Update environment.yml, and replace setup.py with pyproject.toml

.github/workflows/pytest.yml

@@ -4,42 +4,50 @@ on:
   push:
     branches: [ master ]
     paths:
-      - '.github/workflows/pytest.yml'
-      - 'morphct/**'
+      - morphct/**
+      - environment.yml
+      - .github/workflows/pytest.yml
   pull_request:
     branches: [ master ]
     paths:
-      - '.github/workflows/pytest.yml'
-      - 'morphct/**'
-  # Allows workflow to be manually triggered
+      - morphct/**
+      - environment.yml
+      - .github/workflows/pytest.yml
+
   workflow_dispatch:
 
 jobs:
   pytest:
-    runs-on: ubuntu-latest
+    if: github.event.pull_request.draft == false
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.7']
+
+    runs-on: ${{ matrix.os }}
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
- 
+      uses: actions/checkout@v4
+
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment.yml
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
-        use-mamba: true
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Install package
       shell: bash -l {0}
-      run: pip install .
+      run: python -m build && pip install dist/*.whl
 
     - name: Run pytest with coverage report
       shell: bash -l {0}
-      run: python -m pytest --cov=./ --cov-report=xml -v
+      run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

environment.yml

@@ -5,20 +5,20 @@ channels:
 dependencies:
 - blas=*=openblas
 - cython=0.29
-- ele=0.2.0
-- freud=2.6.2
-- gsd=2.4.2
-- h5py=2.10
-- hdf5=1.10
+- ele
+- freud
+- gsd
+- h5py<3.0
+- hdf5
 - libcint=4
-- matplotlib=3.4.2
-- numpy=1.21
-- openbabel=3.1.1
-- pip=21.0.1
-- pyscf=1.7.6
+- matplotlib
+- numpy
+- openbabel
+- pip
+- pyscf<2.0
 - python=3.7
-- scipy=1.7
-- signac=1.6.0      
-- signac-flow=0.13.0
+- scipy
 - pytest
 - pytest-cov
+- pip:
+    - build

morphct/__init__.py

@@ -1,17 +1,23 @@
 from morphct.chromophores import Chromophore
 from morphct.mobility_kmc import Carrier
-from morphct.__version__ import __version__
-from morphct import (chromophores, execute_qcc, helper_functions, kmc_analyze,
-                mobility_kmc, transfer_integrals)
+from morphct import (
+    chromophores,
+    execute_qcc,
+    helper_functions,
+    kmc_analyze,
+    mobility_kmc,
+    transfer_integrals
+)
 
 __all__ = [
-        "__version__",
-        "Chromophore",
-        "Carrier",
-        "chromophores",
-        "execute_qcc",
-        "helper_functions",
-        "kmc_analyze",
-        "mobility_kmc",
-        "transfer_integrals",
-        ]
+    "Chromophore",
+    "Carrier",
+    "chromophores",
+    "execute_qcc",
+    "helper_functions",
+    "kmc_analyze",
+    "mobility_kmc",
+    "transfer_integrals",
+]
+
+__version__ = "0.5.1"

morphct/chromophores.py

@@ -5,7 +5,7 @@
 import sys
 from warnings import warn
 
-import ele
+from ele import element_from_symbol
 import freud
 from openbabel import openbabel
 from openbabel import pybel
@@ -229,7 +229,7 @@ def get_chromo_ids_smiles(snap, smarts_str, conversion_dict=None):
         if conversion_dict is not None:
             element = conversion_dict[snap.particles.types[typeid]]
         else:
-            element = ele.element_from_symbol(snap.particles.types[typeid])
+            element = element_from_symbol(snap.particles.types[typeid])
         a.SetAtomicNum(element.atomic_number)
         a.SetVector(*[float(x) for x in unwrapped_positions[i]])
 
