Integrating ruff precommit (#1473)

* added new categories (#1478)

* added new categories

* added try-except

* bugfix list to dictionary

* added output consistency field and blackened code

* Update columns_information.py

* Generalize Standard Run  (#1411)

* Modify header calculation to choose from predefined example output file or standard example output file

* Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function

* Remove unused method

* Make csv serialization work for any kind of model api response

* Remove the standard flag from the CLI since it is now the default run

* Update tests

* Add Ruff as Linter and Formatter

* Unnecessary files removed

* Unnecessary files removed

* Merge sample command with the example command (#1422)

* Merge sample command with the example command

* Fix example command usage

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Generalize Standard Run  (#1411)

* Modify header calculation to choose from predefined example output file or standard example output file

* Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function

* Remove unused method

* Make csv serialization work for any kind of model api response

* Remove the standard flag from the CLI since it is now the default run

* Update tests

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Generalize Standard Run  (#1411)

* Modify header calculation to choose from predefined example output file or standard example output file

* Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function

* Remove unused method

* Make csv serialization work for any kind of model api response

* Remove the standard flag from the CLI since it is now the default run

* Update tests

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Reconfiguring ruff to make it simple

* Generalize Standard Run  (#1411)

* Modify header calculation to choose from predefined example output file or standard example output file

* Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function

* Remove unused method

* Make csv serialization work for any kind of model api response

* Remove the standard flag from the CLI since it is now the default run

* Update tests

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Unnecessary files removed

* Upstream merge

* Ruff importing sorting

* updating readme for linting guidline

* circular import fix

* example command fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* few code fix

* Code fix

* Code fix

* Code fix

* Code fix

* Code fix

* Update close.py

* Update test.py

* Update information.py

* Update test.py

---------

Co-authored-by: Miquel Duran-Frigola <[email protected]>
Co-authored-by: Dhanshree Arora <[email protected]>

.github/scripts/airtableops.py

@@ -1,13 +1,12 @@
 import os
 
-import requests
 import pyairtable
+import requests
 import yaml
 
-from ersilia.hub.content.card import BaseInformation
-from ersilia.hub.content.card import RepoMetadataFile
-from ersilia.utils.terminal import run_command
+from ersilia.hub.content.card import BaseInformation, RepoMetadataFile
 from ersilia.utils.logging import make_temp_dir
+from ersilia.utils.terminal import run_command
 
 GITHUB_ORG = "ersilia-os"
 AIRTABLE_MODEL_HUB_BASE_ID = "appgxpCzCDNyGjWc8"

.github/scripts/convert_airtable_to_json.py

@@ -1,9 +1,10 @@
-import os
 import json
 import logging
+import os
+
 import boto3
-from botocore.exceptions import ClientError, NoCredentialsError
 import requests
+from botocore.exceptions import ClientError, NoCredentialsError
 
 AIRTABLE_MODEL_HUB_BASE_ID = "appgxpCzCDNyGjWc8"
 AIRTABLE_TABLE_ID = "tblZGe2a2XeBxrEHP"

.github/scripts/generate_eos_identifier.py

@@ -1,8 +1,8 @@
+import json
+import os
 import random
 import string
-import json
 import subprocess
-import os
 
 
 def run_command_check_output(cmd):

.github/scripts/place_a_dockerfile_in_current_eos_repo.py

@@ -1,7 +1,8 @@
 import os
+import shutil
 import sys
+
 import requests
-import shutil
 
 BUILD_VERSIONS = ["ersiliapack", "legacy-bentoml", "multistage-condapack"]
 ENV_TYPES = ["conda", "pip"]

.github/scripts/static_version_writer.py

@@ -12,7 +12,7 @@ def wrapper(package_path):
         with open(toml_path, "r") as f:
             toml_content = f.read()
         toml_content = re.sub(
-            'version\s=\s"[0-9\.]+"', f'version = "{version}"', toml_content
+            r'version\s=\s"[0-9\.]+"', f'version = "{version}"', toml_content
         )
         with open(toml_path, "w") as f:
             f.write(toml_content)

