diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml index 63f407a3..a27828c3 100644 --- a/.github/workflows/publish-docs.yml +++ b/.github/workflows/publish-docs.yml @@ -40,8 +40,8 @@ jobs: - name: Build documentation run: | cd docs - poetry run bash autogen_docs.sh - poetry run make html + poetry run sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/pydna + poetry run sphinx-build -n -W --keep-going -b html ./ ./_build/ - name: Deploy to GitHub pages 🚀 # Deploy only when master changes diff --git a/docs/README.md b/docs/README.md index 8165bab0..d41d043c 100644 --- a/docs/README.md +++ b/docs/README.md @@ -93,3 +93,18 @@ For further customization, you can edit the `custom.css` file. ## Misc Other changes, such as changing the favicon, the css etc., can be made in the `conf.py` file. See the [sphinx docs](https://www.sphinx-doc.org/en/master/usage/configuration.html) and the [sphinx-rtd-theme](https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html) docs for more information. + +## Build docs using Sphinx command line tools + +Command to be run from `path/to/docs`, i.e. from within the `docs` package folder: + +Options: + - `--separate` to build separate pages for each (sub-)module + +```bash +# pwd: docs +# apidoc +sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/pydna +# build docs +sphinx-build -n -W --keep-going -b html ./ ./_build/ +``` diff --git a/docs/conf.py b/docs/conf.py index c2d687c5..15288a26 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -27,31 +27,65 @@ extensions = [ "sphinx.ext.autodoc", + "sphinx.ext.autodoc.typehints", # Automatically document type hints in function signatures "sphinx.ext.coverage", "sphinx.ext.napoleon", + "sphinx.ext.viewcode", # Include links to the source code in the documentation "sphinx.ext.doctest", - "myst_parser", # Allows to use markdown files instead of rst "sphinx.ext.viewcode", "sphinx.ext.autosummary", "numpydoc", "sphinx.ext.intersphinx", - "sphinx_rtd_theme", + # "sphinx_book_theme", + # new: + # "sphinx_new_tab_link", # each link opens in a new tab + "myst_nb", # Markdown and Jupyter Notebook support + # "sphinx_copybutton", # add copy button to code blocks ] + +# https://myst-nb.readthedocs.io/en/latest/computation/execute.html +nb_execution_mode = "auto" + +myst_enable_extensions = ["dollarmath", "amsmath"] + +# Plotly support through require javascript library +# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly +html_js_files = [ + "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js" +] + +# https://myst-nb.readthedocs.io/en/latest/configuration.html +# Execution +nb_execution_raise_on_error = True +# Rendering +nb_merge_streams = True + + # Add mappings https://kev.inburke.com/kevin/sphinx-interlinks intersphinx_mapping = { - "biopython": ("https://biopython.org/docs/latest/api/", None), + "biopython": ("https://biopython.org/docs/latest", None), "python": ("http://docs.python.org/3.8", None), } # Settings to support markdown files source_suffix = { ".rst": "restructuredtext", - ".md": "markdown", } templates_path = ["_templates"] -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", + "future_release_names.md", + "cookbook", # remove once cookbook works + "jupyter_execute", # local build folder for notebooks (dev) + "pydna_cheat_sheet", + "pydna_session", + "Makefile", + "make", + "autogen_docs", + "README.md", + "example_gallery.md", + ] autodoc_member_order = "bysource" autodoc_preserve_defaults = True @@ -61,7 +95,31 @@ # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -html_theme = "sphinx_rtd_theme" +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# See: +# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py +# html_title = "" +html_theme = "sphinx_book_theme" +# html_logo = "_static/logo-wide.svg" +# html_favicon = "_static/logo-square.svg" +html_theme_options = { + "github_url": "https://github.com/pydna-group/pydna", + "repository_url": "https://github.com/pydna-group/pydna", + "repository_branch": "main", + "home_page_in_toc": True, + "path_to_docs": "docs", + "show_navbar_depth": 1, + "use_edit_page_button": True, + "use_repository_button": True, + "use_download_button": True, + "launch_buttons": { + "colab_url": "https://colab.research.google.com" + # "binderhub_url": "https://mybinder.org", + # "notebook_interface": "jupyterlab", + }, + "navigation_with_keys": False, +} html_static_path = ["_static"] texinfo_documents = [ diff --git a/docs/cookbook/cookbook.ipynb b/docs/cookbook/cookbook.ipynb index 6605dcc3..34af1a33 100644 --- a/docs/cookbook/cookbook.ipynb +++ b/docs/cookbook/cookbook.ipynb @@ -74,16 +74,35 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Requirement already satisfied: pydna in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (5.5.3)\n", + "Requirement