Merge branch 'release_22.01' into release_22.05

Makefile

@@ -4,7 +4,6 @@ VENV?=.venv
 IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
 RELEASE_CURR:=22.05
 RELEASE_UPSTREAM:=upstream
-TARGET_BRANCH=$(RELEASE_UPSTREAM)/dev
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy
 DOCS_DIR=doc

doc/Makefile

@@ -54,8 +54,6 @@ source/admin/config_logging_default_yaml.rst: ../lib/galaxy/config/__init__.py
 	printf '      logging:\n        ' >> $@
 	PYTHONPATH=../lib python -c 'from __future__ import print_function; import yaml, galaxy.config; print("\n        ".join(yaml.dump(galaxy.config.LOGGING_CONFIG_DEFAULT, indent=2, default_flow_style=False).splitlines()))' >> $@
 
-# might also want to do
-# cd source/lib; hg revert; rm *.rst.orig;  or not.
 clean:
 	-rm -rf $(BUILDDIR)/* $(GENERATED_RST)
 
@@ -172,4 +170,5 @@ doctest: $(GENERATED_RST)
 
 # Update Sphinx RST files for lib/ to reflect code structure changes
 updaterst:
+	-rm -rf source/lib/
 	$(SPHINXAPIDOC) -M --force -o source/lib/ ../lib/

doc/source/admin/nginx.md

@@ -325,7 +325,7 @@ If you serve Galaxy at a prefix exchange `/api/upload/resumable_upload` with `/p
 
 After reloading the nginx configuration you can verify that this configuration works correctly by uploading a file to Galaxy. Make sure the tusd server logs the request. It should look similar to the following
 
-```log
+```
 [tusd] 2021/10/12 13:30:14 Using '/Users/mvandenb/src/galaxy/database/tmp' as directory storage.
 [tusd] 2021/10/12 13:30:14 Using 0.00MB as maximum size.
 [tusd] 2021/10/12 13:30:14 Using 'http://localhost:8000/api/upload/hooks' as the endpoint for hooks

doc/source/admin/special_topics/performance_tracking.rst

@@ -2,22 +2,21 @@ Galaxy Performance Tracking
 ===========================
 
 Tracking performance over time and identifying slow queries in your Galaxy can be an extremely important thing to do, especially for larger Galaxies.
-[A more in-depth tutorial is available at the Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html).
+A more `in-depth tutorial <https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html>`__ is available at the Galaxy Training Network.
 
 Most performance tracking requires sending metrics to a metrics collection server such as `StatsD <https://github.com/etsy/statsd/>`__. This document assumes you have already deployed StatsD.
 
 Gunicorn
------
+--------
 
 There is some built-in `Gunicorn <https://docs.gunicorn.org/en/stable/instrumentation.html>`__ support for performance logging. You can send Gunicorn's internal metrics to a StatsD server by setting the `--statsd-host` and `--statsd-prefix` command line options for Gunicorn in the `gravity` section of `galaxy.yml`:
 
 .. code-block:: yaml
 
    gravity:
-      ...
+      #...
       gunicorn:
-        extra_args: `--statsd-host 127.0.0.1:8125 --statsd-prefix=gunicorn`
-      ...
+        extra_args: '--statsd-host 127.0.0.1:8125 --statsd-prefix=gunicorn'
 
 API / Route Timing Statistics
 -----------------------------

doc/source/dev/debugging_galaxy_slurm.md

@@ -2,15 +2,15 @@
 # Debugging Galaxy: Slurm Compute Cluster
 
 This document explains how to debug a Galaxy instance that uses a Slurm compute cluster (not the
-default LocalRunner). If you have a MacOS machine, you need to create a Linux VM using Oracle's 
-VirtualBoxVM and run the instructions in the VM. For reference, I created a 64-bit Linux VM with 
-4096 MB of RAM and 32 GB of disk space (all other parameters were left as default) and managed to 
-successfully run the instructions. If using a Linux VM, you may need to install Git, Python, VSCode, 
-and Docker (if using Irods storage). Finally, These instructions are intended for developers who 
-want to debug their Galaxy instance and are not meant for deployment purposes (We have nice Ansible 
+default LocalRunner). If you have a MacOS machine, you need to create a Linux VM using Oracle's
+VirtualBoxVM and run the instructions in the VM. For reference, I created a 64-bit Linux VM with
+4096 MB of RAM and 32 GB of disk space (all other parameters were left as default) and managed to
+successfully run the instructions. If using a Linux VM, you may need to install Git, Python, VSCode,
+and Docker (if using Irods storage). Finally, These instructions are intended for developers who
+want to debug their Galaxy instance and are not meant for deployment purposes (We have nice Ansible
 playbooks for that).
 
