From d0c9ed20c40c71066b636af51796e887377955a4 Mon Sep 17 00:00:00 2001 From: jessicasyu <15913767+jessicasyu@users.noreply.github.com> Date: Mon, 18 Nov 2024 16:45:26 -0500 Subject: [PATCH 1/6] =?UTF-8?q?Bump=20version:=203.1.4=20=E2=86=92=203.2.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- build.gradle | 2 +- version.properties | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/build.gradle b/build.gradle index 1550d5852..db215339f 100644 --- a/build.gradle +++ b/build.gradle @@ -5,7 +5,7 @@ plugins { id "com.diffplug.spotless" version "6.25.0" } -version = "3.1.4" +version = "3.2.0" sourceCompatibility = 1.11 repositories { diff --git a/version.properties b/version.properties index 7784ed7cf..b31914a9c 100644 --- a/version.properties +++ b/version.properties @@ -1,4 +1,4 @@ -#Mon, 26 Feb 2024 14:57:57 -0500 +#Mon, 18 Nov 2024 16:44:50 -0500 major=3 -minor=1 -patch=4 +minor=2 +patch=0 From 40a5028cac8b85025f677f9e9f15143ad14c3532 Mon Sep 17 00:00:00 2001 From: "bagheri-lab-bot[bot]" Date: Mon, 18 Nov 2024 21:46:12 +0000 Subject: [PATCH 2/6] Add changelog for v3.2.0 --- docs/_changelog/v3.2.0.md | 53 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 docs/_changelog/v3.2.0.md diff --git a/docs/_changelog/v3.2.0.md b/docs/_changelog/v3.2.0.md new file mode 100644 index 000000000..f8965b642 --- /dev/null +++ b/docs/_changelog/v3.2.0.md @@ -0,0 +1,53 @@ +--- +title: v3.2.0 +--- + +# [v3.2.0](https://github.com/bagherilab/ARCADE/releases/tag/v3.2.0) - 2024-11-18 + +> Compare with [v3.1.4](https://github.com/bagherilab/ARCADE/compare/v3.1.4...v3.2.0) + +### Features + +- Update cell make method to return container by [@jessicasyu](https://github.com/jessicasyu) in [#74](https://github.com/bagherilab/ARCADE/pull/74) +- Update cell constructors to use container by [@jessicasyu](https://github.com/jessicasyu) in [#75](https://github.com/bagherilab/ARCADE/pull/75) +- Add support for linked populations in setup file by [@jessicasyu](https://github.com/jessicasyu) in [#76](https://github.com/bagherilab/ARCADE/pull/76) +- Add support for parameter distributions by [@jessicasyu](https://github.com/jessicasyu) in [#85](https://github.com/bagherilab/ARCADE/pull/85) + +#### Features: + +- Add support for initialization by percentage by [@jessicasyu](https://github.com/jessicasyu) in [#53](https://github.com/bagherilab/ARCADE/pull/53) +- Add patch cell agent with random state rules by [@jessicasyu](https://github.com/jessicasyu) in [#56](https://github.com/bagherilab/ARCADE/pull/56) +- Add support for different patch initialization schemes by [@jessicasyu](https://github.com/jessicasyu) in [#81](https://github.com/bagherilab/ARCADE/pull/81) +- Pass initial glucose concentration as parameter for metabolism modules by [@allison-li-1016](https://github.com/allison-li-1016) in [#96](https://github.com/bagherilab/ARCADE/pull/96) + +#### Features: + +- Added class key for potts populations by [@Jannetty](https://github.com/Jannetty) in [#11](https://github.com/bagherilab/ARCADE/pull/11) +- Make necessary PottsCell fields public, prepare for abstract setModule() function by [@Jannetty](https://github.com/Jannetty) in [#12](https://github.com/bagherilab/ARCADE/pull/12) +- Convert PottsCell to abstract class by [@Jannetty](https://github.com/Jannetty) in [#13](https://github.com/bagherilab/ARCADE/pull/13) +- Add support for splits with offset, direction, and split probability by [@Jannetty](https://github.com/Jannetty) in [#16](https://github.com/bagherilab/ARCADE/pull/16) +- Add custom plane splitvoxels by [@Jannetty](https://github.com/Jannetty) in [#46](https://github.com/bagherilab/ARCADE/pull/46) +- Refactor plane constructor to take Double3D instead of Int3D by [@Jannetty](https://github.com/Jannetty) in [#83](https://github.com/bagherilab/ARCADE/pull/83) + +### Bug fixes + +- Remove apoptosis checkpoint for potts cells by [@jessicasyu](https://github.com/jessicasyu) in [#18](https://github.com/bagherilab/ARCADE/pull/18) +- Replace instance of wildcard import of Module to prevent clash in Java 9 by [@cainja](https://github.com/cainja) in [#65](https://github.com/bagherilab/ARCADE/pull/65) +- Fix passing in initial glucose as a parameter value by [@allison-li-1016](https://github.com/allison-li-1016) in [#99](https://github.com/bagherilab/ARCADE/pull/99) + +### Tests + +- Remove unnecessary mocking in potts cell stem tests by [@jessicasyu](https://github.com/jessicasyu) in [#57](https://github.com/bagherilab/ARCADE/pull/57) +- Unit tests for core utilities Colors class by [@cainja](https://github.com/cainja) in [#63](https://github.com/bagherilab/ARCADE/pull/63) +- Adding tests for core utilities Solver class by [@cainja](https://github.com/cainja) in [#69](https://github.com/bagherilab/ARCADE/pull/69) +- Improved tests for core utilities Color class by [@cainja](https://github.com/cainja) in [#73](https://github.com/bagherilab/ARCADE/pull/73) +- Adding tests for core utilities Graph class by [@cainja](https://github.com/cainja) in [#64](https://github.com/bagherilab/ARCADE/pull/64) +- Adding tests for core utilities Parameter class by [@cainja](https://github.com/cainja) in [#71](https://github.com/bagherilab/ARCADE/pull/71) + +### Admin + +- Update workflows conditions for main and develop branches by [@jessicasyu](https://github.com/jessicasyu) in [#10](https://github.com/bagherilab/ARCADE/pull/10) +- Change source compatibility from 1.8 to 1.11 by [@jessicasyu](https://github.com/jessicasyu) in [#66](https://github.com/bagherilab/ARCADE/pull/66) +- Migrate to JUnit 5 by [@jessicasyu](https://github.com/jessicasyu) in [#67](https://github.com/bagherilab/ARCADE/pull/67) +- Add spotless autoformatter by [@jessicasyu](https://github.com/jessicasyu) in [#68](https://github.com/bagherilab/ARCADE/pull/68) +- Update workflows for changelog releases and Jekyll docs by [@jessicasyu](https://github.com/jessicasyu) in [#100](https://github.com/bagherilab/ARCADE/pull/100) From 268f5fed2fe9047dc37b1a9122d08021f543b1a7 Mon Sep 17 00:00:00 2001 From: jessicasyu <15913767+jessicasyu@users.noreply.github.com> Date: Mon, 18 Nov 2024 16:50:58 -0500 Subject: [PATCH 3/6] Fix backticks --- .github/workflows/release.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 7425edfbf..a04688457 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -79,13 +79,13 @@ jobs: "exclude_labels": ["package: patch", "package: potts"] }, { - "title": "#### Features: `patch`", + "title": "#### Features: \`patch\`", "labels": ["type: feature", "package: patch"], "exclude_labels": ["package: potts"], "exhaustive": true }, { - "title": "#### Features: `potts`", + "title": "#### Features: \`potts\`", "labels": ["type: feature", "package: potts"], "exclude_labels": ["package: patch"], "exhaustive": true From 44354860402872a138cc1b78f42eea1f40632e46 Mon Sep 17 00:00:00 2001 From: "bagheri-lab-bot[bot]" Date: Mon, 18 Nov 2024 21:51:41 +0000 Subject: [PATCH 4/6] Add changelog for v3.2.0 --- docs/_changelog/v3.2.0.md | 107 +++++++++++++++++++++----------------- 1 file changed, 58 insertions(+), 49 deletions(-) diff --git a/docs/_changelog/v3.2.0.md