From 983ce6f0215a2633442febaf5f179bd9aebb4831 Mon Sep 17 00:00:00 2001 From: Matthew Dillon Date: Sun, 28 Aug 2016 16:30:20 -0700 Subject: [PATCH] TST: Travis/Coveralls setup (#10) - add travis.yml - linting - coveralls - readme --- .coveragerc | 8 ++++- .travis.yml | 18 ++++++++++ README.md | 3 ++ ccdb/api/urls.py | 3 +- ccdb/collections_ccdb/tests/test_models.py | 9 +++-- ccdb/experiments/admin.py | 39 +++++++++++----------- ccdb/experiments/models.py | 18 ++++++---- ccdb/locations/models.py | 6 ++-- ccdb/misc/models.py | 13 +++++--- ccdb/misc/tests/test_models.py | 10 ++++-- ccdb/processing/models.py | 6 ++-- ccdb/processing/tests/test_models.py | 6 ++-- ccdb/projects/tests/factories.py | 1 - ccdb/species/admin.py | 12 ++++--- ccdb/utils/data.py | 5 ++- 15 files changed, 107 insertions(+), 50 deletions(-) create mode 100644 .travis.yml diff --git a/.coveragerc b/.coveragerc index 1a4cfb8..4cfe03e 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,3 +1,9 @@ [run] -omit = ./venv/*,./config/*,manage.py +omit = + */venv/* + */config/* + */migrations/* + manage.py branch = True +source = ccdb +include = */ccdb/* diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..e758a5c --- /dev/null +++ b/.travis.yml @@ -0,0 +1,18 @@ +language: python +python: + - 3.5 +services: + - postgresql +before_install: + - psql -c 'CREATE DATABASE ccdbdjango;' -U postgres + - export DJANGO_SETTINGS_MODULE=config.settings.local + - export DATABASE_URL=postgres://postgres@localhost/ccdbdjango +install: + - pip install -r requirements/local.txt + - pip install coveralls +script: + - python manage.py migrate + - flake8 --exclude=migrations,settings,manage.py,misc/existing.py + - coverage run --rcfile .coveragerc manage.py test +after_success: + - coveralls diff --git a/README.md b/README.md index 552fe02..ebd2278 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,8 @@ # CCDB - Collections and Contaminants Database +[![Build Status](https://travis-ci.org/thermokarst/ccdb.svg?branch=master)](https://travis-ci.org/thermokarst/ccdb) +[![Coverage Status](https://coveralls.io/repos/github/thermokarst/ccdb/badge.svg?branch=master)](https://coveralls.io/github/thermokarst/ccdb?branch=master) + A collections and contaminants database. ## Development Setup diff --git a/ccdb/api/urls.py b/ccdb/api/urls.py index 17243f9..65596b4 100644 --- a/ccdb/api/urls.py +++ b/ccdb/api/urls.py @@ -11,7 +11,8 @@ router.register(r'administrative-urls', api_v.AdminURLs, base_name='adminurls') urlpatterns = [ url(r'^auth/login/', api_v.Login.as_view()), - url(r'^auth/password/reset/confirm/', api_v.PasswordResetConfirm.as_view()), + url(r'^auth/password/reset/confirm/', + api_v.PasswordResetConfirm.as_view()), url(r'^auth/password/reset/', api_v.PasswordReset.as_view()), url(r'^auth/', include('djoser.urls.authtoken')), url(r'^v1/', include(router.urls, namespace='v1')), diff --git a/ccdb/collections_ccdb/tests/test_models.py b/ccdb/collections_ccdb/tests/test_models.py index 849f82d..b35a203 100644 --- a/ccdb/collections_ccdb/tests/test_models.py +++ b/ccdb/collections_ccdb/tests/test_models.py @@ -73,7 +73,8 @@ class CollectionTestCase(TestCase): def test_uniqueness(self): c1 = CollectionFactory() with transaction.atomic(), self.assertRaises(IntegrityError): - CollectionFactory(project=c1.project, study_location=c1.study_location, + CollectionFactory(project=c1.project, + study_location=c1.study_location, collection_type=c1.collection_type, collection_start_date=c1.collection_start_date, collection_end_date=c1.collection_end_date, @@ -99,8 +100,10 @@ class CollectionTrapTestCase(TestCase): def test_uniqueness(self): c1 = CollectionTrapFactory() with transaction.atomic(), self.assertRaises(IntegrityError): - CollectionTrapFactory(collection=c1.collection, date_opened=c1.date_opened, - time_opened=c1.time_opened, date_closed=c1.date_closed, + CollectionTrapFactory(collection=c1.collection, + date_opened=c1.date_opened, + time_opened=c1.time_opened, + date_closed=c1.date_closed, time_closed=c1.time_closed) c3 = CollectionTrapFactory() self.assertTrue(isinstance(c3, CollectionTrap)) diff --git a/ccdb/experiments/admin.py b/ccdb/experiments/admin.py index efdc4a3..3ab6ef5 100644 --- a/ccdb/experiments/admin.py +++ b/ccdb/experiments/admin.py @@ -1,7 +1,7 @@ from django.contrib import admin -from .models import Flaw, Experiment, ProtocolAttachment, TreatmentType, \ - Treatment, TreatmentReplicate, AliveDeadCount +from .models import (Flaw, Experiment, ProtocolAttachment, TreatmentType, + Treatment, TreatmentReplicate, AliveDeadCount) class FlawAdmin(admin.ModelAdmin): @@ -17,7 +17,8 @@ class ExperimentAdmin(admin.ModelAdmin): list_display_links = ('name',) search_fields = ('name', 'code', 'description', 'flaw', 'sort_order') list_per_page = 25 - fields = ('name', 'code', 'description', 'flaw', 'collections', 'sort_order') + fields = ('name', 'code', 'description', 'flaw', 'collections', + 'sort_order') class ProtocolAttachmentAdmin(admin.ModelAdmin): @@ -30,46 +31,46 @@ class ProtocolAttachmentAdmin(admin.ModelAdmin): class TreatmentTypeAdmin(admin.ModelAdmin): list_display = ('experiment', 'name', 'code', 'treatment_type', - 'placement', 'description', 'sort_order') + 'placement', 'description', 'sort_order') list_display_links = ('name',) search_fields = ('experiment', 'name', 'code', 'treatment_type', - 'placement', 'description') + 'placement', 'description') list_per_page = 25 fields = ('experiment', 'name', 'code', 'treatment_type', 'placement', - 'description', 'sort_order') + 'description', 'sort_order') class TreatmentAdmin(admin.ModelAdmin): list_display = ('treatment_type', 'container', 'study_location', 'species', - 'sex', 'flaw') + 'sex', 'flaw') list_display_links = ('treatment_type',) - search_fields = ('treatment_type', 'container', 'study_location', 'species', - 'sex', 'flaw') + search_fields = ('treatment_type', 'container', 'study_location', + 'species', 'sex', 'flaw') list_per_page = 25 fields = ('treatment_type', 'container', 'study_location', 'species', - 'sex', 'flaw') + 'sex', 'flaw') class TreatmentReplicateAdmin(admin.ModelAdmin): list_display = ('treatment', 'name', 'setup_date', 'setup_time', - 'setup_sample_size', 'mass_g', 'flaw') + 'setup_sample_size', 'mass_g', 'flaw') list_display_links = ('name',) search_fields = ('treatment', 'name', 'setup_date', 'setup_time', - 'setup_sample_size', 'mass_g', 'flaw') + 'setup_sample_size', 'mass_g', 'flaw') list_per_page = 25 fields = ('treatment', 'name', 'setup_date', 'setup_time', - 'setup_sample_size', 'mass_g', 'flaw') + 'setup_sample_size', 'mass_g', 'flaw') class AliveDeadCountAdmin(admin.ModelAdmin): - list_display = ('treatment', 'tr', 'status_date', - 'status_time', 'count_alive', 'count_dead', 'flaw') + list_display = ('treatment', 'tr', 'status_date', 'status_time', + 'count_alive', 'count_dead', 'flaw') list_display_links = ('status_date',) search_fields = ('treatment_replicate', 'status_date', 'status_time', - 'count_alive', 'count_dead', 'flaw') + 'count_alive', 