Merge remote-tracking branch 'upstream/main' into ts-tests

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Format Python code with black and isort
+7bcd07db8392ac790d1b0b92f4a377945197e43d

.github/workflows/deploy.yaml

@@ -4,8 +4,8 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
         with:
           python-version: '3.10'
       - name: Install dependencies
@@ -18,7 +18,7 @@ jobs:
           twine check dist/*
       - name: Publish to PyPI
         if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'galaxyproject'
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/lint.yaml

@@ -1,14 +1,17 @@
 name: Lint
 on: [push, pull_request]
+concurrency:
+  group: lint-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   lint:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.6']
+        python-version: ['3.7', '3.10']
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install tox

.github/workflows/test.yaml

@@ -5,6 +5,9 @@ on:
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
+concurrency:
+  group: test-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test-galaxy:
     if: github.event_name != 'schedule' || github.repository_owner == 'galaxyproject'
@@ -29,9 +32,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        tox_env: [py36]
+        tox_env: [py37]
         galaxy_version:
           - dev
+          - release_22.01
           - release_21.09
           - release_21.05
           - release_21.01
@@ -49,22 +53,13 @@ jobs:
           - os: ubuntu-latest
             tox_env: py310
             galaxy_version: dev
-          - os: ubuntu-latest
-            tox_env: py39
-            galaxy_version: dev
-          - os: ubuntu-latest
-            tox_env: py38
-            galaxy_version: dev
-          - os: ubuntu-latest
-            tox_env: py37
-            galaxy_version: dev
           # Cannot test on macOS because service containers are not supported
           # yet: https://github.community/t/github-actions-services-available-on-others-vms/16916
           # - os: macos-latest
-          #   tox_env: py36
+          #   tox_env: py37
           #   galaxy_version: dev
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Cache pip dir
         uses: actions/cache@v2
         with:
@@ -74,7 +69,7 @@ jobs:
         id: get_bioblend_python_version
         run: echo "::set-output name=bioblend_python_version::$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')"
       - name: Set up Python for BioBlend
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
       - name: Install tox
@@ -91,13 +86,15 @@ jobs:
             release_20.0* )
               galaxy_python_version=3.5
               ;;
-            release_21.0* | dev )
+            release_21.0* )
               galaxy_python_version=3.6
               ;;
+            release_22.0* | dev )
+              galaxy_python_version=3.7
           esac
           echo "::set-output name=galaxy_python_version::$galaxy_python_version"
       - name: Set up Python for Galaxy
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
       - name: Run Galaxy tests
@@ -109,31 +106,14 @@ jobs:
           # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
           createdb -U postgres galaxy
           # Install Galaxy
-          wget https://github.com/galaxyproject/galaxy/archive/${{ matrix.galaxy_version }}.tar.gz
-          tar xvzf ${{ matrix.galaxy_version }}.tar.gz | tail
-          cd galaxy-${{ matrix.galaxy_version }}
-          export GALAXY_DIR=$PWD
-          export GALAXY_PYTHON=python${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
-          export GALAXY_VERSION=${{ matrix.galaxy_version }}
-          # Export GALAXY_CONFIG_FILE environment variable to be used by run_galaxy.sh
-          export GALAXY_CONFIG_FILE=config/galaxy.ini
-          # Export BIOBLEND_ environment variables to be used in BioBlend tests
-          export BIOBLEND_GALAXY_MASTER_API_KEY=$(LC_ALL=C tr -dc A-Za-z0-9 < /dev/urandom | head -c 32)
-          export BIOBLEND_GALAXY_USER_EMAIL=${USER}@localhost.localdomain
+          GALAXY_DIR=galaxy-${{ matrix.galaxy_version }}
+          git clone --depth=1 -b ${{ matrix.galaxy_version }} https://github.com/galaxyproject/galaxy $GALAXY_DIR
           export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
-          eval "echo \"$(cat "${{ github.workspace }}/tests/template_galaxy.ini")\"" > "$GALAXY_CONFIG_FILE"
-          # Update psycopg2 requirement to a version compatible with glibc 2.26 for Galaxy releases 16.01-18.01, see https://github.com/psycopg/psycopg2-wheels/issues/2
-          sed -i.bak -e 's/psycopg2==2.6.1/psycopg2==2.7.3.1/' lib/galaxy/dependencies/conditional-requirements.txt
-          # Start Galaxy and wait for successful server start
-          export GALAXY_SKIP_CLIENT_BUILD=1
-          GALAXY_RUN_ALL=1 "${{ github.workspace }}/run_galaxy.sh" --daemon --wait
-          export BIOBLEND_GALAXY_URL=http://localhost:8080
-          cd "${{ github.workspace }}"
-          tox -e ${{ matrix.tox_env }}
+          ./run_bioblend_tests.sh -g $GALAXY_DIR -v python${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }} -e ${{ matrix.tox_env }}
       - name: The job has failed
         if: ${{ failure() }}
         run: |
-          cat galaxy-${{ matrix.galaxy_version }}/main.log
+          cat galaxy-${{ matrix.galaxy_version }}/*.log
   test-toolshed:
     if: (github.event_name != 'schedule' || github.repository_owner == 'galaxyproject') && git diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | grep 'bioblend/toolshed'
     runs-on: ${{ matrix.os }}