b/docs/_changelog/v3.2.0.md index f8965b642..009de7774 100644 --- a/docs/_changelog/v3.2.0.md +++ b/docs/_changelog/v3.2.0.md @@ -2,52 +2,61 @@ title: v3.2.0 --- -# [v3.2.0](https://github.com/bagherilab/ARCADE/releases/tag/v3.2.0) - 2024-11-18 - -> Compare with [v3.1.4](https://github.com/bagherilab/ARCADE/compare/v3.1.4...v3.2.0) - -### Features - -- Update cell make method to return container by [@jessicasyu](https://github.com/jessicasyu) in [#74](https://github.com/bagherilab/ARCADE/pull/74) -- Update cell constructors to use container by [@jessicasyu](https://github.com/jessicasyu) in [#75](https://github.com/bagherilab/ARCADE/pull/75) -- Add support for linked populations in setup file by [@jessicasyu](https://github.com/jessicasyu) in [#76](https://github.com/bagherilab/ARCADE/pull/76) -- Add support for parameter distributions by [@jessicasyu](https://github.com/jessicasyu) in [#85](https://github.com/bagherilab/ARCADE/pull/85) - -#### Features: - -- Add support for initialization by percentage by [@jessicasyu](https://github.com/jessicasyu) in [#53](https://github.com/bagherilab/ARCADE/pull/53) -- Add patch cell agent with random state rules by [@jessicasyu](https://github.com/jessicasyu) in [#56](https://github.com/bagherilab/ARCADE/pull/56) -- Add support for different patch initialization schemes by [@jessicasyu](https://github.com/jessicasyu) in [#81](https://github.com/bagherilab/ARCADE/pull/81) -- Pass initial glucose concentration as parameter for metabolism modules by [@allison-li-1016](https://github.com/allison-li-1016) in [#96](https://github.com/bagherilab/ARCADE/pull/96) - -#### Features: - -- Added class key for potts populations by [@Jannetty](https://github.com/Jannetty) in [#11](https://github.com/bagherilab/ARCADE/pull/11) -- Make necessary PottsCell fields public, prepare for abstract setModule() function by [@Jannetty](https://github.com/Jannetty) in [#12](https://github.com/bagherilab/ARCADE/pull/12) -- Convert PottsCell to abstract class by [@Jannetty](https://github.com/Jannetty) in [#13](https://github.com/bagherilab/ARCADE/pull/13) -- Add support for splits with offset, direction, and split probability by [@Jannetty](https://github.com/Jannetty) in [#16](https://github.com/bagherilab/ARCADE/pull/16) -- Add custom plane splitvoxels by [@Jannetty](https://github.com/Jannetty) in [#46](https://github.com/bagherilab/ARCADE/pull/46) -- Refactor plane constructor to take Double3D instead of Int3D by [@Jannetty](https://github.com/Jannetty) in [#83](https://github.com/bagherilab/ARCADE/pull/83) - -### Bug fixes - -- Remove apoptosis checkpoint for potts cells by [@jessicasyu](https://github.com/jessicasyu) in [#18](https://github.com/bagherilab/ARCADE/pull/18) -- Replace instance of wildcard import of Module to prevent clash in Java 9 by [@cainja](https://github.com/cainja) in [#65](https://github.com/bagherilab/ARCADE/pull/65) -- Fix passing in initial glucose as a parameter value by [@allison-li-1016](https://github.com/allison-li-1016) in [#99](https://github.com/bagherilab/ARCADE/pull/99) - -### Tests - -- Remove unnecessary mocking in potts cell stem tests by [@jessicasyu](https://github.com/jessicasyu) in [#57](https://github.com/bagherilab/ARCADE/pull/57) -- Unit tests for core utilities Colors class by [@cainja](https://github.com/cainja) in [#63](https://github.com/bagherilab/ARCADE/pull/63) -- Adding tests for core utilities Solver class by [@cainja](https://github.com/cainja) in [#69](https://github.com/bagherilab/ARCADE/pull/69) -- Improved tests for core utilities