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commit 877aac1 Author: Jeremy Sadler <[email protected]> Date: Thu Oct 3 01:14:21 2024 +0000 Cleaning up integrated changes commit 6dfd2c0 Author: Jeremy Sadler <[email protected]> Date: Fri Sep 27 22:32:48 2024 +0000 Making blocks more generic commit 164b179 Author: Jeremy Sadler <[email protected]> Date: Wed Sep 18 23:54:45 2024 +0000 Cleaned up some unnecessary methods. commit d42cae2 Author: Jeremy Sadler <[email protected]> Date: Sun Aug 18 00:00:00 2024 +0000 Fixing indexed variables commit 6c648ca Author: Jeremy Sadler <[email protected]> Date: Fri Aug 2 19:52:09 2024 +0000 Removing Julia pieces (for now) and more mypy cleanup commit 905e528 Author: Jeremy Sadler <[email protected]> Date: Thu Aug 1 20:06:31 2024 +0000 Factory classes for vars and constraints commit 8b18e97 Author: Jeremy Sadler <[email protected]> Date: Mon Jul 22 23:41:25 2024 +0000 Improving test coverage commit 069c3ef Author: Jeremy Sadler <[email protected]> Date: Mon Jul 15 21:49:18 2024 +0000 Adding tests commit fe433a3 Author: Jeremy Sadler <[email protected]> Date: Thu Jul 11 22:40:17 2024 +0000 Moving JuMP objects into their own file commit 79af205 Author: Jeremy Sadler <[email protected]> Date: Tue Jul 9 21:20:36 2024 +0000 Fixing an issue with linear trees commit 8c459f1 Author: Jeremy Sadler <[email protected]> Date: Tue Jul 9 19:43:38 2024 +0000 Making block-level modelling language choices percolate through generated variables and constraints commit e01a352 Author: Jeremy Sadler <[email protected]> Date: Mon Jul 8 23:58:06 2024 +0000 Including OmltExpr and OmltConstraints, spreading Omlt classes throughout the codebase. commit c5b866b Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 20:56:23 2024 +0000 linting (2) commit 98518f8 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 20:42:30 2024 +0000 linting (1) commit 6e5292d Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 13:33:16 2024 -0700 Delete .github/workflows/python-package.yml commit 7adf6e4 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 20:22:56 2024 +0000 adding abstract methods to expression interface commit 1a8c124 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 19:06:17 2024 +0000 further fixing commit 2764df1 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 18:58:51 2024 +0000 fixing variable initialization commit dd69394 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 18:47:01 2024 +0000 tidying var.py commit 6e141d4 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 6 18:22:30 2024 +0000 cleanup in expression.py commit ef0885b Author: Jeremy Sadler <[email protected]> Date: Wed Jun 5 20:01:17 2024 +0000 Including OmltExpr expressions for the OmltVars commit a64f6d7 Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:33:14 2024 -0700 Update setup.cfg commit 83ccaef Author: Jeremy Sadler <[email protected]> Date: Sun Apr 21 18:05:47 2024 -0700 Update setup.cfg commit 63f0e5f Author: Jeremy Sadler <[email protected]> Date: Mon Mar 18 22:41:10 2024 -0700 Create python-package.yml commit ea1154c Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:45:42 2024 -0700 Update main.yml commit 7eecd26 Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:44:36 2024 -0700 Update main.yml commit f844c2d Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:42:42 2024 -0700 Update main.yml commit 9ab7fc3 Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:40:35 2024 -0700 Update main.yml commit ab25542 Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:39:03 2024 -0700 Update setup.cfg for Keras version commit 61c8daf Author: Jeremy Sadler <[email protected]> Date: Fri May 17 11:38:30 2024 -0700 Update Python versions in main.yml commit 0ae5b75 Author: Jeremy Sadler <[email protected]> Date: Mon Apr 22 00:35:06 2024 +0000 Fixing some whitespace linting commit cbcefcb Author: Jeremy Sadler <[email protected]> Date: Mon Apr 22 00:20:48 2024 +0000 restoring action workflow file commit c911bb0 Author: Jeremy Sadler <[email protected]> Date: Mon Apr 22 00:16:13 2024 +0000 removing tweaked action file commit c929d54 Author: Jeremy Sadler <[email protected]> Date: Sat Apr 20 23:21:18 2024 -0700 Fix Keras version at 2.9 Keras 3 requires models to have the .keras file format. Going forward we should probably update the test models to use this format, but to unblock I'm holding back the Keras version. commit 738f7fd Author: Jeremy Sadler <[email protected]> Date: Sat Apr 20 23:01:19 2024 -0700 Use tensorflow-cpu for testing to save space commit c4ab257 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 17:43:43 2024 -0700 Make test for JuMP variables conditional on presence of JuMP commit 09c9945 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 17:35:36 2024 -0700 Update var.py commit 991dd37 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 17:29:08 2024 -0700 Update var.py commit b57848a Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 16:58:01 2024 -0700 Getting dependencies lined up correctly commit 1490f42 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 16:52:08 2024 -0700 Removing duplicate line commit ef42ba3 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 19:19:29 2024 +0000 Cleaning up variables - MOI dependency commit fa62661 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 19:19:29 2024 +0000 Cleaning up variables - MOI dependency commit 5dae012 Author: Jeremy Sadler <[email protected]> Date: Fri Apr 19 19:19:29 2024 +0000 Cleaning up variables commit 29b89bc Author: Jeremy Sadler <[email protected]> Date: Mon Apr 8 18:28:49 2024 +0000 Implementing JuMP format scalar and indexed variables. commit 3c20611 Author: Jeremy Sadler <[email protected]> Date: Tue Mar 19 00:58:12 2024 -0700 Removing ipopt from CI workflow commit 6e36c47 Author: Jeremy Sadler <[email protected]> Date: Mon Mar 18 22:16:04 2024 -0700 Create main.yml copying CI workflow over commit 9178a1b Author: Jeremy Sadler <[email protected]> Date: Tue Mar 19 02:05:50 2024 +0000 OmltVar wrapper class commit 0e86c9f Author: Jeremy Sadler <[email protected]> Date: Tue Mar 19 02:05:50 2024 +0000 OmltVar wrapper class commit 7515f57 Author: Jeremy Sadler <[email protected]> Date: Mon Jun 24 05:29:48 2024 +0000 Fixing mypy typing errors commit 7bb6f0d Author: Jeremy Sadler <[email protected]> Date: Mon Jun 24 05:29:48 2024 +0000 Fixing mypy typing errors commit ce6a944 Author: Jeremy Sadler <[email protected]> Date: Sun Jun 23 00:27:31 2024 +0000 Fixing ruff linting errors. commit 8a44751 Author: Jeremy Sadler <[email protected]> Date: Thu Jun 13 22:08:18 2024 +0000 Fixing initial batch of ruff errors commit 0379ec6 Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:32:52 2024 +0100 Add back for mypy commit 2b0f991 Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:31:55 2024 +0100 remove unnecessary things commit 551530d Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:21:20 2024 +0100 wip commit 4c40b8b Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:20:48 2024 +0100 thing commit 8042185 Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:20:00 2024 +0100 wip commit fd4ef72 Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:18:08 2024 +0100 add link commit 5492ddb Author: Lukas Turcani <[email protected]> Date: Thu May 30 18:03:26 2024 +0100 wip commit 3d056e9 Author: Lukas Turcani <[email protected]> Date: Thu May 30 12:57:50 2024 +0100 Add thing commit 0790eb8 Author: Lukas Turcani <[email protected]> Date: Thu May 30 11:37:53 2024 +0100 Thing commit e735707 Author: Lukas Turcani <[email protected]> Date: Thu May 30 11:34:35 2024 +0100 Add conda commit cc07a30 Author: Lukas Turcani <[email protected]> Date: Wed May 29 16:16:38 2024 +0100 wip commit c58ec68 Author: Lukas Turcani <[email protected]> Date: Tue May 28 22:41:59 2024 +0100 wip commit 0a2671f Author: Lukas Turcani <[email protected]> Date: Tue May 28 22:20:10 2024 +0100 Add workflows commit 321a2e2 Author: Jiří Němeček <[email protected]> Date: Sat Aug 24 19:15:47 2024 +0200 Fixing 404 errors of links to notebooks in the documentation (cog-imperial#143) I assume that the notebooks have been moved, but the documentation links did not reflect that **Legal Acknowledgement**\ By contributing to this software project, I agree my contributions are submitted under the BSD license. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer. commit caebfc4 Author: Andrew Lee <[email protected]> Date: Thu Aug 22 13:28:24 2024 -0400 Replace _BlockData with BlockData (cog-imperial#144) Pyomo recently made ComponentData classes public (Pyomo/pyomo#3221) which will be part of the upcoming release. Currently, this causes the following error to occur in OMLT: ``` TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases ``` The Pyomo team is working to try to address this issue, however OMLT should update its code to address this as otherwise deprecation warnings will be emitted when using the old class names. The fix is to replace all instances of `_BlockData` with `BlockData` (just removing the underscore) - this applies to any other instance of Pyomo component data objects as well (although I could only find 2 instances of these in the OMLT code). **Legal Acknowledgement**\ By contributing to this software project, I agree my contributions are submitted under the BSD license. