Merge branch 'develop' into joss_paper

* develop: Update CHANGES.rst Remove dependency in docs on mkvirtualenv. Refs #773 (#775) remove unused dependency #767 op.execute oneline instead of get bind move property to options #767 update language name Flemish to Vlaams rename param #766 add extra id field to language dropdown Update changelog. Update Changelog. #738 more flexible analytics tracking (#762) Upgrade language-tags. (#761) Updates for sqlalchemy 2.0, skosprovider_sqlalchemy 2.0.0 Update contributing.md file. Refs #756 (#757) Update changelog. Remove universal flag for wheel creation. (#753)
OnroerendErfgoed · Feb 23, 2023 · 4a9a684 · 4a9a684
2 parents 2b2cc21 + 293f801
commit 4a9a684
Show file tree

Hide file tree

Showing 83 changed files with 63,904 additions and 58,876 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,14 @@
+in progress
+-----------
+
+- Easier and more flexible configuration of analytics snippets, such as `Plausible Analytics <https://plausible.io>`_. (#738)
+- Show acutal language tags in admin interface drop downs, as opposed to just the labels to reduce confusion. (#766)
+- Update label of default language `vls` to `Vlaams` to be inline with the normal IANA label. (#767)
+- Update language-tags to latest version. (#754)
+- Stop building universal wheels (#752)
+- Update docs to no longer reference mkvirtualenv, use standard venv instead (#773)
+- Update CONTRIBUTING.md file (#756)
+
 1.3.0 (04-01-2023)
 -------------------
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,11 +1,28 @@
 Contributing
 ============
 
-Atramhasis is being developed as open source software by the 
-[Flanders Heritage Agency]. All development is done on the agency's 
-[Github page for Atramhasis].
+Atramhasis is an open source SKOS editor developed by [Flanders Heritage].
+Consult the [Atramhasis documentation] for more information. All development 
+is done through our [Github page for Atramhasis]. If you run into bugs or 
+would like to request a new feature, please open a [Github issue]. Please 
+provide some context to your question such as the operating system, 
+Python and Atramhasis versions you are running. If you have specific questions 
+about the software or the datasets hosted at [Flanders Heritage Thesaurus] 
+you would rather not address in a public forum, please mail us at 
+<ict@onroerenderfgoed.be>.
 
