Merge pull request #492 from PnX-SI/feat/lint

Feat/lint

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# blackify everything!
+c8028f48134dbf07b632c589db900bef1ba6109f

.github/workflows/lint.yml

@@ -0,0 +1,15 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  backend:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Backend code formatting check (Black)
+        uses: psf/black@stable
+        with:
+          src: "setup.py ./atlas"

atlas/app.py

@@ -8,22 +8,35 @@
 
 from atlas.configuration.config_parser import valid_config_from_dict
 from atlas.configuration.config_schema import AtlasConfig, SecretSchemaConf
-from atlas.env import atlas_static_folder, atlas_template_folder, atlas_config_file_path, db, cache
+from atlas.env import (
+    atlas_static_folder,
+    atlas_template_folder,
+    atlas_config_file_path,
+    db,
+    cache,
+)
 
 compress = Compress()
 
+
 def create_app():
     """
     renvoie une instance de l'app Flask
     """
 
-    app = Flask(__name__, template_folder=atlas_template_folder, static_folder=atlas_static_folder)
+    app = Flask(
+        __name__,
+        template_folder=atlas_template_folder,
+        static_folder=atlas_static_folder,
+    )
     # push the config in app config at 'PUBLIC' key
     app.config.from_pyfile(str(atlas_config_file_path))
 
     app.config.from_prefixed_env(prefix="ATLAS")
-    config_valid=valid_config_from_dict(copy.copy(app.config), AtlasConfig)
-    config_secret_valid=valid_config_from_dict(copy.copy(app.config), SecretSchemaConf)
+    config_valid = valid_config_from_dict(copy.copy(app.config), AtlasConfig)
+    config_secret_valid = valid_config_from_dict(
+        copy.copy(app.config), SecretSchemaConf
+    )
 
     app.config.update(config_valid)
     app.config.update(config_secret_valid)
@@ -46,7 +59,9 @@ def get_locale():
         from atlas.atlasRoutes import main as main_blueprint
 
         if app.config["MULTILINGUAL"]:
-            app.register_blueprint(main_blueprint, url_prefix="/<lang_code>", name="multi_lg")
+            app.register_blueprint(
+                main_blueprint, url_prefix="/<lang_code>", name="multi_lg"
+            )
         app.register_blueprint(main_blueprint)
 
         from atlas.atlasAPI import api

atlas/atlasAPI.py

@@ -14,6 +14,7 @@
 
 api = Blueprint("api", __name__)
 
+
 @api.route("/searchTaxon", methods=["GET"])
 def searchTaxonAPI():
     session = db.session
@@ -33,13 +34,15 @@ def searchCommuneAPI():
     session.close()
     return jsonify(results)
 
-if not current_app.config['AFFICHAGE_MAILLE']:
+
+if not current_app.config["AFFICHAGE_MAILLE"]:
+
     @api.route("/observationsMailleAndPoint/<int:cd_ref>", methods=["GET"])
     def getObservationsMailleAndPointAPI(cd_ref):
         """
-            Retourne les observations d'un taxon en point et en maille
+        Retourne les observations d'un taxon en point et en maille
 
-            :returns: dict ({'point:<GeoJson>', 'maille': 'GeoJson})
+        :returns: dict ({'point:<GeoJson>', 'maille': 'GeoJson})
         """
         session = db.session
         observations = {
@@ -55,9 +58,9 @@ def getObservationsMailleAndPointAPI(cd_ref):
 @api.route("/observationsMaille/<int:cd_ref>", methods=["GET"])
 def getObservationsMailleAPI(cd_ref, year_min=None, year_max=None):
     """
-        Retourne les observations d'un taxon par maille (et le nombre d'observation par maille)
+    Retourne les observations d'un taxon par maille (et le nombre d'observation par maille)
 
-        :returns: GeoJson
+    :returns: GeoJson
     """
     session = db.session
     observations = vmObservationsMaillesRepository.getObservationsMaillesChilds(
@@ -70,18 +73,18 @@ def getObservationsMailleAPI(cd_ref, year_min=None, year_max=None):
     return jsonify(observations)
 
 
+if not current_app.config["AFFICHAGE_MAILLE"]:
 
-
-if not current_app.config['AFFICHAGE_MAILLE']:
     @api.route("/observationsPoint/<int:cd_ref>", methods=["GET"])
     def getObservationsPointAPI(cd_ref):
         session = db.session
-        observations = vmObservationsRepository.searchObservationsChilds(session, cd_ref)
+        observations = vmObservationsRepository.searchObservationsChilds(
+            session, cd_ref
+        )
         session.close()
         return jsonify(observations)
 