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer. Co-authored-by: jalving <[email protected]> commit c6d274f Author: Emma Johnson <[email protected]> Date: Thu Aug 22 10:56:10 2024 -0400 Add tolerance to enforce strict inequalities in linear tree formulations (cog-imperial#163) This PR adds a tolerance at which to enforce ``strict'' inequalities in linear model trees: That is, the right branch will require that the feature value be greater than or equal to the bound plus this tolerance (epsilon). This means that users can tune epsilon in order to ensure that the MIP solution will match the tree prediction. Additionally, the PR simplifies the implementation of the hybrid bigm linear tree formulation by using two modern pyomo.gdp transformations. This does mean that the linear tree formulations will rely on pyomo>=6.7.1 though, if that's okay. **Legal Acknowledgement**\ By contributing to this software project, I agree my contributions are submitted under the BSD license. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer. --------- Co-authored-by: Emma Johnson <[email protected]> commit d43643a Author: Lukas Turcani <[email protected]> Date: Tue Aug 20 23:53:51 2024 +0100 Clean up package boilerplate (cog-imperial#149) This PR does a couple of things to clean up the boilerplate related to packaging OMLT, see sections below for detailed explanations of the changes. * Remove `setup.cfg` , `setup.py`, `docs/requirements.txt`, `tox.ini` in favour of `pyproject.toml`. * Place `conda` requirements into `environment.yml` * Create new workflows `tests.yml` and `publish_release.yml` * Add quality checks using `ruff`, `mypy`, `doctest` * Use `just` for developer experience * Updated the `Development` section of `README` to talk about `just` * Clean up `conf.py` * Move `pull_request_template.md` * Allow publishing of package to pypi by pushing a new version tag # Other comments * consider internal package structure * force squash merge of PRs - this keeps git history for the `main` branch nice and clean # Using `pyproject.toml` `pyrpoject.toml` is the simplest way to provide package metadata for a Python package. It is easy to read and also provides sections for configurating tools such as `pytest`, `ruff` and `mypy` all in one place. It works seamlessly with the modern Python ecosystem. I set up `pyproject.toml` to automactically detect the version of the code from git tags. No need to duplicate version numbers across the repo. Just add a new tag and everything will be updated. In addition, when a new git tag is pushed to the GitHub repo, the new `publish_release` workflow will be triggered and a new PYPI version released. (See more on this below). I also set it up so that the version is automatically added to a file called `src/omlt/_version.py` which holds the `__version__` variable. this file is autogenerated and therefore added to `.gitignore`. The `__version__` veriable is then re-exported in `src/omlt/__init__.py` so that our users have access to it. I tried to perserve all the information stored in the `setup.cfg` and other deleted files -- let me know if there is something i missed! ## Optional dependencies The `pyproject.toml` file allows the creation of optional dependencies. For example, our users can install ```bash pip install omlt[keras] # or pip install omlt[torch] # or pip install omlt[linear-tree,keras-gpu] ``` Ofc any combination of optional dependencies is valid too. This allows our users to install the dependencies specific to their use case. Note that: * I made `onnx` and `onnxruntime` a required dependency because from my understanding it is almost always used * I added an optinoal dependency set called `dev` which developers can use to install all developer tools and all dependencies -- you need this to run all the tests for example * There is also `dev-gpu` which installs the GPU version of tensorflow in case the developer has a GPU The available optional dependencies are: * `linear-tree`, installs the linear tree dependency * `keras`, installs tensorflow and keras * `keras-gpu`, installs tensorflow for the gpu