Version 3

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.10.15
+current_version = 3.0.0
 commit = True
 tag = True
 

.ci_support/environment.yml

@@ -9,5 +9,6 @@ dependencies:
   - ipywidgets
   - pytest
   - pytest-cov
-  - h5py
   - pybind11
+  - scipy
+  - spglib

.github/workflows/deploy.yml

@@ -0,0 +1,72 @@
+name: Build and upload to PyPI
+
+# Build on every branch push, tag push, and pull request change:
+#on: [push, pull_request]
+# Alternatively, to publish when a (published) GitHub Release is created, use the following:
+on:
+  push: 
+    branches:
+      - "v3"
+    #tags:
+    #  - "*.dev.*"
+  #release:
+  #  types:
+  #    - published
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: >-
+          python -m pip install --user --upgrade setuptools wheel pybind11
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.12.3
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: >-
+          python -m pip install --user --upgrade setuptools wheel pybind11
+      - name: Build sdist
+        run: |
+          pip install pybind11
+          python setup.py sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    # upload to PyPI on every tag starting with 'v'
+    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    # alternatively, to publish when a GitHub Release is created, use the following rule:
+    #if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          # unpacks default artifact into dist/
+          # if `name: artifact` is omitted, the action will create extra parent dir
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          #repository_url: https://test.pypi.org/legacy/

.github/workflows/testing.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.9]
+        python-version: [3.7, 3.9, '3.10']
 
     runs-on: ${{ matrix.os }}
     steps:

MANIFEST.in

@@ -0,0 +1 @@
+include src/pyscal/data/*.yaml

README.md

@@ -0,0 +1,33 @@
+
+# pyscal - python Structural Environment Calculator
+
+Complete documentation with examples available [here](https://pyscal.org/).
+
+**pyscal** is a python module for the calculation of local atomic structural environments including [Steinhardt's bond orientational order parameters](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.28.784) during post-processing of atomistic simulation data. The core functionality of pyscal is written in C++ with python wrappers using [pybind11](https://pybind11.readthedocs.io/en/stable/intro.html) which allows for fast calculations with possibilities for easy expansion in python.
+
+Steinhardt's order parameters are widely used for [identification of crystal structures](https://aip.scitation.org/doi/full/10.1063/1.4774084). They are also used to identify if an atom is [solid or liquid](https://link.springer.com/chapter/10.1007/b99429).
+
+
+## Installation
+
+pyscal can be installed directly using conda by the following statement-
+
+```
+    conda install -c conda-forge pyscal
+```
+
+**From repository**
+
+pyscal can be built from the repository by-
+
+```
+    git clone https://github.com/pyscal/pyscal.git
+    cd pyscal
+    python setup.py install --user
+```
+
+## Citing the work
+
+If you use pyscal in your work, the citation of the [following article](https://joss.theoj.org/papers/10.21105/joss.01824) will be greatly appreciated:
+
+Sarath Menon, Grisell Díaz Leines and Jutta Rogal (2019). pyscal: A python module for structural analysis of atomic environments. Journal of Open Source Software, 4(43), 1824, https://doi.org/10.21105/joss.01824

docs/requirements.txt

@@ -3,8 +3,14 @@ numpy
 ase
 h5py
 ipywidgets==7.5
-plotly==4.11.0
+sphinx==5.3.0
 sphinx_rtd_theme
-m2r2
+myst_parser
 furo
 nbsphinx
+sphinx_inline_tabs
+sphinx_copybutton
+sphinx_design
+docutils==0.19
+sphinx-gallery
+