Merge pull request #442 from Steinbeck-Lab/development

Development

.github/workflows/dev-build.yml

@@ -4,7 +4,7 @@
 # - Fetch Latest release.
 # - Build the latest docker image in development which needs test to pass first.
 # - Push the docker image to Github Artifact Registry-Dev.
-# 
+#
 # Maintainers:
 #   - name: Nisha Sharma
 #   - email: [email protected]
@@ -28,13 +28,13 @@ jobs:
     steps:
       - name: Check out the repo
         uses: actions/checkout@v4
-      
+
       - name: Log in to Docker Hub
         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
           username: ${{ env.DOCKER_HUB_USERNAME  }}
           password: ${{ env.DOCKER_HUB_PASSWORD  }}
-      
+
       - name: Build and push Docker image
         uses: docker/build-push-action@v4
         with:

.github/workflows/prod-build.yml

@@ -3,7 +3,7 @@
 # - Fetch Latest release.
 # - Build the latest docker image in production.
 # - Push the docker image to Github Artifact Registry-Prod.
-# 
+#
 # Maintainers:
 #   - name: Nisha Sharma
 #   - email: [email protected]
@@ -47,7 +47,7 @@ jobs:
           username: ${{ env.DOCKER_HUB_USERNAME  }}
           password: ${{ env.DOCKER_HUB_PASSWORD  }}
 
-      #Build and push Docker image      
+      #Build and push Docker image
       - name: Build and push Docker image
         uses: docker/build-push-action@v4
         with:
@@ -58,4 +58,4 @@ jobs:
             RELEASE_VERSION=${{ steps.fetch-latest-release.outputs.tag_name }}
           tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:${{ steps.fetch-latest-release.outputs.tag_name }}, ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:latest
           username: ${{ env.DOCKER_HUB_USERNAME  }}
-          password: ${{ env.DOCKER_HUB_PASSWORD  }}
+          password: ${{ env.DOCKER_HUB_PASSWORD  }}

.github/workflows/release-please.yml

@@ -3,7 +3,7 @@
 # - Test linting with pylint.
 # - Test the code with pytest.
 # - Trigger release-please action to create release which needs test to pass first.
-# 
+#
 # Maintainers:
 #   - name: Nisha Sharma
 #   - email: [email protected]

.github/workflows/test-check.yml

@@ -1,11 +1,11 @@
 name: Unit test and Lint check
 
-on:  
+on:
   pull_request:
     branches:
         - development
         - main
 
 jobs:
   test:
-    uses: Steinbeck-Lab/cheminformatics-microservice/.github/workflows/test.yml@main
+    uses: Steinbeck-Lab/cheminformatics-microservice/.github/workflows/test.yml@main

.github/workflows/test.yml

@@ -1,7 +1,7 @@
 name: test
 
 on:
-  workflow_call:  
+  workflow_call:
 
 jobs:
   test:

.gitignore

@@ -135,4 +135,4 @@ node_modules
 docs/_build/
 
 #grafana
-grafana_data/
+grafana_data/

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: requirements-txt-fixer
+-   repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/asottile/reorder-python-imports
+    rev: v3.12.0
+    hooks:
+    -   id: reorder-python-imports
+        exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
+-   repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
+    hooks:
+    -   id: flake8
+        args: [
+            "--per-file-ignores=__init__.py:F401",
+            "--ignore=E402,E501,W503",
+            ".",
+        ]

.readthedocs.yml

@@ -12,7 +12,7 @@ build:
   jobs:
     post_install:
       - python -m pip install --no-deps -r docs/extra-requirements.txt
-      
+
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
    configuration: docs/conf.py
@@ -27,4 +27,3 @@ formats:
 python:
   install:
     - requirements: docs/requirements.txt
-

CITATION.cff

@@ -12,7 +12,7 @@ authors:
   orcid: "https://orcid.org/0000-0003-1554-6666"
 - family-names: "Steinbeck"
   given-names: "Christoph"
-  orcid: "https://orcid.org/0000-0001-6966-0814"  
+  orcid: "https://orcid.org/0000-0001-6966-0814"
 - family-names: "Rajan"
   given-names: "Kohulan"
   orcid: "https://orcid.org/0000-0003-1066-7792"

README.md

@@ -1,4 +1,4 @@
-<p align="center"><a href="https://api.naturalproducts.net/" target="_blank"><img src="/public/img/logo.png" width="400" alt="CMS Logo"></a></p>  
+<p align="center"><a href="https://api.naturalproducts.net/" target="_blank"><img src="/public/img/logo.png" width="400" alt="CMS Logo"></a></p>
 
 [![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/MIT)
 [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-blue.svg)](https://GitHub.com/Steinbeck-Lab/cheminformatics-microservice/graphs/commit-activity)
@@ -48,7 +48,7 @@ https://docs.api.naturalproducts.net/standalone.html
 ## License :scroll:
 
 This project is licensed under the MIT License - see the [LICENSE](https://github.com/Steinbeck-Lab/cheminformatics-microservice/blob/main/LICENSE) file for details
- 
+
 ## Citation :newspaper:
 
