From 42a7d9469aa9360f04a3e7ae71f06eefce5128cf Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 09:53:02 -0500 Subject: [PATCH 01/11] don't use container --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0375112..3fefdbc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,7 +21,6 @@ jobs: - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} - container: pecan/depends:develop services: postgres: image: mdillon/postgis:9.5 From 4e14bd6c317a0294e5ac448265a80f4392bb6849 Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 10:36:03 -0500 Subject: [PATCH 02/11] use sudo --- .github/workflows/ci.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3fefdbc..1d1749f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,7 +2,6 @@ on: push: branches: - master - - "*" pull_request: @@ -48,7 +47,9 @@ jobs: - uses: actions/checkout@v2 - name: install utils - run: apt-get update && apt-get install -y openssh-client postgresql-client curl + run: + - sudo apt-get update + - sudo apt-get install -y openssh-client postgresql-client curl - name: db setup uses: docker://pecan/db:ci From 7a03da3603daa6b3e1e24a1ec2ff69c9ff5fe836 Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 10:36:36 -0500 Subject: [PATCH 03/11] use sudo --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1d1749f..efa111b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,6 +2,7 @@ on: push: branches: - master + - "*" pull_request: From aeacd7fabef899ca9e293f54c083b168524ce8e3 Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 10:38:29 -0500 Subject: [PATCH 04/11] use sudo --- .github/workflows/ci.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index efa111b..ba1f62b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,7 +2,6 @@ on: push: branches: - master - - "*" pull_request: @@ -48,9 +47,9 @@ jobs: - uses: actions/checkout@v2 - name: install utils - run: - - sudo apt-get update - - sudo apt-get install -y openssh-client postgresql-client curl + run: | + sudo apt-get update + sudo apt-get install -y openssh-client postgresql-client curl - name: db setup uses: docker://pecan/db:ci From 9b73dbd37642372e3841a998f6be70b7794550ab Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 16:56:36 -0500 Subject: [PATCH 05/11] more fixes --- .github/workflows/ci.yml | 14 +++++++++----- DESCRIPTION | 3 ++- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ba1f62b..60a3fb6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,14 +46,18 @@ jobs: steps: - uses: actions/checkout@v2 - - name: install utils - run: | - sudo apt-get update - sudo apt-get install -y openssh-client postgresql-client curl + #- name: install utils + # run: | + # sudo apt-get update + # sudo apt-get install -y openssh-client postgresql-client curl - name: db setup uses: docker://pecan/db:ci + - name: create account + uses: docker://pecan/bety:latest + args: user carya illinois "Carya Demo User" carya@example.com 1 1 + - uses: r-lib/actions/setup-r@master with: r-version: ${{ matrix.config.r }} @@ -100,4 +104,4 @@ jobs: uses: actions/upload-artifact@master with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check \ No newline at end of file + path: check diff --git a/DESCRIPTION b/DESCRIPTION index b006d8d..4bd22ae 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,7 +15,8 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific to the PEcAn API server & interact with it. Imports: httr, - jsonlite + jsonlite, + XML License: MIT Copyright: Authors LazyLoad: yes From 42f09fce2961c1b848d8ea70255fd0e8fb47791b Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 17:10:32 -0500 Subject: [PATCH 06/11] fix docker --- .github/workflows/ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 60a3fb6..92651c5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -56,7 +56,8 @@ jobs: - name: create account uses: docker://pecan/bety:latest - args: user carya illinois "Carya Demo User" carya@example.com 1 1 + with: + args: user carya illinois "Carya Demo User" carya@example.com 1 1 - uses: r-lib/actions/setup-r@master with: From caa8c1dcbd2e4a9bd2a8d9bf13f34c3461a2f6ba Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 17:54:04 -0500 Subject: [PATCH 07/11] fix docker --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 92651c5..b753e91 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -55,7 +55,7 @@ jobs: uses: docker://pecan/db:ci - name: create account - uses: docker://pecan/bety:latest + uses: docker://pecan/bety:develop with: args: user carya illinois "Carya Demo User" carya@example.com 1 1 From 17a9d549233a6c8a0f3d6699a621af66c8727d04 Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 18:03:14 -0500 Subject: [PATCH 08/11] fix docker --- .github/workflows/ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b753e91..c1a1870 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -57,7 +57,8 @@ jobs: - name: create account uses: docker://pecan/bety:develop with: - args: user carya illinois "Carya Demo User" carya@example.com 1 1 + entrypoint: /home/bety/script/betyuser.sh + args: carya illinois "Carya Demo User" carya@example.com 1 1 - uses: r-lib/actions/setup-r@master with: From 315f712348013e5f8ec3cb88243cbf261c1f637a Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 18 Aug 2020 18:14:18 -0500 Subject: [PATCH 09/11] install xml2 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4bd22ae..556dea3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific Imports: httr, jsonlite, - XML + xml2 License: MIT Copyright: Authors LazyLoad: yes From 6023efd6ea9b3cb972efa7b0aea509b6aef43ec2 Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Sat, 24 Oct 2020 16:45:40 -0500 Subject: [PATCH 10/11] Update ci.yml --- .github/workflows/ci.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 532feaf..288bd97 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,14 +54,10 @@ jobs: - name: db setup uses: docker://pecan/db:latest - - name: create account - uses: docker://pecan/bety:latest - args: user carya illinois "Carya Demo User" carya@example.com 1 1 - - name: create account uses: docker://pecan/bety:develop with: - entrypoint: /home/bety/script/betyuser.sh + # entrypoint: /home/bety/script/betyuser.sh args: carya illinois "Carya Demo User" carya@example.com 1 1 - uses: r-lib/actions/setup-r@master From f5fbf9906edfc4c1493fffe6acc956668d6e95f7 Mon Sep 17 00:00:00 2001 From: Rob Kooper Date: Tue, 3 Nov 2020 16:52:01 -0600 Subject: [PATCH 11/11] Update .github/workflows/ci.yml Co-authored-by: Alexey Shiklomanov --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 288bd97..4b6d7b3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -58,7 +58,7 @@ jobs: uses: docker://pecan/bety:develop with: # entrypoint: /home/bety/script/betyuser.sh - args: carya illinois "Carya Demo User" carya@example.com 1 1 + args: user carya illinois "Carya Demo User" carya@example.com 1 1 - uses: r-lib/actions/setup-r@master with: