From 4bc80a385d1ff0f30ee4b48495cbb6fba92ac73c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rub=C3=A9n=20Chaves?= Date: Fri, 13 Dec 2024 11:03:02 +0100 Subject: [PATCH 1/3] change docs link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7913c5c..e621b68 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ mdahole2 ============================== [//]: # (Badges) -| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/MDAnalysis/mdahole2.svg)](https://github.com/MDAnalysis/mdahole2/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/MDAnalysis/mdahole2/latest) [![Documentation status](https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml/badge.svg?branch=main)](https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml)| +| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/MDAnalysis/mdahole2.svg)](https://github.com/MDAnalysis/mdahole2/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/MDAnalysis/mdahole2/latest) [![Documentation status]([https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml/badge.svg?branch=main)](https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml](https://www.mdanalysis.org/mdahole2/))| | :------ | :------- | | **Status** | [![GH Actions Status](https://github.com/MDAnalysis/mdahole2/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/MDAnalysis/mdahole2/actions?query=branch%3Amain+workflow%3Agh-ci) [![codecov](https://codecov.io/gh/MDAnalysis/mdahole2/branch/main/graph/badge.svg)](https://codecov.io/gh/MDAnalysis/mdahole2/branch/main)| | **Community** | [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org) | From a67fd8609017792b6c6232418bbd0e894895ffb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rub=C3=A9n=20Chaves?= Date: Fri, 13 Dec 2024 11:11:36 +0100 Subject: [PATCH 2/3] fix link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e621b68..84994ee 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ mdahole2 ============================== [//]: # (Badges) -| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/MDAnalysis/mdahole2.svg)](https://github.com/MDAnalysis/mdahole2/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/MDAnalysis/mdahole2/latest) [![Documentation status]([https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml/badge.svg?branch=main)](https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml](https://www.mdanalysis.org/mdahole2/))| +| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/MDAnalysis/mdahole2.svg)](https://github.com/MDAnalysis/mdahole2/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/MDAnalysis/mdahole2/latest) [![Documentation status](https://github.com/MDAnalysis/mdahole2/actions/workflows/docs.yaml/badge.svg?branch=main)](https://www.mdanalysis.org/mdahole2/)| | :------ | :------- | | **Status** | [![GH Actions Status](https://github.com/MDAnalysis/mdahole2/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/MDAnalysis/mdahole2/actions?query=branch%3Amain+workflow%3Agh-ci) [![codecov](https://codecov.io/gh/MDAnalysis/mdahole2/branch/main/graph/badge.svg)](https://codecov.io/gh/MDAnalysis/mdahole2/branch/main)| | **Community** | [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org) | From b772c8f64812be4a8dddecea3953d0f376901bc9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rub=C3=A9n=20Chaves?= Date: Fri, 13 Dec 2024 14:59:44 +0100 Subject: [PATCH 3/3] Update installation docs --- README.md | 26 +++++++++++++-- docs/source/getting_started.rst | 56 +++++++++++++++++++++++++++------ 2 files changed, 69 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 84994ee..b2cb340 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,26 @@ mdahole2 is bound by a [Code of Conduct](https://github.com/MDAnalysis/mdahole2/ ### Installation +From conda: +``` +conda install conda-forge::mdahole2 +``` + +In case you want to use an already installed version of [hole2](https://www.holeprogram.org/) built from [source](https://github.com/osmart/hole2) or by installing it from conda (`conda install conda-forge:: hole2`), you can use a version without `hole2` as dependency: +``` +conda install conda-forge::mdahole2-base +``` + +Or install from pip: +``` +pip install mdahole2 + +``` + +Note that `mdahole2` is only supported on Linux and macOS. + +#### From source + To build `mdahole2` from source, we highly recommend using virtual environments. If possible, we strongly recommend that you use @@ -20,9 +40,9 @@ If possible, we strongly recommend that you use Below we provide instructions both for `conda` and for `pip`. -Note that `mdahole2` is only supported on Linux and macOS. -#### With conda + +##### With conda Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed. @@ -57,7 +77,7 @@ And when you are finished, you can exit the virtual environment with: conda deactivate ``` -#### With pip +##### With pip To build the package from source, run: diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index c83fe05..e5f9317 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -11,8 +11,37 @@ Documentation is hosted on `GitHub Pages`_. .. _`GitHub Pages`: https://www.mdanalysis.org/mdahole2/ -Download source code -~~~~~~~~~~~~~~~~~~~~ +Installation +~~~~~~~~~~~~~~~~~~~~~~ + +``mdahole2`` can be installed in several ways: + +From conda +---------- + +The recommended way to install ``mdahole2`` is through conda: + +.. code:: bash + + conda install conda-forge::mdahole2 + +If you already have ``hole2`` installed and want to use that version, you can install ``mdahole2`` without the ``hole2`` dependency: + +.. code:: bash + + conda install conda-forge::mdahole2-base + +From pip +-------- + +You can also install ``mdahole2`` using pip: + +.. code:: bash + + pip install mdahole2 + +Download and Build source code +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The ``mdahole2`` source code is hosted on GitHub_ and can be downloaded with @@ -28,23 +57,30 @@ with an SSH key, or with .. _GitHub: https://github.com/MDAnalysis/mdahole2 -Build and installation -~~~~~~~~~~~~~~~~~~~~~~ +To build ``mdahole2`` from source, we highly recommend using virtual environments, preferably with `Anaconda`_. + +With conda: + +.. code:: bash + + conda create --name mdahole2 + conda activate mdahole2 + conda env update --name mdahole2 --file devtools/conda-envs/test_env.yaml --file docs/requirements.yaml + pip install -e . -``mdahole2`` is currently only installable from source (although hosting on conda-forge is planned). -As such ``conda-build`` is required. To download this utility, invoke: +With pip: .. code:: bash - conda install conda-build + pip install -e . -From the repository root directory, run +For development purposes, you can install additional test and documentation dependencies: .. code:: bash - conda build . && conda install --use-local mdahole2 + pip install -e ".[test,doc]" -to build the package and install the local build. +.. _Anaconda: https://docs.conda.io/en/latest/ Installing hole2 ~~~~~~~~~~~~~~~~