.isort.cfg

@@ -0,0 +1,10 @@
+[settings]
+force_alphabetical_sort_within_sections=true
+# Override force_grid_wrap value from profile=black, but black is still happy
+force_grid_wrap=2
+# Same line length as for black
+line_length=120
+no_lines_before=LOCALFOLDER
+profile=black
+reverse_relative=true
+skip_gitignore=true

ABOUT.rst

@@ -3,8 +3,8 @@ interacting with `Galaxy`_ and `CloudMan`_  APIs.
 
 BioBlend is supported and tested on:
 
-- Python 3.6, 3.7, 3.8, 3.9 and 3.10
-- Galaxy release_17.09 and later.
+- Python 3.7, 3.8, 3.9 and 3.10
+- Galaxy release 17.09 and later.
 
 BioBlend's goal is to make it easier to script and automate the running of
 Galaxy analyses, administering of a Galaxy server, and cloud infrastructure

CHANGELOG.md

@@ -1,10 +1,67 @@
-### BioBlend v - unreleased
+### BioBlend v
 
-* Added support for Python 3.10. Added support for Galaxy release 21.09.
+* Format Python code with black and isort.
+
+### BioBlend v0.17.0 - 2022-05-09
+
+* Dropped support for Python 3.6. Added support for Python 3.10. Added support
+  for Galaxy releases 21.09 and 22.01.
+
+* Removed deprecated ``run_workflow()`` method of ``WorkflowClient``.
+
+* Using the deprecated ``history_id`` parameter of the
+  ``HistoryClient.get_histories()`` method now raises a ``ValueError``
+  exception.
+
+* Made ``tool_inputs_update`` parameter of ``JobsClient.rerun_job()`` more
+  flexible.
+
+* Added ``whoami()`` method to ``ConfigClient`` (thanks to
+  [cat-bro](https://github.com/cat-bro)).
 
 * Added ``get_extra_files()`` method to ``HistoryClient``.
 
-* Improvements to type annotations, tests and documentation
+* Added ``build()`` and ``reload()`` methods to ``ToolClient`` (thanks to
+  [Jayadev Joshi](https://github.com/jaidevjoshi83) and
+  [cat-bro](https://github.com/cat-bro) respectively).
+
+* Added ``get_repositories()`` method to ``ToolShedCategoryClient`` (thanks to
+  [cat-bro](https://github.com/cat-bro)).
+
+* Added ``update_repository_metadata()`` method to ``ToolShedRepositoryClient``.
+
+* Added ``order_by`` parameter to ``JobsClient.get_jobs()`` method.
+
+* BioBlend.objects: Removed deprecated ``run()`` method of ``Workflow``.
+
+* BioBlend.objects: Fail if multiple libraries/histories/workflows match when
+  deleting by name, instead of deleting them all.
+
+* BioBlend.objects: in ``HistoryDatasetAssociation.get_stream()``, wait for
+  the dataset to be ready.
+
+* BioBlend.objects: in ``Workflow.invoke()``, check that the workflow is mapped
+  and runnable before invoking, allow the ``inputs`` parameter to be an instance
+  of a ``Dataset`` subclass, and allow the ``history`` parameter to be the name
+  of a new history.
+
+* BioBlend.objects: Added new ``datasets`` and ``dataset_collections``
+  attributes to ``GalaxyInstance`` objects, which are instances of the new
+  ``ObjDatasetClient`` and ``ObjDatasetCollectionClient`` respectively.
+
+* BioBlend.objects: Added ``refresh()``, ``get_outputs()`` and
+  ``get_output_collections()`` methods to ``InvocationStep``.
+
+* Fixed [error](https://github.com/galaxyproject/bioblend/issues/398) when
+  instantiating ``GalaxyInstance`` with ``email`` and ``password`` (reported by
+  [Peter Briggs](https://github.com/pjbriggs)).
+
+* Fixed parameter validation errors for POST requests with attached files on
+  upcoming Galaxy 22.05.
+
+* Code cleanups (thanks to [Martmists](https://github.com/Martmists-GH)).
+
+* Improvements to type annotations, tests and documentation.
 
