Grapevne

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0.4.0

What's Changed
* Bump jinja2 from 3.1.3 to 3.1.4 in /electron-app by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/249
* Bump jinja2 from 3.1.3 to 3.1.4 in /runner by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/248
* Bump jinja2 from 3.1.3 to 3.1.4 in /backend by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/247
* Bump werkzeug from 3.0.1 to 3.0.3 in /backend by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/246
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/244
* Update Electron to 29.4.2 by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/261
* Bump requests from 2.31.0 to 2.32.2 in /runner by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/262
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/260
* Migrate pip to poetry by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/263
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/264
* Bump braces from 3.0.2 to 3.0.3 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/266
* Add icons by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/267
* Replace eval with function evaluations by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/268
* Include Python std libs in environment distributed with GRAPEVNE by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/272
* Bump ws from 8.16.0 to 8.17.1 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/271
* Bump urllib3 from 2.0.7 to 2.2.2 in /builder by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/270
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/269
* Bump ws from 8.17.0 to 8.17.1 in /electron-app by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/273
* Add folder picker to repo URL selection by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/274
* Fix: inputbox looses focus during edits by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/275
* Update version upgrade documentation by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/276
* Add file picker for parameters of type 'file' by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/279
* (builder) Remove deprecated builder_web and ImportWorflow modules by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/283
* (nodemapper) Remove REST support by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/284
* Upgrade to electron 31 by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/285
* Workflow alerts by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/282
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/286
* Add manifest support and selectable configuration files by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/287
* Manifest fix by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/288
* Docs update by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/289
* Bump certifi from 2023.7.22 to 2024.7.4 in /builder by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/295
* Add dev container by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/297
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/299
* Suppress test configs in nodemapper by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/301
* Animate README.md workflow example by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/302
* Fix: Always quote YAML keys in config file by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/309
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/303
* Update documentation by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/312
* Bump requirejs from 2.3.6 to 2.3.7 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/313
* Fix broken links by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/316
* Enable lychee checking across all markdown files by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/315
* Add folder select to 'folder' items; autoformat nodemapper by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/314
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/317
* Migrate mambaforge to miniforge3 by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/320
* Use MUI Alert for email username warning by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/321
* Replace repository list with DataGrid by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/322
* Tidy-up log reports by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/323
* Upgrade dependencies by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/325
* Enable terminal by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/326
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/327
* Add vneyard module search page by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/328
* Bump axios from 1.7.3 to 1.7.4 in /electron-app by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/330
* Move settings into separate reducer slice by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/331
* Fix event listener memory leak by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/333
* Separate macOS-14 and macOS-12 builds by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/334
* Replace deprecated rmdirSync() with rmSync() by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/335
* Provide components overview by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/336
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/338
* Build workflows directly into local repositories by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/339
* Bump axios from 1.7.3 to 1.7.4 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/341
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/342
* Bump webpack from 5.93.0 to 5.94.0 in /electron-app by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/343
* Bump micromatch from 4.0.5 to 4.0.8 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/344
* Bump cryptography from 42.0.4 to 43.0.1 in /electron-app by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/345
* Add GitHub support by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/346
* Auto-load modules on launch by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/348
* Exclude _test rules on workflow imports by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/350
* Bump webpack from 5.93.0 to 5.94.0 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/351
* Bump express from 4.19.2 to 4.20.0 in /nodemapper by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/352
* Bump micromatch from 4.0.7 to 4.0.8 in /electron-app by dependabot in https://github.com/kraemer-lab/GRAPEVNE/pull/353
* Adopt sphinx 'book' theme by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/354
* Upgrade to Python 3.12 / Snakemake 8 by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/355
* Documentation update by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/358
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/359
* Deprecate macOS-12 runners by jsbrittain in https://github.com/kraemer-lab/GRAPEVNE/pull/361
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/kraemer-lab/GRAPEVNE/pull/362


**Full Changelog**: https://github.com/kraemer-lab/GRAPEVNE/compare/v0.3.1...v0.4.0

0.3.1

Usage documentation, including walk-through tutorials are available on the docs pages: [https://grapevne.readthedocs.io/en/latest/](https://grapevne.readthedocs.io/en/latest/).
Please report problems encountered on the [issues page](https://github.com/kraemer-lab/GRAPEVNE/issues).
Suggestions for new features, or ideas for future development, should be raised on the [discussions page](https://github.com/kraemer-lab/GRAPEVNE/discussions).

---

Updates for this build include
- An enhanced Module Editor

0.3.0

Usage documentation, including walk-through tutorials are available on the docs pages: [https://grapevne.readthedocs.io/en/latest/](https://grapevne.readthedocs.io/en/latest/).
Please report problems encountered on the [issues page](https://github.com/kraemer-lab/GRAPEVNE/issues).
Suggestions for new features, or ideas for future development, should be raised on the [discussions page](https://github.com/kraemer-lab/GRAPEVNE/discussions).

---

Updates for this build include
- Updated user-interface
- Template screen for creating New Modules
- Container support for workflow builds
- Parameter mapping between modules
- Code-signed binaries for MacOS builds
- Improved user feedback / reporting
- Optimisations
- Bug fixes

0.2.1

**We strongly recommend using the 'nightly build' which contains the latest features and bug-fixes.**

This version of GRAPEVNE is for testing and early adopters.
Usage documentation, including walk-through tutorials are available on the docs pages: [https://grapevne.readthedocs.io/en/latest/](https://grapevne.readthedocs.io/en/latest/).
Please report problems encountered on the [issues page](https://github.com/kraemer-lab/GRAPEVNE/issues).
Suggestions for new features, or ideas for future development, should be raised on the [discussions page](https://github.com/kraemer-lab/GRAPEVNE/discussions).

---

**NOTE** *If you are having difficulty running GRAPEVNE this is likely because we do not currently have code signing certificates for our builds. We are working to resolve this, but in the meantime it may be easier to follow the instructions to [build from source](https://grapevne.readthedocs.io/en/latest/getting_started/installation.html#developer-build).*

---

Updates for this build include
- [Add dev documentation on upgrading electron](https://github.com/kraemer-lab/GRAPEVNE/commit/239eabdc1a727aa820ef9918959b3a23dd38b6f7)
- [Peg chromedriver version in github workflows](https://github.com/kraemer-lab/GRAPEVNE/commit/54f352c2a85545c4a2e5f589d8dfad3d6dd97fd5)
- [Add text search to module list](https://github.com/kraemer-lab/GRAPEVNE/commit/cf65383ec864e533a6417b9721186ede0963631d)
- [Add delete listener when expanding modules](https://github.com/kraemer-lab/GRAPEVNE/commit/9e5266bcdb2cd344587784d49bf007e465c307ee)
- [Defer module placement on Canvas until configuration loaded](https://github.com/kraemer-lab/GRAPEVNE/commit/0056e5cd4e99322a349d5726952c2a7c40e34bd3)
- [Fix crash on module-list load errors](https://github.com/kraemer-lab/GRAPEVNE/commit/82e392dcdde6b83cbeb69e94a1dc49858d3fcfca)
- [Allow ports to be hidden in interface when namespaces begin with '_'](https://github.com/kraemer-lab/GRAPEVNE/commit/8d8dfd4c3e8b88585f28271e5af1d2df51cd2014)
- [Code tidy-up](https://github.com/kraemer-lab/GRAPEVNE/commit/bf79672e4373d6c617d16db1f1e36915c03d17ca)
- [Formalise electron/nodemapper api types](https://github.com/kraemer-lab/GRAPEVNE/commit/d5fe46b06bbaa771eaf8df8f4c5699f12eeeb0ff)
- [Improve typing (nodemapper)](https://github.com/kraemer-lab/GRAPEVNE/commit/55e6f30763304ec56e76f9e20d300d00f6fa7168)
- [Improve typing (electron-app)](https://github.com/kraemer-lab/GRAPEVNE/commit/094998b863791a5dbfa40a61324603b4eab414ea)
- [Update docs contribution README](https://github.com/kraemer-lab/GRAPEVNE/commit/1a9b2521cc69ea31aad393cae146c8a923407726)
- [Update docs and code tidy-up](https://github.com/kraemer-lab/GRAPEVNE/commit/19960e0926327ee0b5e2cf265c47a63cb2d08900)
- [Add nightly build workflow](https://github.com/kraemer-lab/GRAPEVNE/commit/d02ebccb46c4f87d19202ac019cec49fdea9b173)
- [Reinstate REST mechanism in nodemapper](https://github.com/kraemer-lab/GRAPEVNE/commit/919691e78e7f0de003656fd041e1bf077b6d8f8d)
- [Tidy-up CSS](https://github.com/kraemer-lab/GRAPEVNE/commit/b18ab14455dce0c6d2fb51df053c66b84cdc0bf9)

**Full Changelog**: https://github.com/kraemer-lab/GRAPEVNE/compare/v0.2.0...v0.2.1

nightly
Nightly builds are made available to allow users to stay up-to-date with recent changes in the codebase that have not yet formed part of an official release. These releases are rebuilt only when changes have been commited and accepted into the main branch of the codebase, so may not refresh every night. Nightly builds undergo post-build (end-to-end) testing, but remain more susceptible to bugs than formal releases as they represent on-going development of the project, and do not come with detailed changelog information.

---

**NOTE** *If you are having difficulty running GRAPEVNE this is likely because we do not currently have code signing certificates for our builds. We are working to resolve this, but in the meantime it may be easier to follow the instructions to [build from source](https://grapevne.readthedocs.io/en/latest/getting_started/installation.html#developer-build).*

---

GRAPEVNE usage documentation, including walk-through tutorials, are available on the docs pages: https://grapevne.readthedocs.io/en/latest/.
Please report problems encountered on the [issues page](https://github.com/kraemer-lab/GRAPEVNE/issues).
Suggestions for new features, or ideas for future development, should be raised on the [discussions page](https://github.com/kraemer-lab/GRAPEVNE/discussions).

