From 1c781ec3ef5e5c93c600572e0d134d9bc3043e4d Mon Sep 17 00:00:00 2001 From: Boris Depoortere <118811684+B0r1sD@users.noreply.github.com> Date: Wed, 17 Jul 2024 16:30:03 +0200 Subject: [PATCH 1/6] Update update-trusted.yml Updated tools, removed legacy, kept it in a pull request for now for testing purposes (later: direct commit to main) --- .github/workflows/update-trusted.yml | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/update-trusted.yml b/.github/workflows/update-trusted.yml index 6b333512..690f0219 100644 --- a/.github/workflows/update-trusted.yml +++ b/.github/workflows/update-trusted.yml @@ -1,23 +1,23 @@ name: Update Trusted Tools on: - workflow_dispatch: - push: - pull_request: schedule: - - cron: "0 2 * * THU" + # Runs weekly, every Saturday at 02:00 UTC (alligned with off-peak hours) + - cron: "0 2 * * SAT" jobs: build: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.8] + python-version: [3.7, 3.8, 3.9, 3.10, 3.11] # test to see what Python versons are compatible steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 + with: + fetch-depth: 0 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -25,7 +25,7 @@ jobs: python -m pip install --upgrade pip if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Clone usegalaxy-eu-tools repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: usegalaxy-eu/usegalaxy-eu-tools path: usegalaxy-eu-tools @@ -39,13 +39,13 @@ jobs: run: | # Update the trusted tools. make fix -j $(nproc) - # make lint -j $(nproc) + make lint -j $(nproc) make update_trusted -j $(nproc) - name: Show differences run: "git diff --stat" - name: Create Pull Request id: cpr - uses: peter-evans/create-pull-request@v3 + uses: peter-evans/create-pull-request@v6 with: token: ${{ secrets.GITHUB_TOKEN }} commit-message: Update Galaxy tools @@ -56,7 +56,6 @@ jobs: Please verify if these changes are valid. labels: | automatic PR - reviewers: ieguinoa branch: tools-update base: master - name: Check output From 5b44bc4e079ae43a277cf800b9477c2c4f0dab8f Mon Sep 17 00:00:00 2001 From: Boris Depoortere <118811684+B0r1sD@users.noreply.github.com> Date: Wed, 17 Jul 2024 16:35:25 +0200 Subject: [PATCH 2/6] Update update-trusted.yml Added workflow trigger events --- .github/workflows/update-trusted.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/update-trusted.yml b/.github/workflows/update-trusted.yml index 690f0219..4b6c1ce7 100644 --- a/.github/workflows/update-trusted.yml +++ b/.github/workflows/update-trusted.yml @@ -1,6 +1,10 @@ name: Update Trusted Tools on: + pull_request: + branches: + - main + workflow_dispatch: schedule: # Runs weekly, every Saturday at 02:00 UTC (alligned with off-peak hours) - cron: "0 2 * * SAT" From bd0da39f84f94c3988805a5dc7a23d3a84e27231 Mon Sep 17 00:00:00 2001 From: Boris Depoortere <118811684+B0r1sD@users.noreply.github.com> Date: Wed, 17 Jul 2024 16:36:40 +0200 Subject: [PATCH 3/6] Update update-trusted.yml main branch is still called 'master' --- .github/workflows/update-trusted.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update-trusted.yml b/.github/workflows/update-trusted.yml index 4b6c1ce7..504866bd 100644 --- a/.github/workflows/update-trusted.yml +++ b/.github/workflows/update-trusted.yml @@ -3,7 +3,7 @@ name: Update Trusted Tools on: pull_request: branches: - - main + - master workflow_dispatch: schedule: # Runs weekly, every Saturday at 02:00 UTC (alligned with off-peak hours) From c2fe0b260df9671999e1cf94f6c305c6f71090f2 Mon Sep 17 00:00:00 2001 From: Boris Depoortere <118811684+B0r1sD@users.noreply.github.com> Date: Wed, 17 Jul 2024 16:39:24 +0200 Subject: [PATCH 4/6] Update update-trusted.yml Other Python versions were tested unsuccessfully --- .github/workflows/update-trusted.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update-trusted.yml b/.github/workflows/update-trusted.yml index 504866bd..6276ca89 100644 --- a/.github/workflows/update-trusted.yml +++ b/.github/workflows/update-trusted.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.7, 3.8, 3.9, 3.10, 3.11] # test to see what Python versons are compatible + python-version: [3.8] steps: - name: Checkout uses: actions/checkout@v4 From fc1de455d012efbcde213e0483d348f19f087a75 Mon Sep 17 00:00:00 2001 From: Boris Depoortere <118811684+B0r1sD@users.noreply.github.com> Date: Wed, 17 Jul 2024 16:45:54 +0200 Subject: [PATCH 5/6] Update update-trusted.yml Test if this is needed --- .github/workflows/update-trusted.yml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/.github/workflows/update-trusted.yml b/.github/workflows/update-trusted.yml index 6276ca89..4daae853 100644 --- a/.github/workflows/update-trusted.yml +++ b/.github/workflows/update-trusted.yml @@ -28,17 +28,6 @@ jobs: run: | python -m pip install --upgrade pip if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Clone usegalaxy-eu-tools repository - uses: actions/checkout@v4 - with: - repository: usegalaxy-eu/usegalaxy-eu-tools - path: usegalaxy-eu-tools - ref: master - - name: Update tools_iuc.yaml from tools_iuc_eu.yaml - run: | - python3 process_yaml.py --merge_yaml --base_file tools_iuc.yaml --tools_yaml ${GITHUB_WORKSPACE}/usegalaxy-eu-tools/tools_iuc.yaml --out_file tools_iuc.yaml - - name: Deleting usegalaxy-eu-tools repository - run: rm -r usegalaxy-eu-tools - name: Perform linting run: | # Update the trusted tools. From 5ffd84872b0ba34d8fbb96bf040dc427a5fd92ab Mon Sep 17 00:00:00 2001 From: Boris Depoortere <118811684+B0r1sD@users.noreply.github.com> Date: Wed, 17 Jul 2024 17:04:04 +0200 Subject: [PATCH 6/6] Necessary updating step I've put it back --- .github/workflows/update-trusted.yml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/.github/workflows/update-trusted.yml b/.github/workflows/update-trusted.yml index 4daae853..cd47e56b 100644 --- a/.github/workflows/update-trusted.yml +++ b/.github/workflows/update-trusted.yml @@ -28,11 +28,22 @@ jobs: run: | python -m pip install --upgrade pip if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Clone usegalaxy-eu-tools repository + uses: actions/checkout@v4 + with: + repository: usegalaxy-eu/usegalaxy-eu-tools + path: usegalaxy-eu-tools + ref: master + - name: Update tools_iuc.yaml from tools_iuc_eu.yaml + run: | + python3 process_yaml.py --merge_yaml --base_file tools_iuc.yaml --tools_yaml ${GITHUB_WORKSPACE}/usegalaxy-eu-tools/tools_iuc.yaml --out_file tools_iuc.yaml + - name: Deleting usegalaxy-eu-tools repository + run: rm -r usegalaxy-eu-tools - name: Perform linting run: | # Update the trusted tools. make fix -j $(nproc) - make lint -j $(nproc) + # make lint -j $(nproc) make update_trusted -j $(nproc) - name: Show differences run: "git diff --stat"