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looper 2.0.0 docs release#39

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donaldcampbelljr merged 97 commits intomasterpepkit/pepspec:masterfrom devpepkit/pepspec:devCopy head branch name to clipboardSep 30, 2024

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Commits on Jun 28, 2024

• Begin updating Looper docs for 2.0.0 release

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Commits on Jul 8, 2024

• work towards looper 2.0.0 docs, adding new notebooks,

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Commits on Jul 9, 2024

• update git ignore

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• more updates, re-did looper init docs

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• more shuffling of looper headers

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Commits on Jul 29, 2024

• fix broken link

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• typos, update looper-config.md

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• refactor --looper-config to --config

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• update usage doc and truncate to key examples

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• merge advanced examples

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Commits on Jul 30, 2024

• minor typos and fomratting

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• re-build md files

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Commits on Aug 19, 2024

• Merge branch 'dev' into dev_Looper_2.0.0

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• some looper v2 docs restructing

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• looper docs restructuring.

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Commits on Aug 20, 2024

• consolidate "Defining a project" and "Details of a project"

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• consolidate "Defining a project" and "Details of a project", delete unecessary .md file

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• consolidate items into running a pipeline

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• add clarity to defining looper config

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• merge looper config information

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Commits on Aug 22, 2024

• more work toward new looper 2 docs

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• typos

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• minor typos

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• add looper compute settings tutorial

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• updates on looper tutorial

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Commits on Aug 23, 2024

• rename some sections work on pipestat tutorial for shell-based pipeline

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Commits on Aug 24, 2024

• Lots of work toward a new advanced computing guide

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Commits on Aug 26, 2024

• major work on looper integration with pipestat documentation

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• update items on reporting data to pephub directly

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• changes to advanced computing

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Commits on Aug 27, 2024

• fix links to future hello_looper repository

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• fix pipeline interface in examples

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• fixes to pipestat tutorial

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• update compute settings

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Commits on Aug 28, 2024

• looper docs revamp

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• advanced-run-options clarifications

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• remove redundant looper config items

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• remove warning for advanced-run-options

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• add more complete example for multiple input files

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• merge html report docs and add other pipestat related functions

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• many small changes and link fixes

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• make changes to using-pipestat in how to docs

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Commits on Aug 29, 2024

• remove "using geofetch" from looper as it appears unnecessary

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• remove unused jupyter notebooks (hello looper)

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• add divvy cli tutorial

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• add divvy python api tutorial

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• remove un-used/redundant divvy jupyter notebooks and associated .md files

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• remove linked_pipeline_interfaces, re-do writing-a-pipeline-interface.md

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• remove linked_pipeline_interfaces, re-do writing-a-pipeline-interface.md

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• edit pipeline-interface-specification.md

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• Merge remote-tracking branch 'origin/dev_Looper_2.0.0' into dev_Looper_2.0.0

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• fix pypiper links

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Commits on Aug 30, 2024

• adjustments to advanced metadata

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• clarity added on advanced-metadata

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• finish advanced-metadata.md

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• run typos

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• add divvy links, re-order dev tutorial

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• pipestat tutorial tweaks

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Commits on Sep 3, 2024

• update pipestat docs for new output schemas to use type:array

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Commits on Sep 7, 2024

• looper docs work

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Commits on Sep 10, 2024

• remove pipeline_type from pipestat examples, add portable html report for example

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• minor typos

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Commits on Sep 16, 2024

• some fixes and re-shuffling

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• add link to other project level docs for clarity

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Commits on Sep 18, 2024

• add reporting objects via pipestat and project-level examples, tie into looper link

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• typo corrections, clarification to pipestat.md

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• add changes regarding pipeline interfaces

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• add summary, fix indentation for compute settings

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• add segment regarding pre-submit functions

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• rename pipestat section

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• add pepkit image

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Commits on Sep 19, 2024

• add new image to title page

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• some minor clarifications

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• minor clarifications

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• pipeline interface docs work

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• minor wordsmithing pipestat tutorial

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• Merge remote-tracking branch 'origin/dev_Looper_2.0.0' into dev_Looper_2.0.0

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• typo fix, remove pipeline_type

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• remove pipeline_type from pre-submission-hooks.md

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• split pipestat documentation, create how tos for project level pipelines, reporting objects, and linking objects

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• minor adjustments

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• clean up pipestat tutorial based on suggestions

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• pipeline interface updats

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• Merge branch 'dev_Looper_2.0.0' of github.com:pepkit/pepspec into dev_Looper_2.0.0

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• piface spec updates

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Commits on Sep 23, 2024

• restructure user/developer pipestat docs

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• tutorial tweaks

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• fix links

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• some clean up

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• add information regarding databases in user tutorial and configure-pipestat-backends.md

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Commits on Sep 26, 2024

• add more information to pipestat tutorial wrt database backends

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Commits on Sep 30, 2024

• typo fixes

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• update changelog.md

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• Merge pull request #34 from pepkit/dev_Looper_2.0.0

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• Merge branch 'master' into dev

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• typo fix

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• update eido and peppy changelogs

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