Dependencies: Update requirement to psycopg~=3.0

The connection string for SQLAlchemy needs to change to
`postgres+psycopg://` for it to target psycopg v3.

.docker/aiida-core-base/s6-assets/config-quick-setup.yaml

@@ -1,4 +1,4 @@
-db_engine: postgresql_psycopg2
+db_engine: postgresql_psycopg
 db_backend: core.psql_dos
 db_host: database
 db_port: 5432

.github/config/profile.yaml

@@ -4,7 +4,7 @@ first_name: Giuseppe
 last_name: Verdi
 institution: Khedivial
 db_backend: core.psql_dos
-db_engine: postgresql_psycopg2
+db_engine: postgresql_psycopg
 db_host: localhost
 db_port: 5432
 db_name: test_aiida

docs/source/howto/installation.rst

@@ -55,7 +55,7 @@ To display these parameters, use ``verdi profile show``:
     storage:
         backend: core.psql_dos
         config:
-            database_engine: postgresql_psycopg2
+            database_engine: postgresql_psycopg
             database_hostname: localhost
             database_name: name
             database_password: abc

docs/source/intro/install_conda.rst

@@ -120,7 +120,7 @@ If you want to install AiiDA onto you own personal workstation/laptop, it is rec
             ✓ version:     AiiDA v2.0.0
             ✓ config:      /path/to/.aiida
             ✓ profile:     default
-            ✓ storage:     Storage for 'default' @ postgresql://username:***@localhost:5432/db_name / file:///path/to/repository
+            ✓ storage:     Storage for 'default' @ postgresql+psycopg://username:***@localhost:5432/db_name / file:///path/to/repository
             ✓ rabbitmq:    Connected as amqp://127.0.0.1?heartbeat=600
             ✓ daemon:      Daemon is running as PID 2809 since 2019-03-15 16:27:52
 

docs/source/intro/install_system.rst

@@ -277,7 +277,7 @@ This is the *recommended* installation method to setup AiiDA on a personal lapto
          ✓ version:     AiiDA v2.0.0
          ✓ config:      /path/to/.aiida
          ✓ profile:     default
-         ✓ storage:     Storage for 'default' @ postgresql://username:***@localhost:5432/db_name / file:///path/to/repository
+         ✓ storage:     Storage for 'default' @ postgresql+psycopg://username:***@localhost:5432/db_name / file:///path/to/repository
          ✓ rabbitmq:    Connected as amqp://127.0.0.1?heartbeat=600
          ✓ daemon:      Daemon is running as PID 2809 since 2019-03-15 16:27:52
 

docs/source/intro/installation.rst

@@ -87,7 +87,7 @@ If you use the same names as in the example commands above, then during the ``ve
 
 .. code-block:: console
 
-   $ Database engine: postgresql_psycopg2
+   $ Database engine: postgresql_psycopg
    $ Database host: localhost
    $ Database port: 5432
    $ AiiDA Database name: aiidadb
@@ -142,7 +142,7 @@ During the ``verdi setup`` phase, use ``!`` to leave host empty and specify your
 
 .. code-block:: console
 
-   $ Database engine: postgresql_psycopg2
+   $ Database engine: postgresql_psycopg
    $ Database host: !
    $ Database port: 5432
    $ AiiDA Database name: aiidadb
@@ -209,7 +209,7 @@ Then, the following prompts will help you configure the database. Typical settin
 .. code-block:: console
 
    $ Default user email: [email protected]
-   $ Database engine: postgresql_psycopg2
+   $ Database engine: postgresql_psycopg
    $ PostgreSQL host: localhost
    $ PostgreSQL port: 5432
    $ AiiDA Database name: aiida_dev

docs/source/intro/troubleshooting.rst

@@ -13,7 +13,7 @@ If you experience any problems, first check that all services are up and running
    ✓ version:     AiiDA v2.0.0
    ✓ config:      /path/to/.aiida
    ✓ profile:     default
-   ✓ storage:     Storage for 'default' @ postgresql://username:***@localhost:5432/db_name / file:///path/to/repository
+   ✓ storage:     Storage for 'default' @ postgresql+psycopg://username:***@localhost:5432/db_name / file:///path/to/repository
    ✓ rabbitmq:    Connected as amqp://127.0.0.1?heartbeat=600
    ✓ daemon:      Daemon is running as PID 2809 since 2019-03-15 16:27:52
 

docs/source/nitpick-exceptions

@@ -234,8 +234,6 @@ py:class yaml.nodes.MappingNode
 py:class yaml.nodes.ScalarNode
 py:class uuid.UUID
 