already satisfied: appdirs>=1.4.4 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (1.4.4)\n", + "Requirement already satisfied: biopython>=1.85 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (1.85)\n", + "Requirement already satisfied: networkx>=2.8.8 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (3.5)\n", + "Requirement already satisfied: numpy>=2.3.0 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (2.3.2)\n", + "Requirement already satisfied: prettytable>=3.5.0 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (3.16.0)\n", + "Requirement already satisfied: pydivsufsort>=0.0.14 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (0.0.18)\n", + "Requirement already satisfied: pyfiglet==0.8.post1 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (0.8.post1)\n", + "Requirement already satisfied: regex<2025.0.0,>=2024.11.6 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (2024.11.6)\n", + "Requirement already satisfied: seguid>=0.0.5 in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydna) (0.2.1)\n", + "Requirement already satisfied: wcwidth in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from prettytable>=3.5.0->pydna) (0.2.13)\n", + "Requirement already satisfied: wheel in /Users/heweb/miniforge3/envs/pydna/lib/python3.12/site-packages (from pydivsufsort>=0.0.14->pydna) (0.45.1)\n" + ] + } + ], "source": [ - "#Install pydna for colab.\n", "%%capture\n", + "#Install pydna for colab.\n", "!pip install pydna" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -92,7 +111,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -101,7 +120,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -117,7 +136,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -129,7 +148,7 @@ "Gbnk(o9637 KC562906.1)" ] }, - "execution_count": null, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -140,7 +159,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -151,7 +170,7 @@ "CTTA..AGTT" ] }, - "execution_count": null, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -162,7 +181,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -171,7 +190,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -186,7 +205,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 13, "metadata": {}, "outputs": [], "source": [ @@ -195,7 +214,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 14, "metadata": {}, "outputs": [ { @@ -207,7 +226,7 @@ "Gbnk(-3140 Z72979.1)" ] }, - "execution_count": null, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -218,7 +237,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 15, "metadata": {}, "outputs": [ { @@ -229,7 +248,7 @@ "TACT..TTTT" ] }, - "execution_count": null, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -240,7 +259,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -249,7 +268,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -265,7 +284,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "metadata": {}, "outputs": [ { @@ -279,7 +298,7 @@ " 3ACAAGTCATTAAGTC...GACCTTTTCTGAGAGTAGATT5" ] }, - "execution_count": null, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -290,7 +309,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 19, "metadata": {}, "outputs": [], "source": [ @@ -299,7 +318,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -308,7 +327,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 21, "metadata": {}, "outputs": [ { @@ -317,7 +336,7 @@ "(Dseqrecord(-7), Dseqrecord(-1819), Dseqrecord(-11))" ] }, - "execution_count": null, + "execution_count": 21, "metadata": {}, "output_type": "execute_result" } @@ -328,7 +347,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 22, "metadata": {}, "outputs": [ { @@ -339,7 +358,7 @@ " GAGA..ATTCCTAG" ] }, - "execution_count": null, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } @@ -350,7 +369,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 23, "metadata": {}, "outputs": [], "source": [ @@ -359,7 +378,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 24, "metadata": {}, "outputs": [ { @@ -370,7 +389,7 @@ " AGGG..TTTTCTAG" ] }, - "execution_count": null, + "execution_count": 24, "metadata": {}, "output_type": "execute_result" } @@ -381,7 +400,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 25, "metadata": {}, "outputs": [], "source": [ @@ -390,7 +409,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 26, "metadata": {}, "outputs": [], "source": [ @@ -399,18 +418,19 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 27, "metadata": {}, "outputs": [ { - "data": { - "text/plain": [ - "'t9fs_9UvEuD-Ankyy8XEr1hD5DQ'" - ] - }, - "execution_count": null, - "metadata": {}, - "output_type": "execute_result" + "ename": "AttributeError", + "evalue": "'Dseqrecord' object has no attribute 'cseguid'", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mAttributeError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[27]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m \u001b[43mYEp24PGK_XK\u001b[49m\u001b[43m.