Merge branch 'develop'

Author: bouttier

.flaskenv

@@ -0,0 +1,4 @@
+FLASK_APP=pypnnomenclature:create_app
+FLASK_ENV=development
+FLASK_DEBUG=1
+NOMENCLATURE_SETTINGS=settings.py

.github/workflows/pytest.yml

@@ -0,0 +1,84 @@
+name: pytest
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: "Debian 10"
+            python-version: "3.7"
+            postgres-version: "11-stretch"
+          - name: "Debian 11"
+            python-version: "3.9"
+            postgres-version: "13-bullseye"
+
+    name: ${{ matrix.name }}
+
+    services:
+      postgres:
+        image: postgres:${{ matrix.postgres-version }}
+        env:
+          POSTGRES_PASSWORD: postgres
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+    steps:
+    - name: Add database extensions
+      run: |
+        psql -h localhost -U postgres -d postgres -tc 'CREATE EXTENSION "uuid-ossp";'
+        psql -h localhost -U postgres -d postgres -tc 'CREATE EXTENSION "pg_trgm";'
+      env:
+        PGPASSWORD: postgres
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install \
+          pytest-cov \
+          -e .[tests] \
+          -e file:dependencies/Utils-Flask-SQLAlchemy#egg=utils-flask-sqlalchemy \
+          -e file:dependencies/TaxHub#egg=taxhub \
+          -e file:dependencies/UsersHub-authentification-module#egg=pypnusershub
+    - name: Install database
+      run: |
+        flask db upgrade nomenclatures@head
+        flask db upgrade nomenclatures_inpn_data@head
+        flask db upgrade nomenclatures_taxonomie@head
+        flask db upgrade nomenclatures_taxonomie_inpn_data@head
+      env:
+        NOMENCLATURE_SETTINGS: test_settings.py
+    - name: Test with pytest
+      run: |
+        pytest -v --cov --cov-report xml
+      env:
+        NOMENCLATURE_SETTINGS: test_settings.py
+    - name: Upload coverage to Codecov
+      if: ${{ matrix.name == 'Debian 11' }}
+      uses: codecov/codecov-action@v2
+      with:
+        flags: pytest

.gitignore

@@ -103,3 +103,8 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+*.swp
+*.swo
+
+/*settings.py

.gitmodules

@@ -0,0 +1,9 @@
+[submodule "dependencies/Utils-Flask-SQLAlchemy"]
+	path = dependencies/Utils-Flask-SQLAlchemy
+	url = https://github.com/PnX-SI/Utils-Flask-SQLAlchemy.git
+[submodule "dependencies/TaxHub"]
+	path = dependencies/TaxHub
+	url = https://github.com/PnX-SI/TaxHub.git
+[submodule "dependencies/UsersHub-authentification-module"]
+	path = dependencies/UsersHub-authentification-module
+	url = https://github.com/PnX-SI/UsersHub-authentification-module.git

README.md

@@ -1,5 +1,8 @@
 # Nomenclature-api-module
 
+[![pytest](https://github.com/PnX-SI/Nomenclature-api-module/actions/workflows/pytest.yml/badge.svg)](https://github.com/PnX-SI/Nomenclature-api-module/actions/workflows/pytest.yml)
+[![codecov](https://codecov.io/gh/PnX-SI/Nomenclature-api-module/branch/master/graph/badge.svg?token=KGZRGXFWCK)](https://codecov.io/gh/PnX-SI/Nomenclature-api-module)
+
 Flask (Python) module for Nomenclature API.
 
 It is used in [GeoNature](https://github.com/PnX-SI/GeoNature) but can also be used as a standalone API service to manage and returns various nomenclatures with their hierarchy. 

VERSION

@@ -1 +1 @@
-1.4.5
+1.5.0

admin.py

@@ -2,6 +2,25 @@
 CHANGELOG
 =========
 
+1.5.0 (2022-01-04)
+------------------
+
+**🚀 Nouveautés**
+
+* Possibilité de lancer l’API Nomenclature de manière autonome
+* Possibilité de créer son schéma de base de données de manière autonome
+* Mise en place des tests unitaires
+* Mise en place de l’intégration continue
+* Intégration des dépendances en tant que sous-module Git
+
+  * Utils-Flask-SQLAlchemy
+  * TaxHub (pour la taxonomie)
+  * UsersHub-authentification-module (car requis par TaxHub)
+
+**🐛 Corrections**
+
+* Suppression d’anciens fichiers devenus inutiles suite au paquetage
+
 1.4.5 (2021-01-03)
 ------------------
 

dependencies/TaxHub

@@ -0,0 +1,14 @@
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = [
+    "src",
+]
+
+[tool.coverage.run]
+source = [
+    "pypnnomenclature",
+]
+omit = [
+    "*/tests/*",
+    "*/migrations/*",
+]

dependencies/UsersHub-authentification-module

@@ -1,7 +1,10 @@
+python-dotenv
 flask
 Flask-Admin
 flask-sqlalchemy
+flask-migrate
 psycopg2
-utils-flask-sqlalchemy
+utils-flask-sqlalchemy>=0.2.6
 flask-marshmallow
+marshmallow-sqlalchemy
 

dependencies/Utils-Flask-SQLAlchemy

@@ -13,7 +13,7 @@ COOKIE_EXPIRATION = 3600
 COOKIE_AUTORENEW = True
 
 # Ajouter les filtres taxonomiques à l'API 
-# Nécessite d'avoir exécuté le script 'data/nomenclature_taxonomie.sql' qui installe les tables nécessaires
+# Nécessite d'avoir monté la branche alembic nomenclature_taxonomie
 ENABLE_NOMENCLATURE_TAXONOMIC_FILTERS = True
 
 # URL de l'interface d'administration

docs/changelog.rst

@@ -10,6 +10,7 @@
 with (root_dir / 'requirements.in').open() as f:
     requirements = f.read().splitlines()
 
+
 setuptools.setup(
     name='pypnnomenclature',
     version=version,
@@ -23,6 +24,9 @@
     package_dir={'': 'src'},
     package_data={'pypnnomenclature.migrations': ['data/*.sql']},
     install_requires=requirements,
+    extras_require={
+        'tests': [ 'pytest', 'pytest-flask', ],
+    },
     entry_points={
         'alembic': [
             'migrations = pypnnomenclature.migrations:versions',

install_app.sh

@@ -1 +1,33 @@
-__version__ = "1.1.1"
+from pathlib import Path
+from itertools import chain
+from pkg_resources import iter_entry_points
+
+from flask import Flask
+from flask_migrate import Migrate
+
+from pypnnomenclature.env import db, ma
+from pypnnomenclature.routes import routes
+
+
+migrate = Migrate()
+
+
+@migrate.configure
+def configure_alembic(alembic_config):
+    version_locations = alembic_config.get_main_option('version_locations', default='').split()
+    for entry_point in chain(iter_entry_points('alembic', 'migrations')):
+        _, migrations = str(entry_point).split('=', 1)
+        version_locations += [ migrations.strip() ]
+    alembic_config.set_main_option('version_locations', ' '.join(version_locations))
+    return alembic_config
+
+
+def create_app():
+    app = Flask('Habref')
+    app.config.from_envvar('NOMENCLATURE_SETTINGS')
+    ma.init_app(app)
+    db.init_app(app)
+    migrate.init_app(app, db, directory=Path(__file__).parent / 'migrations')
+    app.register_blueprint(routes, url_prefix='/nomenclatures')
+    # TODO admin
+    return app