Merge pull request #8 from amritagos/develop

Upload to PyPI

Author: amritagos

README.md

@@ -1,12 +1,22 @@
 # solvis
 
-<img src="branding/logo/logo.png" width="300" />
+<img src="https://github.com/amritagos/solvis/blob/main/branding/logo/logo.png?raw=true" width="300" />
 
 ## About
 
 Various ways to analyze and visualize solvation shell structures, which wraps [`PyVista`](https://docs.pyvista.org/version/stable/). Meant primarily for analyzing the outputs produced by LAMMPS here. 
 
-## Installation
+## Installation 
+
+### From PyPI
+
+You can install `solvis` from PyPI like so: 
+
+```bash
+pip install solvis-tools
+```
+
+### From source
 
 We use [`micromamba`](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) as the package manager, but feel free to use your own poison. Create and activate the environment. 
 
@@ -48,10 +58,10 @@ pytest --cov=solvis tests/
 
 ## Image Gallery
 <p float="left">
-    <img src="resources/non_octahedral_shape.png" width="200" />
-    <img src="resources/octahedral_shell.png" width="200" />
+    <img src="https://github.com/amritagos/solvis/blob/main/resources/non_octahedral_shape.png?raw=true" width="200" />
+    <img src="https://github.com/amritagos/solvis/blob/main/resources/octahedral_shell.png?raw=true" width="200" />
 </p>
 <p float="left">
-    <img src="resources/shell_with_hbonds.png" width="200" />
-    <img src="resources/hbond_non_oct.png" width="200" />
+    <img src="https://github.com/amritagos/solvis/blob/main/resources/shell_with_hbonds.png?raw=true" width="200" />
+    <img src="https://github.com/amritagos/solvis/blob/main/resources/hbond_non_oct.png?raw=true" width="200" />
 </p>

environment.yml

@@ -10,10 +10,11 @@ channels:
 #     - {{ compiler('c') }}
 #     - {{ compiler('c++') }}
 dependencies:
-  - python==3.10
-  - ase==3.22.1
-  - numpy==1.22.4
-  - scipy==1.7.3
+  - python>=3.10
+  - build<0.10.0
+  - ase>=3.22.1
+  - numpy>=1.26.4 # 1.22.4
+  - scipy>=1.7.3
   - ipython>=8.26.0
   - pandas>=2.2.2
   - pyvista==0.43.0
@@ -25,6 +26,7 @@ dependencies:
   - pooch==1.8.0
   - scooby==0.9.2
   # Packaging
+  - twine
   - flit==3.9.0
   - pytest==6.2.5
   - coverage==6.1.1
@@ -37,6 +39,6 @@ dependencies:
   - flake8-docstrings==1.6.0 
   - meson-python>=0.16.0
   - pytest-cov>=3.0.0
-  - pip:
-    # works for regular pip packages
-    - lammps-logfile
+  # - pip:
+  #   # works for regular pip packages
+  #   - lammps-logfile

meson.build

@@ -1,7 +1,7 @@
 project('solvis')
 
 py_mod = import('python')
-py = py_mod.find_installation(pure: false)
+py = py_mod.find_installation(pure: true) # This is pure Python, so maybe this should be true
 
 # solvis, main package
 py.install_sources([
@@ -16,6 +16,6 @@ py.install_sources([
     'solvis/vis_initializers.py',
     'solvis/visualization.py'
   ],
-  pure: false, # install next to compiled extension
+  pure: true, # no compiled extension
   subdir: 'solvis'
 )

pyproject.toml

@@ -1,25 +1,27 @@
 [build-system]
-requires = ["meson-python"]
+requires = ["meson-python>=0.16.0"]
 build-backend = "mesonpy"
 # Important, tells pip how to install the package
 
 [project]
-name = "solvis"
-version = "0.0.1"
-description = "A module for analyzing and visualizing solvation shells in LAMMPS output files."
+name = "solvis-tools"
+version = "0.1.4"
+description = "A module for analyzing and visualizing solvation shells in LAMMPS output files, but would work with most files that can be handled by ASE."
 authors = [
     {name = "Amrita Goswami", email = "[email protected]"},
 ]
+classifiers=[
+        'Programming Language :: Python :: 3.10']
 dependencies = [
     "ase == 3.22.1",
-    "numpy == 1.22.4",
-    "scipy == 1.7.3",
+    "numpy",
+    "scipy >= 1.7.3",
     "pyvista == 0.43.0",
     "pillow == 10.0.1",
     "imageio == 2.31.5",
     "pooch==1.8.0",
     "scooby==0.9.2"]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 readme = "README.md"
 license = {text = "MIT"}
 

solvis/visualization.py

@@ -4,7 +4,6 @@
 from scipy.spatial import ConvexHull, Delaunay
 from scipy.spatial import KDTree
 import math
-import pandas as pd
 from pathlib import Path
 from pyvista import PolyData
 import pyvista as pv