-Since we place a lot of importance of code quality, we expect to have a good 
+If you have some
+exerience with Python, Javascript, RDF or SKOS, feel free to contribute
+where you can. If you are unsure if a particular change would be welcome, 
+create a [Github issue] first. When doing so, we recommend you follow these 
+guidelines.
+
+Please setup a local installation according to the [development guidelines] in
+our online documentation, especially if you are looking to make a major 
+contribution. For certain changes, such as updating a part of the documentation 
+this is not necessary.
+
+We place a lot of importance on code quality, expect to have a good 
 amount of code coverage present and run frequent unit tests. All commits and
 pull requests will be tested with [Travis-ci]. Code coverage is being 
 monitored with [Coveralls].
@@ -33,17 +50,21 @@ bugfix/<ticketnumber>_description_of_fix
 feature/<ticketnumber>_description_of_feature
 ````
 
-Branches should be branched from develop and merged back into develop once approved 
-through a pull request.
+Feature and bugfix branches should be branched from develop and will be merged 
+back into develop once approved through a pull request.
 
 Every pull request will be run through [Travis-ci]. When providing a pull 
 request, please run the unit tests first and make sure they all pass. Please 
 provide new unit tests to maintain 100% coverage. If you send us a pull request
-and this build doesn't function, please correct the issue at hand or let us 
+that doesn't pass all tests, please correct the issue at hand or let us 
 know why it's not working.
 
-[Flanders Heritage Agency]: https://www.onroerenderfgoed.be
+[Flanders Heritage]: https://www.onroerenderfgoed.be
+[Atramhasis documentation]: https://atramhasis.readthedocs.io/en/latest
+[Flanders Heritage Thesaurus]: https://thesaurus.onroerenderfgoed.be
 [Github page for Atramhasis]: https://github.com/OnroerendErfgoed/atramhasis
+[Github issue]: https://github.com/OnroerendErfgoed/atramhasis/issues
+[development guidelines]: https://atramhasis.readthedocs.io/en/latest/development.html
 [Travis-ci]: https://travis-ci.org/OnroerendErfgoed/atramhasis
 [Coveralls]: https://coveralls.io/r/OnroerendErfgoed/atramhasis
 [pytest]: http://pytest.org

diff --git a/atramhasis/alembic/env.py b/atramhasis/alembic/env.py
@@ -1,14 +1,14 @@
-try:
-    import configparser
-except ImportError:
-    import ConfigParser as configparser
-from alembic import context
-from sqlalchemy import engine_from_config, pool
+import configparser
 from logging.config import fileConfig
-from atramhasis.data.models import Base
+from os import path
+
+from alembic import context
 from skosprovider_sqlalchemy.models import Base as SkosBase
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
 from sqlalchemy.schema import MetaData
-from os import path
+
+from atramhasis.data.models import Base
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -29,18 +29,22 @@
 # my_important_option = config.get_main_option("my_important_option")
 # ... etc.
 
+
 def load_app_ini(ini_file):
     """Load the settings for the application.ini file."""
     ini = configparser.ConfigParser()
-    ini.readfp(open(ini_file))
+    with open(ini_file) as f:
+        ini.read_file(f)
     here = path.abspath(path.dirname(ini_file))
-    ini.set('app:main', 'here', here)
+    ini.set("app:main", "here", here)
     return ini
 
-app_ini = config.get_main_option('ini_location')
+
+app_ini = config.get_main_option("ini_location")
 app_config = load_app_ini(app_ini)
-sa_url = app_config.get('app:main', 'sqlalchemy.url')
-config.set_main_option('sqlalchemy.url', sa_url)
+sa_url = app_config.get("app:main", "sqlalchemy.url")
+config.set_main_option("sqlalchemy.url", sa_url)
+
 
 def run_migrations_offline():
     """Run migrations in 'offline' mode.
@@ -70,8 +74,9 @@ def run_migrations_online():
     """
     engine = engine_from_config(
         config.get_section(config.config_ini_section),
-        prefix='sqlalchemy.',
-        poolclass=pool.NullPool)
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
 
     metadata = MetaData()
     for md in target_metadata:
@@ -80,9 +85,7 @@ def run_migrations_online():
 
     connection = engine.connect()
     context.configure(
-        connection=connection,
-        target_metadata=metadata,
-        render_as_batch=True
+        connection=connection, target_metadata=metadata, render_as_batch=True
     )
 
     try:
@@ -96,4 +99,3 @@ def run_migrations_online():
     run_migrations_offline()
 else:
     run_migrations_online()
-
diff --git a/atramhasis/alembic/script.py.mako b/atramhasis/alembic/script.py.mako
@@ -6,14 +6,14 @@ Create Date: ${create_date}
 
 """
 
-# revision identifiers, used by Alembic.
-revision = ${repr(up_revision)}
-down_revision = ${repr(down_revision)}
-
 from alembic import op
 import sqlalchemy as sa
 ${imports if imports else ""}
 
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+
 def upgrade():
     ${upgrades if upgrades else "pass"}
 

diff --git a/atramhasis/alembic/versions/0978347c16f9_rename_flemish_vlaams.py b/atramhasis/alembic/versions/0978347c16f9_rename_flemish_vlaams.py
@@ -0,0 +1,21 @@
+"""rename flemish vlaams
+
+
+Revision ID: 0978347c16f9
+Revises: 88214d86a9d1
+Create Date: 2023-02-06 13:23:27.009952
+
+"""
+
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = '0978347c16f9'
+down_revision = '88214d86a9d1'
+
+def upgrade():
+    op.execute("UPDATE language SET name = 'Vlaams' WHERE id = 'vls'")
+
+def downgrade():
+    op.execute("UPDATE language SET name = 'Flemish' WHERE id = 'vls'")
diff --git a/atramhasis/alembic/versions/184f1bbcb916_language_und.py b/atramhasis/alembic/versions/184f1bbcb916_language_und.py
@@ -5,35 +5,27 @@
 Create Date: 2017-07-25 16:38:39.439673
 
 """
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.orm import Session
+from sqlalchemy.sql import column
