Merged
Conversation
matwasilewski
approved these changes
Dec 3, 2025
JacquesVergine
pushed a commit
that referenced
this pull request
Dec 4, 2025
JacquesVergine
added a commit
that referenced
this pull request
Dec 17, 2025
* Rename GT edges' subject_ec_id to source_ec_id * Update test and function to use pyspark * fix typo * feat: docker cloud build for matrix image (#1822) * feat: docker cloud build for matrix image * Refactor cloud build configuration to use dynamic GCP project and environment variables * Update GCP project name in Makefile for production environment * refactor: update build_push_docker to handle environment-specific image pushes * fix: update docker_cloud_build substitutions to use TAG variable * doc: clarify build_push_docker function description to specify cloud image building --------- Co-authored-by: Nelson Alfonso <45660392+Dashing-Nelson@users.noreply.github.com> Co-authored-by: Nelson Alfonso <nelson_alfonso@icloud.com> Co-authored-by: Jacques Vergine <jacques.vergine35@gmail.com> * Fix EC clinical trial ingestion file to parquet (#1972) * Update pipelines/matrix/src/matrix/pipelines/matrix_generation/nodes.py Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> * Remove KG and pandas dataset now that we've movzd to spark * Update pipelines/matrix/src/matrix/pipelines/matrix_generation/nodes.py Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> * Refactor flag adding in functions * bump * Fix off label bug * Fix source and target regexp to only include "source_" + number columns * Set spark checkpoint * Migrate old disease list code to Kedro (v2) (#1943) Migrated the matrix-disease-list repo functionality to kedro with extensive refactoring (see PR) --------- Co-authored-by: Jacques Vergine <jacques.vergine35@gmail.com> * enlarge disk size (#1978) * fix: update OpenAI key reference (#1968) * fix: update OpenAI key reference and set target revision for Helm release * feat: enhance PostgreSQL pooler parameters for improved performance * Fix docker cloud build (#1977) * Revert "feat: docker cloud build for matrix image (#1822)" This reverts commit 09bf859. * bump uv lock * Set spark checkpoint directory (#1979) * Set spark checkpoint * Bump secrets * Fix spark utils * Drop duplicates * Change data leakage test to happen on EC_id * WIP - Update run comparison parameters * Update run comparison file paths * Remove ec_id joins * Fix off label join (thanks Piotr) * Bump off label * Bump to trigger CI again --------- Co-authored-by: Pascal Bro <pascal@everycure.org> Co-authored-by: Nelson Alfonso <45660392+Dashing-Nelson@users.noreply.github.com> Co-authored-by: Nelson Alfonso <nelson_alfonso@icloud.com> Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
JacquesVergine
added a commit
that referenced
this pull request
Dec 18, 2025
* Rename GT edges' subject_ec_id to source_ec_id * Update test and function to use pyspark * fix typo * feat: docker cloud build for matrix image (#1822) * feat: docker cloud build for matrix image * Refactor cloud build configuration to use dynamic GCP project and environment variables * Update GCP project name in Makefile for production environment * refactor: update build_push_docker to handle environment-specific image pushes * fix: update docker_cloud_build substitutions to use TAG variable * doc: clarify build_push_docker function description to specify cloud image building --------- Co-authored-by: Nelson Alfonso <45660392+Dashing-Nelson@users.noreply.github.com> Co-authored-by: Nelson Alfonso <nelson_alfonso@icloud.com> Co-authored-by: Jacques Vergine <jacques.vergine35@gmail.com> * Fix EC clinical trial ingestion file to parquet (#1972) * Update pipelines/matrix/src/matrix/pipelines/matrix_generation/nodes.py Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> * Remove KG and pandas dataset now that we've movzd to spark * Update pipelines/matrix/src/matrix/pipelines/matrix_generation/nodes.py Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> * Refactor flag adding in functions * bump * Fix off label bug * Fix source and target regexp