chipexo sig task test passing

cmatKhan · Dec 16, 2023 · 26e82a7 · 26e82a7
1 parent b1e25fe
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diff --git a/README.md b/README.md
@@ -59,6 +59,10 @@ To run the tests, check your test coverage, and generate an HTML coverage report
   pytest
 ```
 
+**NOTE**: if major changes are made to the database, it may be necesary to
+remove `--reuse-db` from the `addopts` key of the pytest section of
+`pyproject.toml`. It can be added back after a run without it.
+
 ### Live reloading and Sass CSS compilation
 
 Moved to [Live reloading and SASS compilation](https://cookiecutter-django.readthedocs.io/en/latest/developing-locally.html#sass-compilation-live-reloading).

diff --git a/config/api_router.py b/config/api_router.py
@@ -3,12 +3,11 @@
 
 from yeastregulatorydb.regulatory_data.api.views import (
     BindingManualQCViewSet,
-    BindingSourceViewSet,
     BindingViewSet,
     CallingCardsBackgroundViewSet,
     ChrMapViewSet,
+    DataSourceViewSet,
     ExpressionManualQCViewSet,
-    ExpressionSourceViewSet,
     ExpressionViewSet,
     FileFormatViewSet,
     GenomicFeatureViewSet,
@@ -25,12 +24,11 @@
 
 router.register("users", UserViewSet)
 router.register("bindingmanualqc", BindingManualQCViewSet)
-router.register("bindingsource", BindingSourceViewSet)
+router.register("datasource", DataSourceViewSet)
 router.register("binding", BindingViewSet)
 router.register("callingcardsbackground", CallingCardsBackgroundViewSet)
 router.register("chrmap", ChrMapViewSet)
 router.register("expressionmanualqc", ExpressionManualQCViewSet)
-router.register("expressionsource", ExpressionSourceViewSet)
 router.register("expression", ExpressionViewSet)
 router.register("fileformat", FileFormatViewSet)
 router.register("genomicfeature", GenomicFeatureViewSet)

diff --git a/docs/api/yeastregulatorydb.regulatory_data.api.serializers.rst b/docs/api/yeastregulatorydb.regulatory_data.api.serializers.rst
@@ -20,14 +20,6 @@ yeastregulatorydb.regulatory\_data.api.serializers.BindingSerializer module
    :undoc-members:
    :show-inheritance:
 
-yeastregulatorydb.regulatory\_data.api.serializers.BindingSourceSerializer module
----------------------------------------------------------------------------------
-
-.. automodule:: yeastregulatorydb.regulatory_data.api.serializers.BindingSourceSerializer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 yeastregulatorydb.regulatory\_data.api.serializers.CallingCardsBackgroundSerializer module
 ------------------------------------------------------------------------------------------
 
@@ -60,10 +52,10 @@ yeastregulatorydb.regulatory\_data.api.serializers.ExpressionSerializer module
    :undoc-members:
    :show-inheritance:
 
-yeastregulatorydb.regulatory\_data.api.serializers.ExpressionSourceSerializer module
+yeastregulatorydb.regulatory\_data.api.serializers.DataSourceSerializer module
 ------------------------------------------------------------------------------------
 
-.. automodule:: yeastregulatorydb.regulatory_data.api.serializers.ExpressionSourceSerializer
+.. automodule:: yeastregulatorydb.regulatory_data.api.serializers.DataSourceSerializer
    :members:
    :undoc-members:
    :show-inheritance:

diff --git a/docs/api/yeastregulatorydb.regulatory_data.models.mixins.rst b/docs/api/yeastregulatorydb.regulatory_data.models.mixins.rst
@@ -7,7 +7,7 @@ Submodules
 yeastregulatorydb.regulatory\_data.models.mixins.FileUploadWithIdMixin module
 -----------------------------------------------------------------------------
 
-.. automodule:: yeastregulatorydb.regulatory_data.models.mixins.FileUploadWithIdMixin
+.. automodule:: yeastregulatorydb.regulatory_data.models.mixins.GzipFileUploadWithIdMixin
    :members:
    :undoc-members:
    :show-inheritance:

diff --git a/docs/api/yeastregulatorydb.regulatory_data.models.rst b/docs/api/yeastregulatorydb.regulatory_data.models.rst
@@ -36,10 +36,10 @@ yeastregulatorydb.regulatory\_data.models.BindingManualQC module
    :undoc-members:
    :show-inheritance:
 
-yeastregulatorydb.regulatory\_data.models.BindingSource module
+yeastregulatorydb.regulatory\_data.models.DataSource module
 --------------------------------------------------------------
 
-.. automodule:: yeastregulatorydb.regulatory_data.models.BindingSource
+.. automodule:: yeastregulatorydb.regulatory_data.models.DataSource
    :members:
    :undoc-members:
    :show-inheritance:
@@ -76,14 +76,6 @@ yeastregulatorydb.regulatory\_data.models.ExpressionManualQC module
    :undoc-members:
    :show-inheritance:
 
-yeastregulatorydb.regulatory\_data.models.ExpressionSource module
------------------------------------------------------------------
-
-.. automodule:: yeastregulatorydb.regulatory_data.models.ExpressionSource
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 yeastregulatorydb.regulatory\_data.models.FileFormat module
 -----------------------------------------------------------
 

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -27,4 +27,4 @@ django-filter==23.5  # https://github.com/carltongibson/django-filter
 
 # Third Party Software
 # ------------------------------------------------------------------------------
-callingcardstools==1.3.0 # https://github.com/cmatkhan/callingcardstools
+callingcardstools==1.4.1 # https://github.com/cmatkhan/callingcardstools