0.2.0

This version of GRAPEVNE is for testing and early adopters.
Usage documentation, including walk-through tutorials are available on the docs pages: [https://grapevne.readthedocs.io/en/latest/](https://grapevne.readthedocs.io/en/latest/).
Please report problems encountered on the [issues page](https://github.com/kraemer-lab/GRAPEVNE/issues).
Suggestions for new features, or ideas for future development, should be raised on the [discussions page](https://github.com/kraemer-lab/GRAPEVNE/discussions).

---

Updates for this build include
- [Migrate flake8 to ruff](https://github.com/kraemer-lab/GRAPEVNE/commit/028c1e41c17661a82baa353b046399baca9e1081)
- [Add nodemapper lock file](https://github.com/kraemer-lab/GRAPEVNE/commit/48dc9916eda60305e4cbdb4429c6bce156d76bca)
- [Add Python 3.9 to CI](https://github.com/kraemer-lab/GRAPEVNE/commit/7708d62d4724be9614a9efc62e95042f69f9f8bf)
- [Add resizable panes](https://github.com/kraemer-lab/GRAPEVNE/commit/6a8c215722670780fdc2d36bf5dd318cf0c83ca4)
- [Add tabs to lower info pane](https://github.com/kraemer-lab/GRAPEVNE/commit/7accb3d45b10e9ca3c0aec27f86aab245fa207d9)
- [Move statusbar](https://github.com/kraemer-lab/GRAPEVNE/commit/29e2f846b500477fbb2f52b0a0b737fd8f33779a)
- [Enum for settings pane; improve error response when github rate limit exceeded](https://github.com/kraemer-lab/GRAPEVNE/commit/4ebb7a05719faf3fd5fcc27a4d6cebe4f6919060)
- [Provide Idle status](https://github.com/kraemer-lab/GRAPEVNE/commit/9f19a28f76a3336dd3a54358dd16f7737934e6f7)
- [Terminal resizes to container](https://github.com/kraemer-lab/GRAPEVNE/commit/4c547c86bd5b0324c3e88f1027f71a7489eb03ae)
- [Separate Log display and Terminal](https://github.com/kraemer-lab/GRAPEVNE/commit/eb6d1165fe1167efaf59cf3776bbbec1ac912ff3)
- [Migrate build and publish processes to Python3.11 for speedups](https://github.com/kraemer-lab/GRAPEVNE/commit/fcd9d61c018a569f9536d8c6fd43ec8ea3075287)
- [Disable pyinstaller one-file compression (performance optimisation)](https://github.com/kraemer-lab/GRAPEVNE/commit/c9d29de0d4c3ae356dbec48cd717838621ab3a3f)
- [Redirect workflow execution through native shell](https://github.com/kraemer-lab/GRAPEVNE/pull/105/commits/38c93ff9e22a1d66e3cbfae9476f64f37a75d64b)
- [Add selenium testing framework](https://github.com/kraemer-lab/GRAPEVNE/pull/105/commits/a976581b933ede7b6fddf7787c6de425d0b8242c)
- [Add end-to-end / post-build tests](https://github.com/kraemer-lab/GRAPEVNE/pull/105/commits/42a33136856070463e2c7acb1e0306a3fb401ab3)
- [Migrate config import from directory indexing to drag-into-scene (optimisation)](https://github.com/kraemer-lab/GRAPEVNE/pull/105/commits/1a39845686b4a23bf22834063abeabe926aec4c4)
- [Remove built-in conda](https://github.com/kraemer-lab/GRAPEVNE/pull/105/commits/1a39845686b4a23bf22834063abeabe926aec4c4)

0.1.1

This version of the software is for testing and early adopters.
Usage documentation, including walk-through tutorials are available on the docs pages: [https://grapevne.readthedocs.io/en/latest/](https://grapevne.readthedocs.io/en/latest/).
Please report problems encountered on the [issues page](https://github.com/kraemer-lab/GRAPEVNE/issues).
Discussion points, such as suggestions for new features, should be raised on the [discussions page](https://github.com/kraemer-lab/GRAPEVNE/discussions).

---

Updates for this build include
- [X] Bundle conda (mambaforge) with Windows installation
- [X] Snakemake cannot execute Conda when running standalone. Workflows run fine when GRAPEVNE is launched from the terminal.
- [X] This appears to be a PATH issue. Bundling mambaforge with GRAPEVNE resolves the issue. An option has been added to select between the bundled conda, and the system conda (although PATH is not necessarily inherited). Environment variables can instead be passed for runtime execition through GRAPEVNE, which are expecially useful for 1) launching conda in x64 mode, and 2) providing the conda binary path, e.g. "CONDA_SUBDIR=osx-64;PATH=/Path-to-local-conda"
- [X] Bundle conda with GRAPEVNE
- [X] Modify build instructions for bundling across different OSs
- [X] Node validation is failing. Problem was due to improper named argument passing of the snakemake launcher in the GRAPEVNE-builder system.
- [X] Don't create zip file during build & run, only during Build (optimisation; creating the zip file is slow)
- [X] Revert module listing code from python to nodejs (faster / more efficient)

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