diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index af178c68f23a413c3a3521aa7f389e5572532122..e2fbab7a3a56cda5f53298630471551fc1527bbb 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -61,7 +61,8 @@ test-centos7: - coverage run --source='.' manage.py test - coverage report - coverage html - - pip3.6 install sphinx sphinx-argparse sphinxcontrib.bibtex sphinx_rtd_theme + - export LC_CTYPE="en_US.UTF-8" + - pip3.6 install sphinx==3.5.2 sphinx-argparse==0.2.5 sphinxcontrib.bibtex==2.1.4 sphinx_rtd_theme==0.5.1 - cd docs - PYTHON=python3.6 make html artifacts: diff --git a/ippisite/docs/source/conf.py b/ippisite/docs/source/conf.py index a1a1ce100238349db5d46be5be76962191748f29..9169457a512683489b1ff9653c37cce115dab2d7 100644 --- a/ippisite/docs/source/conf.py +++ b/ippisite/docs/source/conf.py @@ -60,6 +60,7 @@ extensions = [ "sphinxcontrib.bibtex", ] + # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] @@ -69,6 +70,9 @@ templates_path = ["_templates"] # source_suffix = ['.rst', '.md'] source_suffix = ".rst" +# The encoding of all reST source files. +source_encoding = "utf-8-sig" + # The master toctree document. master_doc = "index" diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py index e7ed283d59d928dc88c6982bac8c2a7d3cfce40a..f6b478ccc7fbc1d0cb69f16d7d18919762138114 100644 --- a/ippisite/ippidb/admin.py +++ b/ippisite/ippidb/admin.py @@ -179,6 +179,7 @@ class CavityAdmin(admin.ModelAdmin): @admin.register(Distance) class DistanceAdmin(admin.ModelAdmin): list_display = ("similiarity_between", "distance") + search_fields = ("cavity1__full_name", "cavity2__full_name") def similiarity_between(self, obj): return "{} and {}".format(obj.cavity1.full_name, obj.cavity2.full_name) diff --git a/ippisite/ippidb/serializer.py b/ippisite/ippidb/serializer.py index e81cd57c40cc324205f00c7fc5940f1b5458da2e..56d1324135a9a87d2649150d09435c88e255e78a 100644 --- a/ippisite/ippidb/serializer.py +++ b/ippisite/ippidb/serializer.py @@ -114,6 +114,7 @@ class ChainSerializer(serializers.ModelSerializer): class Meta: model = Chain fields = ( + "id", "pdb_chain_id", "protein", "pdb", diff --git a/ippisite/ippidb/tests/tests.py b/ippisite/ippidb/tests/tests.py index 42311209918c0c45fb159f6dc95ae6d334abc468..3fcdf9fb443946b035d696ba8aab12458f8aa277 100644 --- a/ippisite/ippidb/tests/tests.py +++ b/ippisite/ippidb/tests/tests.py @@ -602,7 +602,7 @@ class TestGetUniprotInfo(TestCase): "GO_0005886", "GO_0005905", "GO_0010008", - "GO_0030665", + "GO_0030669", "GO_0031253", "GO_0042470", "GO_0045171", diff --git a/ippisite/requirements-dev.txt b/ippisite/requirements-dev.txt index d9e46e82dac8a42e3e362c1cea5c31e81e60bd81..1549db98da83318c76e564367834cb831570a3f1 100644 --- a/ippisite/requirements-dev.txt +++ b/ippisite/requirements-dev.txt @@ -4,9 +4,9 @@ flake8 black flake8-black # documentation generation -sphinx -sphinx_rtd_theme -sphinxcontrib-bibtex +Sphinx==3.5.2 +sphinx_rtd_theme==0.5.1 +sphinxcontrib-bibtex==2.1.4 # coverage coverage # tests