{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":373502457,"defaultBranch":"main","name":"OMLT","ownerLogin":"cog-imperial","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-06-03T12:39:38.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/30658188?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1724684614.0","currentOid":""},"activityList":{"items":[{"before":"caebfc411a4e3bb43db57cf5c2082e2c7e5e41d0","after":"321a2e213df0a4707184595c399aa52e9bdad69b","ref":"refs/heads/main","pushedAt":"2024-08-24T17:15:47.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"jalving","name":"Jordan Jalving","path":"/jalving","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16785413?s=80&v=4"},"commit":{"message":"Fixing 404 errors of links to notebooks in the documentation (#143)\n\nI assume that the notebooks have been moved, but the documentation links\r\ndid not reflect that\r\n\r\n**Legal Acknowledgement**\\\r\nBy contributing to this software project, I agree my contributions are\r\nsubmitted under the BSD license.\r\nI represent I am authorized to make the contributions and grant the\r\nlicense.\r\nIf my employer has rights to intellectual property that includes these\r\ncontributions,\r\nI represent that I have received permission to make contributions and\r\ngrant the required license on behalf of that employer.","shortMessageHtmlLink":"Fixing 404 errors of links to notebooks in the documentation (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2270565539\" data-permission-text=\"Title is private\" data-url=\"https://github.com/cog-imperial/OMLT/issues/143\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/cog-imperial/OMLT/pull/143/hovercard\" href=\"https://github.com/cog-imperial/OMLT/pull/143\">#143</a>)"}},{"before":"c6d274fbc2ce078827dbabe1e38efeec952eb26d","after":"caebfc411a4e3bb43db57cf5c2082e2c7e5e41d0","ref":"refs/heads/main","pushedAt":"2024-08-22T17:28:25.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"jalving","name":"Jordan Jalving","path":"/jalving","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16785413?s=80&v=4"},"commit":{"message":"Replace _BlockData with BlockData (#144)\n\nPyomo recently made ComponentData classes public\r\n(https://github.com/Pyomo/pyomo/pull/3221) which will be part of the\r\nupcoming release. 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This means that users can tune epsilon in order to ensure\r\nthat the MIP solution will match the tree prediction.\r\n\r\nAdditionally, the PR simplifies the implementation of the hybrid bigm\r\nlinear tree formulation by using two modern pyomo.gdp transformations.\r\nThis does mean that the linear tree formulations will rely on\r\npyomo>=6.7.1 though, if that's okay.\r\n\r\n**Legal Acknowledgement**\\\r\nBy contributing to this software project, I agree my contributions are\r\nsubmitted under the BSD license.\r\nI represent I am authorized to make the contributions and grant the\r\nlicense.\r\nIf my employer has rights to intellectual property that includes these\r\ncontributions,\r\nI represent that I have received permission to make contributions and\r\ngrant the required license on behalf of that employer.\r\n\r\n---------\r\n\r\nCo-authored-by: Emma Johnson <emma58@users.noreply.github.com>","shortMessageHtmlLink":"Add tolerance to enforce strict inequalities in linear tree formulati…"}},{"before":"e60563859a66ac5dd3348bf1763de57eec95171e","after":"d43643a474bca8da9fbfdf53a83cb1a51e4f3780","ref":"refs/heads/main","pushedAt":"2024-08-20T22:53:51.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"jalving","name":"Jordan Jalving","path":"/jalving","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16785413?s=80&v=4"},"commit":{"message":"Clean up package boilerplate (#149)\n\nThis PR does a couple of things to clean up the boilerplate related to\r\npackaging OMLT, see sections below for detailed explanations of the\r\nchanges.\r\n\r\n* Remove `setup.cfg` , `setup.py`, `docs/requirements.txt`, `tox.ini` in\r\nfavour of `pyproject.toml`.\r\n* Place `conda` requirements into `environment.yml` \r\n* Create new workflows `tests.yml` and `publish_release.yml`\r\n* Add quality checks using `ruff`, `mypy`, `doctest`\r\n* Use `just` for developer experience\r\n* Updated the `Development` section of `README`  to talk about `just` \r\n* Clean up `conf.py`\r\n* Move `pull_request_template.md`\r\n* Allow publishing of package to pypi by pushing a new version tag\r\n\r\n# Other comments\r\n\r\n* consider internal package structure\r\n* force squash merge of PRs - this keeps git history for the `main`\r\nbranch nice and clean\r\n\r\n# Using `pyproject.toml`\r\n\r\n`pyrpoject.toml` is the simplest way to provide package metadata for a\r\nPython package. It is easy to read and also provides sections for\r\nconfigurating tools such as `pytest`, `ruff` and `mypy` all in one\r\nplace. It works seamlessly with the modern Python ecosystem.\r\n\r\nI set up `pyproject.toml` to automactically detect the version of the\r\ncode from git tags. No need to duplicate version numbers across the\r\nrepo. Just add a new tag and everything will be updated. In addition,\r\nwhen a new git tag is pushed to the GitHub repo, the new\r\n`publish_release` workflow will be triggered and a new PYPI version\r\nreleased. (See more on this below).\r\n\r\nI also set it up so that the version is automatically added to a file\r\ncalled `src/omlt/_version.py` which holds the `__version__` variable.\r\nthis file is autogenerated and therefore added to `.gitignore`. The\r\n`__version__` veriable is then re-exported in `src/omlt/__init__.py` so\r\nthat our users have access to it.