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
...

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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
...

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>

.github/workflows/ci.yml

@@ -21,20 +21,33 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       # Consider using pre-commit.ci for open source project
       - name: Run pre-commit
         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@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: ${{ matrix.python-version }}
 
       - name: Checkout Code Repository
         uses: actions/checkout@v4
@@ -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@v3
-
-      - name: Upload coverage reports to Codecov
+        if: matrix.os == 'ubuntu-20.04'
         uses: codecov/codecov-action@v3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docs.yml

@@ -10,10 +10,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout main
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 

.vscode/settings.json

@@ -1,7 +1,9 @@
 {
     "editor.formatOnSave": true,
     "cSpell.words": [
+        "arange",
         "dtype",
+        "ndim",
         "pval",
         "pvalues",
         "randperm"

docs/probability_models/GenePopulation.md

@@ -0,0 +1 @@
+::: yeastdnnexplorer.probability_models.generate_data.GenePopulation

docs/probability_models/default_perturbation_effect_adjustment_function.md

@@ -0,0 +1 @@
+::: yeastdnnexplorer.probability_models.generate_data.default_perturbation_effect_adjustment_function