🐛 FIX: CREATE DATABASE with psycopg2 v2.9 (#27)

Addresses aiidateam/aiida-core#5002:
In v2.9, the context manager opens a transaction, but databases cannot be created within them.
The fix is taken from: psycopg/psycopg2#941 (comment)

.github/workflows/ci.yml

@@ -6,7 +6,7 @@ jobs:
 
   pre-commit:
 
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     timeout-minutes: 5
 
     steps:
@@ -17,15 +17,9 @@ jobs:
       with:
         python-version: 3.8
 
-    - name: Install system dependencies
-      run: |
-        sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
-        sudo apt update
-        sudo apt install libkrb5-dev ruby ruby-dev
-
     - name: Install python dependencies
       run: |
-        pip install -e .[pre-commit,testing]
+        pip install -e .[pre_commit,testing]
         pip freeze
 
     - name: Run pre-commit
@@ -40,7 +34,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.5, 3.9]
+        python-version: [3.6, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -76,14 +70,14 @@ jobs:
         file: ./coverage.xml
         fail_ci_if_error: true
 
-  ubuntu-apt-1604:
+  ubuntu-apt-1804:
     # ubuntu using postgresql installed via apt (+ pgtest)
-    runs-on: ubuntu-16.04
+    runs-on: ubuntu-18.04
     timeout-minutes: 5
 
     strategy:
       matrix:
-        python-version: [3.5]
+        python-version: [3.6]
 
     steps:
     - uses: actions/checkout@v2
@@ -97,9 +91,9 @@ jobs:
       run: |
         sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
         sudo apt update
-        sudo apt install postgresql-12
-        sudo cat /etc/postgresql/12/main/pg_hba.conf
-        sudo pg_ctlcluster 12 main start
+        sudo apt install postgresql-10
+        sudo cat /etc/postgresql/10/main/pg_hba.conf
+        sudo pg_ctlcluster 10 main start
 
     - name: Install pgsu
       run: |

.pre-commit-config.yaml

@@ -9,6 +9,11 @@ repos:
   - id: mixed-line-ending
   - id: trailing-whitespace
 
+- repo: https://github.com/asottile/setup-cfg-fmt
+  rev: v1.17.0
+  hooks:
+  - id: setup-cfg-fmt
+
 # yapf = yet another python formatter
 - repo: https://github.com/pre-commit/mirrors-yapf
   rev: v0.30.0

pgsu/__init__.py

@@ -250,16 +250,18 @@ def _execute_psyco(command, dsn):
     """
     import psycopg2  # pylint: disable=import-outside-toplevel
 
+    conn = None
     output = None
-    with psycopg2.connect(**dsn) as conn:
+    try:
+        conn = psycopg2.connect(**dsn)
         conn.autocommit = True
         with conn.cursor() as cursor:
             cursor.execute(command)
             if cursor.description is not None:
                 output = cursor.fetchall()
-
-    # see http://initd.org/psycopg/docs/usage.html#with-statement
-    conn.close()
+    finally:
+        if conn:
+            conn.close()
     return output
 
 
@@ -314,15 +316,15 @@ def _execute_su_psql(command, dsn, interactive=False, stderr=None):
 
     database = dsn.get('database')
     if database:
-        psql_option_str += '-d {}'.format(database)
+        psql_option_str += f'-d {database}'
 
     # to do: Forward password to psql; ignore host only when the password is None.  # pylint: disable=fixme
     # Note: There is currently no known postgresql setup that needs this, though
     # password = dsn.get('password')
 
     host = dsn.pop('host', 'localhost')
     if host and host != 'localhost':
-        psql_option_str += ' -h {}'.format(host)
+        psql_option_str += f' -h {host}'
     else:
         LOGGER.debug(
             "Found host 'localhost' but dropping '-h localhost' option for psql "
@@ -331,7 +333,7 @@ def _execute_su_psql(command, dsn, interactive=False, stderr=None):
 
     port = dsn.get('port')
     if port:
-        psql_option_str += ' -p {}'.format(port)
+        psql_option_str += f' -p {port}'
 
