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Upgrade to 0.99.14 #95

Merged
merged 54 commits into from
Oct 28, 2023
Merged

Upgrade to 0.99.14 #95

merged 54 commits into from
Oct 28, 2023

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bschilder
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@bschilder bschilder commented Oct 27, 2023 •
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rworkflows 0.99.14

New features

  • Add step to enable conda envs: Add step to enable conda envs #78
    • Add subfunction: gha_python_versions() within construct_runners
    • Add new action.yml args:
      • miniforge_variant
      • miniforge_version
      • activate_environment
      • environment_file
      • channels
    • New function to construct conda env yaml files:
      • construct_conda_yml
    • New unit tests to test construct_conda_yml and building conda envs
      from the generated yamls.
  • fill_yaml
    • Add subfunction is_default
  • actions.yml:
    • Add force=TRUE to the remotes::install_local steps. Force new install of local repo #86
    • Add runforesight/workflow-telemetry-action step.
    • Avoid setting rspm explicitly by default.
  • construct_cont:
    • Make registry explicit.
    • New arg: default_registry
    • New subfunction: check_registry
  • Add docker_registry arg to let users choose which registry to push to.
    Defaults to "ghcr.io" instead of "docker.io" so that no additional credentials
    are needed.
    • actions.yml
    • use_workflow
  • get_github_url_desc
    • Improve logic to catch more GH URLs.
  • vignettes/depgraph.Rmd
    • Update plots with new data and resave PNG.
  • New arg free_diskspace
    • actions.yml
    • use_workflow
  • use_workflow
    • template arg can now be "rworkflows_static:dev" to use the "dev" branch's
      version of action.yml as a workflow template.

Bug fixes

  • no visible global function definition for internal function check_miniconda_args
    • This weird error only came up during Rstudio R CMD checks.
      The function check_miniconda_args was clearly defined in its own file.
      The only way to fix it was copying the function into the same one where it
      was called fill_yaml.
    • Thought it might be a permissions issues with check_miniconda_args.R but
      the permissions are identical with all the others.
  • action.yml
    • Remove unnecessary export:echo "GITHUB_TOKEN=${{ inputs.GITHUB_TOKEN }}" >> $GITHUB_ENV
    • Fix runforesight/workflow-telemetry-action step and move to top.

bschilder and others added 30 commits September 14, 2023 15:58
@bschilder
Merge pull request #76 from neurogenomics/master
1add336 
Merge master back into dev
@bschilder
Test dev
bbadb82
@bschilder
Test dev [\nocache]
d45c17d
@bschilder
test miniforge_variant
f9238f7
@bschilder
Fix action defaults
bdea6ba
@bschilder
Fix action defaults 2
713a942
@bschilder
add miniconda arg
c0dabce
@bschilder
Add force=TRUE when installing local repo [skip ci]
059489c
@bschilder
Test conda functions
fed72f5
@bschilder
Fix test typo
ee8d64b
@bschilder
add workflow telemetry
01e183e
@bschilder
Try pushing to ghcr
f05439a
@bschilder
Try pushing to ghcr
c57aa8a
@bschilder
extend check_cont to include no dockerhub registries
065a231
@bschilder
extend check_cont to include no dockerhub registries 2
7ce4579
@bschilder
upgrade docker steps
19a7bd1
@bschilder
remove QEMU steps
5a5d596
@bschilder
Mod docker/setup-buildx-action
1ba91e8
@bschilder
Try docker/setup-buildx-action@v2
9856372
@bschilder
Try docker/setup-buildx-action@v2 2
dbc431b
@bschilder
Try driver: docker
d82cd3d
@bschilder
remove docker buildx step entirely
2da879e
@bschilder
Install docker within docker
3cb6b31
@bschilder
Add volumes to image
78f4611
@bschilder
revert to docker/build-push-action@v1 but enable ghcr
dfd98df
@bschilder
Fix BASE_IMAGE
d0ac808
@bschilder
Fix BASE_IMAGE 2
ca80405
@bschilder
Fix BASE_IMAGE 3
d1a3a42
@bschilder
Fix BASE_IMAGE 4
3c43000
@bschilder
Specify base image when writing Dockerfile
1009041
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Workflow Telemetry - rworkflows_dev / ubuntu-latest (devel)