-## Debugging Galaxy in VS Code 
+## Debugging Galaxy in VS Code
 
 1. Install libslurm-dev
     * `sudo apt install libslurm-dev`
@@ -19,7 +19,7 @@ playbooks for that).
 
 2. Install slurm-drmaa
     * Download slurm-drmaa tar file from https://github.com/natefoo/slurm-drmaa/releases/download/1.1.2/slurm-drmaa-1.1.2.tar.gz
-    * Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~`       
+    * Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~`
     * To compile and install slurm-drmaa
         * `cd ~/slurm-drmaa-1.1.2`
         * `./configure --with-slurm-inc=/usr/include --with-slurm-lib=/usr/lib/x86_64-linux-gpu`
@@ -71,6 +71,6 @@ playbooks for that).
         * `sudo service slurmd start`
         * `sudo service slurmctld start`
 
-6. Follow the instructions [here](./debuging_galaxy.md) to setup VSCode for debugging. 
+6. Follow the instructions [here](debugging_galaxy) to setup VSCode for debugging.
 
-Enjoy debugging session your Galaxy instance backed by a Slurm cluster!        
+Enjoy debugging session your Galaxy instance backed by a Slurm cluster!

doc/source/dev/interactive_environments.rst

@@ -1,5 +1,5 @@
 Interactive Environments
 =========================
 
-Galaxy Interactive Environments are deprecated and were the precursors to the current :doc:`Galaxy Interactive Tools <../admin/special_topics/interactivetools>`.
+Galaxy Interactive Environments are deprecated and were the precursors to the current :ref:`Galaxy Interactive Tools <interactivetools>`.
 You can find information about Galaxy Interactive Environments in `older versions <https://docs.galaxyproject.org/en/release_21.09/admin/special_topics/interactive_environments.html>`__ of this document.

doc/source/dev/translating.rst

@@ -45,19 +45,19 @@ There are a number of ways text gets used in the codebase, especially the new Vu
 
 1. Text within an element:
 
-   .. code-block:: js
+   .. code-block:: html
 
        <b>Some Text</b>
 
 2. Text within a more complex element:
 
-   .. code-block:: javascript
+   .. code-block:: html
 
        <b><icon library>Some Text</b>
 
 3. Attribute or placeholder text
 
-   .. code-block:: javascript
+   .. code-block:: html
 
        <b-form-input v-model="newLibraryForm.synopsis" placeholder="Synopsis of the library" />
 
@@ -88,7 +88,7 @@ The first one is the easiest, we can just add the ``v-localize`` tag and we're d
 
 For those you'll need to have a quick overview of the structure of a Vue component to localize the correct place to set the variable. The exact structure will not always be identical but it should be similar. At the top is a ``<template>`` section which contains what will be rendered, and at the bottom is a ``<script>`` section which contains some code that's run as part of rendering that UI component.
 
-.. code-block:: javascript
+.. code-block:: html
 
     <template>
         <span class="position-relative">

doc/source/lib/galaxy.actions.rst

@@ -9,14 +9,6 @@ galaxy.actions package
 Submodules
 ----------
 
-galaxy.actions.admin module
----------------------------
-
-.. automodule:: galaxy.actions.admin
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 galaxy.actions.library module
 -----------------------------
 

doc/source/lib/galaxy.app_unittest_utils.rst

@@ -0,0 +1,34 @@
+galaxy.app\_unittest\_utils package
+===================================
+
+.. automodule:: galaxy.app_unittest_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+galaxy.app\_unittest\_utils.celery\_helper module
+-------------------------------------------------
+
+.. automodule:: galaxy.app_unittest_utils.celery_helper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.app\_unittest\_utils.galaxy\_mock module
+-----------------------------------------------
+
+.. automodule:: galaxy.app_unittest_utils.galaxy_mock
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.app\_unittest\_utils.tools\_support module
+-------------------------------------------------
+
+.. automodule:: galaxy.app_unittest_utils.tools_support
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/source/lib/galaxy.celery.rst

