From 0f505f20b2fc2f4d70dfc58f6434988258047a3d Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 8 Aug 2024 14:09:07 +0200 Subject: [PATCH 1/6] start setting up lychee --- .lycheeignore | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .lycheeignore diff --git a/.lycheeignore b/.lycheeignore new file mode 100644 index 000000000..9ff7d5612 --- /dev/null +++ b/.lycheeignore @@ -0,0 +1,2 @@ +https://tess.elixir\-europe.org/ +https://github.com/ From b117b0ea95c4d8db7c3ce3db057dfd0018fe68f3 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Wed, 21 Aug 2024 09:34:37 +0200 Subject: [PATCH 2/6] 2 link fixes --- pages/about/outreach.md | 2 +- pages/national_resources/no_resources.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/about/outreach.md b/pages/about/outreach.md index 044974b87..0a0b3fc50 100644 --- a/pages/about/outreach.md +++ b/pages/about/outreach.md @@ -18,7 +18,7 @@ The poster can be found on [F1000Research](https://f1000research.com/posters/12- **2023-01-12** -RDMkit was introduced to the [DSIG]((https://www.dtls.nl/about/community/interest-groups/data-stewards-interest-group/)) at one of their monthly meetings, together with introduction on IDTkit and FAIRCookBook. [Presentation slides on RDMkit (PDF)](https://drive.google.com/file/d/12aHIH0rRU6ogOOacZr3K6PrzXylYgHIo/view). +RDMkit was introduced to the [DSIG](https://www.dtls.nl/about/community/interest-groups/data-stewards-interest-group/) at one of their monthly meetings, together with introduction on IDTkit and FAIRCookBook. [Presentation slides on RDMkit (PDF)](https://drive.google.com/file/d/12aHIH0rRU6ogOOacZr3K6PrzXylYgHIo/view). ### ELIXIR FAIR & Research Data Management know-how ecosystem - All hands 2022 diff --git a/pages/national_resources/no_resources.md b/pages/national_resources/no_resources.md index 2d8fdeb92..b84ba8482 100644 --- a/pages/national_resources/no_resources.md +++ b/pages/national_resources/no_resources.md @@ -278,7 +278,7 @@ A DMP typically contains information about data handling during a project and af -ELIXIR Norway provides access to a [national instance of the Data Stewardship Wizard (DSW)](https://norway.dsw.elixir-europe.org/wizard/), an internationally developed tool that has been adapted to better suit the needs of Norwegian researchers, PIs, and institutions. Both [RCN]((https://www.forskningsradet.no/en/Adviser-research-policy/open-science/open-access-to-research-data/)) and [BOTT (Bergen, Oslo, Trondheim, Tromsø) university libraries](https://zenodo.org/record/7428542) list the DSW as a preferred tool, particularly for life sciences data. DSW provides templates that are compliant with all different funders' regulations and offers machine-actionable DMP exports. To facilitate the adoption of best-practises, the ELIXIR-NO DSW instance also provides a collection of exemplar DMPs. These DMPs are partially pre-filled with domain-specific recommendations and can be used as a starting point for your own projects. +ELIXIR Norway provides access to a [national instance of the Data Stewardship Wizard (DSW)](https://norway.dsw.elixir-europe.org/wizard/), an internationally developed tool that has been adapted to better suit the needs of Norwegian researchers, PIs, and institutions. Both [RCN](https://www.forskningsradet.no/en/Adviser-research-policy/open-science/open-access-to-research-data/) and [BOTT (Bergen, Oslo, Trondheim, Tromsø) university libraries](https://zenodo.org/record/7428542) list the DSW as a preferred tool, particularly for life sciences data. DSW provides templates that are compliant with all different funders' regulations and offers machine-actionable DMP exports. To facilitate the adoption of best-practises, the ELIXIR-NO DSW instance also provides a collection of exemplar DMPs. These DMPs are partially pre-filled with domain-specific recommendations and can be used as a starting point for your own projects. ## Life science-specific infrastructures/resources From 0320136a7cb2cbbe8cd645e6cc033ed0a553039c Mon Sep 17 00:00:00 2001 From: bedroesb Date: Wed, 21 Aug 2024 09:50:16 +0200 Subject: [PATCH 3/6] add action --- .github/workflows/link-checker.yml | 68 ++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 .github/workflows/link-checker.yml diff --git a/.github/workflows/link-checker.yml b/.github/workflows/link-checker.yml new file mode 100644 index 000000000..41055f409 --- /dev/null +++ b/.github/workflows/link-checker.yml @@ -0,0 +1,68 @@ +# .pre-commit-config.yaml +name: Link checker +on: + schedule: + - cron: '0 13 * * 1' + workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + with: + ref: ${{ github.event.inputs.branch }} + + - name: Setup Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: '3.1' + bundler-cache: true + cache-version: 0 + + - name: Setup Pages + id: pages + uses: actions/configure-pages@v2 + + + - name: Install dependencies + run: | + bundle install + + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: | + bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" + env: + PAGES_REPO_NWO: ${{ github.repository }} + JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} + JEKYLL_ENV: production + JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }} + + linkChecker: + runs-on: ubuntu-latest + needs: build + steps: + - uses: actions/checkout@v4 + + - name: Check Links + uses: lycheeverse/lychee-action@v1.6.1 + with: + # For parameter description, see https://github.com/lycheeverse/lychee#commandline-parameters + # Accept 429 for now due