Workflow telemetry for commit 569001f1f4c5a3814ecdf7df36f7e5218455ab62
You can access workflow job details here

Step Trace

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698504458000, 1698504472000
	Pull docker/github-actions-v1 : 1698504472000, 1698504476000
	Initialize containers : 1698504476000, 1698504545000
	Run neurogenomics/rworkflows@dev : crit, 1698504545000, 1698504557000
Loading

CPU Metrics

chart_stacked_area_time_38f1cbdb-eda3-4269-b9f5-929445caf312

Memory Metrics

chart_stacked_area_time_ae8c27f4-0e8e-4ff3-9ab5-0be4ae109ee3

IO Metrics

Read Write
Network I/O chart_line_time_e3d3222a-e1f5-4b99-af96-4d2c3296c20e chart_line_time_9ad4d814-b8ac-4aec-b2ea-fa5438cfeb86
Disk I/O chart_line_time_207674d6-6f5a-4f51-ae0e-b13f8d1b0e8b chart_line_time_ea4d46dc-4997-492a-8752-456f2def795c

Process Trace

Top 100 processes with highest duration

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
Loading

@github-actions
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Workflow Telemetry - rworkflows_dev / macOS-latest (latest)

Workflow telemetry for commit 569001f1f4c5a3814ecdf7df36f7e5218455ab62
You can access workflow job details here

Step Trace

gantt
	title macOS-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698504468000, 1698504516000
	Run neurogenomics/rworkflows@dev : crit, 1698504516000, 1698504606000
Loading

CPU Metrics

chart_stacked_area_time_05566355-7630-4e40-a1eb-4e90ce824892

Memory Metrics

chart_stacked_area_time_175e128f-be60-4976-88b3-cf2b71f33fd1

IO Metrics

Read Write
Network I/O chart_line_time_7b9a6086-3e4c-4431-a93b-0dfe55c9ceb9 chart_line_time_848440ca-8775-49ad-90aa-da77cf714f87
Disk I/O chart_line_time_dc99852b-99a4-49f5-ba03-8a390386be0c chart_line_time_453dc003-52cc-4c9e-80c5-d3d88e37a10c

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Workflow Telemetry - rworkflows_dev / windows-latest (latest)

Workflow telemetry for commit 569001f1f4c5a3814ecdf7df36f7e5218455ab62
You can access workflow job details here

Step Trace

gantt
	title windows-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698504462000, 1698504491000
	Run neurogenomics/rworkflows@dev : crit, 1698504491000, 1698504608000
Loading

CPU Metrics

chart_stacked_area_time_9c8487ab-1ee9-428e-9da9-419cbf3f91c7

Memory Metrics

chart_stacked_area_time_9611b338-e23f-42a6-a25c-341b4d8a13a9

IO Metrics

Read Write
Network I/O chart_line_time_36e5a414-6877-4735-886e-116b892def47 chart_line_time_871dd07d-0d84-46b0-b101-37d7cca0051b

@github-actions
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Workflow Telemetry - rworkflows_dev / windows-latest (latest)

Workflow telemetry for commit a7ae529850b21ce990ebd5c256f5e8b14df0513d
You can access workflow job details here

Step Trace

gantt
	title windows-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698504965000, 1698504994000
	Run neurogenomics/rworkflows@dev : 1698504994000, 1698505279000
Loading

CPU Metrics

chart_stacked_area_time_2e753fd1-e96e-48a5-bb23-05452e57e381

Memory Metrics

chart_stacked_area_time_c6c4dbc8-c2a2-4b0f-8da8-96f9fe57b6c1

IO Metrics

Read Write
Network I/O chart_line_time_fb0585fd-b2d2-486b-961a-0fe5be99935d chart_line_time_2f061c3d-53f2-49a1-8274-c79b7cc5a9c2

@github-actions
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Workflow Telemetry - rworkflows_dev / macOS-latest (latest)

Workflow telemetry for commit a7ae529850b21ce990ebd5c256f5e8b14df0513d
You can access workflow job details here

