Fix submit logic adding for LensingFlow production analyses by disharh · Pull Request #104 · etive-io/asimov

disharh · 2026-02-13T15:23:00Z

Description

Remove some project analyses related submit logic added for handling LensingFlow analyses.

Type of Change

Bug fix (non-breaking change that fixes an issue)
New feature (non-breaking change that adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
Documentation update
Code refactoring
Performance improvement
Test coverage improvement

Motivation and Context

The production analyses submit logic which looks for the production number in analysis name and decides submission priority, has been removed. This was added for the purpose of handling LensingFlow project analyses but LensingFlow now incorporates handling multiple productions internally.

Changes Made

List the main changes:

submit function in manage.py changed (basically reverted to this version with attribute .subjects corrected to ._subjects)
Indent error in review.py line 130 fixed.

Testing

How has this been tested?

Unit tests added/updated
Integration tests added/updated
Manual testing performed :
Tested with pipeline: (LALInference / Bilby / BayesWave / RIFT / N/A) Golum Pipe - here

Test configuration:

Python version(s): 3.10.0
Operating System: Linux (CIT)
Cluster environment (if applicable): /home/disha.hegde/.conda/envs/lfclone

Checklist

My code follows the project's style guidelines
I have performed a self-review of my code
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
My changes generate no new warnings
I have added tests that prove my fix is effective or that my feature works
New and existing unit tests pass locally with my changes
Any dependent changes have been merged and published

Documentation

Documentation updated (if applicable)
Changelog entry added
README updated (if applicable)

Breaking Changes

Does this PR introduce any breaking changes? If yes, describe:

Additional Notes

Any additional information, concerns, or considerations for reviewers.

Screenshots (if applicable)

For UI or output changes, include before/after screenshots or terminal output.

Reviewer Notes:

Does this PR need review from specific domain experts?
Any particular areas that need careful review?

This reverts commit f85978a, reversing changes made to 7b9094d.

Make v0.5.9 release See merge request asimov/asimov!165

DOC Expand the pipelines documentation See merge request asimov/asimov!155

DOCS Analysis remixing See merge request asimov/asimov!169

Fix documentation TOC See merge request asimov/asimov!171

- Introduced a bug report template for users to report issues effectively. - Added a feature request template to gather user suggestions for enhancements. - Created a pull request template to standardize contributions and improve review processes. - Updated the README with comprehensive information about Asimov's features and usage. - Added a CONTRIBUTORS file to acknowledge contributions from the community. - Included a USERS file to showcase research groups and institutions utilizing Asimov. - Established a CITATION file for proper attribution in academic work.

transientlunatic · 2026-02-16T12:23:16Z

NB this MR was made from the main branch, but is a bugfix specific to the 0.6 releases, so I've chnaged the target branch. This means that some additional files are now included in the MR which we'll need to tidy-up before merge.

Copilot

Pull request overview

This PR primarily removes custom submission/priority logic previously added for handling LensingFlow-related productions, reverting asimov manage submit behavior closer to upstream defaults. It also introduces a substantial documentation + repository metadata refresh (new tutorials, README rewrite, community files, and GitHub templates).

Changes:

Reverts/removes specialized submission gating/priority logic in asimov/cli/manage.py for productions and project analyses.
Fixes an indentation issue in asimov/cli/review.py and updates a Bilby config template to skip None-valued prior parameters.
Adds/updates multiple docs pages and repo meta files (tutorials, README, CITATION/USERS/CONTRIBUTORS, GitHub templates).

Reviewed changes

Copilot reviewed 14 out of 16 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
`asimov/cli/manage.py`	Removes specialized submit logic and refactors project-analysis “interest” handling and priority adjustment.
`asimov/cli/review.py`	Fixes indentation in project-analysis review add flow.
`asimov/configs/bilby.ini`	Avoids emitting `None` values when rendering luminosity distance prior kwargs.
`docs/source/index.rst`	Reorganizes docs landing page and adds Tutorials section to navigation.
`docs/source/getting-started.rst`	Adds explicit `Getting Started` ref label and whitespace tidy-ups.
`docs/source/citing.rst`	Fixes link formatting/spacing in citation guide.
`docs/source/tutorials/analysing-gw150914.rst`	Adds a new end-to-end tutorial for GW150914.
`docs/source/tutorials/adding-a-pipeline.rst`	Adds a new tutorial on integrating a pipeline.
`docs/source/tutorials/remixing-analyses.rst`	Adds a new tutorial on remixing published analyses.
`README.md`	Major rewrite/expansion of README content and structure.
`USERS.md`	Adds a users/adopters page for the project.
`CONTRIBUTORS.md`	Adds a contributors listing and contribution guidance.
`CITATION.cff`	Adds a Citation File Format metadata file.
`.github/pull_request_template.md`	Adds a GitHub PR template.
`.github/ISSUE_TEMPLATE/bug_report.md`	Adds a GitHub bug report issue template.
`.github/ISSUE_TEMPLATE/feature_request.md`	Adds a GitHub feature request issue template.

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Copilot · 2026-02-16T12:28:46Z

+            # check if we need to account for extra priority comming from atlenstics
            if "extra priority" in analysis.meta["needs settings"].keys():
-                extra_prio_pipeline = analysis.meta["needs settings"]["extra priority"]
-                if extra_prio_pipeline in interest_dict_project_analyses.keys():
-                    if subj_string in interest_dict_project_analyses[extra_prio_pipeline].keys():
-                        extra_prio = interest_dict_project_analyses[extra_prio_pipeline][subj_string]["interest status"]
-
+                if (
+                    analysis.meta["needs settings"]["extra priority"]
+                    == "atlenstics_compatibility"
+                ):


This extra priority block indexes analysis.meta['needs settings'] without first checking that needs settings exists on the analysis. If a project analysis has dependencies but no needs settings, this will raise and prevent submissions. Add a guard (or use .get) around analysis.meta['needs settings'] before accessing .keys() / fields.

Copilot · 2026-02-16T12:28:47Z

+                        if interest_dict[old_analysis][-1]["interest status"] is True:
                            interested_pipelines += 1


The running-job priority recalculation uses interest_dict[old_analysis][-1] and ignores the stored subjects field. If multiple subject-sets exist per pipeline, this can apply interest from a different subject group and adjust the wrong job’s priority. Filter interest_dict[old_analysis] by matching subjects (as done earlier in the submission gating logic).

Suggested change

if interest_dict[old_analysis][-1]["interest status"] is True:

interested_pipelines += 1

# Filter interest entries by matching subjects, to avoid

# applying interest from a different subject group.

current_subjects = analysis.meta.get("subjects")

matching_entries = [

entry

for entry in interest_dict[old_analysis]

if entry.get("subjects") == current_subjects

] if current_subjects is not None else []

if matching_entries:

if matching_entries[-1].get("interest status") is True:

interested_pipelines += 1

else:

# Fallback to previous behaviour if no subjects match

# (or if subjects are not recorded), to avoid changing

# semantics when subject information is unavailable.

if interest_dict[old_analysis][-1].get("interest status") is True:

interested_pipelines += 1

Copilot · 2026-02-16T12:28:47Z

+            if interested_pipelines < 2:
                theoretical_prio = 0
            else:
-                theoretical_prio = int((interested_pipelines-analysis.meta["needs settings"]["minimum"])*10)
+                theoretical_prio = int((interested_pipelines - 2) * 10)


This priority formula hard-codes a threshold of 2 interested pipelines, rather than using the configured meta['needs settings']['minimum'] value (which is used earlier in the function). This makes the runtime priority behavior inconsistent with the submission gating settings and may mis-prioritize jobs when the minimum differs from 2.

Copilot · 2026-02-16T12:28:47Z

+.. toctree::
+   :maxdepth: 1
+   :Caption: Tutorials
+


The toctree option is written as :Caption: but Sphinx/reST expects :caption: (option names are case-sensitive). As-is, this will likely be ignored and may emit a docs build warning/error.

Copilot · 2026-02-16T12:28:47Z

+
+.. code-block :: console
+
+    $ asimov apply -f get-data.yaml -e GW150914_095045


This command applies get-data.yaml again, but at this point the tutorial says to apply bilby-IMRPhenomPv2.yaml. As written, readers will never add the bilby remix analysis to the project.

Suggested change

$ asimov apply -f get-data.yaml -e GW150914_095045

$ asimov apply -f bilby-IMRPhenomPv2.yaml -e GW150914_095045

Copilot · 2026-02-16T12:28:49Z

-    interest_dict_project_analyses = {}
+    # this should add the required repository field to the project analysis
+    # with the correct type
+    # FIXME: for now, this only accountd for the case where we have multiple analysis


Typo in comment: “only accountd” should be “only accounts”.

Suggested change

# FIXME: for now, this only accountd for the case where we have multiple analysis

# FIXME: for now, this only accounts for the case where we have multiple analysis

Copilot · 2026-02-16T12:28:49Z

@@ -0,0 +1,116 @@
+.. Remixing analyses_


This looks like it was intended to be a reST reference label, but .. Remixing analyses_ is not a valid label directive. If you want this page to be linkable via :ref:, use the label form .. _remixing-analyses: (or similar).

Suggested change

.. Remixing analyses_

.. _remixing-analyses:

Copilot · 2026-02-16T12:28:49Z

+    name: bilby-IMRPhenomPv2
+    pipeline: bilby
+    waveform:
+    approximant: IMRPhenomPv2


The YAML example is invalid as written: approximant is not indented under waveform:. Readers copying this will get a YAML parse error or a mis-specified waveform block. Indent approximant as a child key of waveform.

Suggested change

approximant: IMRPhenomPv2

approximant: IMRPhenomPv2

Copilot · 2026-02-16T12:28:49Z

+   import asimov.pipeline.Pipeline
+
+   class pyRing(asimov.pipeline.Pipeline):


The Python example import is not valid: import asimov.pipeline.Pipeline won’t import the Pipeline symbol, and asimov isn’t imported for asimov.pipeline.Pipeline usage in the class definition. Update the snippet to a valid import pattern so readers can run it as-is.

