Merge pull request #42 from pnnl/ci-fixes

Update conda recipe and actions for continuous integration

.github/workflows/actions.yml

@@ -45,9 +45,10 @@ jobs:
       - name: Install ISiCLE
         run: pip install --no-deps . 
 
-      # - name: Test environment
-      #   run: |
-      #     pytest
+      - name: Test environment
+        run: |
+          python -c "import isicle"
+          # pytest
 
   Test_Mac:
     needs:
@@ -75,10 +76,11 @@ jobs:
       - name: Install ISiCLE
         run: pip install --no-deps . 
 
-      # - name: Test environment
-      #   run: |
-      #     pytest
-
+      - name: Test environment
+        run: |
+          python -c "import isicle"
+          # pytest
+
   Deploy:
     needs:
       - Test_Linux
@@ -100,7 +102,7 @@ jobs:
           miniforge-version: latest
           use-mamba: true
           python-version: 3.12
-          channels: conda-forge,bioconda
+          channels: conda-forge,bioconda,smcolby
           use-only-tar-bz2: false
           auto-activate-base: true
 
@@ -113,13 +115,13 @@ jobs:
           mkdir build/
           conda mambabuild conda-recipe/ --output-folder build/
           conda index build/
-
-      - name: Convert to osx-64
-        run: conda convert -p osx-64 build/linux-64/*.tar.bz2 -o build/
+        
+      - name: Convert to osx-arm64
+        run: conda convert -p osx-arm64 build/linux-64/*.tar.bz2 -o build/
 
       - name: Upload packages
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
           anaconda upload build/linux-64/*.tar.bz2
-          anaconda upload build/osx-64/*.tar.bz2
+          anaconda upload build/osx-arm64/*.tar.bz2

conda-recipe/conda_build_config.yaml

@@ -0,0 +1,6 @@
+
+python:
+    - 3.12
+    - 3.11
+    - 3.10
+    - 3.9

conda-recipe/meta.yaml

@@ -1,9 +1,9 @@
-{% set data = load_setup_py_data(setup_file='../setup.py',
+{% set data = load_setup_py_data(setup_file="../setup.py",
                                  from_recipe_dir=True) %}
 
 package:
   name: isicle
-  version: {{ data.get('version') }}
+  version: {{ data.get("version") }}
 
 source:
   path: ..

isicle/parse.py

@@ -24,7 +24,7 @@ def _find_output_by_header(self, header):
         pattern = (
             r"(-{2,})\n\s{0,}("
             + re.escape(header)
-            + ")\s{0,}\n-{2,}\n([\s\S]*?)(?=-{2,}\n[^\n]*\n-{2,}\n|$)"
+            + r")\s{0,}\n-{2,}\n([\s\S]*?)(?=-{2,}\n[^\n]*\n-{2,}\n|$)"
         )
 
         # Search ORCA output file
@@ -242,8 +242,8 @@ def _parse_spin(self):
 
         # Parse table
         text = [x.strip() for x in text if x.strip() != "" and "*" not in x]
-        columns = [x.replace(" ", "") for x in re.split("\s{2,}", text[0])]
-        body = [re.split("\s{2,}", x)[1:] for x in text[1:-1]]
+        columns = [x.replace(" ", "") for x in re.split(r"\s{2,}", text[0])]
+        body = [re.split(r"\s{2,}", x)[1:] for x in text[1:-1]]
 
         # Construct data frame
         return pd.DataFrame(body, dtype=float, columns=columns, index=columns)

setup.py

@@ -1,30 +1,27 @@
-import os
 from setuptools import setup, find_packages
-import sys
 
-sys.path.append(os.path.dirname(__file__))
+with open("isicle/__init__.py") as f:
+    exec([x for x in f.readlines() if "__version__" in x][0])
 
-import isicle
-
-with open('README.md') as f:
+with open("README.md") as f:
     readme = f.read()
 
-with open('LICENSE') as f:
+with open("LICENSE") as f:
     license = f.read()
 
-with open('requirements.txt', 'r') as f:
+with open("requirements.txt", "r") as f:
     install_requires = f.read().splitlines()
 
-pkgs = find_packages(exclude=('examples', 'docs', 'resources'))
+pkgs = find_packages(exclude=("examples", "docs", "resources"))
 
 setup(
-    name='isicle',
-    version=isicle.__version__,  # TODO: switch to versioneer.get_version() or alternate method
-    description='ISiCLE: in silico chemical library engine',
+    name="isicle",
+    version=__version__,  # TODO: switch to versioneer.get_version() or alternate method
+    description="ISiCLE: in silico chemical library engine",
     long_description=readme,
-    long_description_content_type='text/markdown',
-    author='Sean M. Colby',
-    author_email='sean.colby@pnnl.gov',
+    long_description_content_type="text/markdown",
+    author="Sean M. Colby",
+    author_email="sean.colby@pnnl.gov",
     license=license,
     packages=pkgs,
     python_requires=">=3.9",
@@ -33,6 +30,6 @@
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Chemistry",
         "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License"
-    ]
+        "License :: OSI Approved :: MIT License",
+    ],
 )