Add dockerfile #127

henrikstranneheim · 2024-11-06T09:34:11Z

Description

This PR adds/fixes ...

How to prepare for test

ssh to hasta.scilifelab.se
Use stage: us
Paxa the environment: paxa
Install on stage (example for hasta):
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_hermes -t hermes -b [THIS-BRANCH-NAME]

How to test

Do ...

Expected test outcome

Check that ...
Take a screenshot and attach or copy/paste the output.

Review

Tests executed by
"Merge and deploy" approved by
Thanks for filling in who performed the code review and the test!

This version is a

MAJOR - when you make incompatible API changes
MINOR - when you add functionality in a backwards compatible manner
PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

Document in ...
Deploy this branch
Inform to ...

codecov-commenter · 2024-11-06T10:05:25Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.83%. Comparing base (54ae97a) to head (8e69019).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #127   +/-   ##
=======================================
  Coverage   92.83%   92.83%           
=======================================
  Files          28       28           
  Lines         977      977           
=======================================
  Hits          907      907           
  Misses         70       70

Flag	Coverage Δ
unittests	`92.83% <ø> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚨 Try these New Features:

Flaky Tests Detection - Detect and resolve failed and flaky tests

henrikstranneheim · 2024-11-06T10:10:27Z

Test docker 👍

[henrik.stranneheim@hasta:~] [S_base] $ source /home/proj/stage/servers/config/hasta.scilifelab.se/bashrc
[henrik.stranneheim@hasta:~] [base] $ hermes-test-deploy add-dockerfile
Pulling image for feature branch: add-dockerfile...
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:6dce3b49cfe6dc4b4e0198412bb0578215c86dae41303c47438639853bcba562
 29.97 MiB / 29.97 MiB [====================================================] 0s
Copying blob sha256:8d4dbf8eff6fce7ec6521dea8ec5c57f82c08ca4d8c18f0695aab0f65a96a6e7
 1.03 MiB / 1.03 MiB [======================================================] 0s
Copying blob sha256:f5d1f35bbc6281a31f145940d8353bf0f9f615c5c867101bf44eae6da8861e7a
 12.31 MiB / 12.31 MiB [====================================================] 0s
Copying blob sha256:6821d50670bb17bbbd7d33ad2a15dbc106d3ab46ae6d211795d98e7c7ee2a543
 249 B / 249 B [============================================================] 0s
Copying blob sha256:2aa3976fbd991c705f357e4ea99b303cca0bd66dc79bb8f8094a8cb3928af22b
 93 B / 93 B [==============================================================] 0s
Copying blob sha256:c7d48191456563a0366a507c392e541bc69f7f26566c61cd003e5b1d57f17405
 195.79 KiB / 195.79 KiB [==================================================] 0s
Copying blob sha256:60a5b41e7135ae36a0b61069141c69909cdcc7616e38fb25b38fb08fd87d8b3b
 51.79 MiB / 51.79 MiB [====================================================] 1s
Copying config sha256:1a68e107a16ec4c8b2cf32787ed93b39d933a41547f18127328d47e03ba0b3a7
 6.04 KiB / 6.04 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/stage/singularity_containers/hermes_add-dockerfile.sif
You can now run 'hermes-test --help' to test the feature branch: add-dockerfile.
[henrik.stranneheim@hasta:~] [base] $ hermes-test --help
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:6dce3b49cfe6dc4b4e0198412bb0578215c86dae41303c47438639853bcba562
Skipping fetch of repeat blob sha256:8d4dbf8eff6fce7ec6521dea8ec5c57f82c08ca4d8c18f0695aab0f65a96a6e7
Skipping fetch of repeat blob sha256:f5d1f35bbc6281a31f145940d8353bf0f9f615c5c867101bf44eae6da8861e7a
Skipping fetch of repeat blob sha256:6821d50670bb17bbbd7d33ad2a15dbc106d3ab46ae6d211795d98e7c7ee2a543
Skipping fetch of repeat blob sha256:2aa3976fbd991c705f357e4ea99b303cca0bd66dc79bb8f8094a8cb3928af22b
Skipping fetch of repeat blob sha256:c7d48191456563a0366a507c392e541bc69f7f26566c61cd003e5b1d57f17405
Skipping fetch of repeat blob sha256:60a5b41e7135ae36a0b61069141c69909cdcc7616e38fb25b38fb08fd87d8b3b
Copying config sha256:1a68e107a16ec4c8b2cf32787ed93b39d933a41547f18127328d47e03ba0b3a7
 6.04 KiB / 6.04 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/henrik.stranneheim/.singularity/cache/oci-tmp/224cbf2a1b76515629921bae06fac5788d7d705a971d20fc34f8338396d80655/hermes_add-dockerfile.sif
INFO:    Image cached as SIF at /home/henrik.stranneheim/.singularity/cache/oci-tmp/224cbf2a1b76515629921bae06fac5788d7d705a971d20fc34f8338396d80655/hermes_add-dockerfile.sif