-py:class psycopg2.extensions.cursor
-
 py:class alembic.config.Config
 py:class alembic.op
 py:class alembic.runtime.migration.MigrationContext

docs/source/reference/command_line.rst

@@ -423,7 +423,7 @@ Below is a list with all available subcommands.
       --first-name NONEMPTYSTRING     First name of the user.  [required]
       --last-name NONEMPTYSTRING      Last name of the user.  [required]
       --institution NONEMPTYSTRING    Institution of the user.  [required]
-      --db-engine [postgresql_psycopg2]
+      --db-engine [postgresql_psycopg]
                                       Engine to use to connect to the database.  [required]
       --db-backend [core.psql_dos]    Database backend to use.  [required]
       --db-host HOSTNAME              Database server host. Leave empty for "peer"
@@ -527,7 +527,7 @@ Below is a list with all available subcommands.
       --first-name NONEMPTYSTRING     First name of the user.  [required]
       --last-name NONEMPTYSTRING      Last name of the user.  [required]
       --institution NONEMPTYSTRING    Institution of the user.  [required]
-      --db-engine [postgresql_psycopg2]
+      --db-engine [postgresql_psycopg]
                                       Engine to use to connect to the database.  [required]
       --db-backend [core.psql_dos]    Database backend to use.  [required]
       --db-host HOSTNAME              Database server host. Leave empty for "peer"

environment.yml

@@ -24,9 +24,9 @@ dependencies:
 - numpy~=1.21
 - paramiko>=2.7.2,~=2.7
 - plumpy~=0.21.6
-- pgsu~=0.2.1
+- pgsu~=0.3.0
 - psutil~=5.6
-- psycopg2-binary~=2.8
+- psycopg[binary]~=3.0
 - pydantic~=2.4
 - pytz~=2021.1
 - pyyaml~=6.0

pyproject.toml

@@ -36,9 +36,9 @@ dependencies = [
   'numpy~=1.21',
   'paramiko~=2.7,>=2.7.2',
   'plumpy~=0.21.6',
-  'pgsu~=0.2.1',
+  'pgsu~=0.3.0',
   'psutil~=5.6',
-  'psycopg2-binary~=2.8',
+  'psycopg[binary]~=3.0',
   'pydantic~=2.4',
   'pytz~=2021.1',
   'pyyaml~=6.0',
@@ -327,7 +327,7 @@ module = [
   'pgtest.*',
   'phonopy.*',
   'psutil.*',
-  'psycopg2.*',
+  'psycopg.*',
   'pymatgen.*',
   'pymysql.*',
   'pyparsing.*',

requirements/requirements-py-3.10.txt

@@ -114,7 +114,7 @@ paramiko==2.12.0
 parso==0.8.3
 pexpect==4.8.0
 pg8000==1.29.8
-pgsu==0.2.3
+pgsu==0.3.0
 pgtest==1.3.2
 pickleshare==0.7.5
 pillow==9.5.0
@@ -125,7 +125,7 @@ plumpy==0.21.8
 prometheus-client==0.17.0
 prompt-toolkit==3.0.38
 psutil==5.9.5
-psycopg2-binary==2.9.6
+psycopg[binary]==3.1.18
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0

requirements/requirements-py-3.11.txt

@@ -113,7 +113,7 @@ paramiko==2.12.0
 parso==0.8.3
 pexpect==4.8.0
 pg8000==1.29.8
-pgsu==0.2.3
+pgsu==0.3.0
 pgtest==1.3.2
 pickleshare==0.7.5
 pillow==9.5.0
@@ -124,7 +124,7 @@ plumpy==0.21.8
 prometheus-client==0.17.0
 prompt-toolkit==3.0.38
 psutil==5.9.5
-psycopg2-binary==2.9.6
+psycopg[binary]==3.1.18
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0

requirements/requirements-py-3.12.txt

@@ -111,7 +111,7 @@ paramiko==2.12.0
 parso==0.8.3
 pexpect==4.8.0
 pg8000==1.30.2
-pgsu==0.2.4
+pgsu==0.3.0
 pgtest==1.3.2
 pickleshare==0.7.5
 pillow==10.1.0
@@ -122,7 +122,7 @@ plumpy==0.21.10
 prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 psutil==5.9.6
-psycopg2-binary==2.9.9
+psycopg[binary]==3.1.18
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0

