Hi,
I’m trying to run the tutorial for the LSST Science pipelines and have trouble following these instructions:
Getting started tutorial part 1: setting up the Butler data repository — LSST Science Pipelines
Namely the command:
git clone -b v25_0_1 GitHub - lsst/rc2_subset: A small subset of the RC2 dataset for running DRP
fails with the error:
fatal: Remote branch v25_0_1 not found in upstream origin
and if I ignore the branch and proceed I get the following error when trying to initialize butler:
Failed to instantiate Butler from config file:///home/viitanen/tutorial_lsst_pipelines/rc2_subset/SMALL_HSC/butler.yaml.
Traceback (most recent call last):
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1910, in _execute_context
self.dialect.do_execute(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/default.py”, line 736, in do_execute
cursor.execute(statement, parameters)
sqlite3.DatabaseError: file is not a database
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “”, line 1, in
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/_butler.py”, line 282, in init
self.registry = Registry.fromConfig(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/_registry.py”, line 230, in fromConfig
return registry_cls.fromConfig(config, butlerRoot, writeable, defaults)
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registries/sql.py”, line 207, in fromConfig
managers = managerTypes.loadRepo(database)
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/managers.py”, line 242, in loadRepo
with database.declareStaticTables(create=False) as context:
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/contextlib.py”, line 135, in enter
return next(self.gen)
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/interfaces/_database.py”, line 678, in declareStaticTables
context = StaticTablesContext(self, connection)
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/interfaces/_database.py”, line 118, in init
self._tableNames = frozenset(self._inspector.get_table_names(schema=self._db.namespace))
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/reflection.py”, line 266, in get_table_names
return self.dialect.get_table_names(
File “”, line 2, in get_table_names
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/reflection.py”, line 55, in cache
ret = fn(self, con, *args, **kw)
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/dialects/sqlite/base.py”, line 1993, in get_table_names
rs = connection.exec_driver_sql(s)
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1770, in exec_driver_sql
return self._exec_driver_sql(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1674, in _exec_driver_sql
ret = self._execute_context(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1953, in _execute_context
self.handle_dbapi_exception(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 2134, in handle_dbapi_exception
util.raise(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/util/compat.py”, line 211, in raise
raise exception
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1910, in _execute_context
self.dialect.do_execute(
File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/default.py”, line 736, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.DatabaseError: (sqlite3.DatabaseError) file is not a database
[SQL: SELECT name FROM sqlite_master WHERE type=‘table’ ORDER BY name]
(Background on this error at: Error Messages — SQLAlchemy 1.4 Documentation)
For installing the LSST Science Pipelines I followed the instructions here:
Install with lsstinstall and eups distrib — LSST Science Pipelines
and verified that the issue is not due to git LFS, i.e. running the final git clone here Configuring Git LFS for downloading LSST data packages — LSST Science Pipelines finishes without errors.
Best,
-akke