protocol-timer - v0.4.0

v0.4.0 (2025-03-31)

Feature

• feat: deparaffinization run for prrx1 experiment (#9) (f7ab663)

• feat: deparaffinization run for prrx1 experiment (9c8c06a)

- Jupyter Notebook
Published by github-actions[bot] 12 months ago

protocol-timer - v0.3.0

v0.3.0 (2025-03-25)

Chore

• chore: merge changes from gitea branch (#8) (1e78b98)

Unknown

• Merge branch 'main' into gitea (82e9d95)

- Jupyter Notebook
Published by github-actions[bot] about 1 year ago

protocol-timer - v0.2.0

v0.2.0 (2024-10-21)

Chore

• chore: rename protocol--amend (04c2ba0)

• chore: rename protocol (1bb9c14)

Feature

• feat: add extensions, remove unnecessary mamba env create command (4a9e9ab)

• feat: add semantic versioning (c35a2b7)

• feat: background run now set for facisimilab dockerized environment (50bbb2b)

• feat: deparaffinization protocol from Pranav (ad3336c)

• feat: add 10x Genomics deparaffinization protocol (078152b)

• feat: using facsimilab-main (ab03051)

• feat: revert to self-hosted webhooks testing (5b64ea9)

• feat: add step to pass in all env variables (0753463)

• feat: change to self-hosted webhook server (686f63e)

• feat: add gh action badge (94b8c9b)

• feat: create test tokens file and job summary (716fafe)

• feat: use shell script for testing (cc47c6a)

• feat: add test condition (07b6a16)

• feat: add tests (1b1ad8f)

• feat: automate the workspace directory (c63f924)

• feat: run via facsimilab-main (4094f8f)

• feat: github action to trigger FFPE workflow (914729d)

• feat: try secrets file and fall back to environment variables if not present (77769a8)

• feat: Updated devcontainer; removed dockerfile (ee8d63d)

Fix

• fix: Improve handling of empty string fields (e.g. comments) (d4f8f75)

• fix: deparaffinization protocol with devcontainer (a9558d7)

• fix: testing another way of passing in secrets (2d73fb2)

• fix: run command (6ee939f)

• fix: badge branch (a468292)

• fix: remove docker cache (6b60657)

• fix: papermill and github action directories (376fe0f)

• fix: putting output in the root directory (4e0ae2f)

• fix: create papermill output folder (77a5a65)

• fix: add runs on statement (f66892e)

• fix: location of python env (9239568)

• fix: worspace folders (a3bb426)

Unknown

• Add: deparaffinization, semantic versioning, background run with FacsimiLab (#6) (db709c7)

• Merge branch 'main' into develop (bc53bf5)

• Merge branch 'develop' (6e24209)

• Add devcontainer, GH Actions, Tests (#5)

• fix: add runs on statement

• feat: run via facsimilab-main

• feat: automate the workspace directory

• feat: add tests

• feat: add test condition

• fix: create papermill output folder

• fix: putting output in the root directory

• fix: papermill and github action directories

• fix: remove docker cache

• feat: use shell script for testing

• feat: create test tokens file and job summary

• feat: add gh action badge (69647ae)

• Merge branch 'main' into develop (718e97c)

• Create a static FFPE protocol and update devcontainer (#4)

Create a static FFPE protocol and update devcontainer (820c194)

• trying another method of creating the env (179fd73)

• Update devcontainer.json (3ef6f62)

• add devcontainer secrets declaration (aa0c8a5)

• change docker image to facsimilab (4184a02)

• Add: Automated background run of a protocol using papermill and bash

Why: We want to be able to run a protocol without keeping a computer / browser / VSCode session continuously running.

How:

Bash script will ask for a protocol to run. It will use papermill to execute that notebook. Recommend to run the script in a tmux session

Tags: (debce50)

• Add: adjustment for timezone DST (8f2c579)

• Change docker container to new name (d5ff199)

• Add: papermill to python env (311f2da)

• [DATALAD] Recorded changes (5c0e689)

• Add code-workspace and vscode extensions in devcontainers (a02a9ce)

• Add: Timezone offset (f6c38c9)

• Adding a deparrafinization protocol (5d515be)

• Create a static FFPE protocol (36fc5ba)

• Merge pull request #3 from pranavmishra90/develop

Add: Cleared page at start of protocol. Fix: Rearranged folders. Drop… (3541595)

• Add: Cleared page at start of protocol. Fix: Rearranged folders. Drop unneeded python functions file

(Note, the previous git commit cb134d38855a4691b4a9c1190245b978e1bd0dba did not have all of the files correctly added to the commit.)

Why: 1. We want a clear page on the Matrix chat window so that the start of one protocol does not blend in with the run of the previous protocol

1. I'm considering using static protocols (where the jupyter file already has a protocol loaded) rather than dynamically creating a jupyter notebook for each one. This will allow the code to be easily executed in services like Blender, which do not allow for the iPython libraries needed to dynamically alter the current jupyter notebook.

Tags: jupyter notebook, matrix, element (2365a2a)

• Merge pull request #2 from pranavmishra90/develop

Notifications over Matrix via webhook. Adding additional fields for the protocol. Improved formatting and restructuring. (a08a992)

• Add: Cleared page at start of protocol. Fix: Rearranged folders. Drop: unneeded python functions file

Why: 1. We want a clear page on the Matrix chat window so that the start of one protocol does not blend in with the run of the previous protocol

1. I'm considering using static protocols (where the jupyter file already has a protocol loaded) rather than dynamically creating a jupyter notebook for each one. This will allow the code to be easily executed in services like Blender, which do not allow for the iPython libraries needed to dynamically alter the current jupyter notebook.

Tags: jupyter notebook, matrix, element (cb134d3)

• Add/Fix: Using open-sourced matrix protocol using a secure webhook

Why: Prefer using open-source software over Discord. The matrix messages can also be formatted further (HTML) for better control.

How: new python functions added. Python environment expandeded to to include new libraries

Tags: matrix, element, webhook, notifications (567d479)

• Add / Fix: Improved matrix message webhook formatting (9df861a)

• Removed mailjet api (0756abc)

• Add: environment.yml (e00e097)

• Adding mail API (0f63120)

• Adding devcontainer (e354faf)

• Starting a docker image for this repo (27bafba)

• Added code to improve the json card formatting, use tts, etc (5b91edf)

• Added TTS and rich formatted webhook; CFF, Quarto, bib (7b22a20)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

protocol-timer - Moving "Binder" support to a work-in-progress

- Jupyter Notebook
Published by pranavmishra90 over 2 years ago

protocol-timer - Initial release

Accepting develop branch 0.0.1 as release tag v0.1.0

- Jupyter Notebook
Published by pranavmishra90 over 2 years ago