 
-
 @api.route("/observations/<int:cd_ref>", methods=["GET"])
 def getObservationsGenericApi(cd_ref: int):
     """[summary]
@@ -93,17 +96,22 @@ def getObservationsGenericApi(cd_ref: int):
         [type]: [description]
     """
     session = db.session
-    observations = vmObservationsMaillesRepository.getObservationsMaillesChilds(
-        session,
-        cd_ref,
-        year_min=request.args.get("year_min"),
-        year_max=request.args.get("year_max"),
-    ) if current_app.config['AFFICHAGE_MAILLE'] else vmObservationsRepository.searchObservationsChilds(session, cd_ref)
+    observations = (
+        vmObservationsMaillesRepository.getObservationsMaillesChilds(
+            session,
+            cd_ref,
+            year_min=request.args.get("year_min"),
+            year_max=request.args.get("year_max"),
+        )
+        if current_app.config["AFFICHAGE_MAILLE"]
+        else vmObservationsRepository.searchObservationsChilds(session, cd_ref)
+    )
     session.close()
     return jsonify(observations)
-
 
-if not current_app.config['AFFICHAGE_MAILLE']:
+
+if not current_app.config["AFFICHAGE_MAILLE"]:
+
     @api.route("/observations/<insee>/<int:cd_ref>", methods=["GET"])
     def getObservationsCommuneTaxonAPI(insee, cd_ref):
         connection = db.engine.connect()
@@ -148,18 +156,20 @@ def getPhotosGallery():
     connection.close()
     return jsonify(photos)
 
+
 @api.route("/main_stat", methods=["GET"])
 @cache.cached()
 def main_stat():
     connection = db.engine.connect()
     return vmObservationsRepository.statIndex(connection)
 
+
 @api.route("/rank_stat", methods=["GET"])
 @cache.cached()
 def rank_stat():
     connection = db.engine.connect()
     return jsonify(
-            vmObservationsRepository.genericStat(
+        vmObservationsRepository.genericStat(
             connection, current_app.config["RANG_STAT"]
         )
-    )
+    )

atlas/atlasRoutes.py

@@ -40,18 +40,20 @@
 
     @main.url_defaults
     def add_language_code(endpoint, values):
-        if 'lang_code' in values or not g.get('lang_code', None):
+        if "lang_code" in values or not g.get("lang_code", None):
             return
         # If endpoint expects lang_code, send it forward
-        if current_app.url_map.is_endpoint_expecting(endpoint, 'lang_code'):
-            values['lang_code'] = g.lang_code
+        if current_app.url_map.is_endpoint_expecting(endpoint, "lang_code"):
+            values["lang_code"] = g.lang_code
 
     @main.url_value_preprocessor
     def pull_lang_code(endpoint, values):
         if values is not None:
             # If no language code has been set, get the best language from the browser settings
-            default_lang = request.accept_languages.best_match(current_app.config['LANGUAGES'])
-            g.lang_code = values.pop('lang_code', default_lang)
+            default_lang = request.accept_languages.best_match(
+                current_app.config["LANGUAGES"]
+            )
+            g.lang_code = values.pop("lang_code", default_lang)
 
     @main.before_request
     def redirect_default_language():
@@ -60,7 +62,8 @@ def redirect_default_language():
                 default_lang_code = session["language"]
             else:
                 default_lang_code = request.accept_languages.best_match(
-                    current_app.config["AVAILABLE_LANGUAGES"].keys(), current_app.config["DEFAULT_LANGUAGE"]
+                    current_app.config["AVAILABLE_LANGUAGES"].keys(),
+                    current_app.config["DEFAULT_LANGUAGE"],
                 )
             view_args = request.view_args
             view_args["lang_code"] = default_lang_code
@@ -401,10 +404,15 @@ def photos():
     connection.close()
     return render_template("templates/photoGalery/_main.html", groups=groups)
 
+
 if current_app.config["AFFICHAGE_RECHERCHE_AVANCEE"]:
+
     @main.route("/recherche", methods=["GET"])
     def advanced_search():
-        return render_template("templates/core/advanced_search.html", )
+        return render_template(
+            "templates/core/advanced_search.html",
+        )
+
 
 @main.route("/<page>", methods=["GET", "POST"])
 def get_staticpages(page):

atlas/configuration/config_parser.py

@@ -5,12 +5,12 @@
 from importlib.machinery import SourceFileLoader
 
 
-
 def get_config_module(atlas_config_file_path):
-# imports the module from the given path
+    # imports the module from the given path
     atlas_config = SourceFileLoader("config", atlas_config_file_path).load_module()
     return atlas_config
 
+
 def read_config_file(config_module):
     return {
         var: getattr(config_module, var) for var in remove_reserved_word(config_module)
@@ -22,4 +22,4 @@ def remove_reserved_word(config_module):
 
 
 def valid_config_from_dict(config_dict, config_schema):
-    return config_schema().load(config_dict)
+    return config_schema().load(config_dict)

atlas/configuration/config_schema.py

@@ -95,7 +95,6 @@ class Meta:
     CACHE_TIMEOUT = fields.Number(load_default=3600)
 
