switch to uv (#229)

* use uv

* py311

* uv export

* linting

* tests

* change ci

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* version latest

* uv sync step

* add token

* rename job

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/ci.yml

@@ -18,9 +18,8 @@ concurrency:
 
 jobs:
   # With no caching at all the entire ci process takes 4m 30s to complete!
-  pytest:
+  test:
     runs-on: ubuntu-latest
-
     services:
       redis:
         image: redis:6
@@ -32,59 +31,51 @@ jobs:
           - 5432:5432
         env:
           POSTGRES_PASSWORD: postgres
-
     env:
       CELERY_BROKER_URL: "redis://localhost:6379/0"
       # postgres://user:password@host:port/database
       DATABASE_URL: "postgres://postgres:postgres@localhost:5432/postgres"
-
+      UV_FROZEN: 1
     steps:
       - name: Checkout Code Repository
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v1
         with:
-          python-version: "3.11.4"
-          cache: pip
-          cache-dependency-path: |
-            backend/requirements/base.txt
-            backend/requirements/local.txt
+          version: latest
+          enable-cache: true
 
       - uses: pnpm/action-setup@v4
         name: Install pnpm
         with:
           version: latest
           run_install: false
 
-      - name: Get pnpm store directory
-        id: pnpm-cache
-        shell: bash
-        run: echo "STORE_PATH=$(pnpm store path)" >> $GITHUB_OUTPUT
-
-      - uses: actions/cache@v4
-        name: Setup pnpm cache
+      - name: Install Node.js
+        uses: actions/setup-node@v4
         with:
-          path: ${{ steps.pnpm-cache.outputs.STORE_PATH }}
-          key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
-          restore-keys: ${{ runner.os }}-pnpm-store-
+          node-version-file: package.json
+          cache: "pnpm"
 
-      - name: Install Dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -r backend/requirements/local.txt
-          pnpm install
+      - name: Install node Dependencies
+        run: pnpm install
+
+      - run: uv sync
 
       - name: setup-chromedriver
         uses: nanasess/setup-chromedriver@v2
 
-      - name: Test with pytest
-        working-directory: backend
+      - name: Configure headless display
         run: |
-          export DISPLAY=:99
-          chromedriver --url-base=/wd/hub &
-          sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 & # optional
-          pytest --color=yes -v --cov --cov-report=xml --cov-report=term-missing
+          echo "DISPLAY=:99.0" >> $GITHUB_ENV
+          Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
+          sleep 3
+
+      - name: Test
+        run: uv run pytest --color=yes -v --cov --cov-report=xml --cov-report=term-missing
 
       - name: coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -4,12 +4,12 @@ ci:
   skip: []
   submodules: false
 
-exclude: '^docs/|/migrations/'
-default_stages: [commit]
+exclude: "^docs/|/migrations/"
+default_stages: [pre-commit]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -20,6 +20,12 @@ repos:
       - id: check-docstring-first
       - id: detect-private-key
 
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.6.0
+    hooks:
+      - id: uv-export
+        args: ["--group", "prod", "--no-dev", "--frozen", "--output-file=requirements.txt"]
+
   # - repo: https://github.com/pre-commit/mirrors-prettier
   #   rev: v3.0.0-alpha.9-for-vscode
   #   hooks:
@@ -33,14 +39,14 @@ repos:
   #     - id: djlint-django
 
   - repo: https://github.com/adamchainz/django-upgrade
-    rev: '1.21.0'
+    rev: "1.23.1"
     hooks:
       - id: django-upgrade
-        args: ['--target-version', '4.2']
+        args: ["--target-version", "4.2"]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.6.7'
+    rev: "v0.9.6"
     hooks:
       - id: ruff
-        args: ['--fix']
+        args: ["--fix", "--unsafe-fixes"]
       - id: ruff-format

.python-version

@@ -0,0 +1 @@
+3.11

backend/config/api_router.py

@@ -1,8 +1,9 @@
-import proteins.api.urls
 from django.conf import settings
-from fpbase.users.api.views import UserViewSet
 from rest_framework.routers import DefaultRouter, SimpleRouter
 