Step Trace

gantt
	title macOS-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698504980000, 1698505037000
	Run neurogenomics/rworkflows@dev : 1698505037000, 1698505792000
Loading

CPU Metrics

chart_stacked_area_time_2326b98a-6fd1-4a75-abf8-19758af19a5c

Memory Metrics

chart_stacked_area_time_19fd73ee-25bc-4165-a3df-41246c28b393

IO Metrics

Read Write
Network I/O chart_line_time_4cd4dfad-1511-4fc3-8a3f-f194a27c10c5 chart_line_time_360f1462-e1ab-4001-aaac-af6cde3abac3
Disk I/O chart_line_time_f3b244ac-5264-42bd-8d4a-a683c3f7c4f4 chart_line_time_5bc476ce-bdc7-4a6c-82d3-2665b3930fac

@github-actions
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Workflow Telemetry - rworkflows_dev / ubuntu-latest (devel)

Workflow telemetry for commit a7ae529850b21ce990ebd5c256f5e8b14df0513d
You can access workflow job details here

Step Trace

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698504965000, 1698504984000
	Pull docker/github-actions-v1 : 1698504984000, 1698504990000
	Initialize containers : 1698504990000, 1698505085000
	Run neurogenomics/rworkflows@dev : 1698505085000, 1698505950000
Loading

CPU Metrics

chart_stacked_area_time_41edd37b-0207-4c1e-a2ce-392c6a36fe0a

Memory Metrics

chart_stacked_area_time_9751a408-0585-4dff-88c5-f574b0fb0932

IO Metrics

Read Write
Network I/O chart_line_time_67efdcff-7c5a-4508-a370-161cc51d453a chart_line_time_1b9266b2-e25b-442c-87ad-a9d82080d678
Disk I/O chart_line_time_8f48893d-33b0-4f06-8984-6e4aeb32e431 chart_line_time_f5669a6c-9529-47cd-96b2-f37264fc8ab8

Process Trace

Top 100 processes with highest duration

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
Loading

@github-actions
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Workflow Telemetry - rworkflows_dev / windows-latest (latest)

Workflow telemetry for commit e551b5a02cc69d9a97147fcbe2d9f83c809f770e
You can access workflow job details here

Step Trace

gantt
	title windows-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698506117000, 1698506147000
	Run neurogenomics/rworkflows@dev : 1698506147000, 1698506414000
Loading

CPU Metrics

chart_stacked_area_time_b2b69074-3c84-4823-bb89-6c495370aa53

Memory Metrics

chart_stacked_area_time_7d6a9fa4-d12d-4bca-b36b-46cb91cfef00

IO Metrics

Read Write
Network I/O chart_line_time_0e3aa193-8fff-49b8-8196-ff38a7ad16b4 chart_line_time_35a94bcf-5282-421f-a818-421e4fd7a3ca

@github-actions
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Workflow Telemetry - rworkflows_dev / ubuntu-latest (devel)

Workflow telemetry for commit e551b5a02cc69d9a97147fcbe2d9f83c809f770e
You can access workflow job details here

Step Trace

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698506114000, 1698506133000
	Pull docker/github-actions-v1 : 1698506133000, 1698506138000
	Initialize containers : 1698506138000, 1698506209000
	Run neurogenomics/rworkflows@dev : 1698506210000, 1698506793000
Loading

CPU Metrics

chart_stacked_area_time_e89f8e18-388c-458f-a6f2-6a5fc6d7e4d8

Memory Metrics

chart_stacked_area_time_0ef2512c-ce2b-4b2a-84d8-bf8843570980

IO Metrics

Read Write
Network I/O chart_line_time_ae2c8cea-38e8-43b2-9e38-eb9f8f0e7df8 chart_line_time_e8436bc9-1c02-4cb1-83d9-f804f309c54e
Disk I/O chart_line_time_13313e57-147d-4210-bcc6-9cfc2b1a163e chart_line_time_8792be4b-4b4e-4762-8a39-3296eee17885

Process Trace

Top 100 processes with highest duration

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
Loading

@github-actions
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Workflow Telemetry - rworkflows_dev / macOS-latest (latest)

Workflow telemetry for commit e551b5a02cc69d9a97147fcbe2d9f83c809f770e
You can access workflow job details here

