v1 base branch

.gitignore

@@ -1,7 +1,6 @@
 # project
-notebooks/
 data/
-assets/
+.idea
 
 # ci
 .gitlab-ci.yml

.isort.cfg

@@ -5,4 +5,4 @@ include_trailing_comma=True
 force_grid_wrap=0
 use_parentheses=True
 known_first_party = molecad
-known_third_party = fastapi,loguru,mongordkit,pathlib,pydantic,pymongo,pytest,rdkit,requests,starlette,starlette_context,typing_extensions,uvicorn
+known_third_party = fastapi,loguru,pathlib,pydantic,pymongo,pytest,rdkit,requests,starlette,starlette_context,typing_extensions,uvicorn

CHANGELOG.md

@@ -0,0 +1,19 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+### Added
+* changelog
+### Changed
+* project structure: source code includes three modules – api, cli and db
+* project dependencies
+* mypy config
+
+## [0.1.0] - 2021-08-08
+### Added
+* a command-line interface for fetching Pubchem data and uploading it to your local MongoDB server;
+* API to interact with local MongoDB data where you can run a substructure search and get the results in two different ways: by page or in the summary form.

mypy.ini

@@ -1,14 +1,22 @@
 [mypy]
 python_version = 3.7
+plugins = pydantic.mypy
 
-[mypy-pytest]
-ignore_missing_imports = True
+follow_imports = silent
+warn_redundant_casts = True
+warn_unused_ignores = True
+disallow_any_generics = True
+check_untyped_defs = True
+no_implicit_reexport = True
 
-[mypy-pymongo.*]
-ignore_missing_imports = True
+[pydantic-mypy]
+init_forbid_extra = True
+init_typed = True
+warn_required_dynamic_aliases = True
+warn_untyped_fields = True
 
-[mypy-rdkit.*]
+[mypy-pytest]
 ignore_missing_imports = True
 
-[mypy-pandas]
+[mypy-rdkit.*]
 ignore_missing_imports = True

molecad/api.py → old/api.py

@@ -4,7 +4,7 @@
 from pydantic import BaseModel, NonNegativeInt, PositiveInt
 
 from .api_db import compound_search, compound_search_summary
-from .settings import settings
+from src.settings import settings
 
 
 class Compound(BaseModel):

molecad/api_db.py → old/api_db.py

@@ -5,7 +5,7 @@
 from pymongo.cursor import Cursor
 from rdkit import Chem
 
-from .settings import settings
+from src.settings import settings
 from .utils import timer
 
 db = settings.get_db()

molecad/cli.py → old/cli.py

@@ -9,7 +9,7 @@
 
 from .cli_db import create_molecule, delete_broken, drop_db, upload_data
 from .downloader import execute_requests
-from .settings import Settings, settings
+from src.settings import Settings, settings
 from .utils import (
     check_dir, chunked, converter, file_path, parse_first_and_last, read_json, timer, write_json,
 )

molecad/cli_db.py → old/cli_db.py

@@ -5,7 +5,7 @@
 from pymongo.collection import Collection
 from rdkit import Chem
 
-from .settings import Settings
+from src.settings import Settings
 
 
 def drop_db(setup: Settings) -> None: