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docs: add gentropy first steps guide #449

Merged
merged 12 commits into from
Feb 5, 2024
Merged

docs: add gentropy first steps guide #449

merged 12 commits into from
Feb 5, 2024

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ireneisdoomed
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coauthored with @d0choa

This PR includes changes in the documentation to provide the user with a guide on how to perform basic operations with the package. Inside How-tos/Python API, we have covered:

  • Creating a Session
  • Initialising any Dataset, taking Summary Statistics as an example
  • Applying a method on a Dataset, taking window based clumping and fine mapping as an example
  • Inspecting and writing the content of a Dataset

This will help the user in their journey with the package.

Next steps is to design a more advanced exercise in a Google Colab notebook, with the advantage that it would be run interactively.

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Codecov Report

Attention: 178 lines in your changes are missing coverage. Please review.

Comparison is base (42b366c) 85.67% compared to head (327ff3a) 85.99%.
Report is 94 commits behind head on dev.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #449      +/-   ##
==========================================
+ Coverage   85.67%   85.99%   +0.31%     
==========================================
  Files          89       96       +7     
  Lines        2101     2627     +526     
==========================================
+ Hits         1800     2259     +459     
- Misses        301      368      +67     
Files Coverage Δ
src/airflow/dags/common_airflow.py 90.38% <100.00%> (ø)
src/airflow/dags/dag_preprocess.py 100.00% <ø> (ø)
src/airflow/dags/finngen_preprocess.py 100.00% <100.00%> (ø)
src/airflow/dags/gwas_curation_update.py 100.00% <100.00%> (ø)
src/gentropy/__init__.py 100.00% <ø> (ø)
src/gentropy/assets/__init__.py 100.00% <ø> (ø)
src/gentropy/assets/data/__init__.py 100.00% <ø> (ø)
src/gentropy/assets/schemas/__init__.py 100.00% <ø> (ø)
src/gentropy/cli.py 91.66% <100.00%> (ø)
src/gentropy/common/Liftover.py 80.64% <ø> (ø)
... and 81 more

... and 16 files with indirect coverage changes

d0choa and others added 2 commits February 5, 2024 10:25
* build(deps): bump pandas from 2.1.4 to 2.2.0 (#443)

Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.1.4 to 2.2.0.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.1.4...v2.2.0)

---
updated-dependencies:
- dependency-name: pandas
  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>

* build(deps): bump scikit-learn from 1.3.2 to 1.4.0 (#444)

Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.3.2 to 1.4.0.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.3.2...1.4.0)

---
updated-dependencies:
- dependency-name: scikit-learn
  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>

* test(docs): testing doc snippets proof of concept

* docs: extend and test python snippets to all docs

* fix: correct typing in apply_class_method_clumping

* fix: update imports in doc tests

* chore: harmonizing finngen configuration (#454)

* chore: harmonizing finngen configuration

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* chore: finalising finngen config update

* fix: reverting .env file

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* chore(deps): bump codecov/codecov-action from 3 to 4 (#464)

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>

* ci: ignore patch versions in dependabot (#462)

* build(deps-dev): bump ruff from 0.1.8 to 0.2.0 (#465)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.8 to 0.2.0.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.1.8...v0.2.0)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  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>

* build(deps-dev): bump ipython from 8.20.0 to 8.21.0 (#466)

Bumps [ipython](https://github.com/ipython/ipython) from 8.20.0 to 8.21.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.20.0...8.21.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:development
  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>

* build(deps-dev): bump pytest-sugar from 0.9.7 to 1.0.0 (#467)

Bumps [pytest-sugar](https://github.com/Teemu/pytest-sugar) from 0.9.7 to 1.0.0.
- [Release notes](https://github.com/Teemu/pytest-sugar/releases)
- [Changelog](https://github.com/Teemu/pytest-sugar/blob/main/CHANGES.rst)
- [Commits](Teemu/pytest-sugar@v0.9.7...v1.0.0)

---
updated-dependencies:
- dependency-name: pytest-sugar
  dependency-type: direct:development
  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: Irene López <45119610+ireneisdoomed@users.noreply.github.com>

* build(deps-dev): bump google-cloud-dataproc from 5.8.0 to 5.9.0 (#468)

Bumps [google-cloud-dataproc](https://github.com/googleapis/google-cloud-python) from 5.8.0 to 5.9.0.
- [Release notes](https://github.com/googleapis/google-cloud-python/releases)
- [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/packages/google-cloud-documentai/CHANGELOG.md)
- [Commits](googleapis/google-cloud-python@google-cloud-dataproc-v5.8.0...google-cloud-dataproc-v5.9.0)

---
updated-dependencies:
- dependency-name: google-cloud-dataproc
  dependency-type: direct:development
  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: Irene López <45119610+ireneisdoomed@users.noreply.github.com>

* fix(test): do not create session and pass it as a parameter

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Irene López <irene.lopezs@protonmail.com>
Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com>
@ireneisdoomed ireneisdoomed marked this pull request as ready for review February 5, 2024 10:35
@ireneisdoomed ireneisdoomed requested a review from d0choa February 5, 2024 10:35
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Thank you @ireneisdoomed. I think this will be very valuable for quite a while.

@d0choa d0choa merged commit 40af77f into dev Feb 5, 2024
3 checks passed
@d0choa d0choa deleted the il-howtos branch February 5, 2024 12:10
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3 participants