From 248ab8959ea62106a5966840139fa767ef3196c7 Mon Sep 17 00:00:00 2001 From: Dimitri Yatsenko Date: Mon, 10 Aug 2026 16:20:21 -0500 Subject: [PATCH 1/4] docs: regenerate pipeline diagram with modernized dj.Diagram style Rendered with the restyled dj.Diagram (datajoint-python #1532 / PR #1534): modern tier palette, rounded nodes, master-part entity clustering, corrected edge-weight (cardinality) rule, and Helvetica typography. For visual review of the new diagram style against the LC-MS pipeline. --- docs/pipeline.svg | 251 +++++++++++++++++++++++++--------------------- 1 file changed, 135 insertions(+), 116 deletions(-) diff --git a/docs/pipeline.svg b/docs/pipeline.svg index db68dea..dc24c69 100644 --- a/docs/pipeline.svg +++ b/docs/pipeline.svg @@ -1,193 +1,212 @@ - - - + + + + + + + cluster_cluster_subject - -subject + +subject cluster_cluster_session - -session + +session cluster_cluster_scan - -scan + +scan + + +cluster_cluster_entity_scan_Acquisition + + + +cluster_cluster_entity_scan_PeakDetection + + + +cluster_cluster_entity_scan_MassAnalysis + subject.Subject - - -Subject + + +Subject - + subject.Sample - - -Sample + + +Sample -subject.Subject->subject.Sample - - - - -session.Instrument - - -Instrument - - +subject.Subject->subject.Sample + - + session.Session - - -Session + + +Session - - -session.Instrument->session.Session - - scan.Acquisition - - -Acquisition + + +Acquisition - - -scan.Acquisition.Scan - - -Acquisition.Scan - - - - - -scan.Acquisition->scan.Acquisition.Scan - + + +session.Session->scan.Acquisition + - + scan.MassAnalysis - - -MassAnalysis + + +MassAnalysis -scan.Acquisition->scan.MassAnalysis - +scan.Acquisition->scan.MassAnalysis + - - -subject.Sample->session.Session - + + +scan.Acquisition.Scan + + +Scan + - + + + +scan.Acquisition->scan.Acquisition.Scan + + + -session.AcquisitionMethod - - -AcquisitionMethod +scan.PeakDetection + + +PeakDetection - - -session.AcquisitionMethod->session.Session - + + +scan.MassAnalysis->scan.PeakDetection + scan.MassAnalysis.Spectrum - - -MassAnalysis.Spectrum + + +Spectrum - - -scan.Acquisition.Scan->scan.MassAnalysis.Spectrum - - - - -session.Session->scan.Acquisition - - -scan.MassAnalysis->scan.MassAnalysis.Spectrum - +scan.MassAnalysis->scan.MassAnalysis.Spectrum + - - -scan.PeakDetection - - -PeakDetection + + +scan.PeakDetection.Peak + + +Peak - - -scan.MassAnalysis->scan.PeakDetection - + + +scan.PeakDetection->scan.PeakDetection.Peak + - - -scan.PeakDetection.Peak - - -PeakDetection.Peak + + +subject.Sample->session.Session + + + + +session.Instrument + + +Instrument + + +session.Instrument->session.Session + + + + +scan.Acquisition.Scan->scan.MassAnalysis.Spectrum + + -scan.MassAnalysis.Spectrum->scan.PeakDetection.Peak - +scan.MassAnalysis.Spectrum->scan.PeakDetection.Peak + + + + +session.AcquisitionMethod + + +AcquisitionMethod + + + + + +session.AcquisitionMethod->session.Session + - + scan.PeakDetectionParams - - -PeakDetectionParams + + +PeakDetectionParams - -scan.PeakDetectionParams->scan.PeakDetection - - - -scan.PeakDetection->scan.PeakDetection.Peak - +scan.PeakDetectionParams->scan.PeakDetection + - \ No newline at end of file + From 101a3e97195873b7f8f7729640a9cb4d9bd44f3b Mon Sep 17 00:00:00 2001 From: Dimitri Yatsenko Date: Mon, 10 Aug 2026 16:23:09 -0500 Subject: [PATCH 2/4] =?UTF-8?q?docs:=20regenerate=20pipeline=20diagram=20?= =?UTF-8?q?=E2=80=94=20adaptive=20(auto)=20theme=20+=20sans=20schema=20lab?= =?UTF-8?q?el?