Step Trace

gantt
	title macOS-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698506119000, 1698506157000
	Run neurogenomics/rworkflows@dev : 1698506157000, 1698507050000
Loading

CPU Metrics

chart_stacked_area_time_ed189cad-3932-4075-88f1-a4cb217f9bf0

Memory Metrics

chart_stacked_area_time_e93abd65-309b-4edc-8339-2419fae3ad28

IO Metrics

Read Write
Network I/O chart_line_time_3be0960a-9ecc-452b-908c-663566583513 chart_line_time_be097dc9-5781-48e0-ac85-fb45fca9a966
Disk I/O chart_line_time_f95f95d6-b1a7-4497-ac26-f971ac56d93c chart_line_time_fadb3181-82a5-4ff0-9f3a-5b4f6684db88

@bschilder bschilder mentioned this pull request Oct 28, 2023
Closed
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Workflow Telemetry - rworkflows_dev / windows-latest (latest)

Workflow telemetry for commit 47d35165d499c390b960dc34a903775e9c4ff538
You can access workflow job details here

Step Trace

gantt
	title windows-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698507167000, 1698507213000
	Run neurogenomics/rworkflows@dev : 1698507213000, 1698507540000
Loading

CPU Metrics

chart_stacked_area_time_3bdfa475-ad30-4178-8a4d-29f8b77b4622

Memory Metrics

chart_stacked_area_time_26a5e435-7650-48b6-a4cd-e908bc5f10a6

IO Metrics

Read Write
Network I/O chart_line_time_ad65bba8-97c1-4e45-9775-89dbbfd72cf1 chart_line_time_a9a20716-1f1d-4e1c-bb85-50bbcdb4b5b6

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Workflow Telemetry - rworkflows_dev / ubuntu-latest (devel)

Workflow telemetry for commit 47d35165d499c390b960dc34a903775e9c4ff538
You can access workflow job details here

Step Trace

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698507162000, 1698507180000
	Pull docker/github-actions-v1 : 1698507180000, 1698507184000
	Initialize containers : 1698507184000, 1698507248000
	Run neurogenomics/rworkflows@dev : 1698507248000, 1698507836000
Loading

CPU Metrics

chart_stacked_area_time_75c0f1c5-5db1-4a87-8873-ab82ce380cf8

Memory Metrics

chart_stacked_area_time_62ee6bd8-d0d4-4608-8740-66abd818e746

IO Metrics

Read Write
Network I/O chart_line_time_022831c0-c766-46d4-91eb-769164ff40f7 chart_line_time_b279bed6-a41d-4413-8ee7-a0fae902f211
Disk I/O chart_line_time_529668c7-fb75-4278-87e5-794de8674a79 chart_line_time_f450c5cc-3865-4e08-b466-a8c529d21fe6

Process Trace

Top 100 processes with highest duration

gantt
	title ubuntu-latest (devel)
	dateFormat x
	axisFormat %H:%M:%S
Loading

@github-actions
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Workflow Telemetry - rworkflows_dev / macOS-latest (latest)

Workflow telemetry for commit 47d35165d499c390b960dc34a903775e9c4ff538
You can access workflow job details here

Step Trace

gantt
	title macOS-latest (latest)
	dateFormat x
	axisFormat %H:%M:%S
	Set up job : milestone, 1698507167000, 1698507210000
	Run neurogenomics/rworkflows@dev : 1698507211000, 1698507983000
Loading

CPU Metrics

chart_stacked_area_time_967c21f1-16a1-4e87-a16f-985e73e3ca7d

Memory Metrics

chart_stacked_area_time_acc75d42-3957-42ad-b32c-eff7a12d106b

IO Metrics

Read Write
Network I/O chart_line_time_6ce0a108-fb4a-4900-802a-d72f67d5a64e chart_line_time_f4b7ebb9-2617-4429-b802-772b22bfcf7a
Disk I/O chart_line_time_19088b35-8c1d-4051-9bdb-a45db686f8f3 chart_line_time_2705cb41-1e1f-47fa-81c4-25feec8d5baa

@bschilder bschilder merged commit c6cbf94 into master Oct 28, 2023
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