 *Paper*
@@ -59,7 +59,7 @@ This project is licensed under the MIT License - see the [LICENSE](https://githu
 
 ## Maintained by :wrench:
 
-Cheminformatics Microservice and [Natural Products Online](https://naturalproducts.net) are developed and maintained by the [Steinbeck group](https://cheminf.uni-jena.de) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany. 
+Cheminformatics Microservice and [Natural Products Online](https://naturalproducts.net) are developed and maintained by the [Steinbeck group](https://cheminf.uni-jena.de) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany.
 The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT). Copyright © CC-BY-SA 2023
 <p align="center"><a href="https://cheminf.uni-jena.de/" target="_blank"><img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png" width="800" alt="cheminf Logo"></a></p>
 
@@ -78,5 +78,3 @@ Funded by the [Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
     <img src="https://github.com/Steinbeck-Lab/cheminformatics-microservice/assets/30716951/45c8e153-8322-4563-a51d-cbdbe4e08627" width="30%" alt="Chembiosys Logo">
   </a>
 </div>
-
-

app/__init__.py

@@ -1,5 +1,4 @@
 # -*- coding: utf-8 -*-
-
 """
 Cheminformatics Microservice Python Modules.
 
@@ -8,5 +7,6 @@
 For comments, bug reports or feature requests,
 please raise an issue on our GitHub repository.
 """
+from __future__ import annotations
 
 __version__ = "1.0.0"

app/dependencies.py

@@ -1 +1,2 @@
 # from fastapi import Header, HTTPException
+from __future__ import annotations

app/exception_handlers.py

@@ -1,5 +1,7 @@
-from fastapi.responses import JSONResponse
+from __future__ import annotations
+
 from fastapi import Request
+from fastapi.responses import JSONResponse
 
 
 class InvalidInputException(Exception):

app/main.py

@@ -1,15 +1,22 @@
+from __future__ import annotations
+
 import os
-from fastapi import FastAPI, status
-from fastapi.responses import RedirectResponse
-from fastapi_versioning import VersionedFastAPI
 
-from .routers import tools, depict, converters, chem, ocsr
+from fastapi import FastAPI
+from fastapi import status
 from fastapi.middleware.cors import CORSMiddleware
-
+from fastapi.responses import RedirectResponse
+from fastapi_versioning import VersionedFastAPI
 from prometheus_fastapi_instrumentator import Instrumentator
-from app.schemas import HealthCheck
 
-from app.exception_handlers import InvalidInputException, input_exception_handler
+from .routers import chem
+from .routers import converters
+from .routers import depict
+from .routers import ocsr
+from .routers import tools
+from app.exception_handlers import input_exception_handler
+from app.exception_handlers import InvalidInputException
+from app.schemas import HealthCheck
 
 app = FastAPI(
     title="Cheminformatics Microservice",
@@ -77,7 +84,8 @@ async def add_cors_headers(request, call_next):
 for sub_app in app.routes:
     if hasattr(sub_app.app, "add_exception_handler"):
         sub_app.app.add_exception_handler(
-            InvalidInputException, input_exception_handler
+            InvalidInputException,
+            input_exception_handler,
         )
 
 

app/modules/all_descriptors.py

@@ -1,18 +1,22 @@
-from rdkit.Chem import Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops
+from __future__ import annotations
+
 from typing import Union
-from app.modules.toolkits.rdkit_wrapper import (
-    check_RO5_violations,
-    get_tanimoto_similarity_rdkit,
-)
-from app.modules.toolkits.cdk_wrapper import (
-    get_CDK_SDG,
-    JClass,
-    cdk_base,
-    get_aromatic_ring_count,
-    get_tanimoto_similarity_CDK,
-    get_vander_waals_volume,
-)
+
+from rdkit.Chem import Descriptors
+from rdkit.Chem import Lipinski
+from rdkit.Chem import QED
+from rdkit.Chem import rdMolDescriptors
+from rdkit.Chem import rdmolops
+
+from app.modules.toolkits.cdk_wrapper import cdk_base
+from app.modules.toolkits.cdk_wrapper import get_aromatic_ring_count
+from app.modules.toolkits.cdk_wrapper import get_CDK_SDG
+from app.modules.toolkits.cdk_wrapper import get_tanimoto_similarity_CDK
+from app.modules.toolkits.cdk_wrapper import get_vander_waals_volume
+from app.modules.toolkits.cdk_wrapper import JClass
 from app.modules.toolkits.helpers import parse_input
+from app.modules.toolkits.rdkit_wrapper import check_RO5_violations
+from app.modules.toolkits.rdkit_wrapper import get_tanimoto_similarity_rdkit
 