to github rate limit. + # See https://github.com/lycheeverse/lychee/issues/634 + args: --fallback-extensions=html _site/ + output: out.md + env: + GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} + + - name: Create Issue From File + uses: peter-evans/create-issue-from-file@v4 + with: + title: Broken Link Detected + content-filepath: out.md + +# - name: Fail if there were link errors +# run: exit ${{ steps.lychee.outputs.exit_code }} \ No newline at end of file From d1f89962e4b7044137b318696e0cbc47665e3ab4 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 5 Dec 2024 14:08:23 +0100 Subject: [PATCH 4/6] add link checker --- .github/workflows/link-checker.yml | 74 ++++++++++++------------------ 1 file changed, 30 insertions(+), 44 deletions(-) diff --git a/.github/workflows/link-checker.yml b/.github/workflows/link-checker.yml index 41055f409..c76c6b250 100644 --- a/.github/workflows/link-checker.yml +++ b/.github/workflows/link-checker.yml @@ -1,29 +1,23 @@ -# .pre-commit-config.yaml -name: Link checker +name: Link Checker + on: - schedule: - - cron: '0 13 * * 1' workflow_dispatch: + schedule: + - cron: "00 18 * * *" jobs: - build: - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v3 - with: - ref: ${{ github.event.inputs.branch }} + linkChecker: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Setup Ruby uses: ruby/setup-ruby@v1 with: - ruby-version: '3.1' - bundler-cache: true - cache-version: 0 - - - name: Setup Pages - id: pages - uses: actions/configure-pages@v2 + ruby-version: '3.1' + bundler-cache: true + cache-version: 0 - name: Install dependencies @@ -31,38 +25,30 @@ jobs: bundle install - name: Build with Jekyll - # Outputs to the './_site' directory by default + # Outputs to the './_site' directory by default run: | - bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" + bundle exec jekyll build env: PAGES_REPO_NWO: ${{ github.repository }} JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} JEKYLL_ENV: production JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }} - - linkChecker: - runs-on: ubuntu-latest - needs: build - steps: - - uses: actions/checkout@v4 - - name: Check Links - uses: lycheeverse/lychee-action@v1.6.1 + - name: Link Checker + id: lychee + uses: lycheeverse/lychee-action@2.1.0 with: - # For parameter description, see https://github.com/lycheeverse/lychee#commandline-parameters - # Accept 429 for now due to github rate limit. - # See https://github.com/lycheeverse/lychee/issues/634 - args: --fallback-extensions=html _site/ - output: out.md - env: - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} - - - name: Create Issue From File - uses: peter-evans/create-issue-from-file@v4 + # Check all markdown, html and reStructuredText files in repo (default) + args: _site/ --fallback-extensions .html + # Don't fail action on broken links + fail: false + # Lychee version + lycheeVersion: 0.17.0 + + # Create or Update the issue based on the link check result + - name: Update Comment From File + uses: peter-evans/create-or-update-comment@v4 with: - title: Broken Link Detected - content-filepath: out.md - -# - name: Fail if there were link errors -# run: exit ${{ steps.lychee.outputs.exit_code }} \ No newline at end of file + comment-id: 2520269418 + body-path: ./lychee/out.md + edit-mode: replace From da12bc00873f6e87b58a7568719ceed90ef5c283 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Thu, 5 Dec 2024 15:35:47 +0100 Subject: [PATCH 5/6] Delete .github/workflows/link-checker.yml --- .github/workflows/link-checker.yml | 54 ------------------------------ 1 file changed, 54 deletions(-) delete mode 100644 .github/workflows/link-checker.yml diff --git a/.github/workflows/link-checker.yml b/.github/workflows/link-checker.yml deleted file mode 100644 index c76c6b250..000000000 --- a/.github/workflows/link-checker.yml +++ /dev/null @@ -1,54 +0,0 @@ -name: Link Checker - -on: - workflow_dispatch: - schedule: - - cron: "00 18 * * *" - -jobs: - linkChecker: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - - name: Setup Ruby - uses: ruby/setup-ruby@v1 - with: - ruby-version: '3.1' - bundler-cache: true - cache-version: 0 - - - - name: Install dependencies - run: | - bundle install - - - name: Build with Jekyll - # Outputs to the './_site' directory by default - run: | - bundle exec jekyll build - env: - PAGES_REPO_NWO: ${{ github.repository }} - JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} - JEKYLL_ENV: production - JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - - name: Link Checker - id: lychee - uses: lycheeverse/lychee-action@2.1.0 - with: - # Check all markdown, html and reStructuredText files in repo (default) - args: _site/ --fallback-extensions .html - # Don't fail action on broken links - fail: false - # Lychee version - lycheeVersion: 0.17.0 - - # Create or Update the issue based on the link check result - - name: Update Comment From File - uses: peter-evans/create-or-update-comment@v4 - with: - comment-id: 2520269418 - body-path: ./lychee/out.md - edit-mode: replace From ad65432d959ad578498a99e1e7b32bbf401d21b5 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Thu, 5 Dec 2024 15:35:59 +0100 Subject: [PATCH 6/6] Delete .lycheeignore --- .lycheeignore | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 .lycheeignore diff --git a/.lycheeignore b/.lycheeignore deleted file mode 100644 index 9ff7d5612..000000000 --- a/.lycheeignore +++ /dev/null @@ -1,2 +0,0 @@ -https://tess.elixir\-europe.org/ -https://github.com/