GH actions

.github/workflows/lint.yml

@@ -0,0 +1,25 @@
+name: lint
+
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 6
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+      - name: black
+        run: |
+          black --color ocdata

.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: test
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_call:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 10
+      matrix:
+        python_version: ['3.9', '3.10', '3.11']
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python_version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version:  ${{ matrix.python_version }}
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+            ${{ runner.os }}-
+
+      - name: Install dependencies and package
+        # this can be added along with a dependabot config to run tests with latest versions
+        # pip install -r requirements.txt
+        # pip install -r requirements-optional.txt
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+      - name: Test with pytest
+        run: |
+          pytest tests -vv --cov-report=xml --cov=ocpdata
+
+      - if: ${{ matrix.python_version == '3.11' }}
+        name: codecov-report
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: false # optional (default = false)
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+          verbose: true # optional (default = false)

ocdata/databases/update.py

@@ -2,10 +2,7 @@
 Script for updating ase pkl and db files from v3.19 to v3.21.
 Run it with ase v3.19.
 """
-
-
 import pickle
-from collections import defaultdict
 
 import ase.io
 from ase.atoms import Atoms

pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["setuptools>=69"]
+
+[project]
+name = "oc-data"
+description = "Code for generating adsorbate-catalyst input configurations"
+readme = "README.md"
+license = {text = "MIT License"}
+version = "0.2.0"
+requires-python = ">=3.9, <3.13"
+dependencies = [
+    "scipy",
+    "numpy",
+    "ase==3.22.1",
+    "pymatgen",
+    "tqdm"
+]
+
+[tool.setuptools.packages]
+find = {namespaces = false}  # Disable implicit namespaces
+
+[tool.setuptools_scm]  # for version instrospection based on tags + commit
+
+[project.urls]
+repository = "http://github.com/Open-Catalyst-Project/Open-Catalyst-Dataset"
+
+# include package data
+[tool.setuptools.package-data]
+"ocdata.databases.pkls" = ["*pkl"]
+
+[project.optional-dependencies]
+dev = ["pre-commit", "pytest", "pytest-cov", "coverage", "black"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts  =  "-p no:warnings --import-mode importlib -x --quiet -rxXs --color yes"
+filterwarnings  = [
+    'ignore::UserWarning',
+    'ignore::FutureWarning',
+    'ignore::RuntimeWarning'
+    ]
+testpaths = ["tests"]
+
+[tool.coverage.run]
+source = ["ocdata"]
+
+[tool.isort]
+profile = 'black'
+skip_gitignore = true
+multi_line_output=3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 88

tests/test_bulk.py

@@ -74,7 +74,11 @@ def test_unique_slab_enumeration(self):
             assert slab not in seen
             seen.append(slab)
 
-        # pymatgen-2023.5.10 + ase 3.22.1
+        # pymatgen bug see https://github.com/materialsproject/pymatgen/issues/3747
+        if len(slabs) == 15:
+            pytest.xfail(
+                f"Number of generated slabs {len(slabs)} is off due to pymatgen bug!"
+            )
         assert len(slabs) == 14
 
         with open(self.precomputed_path, "wb") as f:
@@ -86,7 +90,12 @@ def test_precomputed_slab(self):
         precomputed_slabs = self.bulk.get_slabs(
             precomputed_slabs_dir=precomputed_slabs_dir
         )
-        # pymatgen-2023.5.10 + ase 3.22.1
+
+        if len(precomputed_slabs) == 15:
+            pytest.xfail(
+                f"Number of generated slabs {len(precomputed_slabs)} is off due to pymatgen bug!"
+            )
+
         assert len(precomputed_slabs) == 14
 
         slabs = self.bulk.get_slabs()

tests/test_slab.py

@@ -1,6 +1,7 @@
 import random
 
 import numpy as np
+import pytest
 
 from ocdata.core import Bulk, Slab
 
@@ -32,4 +33,4 @@ def test_slab_init_random(self):
 
         assert slab.atoms.get_chemical_formula() == "Sn48"
         assert slab.millers == (2, 1, 0)
-        assert slab.shift == 0.0833333333333334
+        assert slab.shift == pytest.approx(0.0833333333333334)