.github/scripts/update_metadata.py

@@ -1,9 +1,9 @@
 import json
-import yaml
 import logging
 import os
 import time
 
+import yaml
 from github import Github, GithubException
 
 
@@ -43,7 +43,7 @@ def load_json_input(self):
         This is the JSON data parsed from the new model submission request (GitHub issue)
         :return: dict
         """
-        self.log.info(f"loading JSON input from env vars")
+        self.log.info("loading JSON input from env vars")
 
         # Load the JSON input from the env vars and convert it to a dict
         return json.loads(os.environ.get("JSON"))

.github/scripts/update_model_request_template.py

@@ -1,5 +1,3 @@
-import os
-
 # Paths to the tag files and the model_request template
 tag_file = "ersilia/hub/content/metadata/tag.txt"
 model_request_file = ".github/ISSUE_TEMPLATE/model_request.yml"

.github/scripts/update_model_workflows_from_template.py

@@ -1,7 +1,7 @@
-import sys
 import os
 import shutil
 import subprocess
+import sys
 
 model_repo = sys.argv[1]
 

.github/scripts/upload_model_to_s3.py

@@ -1,4 +1,5 @@
 import sys
+
 from ersilia.publish.s3 import S3BucketRepoUploader
 
 model_id = sys.argv[1]

.github/scripts/write_secrets.py

@@ -1,6 +1,6 @@
+import collections
 import json
 import os
-import collections
 
 OUTPUT = "secrets.json"
 

.github/workflows/pr_check.yml

@@ -5,7 +5,6 @@ on:
     branches: [ master ]
   push:
     branches: [ master ]
-
   workflow_dispatch:
 
 permissions:
@@ -14,42 +13,39 @@ permissions:
 jobs:
   build:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # [email protected]
-
-      - name: Add conda to system path
-        run: echo $CONDA/bin >> $GITHUB_PATH
-
-      - name: Set Python to 3.10.10
-        run:
-         conda install -y python=3.10.10 
-
-      - name: Source conda
-        run: source $CONDA/etc/profile.d/conda.sh
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: "3.10.10"
 
       - name: Install dependencies
         run: |
-          source activate
           conda init
           conda install git-lfs -c conda-forge
           git-lfs install
           conda install gh -c conda-forge
 
       - name: Install Ersilia
         run: |
-          source activate
           python --version
           echo "After conda init"
           conda init
           python -m pip install -e .[test]
 
+      - name: Run Ruff
+        run: ruff check --output-format=github .
+
       - name: Hub catalog
         run: |
           ersilia catalog --hub
 
       - name: Fetch model from GitHub
         run: |
-          source activate
           ersilia -v fetch molecular-weight --from_github
           echo "Serving molecular-weight model."
           ersilia serve molecular-weight --track
@@ -59,7 +55,6 @@ jobs:
 
       - name: Fetch model from S3
         run: |
-          source activate
           ersilia -v fetch molecular-weight --from_s3
           echo "Serving molecular-weight model."
           ersilia serve molecular-weight --track
@@ -69,7 +64,6 @@ jobs:
 
       - name: Fetch model from DockerHub
         run: |
-          source activate
           ersilia -v fetch molecular-weight --from_dockerhub
           echo "Serving molecular-weight model." --track
           ersilia serve molecular-weight
@@ -79,4 +73,4 @@ jobs:
 
       - name: Local catalog
         run: |
-          ersilia catalog --local
+          ersilia catalog --local

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

README.md

@@ -108,6 +108,40 @@ The Ersilia Model Hub is a Free, Open Source Software and we highly value new co
 
 The Ersilia Open Source Initiative adheres to the [Contributor Covenant](https://ersilia.gitbook.io/ersilia-wiki/code-of-conduct) code of conduct.
 
