use absolute imports

backend/favit/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from .models import Favorite
+from favit.models import Favorite
 
 
 @admin.register(Favorite)

backend/favit/models.py

@@ -8,7 +8,7 @@
 from django.db import models
 from django.utils.translation import gettext_lazy as _
 
-from .managers import FavoriteManager
+from favit.managers import FavoriteManager
 
 if TYPE_CHECKING:
     from fpbase.users.models import User

backend/favit/templatetags/favit_tags.py

@@ -2,7 +2,7 @@
 from django.contrib.contenttypes.models import ContentType
 from django.template.loader import render_to_string
 
-from ..models import Favorite
+from favit.models import Favorite
 
 register = template.Library()
 

backend/favit/views.py

@@ -4,10 +4,9 @@
 from django.contrib.auth.decorators import login_required
 from django.http import HttpResponseBadRequest, JsonResponse
 
+from favit.models import Favorite
 from fpbase.util import uncache_protein_page
 
-from .models import Favorite
-
 logger = logging.getLogger(__name__)
 
 

backend/fpbase/__init__.py

@@ -1,6 +1,6 @@
 # This will make sure the app is always imported when
 # Django starts so that shared_task will use this app.
-from .celery import app as celery_app
+from fpbase.celery import app as celery_app
 
 __version__ = "0.1.0"
 __version_info__ = tuple([int(num) if num.isdigit() else num for num in __version__.replace("-", ".", 1).split(".")])

backend/fpbase/users/admin.py

@@ -8,7 +8,7 @@
 from django.urls import reverse
 from django.utils.safestring import mark_safe
 
-from .models import User
+from fpbase.users.models import User
 
 
 class MyUserChangeForm(UserChangeForm):

backend/fpbase/users/api/views.py

@@ -5,7 +5,7 @@
 from rest_framework.response import Response
 from rest_framework.viewsets import GenericViewSet
 
-from .serializers import UserSerializer
+from fpbase.users.api.serializers import UserSerializer
 
 User = get_user_model()
 

backend/fpbase/users/urls.py

@@ -1,7 +1,7 @@
 from django.contrib.admin.views.decorators import staff_member_required
 from django.urls import path, re_path
 
-from . import views
+from fpbase.users import views
 
 app_name = "users"
 urlpatterns = [

backend/fpbase/users/views.py

@@ -2,7 +2,7 @@
 from django.urls import reverse
 from django.views.generic import DetailView, ListView, RedirectView, UpdateView
 
-from .models import User
+from fpbase.users.models import User
 
 
 class UserDetailView(LoginRequiredMixin, DetailView):

backend/fpseq/__init__.py

@@ -1,8 +1,8 @@
-from .align import SequenceAlignment, align_seqs
-from .fpseq import FPSeq, from_fpbase
-from .mutations import Mutation, MutationSet, get_mutations, mutate_sequence
-from .skbio_protein import SkbSequence
-from .util import protein_weight
+from fpseq.align import SequenceAlignment, align_seqs
+from fpseq.fpseq import FPSeq, from_fpbase
+from fpseq.mutations import Mutation, MutationSet, get_mutations, mutate_sequence
+from fpseq.skbio_protein import SkbSequence
+from fpseq.util import protein_weight
 
 __all__ = [
     "FPSeq",

backend/fpseq/align.py

@@ -9,7 +9,7 @@
 from Bio import Align
 from Bio.Align import substitution_matrices
 
-from .util import chunked_lines
+from fpseq.util import chunked_lines
 
 
 def align_seqs(query, target, gop=5, gep=1, band_size=0):
@@ -223,7 +223,7 @@ def as_mutations(self, reference=None):
         MutationSet
             Set of mutations between sequences
         """
-        from .mutations import MutationSet, _get_aligned_muts
+        from fpseq.mutations import MutationSet, _get_aligned_muts
 
         seq1, seq2 = self
         mutstring = "/".join(_get_aligned_muts(seq1, seq2))

backend/fpseq/fpseq.py

@@ -2,10 +2,10 @@
 
 import requests
 
-from .align import align_seqs, parental_numbering
-from .mutations import get_mutations, mutate_sequence
-from .skbio_protein import SkbSequence
-from .util import protein_weight, slugify
+from fpseq.align import align_seqs, parental_numbering
+from fpseq.mutations import get_mutations, mutate_sequence
+from fpseq.skbio_protein import SkbSequence
+from fpseq.util import protein_weight, slugify
 
 
 def generate_labels(seq, mods=None, zeroindex=1):

