From 94d1161db3679bc103efc0023894e5246c72b2b1 Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:22:13 -0500 Subject: [PATCH 01/11] initial docs and jb setup --- .gitignore | 1 + .readthedocs.yaml | 32 ++ docs/_config.yml | 39 ++ docs/_toc.yml | 7 + docs/api.rst | 45 ++ docs/intro.md | 11 + docs/requirements.txt | 3 + pixi.lock | 979 ++++++++++++++++++++++++++++++++++++++++++ pixi.toml | 4 + 9 files changed, 1121 insertions(+) create mode 100644 .readthedocs.yaml create mode 100644 docs/_config.yml create mode 100644 docs/_toc.yml create mode 100644 docs/api.rst create mode 100644 docs/intro.md create mode 100644 docs/requirements.txt diff --git a/.gitignore b/.gitignore index a46ba9b..c230166 100644 --- a/.gitignore +++ b/.gitignore @@ -70,6 +70,7 @@ instance/ # Sphinx documentation docs/_build/ +docs/generated/ # PyBuilder .pybuilder/ diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..d25ac0d --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,32 @@ +# .readthedocs.yml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.11" + jobs: + pre_build: + # Generate the Sphinx configuration for this Jupyter Book so it builds. + - "jupyter-book config sphinx docs" + +# Build documentation in the docs/ directory with Sphinx +# sphinx: +# configuration: docs/conf.py + +# Optionally build your docs in additional formats such as PDF and ePub +formats: [] + +# Optionally set the version of Python and requirements required to build your docs +python: + install: + - method: pip + path: . + extra_requirements: + - docs +# system_packages: true \ No newline at end of file diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000..d57610c --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,39 @@ +# Book settings +# Learn more at https://jupyterbook.org/customize/config.html + +title: Phylo2Vec +author: Don Setiawan +# logo: logo.png + +# Force re-execution of notebooks on each build. +# See https://jupyterbook.org/content/execute.html +execute: + execute_notebooks: force + +# Define the name of the latex output file for PDF builds +latex: + latex_documents: + targetname: book.tex + +# Information about where the book exists on the web +repository: + url: https://github.com/uw-ssec/phylo2vec # Online location of your book + path_to_book: docs # Optional path to your book, relative to the repository root + branch: master # Which branch of the repository should be used when creating links (optional) + +# Add GitHub buttons to your book +# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository +html: + use_issues_button: true + use_repository_button: true + + +sphinx: + extra_extensions: + - 'sphinx.ext.autodoc' + - 'sphinx.ext.napoleon' + - 'sphinx.ext.viewcode' + - 'sphinx.ext.autosummary' + config: + add_module_names: True + autosummary_generate: True \ No newline at end of file diff --git a/docs/_toc.yml b/docs/_toc.yml new file mode 100644 index 0000000..abe446b --- /dev/null +++ b/docs/_toc.yml @@ -0,0 +1,7 @@ +# Table of contents +# Learn more at https://jupyterbook.org/customize/toc.html + +format: jb-book +root: intro +chapters: +- file: api.rst diff --git a/docs/api.rst b/docs/api.rst new file mode 100644 index 0000000..129d2f8 --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,45 @@ +API Reference +============= + +.. currentmodule:: phylo2vec + +Base +---------------- + +.. autosummary:: + :nosignatures: + :toctree: generated/ + + base.to_newick + base.to_vector + +Metrics +---------------- + +.. autosummary:: + :nosignatures: + :toctree: generated/ + + metrics.cophenetic_distances + +Utils +---------------- + +.. autosummary:: + :nosignatures: + :toctree: generated/ + + utils.find_num_leaves + utils.create_label_mapping + utils.apply_label_mapping + utils.remove_annotations + utils.remove_parent_labels + utils.sample + utils.seed_everything + utils.check_v + utils.reorder_v + utils.reroot_at_random + utils.remove_leaf + utils.add_leaf + utils.get_common_ancestor + diff --git a/docs/intro.md b/docs/intro.md new file mode 100644 index 0000000..f8cdc73 --- /dev/null +++ b/docs/intro.md @@ -0,0 +1,11 @@ +# Welcome to your Jupyter Book + +This is a small sample book to give you a feel for how book content is +structured. +It shows off a few of the major file types, as well as some sample content. +It does not go in-depth into any particular topic - check out [the Jupyter Book documentation](https://jupyterbook.org) for more information. + +Check out the content pages bundled with this sample book to see more. + +```{tableofcontents} +``` diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..7e821e4 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,3 @@ +jupyter-book +matplotlib +numpy diff --git a/pixi.lock b/pixi.lock index 3bfc03b..3b5860d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -235,6 +235,8 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/noarch/accessible-pygments-0.0.5-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.6.2.post1-pyhd8ed1ab_0.conda - 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greenlet !=0.4.17 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - typing-extensions >=4.6.0 + license: MIT + license_family: MIT + size: 2770491 + timestamp: 1729066732640 +- kind: conda + name: sqlalchemy + version: 2.0.36 + build: py310hf9df320_0 + subdir: osx-arm64 + url: https://conda.anaconda.org/conda-forge/osx-arm64/sqlalchemy-2.0.36-py310hf9df320_0.conda + sha256: e5f765006b2552ce67dc299628c6fadbc3aeb8246f0c629f6a2dc0bad46e7288 + md5: 8302d5d293a28d0b4dd37fc2d3c17d37 + depends: + - __osx >=11.0 + - greenlet !=0.4.17 + - python >=3.10,<3.11.0a0 + - python >=3.10,<3.11.0a0 *_cpython + - python_abi 3.10.* *_cp310 + - typing-extensions >=4.6.0 + license: MIT + license_family: MIT + size: 2805289 + timestamp: 1729066624963 - kind: conda name: sqlite version: 3.47.0 @@ -13995,6 +14942,22 @@ packages: license_family: GPL size: 15500960 timestamp: 1729794510631 +- kind: conda + name: tabulate + version: 0.9.0 + build: pyhd8ed1ab_2 + build_number: 2 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/tabulate-0.9.0-pyhd8ed1ab_2.conda + sha256: 090023bddd40d83468ef86573976af8c514f64119b2bd814ee63a838a542720a + md5: 959484a66b4b76befcddc4fa97c95567 + depends: + - python >=3.9 + license: MIT + license_family: MIT + size: 37554 + timestamp: 1733589854804 - kind: conda name: tapi version: 1300.6.5 @@ -14324,6 +15287,22 @@ packages: license: LicenseRef-Public-Domain size: 122354 timestamp: 1728047496079 +- kind: conda + name: uc-micro-py + version: 1.0.3 + build: pyhd8ed1ab_1 + build_number: 1 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-1.0.3-pyhd8ed1ab_1.conda + sha256: a2f837780af450d633efc052219c31378bcad31356766663fb88a99e8e4c817b + md5: 9c96c9876ba45368a03056ddd0f20431 + depends: + - python >=3.9 + license: MIT + license_family: MIT + size: 11199 + timestamp: 1733784280160 - kind: conda name: ukkonen version: 1.0.1 diff --git a/pixi.toml b/pixi.toml index 00bdf0e..c8dce62 100644 --- a/pixi.toml +++ b/pixi.toml @@ -60,10 +60,14 @@ pip = ">=24.2,<25" maturin = ">=1.7.4,<2" jupyterlab = ">=4.1,<4.2" pytest = ">=8.3.4,<9" +jupyter-book = ">=0.11.0" [feature.python.tasks.install-python] cmd = "maturin develop --manifest-path ./py-phylo2vec/Cargo.toml" +[feature.python.tasks.build-docs] +cmd = "jupyter-book build docs" + [feature.python.tasks.test] cmd = "pytest -vvv ./py-phylo2vec/tests" depends-on = ["install-python"] From e4e6f6e878460be0d3e3dfa5396def7096098abc Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 19 Dec 2024 19:23:11 +0000 Subject: [PATCH 02/11] style: pre-commit fixes --- .readthedocs.yaml | 2 +- docs/_config.yml | 4 ++-- docs/api.rst | 1 - docs/intro.md | 7 ++++--- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index d25ac0d..cb47506 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -29,4 +29,4 @@ python: path: . extra_requirements: - docs -# system_packages: true \ No newline at end of file +# system_packages: true diff --git a/docs/_config.yml b/docs/_config.yml index d57610c..db79cfc 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -26,7 +26,7 @@ repository: html: use_issues_button: true