diff --git a/Makefile b/Makefile index 93e632030d2..a274fd79963 100644 --- a/Makefile +++ b/Makefile @@ -4,7 +4,6 @@ VENV?=.venv IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi; RELEASE_CURR:=22.01 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 @@ -38,8 +37,8 @@ docs-develop: ## Fast doc generation and more warnings (for development) setup-venv: if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi -diff-format: - $(IN_VENV) darker -r $(TARGET_BRANCH) +diff-format: ## Format Python code changes since last commit + $(IN_VENV) darker . list-dependency-updates: setup-venv $(IN_VENV) pip list --outdated --format=columns diff --git a/doc/Makefile b/doc/Makefile index de5921267ad..fc986bd6376 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -54,8 +54,6 @@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/ diff --git a/doc/source/admin/nginx.md b/doc/source/admin/nginx.md index ba377f5a713..377fb039755 100644 --- a/doc/source/admin/nginx.md +++ b/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 diff --git a/doc/source/admin/special_topics/performance_tracking.rst b/doc/source/admin/special_topics/performance_tracking.rst index 5958a0a1614..c354bdd9d2b 100644 --- a/doc/source/admin/special_topics/performance_tracking.rst +++ b/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 `__ is available at the Galaxy Training Network. Most performance tracking requires sending metrics to a metrics collection server such as `StatsD `__. This document assumes you have already deployed StatsD. Gunicorn ------ +-------- There is some built-in `Gunicorn `__ 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 ----------------------------- diff --git a/doc/source/dev/debugging_galaxy_slurm.md b/doc/source/dev/debugging_galaxy_slurm.md index fd0965a7da5..75dc6173ba7 100644 --- a/doc/source/dev/debugging_galaxy_slurm.md +++ b/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! diff --git a/doc/source/dev/interactive_environments.rst b/doc/source/dev/interactive_environments.rst index e7eb5462657..ea66b7794ce 100644 --- a/doc/source/dev/interactive_environments.rst +++ b/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 `. You can find information about Galaxy Interactive Environments in `older versions `__ of this document. diff --git a/doc/source/dev/translating.rst b/doc/source/dev/translating.rst index 2f64ddffc75..6dc19189a61 100644 --- a/doc/source/dev/translating.rst +++ b/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 Some Text 2. Text within a more complex element: - .. code-block:: javascript + .. code-block:: html Some Text 3. Attribute or placeholder text - .. code-block:: javascript + .. code-block:: html @@ -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 ``