\r\n\r\nI tried to perserve all the information stored in the `setup.cfg` and\r\nother deleted files -- let me know if there is something i missed!\r\n\r\n## Optional dependencies\r\n\r\nThe `pyproject.toml` file allows the creation of optional dependencies.\r\nFor example, our users can install\r\n\r\n```bash\r\npip install omlt[keras]\r\n# or\r\npip install omlt[torch]\r\n# or\r\npip install omlt[linear-tree,keras-gpu]\r\n```\r\nOfc any combination of optional dependencies is valid too. This allows\r\nour users to install the dependencies specific to their use case. Note\r\nthat:\r\n\r\n* I made `onnx` and `onnxruntime` a required dependency because from my\r\nunderstanding it is almost always used\r\n* I added an optinoal dependency set called `dev` which developers can\r\nuse to install all developer tools and all dependencies -- you need this\r\nto run all the tests for example\r\n* There is also `dev-gpu` which installs the GPU version of tensorflow\r\nin case the developer has a GPU\r\n\r\nThe available optional dependencies are:\r\n\r\n* `linear-tree`, installs the linear tree dependency\r\n* `keras`, installs tensorflow and keras\r\n* `keras-gpu`, installs tensorflow for the gpu and keras\r\n* `torch`, installs torch and torch geometric\r\n* `dev-tools` - this is not to be used directly but allows easy re-use\r\nof dev tools in other optional dependencies, namely dev and dev-gpu\r\n* `docs` - installs dependencies required to compile docs \r\n* `dev` - dependecies needed for developing the project, such tooling\r\n* `dev-gpu` - same as dev but installed with gpu support\r\n\r\nOur documentation probably needs to be updated to tell users they wanna\r\ninstall omlt with some combination of `linear-tree`, `keras`,\r\n`keras-gpu`, `torch` optional dependencies depending on what features of\r\nthe package they are using\r\n\r\n# Quality checks with `ruff`, `mypy` and `doctest`\r\n\r\nI've enabled `ruff`, `mypy` and `doctest`. Currently there are no\r\ndoctests, but its good to have it set up so that it runs in case any are\r\nadded in the future.\r\n\r\nBoth `ruff` and `mypy` are failing because there are a number of things\r\nwhich need to fixed. For both `ruff` and `mypy` I have disabled some\r\nchecks which it would be good to enable eventually but are probably a\r\nfair amount of work to fix -- these have comments in `pyproject.toml`.\r\nThe remaining failing checks are ones which I would reccomend fixing\r\nASAP. There's two approaches, merge now and fix these errors later. Or\r\nkeep a separate branch where these are incrementally fixed. Up to you to\r\ndecide what you prefer.\r\n\r\nI told ruff to check for `google` style docstrings. I think these are\r\nthe best because they have good readbility and work the best with type\r\nhints in my opinion.\r\n\r\n# Using `just` instead of `tox`\r\n\r\nhttps://github.com/casey/just is a simple command runner. It allows the\r\ndevelopers to define and re-use common operations, for example I can\r\ndefine a `check` recipe and then run\r\n\r\n```bash\r\njust check\r\n```\r\n\r\nin my command line and it will run all the tests. The beauty of this is\r\nthat `just` is extremely simple. If you read the file its basically a\r\nsequence of bash instructions for each recipe. This makes the `recipes`\r\nreally transparent, and easy to understand, and works as\r\ncode-as-documentation. Users can just read the recipe and run the\r\ncommands one by one to get the same effect without having `just`\r\ninstalled. There is no magic which helps with debugging issues. It's\r\nalso language agnostic. `just` comes as a small stand-alone binary,\r\nwhich makes it a very non-intrusive tool to have on your computer that\r\ndoes not need any dependencies.\r\n\r\nThe downside is that it does not provide automatic management for Python\r\nenvironments, which I belive tox does provide. The other side of this is\r\nthat we allow developers to use their favorite tools for managing venvs\r\nrather than proscribing certain tools for this repo. (the difference\r\nwith `just` being that it is essentially optional tool and also serving\r\nas documentation)\r\n\r\nI may be overly opinionated on this one, so feel free to push back.\r\n\r\n# Cleaning up `docs/conf.py`\r\n\r\nI removed a bunch of the commented out code. This makes it easier to see\r\nwhat the configuration is and also prevents the commented out options\r\nfrom becoming out of date when a new release of sphinx is made.\r\n\r\n# Moving `pull_request_template.md`\r\n\r\nI moved this into the `.github` folder because it is GitHub\r\nconfiguration. Very optional, but makes more sense to me.\r\n\r\n# `readthedocs` automated action\r\n\r\nthis guide\r\nhttps://docs.readthedocs.io/en/stable/guides/pull-requests.html shows\r\nhow to set it up. requires admin permissions on readthedocs -- can jump\r\non a call to help with this\r\n\r\n# publishing with to `PYPI` with a git tag\r\n\r\nfor this an API key for PYPI needs to be created and added to the repos\r\nsecrets -- can jump on a call to help with this\r\n\r\n# consider `_internal` package structure\r\n\r\nOne way to make it easier to manage private vs public code in a\r\nrepository is to create an `_internal` folder where all the code goes.\r\nThis way all code can be shared easily and moved between modules and its\r\nby default private, so changes to internal code does not break users.\r\nPublic modules then just re-export code in the `_internal` submodules.\r\nYou can see an example of this structure here\r\nhttps://github.com/lukasturcani/stk. 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