Merge branch 'PDBE-7032' of https://github.com/PDBeurope/ccdutils int…

…o PDBE-7032

.github/workflows/documentation.yml

@@ -21,11 +21,11 @@ jobs:
         with:
           python-version: "3.10"
       - run: |
-          pip install rdkit
-          pip install -e ".[docs]"
+          pip install poetry
+          poetry install --with docs
       - run: |
           cd doc
-          make html
+          poetry run make html
       - name: Deploy pages
         uses: peaceiris/actions-gh-pages@v3
         with:

.github/workflows/publish.yml

@@ -27,10 +27,10 @@ jobs:
           python-version: "3.10"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build
+          pip install poetry
+          poetry install
       - name: Build package
-        run: python -m build
+        run: poetry build
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
         with:

.github/workflows/tests.yml

@@ -20,8 +20,8 @@ jobs:
           python-version: "3.10"
 
       - run: |
-          pip install rdkit==2023.09.6
-          pip install -e ".[tests]"
+          pip install poetry
           pip install pre-commit
-          pre-commit install && pre-commit run --all
-      - run: pytest --cov=pdbeccdutils
+          poetry install --with tests
+          poetry run pre-commit install && pre-commit run --all
+      - run: poetry run pytest --cov=pdbeccdutils

.pre-commit-config.yaml

@@ -14,14 +14,14 @@ repos:
       - id: end-of-file-fixer
       - id: check-ast
 
-  - repo: https://github.com/ambv/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5 # Ruff version.
     hooks:
-      - id: black
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 3.9.1
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: https://github.com/dzhu/rstfmt
+    rev: v0.0.14
     hooks:
-      - id: flake8
-        args: ["--max-line-length=88", "--ignore=E501,W503"]
-        exclude: \.cif$
+      - id: rstfmt
+        name: rST Formatter

pdbeccdutils/core/boundmolecule.py

@@ -46,7 +46,7 @@ def infer_bound_molecules(structure, to_discard, assembly=False):
         bm = BoundMolecule(subgraph)
         bound_molecules.append(bm)
 
-    bound_molecules = sorted(bound_molecules, key=lambda l: -len(l.graph.nodes))
+    bound_molecules = sorted(bound_molecules, key=lambda item: -len(item.graph.nodes))
     return bound_molecules
 
 

pdbeccdutils/core/ccd_writer.py

@@ -22,6 +22,7 @@
     CCDUtilsError: If deemed format is not supported or an unrecoverable
         error occurres.
 """
+
 import json
 import logging
 import math

pdbeccdutils/core/clc_reader.py

@@ -93,7 +93,6 @@ def read_pdb_cif_file(
 
 
 def infer_multiple_chem_comp(path_to_cif, bm, bm_id, sanitize=True):
-
     """Args:
         path_to_cif: Path to input structure
         bm: bound-molecules identified from input structure

pdbeccdutils/core/component.py

@@ -464,11 +464,12 @@ def export_2d_svg(
         Raises:
             CCDUtilsError: If bond or atom does not exist.
         """
-        get_atom_name = (
-            lambda a: a.GetProp("name")
-            if a.HasProp("name")
-            else a.GetSymbol() + str(a.GetIdx())
-        )
+
+        def get_atom_name(atom):
+            if atom.HasProp("name"):
+                return atom.GetProp("name")
+            else:
+                return f"{atom.GetSymbol()}{atom.GetIdx()}"
 
         if self.mol2D is None:
             drawing.save_no_image(file_name, self.id, width)

pdbeccdutils/core/depictions.py

@@ -20,6 +20,7 @@
 quality
 
 """
+
 import logging
 import math
 import os
@@ -118,7 +119,7 @@ def depict_molecule(
 
         results = results + template_res
 
-        results.sort(key=lambda l: (l.score, l.source))
+        results.sort(key=lambda item: (item.score, item.source))
 
         if results:
             to_return = results[0]

pdbeccdutils/core/models.py

@@ -308,7 +308,7 @@ def __eq__(self, other) -> bool:
 class BoundMolecule:
     def __init__(self, graph):
         self.graph = graph
-        self.nodes = sorted(self.graph, key=lambda l: (int(l.res_id), l.chain))
+        self.nodes = sorted(self.graph, key=lambda item: (int(item.res_id), item.chain))
 
     @property
     def id(self) -> str:
@@ -362,7 +362,7 @@ def to_dict(self):
             dict of `str`: dict representation of the object
         """
 