+from sqlalchemy.sql import table
 
 # revision identifiers, used by Alembic.
-revision = '184f1bbcb916'
-down_revision = '6dfc3e2324aa'
+revision = "184f1bbcb916"
+down_revision = "6dfc3e2324aa"
 
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.sql import table, column
-from sqlalchemy.orm import Session
 
-language_table = table('language',
-                       column('id', sa.String),
-                       column('name', sa.String)
-                       )
+language_table = table("language", column("id", sa.String), column("name", sa.String))
 
 
 def upgrade():
 
-    op.bulk_insert(language_table,
-                   [
-                       {'id': 'und', 'name': 'Undetermined'}
-                   ]
-    )
+    op.bulk_insert(language_table, [{"id": "und", "name": "Undetermined"}])
 
 
 def downgrade():
     connection = op.get_bind()
     session = Session(bind=connection)
-    connection.execute(
-        language_table.delete().where(language_table.c.id == 'und')
-    )
+    connection.execute(language_table.delete().where(language_table.c.id == "und"))
     session.flush()
diff --git a/atramhasis/alembic/versions/1a4d62b02630_199_sources.py b/atramhasis/alembic/versions/1a4d62b02630_199_sources.py
@@ -5,42 +5,56 @@
 Create Date: 2015-12-08 12:06:20.303601
 
 """
+import sqlalchemy as sa
+from alembic import op
 
 # revision identifiers, used by Alembic.
-revision = '1a4d62b02630'
-down_revision = '2a38d364113b'
-
-from alembic import op
-import sqlalchemy as sa
+revision = "1a4d62b02630"
+down_revision = "2a38d364113b"
 
 
 def upgrade():
 
-    op.create_table('source',
-        sa.Column('id', sa.Integer(), nullable=False),
-        sa.Column('citation', sa.Text(), nullable=False),
-        sa.PrimaryKeyConstraint('id')
+    op.create_table(
+        "source",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("citation", sa.Text(), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
     )
 
-    op.create_table('conceptscheme_source',
-        sa.Column('conceptscheme_id', sa.Integer(), nullable=False),
-        sa.Column('source_id', sa.Integer(), nullable=False),
-        sa.ForeignKeyConstraint(['conceptscheme_id'], ['conceptscheme.id'], ),
-        sa.ForeignKeyConstraint(['source_id'], ['source.id'], ),
-        sa.PrimaryKeyConstraint('conceptscheme_id', 'source_id')
+    op.create_table(
+        "conceptscheme_source",
+        sa.Column("conceptscheme_id", sa.Integer(), nullable=False),
+        sa.Column("source_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["conceptscheme_id"],
+            ["conceptscheme.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["source_id"],
+            ["source.id"],
+        ),
+        sa.PrimaryKeyConstraint("conceptscheme_id", "source_id"),
     )
 
-    op.create_table('concept_source',
-        sa.Column('concept_id', sa.Integer(), nullable=False),
-        sa.Column('source_id', sa.Integer(), nullable=False),
-        sa.ForeignKeyConstraint(['concept_id'], ['concept.id'], ),
-        sa.ForeignKeyConstraint(['source_id'], ['source.id'], ),
-        sa.PrimaryKeyConstraint('concept_id', 'source_id')
+    op.create_table(
+        "concept_source",
+        sa.Column("concept_id", sa.Integer(), nullable=False),
+        sa.Column("source_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["concept_id"],
+            ["concept.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["source_id"],
+            ["source.id"],
+        ),
+        sa.PrimaryKeyConstraint("concept_id", "source_id"),
     )
 
 
 def downgrade():
 
-    op.drop_table('conceptscheme_source')
-    op.drop_table('concept_source')
-    op.drop_table('source')
+    op.drop_table("conceptscheme_source")
+    op.drop_table("concept_source")
+    op.drop_table("source")
diff --git a/atramhasis/alembic/versions/1ad2b6fbcf22_visit_log.py b/atramhasis/alembic/versions/1ad2b6fbcf22_visit_log.py
@@ -6,30 +6,32 @@
 
 """
 
-# revision identifiers, used by Alembic.
-revision = '1ad2b6fbcf22'
-down_revision = '441c5a16ef8'
-
-from alembic import op
 import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "1ad2b6fbcf22"
+down_revision = "441c5a16ef8"
 
 
 def upgrade():
-    op.create_table('conceptscheme_visit_log',
-                    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True),
-                    sa.Column('conceptscheme_id', sa.String(), nullable=False),
-                    sa.Column('visited_at', sa.DateTime(), nullable=False),
-                    sa.Column('origin', sa.String, nullable=False)
-                    )
-    op.create_table('concept_visit_log',
-                    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True),
-                    sa.Column('concept_id', sa.Integer(), nullable=False),
-                    sa.Column('conceptscheme_id', sa.String(), nullable=False),
-                    sa.Column('visited_at', sa.DateTime(), nullable=False),
-                    sa.Column('origin', sa.String, nullable=False)
-                    )
+    op.create_table(
+        "conceptscheme_visit_log",
+        sa.Column("id", sa.Integer(), primary_key=True, autoincrement=True),
+        sa.Column("conceptscheme_id", sa.String(), nullable=False),
+        sa.Column("visited_at", sa.DateTime(), nullable=False),
+        sa.Column("origin", sa.String, nullable=False),
+    )
+    op.create_table(
+        "concept_visit_log",
+        sa.Column("id", sa.Integer(), primary_key=True, autoincrement=True),
+        sa.Column("concept_id", sa.Integer(), nullable=False),
+        sa.Column("conceptscheme_id", sa.String(), nullable=False),
+        sa.Column("visited_at", sa.DateTime(), nullable=False),
+        sa.Column("origin", sa.String, nullable=False),
+    )
 
 
 def downgrade():
-    op.drop_table('concept_visit_log')
-    op.drop_table('conceptscheme_visit_log')
+    op.drop_table("concept_visit_log")
+    op.drop_table("conceptscheme_visit_log")