to only include "source_" + number columns * Set spark checkpoint * Migrate old disease list code to Kedro (v2) (#1943) Migrated the matrix-disease-list repo functionality to kedro with extensive refactoring (see PR) --------- Co-authored-by: Jacques Vergine <jacques.vergine35@gmail.com> * enlarge disk size (#1978) * fix: update OpenAI key reference (#1968) * fix: update OpenAI key reference and set target revision for Helm release * feat: enhance PostgreSQL pooler parameters for improved performance * Fix docker cloud build (#1977) * Revert "feat: docker cloud build for matrix image (#1822)" This reverts commit 09bf859. * bump uv lock * Set spark checkpoint directory (#1979) * Set spark checkpoint * Bump secrets * Fix spark utils * Drop duplicates * Change data leakage test to happen on EC_id * WIP - Update run comparison parameters * Update run comparison file paths * Remove ec_id joins * Fix off label join (thanks Piotr) * Bump off label * Bump to trigger CI again * Add JaM to matrix pipeline * Update jam columns * Rename ec_ground_truth to medic_ground_truth * Remove on_or_off label --------- Co-authored-by: Pascal Bro <pascal@everycure.org> Co-authored-by: Nelson Alfonso <45660392+Dashing-Nelson@users.noreply.github.com> Co-authored-by: Nelson Alfonso <nelson_alfonso@icloud.com> Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Dashing-Nelson
pushed a commit
that referenced
this pull request
Dec 18, 2025
Dashing-Nelson
added a commit
that referenced
this pull request
Dec 18, 2025
* Rename GT edges' subject_ec_id to source_ec_id * Update test and function to use pyspark * fix typo * feat: docker cloud build for matrix image (#1822) * feat: docker cloud build for matrix image * Refactor cloud build configuration to use dynamic GCP project and environment variables * Update GCP project name in Makefile for production environment * refactor: update build_push_docker to handle environment-specific image pushes * fix: update docker_cloud_build substitutions to use TAG variable * doc: clarify build_push_docker function description to specify cloud image building --------- Co-authored-by: Nelson Alfonso <45660392+Dashing-Nelson@users.noreply.github.com> Co-authored-by: Nelson Alfonso <nelson_alfonso@icloud.com> Co-authored-by: Jacques Vergine <jacques.vergine35@gmail.com> * Fix EC clinical trial ingestion file to parquet (#1972) * Update pipelines/matrix/src/matrix/pipelines/matrix_generation/nodes.py Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> * Remove KG and pandas dataset now that we've movzd to spark * Update pipelines/matrix/src/matrix/pipelines/matrix_generation/nodes.py Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> * Refactor flag adding in functions * bump * Fix off label bug * Fix source and target regexp to only include "source_" + number columns * Set spark checkpoint * Migrate old disease list code to Kedro (v2) (#1943) Migrated the matrix-disease-list repo functionality to kedro with extensive refactoring (see PR) --------- Co-authored-by: Jacques Vergine <jacques.vergine35@gmail.com> * enlarge disk size (#1978) * fix: update OpenAI key reference (#1968) * fix: update OpenAI key reference and set target revision for Helm release * feat: enhance PostgreSQL pooler parameters for improved performance * Fix docker cloud build (#1977) * Revert "feat: docker cloud build for matrix image (#1822)" This reverts commit 09bf859. * bump uv lock * Set spark checkpoint directory (#1979) * Set spark checkpoint * Bump secrets * Fix spark utils * Drop duplicates * Change data leakage test to happen on EC_id * WIP - Update run comparison parameters * Update run comparison file paths * Remove ec_id joins * Fix off label join (thanks Piotr) * Bump off label * Bump to trigger CI again --------- Co-authored-by: Pascal Bro <pascal@everycure.org> Co-authored-by: Nelson Alfonso <45660392+Dashing-Nelson@users.noreply.github.com> Co-authored-by: Nelson Alfonso <nelson_alfonso@icloud.com> Co-authored-by: Alexei Stepanenko <alexei.stepa@gmail.com> Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.