular Dynamics Analysis for Neutron Scattering Experiments
 
-MDANSE is a python application designed for computing neutron observables from molecular dynamics (MD) trajectories that can 
+MDANSE is a Python application designed for computing neutron observables from molecular dynamics (MD) trajectories. The results can 
 be directly compared with neutron scattering experiments, particularly inelastic and quasi-elastic neutron scattering 
 spectroscopies.
 
-To do this, it interfaces with a variety of MD simulation software such as CASTEP, VASP, DMOL, Gromacs, DL_POLY, CHARMM, LAMMPS, PBD, DFTB etc., 
-
-and provides both a graphical user interface (GUI) and a command line interface. 
+To do this, it interfaces with a variety of MD simulation software such as CASTEP, VASP, DMOL, Gromacs, DL_POLY, CHARMM, LAMMPS, PBD, DFTB etc., and provides both a graphical user interface (GUI) and a command line interface. 
 
 This project is built on the development published previously: \
 G. Goret, B. Aoun, E. Pellegrini, "MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations", 
 J Chem Inf Model. 57(1):1-5 (2017).
 
-## Quick start
+## Version information
 
-The easiest way to start using MDANSE is to download a built installer from out latest [github release](https://github.com/ISISNeutronMuon/MDANSE/releases/).
-There, we provide installers for the major operating systems, Windows, Linux and MacOS, which can be downloaded and installed
-any other software on that OS. After that, we recommend starting by using the GUI. The typical workflow will look as follows:
+This is the alpha release of MDANSE 2.0.0. It is the first release since MDANSE has been ported to Python 3.
+Please help us develop MDANSE by reporting any problems you experience when using the code.
+The preferred way of reporting problems is by adding them to the [GitHub issue tracker](https://github.com/ISISNeutronMuon/MDANSE/issues).
 
-1. Convert a trajectory from the file format generated by an MD simulation software into a NetCDF format (File>Trajectory conveters)
-2. Load the converted trajectory into MDANSE (File>Load data)
-3. Perform an analysis of choice (through the Plugins panel)
-4. Check the results with the plotter
+## Quick start: installation
 
+We recommend that you install MDANSE in a Python virtual environment. You can create a virtual environment named mdanse_env by typing
+```
+python3 -m venv mdanse_env
+```
 
-The most complete user documentation of MDANSE can be found on [our Read the Docs page](https://mdanse.readthedocs.io). At the same time, it is still possible to access the original **[MDANSE User Guide](https://epubs.stfc.ac.uk/work/51935555)** \
+To activate your virtual environment, type
+```
+source mdanse_env/bin/activate
+```
+in a bash console, or
+```
+mdanse_end/Scripts/activate.bat
+```
+if you are using cmd.exe on Windows.
 
-Other information including example scripts can be found on the [MDANSE website](https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx) 
+While your virtual environment is active, you can install MDANSE:
+```
+pip install MDANSE
+```
+and see the basic information about its command line interface:
+```
+mdanse --help
+```
+
+If you experience problems with the installation, you may want to upgrade pip
+```
+pip install --upgrade pip
+```
+and try again.
+
+## Quick start: workflow
+
+The typical workflow of MDANSE:
+
+1. Convert a trajectory from the file format generated by an MD simulation software into the MDANSE trajectory format,
+2. Load the converted trajectory into MDANSE,
+3. Perform an analysis,
+4. Check the results with the plotter.
 
-## Installing from source
+The most complete user documentation of MDANSE can be found on [our Read the Docs page](https://mdanse.readthedocs.io/en/protos).
 
-Since MDANSE is currently written in Python 2.7, installing it from the source code can be challenging. There are guides
-for doing this in the [MDANSE User Guide](https://epubs.stfc.ac.uk/work/51935555), 
-[this issue](https://github.com/ISISNeutronMuon/MDANSE/issues/8), and the [Wiki](https://github.com/ISISNeutronMuon/MDANSE/wiki).
-However, if your system is not included in any of these, or you have any difficulties, please don't hesitate to contact us.
+Other information including example scripts can be found on the [MDANSE website](https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx) 
 
 ## What can MDANSE do?
 
-Firstly, MDANSE can interface with MD simulation software. It does this by providing converters for proprietary file formats
-into MMTK-style NetCDF format, which is then used for all calculations. The following MD packages are supported:
+Firstly, MDANSE can interface with MD simulation software. It does this by providing converters for different file formats
+into an .MDT file (HDF format), which is then used for all calculations. The following MD packages are supported:
 
 - CASTEP
 - CHARMM
@@ -55,25 +88,20 @@ into MMTK-style NetCDF format, which is then used for all calculations. The foll
 - PDB
 - VASP
 - XPLOR
+- ASE
 
