Merge remote-tracking branch 'origin/main' into feature/read-value

.github/workflows/CI.yaml

@@ -1,45 +1,36 @@
 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 -r requirements.txt
-        python -m pip install -r 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 }}
+      requirements-file: "tests/requirements-legacy.txt"

.github/workflows/run_tests.yaml

@@ -0,0 +1,37 @@
+name: Run tests
+
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        required: true
+        type: string
+      runs-on:
+        required: true
+        type: string
+      requirements-file:
+        default: "tests/requirements.txt"
+        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 ${{ inputs.requirements-file }}
+    - 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

doc/requirements.in

@@ -0,0 +1,4 @@
+autodocsumm==0.2.12
+furo==2024.5.6
+numpy>=1.26.4
+sphinx==7.3.7

doc/requirements.txt

@@ -1,4 +1,66 @@
+#
+# This file is autogenerated by pip-compile with Python 3.12
+# by the following command:
+#
+#    pip-compile --strip-extras requirements.in
+#
+alabaster==0.7.16
+    # via sphinx
 autodocsumm==0.2.12
+    # via -r requirements.in
+babel==2.15.0
+    # via sphinx
+beautifulsoup4==4.12.3
+    # via furo
+certifi==2024.2.2
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+docutils==0.21.2
+    # via sphinx
 furo==2024.5.6
-numpy>=1.19
+    # via -r requirements.in
+idna==3.7
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+jinja2==3.1.4
+    # via sphinx
+markupsafe==2.1.5
+    # via jinja2
+numpy==1.26.4
+    # via -r requirements.in
+packaging==24.0
+    # via sphinx
+pygments==2.18.0
+    # via
+    #   furo
+    #   sphinx
+requests==2.31.0
+    # via sphinx
+snowballstemmer==2.2.0
+    # via sphinx
+soupsieve==2.5
+    # via beautifulsoup4
 sphinx==7.3.7
+    # via
+    #   -r requirements.in
+    #   autodocsumm
+    #   furo
+    #   sphinx-basic-ng
+sphinx-basic-ng==1.0.0b2
+    # via furo
+sphinxcontrib-applehelp==1.0.8
+    # via sphinx
+sphinxcontrib-devhelp==1.0.6
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.5
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.7
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.10
+    # via sphinx
+urllib3==2.2.1
+    # via requests

parsnip/patterns.py

@@ -67,7 +67,7 @@ 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

@@ -1,5 +1,5 @@
-import dataclasses
 import os
+from collections import namedtuple
 
 import numpy as np
 import pytest
@@ -9,15 +9,7 @@
 data_file_path = os.path.dirname(__file__) + "/sample_data/"
 
 
-@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]
-    single_value_keys: tuple[str]
-
+CifData = namedtuple("CifData", ["filename", "symop_keys", "atom_site_keys"])
 
 # Assorted keys to select from
 assorted_keys = np.loadtxt(data_file_path + "cif_file_keys.txt", dtype=str)

tests/requirements-legacy.in

@@ -0,0 +1,2 @@
+gemmi==0.6.3
+pytest==7.0.1

tests/requirements-legacy.txt

@@ -0,0 +1,32 @@
+#
+# This file is autogenerated by pip-compile with python 3.6
+# To update, run:
+#
+#    pip-compile requirements-legacy.in
+#
+attrs==22.2.0
+    # via pytest
+gemmi==0.6.3
+    # via -r requirements-legacy.in
+importlib-metadata==4.8.3
+    # via
+    #   pluggy
+    #   pytest
+iniconfig==1.1.1
+    # via pytest
+packaging==21.3
+    # via pytest
+pluggy==1.0.0
+    # via pytest
+py==1.11.0
+    # via pytest
+pyparsing==3.1.2
+    # via packaging
+pytest==7.0.1
+    # via -r requirements-legacy.in
+tomli==1.2.3
+    # via pytest
+typing-extensions==4.1.1
+    # via importlib-metadata
+zipp==3.6.0
+    # via importlib-metadata

tests/requirements.in

@@ -0,0 +1,2 @@
+gemmi==0.6.5
+pytest==8.2.0

tests/requirements.txt

@@ -1 +1,16 @@
-gemmi
+#
+# This file is autogenerated by pip-compile with Python 3.12
+# by the following command:
+#
+#    pip-compile --strip-extras requirements.in
+#
+gemmi==0.6.5
+    # via -r requirements.in
+iniconfig==2.0.0
+    # via pytest
+packaging==24.0
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.2.0
+    # via -r requirements.in