+### Development Guidelines
+
+To maintain consistency and code quality, we follow certain coding and linting standards. Please adhere to these guidelines when contributing:
+
+#### Pre-commit Hooks
+
+We use `pre-commit` and `ruff` to automate code quality checks. Ensure you install and set up `pre-commit` and `ruff` before committing any changes:
+
+1. Install pre-commit: `pip install pre-commit`
+2. Set up pre-commit hooks in your local repository by running:
+   ```bash
+   pre-commit install
+   ```
+3. When you commit it automatically fix the issues but will fail for critical error such as missing docstring on a public class and public methods.
+
+#### Manual with Ruff
+
+1. Run `ruff` to check for linting errors:
+   ```bash
+   ruff check .
+   ```
+2. Automatically fix linting issues (where possible):
+   ```bash
+   ruff check . --fix
+   ```
+
+#### Docstring Style
+
+We adhere to the [NumPy-style docstring format](https://numpydoc.readthedocs.io/en/latest/format.html). Please document all public methods and functions using this style.
+
+Consistent documentation ensures the code is easy to understand and maintain.
+
+Thank you for your contributions and for helping make the Ersilia Model Hub a better project!
+
 ### Submit a New Model
 
 If you want to incorporate a new model in the platform, open a new issue using the [model request template](https://github.com/ersilia-os/ersilia/issues/new?assignees=&labels=new-model&template=model_request.yml&title=%F0%9F%A6%A0+Model+Request%3A+%3Cname%3E) or contact us using the following [form](https://www.ersilia.io/request-model).

conftest.py

@@ -1,9 +1,10 @@
-from test.playground.shared import results
-from rich.table import Table
-from rich.console import Console
-from rich.text import Text
 from rich import box
+from rich.console import Console
 from rich.panel import Panel
+from rich.table import Table
+from rich.text import Text
+
+from test.playground.shared import results
 
 
 def pytest_terminal_summary(terminalreporter, exitstatus, config):

docs/conf.py

@@ -1,9 +1,32 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
 import datetime
 
 project = "Ersilia"
-copyright = f"{datetime.datetime.now().year}, Ersilia Open Source Initiative"
-author = "Miquel Duran-Frigola and Abel Legese"
 
+now = datetime.datetime.now()
+copyright = "{0}, Ersilia Open Source Initiative".format(now.year)
+author = "Miquel Duran-Frigola"
+
+# The short X.Y version
 version = ""
 release = ""
 

ersilia/__init__.py

@@ -1,4 +1,5 @@
 # External imports
+# ruff: noqa
 import os
 from ._version import __version__
 import warnings

ersilia/_version.py

@@ -1,6 +1,6 @@
-from urllib.request import urlopen
 import json
 import os
+from urllib.request import urlopen
 
 STATIC_VERSION_FILE = "_static_version.py"
 PACKAGE_NAME = "ersilia"

ersilia/auth/auth.py

@@ -1,16 +1,12 @@
-"""
-Deal with privileges in Ersilia.
-Base on GitHub login.
-"""
-
-from pathlib import Path
 import os
+from pathlib import Path
+
 import yaml
 
 try:
     from github import Github
     from github.GithubException import UnknownObjectException
-except ModuleNotFoundError as err:
+except ModuleNotFoundError:
     Github = None
     UnknownObjectException = None
 
@@ -19,7 +15,11 @@
 SECRET_REPO = "ersilia-os/ersilia-secrets"
 
 
-class Auth(object):
+class Auth:
+    """
+    This class handles authentication.
+    """
+
     def __init__(self):
         self.hosts_yml = os.path.join(str(Path.home()), ".config", "gh", "hosts.yml")
         if os.path.exists(self.hosts_yml):

ersilia/cli/__init__.py

@@ -1,8 +1,10 @@
+from ..utils.session import create_session_dir
 from .create_cli import create_ersilia_cli
 from .echo import echo
-from ..utils.session import create_session_dir
 
 cli = create_ersilia_cli()
 create_session_dir()
 if __name__ == "__main__":
     cli()
+
+__all__ = ["echo"]