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Fix documentation auto implementation of version release #278

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Apr 22, 2024
Merged

Fix documentation auto implementation of version release #278

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1 change: 1 addition & 0 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
rst_prolog = f"""
.. |pkgurl| replace:: https://github.com/NCI-CGR/GwasQcPipeline/releases/download/{__version__}/{pkg}
.. |cgr| replace:: *CGR GwasQcPipeline*
.. |pkg_version| replace:: {__version__}
"""

rst_epilog = ".. include:: /common_urls.rst"
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23 changes: 15 additions & 8 deletions docs/getting_started/installation.rst
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Expand Up @@ -45,26 +45,31 @@ To update the latest version of ``GwasQcPipeline``:
Installing on ccad2
-------------------------

- Install miniconda and then create a GwasQcPipeline production environment
Install miniconda and then create a GwasQcPipeline production environment:

.. code-block::
:substitutions:

$ mkdir /scratch/myfolder/GwasQcPipeline_v1.2
$ cd /scratch/myfolder/GwasQcPipeline_v1.2
$ mkdir /scratch/myfolder/GwasQcPipeline_|pkg_version|
$ cd /scratch/myfolder/GwasQcPipeline_|pkg_version|
$ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
$ bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /scratch/myfolder/GwasQcPipeline_v1.2/conda -b
$ bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /scratch/myfolder/GwasQcPipeline_|pkg_version|/conda -b
$ source conda/bin/activate base
(base) $ conda update -n base -c defaults conda
(base) $ conda install -n base -c conda-forge mamba
(base) $ conda create -n GwasQcPipeline -y python=3.8 pip
(base) $ conda deactivate

Next install the latest version of the GwasQcPipeline environment:

.. code-block::
$ source /scratch/myfolder/GwasQcPipeline_v1.2/conda/bin/activate GwasQcPipeline
(GwasQcPipeline) $ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.2.0/cgr_gwas_qc-1.2.0-py3-none-any.whl
:substitutions:

$ source /scratch/myfolder/GwasQcPipeline_|pkg_version|/conda/bin/activate GwasQcPipeline
(GwasQcPipeline) $ pip install |pkgurl|
(GwasQcPipeline) $ cgr --help
(GwasQcPipeline) $ cgr version
v1.2.0
|pkg_version|

Installing on NIH Biowulf
-------------------------
Expand All @@ -76,6 +81,7 @@ description is provided on the `Biowulf python env website`_.


.. code-block::
:substitutions:

$ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh

Expand All @@ -91,9 +97,10 @@ description is provided on the `Biowulf python env website`_.
Next install the latest version of the GwasQcPipeline environment:

.. code-block::
:substitutions:

$ source /<location of miniconda installation>/conda/bin/activate GwasQcPipeline
$ pip install --force-reinstall https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.2.0/cgr_gwas_qc-1.2.0-py3-none-any.whl
$ pip install --force-reinstall |pkgurl|
$ cgr --help
$ cgr version

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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[tool.poetry]
name = "cgr_gwas_qc"
version = "1.3.0"
version = "1.4.0"
description = "The CGR GWAS QC Pipeline"
authors = [
"Justin Fear <justin.fear@nih.gov>",
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