diff --git a/.github/workflows/cont_int.yml b/.github/workflows/cont_int.yml index a812e37ce1..a0662b3ed5 100644 --- a/.github/workflows/cont_int.yml +++ b/.github/workflows/cont_int.yml @@ -4,7 +4,7 @@ on: push: pull_request: branches: - - master + - main types: [opened, synchronize, reopened, ready_for_review, review_requested] jobs: diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 0572f364a2..72e2d086f4 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -3,7 +3,7 @@ name: github pages on: push: branches: - - master + - main - docs jobs: diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml index d02d55babe..bc1fce176d 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -1,6 +1,6 @@ # This workflow will triage pull requests and apply a label based on the # paths that are modified in the pull request. -# See: https://github.com/actions/labeler/blob/master/README.md +# See: https://github.com/actions/labeler/blob/main/README.md name: Labeler on: [pull_request] diff --git a/README.md b/README.md index f8640bc175..509ca3dcaa 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # Automated Rate Calculator | ARC ![Build Status](https://github.com/ReactionMechanismGenerator/ARC/actions/workflows/cont_int.yml/badge.svg) -[![codecov](https://codecov.io/gh/ReactionMechanismGenerator/ARC/branch/master/graph/badge.svg)](https://codecov.io/gh/ReactionMechanismGenerator/ARC) +[![codecov](https://codecov.io/gh/ReactionMechanismGenerator/ARC/branch/main/graph/badge.svg)](https://codecov.io/gh/ReactionMechanismGenerator/ARC) [![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT) ![Release](https://img.shields.io/badge/version-1.1.0-blue.svg) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3356849.svg)](https://doi.org/10.5281/zenodo.3356849) -arc logo +arc logo The **A**utomated **R**ate **C**alculator (**ARC**) software is a tool for automating electronic structure calculations and attaining thermo-kinetic data @@ -32,7 +32,7 @@ Visit out ## Licence -This project is licensed under the MIT License - see the LICENSE file for details. +This project is licensed under the MIT License - see the LICENSE file for details. ## Contributing diff --git a/arc/common.py b/arc/common.py index 353729a8e9..36682404f5 100644 --- a/arc/common.py +++ b/arc/common.py @@ -281,7 +281,7 @@ def log_header(project: str, if head != '' and date != '': logger.log(level, f'The current git HEAD for {repo} is:') logger.log(level, f' {head}\n {date}') - if branch_name and branch_name != 'master': + if branch_name and branch_name != 'main': logger.log(level, f' (running on the {branch_name} branch)\n') else: logger.log(level, '\n') diff --git a/docs/source/conf.py b/docs/source/conf.py index 8b0761d27f..bda22b4eca 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -63,8 +63,8 @@ # source_suffix = ['.rst', '.md'] source_suffix = '.rst' -# The master toctree document. -master_doc = 'index' +# The main toctree document. +main_doc = 'index' # A list of default flags for automatically documented items. @@ -154,7 +154,7 @@ # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (master_doc, 'ARC.tex', u'ARC Documentation', + (main_doc, 'ARC.tex', u'ARC Documentation', u'Alon Grinberg Dana', 'manual'), ] @@ -164,7 +164,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'arc', u'ARC Documentation', + (main_doc, 'arc', u'ARC Documentation', [author], 1) ] @@ -175,7 +175,7 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'ARC', u'ARC Documentation', + (main_doc, 'ARC', u'ARC Documentation', author, 'ARC', 'One line description of project.', 'Miscellaneous'), ] diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 5b7c7e8bfb..a6485cfee9 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -95,7 +95,7 @@ The first two directives are only required if you'd like ARC to access remote se - Copy the RSA SSH key path/s on your local machine to ``settings.py`` in the servers dictionary under keys. - Update the ``servers`` dictionary in your copy of ARC's `settings.py - `_. + `_. * A local server must be named with the reserved keyword ``local``. ``cluster_soft`` and username (``un``) are mandatory. @@ -111,7 +111,7 @@ The first two directives