Build a docker image in the pipeline #14
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- Created a script 'bootstrap_dev.sh' that installs Nix and all project dependencies for you.
- To run it, from main poretitioner git directory, run:
- $ export PORETITIONER_DIR=/home/jdunstan/Developer/poretitioner; bash ./bootstrap_dev
- Added project directory structure stubs.
#2
- Created a script 'bootstrap_dev.sh' that installs Nix and all project dependencies for you.
- To run it, from main poretitioner git directory, run:
- $ export PORETITIONER_DIR=/home/jdunstan/Developer/poretitioner; bash ./bootstrap_dev
- Added project directory structure stubs.
- Introduce test runner and code coverage. - Set up pre-commit hooks to run before git commit and push. - Create setup.py and add a LICENSE file (using MIT by default, subject to change). #4
- Introduce test runner and code coverage. - Set up pre-commit hooks to run before git commit and push. - Create setup.py and add a LICENSE file (using MIT by default, subject to change). #4
…ithub.com/uwmisl/poretitioner into jdunstan/scaffolding-and-pre-commit-hooks
…e trailing whitespace.
…ilable on VM. Final size: 302.1 MB (compressed)
I really wish github offered a way to test workflow changes without polluting the branch with extraneous commits -__-. I'm sorry.
I really wish this were easy to test locally...
I really wish this were easier to test
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Feel free to merge whenever you're ready; my changes won't conflict with this in the slightest. |
thequicksort
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kdoroschak
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Apr 27, 2020
Run "nix-build" or "nix-build -A docker" to build a docker image. Run "nix-build -A app" to build Poretitioner locally without Docker. #14
kdoroschak
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Apr 28, 2020
* begin quantifier refactor; absolutely does not run attempting to get a basic test set up for calc_time_until_capture. test comes from 20180618 data, run on the original version. moved voltage utility function to segmenter. * rewrite calc_time_until_capture to be conceptually easier to follow * fix relative import . * remove orig version of calc_time_until_capture * add init so pytest can find tests; minor flake compliance * add test for get_overlapping_regions; fixed edge case bug * docstrings * update parameterized fn * remove calc_time_until_capture_blockages * minor flake change, star import, & add test file * open_pore --> _channel; docstrings raw utils; rm multi path choice raw utils * python 3 import * fix import * method to create the capture fast5 + tests * rm plotting in utils * rm example test * add filters (+tests) & find capture fn (untested) * make fn call more generic * window-only segmentation core fn * functional segmenter + tests + parallel * finish doc for segment, move fn to raw_signal_utils * rm placeholder test * reorganize module names for downstream changes * Build docker image * Upload the docker image as a build artifact * rewrite calc_time_until_capture to be conceptually easier to follow * fix relative import . * remove orig version of calc_time_until_capture * add init so pytest can find tests; minor flake compliance * add test for get_overlapping_regions; fixed edge case bug * Build the application's docker image 🐳 (#14) Run "nix-build" or "nix-build -A docker" to build a docker image. Run "nix-build -A app" to build Poretitioner locally without Docker. #14 * Adding build steps to the Readme * Added more build steps * Update Readme.md * Added NanoporTER paper * Update Readme.md * docstrings * update parameterized fn * remove calc_time_until_capture_blockages * minor flake change, star import, & add test file * open_pore --> _channel; docstrings raw utils; rm multi path choice raw utils * python 3 import * fix import * Import pytorch and torchvision (#25) Add pytorch dependency. #8 Co-authored-by: Jessica Dunstan <jdunstan@cs.washington.edu> * method to create the capture fast5 + tests * Update Readme.md * Added continuous integration badge * Add uninstall steps * rm plotting in utils * rm example test * add filters (+tests) & find capture fn (untested) * make fn call more generic * window-only segmentation core fn * functional segmenter + tests + parallel * finish doc for segment, move fn to raw_signal_utils * rm placeholder test * reorganize module names for downstream changes Co-authored-by: J.D <thequicksort@gmail.com> Co-authored-by: Jessica Dunstan <jdunstan@cs.washington.edu>
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Update: Sorry for the lateness, I turns out Github actions double-archive if your build output is already an archive file, which makes the testing steps here a little more complicated.
Description
Building a docker image as part of our build process. Running
nix-build -A dockerlocally will return a path to a docker image in the Nix store. You can copy this artifact wherever you'd like.Pushing to master will now result in a docker image being built.
I also refactored the dependency structure a little bit. Now all dependencies are managed in one file, as I figure this will be easier as it mimics setup.py/requirements.txt (if you disagree, let me know!).
Once we're ready to merge, I'll switch the build branch over from
jdunstan/docker-imagetomaster.Issues
#6
Testing
Test case: Docker image produced by
Download Docker, if it's not already installed.
Download the Poretitioner docker image here, which was produced automatically by our build pipeline, to a known path, hereto referred to as
DOCKER_IMAGE_PATHLoad the image into docker, e.g.