Adding sanity check to tutorial #38
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Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v1.1.0a0...v2.2.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com>
Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.12.1...24.1.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com>
Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.39.1 to 0.40.0. - [Release notes](https://github.com/mkdocstrings/griffe/releases) - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/griffe@0.39.1...0.40.0) --- updated-dependencies: - dependency-name: griffe dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com>
Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.5 to 9.5.7. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.5.5...9.5.7) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com>
…to dev pulling from remote
…to dev bringing local dev up to remote HEAD
…hat relates binding strength to purturbation effect
cmatKhan
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Apr 30, 2024
* Bump codecov/codecov-action from 3 to 4 (#13) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update torch requirement from ^1.0.2 to ^2.2.0 (#12) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v1.1.0a0...v2.2.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Bump actions/checkout from 2 to 4 (#2) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump actions/setup-python from 2 to 5 (#1) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Update black requirement from ^23.12.1 to ^24.1.1 (#9) Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.12.1...24.1.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump griffe from 0.39.1 to 0.40.0 (#11) Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.39.1 to 0.40.0. - [Release notes](https://github.com/mkdocstrings/griffe/releases) - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/griffe@0.39.1...0.40.0) --- updated-dependencies: - dependency-name: griffe dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump mkdocs-material from 9.5.5 to 9.5.7 (#14) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.5 to 9.5.7. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.5.5...9.5.7) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * updating pytest CI to include multiple OS * fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * correcting error in data generation regarding tf indexing * adding another cell to the tutorial to show how to use the function that relates binding strength to purturbation effect * improved plot for the tf effect on perturbation * changing colors for aesthetics * changing colors for aesthetics x2 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com>
cmatKhan
added a commit
that referenced
this pull request
May 1, 2024
* fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * Fix binding effects (#27) * Bump codecov/codecov-action from 3 to 4 (#13) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update torch requirement from ^1.0.2 to ^2.2.0 (#12) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v1.1.0a0...v2.2.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Bump actions/checkout from 2 to 4 (#2) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump actions/setup-python from 2 to 5 (#1) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Update black requirement from ^23.12.1 to ^24.1.1 (#9) Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.12.1...24.1.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump griffe from 0.39.1 to 0.40.0 (#11) Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.39.1 to 0.40.0. - [Release notes](https://github.com/mkdocstrings/griffe/releases) - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/griffe@0.39.1...0.40.0) --- updated-dependencies: - dependency-name: griffe dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump mkdocs-material from 9.5.5 to 9.5.7 (#14) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.5 to 9.5.7. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.5.5...9.5.7) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * updating pytest CI to include multiple OS * fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * major re-write of probability_models and associated documentation * fixing typo in generate_pert_effects docstring; adding error handling on Callable * removing python 3.10 from CI --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * fix torch install issue for macs, closes #18 (#19) * Simple linear model, Synthetic data DataLoader, a couple scripts, lots of setup (#31) * installed lightning and outlined file structure * forgot to outline testing files * created incredibly basic linear model * made basic outline for data loader * outlined idea for processin dataset * wrote script to run simple model experiment * fixed bug in gitignore that caused tmp files to not be ignored * simple model is working * added basic script to load in model checkpoint and print off params and hyperparams * added logic for checkpointing * added support for logging with tensorboard * now supports csv and tensorboard logging * added typing to simple model * added type hints to dataLoader * added type hinting to simple_model_synthetic_data.py * rewrote to use new data generation functions * added assertions for type checking and valid ranges for params / inputs * docstrings added * added new docs to mkdocs * added tests for simple model and synthetic data loader * now passes all pre-commit checks * addressing all comments on PR * add all log folders to gitignore * formatting * Adding sanity check to tutorial (#38) * Bump codecov/codecov-action from 3 to 4 (#13) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update torch requirement from ^1.0.2 to ^2.2.0 (#12) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v1.1.0a0...v2.2.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Bump actions/checkout from 2 to 4 (#2) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump actions/setup-python from 2 to 5 (#1) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Update black requirement from ^23.12.1 to ^24.1.1 (#9) Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.12.1...24.1.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump griffe from 0.39.1 to 0.40.0 (#11) Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.39.1 to 0.40.0. - [Release notes](https://github.com/mkdocstrings/griffe/releases) - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/griffe@0.39.1...0.40.0) --- updated-dependencies: - dependency-name: griffe dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump mkdocs-material from 9.5.5 to 9.5.7 (#14) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.5 to 9.5.7. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.5.5...9.5.7) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * updating pytest CI to include multiple OS * fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * correcting error in data generation regarding tf indexing * adding another cell to the tutorial to show how to use the function that relates binding strength to purturbation effect * improved plot for the tf effect on perturbation * changing colors for aesthetics * changing colors for aesthetics x2 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Fixing (#68) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * Adding in files (#70) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * uncomment tests * pyproject now matches * fix indent error in tests * added the dataLoaders * add in models * formatting * linting * Rewrite generate_in_silico_data.ipynb to match new methods we are using, also delete old unused mean adjustment function (#73) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * uncomment tests * pyproject now matches * fix indent error in tests * added the dataLoaders * add in models * formatting * linting * delete old unused adjustment function * rewrite in silico data generation tutorial notebook to match current methods * cleaning up generate_perturbation_effects * passing precommit * Cleaning up notebooks (#74) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * uncomment tests * pyproject now matches * fix indent error in tests * added the dataLoaders * add in models * formatting * linting * delete old unused adjustment function * rewrite in silico data generation tutorial notebook to match current methods * cleaning up generate_perturbation_effects * passing precommit * cleaned up hyperparameter sweep notebook and added better explanations * added dataset directory and logs to gitignore * added notebook for visualizing data generation methods * finished adding in data visualization experiment * renamed loss to mse in simpleModel * finished the data generation method experiment notebook, added in experiment comparing model performance * added and cleaned up the testing_model_metrics notebook * real data loader choice of perturbation effect dataset is now a param you can pass in * added lightning crash course notebook * linting * removing experiments from src dir; updating docs md and index files (#76) * removing experiments from src dir; updating docs md and index files * fixing stupid mkdocs docs text added to readme * setting version to 0.0.1 * fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * Fix binding effects (#27) * Bump codecov/codecov-action from 3 to 4 (#13) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update torch requirement from ^1.0.2 to ^2.2.0 (#12) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v1.1.0a0...v2.2.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Bump actions/checkout from 2 to 4 (#2) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump actions/setup-python from 2 to 5 (#1) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Update black requirement from ^23.12.1 to ^24.1.1 (#9) Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.12.1...24.1.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump griffe from 0.39.1 to 0.40.0 (#11) Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.39.1 to 0.40.0. - [Release notes](https://github.com/mkdocstrings/griffe/releases) - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/griffe@0.39.1...0.40.0) --- updated-dependencies: - dependency-name: griffe dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump mkdocs-material from 9.5.5 to 9.5.7 (#14) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.5 to 9.5.7. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.5.5...9.5.7) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * updating pytest CI to include multiple OS * fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * major re-write of probability_models and associated documentation * fixing typo in generate_pert_effects docstring; adding error handling on Callable * removing python 3.10 from CI --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * fix torch install issue for macs, closes #18 (#19) * Simple linear model, Synthetic data DataLoader, a couple scripts, lots of setup (#31) * installed lightning and outlined file structure * forgot to outline testing files * created incredibly basic linear model * made basic outline for data loader * outlined idea for processin dataset * wrote script to run simple model experiment * fixed bug in gitignore that caused tmp files to not be ignored * simple model is working * added basic script to load in model checkpoint and print off params and hyperparams * added logic for checkpointing * added support for logging with tensorboard * now supports csv and tensorboard logging * added typing to simple model * added type hints to dataLoader * added type hinting to simple_model_synthetic_data.py * rewrote to use new data generation functions * added assertions for type checking and valid ranges for params / inputs * docstrings added * added new docs to mkdocs * added tests for simple model and synthetic data loader * now passes all pre-commit checks * addressing all comments on PR * add all log folders to gitignore * formatting * Adding sanity check to tutorial (#38) * Bump codecov/codecov-action from 3 to 4 (#13) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update torch requirement from ^1.0.2 to ^2.2.0 (#12) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v1.1.0a0...v2.2.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Bump actions/checkout from 2 to 4 (#2) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump actions/setup-python from 2 to 5 (#1) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Update black requirement from ^23.12.1 to ^24.1.1 (#9) Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.12.1...24.1.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump griffe from 0.39.1 to 0.40.0 (#11) Bumps [griffe](https://github.com/mkdocstrings/griffe) from 0.39.1 to 0.40.0. - [Release notes](https://github.com/mkdocstrings/griffe/releases) - [Changelog](https://github.com/mkdocstrings/griffe/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/griffe@0.39.1...0.40.0) --- updated-dependencies: - dependency-name: griffe dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * Bump mkdocs-material from 9.5.5 to 9.5.7 (#14) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.5.5 to 9.5.7. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.5.5...9.5.7) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chase.mateusiak@gmail.com> * updating pytest CI to include multiple OS * fixing readme badge order; adding codecove badge (#5) resolves #4 * removing plural from gene_populations; resolves #6 (#7) * correcting error in data generation regarding tf indexing * adding another cell to the tutorial to show how to use the function that relates binding strength to purturbation effect * improved plot for the tf effect on perturbation * changing colors for aesthetics * changing colors for aesthetics x2 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com> * Fixing (#68) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * Adding in files (#70) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * uncomment tests * pyproject now matches * fix indent error in tests * added the dataLoaders * add in models * formatting * linting * Rewrite generate_in_silico_data.ipynb to match new methods we are using, also delete old unused mean adjustment function (#73) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * uncomment tests * pyproject now matches * fix indent error in tests * added the dataLoaders * add in models * formatting * linting * delete old unused adjustment function * rewrite in silico data generation tutorial notebook to match current methods * cleaning up generate_perturbation_effects * passing precommit * Cleaning up notebooks (#74) * need to update pre commit config since were now using python3.11 * added in current generate_data file, commented out test_generate_data, also had to add relation_classes * fix lint issue * attempt to fix by downgrading default language version * new attempt to fix by changing specified torch version * try limiting to install torch beneath 2.3.0 * uncomment tests * pyproject now matches * fix indent error in tests * added the dataLoaders * add in models * formatting * linting * delete old unused adjustment function * rewrite in silico data generation tutorial notebook to match current methods * cleaning up generate_perturbation_effects * passing precommit * cleaned up hyperparameter sweep notebook and added better explanations * added dataset directory and logs to gitignore * added notebook for visualizing data generation methods * finished adding in data visualization experiment * renamed loss to mse in simpleModel * finished the data generation method experiment notebook, added in experiment comparing model performance * added and cleaned up the testing_model_metrics notebook * real data loader choice of perturbation effect dataset is now a param you can pass in * added lightning crash course notebook * linting * removing experiments from src dir; updating docs md and index files (#76) * removing experiments from src dir; updating docs md and index files * fixing stupid mkdocs docs text added to readme * setting version to 0.0.1 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Mueller <57322122+BenMueller1@users.noreply.github.com>
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this adds some sanity checks and graphing to the in silico data generation tutorial.
in doing that i also found and corrected a bug with regards to the tf indexing in generate_perturbation effects