 ### BioBlend v0.16.0 - 2021-06-13
 
@@ -276,7 +333,7 @@
 * BioBlend.objects: added ``update()`` method to ``LibraryDataset`` (thanks to
   [Anthony Bretaudeau](https://github.com/abretaud)).
 
-* Run tests with pytest instead of nose
+* Run tests with pytest instead of nose.
 
 ### BioBlend v0.11.0 - 2018-04-18
 
@@ -409,7 +466,7 @@
 
 * Added ``install_resolver_dependencies`` parameter to
   ``ToolShedClient.install_repository_revision()``, applicable for Galaxy
-  release_16.07 and later (thanks to
+  release 16.07 and later (thanks to
   [Marius van den Beek](https://github.com/mvdbeek)).
 
 * Improve ``DatasetClient.download_dataset()`` by downloading the dataset in
@@ -525,7 +582,7 @@
 * Project source moved to new URL - https://github.com/galaxyproject/bioblend
 
 * Huge improvements to automated testing, tests now run against Galaxy
-  release_14.02 and all later versions to ensure backward compatibility
+  release 14.02 and all later versions to ensure backward compatibility
   (see `.travis.yml` for details).
 
 * Many documentation improvements (thanks to
@@ -549,7 +606,7 @@
   deployments.
 
 * Made ``LibraryClient._get_root_folder_id()`` method safer and faster for
-  Galaxy release_13.06 and later.
+  Galaxy release 13.06 and later.
 
 * Deprecate and ignore invalid ``deleted`` parameter to
   ``WorkflowClient.get_workflows()``.

README.rst

@@ -16,8 +16,8 @@ APIs.
 
 BioBlend is supported and tested on:
 
-- Python 3.6, 3.7, 3.8, 3.9 and 3.10
-- Galaxy release_17.09 and later.
+- Python 3.7, 3.8, 3.9 and 3.10
+- Galaxy release 17.09 and later.
 
 Full docs are available at https://bioblend.readthedocs.io/ with a quick library
 overview also available in `ABOUT.rst <./ABOUT.rst>`_.

bioblend/__init__.py

@@ -8,11 +8,12 @@
 )
 
 # Current version of the library
-__version__ = '0.16.0'
+__version__ = "0.17.0"
 
 # default chunk size (in bytes) for reading remote data
 try:
     import resource
+
     CHUNK_SIZE = resource.getpagesize()
 except Exception:
     CHUNK_SIZE = 4096
@@ -47,7 +48,7 @@ def emit(self, record):
 #   import logging
 #   logging.basicConfig(filename="bioblend.log", level=logging.DEBUG)
 default_format_string = "%(asctime)s %(name)s [%(levelname)s]: %(message)s"
-log = logging.getLogger('bioblend')
+log = logging.getLogger("bioblend")
 log.addHandler(NullHandler())
 init_logging()
 
@@ -94,6 +95,7 @@ class ConnectionError(Exception):
     proxy server getting in the way of the request etc.
     @see: body attribute to see the content of the http response
     """
+
     def __init__(self, message, body=None, status_code=None):
         super().__init__(message)
         self.body = body