     # Note: This is *both* the UNIX user to become *and* the database user
     user = dsn.get('user')
@@ -382,7 +384,7 @@ def escape_for_bash(str_to_escape):
     string found below.
     """
     escaped_quotes = str_to_escape.replace("'", """'"'"'""")
-    return "'{}'".format(escaped_quotes)
+    return f"'{escaped_quotes}'"
 
 
 def unique_list(non_unique_list):

pgsu/cli.py

@@ -14,6 +14,6 @@
 def run(query):
     """Execute SQL command as PostrgreSQL superuser."""
     pgsu = PGSU(interactive=True, quiet=False)
-    click.echo('Executing query: {}'.format(query))
+    click.echo(f'Executing query: {query}')
     dbs = pgsu.execute(query)
     click.echo(pprint.pformat(dbs))

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["setuptools>=46.4.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
 [tool.pylint.format]
 max-line-length = 120
 max-args = 7

setup.cfg

@@ -1,2 +1,51 @@
+[metadata]
+name = pgsu
+version = 0.2.0
+description = Connect to an existing PostgreSQL cluster as a postgres superuser and execute SQL commands.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/aiidateam/pgsu
+author = AiiDA Team
+author_email = aiidateam@gmail.com
+license = MIT
+license_file = LICENSE
+classifiers =
+    License :: OSI Approved :: MIT License
+    Operating System :: MacOS :: MacOS X
+    Operating System :: Microsoft :: Windows
+    Operating System :: POSIX :: Linux
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: Implementation :: CPython
+
+[options]
+packages = find:
+install_requires =
+    click
+    psycopg2-binary>=2.8.3
+python_requires = ~=3.6
+
+[options.packages.find]
+exclude =
+    test*
+
+[options.entry_points]
+console_scripts =
+    pgsu = pgsu.cli:run
+
+[options.extras_require]
+pre_commit =
+    pre-commit~=2.2
+    pylint~=2.5.0
+testing =
+    pgtest>=1.3.1
+    pytest
+    pytest-cov
+
 [coverage:run]
-parallel=true
+parallel = true

setup.py

@@ -1,42 +1,9 @@
 # -*- coding: utf-8 -*-
-"""Setup script for pgsu python package"""
-import os
-from setuptools import setup, find_packages
+"""This file is needed for editable installs (`pip install -e .`).
 
-THIS_FOLDER = os.path.split(os.path.abspath(__file__))[0]
+Can be removed once the following is resolved
+https://github.com/pypa/packaging-problems/issues/256
+"""
+from setuptools import setup
 
-setup(
-    name='pgsu',
-    version='0.2.0',
-    description=
-    ('Connect to an existing PostgreSQL cluster as a postgres superuser and execute SQL commands.'
-     ),
-    long_description=open(os.path.join(THIS_FOLDER, 'README.md')).read(),
-    long_description_content_type='text/markdown',
-    url='https://github.com/aiidateam/pgsu',
-    author='AiiDA Team',
-    author_email='aiidateam@gmail.com',
-    classifiers=[
-        'License :: OSI Approved :: MIT License',
-        'Operating System :: POSIX :: Linux',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: Microsoft :: Windows',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-    ],
-    license='MIT',
-    packages=find_packages(),
-    install_requires=[
-        'psycopg2-binary>=2.8.3',
-        'click',
-    ],
-    extras_require={
-        'testing': ['pytest', 'pgtest>=1.3.1', 'pytest-cov'],
-        # note: pre-commit hooks require python3
-        'pre-commit': ['pre-commit~=2.2', 'pylint~=2.5.0']
-    },
-    entry_points={'console_scripts': ['pgsu=pgsu.cli:run']})
+setup()

tox.ini

@@ -0,0 +1,16 @@
+# To use tox, see https://tox.readthedocs.io
+# Simply pip or conda install tox
+# If you use conda, you may also want to install tox-conda
+# then run `tox` or `tox -- {pytest args}`
+# run in parallel using `tox -p`
+[tox]
+envlist = py38
+
+[testenv]
+usedevelop = true
+
+[testenv:py{37,38,39}]
+description = Run unit tests with this Python version
+extras =
+    testing
+commands = pytest {posargs}