+import proteins.api.urls
+from fpbase.users.api.views import UserViewSet
+
 if settings.DEBUG:
     router = DefaultRouter()
 else:

backend/config/settings/production.py

@@ -199,7 +199,7 @@
     "disable_existing_loggers": True,
     "root": {"level": "WARNING"},
     "formatters": {
-        "verbose": {"format": "%(levelname)s %(asctime)s %(module)s " "%(process)d %(thread)d %(message)s"},
+        "verbose": {"format": "%(levelname)s %(asctime)s %(module)s %(process)d %(thread)d %(message)s"},
     },
     "handlers": {
         "console": {

backend/config/urls.py

@@ -1,4 +1,3 @@
-import fpbase.views
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
@@ -10,6 +9,9 @@
 from django.views.generic import TemplateView
 from django.views.generic.base import RedirectView
 from drf_spectacular.views import SpectacularAPIView, SpectacularSwaggerView
+from graphene_django.views import GraphQLView
+
+import fpbase.views
 from fpbase.sitemaps import (
     AuthorsSitemap,
     MicroscopeSitemap,
@@ -19,7 +21,6 @@
     ReferencesSitemap,
     StaticSitemap,
 )
-from graphene_django.views import GraphQLView
 from references.views import ReferenceListView
 
 sitemaps = {

backend/favit/views.py

@@ -1,6 +1,7 @@
 from django.apps import apps
 from django.contrib.auth.decorators import login_required
 from django.http import HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
+
 from fpbase.util import is_ajax, uncache_protein_page
 
 from .models import Favorite

backend/fpbase/forms.py

@@ -29,7 +29,7 @@ def friendly_email(self):
 
     def send_email(self):
         EmailMessage(
-            f'FPbase contact from {self.cleaned_data["name"]}',
+            f"FPbase contact from {self.cleaned_data['name']}",
             self.cleaned_data["message"],
             to=[a[1] for a in settings.ADMINS],
             headers={"Reply-To": self.friendly_email()},

backend/fpbase/schema.py

@@ -1,4 +1,5 @@
 import graphene
+
 import proteins.schema
 import references.schema
 

backend/fpbase/sitemaps.py

@@ -1,5 +1,6 @@
 from django.contrib.sitemaps import Sitemap
 from django.urls import reverse
+
 from proteins.models import Microscope, Organism, Protein, ProteinCollection
 from references.models import Author, Reference
 

backend/fpbase/tests/test_end2end.py

@@ -5,14 +5,15 @@
 import pytest
 from django.contrib.staticfiles.testing import StaticLiveServerTestCase
 from django.urls import reverse
-from proteins.factories import MicroscopeFactory, OpticalConfigWithFiltersFactory, ProteinFactory
-from proteins.models.protein import Protein
-from proteins.util.blast import _get_binary
 from selenium import webdriver
 from selenium.webdriver.common.keys import Keys
 from selenium.webdriver.support.ui import Select
 from selenium.webdriver.support.wait import WebDriverWait
 
+from proteins.factories import MicroscopeFactory, OpticalConfigWithFiltersFactory, ProteinFactory
+from proteins.models.protein import Protein
+from proteins.util.blast import _get_binary
+
 SEQ = "MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFS"
 # reverse translation of DGDVNGHKFSVSGEGEGDATYGKLTLKFICT
 cDNA = "gatggcgatgtgaacggccataaatttagcgtgagcggcgaaggcgaaggcgatgcgacctatggcaaactgaccctgaaatttatttgcacc"
@@ -48,13 +49,8 @@ def _load_reverse(self, url_name, **kwargs):
 
     def _assert_no_console_errors(self):
         logs = self.browser.get_log("browser")
-        acceptable_errors = (
-            "GPU stall due to ReadPixels",
-            "favicon.ico",
-            "Failed to decode downloaded font",
-        )
         for lg in logs:
-            if all(err not in lg["message"] for err in acceptable_errors):
+            if lg["level"] == "SEVERE":
                 raise AssertionError(f"Console errors occurred: {logs}")
 
     def test_spectra(self):

backend/fpbase/tests/test_schema.py

@@ -1,6 +1,7 @@
 import json
 
 from graphene_django.utils.testing import GraphQLTestCase
+
 from proteins import models
 
 from ..schema import schema

backend/fpbase/views.py

@@ -4,10 +4,10 @@
 from django.views.decorators.cache import cache_page
 from django.views.generic import TemplateView
 from django.views.generic.edit import FormView
-from proteins.models import Protein, Spectrum
 from sentry_sdk import last_event_id
 
 from fpbase.forms import ContactForm
+from proteins.models import Protein, Spectrum
 
 
 class HomeView(TemplateView):