@@ -335,90 +335,90 @@ def set_neighbors_voronoi(chromo_list, snap, conversion_dict=None, d_cut=10):
 
 
 conversion_dict = {
-    "S1": ele.element_from_symbol("S"),
-    "H1": ele.element_from_symbol("H"),
-    "C5": ele.element_from_symbol("C"),
-    "C1": ele.element_from_symbol("C"),
-    "C4": ele.element_from_symbol("C"),
-    "C6": ele.element_from_symbol("C"),
-    "C8": ele.element_from_symbol("C"),
-    "C9": ele.element_from_symbol("C"),
-    "C3": ele.element_from_symbol("C"),
-    "C7": ele.element_from_symbol("C"),
-    "C2": ele.element_from_symbol("C"),
-    "C10": ele.element_from_symbol("C"),
+    "S1": element_from_symbol("S"),
+    "H1": element_from_symbol("H"),
+    "C5": element_from_symbol("C"),
+    "C1": element_from_symbol("C"),
+    "C4": element_from_symbol("C"),
+    "C6": element_from_symbol("C"),
+    "C8": element_from_symbol("C"),
+    "C9": element_from_symbol("C"),
+    "C3": element_from_symbol("C"),
+    "C7": element_from_symbol("C"),
+    "C2": element_from_symbol("C"),
+    "C10":element_from_symbol("C"),
 }
 