requirements/requirements-py-3.9.txt

@@ -116,7 +116,7 @@ paramiko==2.12.0
 parso==0.8.3
 pexpect==4.8.0
 pg8000==1.29.8
-pgsu==0.2.3
+pgsu==0.3.0
 pgtest==1.3.2
 pickleshare==0.7.5
 pillow==9.5.0
@@ -127,7 +127,7 @@ plumpy==0.21.8
 prometheus-client==0.17.0
 prompt-toolkit==3.0.38
 psutil==5.9.5
-psycopg2-binary==2.9.6
+psycopg[binary]==3.1.18
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0

src/aiida/cmdline/commands/cmd_setup.py

@@ -237,8 +237,8 @@ def quicksetup(
         'db_backend': db_backend,
         'db_name': db_name,
         # from now on we connect as the AiiDA DB user, which may be forbidden when going via sockets
-        'db_host': postgres.host_for_psycopg2,
-        'db_port': postgres.port_for_psycopg2,
+        'db_host': postgres.host_for_psycopg,
+        'db_port': postgres.port_for_psycopg,
         'db_username': db_username,
         'db_password': db_password,
         'broker_protocol': broker_protocol,

src/aiida/cmdline/params/options/commands/setup.py

@@ -245,7 +245,7 @@ def get_quicksetup_password(ctx, param, value):
     '--su-db-name',
     help='Name of the template database to connect to as the database superuser.',
     type=click.STRING,
-    default=DEFAULT_DBINFO['database'],
+    default=DEFAULT_DBINFO['dbname'],
 )
 
 QUICKSETUP_SUPERUSER_DATABASE_PASSWORD = options.OverridableOption(
@@ -275,7 +275,7 @@ def get_quicksetup_password(ctx, param, value):
 SETUP_DATABASE_ENGINE = QUICKSETUP_DATABASE_ENGINE.clone(
     prompt='Database engine',
     contextual_default=functools.partial(
-        get_profile_attribute_default, ('storage.config.database_engine', 'postgresql_psycopg2')
+        get_profile_attribute_default, ('storage.config.database_engine', 'postgresql_psycopg')
     ),
     cls=options.interactive.InteractiveOption,
 )

src/aiida/cmdline/params/options/main.py

@@ -375,8 +375,8 @@ def set_log_level(_ctx, _param, value):
     '--db-engine',
     required=True,
     help='Engine to use to connect to the database.',
-    default='postgresql_psycopg2',
-    type=click.Choice(['postgresql_psycopg2']),
+    default='postgresql_psycopg',
+    type=click.Choice(['postgresql_psycopg']),
 )
 
 DB_BACKEND = OverridableOption(

src/aiida/manage/external/postgres.py

@@ -96,7 +96,7 @@ def create_dbuser(self, dbuser, dbpass, privileges=''):
 
         :param str dbuser: Name of the user to be created.
         :param str dbpass: Password the user should be given.
-        :raises: psycopg2.errors.DuplicateObject if user already exists and
+        :raises: psycopg.errors.DuplicateObject if user already exists and
             self.connection_mode == PostgresConnectionMode.PSYCOPG
         """
         self.execute(_CREATE_USER_COMMAND.format(dbuser, dbpass, privileges))
@@ -130,14 +130,13 @@ def find_new_dbuser(self, start_from='aiida'):
     def can_user_authenticate(self, dbuser, dbpass):
         """Check whether the database user credentials are valid.
 
-        Checks whether dbuser has access to the `template1` postgres database
-        via psycopg2.
+        Checks whether dbuser has access to the `template1` postgres database via psycopg.
 
         :param dbuser: the database user
         :param dbpass: the database password
         :return: True if the credentials are valid, False otherwise
         """
-        import psycopg2
+        import psycopg
         from pgsu import _execute_psyco
 
         dsn = self.dsn.copy()
@@ -146,7 +145,7 @@ def can_user_authenticate(self, dbuser, dbpass):
 
         try:
             _execute_psyco('SELECT 1', dsn)
-        except psycopg2.OperationalError:
+        except psycopg.OperationalError:
             return False
 
         return True
@@ -227,8 +226,8 @@ def create_dbuser_db_safe(self, dbname, dbuser, dbpass):
         return dbuser, dbname
 
     @property
-    def host_for_psycopg2(self):
-        """Return correct host for psycopg2 connection (as required by regular AiiDA operation)."""
+    def host_for_psycopg(self):
+        """Return correct host for psycopg connection (as required by regular AiiDA operation)."""
         host = self.dsn.get('host')
         if self.connection_mode == PostgresConnectionMode.PSQL:
             # If "sudo su postgres" was needed to create the DB, we are likely on Ubuntu, where
@@ -238,8 +237,8 @@ def host_for_psycopg2(self):
         return host
 
     @property
-    def port_for_psycopg2(self):
-        """Return port for psycopg2 connection (as required by regular AiiDA operation)."""
+    def port_for_psycopg(self):
+        """Return port for psycopg connection (as required by regular AiiDA operation)."""
         return self.dsn.get('port')
 
     @property

src/aiida/manage/tests/pytest_fixtures.py

@@ -96,7 +96,7 @@ def create_database(
         from aiida.manage.external.postgres import Postgres
 
         postgres_config = {
-            'database_engine': 'postgresql_psycopg2',
+            'database_engine': 'postgresql_psycopg',
             'database_name': database_name or str(uuid.uuid4()),
             'database_username': database_username or 'guest',
             'database_password': database_password or 'guest',
@@ -109,8 +109,8 @@ def create_database(
             )
         postgres.create_db(postgres_config['database_username'], postgres_config['database_name'])
 
-        postgres_config['database_hostname'] = postgres.host_for_psycopg2
-        postgres_config['database_port'] = postgres.port_for_psycopg2
+        postgres_config['database_hostname'] = postgres.host_for_psycopg
+        postgres_config['database_port'] = postgres.port_for_psycopg
 
         return postgres_config
 

src/aiida/restapi/common/utils.py

@@ -9,7 +9,7 @@
 """Util methods"""
 
 import urllib.parse
-from datetime import datetime, timedelta
+from datetime import datetime, timedelta, timezone
 
 from flask import jsonify
 from flask.json.provider import DefaultJSONProvider
@@ -670,7 +670,6 @@ def parse_query_string(self, query_string):
         :param query_string (as obtained from request.query_string)
         :return: parsed values for the querykeys
         """
-        from psycopg2.tz import FixedOffsetTimezone
         from pyparsing import (
             Combine,
             Group,
@@ -774,10 +773,10 @@ def validate_time(toks):
             if dtobj.tzinfo is not None and dtobj.utcoffset() is not None:
                 tzoffset_minutes = int(dtobj.utcoffset().total_seconds() // 60)
                 return DatetimePrecision(
-                    dtobj.replace(tzinfo=FixedOffsetTimezone(offset=tzoffset_minutes, name=None)), precision
+                    dtobj.replace(tzinfo=timezone(offset=timedelta(minutes=tzoffset_minutes), name='UTC')), precision
                 )
 
-            return DatetimePrecision(dtobj.replace(tzinfo=FixedOffsetTimezone(offset=0, name=None)), precision)
+            return DatetimePrecision(dtobj.replace(tzinfo=timezone(offset=timedelta(minutes=0), name='UTC')), precision)
 
         ########################################################################
 

src/aiida/storage/psql_dos/backend.py

@@ -80,7 +80,7 @@ class Model(BaseModel, defer_build=True):
         database_engine: str = Field(
             title='PostgreSQL engine',
             description='The engine to use to connect to the database.',
-            default='postgresql_psycopg2',
+            default='postgresql_psycopg',
         )
         database_hostname: str = Field(
             title='PostgreSQL hostname', description='The hostname of the PostgreSQL server.', default='localhost'

src/aiida/storage/psql_dos/utils.py

@@ -42,7 +42,7 @@ def create_sqlalchemy_engine(config: PsqlConfig):
     separator = ':' if config['database_port'] else ''
     password = quote_plus(config['database_password'])
 
-    engine_url = 'postgresql://{user}:{password}@{hostname}{separator}{port}/{name}'.format(
+    engine_url = 'postgresql+psycopg://{user}:{password}@{hostname}{separator}{port}/{name}'.format(
         separator=separator,
         user=config['database_username'],
         password=password,

src/aiida/tools/pytest_fixtures/storage.py

@@ -29,7 +29,7 @@ def create_database(
         from aiida.manage.external.postgres import Postgres
 
         postgres_config = {
-            'database_engine': 'postgresql_psycopg2',
+            'database_engine': 'postgresql_psycopg',
             'database_name': database_name or str(uuid4()),
             'database_username': database_username or 'guest',
             'database_password': database_password or 'guest',
@@ -42,8 +42,8 @@ def create_database(
             )
         postgres.create_db(postgres_config['database_username'], postgres_config['database_name'])
 
-        postgres_config['database_hostname'] = postgres.host_for_psycopg2
-        postgres_config['database_port'] = postgres.port_for_psycopg2
+        postgres_config['database_hostname'] = postgres.host_for_psycopg
+        postgres_config['database_port'] = postgres.port_for_psycopg
 
         return postgres_config