feat: setup Lintes for repo

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "bug( ):"
+labels: bug
+assignees: ""
+---
+
+## Describe the bug
+
+A clear and concise description of what the bug is.
+
+## To Reproduce
+
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+## Expected behavior
+
+A clear and concise description of what you expected to happen.
+
+## Environment
+
+**Desktop (please complete the following information):**
+
+- OS: [e.g. iOS]
+- Version [e.g. 22]
+
+**Python Version (please complete the following information):**
+
+- Version [e.g. 22]
+
+## Additional context
+
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "feat( ):"
+labels: ""
+assignees: ""
+---
+
+## Need
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+## Approach
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+
+## Definition of Done
+
+    • This is what I will demo
+    • This is what it will do.

.github/ISSUE_TEMPLATE/tech-issue.md

@@ -0,0 +1,25 @@
+---
+name: Tech Issue
+about:
+  Engineering-specific technical work that is not product-specific. Engineering
+  team "owns" these issues.
+title: ""
+labels: tech
+assignees: ""
+---
+
+## Motivation
+
+Why is this work important to engineers?
+
+## Definition of Done
+
+What should the end result look like? What will have been changed?
+
+## Tasks
+
+Detail the specific tasks that can be used to accomplish the desired changes.
+If detailed steps cannot be provided at this time, please file a [Tech Proposal](https://docs.google.com/document/d/1o2vuvl-kXwRJN1nBoPzJS_MAQgDGYnjmPZWa4qRDi-I/edit#heading=h.7dvzhm7gqc3v) instead.
+
+- [ ]
+- [ ]

.github/workflows/generate_all_ontology.yml

@@ -3,7 +3,7 @@ name: Updates to Ontology Files
 on:
   push:
     paths:
-      - '**/tools/ontology-builder/ontology-references/owl_info.yml'
+      - "**/tools/ontology-builder/ontology-references/owl_info.yml"
     branches-ignore:
       - main
 

.github/workflows/push-tests.yml

@@ -0,0 +1,27 @@
+name: Push Tests
+
+on:
+  pull_request:
+    branches:
+      - "*"
+  push:
+    branches:
+      - "main"
+
+env:
+  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+permissions:
+  id-token: write
+  contents: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+      - uses: actions/setup-python@v5
+      - name: lint checks
+        uses: pre-commit/action@v3.0.0

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.2.0 # Must be kept in sync with black version in requirements.txt
+    hooks:
+      - id: black
+        stages: [commit]
+        files: ^(api/python|tools)/
+        args: ["--config", "pyproject.toml"]
+        exclude_types: ["json"]
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.2.1
+    hooks:
+      - id: ruff
+        args: ["--config=pyproject.toml", "--fix"]
+        stages: [commit]
+        files: ^(api/python|tools)/
+        exclude_types: ["json"]
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        args: [--write]
+        stages: [commit]
+        exclude_types: ["json"]
+        additional_dependencies:
+          - prettier@3.0.2
+          - prettier-plugin-organize-imports@2.3.3
+          - typescript@4.9.5
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.8.0"
+    hooks:
+      - id: mypy
+        args: [--strict, --ignore-missing-imports]
+        additional_dependencies: [types-PyYAML]

Makefile

@@ -0,0 +1,3 @@
+lint:
+	pre-commit run --all-files
+

PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,17 @@
+## Reason for Change
+
+- #TICKET_NUMBER
+- If the reason for this PR's code changes are not clear in the issue, state value/impact
+
+## Changes
+
+- add
+- remove
+- modify
+
+## Testing steps
+
+- Either list QA steps or reasoning you feel QA is unnecessary
+- Describe how you made sure to know that your changes worked. Should allow someone else to go verify your code without in depth knowledge.
+
+## Notes for Reviewer

README.md

@@ -1,4 +1,5 @@
 # cellxgene-ontology
+
 starter template for CZI open source projects
 
 ## Code of Conduct

pyproject.toml

@@ -0,0 +1,31 @@
+[tool.black]
+line-length = 120
+target_version = ['py38']
+include = '\.pyi?$'
+exclude = '''
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | venv
+    | virtualenv
+    | _build
+    | buck-out
+    | build
+    | dist
+    | vendor
+    | vendor.in
+    | node_modules
+  )/
+)
+'''
+
+[tool.ruff]
+select = ["E", "F", "B", "SIM", "C4", "I"]
+ignore = ["E501", "E402", "C408", ]
+line-length = 120
+target-version = "py38"

tools/ontology-builder/all_ontology_generator.py

@@ -1,18 +1,18 @@
-import env
 import gzip
 import json
 import os
 import re
 import urllib.request
 from threading import Thread
-from typing import List
+from typing import Any, Dict, List
 from urllib.error import HTTPError, URLError
 
+import env
 import owlready2
 import yaml
 
 
-def _download_owls(owl_info_yml: str = env.OWL_INFO_YAML, output_dir: str = env.ONTOLOGY_DIR):
+def _download_owls(owl_info_yml: str = env.OWL_INFO_YAML, output_dir: str = env.ONTOLOGY_DIR) -> None:
     """
     Downloads the ontology owl files specified in 'owl_info_yml' into 'output_dir'
 
@@ -25,7 +25,7 @@ def _download_owls(owl_info_yml: str = env.OWL_INFO_YAML, output_dir: str = env.
     with open(owl_info_yml, "r") as owl_info_handle:
         owl_info = yaml.safe_load(owl_info_handle)
 
-    def download(_ontology, _url):
+    def download(_ontology: str, _url: str) -> None:
         print(f"Start Downloading {_ontology}")
         # Format of owl (handles cases where they are compressed)
         download_format = _url.split(".")[-1]
@@ -58,7 +58,7 @@ def download(_ontology, _url):
         t.join()
 
 
-def _decompress(infile: str, tofile: str):
+def _decompress(infile: str, tofile: str) -> None:
     """
     Decompresses a gziped file
 
@@ -76,7 +76,7 @@ def _parse_owls(
     working_dir: str = env.ONTOLOGY_DIR,
     owl_info_yml: str = env.OWL_INFO_YAML,
     output_json_file: str = env.PARSED_ONTOLOGIES_FILE,
-):
+) -> None:
     """
     Parser all owl files in working_dir. Extracts information from all classes in the owl file.
     The extracted information is written into a gzipped a json file with the following structure:
@@ -118,7 +118,7 @@ def _parse_owls(
             owl_files.append(os.path.join(working_dir, owl_file))
 
     # Parse owl files
-    onto_dict = {}
+    onto_dict: Dict[str, Any] = {}
     for owl_file in owl_files:
         world = owlready2.World()
         onto = world.get_ontology(owl_file)