 Usage: hermes [OPTIONS] COMMAND [ARGS]...

 Manage users in the awesome CLI app.

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --loglevel                  [DEBUG|INFO|WARNING]  Set the log level [default: INFO]                                                      │
│ --version                                                                                                                                │
│ --install-completion                              Install completion for the current shell.                                              │
│ --show-completion                                 Show completion for the current shell, to copy it or customize the installation.       │
│ --help                                            Show this message and exit.                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ convert                                                                                                                                  │
│ export                                                                                                                                   │
│ validate                                                                                                                                 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

henrikstranneheim · 2024-11-06T10:22:26Z

Alias 👍

enrik.stranneheim@hasta:~] [base] $ which hermes
/usr/bin/which: no hermes in (/home/henrik.stranneheim/.local/bin:/home/proj/production/bin/miniconda3/bin:/home/henrik.stranneheim/.local/bin:/home/proj/production/bin/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/dell/srvadmin/bin)
[henrik.stranneheim@hasta:~] [base] $ ^Curce /home/proj/stage/servers/resources/hasta.scilifelab.se/usestage.sh
[henrik.stranneheim@hasta:~] [base] $ us
[henrik.stranneheim@hasta:~] [S_base] $ which hermes
alias hermes='/home/proj/stage/bin/miniconda3/envs/S_hermes/bin/hermes'
	/home/proj/stage/bin/miniconda3/envs/S_hermes/bin/hermes
[henrik.stranneheim@hasta:~] [S_base] $ source /home/proj/stage/servers/resources/hasta.scilifelab.se/usestage.sh
[henrik.stranneheim@hasta:~] [S_base] $ which hermes
alias hermes='singularity run --bind /home/proj/stage:/home/proj/stage /home/proj/stage/singularity_containers/hermes_latest.sif'
	/usr/bin/singularity
[henrik.stranneheim@hasta:~] [S_base] $ hermes --help
FATAL:   failed to retrieved path for /home/proj/stage/singularity_containers/hermes_latest.sif: lstat /home/proj/stage/singularity_containers/hermes_latest.sif: no such file or directory
[henrik.stranneheim@hasta:~] [S_base] $ ls  /home/proj/stage/singularity_containers/
cg_add-default-command.sif                     housekeeper_refactor-sql-filter-function-attr.sif
cg_lessen-archiving-limit.sif                  housekeeper_refactor-sql-handlers.sif
hermes_add-dockerfile.sif                      housekeeper_refactorto-PEP-0604_2.sif
housekeeper_197-improve-visualisation.sif      housekeeper_refactorto-PEP-0604.sif
housekeeper_add-cryptography.sif               housekeeper_separate-remote-files.sif
housekeeper_archiving-do-not-delete.sif        housekeeper_update-python.sif
housekeeper_archiving-fetch-limited-files.sif  housekeeper_use-poetry-instead-of-pip.sif
housekeeper_archiving-filter-on-tags.sif       trailblazer-cli_rm-conda-env-and-use-container.sif
housekeeper_archiving-get-retrieved-files.sif  trailblazer_dockerize-cli.sif
housekeeper_cascade-archive.sif                trailblazer_fix-cli-images.sif
housekeeper_fix-python-syntax-warning.sif      trailblazer_latest.sif
housekeeper_latest.sif                         trailblazer_upgrade-deploy-instructions.sif
housekeeper_master.sif
[henrik.stranneheim@hasta:~] [S_base] $ hermes-deploy
-bash: /home/proj/production/servers/resources/hasta.scilifelab.se/deployment/hermes-deploy.sh: No such file or directory
[henrik.stranneheim@hasta:~] [S_base] $ cp  /home/proj/stage/singularity_containers/hermes_add-dockerfile.sif /home/proj/stage/singularity_containers/hermes_latest.sif
[henrik.stranneheim@hasta:~] [S_base] $ hermes --help

 Usage: hermes [OPTIONS] COMMAND [ARGS]...

