From f80e29bd32cc35ef0e38022e29d7c7c78a12ce2b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 11 Dec 2023 14:00:37 +0100 Subject: [PATCH 1/5] Unset en variable JAVA_TOOL_OPTIONS in gitpod --- .gitpod.yml | 3 +++ CHANGELOG.md | 2 ++ nf_core/pipeline-template/.gitpod.yml | 4 +++- 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index 1cc63b197f..3c8b6b5303 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -6,6 +6,9 @@ tasks: python -m pip install -r requirements-dev.txt pre-commit install --install-hooks nextflow self-update + - name: unset JAVA_TOOL_OPTIONS + command: | + unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/CHANGELOG.md b/CHANGELOG.md index c1279e9249..ef414cf8e5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503)) - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509)) - Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540)) +- Unset en variable JAVA_TOOL_OPTIONS in gitpod ([]()) ### Download @@ -41,6 +42,7 @@ - Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545)) - Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)). - GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)). +- Unset en variable JAVA_TOOL_OPTIONS in gitpod ([]()) # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25] diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 25488dcc08..acf7269536 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -4,7 +4,9 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - + - name: unset JAVA_TOOL_OPTIONS + command: | + unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files From 92f5f1dc26489b8c5e2409dbe1451ebbeab7f558 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 11 Dec 2023 14:02:24 +0100 Subject: [PATCH 2/5] update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ef414cf8e5..c453c79abd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503)) - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509)) - Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540)) -- Unset en variable JAVA_TOOL_OPTIONS in gitpod ([]()) +- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569)) ### Download @@ -42,7 +42,7 @@ - Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545)) - Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)). - GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)). -- Unset en variable JAVA_TOOL_OPTIONS in gitpod ([]()) +- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569)) # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25] From 420a6413bef6eb3de9d0f878318c5f9689962391 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 14 Dec 2023 10:07:58 +0000 Subject: [PATCH 3/5] No need for setup steps in setup job --- .github/workflows/pytest.yml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 9f8172a3be..3499c99e66 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -39,16 +39,6 @@ jobs: id: conditions run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV - - name: Check out source-code repository - uses: actions/checkout@v4 - if: ${{ env.run-tests == 'true' }} - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - if: ${{ env.run-tests == 'true' }} outputs: python-version: ${{ matrix.python-version }} runner: ${{ matrix.runner }} From fc99c0c9d70cfcb8e4175da3c27e5d1bdf0da723 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 14 Dec 2023 10:15:42 +0000 Subject: [PATCH 4/5] limit nf-test cache to once per month --- .github/workflows/pytest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 3499c99e66..e2a5d5be7f 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -87,7 +87,7 @@ jobs: path: | /usr/local/bin/nf-test /home/runner/.nf-test/nf-test.jar - key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest + key: ${{ runner.os }}-nftest-${{ needs.date.outputs.date }} - name: Install nf-test if: steps.cache-software.outputs.cache-hit != 'true' From e62d11344eb5ad95bdf4ca208d7e4d19be01c283 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 14 Dec 2023 10:18:35 +0000 Subject: [PATCH 5/5] fix date key --- .github/workflows/pytest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index e2a5d5be7f..23d052dc03 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -87,7 +87,7 @@ jobs: path: | /usr/local/bin/nf-test /home/runner/.nf-test/nf-test.jar - key: ${{ runner.os }}-nftest-${{ needs.date.outputs.date }} + key: ${{ runner.os }}-nftest-${{ env.date }} - name: Install nf-test if: steps.cache-software.outputs.cache-hit != 'true'