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* 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
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* 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)

---
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- dependency-name: torch
  dependency-type: direct:production
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* 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
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* 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)

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updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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* 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)

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  dependency-type: direct:development
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* 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
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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
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* 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

---------

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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* 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
...

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* 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
...

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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
...

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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
...

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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
...

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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
...

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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

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* 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
...

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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
...

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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
...

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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
...

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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>
  • Loading branch information
@cmatKhan @dependabot @BenMueller1
3 people authored May 1, 2024
1 parent c23a8f6 commit 17e4ffe
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26 changes: 17 additions & 9 deletions .github/workflows/ci.yml
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Expand Up @@ -29,12 +29,25 @@ jobs:
uses: pre-commit/action@v3.0.0

pytest:
runs-on: ubuntu-latest
strategy:
matrix:
# see https://github.com/actions/runner-images
os:
[
ubuntu-22.04,
ubuntu-20.04,
macos-13,
macos-12,
windows-2022,
windows-2019,
]
python-version: ["3.11"]
runs-on: ${{ matrix.os }}
steps:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
python-version: ${{ matrix.python-version }}

- name: Checkout Code Repository
uses: actions/checkout@v4
Expand All @@ -45,13 +58,8 @@ jobs:
pip install poetry
poetry install
- name: Run tests and collect coverage
run: poetry run pytest --cov=./ --cov-report=xml

- name: Upload coverage reports to Codecov with GitHub Action
uses: codecov/codecov-action@v4

- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v4
if: matrix.os == 'ubuntu-20.04'
uses: codecov/codecov-action@v3
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
14 changes: 13 additions & 1 deletion .gitignore
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@@ -1,5 +1,11 @@
# Dataset directory
data/

# logs
logs/

# local tmp files
./tmp/*
tmp/*
# But do not ignore README.md in the tmp directory
!/tmp/README.md

Expand Down Expand Up @@ -31,6 +37,10 @@ share/python-wheels/
*.egg
MANIFEST

# ignore any log folders anywhere in repo
**/logs/
**/lightning_logs/

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
Expand Down Expand Up @@ -157,6 +167,8 @@ dmypy.json
# Cython debug symbols
cython_debug/

logs

# PyCharm
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
Expand Down
4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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@@ -1,8 +1,8 @@
exclude: '^docs/|devcontainer.json'
exclude: "^docs/|devcontainer.json"
default_stages: [commit]

default_language_version:
python: python3.10
python: python3.11

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
Expand Down
9 changes: 8 additions & 1 deletion .vscode/settings.json
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@@ -1,12 +1,19 @@
{
"editor.formatOnSave": true,
"cSpell.words": [
"arange",
"dtype",
"ndim",
"pval",
"pvalues",
"randperm"
],
"[markdown]": {
"editor.formatOnSave": false
}
},
"python.testing.pytestArgs": [
"."
],
"python.testing.unittestEnabled": false,
"python.testing.pytestEnabled": true
}
35 changes: 27 additions & 8 deletions README.md
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@@ -1,25 +1,26 @@
# yeastdnnexplorer

[![gh-pages](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/docs.yml/badge.svg)](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/docs.yml)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![style](https://img.shields.io/badge/%20style-sphinx-0a507a.svg)](https://www.sphinx-doc.org/en/master/usage/index.html)
[![Pytest](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/BrentLab/yeastdnnexplorer/graph/badge.svg?token=D2AB7IUY7F)](https://codecov.io/gh/BrentLab/yeastdnnexplorer)
[![gh-pages](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/docs.yml/badge.svg)](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/docs.yml)

## Documentation

See [here]() for more complete documentation
See [here](https://brentlab.github.io/yeastdnnexplorer/) for more complete documentation

## Installation

(no user installation instructions yet)
This repo has not yet been added to PyPI. See the developer installation below.

### Development

1. git clone the repo
1. `cd` into the local version of the repo
1. choose one (or more) of the following
1. choose one (or more) of the following (only poetry currently supported)

#### vscode
<!-- #### vscode
I strongly recommend using vscode in the `devcontainer` environment. This will
ensure that you have all the necessary dependencies installed and configured,
Expand All @@ -32,7 +33,7 @@ but not the tookit, see the section on installing with docker:
If you don't want GPU access in the devcontainer, you can also change the
value of `dockerComposeFile` from `gpu.yml` to `cpu.yml` in the
[devcontainer.json](.devcontainer/devcontainer.json).
[devcontainer.json](.devcontainer/devcontainer.json). -->