 Manage users in the awesome CLI app.

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --loglevel                  [DEBUG|INFO|WARNING]  Set the log level [default: INFO]                                                      │
│ --version                                                                                                                                │
│ --install-completion                              Install completion for the current shell.                                              │
│ --show-completion                                 Show completion for the current shell, to copy it or customize the installation.       │
│ --help                                            Show this message and exit.                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ convert                                                                                                                                  │
│ export                                                                                                                                   │
│ validate                                                                                                                                 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

jemten

Great to get a dockerfile going for hermes and nice update to the PR template

Dockerfile

ChrOertlin

Looks good!

jemten

👍

henrikstranneheim · 2024-11-21T08:26:49Z

Dockerfile builds and runs

(cg-hermes-py3.12) henrikstranneheim in ~/git/hermes on branch add-dockerfile >  docker build -t hermes:latest .

[+] Building 10.6s (9/9) FINISHED                                                                                  docker:desktop-linux
 => [internal] load .dockerignore                                                                                                  0.0s
 => => transferring context: 2B                                                                                                    0.0s
 => [internal] load build definition from Dockerfile                                                                               0.0s
 => => transferring dockerfile: 328B                                                                                               0.0s
 => [internal] load metadata for docker.io/library/python:3.12-slim-bullseye                                                       0.7s
 => [1/4] FROM docker.io/library/python:3.12-slim-bullseye@sha256:6e2d8a88c5c53efe7d59b8b83b7d5bc2c066fc7d28d7db704c8479424cd4346  0.0s
 => [internal] load build context                                                                                                  0.4s
 => => transferring context: 943.03kB                                                                                              0.4s
 => CACHED [2/4] WORKDIR /app                                                                                                      0.0s
 => [3/4] COPY . /app/                                                                                                             0.6s
 => [4/4] RUN pip install --no-cache-dir --ignore-installed poetry     && poetry config virtualenvs.create false     && poetry in  8.5s
 => exporting to image                                                                                                             0.4s
 => => exporting layers                                                                                                            0.4s
 => => writing image sha256:0340a5bc757b96262ac1c5a3b6dc4e63421ea049f2220dad21c534b951a0166f                                       0.0s
 => => naming to docker.io/library/hermes:latest                                                                                   0.0s

What's Next?
  View summary of image vulnerabilities and recommendations → docker scout quickview
(cg-hermes-py3.12) henrikstranneheim in ~/git/hermes on branch add-dockerfile >  docker run hermes:latest export --help

                                                                                
 Usage: hermes export [OPTIONS] COMMAND [ARGS]...                               
                                                                                
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help          Show this message and exit.                                  │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────╮
│ tags   Export tag definitions from Hermes.                                   │
╰──────────────────────────────────────────────────────────────────────────────╯

(cg-hermes-py3.12) henrikstranneheim in ~/git/hermes on branch add-dockerfile >

henrikstranneheim · 2024-11-21T08:43:53Z

Redid tests using servers PR - passed as before.

henrikstranneheim · 2024-11-21T09:42:08Z

Deployed to prod

enrik.stranneheim@hasta:~] [base] $  hermes-deploy
Are you sure you want to pull the latest Hermes image? [Y/n] y
Pulling the latest Hermes image which will be used in stage and prod
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:55ab1b300d4b4b00c98fb396b36f0f7ba5dab2f7d18927e3742d364632723cbe
Skipping fetch of repeat blob sha256:0649af9ad5efea5dc7abeb426e4a4c7015ec86bba77b1d0e8ac3baca625ab82a
Skipping fetch of repeat blob sha256:07e281a95857e20e0dab09ba34ef88079e8666145a374c9757ea28d06d8ca9ac
Skipping fetch of repeat blob sha256:fb9990d14d0dbdfb200c5cddd2b531c36d758cdf6a4d43c26d9c1f3c5d9b19a7
Copying blob sha256:6e23a4f0c95c159ee39d3d50ea20fea96847662fd1e7a9d44ead0858f483fab4
 93 B / 93 B [==============================================================] 0s
Copying blob sha256:b74a1e6c703129172e72883217665444a81034ab2febea93e6ef7bf436ec267f
 201.63 KiB / 201.63 KiB [==================================================] 0s
Copying blob sha256:00a800db0f9c59b475dbaf6aa23181573e40fe559223b11916b15ae186c763cf
 30.76 MiB / 30.76 MiB [====================================================] 0s
Copying config sha256:7f931562bfcc4fc7f4a0c88b30c48c7cc23ef8cc2cd19c1ba89854a4f642baef
 6.03 KiB / 6.03 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/stage/singularity_containers/hermes_temp.sif
Successfully pulled the latest Hermes image.
[henrik.stranneheim@hasta:~] [base] $ up
[henrik.stranneheim@hasta:~] [P_base] $ which hermes
alias hermes='singularity run --bind /home/proj/production:/home/proj/production /home/proj/stage/singularity_containers/hermes_latest.sif'
	/usr/bin/singularity
[henrik.stranneheim@hasta:~] [P_base] $ hermes --help

 Usage: hermes [OPTIONS] COMMAND [ARGS]...

 Manage users in the awesome CLI app.

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --loglevel                  [DEBUG|INFO|WARNING]  Set the log level [default: INFO]                                                      │
│ --version                                                                                                                                │
│ --install-completion                              Install completion for the current shell.                                              │
│ --show-completion                                 Show completion for the current shell, to copy it or customize the installation.       │
│ --help                                            Show this message and exit.                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ convert                                                                                                                                  │
│ export                                                                                                                                   │
│ validate                                                                                                                                 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

henrikstranneheim added 5 commits November 6, 2024 09:24

feat(docker): Add

ac14c96

feat(docker): Update PR template

c253b86

feat(docker): Add docker actions

072a6a4

feat(docker): Add docker actions

673b326

feat(docker): Add docker actions

7f85e1b

henrikstranneheim marked this pull request as ready for review November 6, 2024 10:23

henrikstranneheim requested a review from a team as a code owner November 6, 2024 10:23

jemten reviewed Nov 11, 2024

View reviewed changes

Dockerfile Outdated Show resolved Hide resolved

Dockerfile Outdated Show resolved Hide resolved

ChrOertlin approved these changes Nov 20, 2024

View reviewed changes

Merge branch 'main' into add-dockerfile

0814368

jemten approved these changes Nov 21, 2024

View reviewed changes

fix(review)

78d5ff9

henrikstranneheim added 2 commits November 21, 2024 10:06

feat(deployment): Add

183cdc1

feat(deployment): Add

8e69019

henrikstranneheim merged commit e0a6b15 into main Nov 21, 2024
3 checks passed

henrikstranneheim deleted the add-dockerfile branch November 21, 2024 09:25

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add dockerfile #127

Add dockerfile #127

henrikstranneheim commented Nov 6, 2024 •

edited

Loading

codecov-commenter commented Nov 6, 2024 •

edited

Loading

henrikstranneheim commented Nov 6, 2024

henrikstranneheim commented Nov 6, 2024

jemten left a comment

ChrOertlin left a comment

jemten left a comment

henrikstranneheim commented Nov 21, 2024

henrikstranneheim commented Nov 21, 2024

henrikstranneheim commented Nov 21, 2024

Add dockerfile #127

Add dockerfile #127

Conversation

henrikstranneheim commented Nov 6, 2024 • edited Loading

Description

How to prepare for test

How to test

Expected test outcome

Review

This version is a

Implementation Plan

codecov-commenter commented Nov 6, 2024 • edited Loading

Codecov Report

henrikstranneheim commented Nov 6, 2024

Test docker 👍

henrikstranneheim commented Nov 6, 2024

Alias 👍

jemten left a comment

Choose a reason for hiding this comment

ChrOertlin left a comment

Choose a reason for hiding this comment

jemten left a comment

Choose a reason for hiding this comment

henrikstranneheim commented Nov 21, 2024

Dockerfile builds and runs

henrikstranneheim commented Nov 21, 2024

henrikstranneheim commented Nov 21, 2024

Deployed to prod

henrikstranneheim commented Nov 6, 2024 •

edited

Loading

codecov-commenter commented Nov 6, 2024 •

edited

Loading