From a77e0f842883b0a06581cec597508c444eb0f094 Mon Sep 17 00:00:00 2001 From: Julian Pistorius Date: Thu, 29 Oct 2020 18:09:47 +0000 Subject: [PATCH 1/4] Docker build instructions will break by default Not everybody has a Docker daemon recent enough for `--progress` to work by default. Solution: Remove the `--progress` flag Related commit: https://github.com/AgPipeline/drone-makeflow/pull/1/commits/0171237a4c1f1642a995e974ec7563d58c09636f --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6feb4e7..5c3a0d6 100644 --- a/README.md +++ b/README.md @@ -215,7 +215,7 @@ Please refer to the [Docker](https://www.docker.com/) documentation for more inf ```bash cp jx-args.json.example jx-args.json -docker build --progress=plain -t agdrone/canopycover-workflow:latest . +docker build -t agdrone/canopycover-workflow:latest . ``` ## Monitoring the Workflow From dc6ed84a9e9af1f04822eea6bf6d068c273e8d47 Mon Sep 17 00:00:00 2001 From: Chris Schnaufer Date: Tue, 17 Nov 2020 13:38:50 -0700 Subject: [PATCH 2/4] Updating canopy cover code tag --- scif_app_recipes/canopycover_v0.0.1_ubuntu16.04.scif | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scif_app_recipes/canopycover_v0.0.1_ubuntu16.04.scif b/scif_app_recipes/canopycover_v0.0.1_ubuntu16.04.scif index 8ba92d6..2f7e099 100644 --- a/scif_app_recipes/canopycover_v0.0.1_ubuntu16.04.scif +++ b/scif_app_recipes/canopycover_v0.0.1_ubuntu16.04.scif @@ -1,8 +1,8 @@ %appinstall canopycover # Download canopycover code. In the future use pip/conda install. - wget -O canopycover.tar.gz https://github.com/AgPipeline/transformer-canopycover/archive/v1.3.tar.gz + wget -O canopycover.tar.gz https://github.com/AgPipeline/transformer-canopycover/archive/v1.4.tar.gz tar xvf canopycover.tar.gz - mv transformer-canopycover-1.3 src + mv transformer-canopycover-1.4 src # Install packages needed python3 -m venv --system-site-packages .venv From ad7163157eb7ed5225ac5b14b290ed117c7d2c9f Mon Sep 17 00:00:00 2001 From: Chris Schnaufer Date: Tue, 17 Nov 2020 14:10:00 -0700 Subject: [PATCH 3/4] Count adjutment --- .github/workflows/short_workflow_check.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/short_workflow_check.sh b/.github/workflows/short_workflow_check.sh index 24a8b2d..cf1e619 100755 --- a/.github/workflows/short_workflow_check.sh +++ b/.github/workflows/short_workflow_check.sh @@ -2,7 +2,7 @@ # Define some counts that we expect (the number of sub-folders plus the top folder) EXPECTED_NUM_FOLDERS=58 -EXPECTED_NUM_CANOPYCOVER_CSV=56 +EXPECTED_NUM_CANOPYCOVER_CSV=57 # The same number of CSV files + original, un-clipped mask file EXPECTED_NUM_MASK_TIF=$((EXPECTED_NUM_CANOPYCOVER_CSV + 1)) From 6ad52dee3808b624d87dc3d6464208a5f2d5fbbb Mon Sep 17 00:00:00 2001 From: Chris Schnaufer Date: Tue, 17 Nov 2020 15:17:45 -0700 Subject: [PATCH 4/4] Count adjust --- .github/workflows/docker_build_test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_build_test.yaml b/.github/workflows/docker_build_test.yaml index 6c9beff..35510b6 100644 --- a/.github/workflows/docker_build_test.yaml +++ b/.github/workflows/docker_build_test.yaml @@ -81,7 +81,7 @@ jobs: docker_params: -v "${PWD}/inputs:/scif/data/odm_workflow/images" -v "${PWD}/outputs:/output" -v "${PWD}/checkpoints:/scif/data/short_workflow" parameters: orthomosaic plot_shapes.shp result_check_script: "short_workflow_check.sh" - clean_leftover_output_count: "3" + clean_leftover_output_count: "1" clean_leftover_makeflow_count: "2" steps: - name: Fetch source code