From 8caa214d50ee301c429439ecd9ee888575980b78 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Thu, 15 Feb 2024 11:23:39 +0100 Subject: [PATCH 1/3] fix environment_script for private plugins I found that patch 54.sql for the test database uses an old conda activate mechanism for travis. We might want to fix this to the latest github action method of choice? --- .github/workflows/qiita-ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml index bbc6c25f5..dd9ab2c88 100644 --- a/.github/workflows/qiita-ci.yml +++ b/.github/workflows/qiita-ci.yml @@ -154,6 +154,8 @@ jobs: echo "5. Setting up qiita" conda activate qiita + # adapt environment_script for private qiita plugins from travis to github actions. + sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"#source /home/runner/.profile#' -i qiita_db/support_files/patches/54.sql qiita-env make --no-load-ontologies qiita-test-install qiita plugins update From 6f027ada1d2d61901af5545c47e580e1272a933b Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Thu, 15 Feb 2024 11:27:56 +0100 Subject: [PATCH 2/3] Update qiita-ci.yml --- .github/workflows/qiita-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml index dd9ab2c88..988ebde22 100644 --- a/.github/workflows/qiita-ci.yml +++ b/.github/workflows/qiita-ci.yml @@ -155,7 +155,7 @@ jobs: echo "5. Setting up qiita" conda activate qiita # adapt environment_script for private qiita plugins from travis to github actions. - sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"#source /home/runner/.profile#' -i qiita_db/support_files/patches/54.sql + sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile#; conda ' -i qiita_db/support_files/patches/54.sql qiita-env make --no-load-ontologies qiita-test-install qiita plugins update From 9aff1e4870c871408c8e6626c348209fa948ae86 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 16 Feb 2024 08:50:38 +0100 Subject: [PATCH 3/3] Update qiita-ci.yml fix quoting --- .github/workflows/qiita-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml index 988ebde22..6c3b06be1 100644 --- a/.github/workflows/qiita-ci.yml +++ b/.github/workflows/qiita-ci.yml @@ -155,7 +155,7 @@ jobs: echo "5. Setting up qiita" conda activate qiita # adapt environment_script for private qiita plugins from travis to github actions. - sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile#; conda ' -i qiita_db/support_files/patches/54.sql + sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile; conda #' -i qiita_db/support_files/patches/54.sql qiita-env make --no-load-ontologies qiita-test-install qiita plugins update