Replaces yarn with pnpm throughout the Makefile and common_startup.sh.
The startup script now installs pnpm via conda, corepack, or npm
depending on the environment.
by runnig:
```shell
make pyupgrade
ruff check --fix .
make format
```
Also update ruff configuration to:
- Enable UP006 and UP035 error codes for PEP 585 type annotations
- Ignore UP045 for the packages which need to stay compatible with Python 3.8
- Add tool-util-models paths to those that need to stay compatible with Python 3.8
Updates repository_metadata.tools with new and correct file locations.
The test toolshed moved around `file_path` multiple times since its
inception, and old revisions might point at old location. This is a
simple script that fixes the locations. It has a dry run mode that I've
run successfully:
```
----------------------------------------------------------------------
Dry run complete - no changes made to database
======================================================================
SUMMARY
======================================================================
Total RepositoryMetadata records processed: 25414
RepositoryMetadata with tools: 22497
Total tools examined: 40470
Tools with correct paths (unchanged): 3898
Tools with paths updated: 36572
- Tool file exists on disk: 33297
- Tool file missing (removed in later changeset): 3275
Tools with path construction errors: 0
======================================================================
```
it also write out json files for each repository as backups should
this be needed.
Closes https://github.com/galaxyproject/galaxy/issues/21454
Found by running:
```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```
The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases
Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
packages needed by Pulsar, including the new galaxy-tool-util-models
package.
This statement is prepared for SQLAlchemy but executed via psycopg2 in
the `pgcleanup.py` script. For psycopg2, the "%" character should be replaced
with %% (see docs
https://www.psycopg.org/docs/usage.html#passing-parameters-to-sql-queries).
SQLAlchemy already takes care of it automatically.
for proper type annotation of query results.
Also:
- Drop unused code from `lib/tool_shed/webapp/controllers/user.py`
- Drop Galaxy model code from
`lib/tool_shed/util/admin_util.py:Admin.purge_user()`
John Davis