 
 def get_all_rdkit_descriptors(molecule: any) -> Union[tuple, str]:
@@ -105,7 +109,7 @@ def get_all_cdk_descriptors(molecule: any) -> Union[tuple, str]:
             .toString()
         )
         TotalExactMass = JClass(
-            cdk_base + ".tools.manipulator.AtomContainerManipulator"
+            cdk_base + ".tools.manipulator.AtomContainerManipulator",
         ).getTotalExactMass(SDGMol)
         ALogP = (
             JClass(cdk_base + ".qsar.descriptors.molecular.ALOGPDescriptor")()
@@ -114,7 +118,7 @@ def get_all_cdk_descriptors(molecule: any) -> Union[tuple, str]:
         )
         NumRotatableBonds = (
             JClass(
-                cdk_base + ".qsar.descriptors.molecular.RotatableBondsCountDescriptor"
+                cdk_base + ".qsar.descriptors.molecular.RotatableBondsCountDescriptor",
             )()
             .calculate(SDGMol)
             .getValue()
@@ -127,7 +131,7 @@ def get_all_cdk_descriptors(molecule: any) -> Union[tuple, str]:
         )
         HBondAcceptorCountDescriptor = (
             JClass(
-                cdk_base + ".qsar.descriptors.molecular.HBondAcceptorCountDescriptor"
+                cdk_base + ".qsar.descriptors.molecular.HBondAcceptorCountDescriptor",
             )()
             .calculate(SDGMol)
             .getValue()
@@ -145,15 +149,21 @@ def get_all_cdk_descriptors(molecule: any) -> Union[tuple, str]:
         AromaticRings = get_aromatic_ring_count(SDGMol)
         QEDWeighted = None
         FormalCharge = JClass(
-            cdk_base + ".tools.manipulator.AtomContainerManipulator"
+            cdk_base + ".tools.manipulator.AtomContainerManipulator",
         ).getTotalFormalCharge(SDGMol)
         FractionalCSP3Descriptor = (
             JClass(cdk_base + ".qsar.descriptors.molecular.FractionalCSP3Descriptor")()
             .calculate(SDGMol)
             .getValue()
             .toString()
         )
-        NumRings = JClass(cdk_base + ".graph.Cycles").mcb(SDGMol).numberOfCycles()
+        NumRings = (
+            JClass(
+                cdk_base + ".graph.Cycles",
+            )
+            .mcb(SDGMol)
+            .numberOfCycles()
+        )
         VABCVolume = get_vander_waals_volume(SDGMol)
 
         return (
@@ -229,7 +239,9 @@ def get_cdk_rdkit_combined_descriptors(
         combined_dict = {
             descriptor: (rdkit_desc, cdk_desc)
             for descriptor, rdkit_desc, cdk_desc in zip(
-                all_descriptors, rdkit_descriptors, cdk_descriptors
+                all_descriptors,
+                rdkit_descriptors,
+                cdk_descriptors,
             )
         }
         return combined_dict

app/modules/classyfire.py

@@ -1,6 +1,9 @@
-import requests
+from __future__ import annotations
+
 import json
 
+import requests
+
 
 async def classify(smiles: str) -> dict:
     """
@@ -22,7 +25,7 @@ async def classify(smiles: str) -> dict:
 
     # Prepare payload for the API request
     payload = json.dumps(
-        {"label": "query", "query_input": smiles, "query_type": "STRUCTURE"}
+        {"label": "query", "query_input": smiles, "query_type": "STRUCTURE"},
     )
 
     # Set headers for the API request

app/modules/coconut/descriptors.py

@@ -1,13 +1,15 @@
-from app.modules.toolkits.rdkit_wrapper import get_rdkit_descriptors
-from typing import Dict, Union
-from app.modules.toolkits.cdk_wrapper import (
-    get_murko_framework,
-    get_CDK_descriptors,
-)
+from __future__ import annotations
+
+from typing import Dict
+from typing import Union
+
 from app.modules.all_descriptors import get_cdk_rdkit_combined_descriptors
 from app.modules.npscorer import get_np_score
-from app.modules.tools.sugar_removal import get_sugar_info
+from app.modules.toolkits.cdk_wrapper import get_CDK_descriptors
+from app.modules.toolkits.cdk_wrapper import get_murko_framework
 from app.modules.toolkits.helpers import parse_input
+from app.modules.toolkits.rdkit_wrapper import get_rdkit_descriptors
+from app.modules.tools.sugar_removal import get_sugar_info
 
 
 def get_descriptors(smiles: str, toolkit: str) -> Union[tuple, str]:
@@ -60,7 +62,7 @@ def get_COCONUT_descriptors(smiles: str, toolkit: str) -> Union[Dict[str, float]
 
         CombinedDescriptors = list(Descriptors)
         CombinedDescriptors.extend(
-            [hasLinearSugar, hasCircularSugars, framework, nplikeliness]
+            [hasLinearSugar, hasCircularSugars, framework, nplikeliness],
         )
 
         DescriptorList = (
@@ -91,7 +93,7 @@ def get_COCONUT_descriptors(smiles: str, toolkit: str) -> Union[Dict[str, float]
             "circular_sugars": hasCircularSugars,
             "murko_framework": framework,
             "nplikeness": nplikeliness,
-        }
+        },
     )
 
     return (