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Re-rendered with the updated #1534 defaults: 'auto' color theme (single SVG that adapts to the viewer's light/dark mode via prefers-color-scheme) and Helvetica schema (cluster) labels. --- docs/pipeline.svg | 75 ++++++++++++++++++++++++++++++++++------------- 1 file changed, 54 insertions(+), 21 deletions(-) diff --git a/docs/pipeline.svg b/docs/pipeline.svg index dc24c69..fbbd5de 100644 --- a/docs/pipeline.svg +++ b/docs/pipeline.svg @@ -4,43 +4,76 @@ - - - + + + + cluster_cluster_subject - -subject + +subject cluster_cluster_session - -session + +session cluster_cluster_scan - -scan + +scan -cluster_cluster_entity_scan_Acquisition - - - cluster_cluster_entity_scan_PeakDetection - + cluster_cluster_entity_scan_MassAnalysis + +cluster_cluster_entity_scan_Acquisition + + subject.Subject - -Subject + +Subject @@ -48,15 +81,15 @@ subject.Sample - -Sample + +Sample subject.Subject->subject.Sample - + @@ -154,7 +187,7 @@ subject.Sample->session.Session - + From 9fe43bb9684155b073e7a348b3c297a6590e37c7 Mon Sep 17 00:00:00 2001 From: Dimitri Yatsenko Date: Mon, 10 Aug 2026 16:42:21 -0500 Subject: [PATCH 3/4] docs: update DataJoint version references to 2.3 Bump the README's 'DataJoint 2.1' mentions and the dependency floor (datajoint[postgres]>=2.1.0 -> >=2.3.0) to the current 2.3 line. --- README.md | 6 +++--- pyproject.toml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d657a50..c8b1080 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ A demonstration DataJoint pipeline for LC-MS (Liquid Chromatography-Mass Spectrometry) data processing. -This project showcases DataJoint 2.1 best practices with a realistic scientific workflow. +This project showcases DataJoint 2.3 best practices with a realistic scientific workflow. ## Pipeline Overview @@ -52,9 +52,9 @@ uv sync --group dev ## Quick Start -### 1. Configure Database (DataJoint 2.1) +### 1. Configure Database (DataJoint 2.3) -DataJoint 2.1 uses a layered configuration system. Non-sensitive settings go in `datajoint.json`, while credentials come from secrets or environment variables. +DataJoint 2.3 uses a layered configuration system. Non-sensitive settings go in `datajoint.json`, while credentials come from secrets or environment variables. **Configuration sources (in priority order):** 1. Environment variables (`DJ_HOST`, `DJ_USER`, `DJ_PASS`, etc.) diff --git a/pyproject.toml b/pyproject.toml index 3ffa8b0..ba1f959 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ classifiers = [ "Topic :: Scientific/Engineering :: Bio-Informatics", ] dependencies = [ - "datajoint[postgres]>=2.1.0", + "datajoint[postgres]>=2.3.0", "numpy", "pandas", "scipy", From 303be06fe350914628176d37bdd24928299a4395 Mon Sep 17 00:00:00 2001 From: Dimitri Yatsenko Date: Mon, 10 Aug 2026 18:11:59 -0500 Subject: [PATCH 4/4] docs: regenerate pipeline diagram with top-right schema labels Re-render against datajoint-python #1534 (fix/1532-diagram-restyle) so the schema name sits in the top-right corner of each schema cluster. --- docs/pipeline.svg | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/pipeline.svg b/docs/pipeline.svg index fbbd5de..4ff99c1 100644 --- a/docs/pipeline.svg +++ b/docs/pipeline.svg @@ -44,30 +44,30 @@ cluster_cluster_subject -subject +subject cluster_cluster_session -session +session cluster_cluster_scan -scan +scan cluster_cluster_entity_scan_PeakDetection -cluster_cluster_entity_scan_MassAnalysis - - - cluster_cluster_entity_scan_Acquisition + +cluster_cluster_entity_scan_MassAnalysis + + subject.Subject