From 99dc1c5487fa004d4476468eab269fb4c3e17c26 Mon Sep 17 00:00:00 2001 From: thalassemia Date: Fri, 29 Nov 2024 03:04:31 -0800 Subject: [PATCH] Fix documentation formatting --- doc/ci.rst | 12 +++++++----- doc/gcloud.rst | 16 ++++++++-------- doc/workflows.rst | 2 +- 3 files changed, 16 insertions(+), 14 deletions(-) diff --git a/doc/ci.rst b/doc/ci.rst index ab41a1ff6..c27b66e69 100644 --- a/doc/ci.rst +++ b/doc/ci.rst @@ -23,11 +23,13 @@ tasks are: - ``docs_test.yml``: ``test-docs`` job ensures that the documentation builds properly (Sphinx) on PRs and changes to ``master`` - ``pr_tests.yml``: tests that run on PRs and changes to ``master`` - - ``Reproducibility`` ensures that two runs of the ParCa and simulation - with the same settings produce the same output - - ``two-gens`` runs a two-generation workflow on glucose minimal media + + - ``Reproducibility`` ensures that two runs of the ParCa and simulation + with the same settings produce the same output + - ``two-gens`` runs a two-generation workflow on glucose minimal media - ``pytest.yml``: code quality and functionality tests that run on PRs and changes to master + - ``Pytest`` runs ``pytest`` (all functions with ``test_`` prefix) - ``Mypy`` checks types with ``mypy`` - ``Lint`` checks code style and formatting with ``ruff`` @@ -67,8 +69,8 @@ view the logs in two steps. First, SSH into Sherlock and run the following comma squeue -p mcovert -o '%.10i %.9P %.50j %.8u %.2t %.10M %.3C %.6D %.20R %k' .. tip:: - Create an alias ``sqp`` for the command above by adding ``alias sqp="..."`` - to your ``~/.bashrc``. + Create an alias ``sqp`` for the command above by adding + ``alias sqp="{insert command here}"`` to your ``~/.bashrc``. Look for a job called ``jenkins_new``. Under the ``COMMENT`` column, there should be a login node of the format ``shXX-lnXX``. Close your SSH connection diff --git a/doc/gcloud.rst b/doc/gcloud.rst index 487da3db4..bcf30bb52 100644 --- a/doc/gcloud.rst +++ b/doc/gcloud.rst @@ -36,17 +36,17 @@ You will be asked to link a billing account at this time. ``runscripts/nextflow/config.template``. Set a default region and zone for Compute Engine following -`these instructions`. +`these instructions `_. This avoids unnecessary charges for multi-region data availability and access, improves latency, and is required for some of vEcoli's code to work. Create a new repository in Artifact Registry following the steps -on `this page`_. +on `this page `_. Make sure to name the repository ``vecoli`` and create it in the same region as your Compute Engine default. This is where the Docker images used to run the workflow will be stored (see `Build Docker Images`_). -Compute Engine VMs come with `service accounts ` +Compute Engine VMs come with `service accounts `_ allow users to control access to project resources (compute, storage, etc.). To run vEcoli workflows, only a small subset of the default service account permissions are necessary. For that reason, we strongly @@ -79,7 +79,7 @@ Create Your VM -------------- Click on the terminal shell icon near the top-right corner of the -`Cloud console `. Run the command +`Cloud console `_. Run the command ``gcloud init`` and choose to reinitialize your configuration. Choose the right account and project, allowing ``gcloud`` to pull in the project's default Compute Engine zone and region. @@ -142,7 +142,7 @@ requirements.txt for correct versions):: make clean compile Then, install Java (through SDKMAN) and Nextflow following -`these instructions`. +`these instructions `_. ------------------ Create Your Bucket @@ -150,7 +150,7 @@ Create Your Bucket vEcoli workflows persist their final outputs to a Cloud Storage bucket. To create a bucket, follow the steps on -`this page`_. By default, +`this page `_. By default, buckets are created in the US multi-region. We strongly recommend changing this to the same single region as your Compute Engine default (``us-west1`` for Covert Lab). All other settings can be kept as default. @@ -159,7 +159,7 @@ All other settings can be kept as default. Do NOT use underscores or special characters in your bucket name. Hyphens are OK. Once you have created your bucket, tell vEcoli to use that bucket by setting the -``out_uri`` key under the ``emitter_arg`` key in your config JSON (see `json_config`_). +``out_uri`` key under the ``emitter_arg`` key in your config JSON (see :ref:`json_config`). The URI should be in the form ``gs://{bucket name}``. Remember to remove the ``out_dir`` key under ``emitter_arg`` if present. @@ -205,7 +205,7 @@ keys in your configuration JSON:: These configuration keys, in addition to the ``out_uri`` key under ``emitter_arg``, are necessary and sufficient to tell :py:mod:`runscripts.workflow` that you intend to run the workflow on Google Cloud. After setting these options in your configuration JSON, -you can use ```screen`` to open a virtual console that will persist even after your SSH +you can use ``screen`` to open a virtual console that will persist even after your SSH connection is closed. In that virtual console, invoke :py:mod:`runscripts.workflow` as normal to start your workflow:: diff --git a/doc/workflows.rst b/doc/workflows.rst index a602202d3..792120f8c 100644 --- a/doc/workflows.rst +++ b/doc/workflows.rst @@ -561,7 +561,7 @@ be absolute because Nextflow does not resolve environment variables like to the correct SLURM queue. If your HPC cluster uses a different scheduler, you will have to change many options in the ``sherlock`` configuration profile starting with ``process.executor``. Refer to the Nextflow - `executor documentation`_. + `executor documentation `_. .. _progress: