Add ruff (libAtoms#120)

* Add pre-commit and ruff dependencies

* Add pre-commit

* Add pre-commit CI

* Apply pre-commit

* Apply ruff format and fixes

* Apply ruff unsafe fixes

* Update ruff

* Update ruff

* Apply ruff fixes

---------

Co-authored-by: ElliottKasoar <[email protected]>

Author: ElliottKasoar

.github/workflows/ci.yml

@@ -4,7 +4,7 @@ on: [ push, pull_request ]
 
 jobs:
 
-  build:
+  tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -35,3 +35,25 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install poetry
+        run: pipx install poetry
+
+      - name: Install python dependencies
+        run: |
+          poetry env use 3.11
+          poetry install --with pre-commit,dev
+
+      - name: Run pre-commit
+        run: |
+          poetry run pre-commit install
+          poetry run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+# Install pre-commit hooks via:
+# pre-commit install
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+    - id: check-json
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.9.6
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

Dockerfile

@@ -13,5 +13,3 @@ RUN python setup.py develop
 #CMD ["/bin/bash"]
 CMD [ "python", "abcd/server/__init__.py" ]
 #CMD ["gunicorn", "-w 4", "-b 0.0.0.0:8000", "server:app"]
-
-

README.md

@@ -3,17 +3,17 @@
 [![Doc](https://img.shields.io/badge/docs-master-green.svg)](https://libatoms.github.io/abcd/)
 [![Build Status](https://travis-ci.org/libAtoms/abcd.svg?branch=master)](https://travis-ci.org/libAtoms/abcd)
 
-Database storage and discovery of atomistic data. 
+Database storage and discovery of atomistic data.
 
 Take a look at the `examples.md` file for.. examples!
 
 Main features:
 
-- Configurations that consist of atom positions, elements, forces, and various metadata are stored as a dictionary by a MongoDB backend. 
-- There is no predefined schema, any combination of keys are allowed for all configurations. 
-- Two modes: "discovery" and "download". Both use filter-type queries, but in "discovery" mode, summary statistics of the configurations that pass the filter are reported. In "download" mode, the matching configurations are downloaded and exported to a file. 
-- The "discovery" mode can be used to learn what keys exist in the set of configurations that have passed the current quiery filter. The user can use this to refine the query. 
-- Complex queries on dictionary key-value pairs are allowed, and their logical combinations. 
+- Configurations that consist of atom positions, elements, forces, and various metadata are stored as a dictionary by a MongoDB backend.
+- There is no predefined schema, any combination of keys are allowed for all configurations.
+- Two modes: "discovery" and "download". Both use filter-type queries, but in "discovery" mode, summary statistics of the configurations that pass the filter are reported. In "download" mode, the matching configurations are downloaded and exported to a file.
+- The "discovery" mode can be used to learn what keys exist in the set of configurations that have passed the current quiery filter. The user can use this to refine the query.
+- Complex queries on dictionary key-value pairs are allowed, and their logical combinations.
 
 ## Installation
 
@@ -24,13 +24,13 @@ $ pip install git+https://github.com/libAtoms/abcd.git
 
 ## Setup
 
-If you have an already running mongo server, or install your own, they you are ready to go. Alternatively, 
+If you have an already running mongo server, or install your own, they you are ready to go. Alternatively,
 
 ```
 docker run -d --rm --name abcd-mongodb -v <path-on-your-machine-to-store-database>:/data/db -p 27017:27017 mongo
 ```
 
-will download and install a docker and run a database in it. 
+will download and install a docker and run a database in it.
 
 To connect to a mongodb that is already running, use
 ```
@@ -56,7 +56,7 @@ You can set up an `abcd` user on your machine where the database is running, and
 command="/path/to/abcd --remote  ${SSH_ORIGINAL_COMMAND}",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty ssh-rsa <public-key> your@email
 ```
 
-Then you'll be able to access the database remotely using, e.g. 
+Then you'll be able to access the database remotely using, e.g.
 ```
 ssh [email protected] summary
 ```
@@ -74,18 +74,18 @@ To access it:
     docker pull stenczelt/projection-abcd:latest
     ```
 
-2. create a docker network, which enables the containers to communicate with each other and the outside world as well 
+2. create a docker network, which enables the containers to communicate with each other and the outside world as well
     ```
     docker network create --driver bridge abcd-network
     ```
 
 3. run the mongo (ABCD) and the visualiser as well
     ```
     docker run -d --rm --name abcd-mongodb-net -v <path-on-your-machine-to-store-database>:/data/db -p 27017:27017 --network abcd-network mongo
-    
+
     docker run -it --rm --name visualiser-dev -p 9999:9999 --network abcd-network stenczelt/projection-abcd
     ```
-    NB: You need a a directory where the database files are kept locally and you need to connect this to the mongo 
+    NB: You need a a directory where the database files are kept locally and you need to connect this to the mongo
     container. More info about this can be found in the original ABCD repo
 
 This will start the visualiser with ABCD integration! Have fun!

abcd/__init__.py

@@ -1,6 +1,6 @@
+from enum import Enum
 import logging
 from urllib import parse
-from enum import Enum
 
 logger = logging.getLogger(__name__)
 
@@ -10,7 +10,7 @@ class ConnectionType(Enum):
     http = 2
 
 
-class ABCD(object):
+class ABCD:
     @classmethod
     def from_config(cls, config):
         # Factory method
@@ -24,7 +24,6 @@ def from_url(cls, url, **kwargs):
         logger.info(r)
 
         if r.scheme == "mongodb":
-
             conn_settings = {
                 "host": r.hostname,
                 "port": r.port,
@@ -39,20 +38,19 @@ def from_url(cls, url, **kwargs):
             from abcd.backends.atoms_pymongo import MongoDatabase
 
             return MongoDatabase(db_name=db, **conn_settings, **kwargs)
-        elif r.scheme == "mongodb+srv":
+        if r.scheme == "mongodb+srv":
             db = r.path.split("/")[1] if r.path else None
             db = db if db else "abcd"
             from abcd.backends.atoms_pymongo import MongoDatabase
 
             return MongoDatabase(db_name=db, host=r.geturl(), uri_mode=True, **kwargs)
-        elif r.scheme == "http" or r.scheme == "https":
+        if r.scheme == "http" or r.scheme == "https":
             raise NotImplementedError("http not yet supported! soon...")
-        elif r.scheme == "ssh":
+        if r.scheme == "ssh":
             raise NotImplementedError("ssh not yet supported! soon...")
-        else:
-            raise NotImplementedError(
-                "Unable to recognise the type of connection. (url: {})".format(url)
-            )
+        raise NotImplementedError(
+            f"Unable to recognise the type of connection. (url: {url})"
+        )
 
 
 if __name__ == "__main__":
@@ -62,11 +60,3 @@ def from_url(cls, url, **kwargs):
     url = "mongodb://mongoadmin:secret@localhost:27017/abcd_new"
     abcd = ABCD.from_url(url)
     abcd.print_info()
-
-    # from ase.io import iread
-    # for atoms in iread('../tutorials/data/bcc_bulk_54_expanded_2_high.xyz', index=slice(1)):
-    #     # Hack to fix the representation of forces
-    #     atoms.calc.results['forces'] = atoms.arrays['force']
-    #
-    #     abcd.push(atoms)
-    #     print(atoms)

abcd/backends/atoms_http.py

@@ -1,10 +1,10 @@
 import json
 import logging
-import requests
 from os import linesep
-from typing import List
 
 import ase
+import requests
+
 from abcd.backends.abstract import Database
 
 logger = logging.getLogger(__name__)
@@ -44,17 +44,15 @@ def pull(self, query=None, properties=None):
     def query(self, query_string):
         pass
 
-    def search(self, query_string: str) -> List[str]:
-        results = requests.get(self.url + "/calculation").json()
-        return results
+    def search(self, query_string: str) -> list[str]:
+        return requests.get(self.url + "/calculation").json()
 
     def get_atoms(self, id: str) -> Atoms:
-        data = requests.get(self.url + "/calculation/{}".format(id)).json()
-        atoms = Atoms.from_dict(data)
-        return atoms
+        data = requests.get(self.url + f"/calculation/{id}").json()
+        return Atoms.from_dict(data)
 
     def __repr__(self):
-        return "ABCD(type={}, url={}, ...)".format(self.__class__.__name__, self.url)
+        return f"ABCD(type={self.__class__.__name__}, url={self.url}, ...)"
 
     def _repr_html_(self):
         """jupyter notebook representation"""
@@ -67,9 +65,7 @@ def print_info(self):
             [
                 "{:=^50}".format(" ABCD Database "),
                 "{:>10}: {}".format("type", "remote (http/https)"),
-                linesep.join(
-                    "{:>10}: {}".format(k, v) for k, v in self.db.info().items()
-                ),
+                linesep.join(f"{k:>10}: {v}" for k, v in self.db.info().items()),
             ]
         )