use_repository_button: true - + sphinx: extra_extensions: @@ -36,4 +36,4 @@ sphinx: - 'sphinx.ext.autosummary' config: add_module_names: True - autosummary_generate: True \ No newline at end of file + autosummary_generate: True diff --git a/docs/api.rst b/docs/api.rst index 129d2f8..94d09c3 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -42,4 +42,3 @@ Utils utils.remove_leaf utils.add_leaf utils.get_common_ancestor - diff --git a/docs/intro.md b/docs/intro.md index f8cdc73..0efca76 100644 --- a/docs/intro.md +++ b/docs/intro.md @@ -1,11 +1,12 @@ # Welcome to your Jupyter Book This is a small sample book to give you a feel for how book content is -structured. -It shows off a few of the major file types, as well as some sample content. -It does not go in-depth into any particular topic - check out [the Jupyter Book documentation](https://jupyterbook.org) for more information. +structured. It shows off a few of the major file types, as well as some sample +content. It does not go in-depth into any particular topic - check out +[the Jupyter Book documentation](https://jupyterbook.org) for more information. Check out the content pages bundled with this sample book to see more. ```{tableofcontents} + ``` From 3caa560b27c90e5c438a3d98d4377e79850bc269 Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:41:38 -0500 Subject: [PATCH 03/11] add rtd workflow .yml --- .github/workflows/documentation-links.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 .github/workflows/documentation-links.yml diff --git a/.github/workflows/documentation-links.yml b/.github/workflows/documentation-links.yml new file mode 100644 index 0000000..32455de --- /dev/null +++ b/.github/workflows/documentation-links.yml @@ -0,0 +1,22 @@ +# .github/workflows/documentation-links.yml + +name: readthedocs/actions +on: + pull_request_target: + types: + - opened + # Execute this action only on PRs that touch + # documentation files. + paths: + - "docs/**" + +permissions: + pull-requests: write + +jobs: + documentation-links: + runs-on: ubuntu-latest + steps: + - uses: readthedocs/actions/preview@v1 + with: + project-slug: "phylo2vec" \ No newline at end of file From 03278195f84d9b997260de047672137059a911bb Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 15:16:11 -0500 Subject: [PATCH 04/11] refactor: remove rtd workflow yml --- .github/workflows/documentation-links.yml | 22 ---------------------- 1 file changed, 22 deletions(-) delete mode 100644 .github/workflows/documentation-links.yml diff --git a/.github/workflows/documentation-links.yml b/.github/workflows/documentation-links.yml deleted file mode 100644 index 32455de..0000000 --- a/.github/workflows/documentation-links.yml +++ /dev/null @@ -1,22 +0,0 @@ -# .github/workflows/documentation-links.yml - -name: readthedocs/actions -on: - pull_request_target: - types: - - opened - # Execute this action only on PRs that touch - # documentation files. - paths: - - "docs/**" - -permissions: - pull-requests: write - -jobs: - documentation-links: - runs-on: ubuntu-latest - steps: - - uses: readthedocs/actions/preview@v1 - with: - project-slug: "phylo2vec" \ No newline at end of file From ed9ad6cfc2853bfbecd1512c4e9a39993172c298 Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 15:39:33 -0500 Subject: [PATCH 05/11] chore: add pixi install to rtd yml --- .readthedocs.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index cb47506..db15ba1 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,6 +11,8 @@ build: tools: python: "3.11" jobs: + install: + - "pixi install jupyter-book" pre_build: # Generate the Sphinx configuration for this Jupyter Book so it builds. - "jupyter-book config sphinx docs" @@ -25,8 +27,4 @@ formats: [] # Optionally set the version of Python and requirements required to build your docs python: install: - - method: pip - path: . - extra_requirements: - - docs -# system_packages: true + - requirements: docs/requirements.txt From 7296bdc2307af8ef0ffb39d2905617bc2b03984e Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 19:09:51 -0500 Subject: [PATCH 06/11] chore: test pixi rtd --- .readthedocs.yaml | 21 +++++++-------------- docs/requirements.txt | 2 -- 2 files changed, 7 insertions(+), 16 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index db15ba1..a259da7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,20 +11,13 @@ build: tools: python: "3.11" jobs: - install: - - "pixi install jupyter-book" - pre_build: - # Generate the Sphinx configuration for this Jupyter Book so it builds. - - "jupyter-book config sphinx docs" - -# Build documentation in the docs/ directory with Sphinx -# sphinx: -# configuration: docs/conf.py + commands: + - asdf plugin add pixi + - asdf install pixi latest + - asdf global pixi latest + - pixi run build-docs + - mkdir -p $READTHEDOCS_OUTPUT/html/ + - cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/ # Optionally build your docs in additional formats such as PDF and ePub formats: [] - -# Optionally set the version of Python and requirements required to build your docs -python: - install: - - requirements: docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt index 7e821e4..9fc0428 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1 @@ jupyter-book -matplotlib -numpy From cc2b56074e6102fba8efe44f8f3a8bd459387dd1 Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 19:13:33 -0500 Subject: [PATCH 07/11] chore: change rtd job type --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index a259da7..4212819 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,7 +11,7 @@ build: tools: python: "3.11" jobs: - commands: + install: - asdf plugin add pixi - asdf install pixi latest - asdf global pixi latest From b52883fbc23c004e9e4cc4a9a0b5f10282466df5 Mon Sep 17 00:00:00 2001 From: Don Setiawan Date: Thu, 19 Dec 2024 16:52:16 -0800 Subject: [PATCH 08/11] Update .readthedocs.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4212819..84824de 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,7 +15,7 @@ build: - asdf plugin add pixi - asdf install pixi latest - asdf global pixi latest - - pixi run build-docs + - pixi run -e py-phylo2vec build-docs - mkdir -p $READTHEDOCS_OUTPUT/html/ - cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/ From 86d91cacf33687f0127f93bfe5a6ff4e91e7bdf5 Mon Sep 17 00:00:00 2001 From: Don Setiawan Date: Thu, 19 Dec 2024 16:54:37 -0800 Subject: [PATCH 09/11] Update pixi.toml --- pixi.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pixi.toml b/pixi.toml index c8dce62..f590ae4 100644 --- a/pixi.toml +++ b/pixi.toml @@ -67,6 +67,7 @@ cmd = "maturin develop --manifest-path ./py-phylo2vec/Cargo.toml" [feature.python.tasks.build-docs] cmd = "jupyter-book build docs" +depends-on = ["install-python"] [feature.python.tasks.test] cmd = "pytest -vvv ./py-phylo2vec/tests" From fc98ccdd9617c8bcf6478cda9d9aaeabfb3ecccc Mon Sep 17 00:00:00 2001 From: Don Setiawan Date: Thu, 19 Dec 2024 17:05:05 -0800 Subject: [PATCH 10/11] Update .readthedocs.yaml job commands --- .readthedocs.yaml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 84824de..a68db76 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,14 +10,13 @@ build: os: ubuntu-22.04 tools: python: "3.11" - jobs: - install: - - asdf plugin add pixi - - asdf install pixi latest - - asdf global pixi latest - - pixi run -e py-phylo2vec build-docs - - mkdir -p $READTHEDOCS_OUTPUT/html/ - - cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/ + commands: + - asdf plugin add pixi + - asdf install pixi latest + - asdf global pixi latest + - pixi run -e py-phylo2vec build-docs + - mkdir -p $READTHEDOCS_OUTPUT/html/ + - cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/ # Optionally build your docs in additional formats such as PDF and ePub formats: [] From 386f6ea615b0b9719535c6b6ad3a1a1a0dff89c6 Mon Sep 17 00:00:00 2001 From: ayushnag <35325113+ayushnag@users.noreply.github.com> Date: Thu, 19 Dec 2024 20:10:50 -0500 Subject: [PATCH 11/11] chore: remove extra deps file --- docs/requirements.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 9fc0428..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -jupyter-book