Merge pull request isambard-uob#19 from universvm/master

Add cython as dependency to the install

.github/workflows/python-package.yml

@@ -27,8 +27,8 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install flake8 pytest hypothesis cython
-        python setup.py install
+        pip install .
+        pip install -r dev-requirements.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

pyproject.toml

@@ -0,0 +1,15 @@
+[build-system]
+requires = ["setuptools", "wheel", "Cython"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "AMPAL"
+version = "1.5.1"
+requires-python = ">= 3.8"
+readme = "README.md"
+dependencies = [
+  "Cython",
+  "networkx==3.1",
+  "numpy==1.22",
+  "requests",
+]

setup.py

@@ -13,7 +13,7 @@ def readme():
 
 setup(
     name="AMPAL",
-    version="1.5.0",
+    version="1.5.1",
     description="A simple framework for representing biomolecular structure.",
     long_description=readme(),
     long_description_content_type="text/markdown; charset=UTF-8; variant=GFM",
@@ -31,12 +31,15 @@ def readme():
     packages=find_packages("src"),
     package_dir={"": "src"},
     include_package_data=True,
+    setup_requires=[
+        "Cython",
+    ],
     # This code automatically builds the Cython extensions.
     ext_modules=cythonize(
         [
             Extension("ampal.geometry", ["src/ampal/geometry.pyx"]),
         ]
     ),
-    install_requires=["Cython", "networkx", "numpy==1.22", "requests"],
+    install_requires=["Cython", "networkx==3.1", "numpy==1.22", "requests"],
     zip_safe=False,
 )

src/ampal/amino_acids.py

@@ -763,7 +763,6 @@ def get_aa_letter(aa_code):
 
     return aa_letter
 
-
 def get_aa_info(code):
     """Get dictionary of information relating to a new amino acid code not currently in the database.
 
@@ -795,7 +794,7 @@ def get_aa_info(code):
     )
     r = requests.get(url_string)
     # Raise error if content not obtained.
-    if not r.ok:
+    if not r.ok or "does not exist" in r.text:
         raise IOError("Could not get to url {0}".format(url_string))
 
     # Parse r.text in an ugly way to get the required information.
@@ -814,7 +813,6 @@ def get_aa_info(code):
     }
     return aa_dict
 
-
 def add_amino_acid_to_json(
     code, description, letter="X", modified=None, force_add=False
 ):