'count_dead', 'flaw') list_per_page = 25 fields = ('treatment_replicate', 'status_date', 'status_time', - 'count_alive', 'count_dead', 'flaw') + 'count_alive', 'count_dead', 'flaw') def treatment(self, obj): return obj.treatment_replicate.treatment @@ -77,8 +78,8 @@ class AliveDeadCountAdmin(admin.ModelAdmin): def tr(self, obj): return "{}_{}_{}".format(obj.treatment_replicate.setup_date, - obj.treatment_replicate.name, - obj.treatment_replicate.setup_sample_size) + obj.treatment_replicate.name, + obj.treatment_replicate.setup_sample_size) tr.short_description = 'Treatment Replicate' diff --git a/ccdb/experiments/models.py b/ccdb/experiments/models.py index 3af990c..ad2373a 100644 --- a/ccdb/experiments/models.py +++ b/ccdb/experiments/models.py @@ -17,7 +17,8 @@ class Experiment(models.Model): name = models.CharField(max_length=150) code = models.CharField(max_length=10, blank=True) description = models.CharField(max_length=255, blank=True) - flaw = models.ForeignKey(Flaw, blank=True, null=True, related_name='experiments') + flaw = models.ForeignKey(Flaw, blank=True, null=True, + related_name='experiments') sort_order = models.IntegerField(blank=True, null=True) collections = models.ManyToManyField('collections_ccdb.Collection') @@ -63,19 +64,22 @@ class TreatmentType(models.Model): class Treatment(models.Model): - treatment_type = models.ForeignKey(TreatmentType, related_name='treatments') + treatment_type = models.ForeignKey(TreatmentType, + related_name='treatments') container = models.ForeignKey('misc.Container', blank=True, null=True, related_name='treatments') study_location = models.ForeignKey('locations.StudyLocation', related_name='treatments') species = models.ForeignKey('species.Species', related_name='treatments') sex = models.CharField(max_length=25) - flaw = models.ForeignKey(Flaw, blank=True, null=True, related_name='treatments') + flaw = models.ForeignKey(Flaw, blank=True, null=True, + related_name='treatments') display_name = models.CharField(max_length=255, editable=False) def save(self, *args, **kwargs): self.display_name = "{}_{}_{}_{}".format(self.treatment_type, - self.study_location, self.species, + self.study_location, + self.species, self.sex) super(Treatment, self).save(*args, **kwargs) @@ -88,13 +92,15 @@ class Treatment(models.Model): class TreatmentReplicate(models.Model): - treatment = models.ForeignKey(Treatment, related_name='treatment_replicates') + treatment = models.ForeignKey(Treatment, + related_name='treatment_replicates') name = models.CharField(max_length=50) setup_date = models.DateField(blank=True, null=True) setup_time = models.TimeField(blank=True, null=True) setup_sample_size = models.IntegerField(blank=True, null=True) mass_g = models.FloatField(blank=True, null=True) - flaw = models.ForeignKey(Flaw, blank=True, null=True, related_name='treatment_replicates') + flaw = models.ForeignKey(Flaw, blank=True, null=True, + related_name='treatment_replicates') display_name = models.CharField(max_length=255, editable=False) def save(self, *args, **kwargs): diff --git a/ccdb/locations/models.py b/ccdb/locations/models.py index 3e4eda2..021ed17 100644 --- a/ccdb/locations/models.py +++ b/ccdb/locations/models.py @@ -15,7 +15,8 @@ class Region(models.Model): class Site(models.Model): - region = models.ForeignKey(Region, blank=True, null=True, related_name='sites') + region = models.ForeignKey(Region, blank=True, null=True, + related_name='sites') name = models.CharField(max_length=100) code = models.CharField(max_length=10, blank=True) description = models.CharField(max_length=255, blank=True) @@ -51,7 +52,8 @@ class StudyLocation(models.Model): study_location_type = models.CharField(max_length=50, blank=True) treatment_type = models.CharField(max_length=100, blank=True) municipal_location = models.ForeignKey(MunicipalLocation, - blank=True, null=True, related_name='study_locations') + blank=True, null=True, + related_name='study_locations') collecting_location = models.BooleanField(default=False) description = models.CharField(max_length=255, blank=True) sort_order = models.IntegerField(blank=True, null=True) diff --git a/ccdb/misc/models.py b/ccdb/misc/models.py index 5118500..27bed5a 100644 --- a/ccdb/misc/models.py +++ b/ccdb/misc/models.py @@ -21,9 +21,12 @@ class MeasurementType(models.Model): code = models.CharField(max_length=10, blank=True) measurement_type_class = models.CharField(max_length=50, blank=True) description = models.CharField(max_length=255, blank=True) - default_measurement_unit = models.ForeignKey('MeasurementUnit', blank=True, - null=True, - related_name='measurement_types') + default_measurement_unit = models.ForeignKey( + 'MeasurementUnit', + blank=True, + null=True, + related_name='measurement_types' + ) sort_order = models.IntegerField(blank=True, null=True) def __str__(self): @@ -72,8 +75,8 @@ class Container(models.Model): material = models.ForeignKey(Material, blank=True, null=True, related_name='containers') volume = models.FloatField(blank=True, null=True) - measurement_unit = models.ForeignKey(MeasurementUnit, blank=True, null=True, - related_name='containers') + measurement_unit = models.ForeignKey(MeasurementUnit, blank=True, + null=True, related_name='containers') sort_order = models.IntegerField(blank=True, null=True) def __str__(self): diff --git a/ccdb/misc/tests/test_models.py b/ccdb/misc/tests/test_models.py index d3a95f7..363dbaa 100644 --- a/ccdb/misc/tests/test_models.py +++ b/ccdb/misc/tests/test_models.py @@ -30,8 +30,11 @@ class MeasurementTypeTestCase(TestCase): def test_uniqueness(self): m1 = MeasurementTypeFactory() with transaction.atomic(), self.assertRaises(IntegrityError): - MeasurementTypeFactory(name=m1.name, code=m1.code, - measurement_type_class=m1.measurement_type_class) + MeasurementTypeFactory( + name=m1.name, + code=m1.code, + measurement_type_class=m1.measurement_type_class + ) m3 = MeasurementTypeFactory() self.assertTrue(isinstance(m3, MeasurementType)) @@ -59,7 +62,8 @@ class ColorTestCase(TestCase): def test_uniqueness(self): c1 = ColorFactory() with transaction.atomic(), self.assertRaises(IntegrityError): - ColorFactory(name=c1.name, code=c1.code, color_number=c1.color_number) + ColorFactory(name=c1.name, code=c1.code, + color_number=c1.color_number) c3 = ColorFactory() self.assertTrue(isinstance(c3, Color)) diff --git a/ccdb/processing/models.py b/ccdb/processing/models.py index 4833f18..33b62ec 100644 --- a/ccdb/processing/models.py +++ b/ccdb/processing/models.py @@ -53,10 +53,12 @@ class Processing(models.Model): measurement_unit = models.ForeignKey('misc.MeasurementUnit', blank=True, null=True, related_name='processings') minutes_in_reagent = models.IntegerField(blank=True, null=True) - flaw = models.ForeignKey(Flaw, blank=True, null=True, related_name='processings') + flaw = models.ForeignKey(Flaw, blank=True, null=True, + related_name='processings') def __str__(self): - return "{} {} {}".format(self.process_date, self.process_type, self.container_label) + return "{} {} {}".format(self.process_date, self.process_type, + self.container_label) class Meta: unique_together = ('process_type', 'container', 'container_label', diff --git a/ccdb/processing/tests/test_models.py b/ccdb/processing/tests/test_models.py index eb39456..49b1f29 100644 --- a/ccdb/processing/tests/test_models.py +++ b/ccdb/processing/tests/test_models.py @@ -52,13 +52,15 @@ class ProcessingTestCase(TestCase): def test_creation(self): p = ProcessingFactory() self.assertTrue(isinstance(p, Processing)) - name = "{} {} {}".format(p.process_date, p.process_type, p.container_label) + name = "{} {} {}".format(p.process_date, p.process_type, + p.container_label) self.assertEqual(p.__str__(), name) def test_uniqueness(self): p1 = ProcessingFactory() with transaction.atomic(), self.assertRaises(IntegrityError): - ProcessingFactory(process_type=p1.process_type, container=p1.container, + ProcessingFactory(process_type=p1.process_type, + container=p1.container, container_label=p1.container_label, process_date=p1.process_date, process_time=p1.process_time, reagent=p1.reagent) diff --git a/ccdb/projects/tests/factories.py b/ccdb/projects/tests/factories.py index 15c6c86..2941dab 100644 --- a/ccdb/projects/tests/factories.py +++ b/ccdb/projects/tests/factories.py @@ -37,4 +37,3 @@ class GrantReportFactory(factory.DjangoModelFactory): due_date = factory.LazyFunction(datetime.now) submitted_date = factory.LazyFunction(datetime.now) sort_order = factory.Sequence(lambda n: n) - diff --git a/ccdb/species/admin.py b/ccdb/species/admin.py index 71b3995..cbee00e 100644 --- a/ccdb/species/admin.py +++ b/ccdb/species/admin.py @@ -4,7 +4,8 @@ from .models import Species, TrapSpecies, CollectionSpecies class SpeciesAdmin(admin.ModelAdmin): - list_display = ('common_name', 'genus', 'species', 'parasite', 'sort_order') + list_display = ('common_name', 'genus', 'species', 'parasite', + 'sort_order') list_display_links = ('common_name',) search_fields = ('common_name', 'genus', 'species', 'parasite') list_per_page = 25 @@ -12,9 +13,11 @@ class SpeciesAdmin(admin.ModelAdmin): class TrapSpeciesAdmin(admin.ModelAdmin): - list_display = ('collection_trap', 'species', 'sex', 'count', 'count_estimated') + list_display = ('collection_trap', 'species', 'sex', 'count', + 'count_estimated') list_display_links = ('count',) - search_fields = ('collection_trap', 'species', 'sex', 'count', 'count_estimated') + search_fields = ('collection_trap', 'species', 'sex', 'count', + 'count_estimated') list_per_page = 25 fields = ('collection_trap', 'species', 'sex', 'count', 'count_estimated') @@ -22,7 +25,8 @@ class TrapSpeciesAdmin(admin.ModelAdmin): class CollectionSpeciesAdmin(admin.ModelAdmin): list_display = ('collection', 'species', 'sex', 'count', 'count_estimated') list_display_links = ('count',) - search_fields = ('collection', 'species', 'sex', 'count', 'count_estimated') + search_fields = ('collection', 'species', 'sex', 'count', + 'count_estimated') list_per_page = 25 fields = ('collection', 'species', 'sex', 'count', 'count_estimated') diff --git a/ccdb/utils/data.py b/ccdb/utils/data.py index 7074cb9..1e4bd60 100644 --- a/ccdb/utils/data.py +++ b/ccdb/utils/data.py @@ -62,7 +62,10 @@ sqlite3.register_converter("dtdt", dtdt) def setup_sqlite(dbfile): if os.path.exists(dbfile): - db = sqlite3.connect(dbfile, detect_types=sqlite3.PARSE_DECLTYPES | sqlite3.PARSE_COLNAMES) + db = sqlite3.connect( + dbfile, + detect_types=sqlite3.PARSE_DECLTYPES | sqlite3.PARSE_COLNAMES + ) db.row_factory = sqlite3.Row return db.cursor() else: