Merge remote-tracking branch 'upstream/master' into serve-test

Author: simonbray

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Code formatting with black and isort
+4d8fc5a87a4b9f544a8d099eb2e97dbff505e3db

.github/workflows/ci.yaml

@@ -13,11 +13,11 @@ env:
 jobs:
   test:
     runs-on: ubuntu-latest
-    timeout-minutes: 90
+    timeout-minutes: 100
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.6']
+        python-version: ['3.7']
         tox-action:
           - lint
           - lint_docs
@@ -30,8 +30,8 @@ jobs:
           #- unit-diagnostic-servetraining
           #- unit-diagnostic-servecmd
           #- unit-diagnostic-trainingwfcmd
-          - unit-nonredundant-noclientbuild-noshed-gx-2005
-          - unit-nonredundant-noclientbuild-noshed-gx-2009
+          - unit-nonredundant-noclientbuild-noshed-gx-2105
+          - unit-nonredundant-noclientbuild-noshed-gx-2109
           - unit-nonredundant-noclientbuild-noshed-gx-dev
           - unit-nonredundant-noclientbuild-noshed
           - unit-diagnostic-serveclientcmd
@@ -47,20 +47,20 @@ jobs:
         # needed because the postgres container does not provide a healthcheck
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 1
           submodules: true
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Test psql
         run: |
           psql --tuples-only --username postgres -P pager=off --list
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install tox coveralls
+          python -m pip install --upgrade pip setuptools
+          python -m pip install tox coveralls
       - name: Checkout system space
         run: |
           df
@@ -72,11 +72,11 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 1
           submodules: true
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v3
         with:
           python-version: '3.7'
       - name: Install dependencies
@@ -88,6 +88,6 @@ jobs:
           make dist
       - name: Publish to PyPI
         if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.0.0a0
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.pypi_password }}

.isort.cfg

@@ -0,0 +1,11 @@
+[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
+skip_glob=docs/standards/*

HISTORY.rst

@@ -11,6 +11,14 @@ History
 
 
 
+---------------------
+0.74.9 (2021-11-03)
+---------------------
+* Fix rendering of subworkflow steps for workflow testing report (thanks to
+  `@simonbray`_). `Pull Request 1200`_
+* Replace Galaxy interactor galaxy_requests_post with make_post_request from
+  BioBlend (thanks to `@simonbray`_). `Pull Request 1201`_
+
 ---------------------
 0.74.8 (2021-10-10)
 ---------------------
@@ -27,7 +35,7 @@ History
 0.74.7 (2021-09-21)
 ---------------------
 
-* Fix documentation to include `--download_outputs` flag (thanks to
+* Fix documentation to include ``--download_outputs`` flag (thanks to
   `@simonbray`_). `Pull Request 1184`_
 * Select refgenie config based on Galaxy version `Pull Request 1187`_
 * Extend autoupdate subcommand to workflows (thanks to `@simonbray`_). `Pull
@@ -1761,6 +1769,8 @@ History
   tools - and more experimental features involving Docker and Homebrew. 7d07782_
 
 .. github_links
+.. _Pull Request 1200: https://github.com/galaxyproject/planemo/pull/1200
+.. _Pull Request 1201: https://github.com/galaxyproject/planemo/pull/1201
 .. _Pull Request 1188: https://github.com/galaxyproject/planemo/pull/1188
 .. _Pull Request 1193: https://github.com/galaxyproject/planemo/pull/1193
 .. _Pull Request 1195: https://github.com/galaxyproject/planemo/pull/1195

cwl-runner/setup.py

@@ -5,24 +5,24 @@
 from setuptools import setup
 
 SETUP_DIR = os.path.dirname(__file__)
-README = os.path.join(SETUP_DIR, 'README')
+README = os.path.join(SETUP_DIR, "README")
 
 scripts = ["cwl-runner"]
 
 with open(README) as fh:
     readme_content = fh.read()
 
-setup(name='cwl_runner',
-      version='1.0',
-      description='Common workflow language interpreter implementation (for Galaxy + Planemo)',
-      long_description=readme_content,
-      author='John Chilton',
-      author_email='[email protected]',
-      url="https://github.com/galaxyproject/planemo",
-      download_url="https://github.com/galaxyproject/planemo",
-      license="MIT",
-      install_requires=[
-          'planemo'
-        ],
-      scripts=scripts,
-      zip_safe=True)
+setup(
+    name="cwl_runner",
+    version="1.0",
+    description="Common workflow language interpreter implementation (for Galaxy + Planemo)",
+    long_description=readme_content,
+    author="John Chilton",
+    author_email="jmchilton@gmail.com",
+    url="https://github.com/galaxyproject/planemo",
+    download_url="https://github.com/galaxyproject/planemo",
+    license="MIT",
+    install_requires=["planemo"],
+    scripts=scripts,
+    zip_safe=True,
+)

dev-requirements.txt

@@ -11,17 +11,15 @@ pytest
 coverage
 
 #Building Docs
+docutils
 sphinx
 sphinx_rtd_theme
 recommonmark
 
-# Used to check readme.
-readme
-
 # Used for code checking.
-pyflakes
+black
 flake8
-flake8-import-order
+isort
 
 # For release
 wheel

docs/_running_external.rst

@@ -300,3 +300,26 @@ You can also delete unwanted profiles or aliases with these commands:
 
     $ planemo delete_alias --alias my_favorite_workflow --profile tutorial_profile
     $ planemo profile_delete tutorial_profile
+
+
+Rerunning failed jobs
+===============================================
+
+A frequent issue that arises when running a complex workflow is that component
+jobs can fail, resulting in failure of the entire workflow. These jobs can be
+rerun in the graphical interface, selecting the ``Resume dependencies from this
+job ?`` option, which restarts the paused workflow (so-called 'remapping' of the
+failed job over the previously created output dataset(s)). However, if there are
+a large number of failures, and you believe the errors are transitory, e.g. due
+to some temporary server issue, you can rerun several failed jobs simultaneously
+using the ``planemo rerun`` command:
+
+::
+
+    $ planemo rerun --history 68008488b4fb94de
+    $ planemo rerun --invocation 27267240b7d1f22a a9b086729787c907c
+    $ planemo rerun --job a2b39deaa34509bb 3318707f2f0ff1fd
+
+In the first two cases, all failed, remappable jobs which are associated with
+the specified history(s) or invocation(s) will be rerun. In the third case,
+the specified jobs will simply be rerun.

docs/_writing_dependencies_conda.rst

@@ -164,7 +164,7 @@ demonstrating using this tool.
     2017-02-22 10:13:29,064 INFO  [galaxy.jobs.handler] (2) Job dispatched
     2017-02-22 10:13:29,281 DEBUG [galaxy.tools.deps] Using dependency seqtk version 1.2 of type conda
     2017-02-22 10:13:29,282 DEBUG [galaxy.tools.deps] Using dependency seqtk version 1.2 of type conda
-    2017-02-22 10:13:29,317 INFO  [galaxy.jobs.command_factory] Built script [/tmp/tmpLvKwta/job_working_directory/000/2/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/Users/john/miniconda2/envs/[email protected]" ] || . /Users/john/miniconda2/bin/activate '/Users/john/miniconda2/envs/[email protected]' >conda_activate.log 2>&1 ; seqtk seq -a '/tmp/tmpLvKwta/files/000/dataset_1.dat' > '/tmp/tmpLvKwta/files/000/dataset_2.dat']
+    2017-02-22 10:13:29,317 INFO  [galaxy.jobs.command_factory] Built script [/tmp/tmpLvKwta/job_working_directory/000/2/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/Users/john/miniconda2/envs/[email protected]" ] || . /Users/john/miniconda2/bin/activate '/Users/john/miniconda2/envs/[email protected]' >conda_activate.log 2>&1 ; seqtk seq -A '/tmp/tmpLvKwta/files/000/dataset_1.dat' > '/tmp/tmpLvKwta/files/000/dataset_2.dat']
     2017-02-22 10:13:29,516 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
     2017-02-22 10:13:29,516 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
     ok

docs/_writing_dependencies_containers.rst

@@ -102,7 +102,7 @@ tool from the introductory tutorial.
     2017-03-01 08:18:20,325 INFO  [galaxy.tools.deps.containers] Checking with container resolver [ExplicitDockerContainerResolver[]] found description [None]
     2017-03-01 08:18:20,468 INFO  [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledDockerContainerResolver[namespace=None]] found description [None]
     2017-03-01 08:18:20,881 INFO  [galaxy.tools.deps.containers] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]]
-    2017-03-01 08:18:20,904 INFO  [galaxy.jobs.command_factory] Built script [/tmp/tmpw8_UQm/job_working_directory/000/2/tool_script.sh] for tool command [seqtk seq -a '/tmp/tmpw8_UQm/files/000/dataset_1.dat' > '/tmp/tmpw8_UQm/files/000/dataset_2.dat']
+    2017-03-01 08:18:20,904 INFO  [galaxy.jobs.command_factory] Built script [/tmp/tmpw8_UQm/job_working_directory/000/2/tool_script.sh] for tool command [seqtk seq -A '/tmp/tmpw8_UQm/files/000/dataset_1.dat' > '/tmp/tmpw8_UQm/files/000/dataset_2.dat']
     2017-03-01 08:18:21,060 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
     2017-03-01 08:18:21,061 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
     ok

docs/_writing_intro.rst

@@ -34,7 +34,7 @@ still need to open up the editor and fill out the command template, describe
 input parameters, tool outputs, write a help section, etc.
 
 The ``tool_init`` command can do a little bit better than this as well. We can
-use the test command we tried above ``seqtk seq -a 2.fastq > 2.fasta`` as
+use the test command we tried above ``seqtk seq -A 2.fastq > 2.fasta`` as
 an example to generate a command block by specifing the inputs and the outputs
 as follows.
 
@@ -44,7 +44,7 @@ as follows.
                         --id 'seqtk_seq' \
                         --name 'Convert to FASTA (seqtk)' \
                         --requirement [email protected] \
-                        --example_command 'seqtk seq -a 2.fastq > 2.fasta' \
+                        --example_command 'seqtk seq -A 2.fastq > 2.fasta' \
                         --example_input 2.fastq \
                         --example_output 2.fasta
 
@@ -63,7 +63,7 @@ definitions for the input and output as well as an actual command template.
                         --id 'seqtk_seq' \
                         --name 'Convert to FASTA (seqtk)' \
                         --requirement [email protected] \
-                        --example_command 'seqtk seq -a 2.fastq > 2.fasta' \
+                        --example_command 'seqtk seq -A 2.fastq > 2.fasta' \
                         --example_input 2.fastq \
                         --example_output 2.fasta \
                         --test_case \