Suggested change

import asimov.pipeline.Pipeline

class pyRing(asimov.pipeline.Pipeline):

from asimov.pipeline import Pipeline

class pyRing(Pipeline):

Copilot · 2026-02-16T12:28:50Z

+## Table of Contents

-### Job monitoring and management
+- [What is Asimov?](#what-is-asimov)
+- [Why Asimov?](#why-asimov)
+- [Key Features](#-key-features)
+- [Primary Use Case: Gravitational Waves](#-primary-use-case-gravitational-waves)
+- [Beyond Gravitational Waves](#-beyond-gravitational-waves)
+- [Installing Asimov](#-installing-asimov)
+- [Quick Start](#-quick-start)
+- [Do I Need Asimov?](#-do-i-need-asimov)
+- [Example Workflow](#-example-workflow)
+- [Extensibility](#-extensibility)
+- [Roadmap](#-roadmap)
+- [Contributing](#-contributing)
+- [Citation](#-citation)
+- [Authors](#-authors)


The PR description focuses on reverting submit logic and fixing an indentation error, but this PR also introduces substantial new documentation/tutorial pages and repository meta files (README rewrite, new templates, CITATION/USERS/CONTRIBUTORS). Consider updating the PR description to reflect these additional changes or splitting them into separate PRs to keep review scope focused.

transientlunatic and others added 26 commits November 2, 2023 14:03

Merge branch 'review'

b70a268

Merge branch 'v0.5-release'

1fc9448

Merge branch 'master' of git.ligo.org:asimov/asimov

a4d830f

Updates to pipeline development documentation.

26cfc0d

Update the index.

e9317f9

Add the start of the tutorial.

388f66e

Completed the pipeline tutorial.

954108c

Added authorship note.

ca2d867

Added GW150914 tutorial.

2eb4aa9

Merge branch 'master' of git.ligo.org:asimov/asimov

0065491

Merge branch 'master' of github.com:transientlunatic/asimov

7b9094d

Merge branch 'doc-pipelines'

f85978a

Revert "Merge branch 'doc-pipelines'"

814fb2d

This reverts commit f85978a, reversing changes made to 7b9094d.

Make v0.5.9 release

f784b57

Merge branch 'v0.5-release' into 'master'

148e30e

Make v0.5.9 release See merge request asimov/asimov!165

DOC Expand the pipelines documentation

28f3076

Merge branch 'doc-pipelines' into 'master'

9c383bb

DOC Expand the pipelines documentation See merge request asimov/asimov!155

DOCS Analysis remixing

0d1a721

Merge branch 'docs-cookbook' into 'master'

822fdb0

DOCS Analysis remixing See merge request asimov/asimov!169

Fix documentation TOC

0c6e052

Merge branch 'docs-cookbook' into 'master'

1d92c1b

Fix documentation TOC See merge request asimov/asimov!171

Merge branch 'master' of git.ligo.org:asimov/asimov

fc5aa16

Merge branch 'v0.6-release'

bda345d

remove submit logic added for LensingFlow

21f22ca

fix indent error

581b1a8

transientlunatic changed the base branch from main to v0.6-release February 16, 2026 12:20

transientlunatic added the bug Something isn't working label Feb 16, 2026

transientlunatic mentioned this pull request Feb 16, 2026

Pip Install of v0.6/v0.6.1 #102

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Fix submit logic adding for LensingFlow production analyses#104

Fix submit logic adding for LensingFlow production analyses#104
disharh wants to merge 26 commits intoetive-io:v0.6-releasefrom
disharh:fix-submit

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		if interest_dict[old_analysis][-1]["interest status"] is True:
		interested_pipelines += 1

-                        if interest_dict[old_analysis][-1]["interest status"] is True:
-                            interested_pipelines += 1
+                        # Filter interest entries by matching subjects, to avoid
+                        # applying interest from a different subject group.
+                        current_subjects = analysis.meta.get("subjects")
+                        matching_entries = [
+                            entry
+                            for entry in interest_dict[old_analysis]
+                            if entry.get("subjects") == current_subjects
+                        ] if current_subjects is not None else []
+                        if matching_entries:
+                            if matching_entries[-1].get("interest status") is True:
+                                interested_pipelines += 1
+                        else:
+                            # Fallback to previous behaviour if no subjects match
+                            # (or if subjects are not recorded), to avoid changing
+                            # semantics when subject information is unavailable.
+                            if interest_dict[old_analysis][-1].get("interest status") is True:
+                                interested_pipelines += 1


		.. code-block :: console

		$ asimov apply -f get-data.yaml -e GW150914_095045

	$ asimov apply -f get-data.yaml -e GW150914_095045
	$ asimov apply -f bilby-IMRPhenomPv2.yaml -e GW150914_095045

	# FIXME: for now, this only accountd for the case where we have multiple analysis
	# FIXME: for now, this only accounts for the case where we have multiple analysis

		import asimov.pipeline.Pipeline

		class pyRing(asimov.pipeline.Pipeline):

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disharh commented Feb 13, 2026

Description

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