feat!: change default postgresql port to 5432 (#292)

* close #288

docs/source/install.rst

@@ -42,9 +42,9 @@ Cool-Seq-Tool requires an available instance of the Universal Transcript Archive
 
    export UTA_VERSION=uta_20210129b.pgd.gz  # most recent as of 2023/12/05
    curl -O https://dl.biocommons.org/uta/$UTA_VERSION
-   gzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5433
+   gzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432
 
-By default, Cool-Seq-Tool expects to connect to the UTA database via a PostgreSQL connection served local on port 5433, under the PostgreSQL username ``uta_admin`` and the schema ``uta_20210129b``.
+By default, Cool-Seq-Tool expects to connect to the UTA database via a PostgreSQL connection served local on port 5432, under the PostgreSQL username ``uta_admin`` and the schema ``uta_20210129b``.
 
 Set up SeqRepo
 --------------

docs/source/usage.rst

@@ -101,7 +101,7 @@ Individual classes will accept arguments upon initialization to set parameters r
    * - ``SEQREPO_ROOT_DIR``
      - Path to SeqRepo directory (i.e. contains ``aliases.sqlite3`` database file, and ``sequences`` directory). Used by :py:class:`SeqRepoAccess <cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess`. If not defined, defaults to ``/usr/local/share/seqrepo/latest``.
    * - ``UTA_DB_URL``
-     - A `libpq connection string <https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING>`_, i.e. of the form ``postgresql://<user>:<password>@<host>:<port>/<database>/<schema>``, used by the :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b``.
+     - A `libpq connection string <https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING>`_, i.e. of the form ``postgresql://<user>:<password>@<host>:<port>/<database>/<schema>``, used by the :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b``.
    * - ``LIFTOVER_CHAIN_37_TO_38``
      - A path to a `chainfile <https://genome.ucsc.edu/goldenPath/help/chain.html>`_ for lifting from GRCh37 to GRCh38. Used by :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` as input to `agct <https://pypi.org/project/agct/>`_. If not provided, agct will fetch it automatically from UCSC.
    * - ``LIFTOVER_CHAIN_38_TO_37``

src/cool_seq_tool/sources/uta_database.py

@@ -24,7 +24,7 @@
 LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37")
 
 UTA_DB_URL = environ.get(
-    "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b"
+    "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b"
 )
 
 logger = logging.getLogger(__name__)

src/cool_seq_tool/version.py

@@ -1,2 +1,2 @@
 """Define package version."""
-__version__ = "0.4.0-dev3"
+__version__ = "0.4.0-dev4"