and keras * `torch`, installs torch and torch geometric * `dev-tools` - this is not to be used directly but allows easy re-use of dev tools in other optional dependencies, namely dev and dev-gpu * `docs` - installs dependencies required to compile docs * `dev` - dependecies needed for developing the project, such tooling * `dev-gpu` - same as dev but installed with gpu support Our documentation probably needs to be updated to tell users they wanna install omlt with some combination of `linear-tree`, `keras`, `keras-gpu`, `torch` optional dependencies depending on what features of the package they are using # Quality checks with `ruff`, `mypy` and `doctest` I've enabled `ruff`, `mypy` and `doctest`. Currently there are no doctests, but its good to have it set up so that it runs in case any are added in the future. Both `ruff` and `mypy` are failing because there are a number of things which need to fixed. For both `ruff` and `mypy` I have disabled some checks which it would be good to enable eventually but are probably a fair amount of work to fix -- these have comments in `pyproject.toml`. The remaining failing checks are ones which I would reccomend fixing ASAP. There's two approaches, merge now and fix these errors later. Or keep a separate branch where these are incrementally fixed. Up to you to decide what you prefer. I told ruff to check for `google` style docstrings. I think these are the best because they have good readbility and work the best with type hints in my opinion. # Using `just` instead of `tox` https://github.com/casey/just is a simple command runner. It allows the developers to define and re-use common operations, for example I can define a `check` recipe and then run ```bash just check ``` in my command line and it will run all the tests. The beauty of this is that `just` is extremely simple. If you read the file its basically a sequence of bash instructions for each recipe. This makes the `recipes` really transparent, and easy to understand, and works as code-as-documentation. Users can just read the recipe and run the commands one by one to get the same effect without having `just` installed. There is no magic which helps with debugging issues. It's also language agnostic. `just` comes as a small stand-alone binary, which makes it a very non-intrusive tool to have on your computer that does not need any dependencies. The downside is that it does not provide automatic management for Python environments, which I belive tox does provide. The other side of this is that we allow developers to use their favorite tools for managing venvs rather than proscribing certain tools for this repo. (the difference with `just` being that it is essentially optional tool and also serving as documentation) I may be overly opinionated on this one, so feel free to push back. # Cleaning up `docs/conf.py` I removed a bunch of the commented out code. This makes it easier to see what the configuration is and also prevents the commented out options from becoming out of date when a new release of sphinx is made. # Moving `pull_request_template.md` I moved this into the `.github` folder because it is GitHub configuration. Very optional, but makes more sense to me. # `readthedocs` automated action this guide https://docs.readthedocs.io/en/stable/guides/pull-requests.html shows how to set it up. requires admin permissions on readthedocs -- can jump on a call to help with this # publishing with to `PYPI` with a git tag for this an API key for PYPI needs to be created and added to the repos secrets -- can jump on a call to help with this # consider `_internal` package structure One way to make it easier to manage private vs public code in a repository is to create an `_internal` folder where all the code goes. This way all code can be shared easily and moved between modules and its by default private, so changes to internal code does not break users. Public modules then just re-export code in the `_internal` submodules. You can see an example of this structure here https://github.com/lukasturcani/stk. Not a huge issue but I find it very helpful for managing what things are actually exposed to users the code-base grows. **Legal Acknowledgement**\ By contributing to this software project, I agree my contributions are submitted under the BSD license. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer. --------- Co-authored-by: Jeremy Sadler <[email protected]>
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