From ee5894eaf00e13c1173f7e21dae82cb96e39d4f4 Mon Sep 17 00:00:00 2001
From: Jen Bradley <55467578+janbridley@users.noreply.github.com>
Date: Thu, 16 May 2024 13:24:11 -0400
Subject: [PATCH] Support Python 3.6+ (#13)

* Add minimal setup.py

* Switch dataclass to namedtuple

* Fix typing for python < 3.7

* Split tests into two blocks

* Add required workflow steps

* pip install -r

* Add pytest to reqs

* Rename CI features

* Properly implement workflow_call procedure

* Remove incorrect runs_on key

* Rename action

* Fix syntax in CI

* Set legacy tests to run after modern versions pass

* Clean up CI script

* Clean up action names

* Parameterize runs-on

* Add runs-on input to workflow callable

* Move python 3.6 tests to ubuntu 20.04

* Test python 3.5

* Remove broken python 3.5

* Update install files

* Swapped requirements.txt with requirements.in

* Swapped tests requirements.txt with requirements.in

* Added legacy test requirements file

* Fixed pin and reran pip-compile on python 3.6

* Set default value for requirements-file
---
 .github/workflows/CI.yaml        | 53 +++++++++++---------------
 .github/workflows/run_tests.yaml | 37 ++++++++++++++++++
 doc/requirements.in              |  4 ++
 doc/requirements.txt             | 64 +++++++++++++++++++++++++++++++-
 parsnip/parse.py                 | 11 +++---
 parsnip/patterns.py              |  6 +--
 pyproject.toml                   |  2 +-
 setup.py                         |  4 ++
 tests/conftest.py                | 10 +----
 tests/requirements-legacy.in     |  2 +
 tests/requirements-legacy.txt    | 32 ++++++++++++++++
 tests/requirements.in            |  2 +
 tests/requirements.txt           | 17 ++++++++-
 13 files changed, 193 insertions(+), 51 deletions(-)
 create mode 100644 .github/workflows/run_tests.yaml
 create mode 100644 doc/requirements.in
 create mode 100644 setup.py
 create mode 100644 tests/requirements-legacy.in
 create mode 100644 tests/requirements-legacy.txt
 create mode 100644 tests/requirements.in

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 9c5fe9e..3f390ee 100644
--- a/.github/workflows/CI.yaml
+++ b/.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 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 }}
+      requirements-file: "tests/requirements-legacy.txt"
diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml
new file mode 100644
index 0000000..e3e125a
--- /dev/null
+++ b/.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
diff --git a/doc/requirements.in b/doc/requirements.in
new file mode 100644
index 0000000..6480824
--- /dev/null
+++ b/doc/requirements.in
@@ -0,0 +1,4 @@
+autodocsumm==0.2.12
+furo==2024.5.6
+numpy>=1.26.4
+sphinx==7.3.7
diff --git a/doc/requirements.txt b/doc/requirements.txt
index 26cd033..3be342f 100644
--- a/doc/requirements.txt
+++ b/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
diff --git a/parsnip/parse.py b/parsnip/parse.py
index baca349..8d7712c 100644
--- a/parsnip/parse.py
+++ b/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+",",")) )
 
diff --git a/parsnip/patterns.py b/parsnip/patterns.py
index f81923a..430a6ff 100644
--- a/parsnip/patterns.py
+++ b/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
diff --git a/pyproject.toml b/pyproject.toml
index 8e6412d..2fb22f2 100644
--- a/pyproject.toml
+++ b/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" }
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..1c7fac8
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,4 @@
+# ruff: noqa: D100
+from setuptools import setup
+
+setup(name="parsnip")
diff --git a/tests/conftest.py b/tests/conftest.py
index 5852b37..4589560 100644
--- a/tests/conftest.py
+++ b/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 = (
diff --git a/tests/requirements-legacy.in b/tests/requirements-legacy.in
new file mode 100644
index 0000000..c9e5797
--- /dev/null
+++ b/tests/requirements-legacy.in
@@ -0,0 +1,2 @@
+gemmi==0.6.3
+pytest==7.0.1
diff --git a/tests/requirements-legacy.txt b/tests/requirements-legacy.txt
new file mode 100644
index 0000000..1f9c539
--- /dev/null
+++ b/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
diff --git a/tests/requirements.in b/tests/requirements.in
new file mode 100644
index 0000000..946cb29
--- /dev/null
+++ b/tests/requirements.in
@@ -0,0 +1,2 @@
+gemmi==0.6.5
+pytest==8.2.0
diff --git a/tests/requirements.txt b/tests/requirements.txt
index b6d2376..ee7a087 100644
--- a/tests/requirements.txt
+++ b/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