 
 amber_dict = {
-    "c": ele.element_from_symbol("C"),
-    "c1": ele.element_from_symbol("C"),
-    "c2": ele.element_from_symbol("C"),
-    "c3": ele.element_from_symbol("C"),
-    "ca": ele.element_from_symbol("C"),
-    "cp": ele.element_from_symbol("C"),
-    "cq": ele.element_from_symbol("C"),
-    "cc": ele.element_from_symbol("C"),
-    "cd": ele.element_from_symbol("C"),
-    "ce": ele.element_from_symbol("C"),
-    "cf": ele.element_from_symbol("C"),
-    "cg": ele.element_from_symbol("C"),
-    "ch": ele.element_from_symbol("C"),
-    "cx": ele.element_from_symbol("C"),
-    "cy": ele.element_from_symbol("C"),
-    "cu": ele.element_from_symbol("C"),
-    "cv": ele.element_from_symbol("C"),
-    "h1": ele.element_from_symbol("H"),
-    "h2": ele.element_from_symbol("H"),
-    "h3": ele.element_from_symbol("H"),
-    "h4": ele.element_from_symbol("H"),
-    "h5": ele.element_from_symbol("H"),
-    "ha": ele.element_from_symbol("H"),
-    "hc": ele.element_from_symbol("H"),
-    "hn": ele.element_from_symbol("H"),
-    "ho": ele.element_from_symbol("H"),
-    "hp": ele.element_from_symbol("H"),
-    "hs": ele.element_from_symbol("H"),
-    "hw": ele.element_from_symbol("H"),
-    "hx": ele.element_from_symbol("H"),
-    "f": ele.element_from_symbol("F"),
-    "cl": ele.element_from_symbol("Cl"),
-    "br": ele.element_from_symbol("Br"),
-    "i": ele.element_from_symbol("I"),
-    "n": ele.element_from_symbol("N"),
-    "n1": ele.element_from_symbol("N"),
-    "n2": ele.element_from_symbol("N"),
-    "n3": ele.element_from_symbol("N"),
-    "n4": ele.element_from_symbol("N"),
-    "na": ele.element_from_symbol("N"),
-    "nb": ele.element_from_symbol("N"),
-    "nc": ele.element_from_symbol("N"),
-    "nd": ele.element_from_symbol("N"),
-    "ne": ele.element_from_symbol("N"),
-    "nf": ele.element_from_symbol("N"),
-    "nh": ele.element_from_symbol("N"),
-    "no": ele.element_from_symbol("N"),
-    "o": ele.element_from_symbol("O"),
-    "oh": ele.element_from_symbol("O"),
-    "os": ele.element_from_symbol("O"),
-    "ow": ele.element_from_symbol("O"),
-    "p2": ele.element_from_symbol("P"),
-    "p3": ele.element_from_symbol("P"),
-    "p4": ele.element_from_symbol("P"),
-    "p5": ele.element_from_symbol("P"),
-    "pb": ele.element_from_symbol("P"),
-    "pc": ele.element_from_symbol("P"),
-    "pd": ele.element_from_symbol("P"),
-    "pe": ele.element_from_symbol("P"),
-    "pf": ele.element_from_symbol("P"),
-    "px": ele.element_from_symbol("P"),
-    "py": ele.element_from_symbol("P"),
-    "s": ele.element_from_symbol("S"),
-    "s2": ele.element_from_symbol("S"),
-    "s4": ele.element_from_symbol("S"),
-    "s6": ele.element_from_symbol("S"),
-    "sh": ele.element_from_symbol("S"),
-    "ss": ele.element_from_symbol("S"),
-    "sx": ele.element_from_symbol("S"),
-    "sy": ele.element_from_symbol("S"),
+    "c": element_from_symbol("C"),
+    "c1": element_from_symbol("C"),
+    "c2": element_from_symbol("C"),
+    "c3": element_from_symbol("C"),
+    "ca": element_from_symbol("C"),
+    "cp": element_from_symbol("C"),
+    "cq": element_from_symbol("C"),
+    "cc": element_from_symbol("C"),
+    "cd": element_from_symbol("C"),
+    "ce": element_from_symbol("C"),
+    "cf": element_from_symbol("C"),
+    "cg": element_from_symbol("C"),
+    "ch": element_from_symbol("C"),
+    "cx": element_from_symbol("C"),
+    "cy": element_from_symbol("C"),
+    "cu": element_from_symbol("C"),
+    "cv": element_from_symbol("C"),
+    "h1": element_from_symbol("H"),
+    "h2": element_from_symbol("H"),
+    "h3": element_from_symbol("H"),
+    "h4": element_from_symbol("H"),
+    "h5": element_from_symbol("H"),
+    "ha": element_from_symbol("H"),
+    "hc": element_from_symbol("H"),
+    "hn": element_from_symbol("H"),
+    "ho": element_from_symbol("H"),
+    "hp": element_from_symbol("H"),
+    "hs": element_from_symbol("H"),
+    "hw": element_from_symbol("H"),
+    "hx": element_from_symbol("H"),
+    "f": element_from_symbol("F"),
+    "cl": element_from_symbol("Cl"),
+    "br": element_from_symbol("Br"),
+    "i": element_from_symbol("I"),
+    "n": element_from_symbol("N"),
+    "n1":element_from_symbol("N"),
+    "n2":element_from_symbol("N"),
+    "n3":element_from_symbol("N"),
+    "n4": element_from_symbol("N"),
+    "na": element_from_symbol("N"),
+    "nb": element_from_symbol("N"),
+    "nc": element_from_symbol("N"),
+    "nd": element_from_symbol("N"),
+    "ne": element_from_symbol("N"),
+    "nf": element_from_symbol("N"),
+    "nh": element_from_symbol("N"),
+    "no": element_from_symbol("N"),
+    "o": element_from_symbol("O"),
+    "oh": element_from_symbol("O"),
+    "os": element_from_symbol("O"),
+    "ow": element_from_symbol("O"),
+    "p2": element_from_symbol("P"),
+    "p3": element_from_symbol("P"),
+    "p4": element_from_symbol("P"),
+    "p5": element_from_symbol("P"),
+    "pb": element_from_symbol("P"),
+    "pc": element_from_symbol("P"),
+    "pd": element_from_symbol("P"),
+    "pe": element_from_symbol("P"),
+    "pf": element_from_symbol("P"),
+    "px": element_from_symbol("P"),
+    "py": element_from_symbol("P"),
+    "s": element_from_symbol("S"),
+    "s2": element_from_symbol("S"),
+    "s4": element_from_symbol("S"),
+    "s6": element_from_symbol("S"),
+    "sh": element_from_symbol("S"),
+    "ss": element_from_symbol("S"),
+    "sx": element_from_symbol("S"),
+    "sy": element_from_symbol("S"),
 }

pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools>=61.2", "versioningit"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "MorphCT"
+description = "Using the Marcus Hoping model, caclulates charge mobility from atomistic molecular dynamics morphologies."
+readme = "README.md"
+authors = [
+  {name = "Eric Jankowski", email = "ericjankowski@boisestate.edu"}
+]
+license= {text = "GPLv3"}
+classifiers=[
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+urls = {Homepage = "https://github.com/cmelab/morphct"}
+requires-python = ">=3.7"
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["morphct*"]
+exclude = ["tests*"]
+
+[tool.setuptools.dynamic]
+version = {attr = "morphct.__version__"}