Support Python 3.6+

.github/workflows/CI.yaml

@@ -1,45 +1,35 @@
 name: Run Tests
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
 on:
-  # trigger on pull requests
   pull_request:
-
-  # trigger on all commits to master
   push:
     branches:
       - "main"
       - "breaking"
-
-  # trigger on request
   workflow_dispatch:
 
+
 jobs:
-  run_tests:
-    name: Run tests on ubuntu-latest with Python ${{ matrix.python-version }}
-    runs-on: ubuntu-latest
+  run-tests-modern-python:
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        runs-on: ["ubuntu-latest"]
+    # Pull in the test script from run_tests and distribute python from matrix versions
+    uses: ./.github/workflows/run_tests.yaml
+    with:
+      python-version: ${{ matrix.python-version }}
+      runs-on: ${{ matrix.runs-on }}
+
+  run-tests-legacy-python:
+    needs: run-tests-modern-python # Wait until tests pass on python 3.9+
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9","3.10","3.11","3.12"]
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install requirements.txt
-        python -m pip install tests/requirements.txt
-    - name: Install package
-      run: |
-        python --version
-        python -c "import numpy; print('numpy', numpy.__version__)"
-        python -m pip install . -v --progress-bar off
-    - name: Test with pytest
-      run: |
-        python -m pytest -v
+        python-version: ["3.6", "3.7", "3.8"]
+        runs-on: ["ubuntu-20.04"]
+    uses: ./.github/workflows/run_tests.yaml
+    with:
+      python-version: ${{ matrix.python-version }}
+      runs-on: ${{ matrix.runs-on }}

.github/workflows/run_tests.yaml

@@ -0,0 +1,34 @@
+name: Run tests
+
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        required: true
+        type: string
+      runs-on:
+        required: true
+        type: string
+
+jobs:
+  run_test:
+    runs-on: ${{ inputs.runs-on }}
+    steps:
+      # Steps common to both groups
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install -r requirements.txt
+        python -m pip install -r tests/requirements.txt
+    - name: Install package
+      run: |
+        python --version
+        python -m pip install . -v --progress-bar off
+        python -c "import parsnip; print('parsnip', parsnip.__version__)"
+    - name: Test with pytest
+      run: |
+        python -m pytest -v

parsnip/parse.py

@@ -1,5 +1,4 @@
 """CIF parsing tools."""
-
 import warnings
 
 import numpy as np
@@ -15,9 +14,9 @@ def _remove_comments_from_line(line):
 def read_table(
     filename: str,
     keys: str,
-    filter_line: tuple[tuple[str, str]] = ((r",\s+", ",")),
+    filter_line: tuple = ((r",\s+", ",")),
     keep_original_key_order=False,
-) -> np.ndarray[str]:
+) -> np.ndarray:
     r"""Extract data from a CIF file loop_ table.
 
     CIF files store tabular data as whitespace-delimited blocks that start with `loop_`.
@@ -61,7 +60,7 @@ def read_table(
     Args:
         filename (str): The name of the .cif file to be parsed.
         keys (tuple[str]): The names of the keys to be parsed.
-        filter_line (tuple[tuple[str]], optional):
+        filter_line (tuple[tuple[str,str]], optional):
             A tuple of strings that are compiled to a regex filter and applied to each
             data line. (Default value: ((r",\s+",",")) )
         keep_original_key_order (bool, optional):
@@ -146,13 +145,13 @@ def read_table(
 
 def read_fractional_positions(
     filename: str,
-    filter_line: tuple[tuple[str, str]] = ((r",\s+", ",")),
+    filter_line: tuple = ((r",\s+", ",")),
 ):
     r"""Extract the fractional X,Y,Z coordinates from a CIF file.
 
     Args:
         filename (str): The name of the .cif file to be parsed.
-        filter_line (tuple[tuple[str]], optional):
+        filter_line (tuple[tuple[str,str]], optional):
             A tuple of strings that are compiled to a regex filter and applied to each
             data line. (Default value: ((r",\s+",",")) )
 

parsnip/patterns.py

@@ -8,11 +8,11 @@
 _comma_prune_spaces = re.compile(r",\s+")
 
 
-def compile_pattern_from_strings(filter_patterns: tuple[str]):
+def compile_pattern_from_strings(filter_patterns: tuple):
     """Return a regex pattern that matches any of the characters in the filter.
 
     Args:
-        filter_patterns (list[str]): Description
+        filter_patterns (tuple[str]): Description
 
     Returns:
         re.Pattern: Pattern matching any of the input characters.
@@ -46,7 +46,7 @@ class LineCleaner:
             what that pattern will be replaced with.
     """
 
-    def __init__(self, patterns: tuple[tuple[str, str]]):
+    def __init__(self, patterns: tuple):
         self.patterns, self.replacements = [], []
 
         # If we only have a single tuple

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "parsnip"
 version = "0.0.2"
-requires-python = ">=3.9"
+requires-python = ">=3.6"
 description = "Minimal library for parsing CIF/mmCIF files in Python."
 readme = "README.md"
 license = { file = "LICENSE" }

setup.py

@@ -0,0 +1,4 @@
+# ruff: noqa: D100
+from setuptools import setup
+
+setup(name="parsnip")

tests/conftest.py

@@ -1,18 +1,12 @@
-import dataclasses
 import os
+from collections import namedtuple
 
 import pytest
 
 # ruff: noqa: N816. Allow mixed-case global variables
 
 
-@dataclasses.dataclass
-class CifData:
-    """Class to hold the filename and stored keys for a CIF file."""
-
-    filename: str
-    symop_keys: tuple[str]
-    atom_site_keys: tuple[str]
+CifData = namedtuple("CifData", ["filename", "symop_keys", "atom_site_keys"])
 
 
 box_keys = (

tests/requirements.txt

@@ -1 +1,2 @@
 gemmi
+pytest