backend/fpseq/__init__.py

@@ -6,12 +6,12 @@
 
 __all__ = [
     "FPSeq",
-    "from_fpbase",
-    "SkbSequence",
-    "ParasailAlignment",
-    "align_seqs",
     "Mutation",
     "MutationSet",
+    "ParasailAlignment",
+    "SkbSequence",
+    "align_seqs",
+    "from_fpbase",
     "get_mutations",
     "mutate_sequence",
     "protein_weight",

backend/fpseq/skbio_protein.py

@@ -138,7 +138,7 @@ def _munge_to_sequence(self, other, method):
         if isinstance(other, SkbSequence):
             if type(other) is not type(self):
                 raise TypeError(
-                    f"Cannot use {self.__class__.__name__} and " f"{other.__class__.__name__} together with `{method}`"
+                    f"Cannot use {self.__class__.__name__} and {other.__class__.__name__} together with `{method}`"
                 )
             else:
                 return other
@@ -216,8 +216,7 @@ def __getitem__(self, indexable):
 
         if isinstance(indexable, np.ndarray) and indexable.dtype == bool and len(indexable) != len(self):
             raise IndexError(
-                "An boolean vector index must be the same length"
-                " as the sequence (%d, not %d)." % (len(self), len(indexable))
+                f"An boolean vector index must be the same length as the sequence ({len(self)}, not {len(indexable)})."
             )
 
         if isinstance(indexable, np.ndarray) and indexable.size == 0:
@@ -362,6 +361,6 @@ def _slices_from_iter(array, indexables):
         elif _is_single_index(i):
             i = _single_index_to_slice(i)
         else:
-            raise IndexError("Cannot slice sequence from iterable " f"containing {i!r}.")
+            raise IndexError(f"Cannot slice sequence from iterable containing {i!r}.")
 
         yield array[i]

backend/proteins/admin.py

@@ -4,11 +4,11 @@
 from django.forms import TextInput
 from django.urls import reverse
 from django.utils.safestring import mark_safe
-from fpbase.util import uncache_protein_page
 from mptt.admin import MPTTModelAdmin
 from reversion.admin import VersionAdmin
 from reversion_compare.admin import CompareVersionAdmin
 
+from fpbase.util import uncache_protein_page
 from proteins.models import (
     BleachMeasurement,
     Camera,

backend/proteins/extrest/entrez.py

@@ -6,6 +6,7 @@
 
 from Bio import Entrez, SeqIO
 from django.core.cache import cache
+
 from references.helpers import pmid2doi
 
 logger = logging.getLogger(__name__)
@@ -129,9 +130,9 @@ def fetch_ipg_sequence(protein_name=None, uid=None):
     assert len(record) == 1, "More than one record returned from protein database"
     record = record[0]
     prot_seq = record["GBSeq_sequence"].upper()
-    assert len(prot_seq) == int(
-        seq_len
-    ), f"Protein database sequence different length {len(prot_seq)} than IPG database{int(seq_len)}"
+    assert len(prot_seq) == int(seq_len), (
+        f"Protein database sequence different length {len(prot_seq)} than IPG database{int(seq_len)}"
+    )
     return (ipg_uid, prot_seq)
 
 

backend/proteins/factories.py

@@ -5,8 +5,8 @@
 import factory.fuzzy
 import numpy as np
 from django.utils.text import slugify
-from fpseq import FPSeq
 
+from fpseq import FPSeq
 from proteins.util.helpers import wave_to_hex
 
 from .models import Filter, FilterPlacement, Microscope, OpticalConfig, Protein, Spectrum, State

backend/proteins/forms/forms.py

@@ -7,7 +7,6 @@
 from django.forms.models import inlineformset_factory  # ,BaseInlineFormSet
 from django.utils.safestring import mark_safe
 from django.utils.text import slugify
-from references.models import Reference  # breaks application modularity
 
 from proteins.models import (
     BleachMeasurement,
@@ -18,6 +17,7 @@
     StateTransition,
 )
 from proteins.validators import protein_sequence_validator, validate_doi
+from references.models import Reference  # breaks application modularity
 
 
 def popover_html(label, content, side="right"):
@@ -390,7 +390,7 @@ def clean(self):
         parent = self.cleaned_data.get("parent")
         mutation = self.cleaned_data.get("mutation")
         if (parent and not mutation) or (mutation and not parent):
-            raise forms.ValidationError("Both parent and mutation are " "required when providing lineage information")
+            raise forms.ValidationError("Both parent and mutation are required when providing lineage information")
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)