backend/fpseq/mutations.py

@@ -38,8 +38,8 @@
 
 import numpy as np
 
-from .align import align_seqs, parental_numbering
-from .skbio_protein import SkbSequence
+from fpseq.align import align_seqs, parental_numbering
+from fpseq.skbio_protein import SkbSequence
 
 if TYPE_CHECKING:
     from collections.abc import Sequence

backend/fpseq/skbio_protein.py

@@ -36,7 +36,7 @@
 
 import numpy as np
 
-from .util import chunk_string
+from fpseq.util import chunk_string
 
 
 class classproperty(property):

backend/proteins/api/urls.py

@@ -2,7 +2,7 @@
 from django.views.generic import TemplateView
 from django.views.generic.base import RedirectView
 
-from . import views
+from proteins.api import views
 
 app_name = "api"
 

backend/proteins/api/views.py

@@ -15,11 +15,7 @@
 
 import proteins.models as pm
 from fpbase.cache_utils import get_model_version
-
-from ..filters import ProteinFilter, SpectrumFilter, StateFilter
-from ..models.microscope import get_cached_optical_configs
-from ..models.spectrum import get_cached_spectra_info
-from .serializers import (
+from proteins.api.serializers import (
     BasicProteinSerializer,
     ProteinSerializer,
     ProteinSerializer2,
@@ -28,6 +24,9 @@
     SpectrumSerializer,
     StateSerializer,
 )
+from proteins.filters import ProteinFilter, SpectrumFilter, StateFilter
+from proteins.models.microscope import get_cached_optical_configs
+from proteins.models.spectrum import get_cached_spectra_info
 
 
 def _spectra_etag(request: HttpRequest) -> str:

backend/proteins/fields.py

@@ -3,7 +3,7 @@
 from django.core.exceptions import ValidationError
 from django.db.models import Lookup, TextField, fields
 
-from .util.helpers import wave_to_hex
+from proteins.util.helpers import wave_to_hex
 
 
 class Around(Lookup):

backend/proteins/filters.py

@@ -3,8 +3,8 @@
 from django import forms
 from django_filters import rest_framework as filters
 
-from .models import Organism, Protein, Spectrum, State
-from .validators import cdna_sequence_validator
+from proteins.models import Organism, Protein, Spectrum, State
+from proteins.validators import cdna_sequence_validator
 
 
 class SpectrumFilter(filters.FilterSet):

backend/proteins/forms/microscope.py

@@ -6,20 +6,8 @@
 from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
 from django.forms.models import inlineformset_factory
 
-from ..models import (
-    Camera,
-    Filter,
-    FilterPlacement,
-    Light,
-    Microscope,
-    OpticalConfig,
-    ProteinCollection,
-)
-from ..util.importers import (
-    add_filter_to_database,
-    check_chroma_for_part,
-    check_semrock_for_part,
-)
+from proteins.models import Camera, Filter, FilterPlacement, Light, Microscope, OpticalConfig, ProteinCollection
+from proteins.util.importers import add_filter_to_database, check_chroma_for_part, check_semrock_for_part
 
 User = get_user_model()
 

backend/proteins/index.py

@@ -1,7 +1,7 @@
 from algoliasearch_django import AlgoliaIndex
 from algoliasearch_django.decorators import register
 
-from .models import Organism, Protein
+from proteins.models import Organism, Protein
 
 
 @register(Protein)

backend/proteins/models/__init__.py

@@ -1,18 +1,18 @@
-from .bleach import BleachMeasurement
-from .collection import ProteinCollection
-from .dye import Dye, DyeState
-from .efficiency import OcFluorEff
-from .excerpt import Excerpt
-from .fluorescence_measurement import FluorescenceMeasurement
-from .fluorophore import FluorState
-from .lineage import Lineage
-from .microscope import FilterPlacement, Microscope, OpticalConfig
-from .organism import Organism
-from .oser import OSERMeasurement
-from .protein import Protein, State
-from .snapgene import SnapGenePlasmid
-from .spectrum import Camera, Filter, Light, Spectrum
-from .transition import StateTransition
+from proteins.models.bleach import BleachMeasurement
+from proteins.models.collection import ProteinCollection
+from proteins.models.dye import Dye, DyeState
+from proteins.models.efficiency import OcFluorEff
+from proteins.models.excerpt import Excerpt
+from proteins.models.fluorescence_measurement import FluorescenceMeasurement
+from proteins.models.fluorophore import FluorState
+from proteins.models.lineage import Lineage
+from proteins.models.microscope import FilterPlacement, Microscope, OpticalConfig
+from proteins.models.organism import Organism
+from proteins.models.oser import OSERMeasurement
+from proteins.models.protein import Protein, State
+from proteins.models.snapgene import SnapGenePlasmid
+from proteins.models.spectrum import Camera, Filter, Light, Spectrum
+from proteins.models.transition import StateTransition
 
 __all__ = [
     "BleachMeasurement",

backend/proteins/schema/__init__.py

@@ -1,3 +1,3 @@
-from .query import Query
+from proteins.schema.query import Query
 
 __all__ = ["Query"]

backend/proteins/schema/query.py

@@ -5,10 +5,10 @@
 from graphene_django.filter import DjangoFilterConnectionField
 from graphql import FieldNode, GraphQLError, GraphQLResolveInfo
 
-from .. import models
-from ..filters import ProteinFilter
-from ..models.spectrum import get_spectra_list
-from . import relay, types
+from proteins import models
+from proteins.filters import ProteinFilter
+from proteins.models.spectrum import get_spectra_list
+from proteins.schema import relay, types
 
 
 def get_cached_spectrum(id, timeout=60 * 60 * 24):

backend/proteins/schema/relay.py

@@ -1,7 +1,7 @@
 import graphene
 
-from .. import models
-from .types import Protein
+from proteins import models
+from proteins.schema.types import Protein
 
 
 class ProteinNode(Protein):

backend/proteins/schema/types.py

@@ -5,10 +5,9 @@
 from graphene_django.converter import get_choices
 from graphene_django.types import DjangoObjectType
 
+from proteins import models
 from references.schema import Reference
 
-from .. import models
-
 
 def nullable_enum_from_field(_model, _field):
     field = _model._meta.get_field(_field)

backend/proteins/tasks.py

@@ -1,7 +1,7 @@
 from celery import shared_task
 from sentry_sdk import capture_exception
 
-from .util.helpers import forster_list
+from proteins.util.helpers import forster_list
 
 
 @shared_task

backend/proteins/urls.py

@@ -4,8 +4,7 @@
 from django.views.generic import TemplateView
 
 from fpbase.decorators import login_required_message_and_redirect as login_required
-
-from . import views
+from proteins import views
 
 app_name = "proteins"
 

backend/proteins/util/__init__.py

@@ -1,4 +1,4 @@
-from .blurb import long_blurb
-from .helpers import getprot
+from proteins.util.blurb import long_blurb
+from proteins.util.helpers import getprot
 
 __all__ = ["getprot", "long_blurb"]

backend/proteins/util/blast.py

@@ -9,7 +9,7 @@
 from shutil import copyfileobj
 from subprocess import run
 
-from ..models import Protein
+from proteins.models import Protein
 
 ROOT = Path(__file__).parent.parent.parent
 BIN_DIR = ROOT / "bin"

backend/proteins/util/helpers.py

@@ -331,7 +331,7 @@ def forster_list():
 
     from django.core.cache import cache
 
-    from ..models import Protein
+    from proteins.models import Protein
 
     # Try to get cached results first
     cache_key = "forster_list_results"

backend/proteins/util/importers.py

@@ -7,7 +7,7 @@
 from django.core.validators import URLValidator
 from django.template.defaultfilters import slugify
 
-from ..models import Filter
+from proteins.models import Filter
 
 ############################################
 #       Importing Tools
@@ -266,7 +266,7 @@ def text_to_spectra(text, wavecol=0):
 
 
 def import_chroma_spectra(part=None, url=None, **kwargs):
-    from ..util.spectra_import import import_spectral_data
+    from proteins.util.spectra_import import import_spectral_data
 
     if isinstance(part, str):
         text = fetch_chroma_part(part)
@@ -305,7 +305,7 @@ def import_chroma_spectra(part=None, url=None, **kwargs):
 
 
 def import_semrock_spectra(part=None, **kwargs):
-    from ..util.spectra_import import import_spectral_data
+    from proteins.util.spectra_import import import_spectral_data
 
     if isinstance(part, str):
         part = normalize_semrock_part(part)

backend/proteins/util/maintain.py

@@ -91,7 +91,7 @@ def check_lineages(qs=None, correct_offset=False):
     good = set()
 
     if not qs:
-        from ..models import Lineage
+        from proteins.models import Lineage
 
         qs = Lineage.objects.all()
 

backend/proteins/util/spectra.py

@@ -6,7 +6,7 @@
 import numpy as np
 from django.http import HttpResponse
 
-from . import _scipy as scipy
+from proteins.util import _scipy as scipy
 
 if TYPE_CHECKING:
     from collections.abc import Iterable