@@ -0,0 +1,18 @@
+galaxy.celery package
+=====================
+
+.. automodule:: galaxy.celery
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+galaxy.celery.tasks module
+--------------------------
+
+.. automodule:: galaxy.celery.tasks
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/source/lib/galaxy.datatypes.converters.rst

@@ -161,6 +161,14 @@ galaxy.datatypes.converters.maf\_to\_interval\_converter module
    :undoc-members:
    :show-inheritance:
 
+galaxy.datatypes.converters.parquet\_to\_csv\_converter module
+--------------------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.parquet_to_csv_converter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.datatypes.converters.pbed\_ldreduced\_converter module
 -------------------------------------------------------------
 

doc/source/lib/galaxy.datatypes.rst

@@ -100,6 +100,14 @@ galaxy.datatypes.data module
    :undoc-members:
    :show-inheritance:
 
+galaxy.datatypes.flow module
+----------------------------
+
+.. automodule:: galaxy.datatypes.flow
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.datatypes.genetics module
 --------------------------------
 
@@ -116,6 +124,14 @@ galaxy.datatypes.gis module
    :undoc-members:
    :show-inheritance:
 
+galaxy.datatypes.goldenpath module
+----------------------------------
+
+.. automodule:: galaxy.datatypes.goldenpath
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.datatypes.graph module
 -----------------------------
 
@@ -124,6 +140,14 @@ galaxy.datatypes.graph module
    :undoc-members:
    :show-inheritance:
 
+galaxy.datatypes.hdf5 module
+----------------------------
+
+.. automodule:: galaxy.datatypes.hdf5
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.datatypes.images module
 ------------------------------
 
@@ -156,6 +180,14 @@ galaxy.datatypes.media module
    :undoc-members:
    :show-inheritance:
 
+galaxy.datatypes.metacyto module
+--------------------------------
+
+.. automodule:: galaxy.datatypes.metacyto
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.datatypes.metadata module
 --------------------------------
 

doc/source/lib/galaxy.files.rst

@@ -13,3 +13,4 @@ Subpackages
    :maxdepth: 4
 
    galaxy.files.sources
+   galaxy.files.unittest_utils

doc/source/lib/galaxy.files.sources.rst

@@ -9,6 +9,22 @@ galaxy.files.sources package
 Submodules
 ----------
 
+galaxy.files.sources.anvil module
+---------------------------------
+
+.. automodule:: galaxy.files.sources.anvil
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.files.sources.basespace module
+-------------------------------------
+
+.. automodule:: galaxy.files.sources.basespace
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.files.sources.dropbox module
 -----------------------------------
 
@@ -17,6 +33,14 @@ galaxy.files.sources.dropbox module
    :undoc-members:
    :show-inheritance:
 
+galaxy.files.sources.ftp module
+-------------------------------
+
+.. automodule:: galaxy.files.sources.ftp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.files.sources.galaxy module
 ----------------------------------
 
@@ -25,6 +49,30 @@ galaxy.files.sources.galaxy module
    :undoc-members:
    :show-inheritance:
 
+galaxy.files.sources.googlecloudstorage module
+----------------------------------------------
+
+.. automodule:: galaxy.files.sources.googlecloudstorage
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.files.sources.googledrive module
+---------------------------------------
+
+.. automodule:: galaxy.files.sources.googledrive
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.files.sources.onedata module
+-----------------------------------
+
+.. automodule:: galaxy.files.sources.onedata
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.files.sources.posix module
 ---------------------------------
 
@@ -41,6 +89,22 @@ galaxy.files.sources.s3 module
    :undoc-members:
    :show-inheritance:
 
+galaxy.files.sources.s3fs module
+--------------------------------
+
+.. automodule:: galaxy.files.sources.s3fs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.files.sources.ssh module
+-------------------------------
+
+.. automodule:: galaxy.files.sources.ssh
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.files.sources.webdav module
 ----------------------------------
 

doc/source/lib/galaxy.tools.toolbox.filters.rst → doc/source/lib/galaxy.files.unittest_utils.rst

@@ -1,7 +1,7 @@
-galaxy.tools.toolbox.filters package
+galaxy.files.unittest\_utils package
 ====================================
 
-.. automodule:: galaxy.tools.toolbox.filters
+.. automodule:: galaxy.files.unittest_utils
    :members:
    :undoc-members:
    :show-inheritance: