From 45433aaf8d32f91e92f3d08606cbe76f06d57bd7 Mon Sep 17 00:00:00 2001 From: Sebastian Lobentanzer Date: Fri, 27 Oct 2023 09:59:19 +0200 Subject: [PATCH] Brand repo to biocypher/biochatter-paper --- .appveyor.yml | 84 --------------------------------------------------- README.md | 16 +++++----- ci/install.sh | 25 --------------- 3 files changed, 8 insertions(+), 117 deletions(-) delete mode 100644 .appveyor.yml delete mode 100755 ci/install.sh diff --git a/.appveyor.yml b/.appveyor.yml deleted file mode 100644 index 69d6e6c..0000000 --- a/.appveyor.yml +++ /dev/null @@ -1,84 +0,0 @@ -# See https://www.appveyor.com/docs/getting-started-with-appveyor-for-linux/ -# Don't build branches with a PR, since their build will be created with the PR itself. -# Otherwise there would be two builds -- one for the PR and one for the branch. -# If you're having issues with getting your PR to build, make sure there are no merge conflicts. -skip_branch_with_pr: true - -# Enable 'Do not build on "Push" events' in the AppVeyor project settings -# to only build commits from pull requests -branches: - only: - - main - - master - -# Only run AppVeyor on commits that modify at least one of the following files -# Delete these lines to run AppVeyor on all main/master branch commits -only_commits: - files: - - .appveyor.yml - - build/ - - ci/install.sh - - content/ - -image: ubuntu -services: - - docker - -# Set SPELLCHECK to true to enable Pandoc spellchecking -environment: - SPELLCHECK: true - -install: - # Create the message with the triggering commit before install so it is - # available if the build fails - - TRIGGERING_COMMIT=${APPVEYOR_PULL_REQUEST_HEAD_COMMIT:-APPVEYOR_REPO_COMMIT} - - JOB_MESSAGE=" for commit $TRIGGERING_COMMIT " - - source ci/install.sh - -test_script: - - bash build/build.sh - - MANUSCRIPT_FILENAME=manuscript-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7} - - cp output/manuscript.html $MANUSCRIPT_FILENAME.html - - cp output/manuscript.pdf $MANUSCRIPT_FILENAME.pdf - - appveyor PushArtifact $MANUSCRIPT_FILENAME.html - - appveyor PushArtifact $MANUSCRIPT_FILENAME.pdf - - | - if [ "${SPELLCHECK:-}" = "true" ]; then - SPELLING_ERRORS_FILENAME=spelling-errors-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt - cp output/spelling-errors.txt $SPELLING_ERRORS_FILENAME - appveyor PushArtifact $SPELLING_ERRORS_FILENAME - SPELLING_ERROR_LOCATIONS_FILENAME=spelling-error-locations-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt - cp output/spelling-error-locations.txt $SPELLING_ERROR_LOCATIONS_FILENAME - appveyor PushArtifact $SPELLING_ERROR_LOCATIONS_FILENAME - fi - -build: off - -cache: - - ci/cache - -on_success: - - echo "Artifacts available from $APPVEYOR_URL/project/$APPVEYOR_ACCOUNT_NAME/$APPVEYOR_PROJECT_SLUG/builds/$APPVEYOR_BUILD_ID/artifacts" - - echo "Updated PDF available from $APPVEYOR_URL/api/buildjobs/$APPVEYOR_JOB_ID/artifacts/$MANUSCRIPT_FILENAME.pdf" - - appveyor AddMessage "$JOB_MESSAGE is now complete." - - | - if [ "${SPELLCHECK:-}" = "true" ]; then - SPELLING_ERROR_COUNT=($(wc -l $SPELLING_ERROR_LOCATIONS_FILENAME)) - appveyor AddMessage "
Found $SPELLING_ERROR_COUNT potential spelling error(s). Preview:$(head -n 100 $SPELLING_ERROR_LOCATIONS_FILENAME)" - appveyor AddMessage "...
" - fi - -on_failure: - - appveyor AddMessage "$JOB_MESSAGE failed." - -# The following lines can be safely deleted, which will disable AppVeyorBot -# notifications in GitHub pull requests -# Notifications use Mustache templates http://mustache.github.io/mustache.5.html -# See https://www.appveyor.com/docs/notifications/#customizing-message-template -# for available variables -notifications: - - provider: GitHubPullRequest - template: "AppVeyor [build {{buildVersion}}]({{buildUrl}}) - {{#jobs}}{{#messages}}{{{message}}}{{/messages}}{{/jobs}} - {{#passed}}The rendered manuscript from this build is temporarily available for download at:\n\n - {{#jobs}}{{#artifacts}}- [`{{fileName}}`]({{permalink}})\n{{/artifacts}}{{/jobs}}{{/passed}}" diff --git a/README.md b/README.md index 73197a6..17dfb42 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,9 @@ -[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://manubot.github.io/rootstock/) -[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://manubot.github.io/rootstock/manuscript.pdf) -[![GitHub Actions Status](https://github.com/manubot/rootstock/workflows/Manubot/badge.svg)](https://github.com/manubot/rootstock/actions) +[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://biocypher.github.io/biochatter-paper/) +[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://biocypher.github.io/biochatter-paper/manuscript.pdf) +[![GitHub Actions Status](https://github.com/biocypher/biochatter-paper/workflows/Manubot/badge.svg)](https://github.com/biocypher/biochatter-paper/actions) ## Manuscript description @@ -77,11 +77,11 @@ Whenever a pull request is opened, CI (continuous integration) will test whether The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly. -When a commit to the `main` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches. +When a commit to the `main` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/biocypher/biochatter-paper/tree/gh-pages) and [`output`](https://github.com/biocypher/biochatter-paper/tree/output) branches. The `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs: -+ **HTML manuscript** at https://manubot.github.io/rootstock/ -+ **PDF manuscript** at https://manubot.github.io/rootstock/manuscript.pdf ++ **HTML manuscript** at https://biocypher.github.io/biochatter-paper/ ++ **PDF manuscript** at https://biocypher.github.io/biochatter-paper/manuscript.pdf For continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml). @@ -96,7 +96,7 @@ We encourage users to openly license their manuscripts, which is the default as [![License: CC0 1.0](https://img.shields.io/badge/License%20Parts-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/) Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution. -Please attribute by linking to https://github.com/manubot/rootstock. +Please attribute by linking to https://github.com/biocypher/biochatter-paper. Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication ([`LICENSE-CC0.md`](LICENSE-CC0.md)). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0: @@ -116,4 +116,4 @@ All other files are only available under CC BY 4.0, including: + `*.pdf` + `*.docx` -Please open [an issue](https://github.com/manubot/rootstock/issues) for any question related to licensing. +Please open [an issue](https://github.com/biocypher/biochatter-paper/issues) for any question related to licensing. diff --git a/ci/install.sh b/ci/install.sh deleted file mode 100755 index 6b20f0e..0000000 --- a/ci/install.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env bash - -## install.sh: run during an AppVeyor build to install the conda environment -## and the optional Pandoc spellcheck dependencies. - -# Set options for extra caution & debugging -set -o errexit \ - -o pipefail - -wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh \ - --output-document miniforge.sh -bash miniforge.sh -b -p $HOME/miniconda -source $HOME/miniconda/etc/profile.d/conda.sh -hash -r -conda config \ - --set always_yes yes \ - --set changeps1 no -mamba env create --quiet --file build/environment.yml -mamba list --name manubot -conda activate manubot - -# Install Spellcheck filter for Pandoc -if [ "${SPELLCHECK:-}" = "true" ]; then - bash ci/install-spellcheck.sh -fi