diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..139b7b1 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,68 @@ +name: Deploy documentation + +on: + # Runs on pushes targeting the default branch + push: + branches: ["main"] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: read + pages: write + id-token: write + +# Allow one concurrent deployment +concurrency: + group: "pages" + cancel-in-progress: true + +jobs: + deploy: + name: docs + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Install miniconda + uses: conda-incubator/setup-miniconda@v3 + with: + miniconda-version: "latest" + auto-update-conda: true + python-version: "3.12" + + - name: Initialize conda environment + run: make conda-create + + - name: Setup conda + run: make conda-setup + + - name: Install conda dependencies + run: make from-conda-lock + + - name: Install docs dependenices + run: make install + + - name: Build documentation + run: make docs + + - name: Setup Pages + uses: actions/configure-pages@v5 + + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + path: 'public/' + + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index 868e0b2..0000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,19 +0,0 @@ -default: - image: continuumio/miniconda3 - before_script: - - apt-get update - - apt-get install build-essential -y - - apt-get install curl -y - -pages: - stage: deploy - script: - - make environment - - make docs - artifacts: - paths: - - public/ - rules: - - if: $CI_PIPELINE_SOURCE == 'merge_request_event' - - if: $CI_COMMIT_TAG - - if: "$CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH" diff --git a/CODEOWNERS b/CODEOWNERS deleted file mode 100644 index fb80d88..0000000 --- a/CODEOWNERS +++ /dev/null @@ -1 +0,0 @@ -* @aalexmmaldonado diff --git a/README.md b/README.md index 1153c6f..63e6952 100644 --- a/README.md +++ b/README.md @@ -22,12 +22,12 @@ git push --follow-tags ## License -Code contained in this project is released under the [MIT License](https://spdx.org/licenses/MIT.html) as specified in [`LICENSE_CODE`](https://gitlab.com/oasci/breadcrumbs/compbio/-/blob/main/LICENSE_CODE.md). -This license grants you the freedom to use, modify, and distribute it as long as you include the original copyright notice contained in [`LICENSE_CODE`](https://gitlab.com/oasci/breadcrumbs/compbio/-/blob/main/LICENSE_CODE.md) and the following notice. +Code contained in this project is released under the [MIT License](https://spdx.org/licenses/MIT.html) as specified in [`LICENSE_CODE`](https://github.com/oasci-bc/compbio/blob/main/LICENSE_CODE.md). +This license grants you the freedom to use, modify, and distribute it as long as you include the original copyright notice contained in [`LICENSE_CODE`](https://github.com/oasci-bc/compbio/blob/main/LICENSE_CODE.md) and the following notice. -> Portions of this code were incorporated and adapted with permission from [Computational Biology Breadcrumbs](https://gitlab.com/oasci/compbio) by OASCI licensed under the [MIT license](https://gitlab.com/oasci/breadcrumbs/compbio/-/blob/main/LICENSE_CODE.md). +> Portions of this code were incorporated and adapted with permission from [Computational Biology Breadcrumbs](https://gitlab.com/oasci/compbio) by OASCI licensed under the [MIT license](https://github.com/oasci-bc/compbio/blob/main/LICENSE_CODE.md). -All other data, information, documentation, and associated content provided within this project are released under the [Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0)](https://creativecommons.org/licenses/by-sa/4.0/) as specified in [`LICENSE_INFO`](https://gitlab.com/oasci/breadcrumbs/compbio/-/blob/main/LICENSE_INFO.md). +All other data, information, documentation, and associated content provided within this project are released under the [Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0)](https://creativecommons.org/licenses/by-sa/4.0/) as specified in [`LICENSE_INFO`](https://github.com/oasci-bc/compbio/blob/main/LICENSE_INFO.md). This means you are free to share and adapt the non-code elements, but you must give appropriate credit to the original source and indicate if changes were made. -> Some content was incorporated and adapted with permission [Computational Biology Breadcrumbs](https://gitlab.com/oasci/compbio) by OASCI licensed under the [CC BY-SA 4.0 license](https://gitlab.com/oasci/breadcrumbs/compbio/-/blob/main/LICENSE_INFO.md) +> Some content was incorporated and adapted with permission [Computational Biology Breadcrumbs](https://gitlab.com/oasci/compbio) by OASCI licensed under the [CC BY-SA 4.0 license](https://github.com/oasci-bc/compbio/blob/main/LICENSE_INFO.md) diff --git a/mkdocs.yml b/mkdocs.yml index affacee..0327d2a 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -3,9 +3,8 @@ docs_dir: docs site_name: Computational Biology - Breadcrumbs site_author: OASCI -repo_name: oasci/breadcrumbs/python-bc -repo_url: https://gitlab.com/oasci/breadcrumbs/python-bc -edit_uri: -/edit/main/python-bc +repo_name: oasci/compbio +repo_url: https://github.com/oasci-bc/compbio copyright: CC BY-NC-SA 4.0 by OASCI # https://squidfunk.github.io/mkdocs-material/ @@ -29,7 +28,7 @@ theme: text: Roboto code: Roboto Mono icon: - repo: fontawesome/brands/gitlab + repo: fontawesome/brands/github annotation: material/star-four-points-circle features: - content.code.annotate