Color class by [@cainja](https://github.com/cainja) in [#73](https://github.com/bagherilab/ARCADE/pull/73) -- Adding tests for core utilities Graph class by [@cainja](https://github.com/cainja) in [#64](https://github.com/bagherilab/ARCADE/pull/64) -- Adding tests for core utilities Parameter class by [@cainja](https://github.com/cainja) in [#71](https://github.com/bagherilab/ARCADE/pull/71) - -### Admin - -- Update workflows conditions for main and develop branches by [@jessicasyu](https://github.com/jessicasyu) in [#10](https://github.com/bagherilab/ARCADE/pull/10) -- Change source compatibility from 1.8 to 1.11 by [@jessicasyu](https://github.com/jessicasyu) in [#66](https://github.com/bagherilab/ARCADE/pull/66) -- Migrate to JUnit 5 by [@jessicasyu](https://github.com/jessicasyu) in [#67](https://github.com/bagherilab/ARCADE/pull/67) -- Add spotless autoformatter by [@jessicasyu](https://github.com/jessicasyu) in [#68](https://github.com/bagherilab/ARCADE/pull/68) -- Update workflows for changelog releases and Jekyll docs by [@jessicasyu](https://github.com/jessicasyu) in [#100](https://github.com/bagherilab/ARCADE/pull/100) +## 📦 Uncategorized + +- Update workflows conditions for main and develop branches + - PR: #10 +- Added class key for potts populations + - PR: #11 +- Make necessary PottsCell fields public, prepare for abstract setModule() function + - PR: #12 +- Convert PottsCell to abstract class + - PR: #13 +- Add support for splits with offset, direction, and split probability + - PR: #16 +- Remove apoptosis checkpoint for potts cells + - PR: #18 +- Add support for initialization by percentage + - PR: #53 +- Add custom plane splitvoxels + - PR: #46 +- Replace instance of wildcard import of Module to prevent clash in Java 9 + - PR: #65 +- Remove unnecessary mocking in potts cell stem tests + - PR: #57 +- Add patch cell agent with random state rules + - PR: #56 +- Change source compatibility from 1.8 to 1.11 + - PR: #66 +- Migrate to JUnit 5 + - PR: #67 +- Add spotless autoformatter + - PR: #68 +- Unit tests for core utilities Colors class + - PR: #63 +- Adding tests for core utilities Solver class + - PR: #69 +- Improved tests for core utilities Color class + - PR: #73 +- Adding tests for core utilities Graph class + - PR: #64 +- Adding tests for core utilities Parameter class + - PR: #71 +- Update cell make method to return container + - PR: #74 +- Add support for different patch initialization schemes + - PR: #81 +- Update cell constructors to use container + - PR: #75 +- Add support for linked populations in setup file + - PR: #76 +- Refactor plane constructor to take Double3D instead of Int3D + - PR: #83 +- Add support for parameter distributions + - PR: #85 +- Pass initial glucose concentration as parameter for metabolism modules + - PR: #96 +- Fix passing in initial glucose as a parameter value + - PR: #99 +- Update workflows for changelog releases and Jekyll docs + - PR: #100 From 6049312e839e499fb61c8599e4ac803ae3bed5bb Mon Sep 17 00:00:00 2001 From: jessicasyu <15913767+jessicasyu@users.noreply.github.com> Date: Mon, 18 Nov 2024 17:05:11 -0500 Subject: [PATCH 5/6] Actually fix backticks --- .github/workflows/release.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index a04688457..e00467ce3 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -79,13 +79,13 @@ jobs: "exclude_labels": ["package: patch", "package: potts"] }, { - "title": "#### Features: \`patch\`", + "title": "#### Features: \\x60patch\\x60", "labels": ["type: feature", "package: patch"], "exclude_labels": ["package: potts"], "exhaustive": true }, { - "title": "#### Features: \`potts\`", + "title": "#### Features: \\x60potts\\x60", "labels": ["type: feature", "package: potts"], "exclude_labels": ["package: patch"], "exhaustive": true From c917f191cc716c354dde93454b20fa986ab00dfd Mon Sep 17 00:00:00 2001 From: jessicasyu <15913767+jessicasyu@users.noreply.github.com> Date: Mon, 18 Nov 2024 17:05:56 -0500 Subject: [PATCH 6/6] Update changelog --- docs/_changelog/v3.2.0.md | 107 +++++++++++++++++--------------------- 1 file changed, 49 insertions(+), 58 deletions(-) diff --git a/docs/_changelog/v3.2.0.md b/docs/_changelog/v3.2.0.md index 009de7774..1a5614192 100644 --- a/docs/_changelog/v3.2.0.md +++ b/docs/_changelog/v3.2.0.md @@ -2,61 +2,52 @@ title: v3.2.0 --- -## 📦 Uncategorized - -- Update workflows conditions for main and develop branches - - PR: #10 -- Added class key for potts populations - - PR: #11 -- Make necessary PottsCell fields public, prepare for abstract setModule() function - - PR: #12 -- Convert PottsCell to abstract class - - PR: #13 -- Add support for splits with offset, direction, and split probability - - PR: #16 -- Remove apoptosis checkpoint for potts cells - - PR: #18 -- Add support for initialization by percentage - - PR: #53 -- Add custom plane splitvoxels - - PR: #46 -- Replace instance of wildcard import of Module to prevent clash in Java 9 - - PR: #65 -- Remove unnecessary mocking in potts cell stem tests - - PR: #57 -- Add patch cell agent with random state rules - - PR: #56 -- Change source compatibility from 1.8 to 1.11 - - PR: #66 -- Migrate to JUnit 5 - - PR: #67 -- Add spotless autoformatter - - PR: #68 -- Unit tests for core utilities Colors class - - PR: #63 -- Adding tests for core utilities Solver class - - PR: #69 -- Improved tests for core utilities Color class - - PR: #73 -- Adding tests for core utilities Graph class - - PR: #64 -- Adding tests for core utilities Parameter class - - PR: #71 -- Update cell make method to return container - - PR: #74 -- Add support for different patch initialization schemes - - PR: #81 -- Update cell constructors to use container - - PR: #75 -- Add support for linked populations in setup file - - PR: #76 -- Refactor plane constructor to take Double3D instead of Int3D - - PR: #83 -- Add support for parameter distributions - - PR: #85 -- Pass initial glucose concentration as parameter for metabolism modules - - PR: #96 -- Fix passing in initial glucose as a parameter value - - PR: #99 -- Update workflows for changelog releases and Jekyll docs - - PR: #100 +# [v3.2.0](https://github.com/bagherilab/ARCADE/releases/tag/v3.2.0) - 2024-11-18 + +> Compare with [v3.1.4](https://github.com/bagherilab/ARCADE/compare/v3.1.4...v3.2.0) + +### Features + +- Update cell make method to return container by [@jessicasyu](https://github.com/jessicasyu) in [#74](https://github.com/bagherilab/ARCADE/pull/74) +- Update cell constructors to use container by [@jessicasyu](https://github.com/jessicasyu) in [#75](https://github.com/bagherilab/ARCADE/pull/75) +- Add support for linked populations in setup file by [@jessicasyu](https://github.com/jessicasyu) in [#76](https://github.com/bagherilab/ARCADE/pull/76) +- Add support for parameter distributions by [@jessicasyu](https://github.com/jessicasyu) in [#85](https://github.com/bagherilab/ARCADE/pull/85) + +#### Features: `patch` + +- Add support for initialization by percentage by [@jessicasyu](https://github.com/jessicasyu) in [#53](https://github.com/bagherilab/ARCADE/pull/53) +- Add patch cell agent with random state rules by [@jessicasyu](https://github.com/jessicasyu) in [#56](https://github.com/bagherilab/ARCADE/pull/56) +- Add support for different patch initialization schemes by [@jessicasyu](https://github.com/jessicasyu) in [#81](https://github.com/bagherilab/ARCADE/pull/81) +- Pass initial glucose concentration as parameter for metabolism modules by [@allison-li-1016](https://github.com/allison-li-1016) in [#96](https://github.com/bagherilab/ARCADE/pull/96) + +#### Features: `potts` + +- Added class key for potts populations by [@Jannetty](https://github.com/Jannetty) in [#11](https://github.com/bagherilab/ARCADE/pull/11) +- Make necessary PottsCell fields public, prepare for abstract setModule() function by [@Jannetty](https://github.com/Jannetty) in [#12](https://github.com/bagherilab/ARCADE/pull/12) +- Convert PottsCell to abstract class by [@Jannetty](https://github.com/Jannetty) in [#13](https://github.com/bagherilab/ARCADE/pull/13) +- Add support for splits with offset, direction, and split probability by [@Jannetty](https://github.com/Jannetty) in [#16](https://github.com/bagherilab/ARCADE/pull/16) +- Add custom plane splitvoxels by [@Jannetty](https://github.com/Jannetty) in [#46](https://github.com/bagherilab/ARCADE/pull/46) +- Refactor plane constructor to take Double3D instead of Int3D by [@Jannetty](https://github.com/Jannetty) in [#83](https://github.com/bagherilab/ARCADE/pull/83) + +### Bug fixes + +- Remove apoptosis checkpoint for potts cells by [@jessicasyu](https://github.com/jessicasyu) in [#18](https://github.com/bagherilab/ARCADE/pull/18) +- Replace instance of wildcard import of Module to prevent clash in Java 9 by [@cainja](https://github.com/cainja) in [#65](https://github.com/bagherilab/ARCADE/pull/65) +- Fix passing in initial glucose as a parameter value by [@allison-li-1016](https://github.com/allison-li-1016) in [#99](https://github.com/bagherilab/ARCADE/pull/99) + +### Tests + +- Remove unnecessary mocking in potts cell stem tests by [@jessicasyu](https://github.com/jessicasyu) in [#57](https://github.com/bagherilab/ARCADE/pull/57) +- Unit tests for core utilities Colors class by [@cainja](https://github.com/cainja) in [#63](https://github.com/bagherilab/ARCADE/pull/63) +- Adding tests for core utilities Solver class by [@cainja](https://github.com/cainja) in [#69](https://github.com/bagherilab/ARCADE/pull/69) +- Improved tests for core utilities Color class by [@cainja](https://github.com/cainja) in [#73](https://github.com/bagherilab/ARCADE/pull/73) +- Adding tests for core utilities Graph class by [@cainja](https://github.com/cainja) in [#64](https://github.com/bagherilab/ARCADE/pull/64) +- Adding tests for core utilities Parameter class by [@cainja](https://github.com/cainja) in [#71](https://github.com/bagherilab/ARCADE/pull/71) + +### Admin + +- Update workflows conditions for main and develop branches by [@jessicasyu](https://github.com/jessicasyu) in [#10](https://github.com/bagherilab/ARCADE/pull/10) +- Change source compatibility from 1.8 to 1.11 by [@jessicasyu](https://github.com/jessicasyu) in [#66](https://github.com/bagherilab/ARCADE/pull/66) +- Migrate to JUnit 5 by [@jessicasyu](https://github.com/jessicasyu) in [#67](https://github.com/bagherilab/ARCADE/pull/67) +- Add spotless autoformatter by [@jessicasyu](https://github.com/jessicasyu) in [#68](https://github.com/bagherilab/ARCADE/pull/68) +- Update workflows for changelog releases and Jekyll docs by [@jessicasyu](https://github.com/jessicasyu) in [#100](https://github.com/bagherilab/ARCADE/pull/100)