-        nodes = sorted(self.graph, key=lambda l: (int(l.res_id), l.chain))
+        nodes = sorted(self.graph, key=lambda item: (int(item.res_id), item.chain))
 
         results_bag = {}
         results_bag["residues"] = [x.to_dict() for x in nodes]

pdbeccdutils/core/prd_writer.py

@@ -22,6 +22,7 @@
     CCDUtilsError: If deemed format is not supported or an unrecoverable
         error occurres.
 """
+
 import json
 import math
 from pathlib import Path

pdbeccdutils/helpers/drawing.py

@@ -15,8 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
-"""Module helper providing drawing functionality based on RDKit
-"""
+"""Module helper providing drawing functionality based on RDKit"""
 
 import os
 import re

pdbeccdutils/helpers/helper.py

@@ -15,8 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
-"""Generic helper functions that may be re-used
-"""
+"""Generic helper functions that may be re-used"""
 
 import os
 import sys
@@ -145,7 +144,6 @@ def requests_retry_session(
     status_forcelist=(429, 500, 502, 503, 504),
     session=None,
 ):
-
     session = session or requests.Session()
     retry = Retry(
         total=retries,

pdbeccdutils/scripts/process_components_cif_cli.py

@@ -28,6 +28,7 @@
 
 https://gitlab.ebi.ac.uk/pdbe/release/pdbechem
 """
+
 import argparse
 import logging
 import os

pdbeccdutils/scripts/setup_pubchem_library_cli.py

@@ -2,6 +2,7 @@
 the pdbeccdutils. Based on the inchikey provided in the CCD
 a corresponding 2D layout is downloaded from PubChem database.
 """
+
 import argparse
 import os
 import sys

pdbeccdutils/tests/conftest.py

@@ -1,5 +1,5 @@
-"""Common fixtures shared among all the tests
-"""
+"""Common fixtures shared among all the tests"""
+
 import pytest
 from pdbeccdutils.core import ccd_reader, clc_reader
 from pdbeccdutils.core.fragment_library import FragmentLibrary

pdbeccdutils/tests/test_bound_molecule.py

@@ -1,5 +1,4 @@
-"""Common fixtures shared among all the tests
-"""
+"""Common fixtures shared among all the tests"""
 
 import json
 import pytest

pdbeccdutils/tests/test_clc_reader.py

@@ -1,6 +1,7 @@
 """
 load 6lq4_updated.cif from file and test important cif item.
 """
+
 import pytest
 from pdbeccdutils.core import clc_reader
 from pdbeccdutils.core.models import ReleaseStatus

pdbeccdutils/tests/test_fragment_library.py

@@ -1,5 +1,4 @@
-"""Test fragment library functionality
-"""
+"""Test fragment library functionality"""
 
 import os
 

pdbeccdutils/tests/test_load_eoh_cif.py

@@ -1,6 +1,7 @@
 """
 load EOH.cif from file and test important cif item.
 """
+
 import pytest
 
 from pdbeccdutils.core import ccd_reader, ccd_writer

pdbeccdutils/tests/test_parity.py

@@ -1,5 +1,4 @@
-"""Test of PARITY method
-"""
+"""Test of PARITY method"""
 
 import pytest
 

pdbeccdutils/tests/test_process_components_cif_cli.py

@@ -5,6 +5,7 @@
 http://dustinrcollins.com/testing-python-command-line-apps
 adapted to use nose then converted to pytest
 """
+
 import json
 import os
 import re

pdbeccdutils/tests/test_web_services.py

@@ -1,5 +1,4 @@
-"""Test of routine for retrieving 2D layouts of the CCDs.
-"""
+"""Test of routine for retrieving 2D layouts of the CCDs."""
 
 import os
 

pdbeccdutils/tests/test_write_img.py

@@ -1,6 +1,4 @@
-"""Unit tests for checking whether or not depictions are written properly.
-"""
-
+"""Unit tests for checking whether or not depictions are written properly."""
 
 import json
 import os

pdbeccdutils/utils/config.py

@@ -1,5 +1,5 @@
-"""Package configuration with the paths to the templates
-"""
+"""Package configuration with the paths to the templates"""
+
 import os
 import pdbeccdutils
 

pdbeccdutils/utils/web_services.py

@@ -15,8 +15,7 @@
 # specific language governing permissions and limitations
 # under the License.
 
-"""module handling UniChem mapping
-"""
+"""module handling UniChem mapping"""
 
 from pdbeccdutils.helpers import helper