Merge pull request #86 from GMPavanLab/revert-85-modify_readme

Revert "Renaming to cpctools"

Changelog.md

@@ -2,11 +2,6 @@
 
 Until we get to a release version you may encounter different broken interface problem each time we increase a minor version.
 
-## Changes since v0.2.0
-
-- Rename SOAPify to cpctools
-- Clarify README
-
 ## Changes since v0.1.0rc0
 
 - `SOAPify.HDF5er.isTrajectoryGroup` now returns `False` with Datasets

Readme.md

@@ -1,4 +1,4 @@
-# cpctools
+# cpctools: SOAPify and SOAPify.HDF5er
 
 ![PyPI - License](https://img.shields.io/pypi/l/cpctools)
 [![PyPI](https://img.shields.io/pypi/v/cpctools)](https://pypi.org/project/cpctools/)
@@ -9,43 +9,65 @@
 [![Coverage Status](https://coveralls.io/repos/github/GMPavanLab/SOAPify/badge.svg?branch=main)](https://coveralls.io/github/GMPavanLab/SOAPify?branch=main)
 [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
 
+SOAPify is a python 3.8/3.9/3.10 library aimed at simplifying the analysis of Molecular Dynamics simulation using the Smooth Overlap of Atomic Position (SOAP) in the context that includes the time along the geometrical information of the frames of the simulation.
 
-### **We are no longer developing in this project. Future works will be in [dynsight](https://github.com/GMPavanLab/dynsight).**
+SOAPify uses `h5py` to store the trajectories, the SOAP fingerprints, and the analysis results in a binary format.
 
-
-`cpctools` is a python 3.8/3.9/3.10 library aimed at simplifying the analysis of Molecular Dynamics simulations.
-
-_cpctools_ stands for **C**omputational **P**hysical **C**hemistry **TOOLS**, or, if you prefer, for **C**hemical **P**hysics **C**omputational **TOOLS**.
-
-It contains two packages, `SOAPify` and `SOAPify.HDF5er`.
-
-`cpctools` uses `h5py` to store the trajectories, the SOAP fingerprints, and the analysis results in a binary format, facilitated by `HDF5er`.
-
-The documentation is available on [read the docs](https://cpctools.readthedocs.io/en/latest/). There you can consult the documentation for each available version of the package.
+SOAPify also offers a suite for  (simple) state analysis for your simulations.
 
 ## How To Install
 
-To install the stable version of `cpctools` just type:
+To install the stable version of SOAPify just type:
 ```bash
 pip install cpctools
 ```
+_cpctools_ stands for **C**omputational **P**hysical **C**hemistry **TOOLS**, or, if you prefer, for **C**hemical **P**hysics **C**omputational **TOOLS**.
 
 If you want to use _dscribe_ or _quippy_ for calculating the SOAP features you should install them separately, since they are quite heavy packages on their own, and usually you would use only one of these packages:
 
 ```bash
 pip install "dscribe<=1.2.2,>1.2.0"
 pip install "quippy-ase==0.9.10"
 ```
----
-### package: SOAPify
+
+### Installing the latest version
+
+We always recommend to install your code in a dedicated environment:
+
+```bash
+python3 -m venv /path/to/new/venv --prompt SOAPify
+source /path/to/new/venv/bin/activate
+pip install --upgrade pip
+```
+
+Then to install SOAPify you can simply go to the repository directory and run the following:
+```bash
+cd /path/to/SOAPify/directory
+pip install .
+```
+or if you do not want to download the repo, you can have pip install from source:
+```bash
+pip install 'cpctools @ git+https://github.com/GMPavanLab/SOAPify.git'
+```
+Or if you desire an older version you can install it from a tag:
+```bash
+pip install 'cpctools @ git+https://github.com/GMPavanLab/[email protected]'
+```
+
+We have a (very basic) [documentation](https://gmpavanlab.github.io/SOAPify/SOAPify.html) of the latest version available on the GitHub pages.
+
+A more complete history of the documentation is available on [read the docs](https://soapify.readthedocs.io/en/latest/). There you can consult the documentation for each available version of the package.
+
+
+## SOAPify
 
 This package contains:
  - a toolbox to calculate the [SOAP fingerprints](https://doi.org/10.1103/PhysRevB.87.184115) of a system of atoms. The principal aim is to simplify the setup of the calculation. This toolbox depends on `dscribe` or `quippy` and 'unify' the output of the two codes.
  - a toolbox to calculate the distances between SOAP fingerprints
  - a simple analysis tool for trajectories of classified atoms
 
 
-### package: SOAPify.HDF5er
+## SOAPify.HDF5er
 
 This package is a toolbox to create [hdf5 files](https://www.hdfgroup.org/) with [h5py](https://www.h5py.org/) from the trajectory and topology files. The format we use **do not** align with [h5md](https://www.nongnu.org/h5md/h5md.html)
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "cpctools"
-description = "A package for analysing molecular systems"
+description = "A package for creating and studying SOAP fingerprints"
 readme = "Readme.md"
 requires-python = "<3.11,>=3.8"
 license = "MIT"
@@ -18,9 +18,9 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
 ]
 dependencies = [
-    "ase==3.22.1",
+    "ase==3.22.1", 
     "MDAnalysis==2.4.2",
-    "h5py==3.8.0",
+    "h5py==3.8.0", 
     "Deprecated==1.2.13",
     "numpy<1.24,>=1.18", #problems with numba and f90wrap
     ]
@@ -37,7 +37,7 @@ docs = [
     "sphinx_gallery==0.12.2",
     "ipython"
 ]
-dscribe=["dscribe >1.2.0, <=1.2.2",]
+dscribe=["dscribe >1.2.0, <=12.2",]
 quippy=["quippy-ase==0.9.10",]
 tests = [
     "coverage[toml]",
@@ -47,10 +47,11 @@ tests = [
 
 
 [project.urls]
-Homepage = "https://github.com/GMPavanLab/cpctools"
-ReadTheDocs = "https://cpctools.readthedocs.io/en/latest/"
-Issues = "https://github.com/GMPavanLab/cpctools/issues"
-Source = "https://github.com/GMPavanLab/cpctools"
+Homepage = "https://github.com/GMPavanLab/SOAPify"
+Documentation = "https://gmpavanlab.github.io/SOAPify/"
+ReadTheDocs = "https://soapify.readthedocs.io/en/latest/"
+Issues = "https://github.com/GMPavanLab/SOAPify/issues"
+Source = "https://github.com/GMPavanLab/SOAPify"
 
 #TODO: define some cli scripts that can be useful!
 [project.scripts]
@@ -84,7 +85,7 @@ cleanbuild = 'cd docs && make clean build'
 
 [tool.hatch.envs.livedocs]
 template="docs"
-extra-dependencies = [
+extra-dependencies = [   
     "sphinx-autobuild",
     ]
 

src/SOAPify/__init__.py

@@ -13,4 +13,4 @@
 from .engine import *
 from .analysis import *
 
-__version__ = "v0.2.0"
+__version__ = "v0.1.0"