are only required if you'd like ARC to access remote se for this reason, ARC will attempt to re-run the job with fewer CPU cores. - Update the ``default_job_settings`` dictionary in your copy of ARC's `settings.py - `_. + `_. * This dictionary contains default job memory, cpu, and time settings. * A default ESS job in ARC has 14 GB of memory, 8 cpu cores, and 120 hours of maximum execution time. The default @@ -122,7 +122,7 @@ The first two directives are only required if you'd like ARC to access remote se use when troubleshoot a job. The default value is 80%. - Update the submit scripts in your copy of ARC's `submit.py - `_ + `_ according to your servers' definitions. * See the given template examples, and follow the structure of nested dictionaries (by server name, then by ESS name). * Preserve the variables in curly braces (e.g., ``{memory}``), so that ARC is able to auto-complete them. @@ -134,7 +134,7 @@ ARC keeps track of software location on servers using a Python dictionary associ with the servers they are installed on (values). The server name must be consistent with the respective definition in the ``servers`` dictionary mentioned above. Typically, you would update the ``global_ess_settings`` dictionary in your copy of ARC's -`settings.py `_ +`settings.py `_ to reflect your software and servers, for example:: global_ess_settings = { @@ -170,7 +170,7 @@ Cluster software definitions ARC supports Slurm and Oracle/Sun Grid Engine (OGE / SGE). If you're using other `cluster software`__, or if your server's definitions are different that ARC's, you should also modify the following variables in your copy of ARC's -`settings.py `_: +`settings.py `_: - ``check_status_command`` - ``submit_command`` @@ -245,10 +245,10 @@ To get the most recent developer version, do the following cd ~/Path/to/ARC/ git stash git fetch origin - git pull origin master + git pull origin main git stash pop -The above will update your `master` branch of ARC. +The above will update your `main` branch of ARC. To update to a specific version (e.g., version 1.1.0), do the following (and make sure to change `~/Path/to/ARC/` accordingly):: @@ -291,7 +291,7 @@ Resolving a merge conflict consists of three stages: updated ARC code). Make the changes and get rid of the unneeded ``<<<<<<< HEAD``, ``=======``, and ``>>>>>>> new_branch_to_merge_later`` markings. Repeat for all conflicts. - Stage the changed by typing: ``git add .`` -- If you don't plan to commit your changes, unstage them by typing: ``git reset --soft origin/master`` +- If you don't plan to commit your changes, unstage them by typing: ``git reset --soft origin/main`` .. include:: links.txt diff --git a/docs/source/links.txt b/docs/source/links.txt index 86e3a10054..e6e4b10879 100644 --- a/docs/source/links.txt +++ b/docs/source/links.txt @@ -6,7 +6,7 @@ .. _anaconda: https://www.anaconda.com/distribution/ .. _yaml: https://yaml.org/ .. _jupyter: https://jupyter.org/ -.. _examplesGitHub: https://github.com/ReactionMechanismGenerator/ARC/tree/master/examples +.. _examplesGitHub: https://github.com/ReactionMechanismGenerator/ARC/tree/main/examples .. _xyz_format: https://en.wikipedia.org/wiki/XYZ_file_format .. _Arkane: http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/input.html .. _semantic: https://semver.org/ diff --git a/docs/source/running.rst b/docs/source/running.rst index 69eb61301e..92c397bb7d 100644 --- a/docs/source/running.rst +++ b/docs/source/running.rst @@ -52,7 +52,7 @@ object. See ARC's API for a complete and updated list of keywords along with the Additional input file examples are available in ARC's examples folder -(`ARC/examples `_). +(`ARC/examples `_). Another convenient way to see a valid and detailed input file is to run an ARC job and peak at the automatically generated ``restart.yml`` file. @@ -104,7 +104,7 @@ has the benefit of displaying "live" and interactive __ jupyter_ Example iPython notebooks are available in the -`ipython/Demo `_ +`ipython/Demo `_ folder. Various :ref:`standalone tools ` in an iPython format are also available, demonstrating different utilizations of the API. Users are of course directed to read :ref:`ARC's API `.