#### poetry

Expand All @@ -50,7 +51,7 @@ After cloning and `cd`ing into the repo, you can install the dependencies with:
poetry install
```

#### docker compose
<!-- #### docker compose
You can create an environment using docker compose. There are two compose
configuration files:
Expand All @@ -75,4 +76,22 @@ docker-compose -f <gpu/cpu>.yml run --rm app bash
you don't need to clone the repo to your local for this, but you will
need to fork the repo into your local github account. Make sure you change
the `dockerComposeFile` in the [devcontainer.json](.devcontainer/devcontainer.json)
to `cpu.yml` and then launch a codespace.
to `cpu.yml` and then launch a codespace. -->

#### mkdocs

The documentation is build with mkdocs:

##### Commands

* `mkdocs new [dir-name]` - Create a new project.
* `mkdocs serve` - Start the live-reloading docs server.
* `mkdocs build` - Build the documentation site.
* `mkdocs -h` - Print help message and exit.

##### Project layout

* mkdocs.yml # The configuration file.
* docs/
* index.md # The documentation homepage.
* ... # Other markdown pages, images and other files.
1 change: 1 addition & 0 deletions docs/data_loaders/real_data_loader.md
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::: yeastdnnexplorer.data_loaders.real_data_loader.RealDataLoader
1 change: 1 addition & 0 deletions docs/data_loaders/synthetic_data_loader.md
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::: yeastdnnexplorer.data_loaders.synthetic_data_loader.SyntheticDataLoader
95 changes: 90 additions & 5 deletions docs/index.md
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@@ -1,17 +1,102 @@
# Welcome to MkDocs
# yeastdnnexplorer

For full documentation visit [mkdocs.org](https://www.mkdocs.org).
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![style](https://img.shields.io/badge/%20style-sphinx-0a507a.svg)](https://www.sphinx-doc.org/en/master/usage/index.html)
[![Pytest](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/BrentLab/yeastdnnexplorer/graph/badge.svg?token=D2AB7IUY7F)](https://codecov.io/gh/BrentLab/yeastdnnexplorer)
[![gh-pages](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/docs.yml/badge.svg)](https://github.com/BrentLab/yeastdnnexplorer/actions/workflows/docs.yml)

## Commands
## Introduction

`yeastdnnexplorer` is intended to serve as a development environment for exploring
different DNN models to infer the relationship between transcription factors and
target genes using binding and perturbation expression data.

## Installation

This repo has not yet been added to PyPI. See the developer installation below.

### Development

1. git clone the repo
1. `cd` into the local version of the repo
1. choose one (or more) of the following (only poetry currently supported)

<!-- #### vscode
I strongly recommend using vscode in the `devcontainer` environment. This will
ensure that you have all the necessary dependencies installed and configured,
as well as your vscode environment set up for automatic linting/formatting.
By default, the `devcontainer` expects that you have Nvidia GPUs with the
Nvidia Container Tookit installed and docker enabled. If you have Nvidia GPUs,
but not the tookit, see the section on installing with docker:
[Nvidia Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html?highlight=docker#configuring-docker)
If you don't want GPU access in the devcontainer, you can also change the
value of `dockerComposeFile` from `gpu.yml` to `cpu.yml` in the
[devcontainer.json](.devcontainer/devcontainer.json). -->

#### poetry

You can also install the dependencies using poetry. I prefer setting the following:

```bash
poetry config virtualenvs.in-project true
```

So that the virtual environments are installed in the project directory as `.venv`

After cloning and `cd`ing into the repo, you can install the dependencies with:

```bash
poetry install
```

<!-- #### docker compose
You can create an environment using docker compose. There are two compose
configuration files:
- `gpu.yml`: for use with Nvidia GPUs
- `cpu.yml`: for use without GPUs
You can build the environment with:
```bash
docker-compose -f <gpu/cpu>.yml build
```
After that you can start a shell with:
```bash
docker-compose -f <gpu/cpu>.yml run --rm app bash
```
#### github codespaces
you don't need to clone the repo to your local for this, but you will
need to fork the repo into your local github account. Make sure you change
the `dockerComposeFile` in the [devcontainer.json](.devcontainer/devcontainer.json)
to `cpu.yml` and then launch a codespace. -->

#### mkdocs

The documentation is build with mkdocs:

##### Commands

After building the environment with poetry, you can use `poetry run` or a poetry shell
to execute the following:

* `mkdocs new [dir-name]` - Create a new project.
* `mkdocs serve` - Start the live-reloading docs server.
* `mkdocs build` - Build the documentation site.
* `mkdocs -h` - Print help message and exit.

## Project layout
##### Project layout

mkdocs.yml # The configuration file.
docs/
index.md # The documentation homepage.
... # Other markdown pages, images and other files.
... # Other markdown pages, images and other files.
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::: yeastdnnexplorer.ml_models.customizable_model.CustomizableModel
1 change: 1 addition & 0 deletions docs/ml_models/metrics_compute_nrmse.md
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::: yeastdnnexplorer.ml_models.metrics.compute_nrmse
1 change: 1 addition & 0 deletions docs/ml_models/metrics_smse.md
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::: yeastdnnexplorer.ml_models.metrics.SMSE
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::: yeastdnnexplorer.ml_models.simple_model
1 change: 1 addition & 0 deletions docs/probability_models/GenePopulation.md
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::: yeastdnnexplorer.probability_models.generate_data.GenePopulation
1 change: 1 addition & 0 deletions docs/probability_models/default_perturbation_effect_adjustment_function.md
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::: yeastdnnexplorer.probability_models.generate_data.default_perturbation_effect_adjustment_function
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1 change: 1 addition & 0 deletions ...ability_models/perturbation_effect_adjustment_function_with_tf_relationships.md
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::: yeastdnnexplorer.probability_models.generate_data.perturbation_effect_adjustment_function_with_tf_relationships
1 change: 1 addition & 0 deletions .../perturbation_effect_adjustment_function_with_tf_relationships_boolean_logic.md
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::: yeastdnnexplorer.probability_models.generate_data.perturbation_effect_adjustment_function_with_tf_relationships_boolean_logic
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::: yeastdnnexplorer.probability_models.relation_classes
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