From 58f44ca77a2ec13dc017bf60166a1b48c656c465 Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Fri, 19 Jul 2024 15:00:31 +0800 Subject: [PATCH 1/5] update README.rst --- README.rst | 122 ++++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 117 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 8dee78edf..aaf882979 100644 --- a/README.rst +++ b/README.rst @@ -1,8 +1,120 @@ -Regolith +|Icon| |title|_ +=============== + +.. |title| replace:: regolith +.. _title: https://regro.github.io/regolith + +.. |Icon| image:: https://avatars.githubusercontent.com/regro + :target: https://regro.github.io/regolith + :height: 100px + +|PyPi| |Forge| |PythonVersion| |PR| + +|CI| |Codecov| |Black| |Tracking| + +.. |Black| image:: https://img.shields.io/badge/code_style-black-black + :target: https://github.com/psf/black + +.. |CI| image:: https://github.com/regro/regolith/actions/workflows/main.yml/badge.svg + :target: https://github.com/regro/regolith/actions/workflows/main.yml + +.. |Codecov| image:: https://codecov.io/gh/regro/regolith/branch/main/graph/badge.svg + :target: https://codecov.io/gh/regro/regolith + +.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/regolith + :target: https://anaconda.org/conda-forge/regolith + +.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + +.. |PyPi| image:: https://img.shields.io/pypi/v/regolith + :target: https://pypi.org/project/regolith/ + +.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/regolith + :target: https://pypi.org/project/regolith/ + +.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue + :target: https://github.com/regro/regolith/issues + +A Group Content Management System + + +For more information about the regolith library, please consult our `online documentation `_. + +Citation -------- -Research Group Content Management System +If you use regolith in a scientific publication, we would like you to cite this package as + + regolith Package, https://github.com/regro/regolith + +Installation +------------ + +The preferred method is to use `Miniconda Python +`_ +and install from the "conda-forge" channel of Conda packages. + +To add "conda-forge" to the conda channels, run the following in a terminal. :: + + conda config --add channels conda-forge + +We want to install our packages in a suitable conda environment. +The following creates and activates a new environment named ``regolith_env`` :: + + conda create -n regolith_env python=3 + conda activate regolith_env + +Then, to fully install ``regolith`` in our active environment, run :: + + conda install regolith + +Another option is to use ``pip`` to download and install the latest release from +`Python Package Index `_. +To install using ``pip`` into your ``regolith_env`` environment, we will also have to install dependencies :: + + pip install -r https://raw.githubusercontent.com/regro/regolith/main/requirements/run.txt + +and then install the package :: + + pip install regolith + +If you prefer to install from sources, after installing the dependencies, obtain the source archive from +`GitHub `_. Once installed, ``cd`` into your ``regolith`` directory +and run the following :: + + pip install . + +Support and Contribute +---------------------- + +`Diffpy user group `_ is the discussion forum for general questions and discussions about the use of regolith. Please join the regolith users community by joining the Google group. The regolith project welcomes your expertise and enthusiasm! + +If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. You can also post it to the `Diffpy user group `_. + +Feel free to fork the project and contribute. To install regolith +in a development mode, with its sources being directly used by Python +rather than copied to a package directory, use the following in the root +directory :: + + pip install -e . + +To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit +hooks. + +1. Install pre-commit in your working environment by running ``conda install pre-commit``. + +2. Initialize pre-commit (one time only) ``pre-commit install``. + +Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. +If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should +pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before +trying to commit again. + +Improvements and fixes are always appreciated. + +Before contribuing, please read our `Code of Conduct `_. + +Contact +------- -Docs: ------ -https://regro.github.io/regolith-docs/ +For more information on regolith please visit the project `web-page `_ or email Prof. Simon Billinge at sb2896@columbia.edu. From baca2026358c5d9eabea660a4b0b80c8c0961f72 Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Fri, 19 Jul 2024 15:05:37 +0800 Subject: [PATCH 2/5] update conf.py with autodoc_mock_imports inserted --- doc/source/conf.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/source/conf.py b/doc/source/conf.py index 5f7abb709..c990027b6 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -19,11 +19,16 @@ import cloud_sptheme as csp +import regolith from regolith import __version__ as REGOLITH_VERSION from regolith.fsclient import _id_key, dump_json, json_to_yaml from regolith.main import CONNECTED_COMMANDS, DISCONNECTED_COMMANDS from regolith.schemas import EXEMPLARS, SCHEMAS +autodoc_mock_imports = [ + regolith, +] + # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. From 94e8b7edaad77d16f0169a7e6b0a7b18fbac1f39 Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Fri, 19 Jul 2024 17:59:08 +0800 Subject: [PATCH 3/5] update schemas.json with "_description" key in software added --- src/regolith/schemas.json | 1 + 1 file changed, 1 insertion(+) diff --git a/src/regolith/schemas.json b/src/regolith/schemas.json index a9488d731..e2dea6d7f 100644 --- a/src/regolith/schemas.json +++ b/src/regolith/schemas.json @@ -2877,6 +2877,7 @@ } }, "software": { + "_description": {"description": "Information about software, such as active, grants, etc."}, "_id": { "description": "package id", "required": true, From 0194bf11ca099d5792277d6aa47d60713807aa40 Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Fri, 19 Jul 2024 18:19:17 +0800 Subject: [PATCH 4/5] change from "redcloud" to "sphinx_rtd_theme" --- doc/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index c990027b6..e6e99d585 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -118,7 +118,7 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = "redcloud" +html_theme = "sphinx_rtd_theme" # html_theme = 'blackcloud' # Theme options are theme-specific and customize the look and feel of a theme From 1b617a9975ecc441de8d4db9b5d437d9e47ad705 Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Fri, 19 Jul 2024 21:56:36 +0800 Subject: [PATCH 5/5] update the web-page link --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index aaf882979..42c9a06a2 100644 --- a/README.rst +++ b/README.rst @@ -117,4 +117,4 @@ Before contribuing, please read our `Code of Conduct `_ or email Prof. Simon Billinge at sb2896@columbia.edu. +For more information on regolith please visit the project `web-page `_ or email Prof. Simon Billinge at sb2896@columbia.edu.