 
-
 class MapConfig(Schema):
     LAT_LONG = fields.List(fields.Float(), load_default=[44.7952, 6.2287])
     MIN_ZOOM = fields.Integer(load_default=1)
@@ -207,7 +206,7 @@ class Meta:
     SPLIT_NOM_VERN = fields.Boolean(load_default=True)
     INTERACTIVE_MAP_LIST = fields.Boolean(load_default=True)
     AVAILABLE_LANGUAGES = fields.Dict(load_default=LANGUAGES)
-    # Flask parameter enabling auto reload of templates 
+    # Flask parameter enabling auto reload of templates
     # (no need to restart the atlas service when updating templates)
     # Defaults to False to have the best performance in production
     TEMPLATES_AUTO_RELOAD = fields.Boolean(load_default=False)

atlas/env.py

@@ -7,17 +7,23 @@
 
 babel = Babel()
 
-cache = Cache(config={
-    'CACHE_TYPE': 'SimpleCache',
-})
+cache = Cache(
+    config={
+        "CACHE_TYPE": "SimpleCache",
+    }
+)
 
 db = SQLAlchemy()
 
-default_atlas_config_file_path=Path(__file__).parent / 'configuration/config.py'
-default_atlas_static_folder=Path(__file__).parent / 'static'
-default_atlas_template_folder=Path(__file__).parent
+default_atlas_config_file_path = Path(__file__).parent / "configuration/config.py"
+default_atlas_static_folder = Path(__file__).parent / "static"
+default_atlas_template_folder = Path(__file__).parent
 
 
-atlas_config_file_path=os.environ.get("ATLAS_SETTINGS", default_atlas_config_file_path)
+atlas_config_file_path = os.environ.get(
+    "ATLAS_SETTINGS", default_atlas_config_file_path
+)
 atlas_static_folder = os.environ.get("ATLAS_STATIC_FOLDER", default_atlas_static_folder)
-atlas_template_folder = os.environ.get("ATLAS_TEMPLATE_FOLDER", default_atlas_template_folder)
+atlas_template_folder = os.environ.get(
+    "ATLAS_TEMPLATE_FOLDER", default_atlas_template_folder
+)

atlas/modeles/entities/tBibTaxrefRang.py

@@ -8,9 +8,10 @@
 
 class TBibTaxrefRang(Base):
     __table__ = Table(
-        'bib_taxref_rangs', metadata,
-        Column('id_rang', String(4), nullable=False, primary_key=True),
-        Column('nom_rang', String(20), nullable=False),
-        Column('tri_rang', Integer),
-        schema='atlas'
+        "bib_taxref_rangs",
+        metadata,
+        Column("id_rang", String(4), nullable=False, primary_key=True),
+        Column("nom_rang", String(20), nullable=False),
+        Column("tri_rang", Integer),
+        schema="atlas",
     )

atlas/modeles/entities/tCommunes.py

@@ -8,8 +8,8 @@
 
 
 class LCommune(Base):
-    __tablename__ = 'l_communes'
-    __table_args__ = {u'schema': 'layers'}
+    __tablename__ = "l_communes"
+    __table_args__ = {"schema": "layers"}
 
     insee = Column(String(5), primary_key=True)
     commune_maj = Column(String(50))

atlas/modeles/entities/vmAreas.py

@@ -34,7 +34,7 @@ class VmAreas(Base):
         Column("area_code", String(50)),
         Column("area_name", String(50)),
         Column("id_type", Integer(), ForeignKey("atlas.vm_bib_areas_types.id_type")),
-        Column("the_geom", Geometry(u"MULTIPOLYGON", 4326), index=True),
+        Column("the_geom", Geometry("MULTIPOLYGON", 4326), index=True),
         Column("area_geojson", Text()),
         schema="atlas",
         autoload=True,

atlas/modeles/entities/vmCommunes.py

@@ -11,10 +11,13 @@
 
 class VmCommunes(Base):
     __table__ = Table(
-        'vm_communes', metadata,
-        Column('insee', String(5), primary_key=True, unique=True),
-        Column('commune_maj', String(50)),
+        "vm_communes",
+        metadata,
+        Column("insee", String(5), primary_key=True, unique=True),
+        Column("commune_maj", String(50)),
         # Column('commune_min', String(50)),
-        Column('the_geom', Geometry(u'MULTIPOLYGON'), index=True),
-        schema='atlas', autoload=True, autoload_with=db.engine
+        Column("the_geom", Geometry("MULTIPOLYGON"), index=True),
+        schema="atlas",
+        autoload=True,
+        autoload_with=db.engine,
     )