Run CI tests on Windows and macOS

.github/requirements-3.10.txt

@@ -8,21 +8,21 @@ cycler==0.12.1
     # via matplotlib
 exceptiongroup==1.2.2
     # via pytest
-fonttools==4.55.3
+fonttools==4.56.0
     # via matplotlib
 gemmi==0.7.0
     # via -r tests/requirements.in
 iniconfig==2.0.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
-matplotlib==3.10.0
+matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
-    # via parsnip (pyproject.toml)
-numpy==2.2.1
+    # via parsnip-cif (pyproject.toml)
+numpy==2.2.3
     # via
-    #   parsnip (pyproject.toml)
+    #   parsnip-cif (pyproject.toml)
     #   ase
     #   contourpy
     #   matplotlib
@@ -43,15 +43,15 @@ pycifrw==4.4.6
     # via -r tests/requirements.in
 pyparsing==3.2.1
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   -r tests/requirements.in
     #   pytest-doctestplus
-pytest-doctestplus==1.3.0
+pytest-doctestplus==1.4.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.15.1
+scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.11.txt

@@ -6,21 +6,21 @@ contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.55.3
+fonttools==4.56.0
     # via matplotlib
 gemmi==0.7.0
     # via -r tests/requirements.in
 iniconfig==2.0.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
-matplotlib==3.10.0
+matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
-    # via parsnip (pyproject.toml)
-numpy==2.2.1
+    # via parsnip-cif (pyproject.toml)
+numpy==2.2.3
     # via
-    #   parsnip (pyproject.toml)
+    #   parsnip-cif (pyproject.toml)
     #   ase
     #   contourpy
     #   matplotlib
@@ -41,15 +41,15 @@ pycifrw==4.4.6
     # via -r tests/requirements.in
 pyparsing==3.2.1
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   -r tests/requirements.in
     #   pytest-doctestplus
-pytest-doctestplus==1.3.0
+pytest-doctestplus==1.4.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.15.1
+scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.12.txt

@@ -6,21 +6,21 @@ contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.55.3
+fonttools==4.56.0
     # via matplotlib
 gemmi==0.7.0
     # via -r tests/requirements.in
 iniconfig==2.0.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
-matplotlib==3.10.0
+matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
-    # via parsnip (pyproject.toml)
-numpy==2.2.1
+    # via parsnip-cif (pyproject.toml)
+numpy==2.2.3
     # via
-    #   parsnip (pyproject.toml)
+    #   parsnip-cif (pyproject.toml)
     #   ase
     #   contourpy
     #   matplotlib
@@ -41,15 +41,15 @@ pycifrw==4.4.6
     # via -r tests/requirements.in
 pyparsing==3.2.1
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   -r tests/requirements.in
     #   pytest-doctestplus
-pytest-doctestplus==1.3.0
+pytest-doctestplus==1.4.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.15.1
+scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.13.txt

@@ -6,21 +6,21 @@ contourpy==1.3.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.55.3
+fonttools==4.56.0
     # via matplotlib
 gemmi==0.7.0
     # via -r tests/requirements.in
 iniconfig==2.0.0
     # via pytest
 kiwisolver==1.4.8
     # via matplotlib
-matplotlib==3.10.0
+matplotlib==3.10.1
     # via ase
 more-itertools==10.6.0
-    # via parsnip (pyproject.toml)
-numpy==2.2.1
+    # via parsnip-cif (pyproject.toml)
+numpy==2.2.3
     # via
-    #   parsnip (pyproject.toml)
+    #   parsnip-cif (pyproject.toml)
     #   ase
     #   contourpy
     #   matplotlib
@@ -41,15 +41,15 @@ pycifrw==4.4.6
     # via -r tests/requirements.in
 pyparsing==3.2.1
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   -r tests/requirements.in
     #   pytest-doctestplus
-pytest-doctestplus==1.3.0
+pytest-doctestplus==1.4.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.15.1
+scipy==1.15.2
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.9.txt

@@ -8,7 +8,7 @@ cycler==0.12.1
     # via matplotlib
 exceptiongroup==1.2.2
     # via pytest
-fonttools==4.55.3
+fonttools==4.56.0
     # via matplotlib
 gemmi==0.7.0
     # via -r tests/requirements.in
@@ -21,10 +21,10 @@ kiwisolver==1.4.7
 matplotlib==3.9.4
     # via ase
 more-itertools==10.6.0
-    # via parsnip (pyproject.toml)
+    # via parsnip-cif (pyproject.toml)
 numpy==2.0.2
     # via
-    #   parsnip (pyproject.toml)
+    #   parsnip-cif (pyproject.toml)
     #   ase
     #   contourpy
     #   matplotlib
@@ -45,11 +45,11 @@ pycifrw==4.4.6
     # via -r tests/requirements.in
 pyparsing==3.2.1
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   -r tests/requirements.in
     #   pytest-doctestplus
-pytest-doctestplus==1.3.0
+pytest-doctestplus==1.4.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib

.github/workflows/CI.yaml

@@ -15,6 +15,11 @@ jobs:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         runs-on: ["ubuntu-latest"]
+        include:
+          - runs-on: "macos-latest"
+            python-version: "3.13"
+          - runs-on: "macos-latest"
+            python-version: "3.9"
     # Pull in the test script from run_tests and distribute python from matrix versions
     uses: ./.github/workflows/run_tests.yaml
     with:
@@ -29,6 +34,22 @@ jobs:
       matrix: # Code works on py3.6, but type annotations are broken
         python-version: ["3.7", "3.8"]
         runs-on: ["ubuntu-20.04"]
+        include:
+          - runs-on: "macos-14"
+            python-version: "3.8"
+    uses: ./.github/workflows/run_tests.yaml
+    with:
+      python-version: ${{ matrix.python-version }}
+      runs-on: ${{ matrix.runs-on }}
+      requirements-file: ".github/requirements-${{ matrix.python-version }}.txt"
+
+  run-tests-windows:
+    needs: run-tests-modern-python
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.9", "3.13"]
+        runs-on: ["windows-latest"]
     uses: ./.github/workflows/run_tests.yaml
     with:
       python-version: ${{ matrix.python-version }}

.github/workflows/run_tests.yaml

@@ -18,20 +18,20 @@ jobs:
     runs-on: ${{ inputs.runs-on }}
     steps:
     - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
     - name: Install uv
       uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ inputs.python-version }}
-        version: "0.5.11"
-    - name: Set up environment with dependencies
-      run: |
-        uv venv && . .venv/bin/activate
-        echo PATH=$PATH >> $GITHUB_ENV
+        version: "0.6.6"
+
     - name: Install package
       run: |
+        which python
         python --version
-        uv pip install . -r ${{ inputs.requirements-file }} -v
+        uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --system
         python -c "import parsnip; print('parsnip', parsnip.__version__)"
+
     - name: Test with pytest
-      run: |
-        python -m pytest -v
+      run: python -m ${{ runner.os != 'Windows' && 'pytest' || 'pytest tests' }} -v

.github/workflows/update-uv-lockfiles.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+for version in 3.{9..13}; do
+    uv pip compile --python-version="$version" pyproject.toml tests/requirements.in > ".github/requirements-$version.txt"
+done

changelog.rst

@@ -12,6 +12,7 @@ Added
 - New ``additional_columns`` parameter for ``build_unit_cell`` that allows the return of
   atom site labels and similar data alongside unit cell positions.
 - Ensured consistent ordering of lattice positions returned from ``build_unit_cell``.
+- CI testing on Windows and macOS
 
 Fixed
 ~~~~~

tests/conftest.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import os
+import re
 from dataclasses import dataclass
 
 import numpy as np
@@ -14,6 +15,10 @@
 data_file_path = os.path.dirname(__file__) + "/sample_data/"
 
 
+def _arrstrip(arr: np.ndarray, pattern: str):
+    return np.vectorize(lambda x: re.sub(pattern, "", x))(arr)
+
+
 @dataclass
 class CifData:
     filename: str

tests/requirements.in

@@ -1,5 +1,5 @@
 ase
 gemmi
-pycifrw
+pycifrw<5.0.0
 pytest
 pytest-doctestplus

tests/test_patterns.py

@@ -206,7 +206,7 @@ def test_try_cast_to_numeric(s):
 def test_repr(cif_data):
     import re
 
-    repr = re.sub(r"[a-z\s]*", "", cif_data.file.__repr__().split(":")[1]).split(",")
+    repr = re.sub(r"[a-z\s]*", "", cif_data.file.__repr__().split(" : ")[1]).split(",")
     n_pairs, n_tabs = [int(i) for i in repr]
     assert n_pairs == len(cif_data.file.pairs)
     assert n_tabs == len(cif_data.file.loops)

tests/test_table_reader.py

@@ -4,7 +4,7 @@
 import pytest
 from ase.io import cif as asecif
 from CifFile import CifFile as pycifRW
-from conftest import bad_cif, cif_files_mark
+from conftest import _arrstrip, bad_cif, cif_files_mark
 from gemmi import cif
 from more_itertools import flatten
 
@@ -34,7 +34,7 @@ def test_reads_all_keys(cif_data):
         loop = [pycif.true_case[key] for key in loop]
         parsnip_data = cif_data.file.get_from_loops(loop)
         gemmi_data = _gemmi_read_table(cif_data.filename, loop)
-        np.testing.assert_array_equal(parsnip_data, gemmi_data)
+        np.testing.assert_array_equal(parsnip_data, _arrstrip(gemmi_data, r"\r"))
 
 
 @cif_files_mark

tests/test_unitcells.py

@@ -1,12 +1,11 @@
-import re
 import warnings
 from contextlib import nullcontext
 
 import numpy as np
 import pytest
 from ase import io
 from ase.build import supercells
-from conftest import box_keys, cif_files_mark
+from conftest import _arrstrip, box_keys, cif_files_mark
 from gemmi import cif
 from more_itertools import flatten
 
@@ -22,10 +21,6 @@ def _gemmi_read_keys(filename, keys, as_number=True):
     return np.array([file_block.find_value(key) for key in keys])
 
 
-def _arrstrip(arr: np.ndarray, pattern: str):
-    return np.vectorize(lambda x: re.sub(pattern, "", x))(arr)
-
-
 @cif_files_mark  # TODO: test with conversions to numeric as well
 def test_read_wyckoff_positions(cif_data):
     if "PDB_4INS_head.cif" in cif_data.filename: