Skip to content
Permalink
Branch: dev
Commits on Aug 19, 2019
  1. Merge pull request #8409 from bernt-matthias/topic/argument-dashes

    mvdbeek committed Aug 19, 2019
    argument tag: automatically replace dashes by underscores
  2. Merge pull request #8334 from WilliamHolden/nav_cues

    martenson committed Aug 19, 2019
    Update anchor tags and enhance navigation cues for screen readers
  3. Merge pull request #8315 from natefoo/installable-config

    mvdbeek committed Aug 19, 2019
    Config updates for installable Galaxy
  4. Merge pull request #8473 from nsoranzo/restore_mysql

    mvdbeek committed Aug 19, 2019
    Fix MySQL database creation and migrations
  5. documentation improvements

    bernt-matthias and nsoranzo committed Aug 14, 2019
    Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
  6. Merge pull request #8477 from nsoranzo/conda_common_startup_fixes

    mvdbeek committed Aug 19, 2019
    Fix startup checks when using a Conda env
  7. fix apparent copy paste error

    bernt-matthias and nsoranzo committed Aug 14, 2019
    Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
  8. argument tag: move name+argument parsing

    bernt-matthias and nsoranzo committed Aug 14, 2019
    - to tool_util.parser.util
    - make ToolParameter.build work with InputSource
      instead of plain XML as commonly done in tests
    - refactor stdio related function to tool_util.parser.stdio
      to avoid circular import
    
    Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
  9. add linting of input and output names

    3 people committed Aug 5, 2019
    checks if input and output names are valid cheetah placeholders
    
    Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
    Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
  10. Fix startup checks when using a Conda env

    nsoranzo committed Aug 19, 2019
    Unless `--skip-venv` is specified, Galaxy creates/activates a virtualenv
    also when using a Conda environment.
Commits on Aug 18, 2019
  1. Merge pull request #8104 from dannon/ordereddicts

    nsoranzo committed Aug 18, 2019
    Swap out galaxy.util.odict for core python collections.OrderedDicts
  2. Reimplement `MetadataSpecCollection` as subclass of `OrderedDict`

    nsoranzo committed Aug 18, 2019
  3. Fix symlink busted in rebase.

    dannon authored and nsoranzo committed Aug 15, 2019
  4. Retain odict module for use in tool panel and metadata extensions, note

    dannon authored and nsoranzo committed Aug 15, 2019
    that it likely should not be used *unless* insert functionality is
    specifically required.
  5. Attempt to fix a TODO in cwl/representation since OrderedDict is json…

    dannon authored and nsoranzo committed Jun 6, 2019
    … serializable.
  6. Merge pull request #8456 from selten/data-libraries-file-extension

    bgruening committed Aug 18, 2019
    Add file extensions when downloading from data libraries
  7. Fix MySQL database creation and migrations

    nsoranzo committed Aug 15, 2019
    Fix #6401 .
    Fix #8400 .
    
    Remove `index=True` from some `Column()` definitions in
    lib/galaxy/model/mapping.py when the index was not part of any migration.
  8. Handle better an SQLAlchemy Migrate issue

    nsoranzo committed Aug 14, 2019
    when adding a column with both a ForeignKey and an index in SQLite.
  9. Another round of migration refactoring

    nsoranzo committed Aug 14, 2019
    Allow `table` to be a string in `drop_table()`.
    
    Sync definition of `form_definition` and `form_definition_current` tables
    between migration 8 and `mapping.py` .
    
    Drop unnecessary logging configurations.
  10. Fix create_db.sh

    nsoranzo committed Aug 14, 2019
    Broken in commit d34142e .
    
    Traceback:
    
    ```
    $ rm -f database/universe.sqlite && sqlite3 database/universe.sqlite 'VACUUM;' && ./create_db.sh
    Activating virtualenv at .venv
    Traceback (most recent call last):
      File "./scripts/create_db.py", line 44, in <module>
        invoke_create()
      File "./scripts/create_db.py", line 36, in invoke_create
        create_db(config['db_url'], config['config_file'])
      File "/opt/galaxy/lib/galaxy/model/migrate/check.py", line 74, in create_or_verify_database
        elif getattr(app.config, 'database_auto_migrate', False):
    AttributeError: 'NoneType' object has no attribute 'config'
    ```
Commits on Aug 17, 2019
  1. Merge pull request #8469 from jmchilton/amqp_sep

    nsoranzo committed Aug 17, 2019
    Try separate amqp connection from database for integration testing.
Commits on Aug 16, 2019
  1. Merge pull request #8470 from erasche/fix-975

    jmchilton committed Aug 16, 2019
    Fix #975
  2. Merge pull request #8465 from erasche/remove-deprecated

    jmchilton committed Aug 16, 2019
    Remove deprecated scripts
  3. Merge pull request #8468 from jmchilton/cleanup_integraiton

    jmchilton committed Aug 16, 2019
    Don't cleanup integration tests twice.
  4. Fix #975

    erasche committed Aug 16, 2019
Commits on Aug 15, 2019
  1. Merge pull request #8466 from dannon/fix-style-overhaul-positioning

    guerler committed Aug 15, 2019
    Fix absolutely positioned elements and children from displaying off-screen.
  2. Try separate amqp connection from database for integration testing.

    jmchilton committed Aug 15, 2019
    In case this is what is holding on to the connection causing tests to fail.
Older
You can’t perform that action at this time.