 The converted trajectory can then be loaded into MDANSE, where it can be visualised via the Molecular Viewer and animated.
-Various trajectory variables (positions, velocities, and forces) can also be plotted for each particle. Then, if the 
-trajectory is as expected, various properties can be calculated, which can be compared with neutron (or, some, with X-ray)
-experimental data, or used as new data to draw conclusions from. The following properties can be computed:
+Various trajectory variables (positions, velocities, and forces) can also be plotted for each particle. Then, various properties can be calculated, which can be compared with neutron (or, for some analysis types, with X-ray)
+experimental data, or used as a prediction of results of a potential experiment. The following properties can be computed:
 
 <details><summary>Dynamics</summary><ul>
 <li>Angular correlation</li>
 <li>Density of states</li>
 <li>Mean Square Displacement</li>
-<li>Order parameter</li>
 <li>Position Autocorrelation Function</li>
 <li>Velocity Autocorrelation Function</li>
 </ul></details>
 
-<details><summary>Infrared</summary><ul>
-<li>Dipole Autocorrelation Function</li>
-</ul></details>
-
 <details><summary>Scattering</summary><ul>
 <li>Current correlation function</li>
 <li>Dynamic Coherent Structure Factor</li>
@@ -96,7 +124,7 @@ experimental data, or used as new data to draw conclusions from. The following p
 <li>Solvent Accessible Surface</li>
 <li>Spatial Density</li>
 <li>Static Structure Factor</li>
-<li>Voronoi</li>
+<li>Voronoi (volume per atom)</li>
 <li>X-Ray Static Structure Factor</li>
 </ul></details>
 
@@ -105,13 +133,10 @@ experimental data, or used as new data to draw conclusions from. The following p
 <li>Temperature</li>
 </ul></details>
 
-Each of these analyses can be configured in various ways. For example, the frames that are used can be changed, certain
-atoms can be specified to be the only ones for which the property is computed, or specified atoms can be substituted with
-different elements/isotopes. Finally, their results can be outputted in a NetCDF file, an HDF5 file, or a set of DAT 
-files, and those can then be plotted directly in MDANSE.
+Each of these analyses can be controlled using a number of parameters. For example, the user can select a subset of trajectory frames or a subset of atoms on which to perform the calculation, or specified atoms can be substituted with
+different elements/isotopes. Finally, their results can be saved in an MDA file (HDF5 format), or a set of DAT files (text format), and those can then be plotted directly in MDANSE.
 
-More detailed information on how MDANSE works, what it can do, and the science can all be found in the 
-**[MDANSE User Guide](https://epubs.stfc.ac.uk/work/51935555)**
+More detailed information on how MDANSE works, what it can do, and the science can all be found on [our Read the Docs page](https://mdanse.readthedocs.io/en/protos).
 
 ## Citing MDANSE
 
@@ -131,8 +156,8 @@ information.
 MDANSE started as a fork of [version 3 of the nMOLDYN program](https://github.com/khinsen/nMOLDYN3).
 nMOLDYN was originally developed by Gerald Kneller in 1995 and subsequently also by Konrad Hinsen, Tomasz Rog,
 Krzysztof Murzyn, Slawomir Stachura, and Eric Pellegrini. MDANSE includes most of the code of nMOLDYN3, and also code
-from the libraries [MMTK](https://github.com/khinsen/MMTK) and [ScientificPython](https://github.com/khinsen/ScientificPython),
-in order to reduce dependencies and thus facilitate installation.
+from the libraries [MMTK](https://github.com/khinsen/MMTK), [ScientificPython](https://github.com/khinsen/ScientificPython)
+and [MDTraj](https://github.com/mdtraj/mdtraj).
 
 For more information see:
 
@@ -141,7 +166,7 @@ K. Hinsen, E. Pellegrini, S. Stachura, G.R. Kneller J. Comput. Chem. (2012) 33:2
 
 We are grateful to all the people who have helped in some way or another to improve nMOLDYN and/or MDANSE along those years. 
 Apart from the main developers mentioned above, we would like to acknowledge explicitly the contributions done in the past 
-by Bachir Aoun, Vania Calandrini, Paolo Calligari, Gael Goret and Remi Perenon.
+by Bachir Aoun, Vania Calandrini, Paolo Calligari, Gael Goret, Remi Perenon and Rastislav Turanyi.
 
 The MDANSE project is supported by Ada Lovelace Centre, ISIS Neutron and Muon Source, Science
 and Technology Facilities Council, UKRI, and the Institut Laue-Langevin (Grenoble, France). 
@@ -159,3 +184,12 @@ If you want to join the project contact:
 ISIS Neutron and Muon Source \
 Rutherford Appleton Laboratory \
 Didcot, UK
+
+## Software Inquiries
+
+For questions or contributions related to the software, please contact:
+
+>Dr. Maciej Bartkowiak ([email protected])\
+ISIS Neutron and Muon Source \
+Rutherford Appleton Laboratory \
+Didcot, UK

MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py

@@ -2628,6 +2628,8 @@ def copy(self) -> "ChemicalSystem":
 
         if self._atoms is not None:
             _ = cs.atoms
+        else:
+            cs._atoms = None
 
         return cs
 

MDANSE/Src/MDANSE/Extensions/.gitignore

@@ -1,2 +1,3 @@
 *.o
 *.so
+*.pyd