Fixed merge conflicts

.github/workflows/build_deploy.yml

@@ -50,7 +50,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -74,10 +74,12 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
 
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
         env:
           CIBW_BUILD: ${{ matrix.cibw_build }}
           CIBW_SKIP: ${{ matrix.cibw_skip }}
@@ -95,7 +97,9 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
 
       - name: Install dependencies
         run: python -m pip install twine build
@@ -115,15 +119,17 @@ jobs:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
 
       - uses: actions/download-artifact@v2
         with:
           name: artifact
           path: dist
 
       - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/matrix_includes.json

@@ -3,37 +3,37 @@
         "runOn": "master",
         "os": "ubuntu-latest",
         "cibw_skip": "",
-        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
+        "cibw_build": "cp39-* cp310-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "master",
         "os": "windows-latest",
         "cibw_skip": "",
-        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
+        "cibw_build": "cp39-* cp310-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "master",
         "os": "macos-latest",
         "cibw_skip": "",
-        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
+        "cibw_build": "cp39-* cp310-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "release-",
         "os": "ubuntu-latest",
         "cibw_skip": "",
-        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
+        "cibw_build": "cp39-* cp310-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "release-",
         "os": "windows-latest",
         "cibw_skip": "",
-        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
+        "cibw_build": "cp39-* cp310-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "release-",
         "os": "macos-latest",
         "cibw_skip": "",
-        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
+        "cibw_build": "cp39-* cp310-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "always",

prospr/__init__.py

@@ -1,3 +1,11 @@
-from prospr_core import Protein, depth_first, depth_first_bnb
+from prospr_core import AminoAcid, Protein, depth_first, depth_first_bnb
+from .datasets import load_vanEck250, load_vanEck1000
 
-__all__ = ["Protein", "depth_first", "depth_first_bnb"]
+__all__ = [
+    "AminoAcid",
+    "Protein",
+    "depth_first",
+    "depth_first_bnb",
+    "load_vanEck250",
+    "load_vanEck1000",
+]

pyproject.toml

@@ -13,4 +13,4 @@ build-backend = "setuptools.build_meta"
 line-length = 79
 
 [tool.pytest]
-minversion = 6.2
+minversion = 7.1

setup.py

@@ -12,7 +12,7 @@
 from setuptools import setup
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 
-__version__ = "0.2a3"
+__version__ = "0.2a4"
 
 # Define core module extension.
 ext_modules = [

tests/core/test_depth_first.py

@@ -2,7 +2,10 @@
 """
 File:           test_depth_first.py
 Description:    This file contains the pytest tests for the depth_first search
-                    core code.
+                core code.
+License:        This file is licensed under the GNU LGPL V3 license by
+                Okke van Eck (2020 - 2022). See the LICENSE file for the
+                specifics.
 """
 
 from prospr import Protein, depth_first
@@ -19,7 +22,6 @@ def protein_3d():
     return Protein("HPPHPHPHPH", 3, model="HP")
 
 
-# @pytest.mark.order(after="test_protein.TestProtein")
 @pytest.mark.order(order=2)
 class TestDepthFirst:
     def test_protein_2d_depth_first(self, protein_2d):

tests/core/test_depth_first_bnb.py

@@ -2,7 +2,10 @@
 """
 File:           test_depth_first_bnb.py
 Description:    This file contains the pytest tests for the depth_first_bnb
-                    search core code.
+                search core code.
+License:        This file is licensed under the GNU LGPL V3 license by
+                Okke van Eck (2020 - 2022). See the LICENSE file for the
+                specifics.
 """
 
 from prospr import Protein, depth_first_bnb
@@ -19,7 +22,6 @@ def protein_3d():
     return Protein("HPPHPHPHPH", 3, model="HP")
 
 
-# @pytest.mark.order(after="test_protein.TestProtein")
 @pytest.mark.order(order=2)
 class TestDepthFirstBnB:
     def test_protein_2d_depth_first_bnb(self, protein_2d):

tests/core/test_protein.py

@@ -2,6 +2,9 @@
 """
 File:           test_protein.py
 Description:    This file contains the pytest tests for the Protein core code.
+License:        This file is licensed under the GNU LGPL V3 license by
+                Okke van Eck (2020 - 2022). See the LICENSE file for the
+                specifics.
 """
 
 from prospr import Protein

tests/data/test_datasets.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+"""
+File:           test_depth_first.py
+Description:    This file contains the pytest tests for loading data from the
+                datasets.
+License:        This file is licensed under the GNU LGPL V3 license by
+                Okke van Eck (2020 - 2022). See the LICENSE file for the
+                specifics.
+"""
+
+from prospr import load_vanEck250, load_vanEck1000
+
+
+class TestDatasets:
+    def test_vanEck250(self):
+        """
+        Test loading data from vanEck250 works.
+        """
+        l10 = load_vanEck250()
+        l10_2 = load_vanEck250(10)
+        l20 = load_vanEck250(20)
+        l30 = load_vanEck250(30)
+        l40 = load_vanEck250(40)
+        l50 = load_vanEck250(50)
+        l60 = load_vanEck250(60)
+        l70 = load_vanEck250(70)
+        l80 = load_vanEck250(80)
+        l90 = load_vanEck250(90)
+        l100 = load_vanEck250(100)
+
+        assert not l10.empty
+        assert not l10_2.empty
+        assert not l20.empty
+        assert not l30.empty
+        assert not l40.empty
+        assert not l50.empty
+        assert not l60.empty
+        assert not l70.empty
+        assert not l80.empty
+        assert not l90.empty
+        assert not l100.empty
+
+    def test_vanEck1000(self):
+        """
+        Test loading data from vanEck1000 works.
+        """
+        l10 = load_vanEck1000()
+        l10_2 = load_vanEck1000(10)
+        l20 = load_vanEck1000(20)
+        l30 = load_vanEck1000(30)
+        l40 = load_vanEck1000(40)
+        l50 = load_vanEck1000(50)
+        l60 = load_vanEck1000(60)
+        l70 = load_vanEck1000(70)
+        l80 = load_vanEck1000(80)
+        l90 = load_vanEck1000(90)
+        l100 = load_vanEck1000(100)
+
+        assert not l10.empty
+        assert not l10_2.empty
+        assert not l20.empty
+        assert not l30.empty
+        assert not l40.empty
+        assert not l50.empty
+        assert not l60.empty
+        assert not l70.empty
+        assert not l80.empty
+        assert not l90.empty
+        assert not l100.empty