\u001b[49m\u001b[43mcseguid\u001b[49m()\n", + "\u001b[31mAttributeError\u001b[39m: 'Dseqrecord' object has no attribute 'cseguid'" + ] } ], "source": [ @@ -770,10 +790,15 @@ } ], "metadata": { + "jupytext": { + "cell_metadata_filter": "-all", + "main_language": "python", + "notebook_metadata_filter": "-all" + }, "kernelspec": { - "display_name": "Python [conda env:bjorn311]", + "display_name": "pydna", "language": "python", - "name": "conda-env-bjorn311-py" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -785,7 +810,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.0" + "version": "3.12.11" } }, "nbformat": 4, diff --git a/docs/index.rst b/docs/index.rst index 69ab1aa0..a7f5399d 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -16,11 +16,24 @@ Welcome to pydna's documentation! :maxdepth: 1 :hidden: - self installation - modules/index getting_started - example_gallery + +.. toctree:: + :caption: Examples: + :maxdepth: 1 + :hidden: + :glob: + + notebooks/* + +.. toctree:: + :caption: package + :maxdepth: 2 + :hidden: + + reference/pydna + CHANGELOG .. Indices and tables .. ================== diff --git a/docs/notebooks/Example_HT_cazyme_primer_design.ipynb b/docs/notebooks/Example_HT_cazyme_primer_design.ipynb index eae36ef4..e2c0f74e 100644 --- a/docs/notebooks/Example_HT_cazyme_primer_design.ipynb +++ b/docs/notebooks/Example_HT_cazyme_primer_design.ipynb @@ -305,7 +305,7 @@ "id": "8", "metadata": {}, "source": [ - "# Steps\n", + "## Steps\n", "\n", "I would like:\n", "1) Read sequences from a text file\n", @@ -320,7 +320,7 @@ "id": "9", "metadata": {}, "source": [ - "# 1 - Read sequences" + "## 1 - Read sequences" ] }, { @@ -440,7 +440,7 @@ "id": "13", "metadata": {}, "source": [ - "# 2 - Translate sequences" + "## 2 - Translate sequences" ] }, { @@ -528,7 +528,7 @@ "id": "15", "metadata": {}, "source": [ - "# 3 - Read in SignalP output" + "## 3 - Read in SignalP output" ] }, { @@ -686,7 +686,7 @@ "id": "18", "metadata": {}, "source": [ - "# 4 - Remove signal peptides" + "## 4 - Remove signal peptides" ] }, { @@ -801,7 +801,7 @@ "id": "24", "metadata": {}, "source": [ - "# 5 - Generate primers " + "## 5 - Generate primers " ] }, { diff --git a/poetry.lock b/poetry.lock index d2eda781..2286023a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,23 @@ -# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.4 and should not be changed by hand. + +[[package]] +name = "accessible-pygments" +version = "0.0.5" +description = "A collection of accessible pygments styles" +optional = false +python-versions = ">=3.9" +groups = ["docs"] +files = [ + {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, + {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, +] + +[package.dependencies] +pygments = ">=1.5" + +[package.extras] +dev = ["pillow", "pkginfo (>=1.10)", "playwright", "pre-commit", "setuptools", "twine (>=5.0)"] +tests = ["hypothesis", "pytest"] [[package]] name = "alabaster" @@ -7,7 +26,7 @@ description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.9" groups = ["docs"] -markers = "python_version == \"3.9\"" +markers = "python_version < \"3.11\"" files = [ {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, @@ -20,7 +39,7 @@ description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.10" groups = ["docs"] -markers = "python_version >= \"3.10\"" +markers = "python_version >= \"3.11\"" files = [ {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, @@ -44,7 +63,7 @@ version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" optional = false python-versions = ">=3.6" -groups = ["test"] +groups = ["docs", "test"] markers = "platform_system == \"Darwin\"" files = [ {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, @@ -57,7 +76,7 @@ version = "3.0.0" description = "Annotate AST trees with source code positions" optional = false python-versions = ">=3.8" -groups = ["test"] +groups = ["docs", "test"] files = [ {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, @@ -233,25 +252,6 @@ d = ["aiohttp (>=3.10)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] uvloop = ["uvloop (>=0.15.2)"] -[[package]] -name = "bleach" -version = "6.2.0" -description = "An easy safelist-based HTML-sanitizing tool." -optional = false -python-versions = ">=3.9" -groups = ["docs"] -files = [ - {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"}, - {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"}, -] - -[package.dependencies] -tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""} -webencodings = "*" - -[package.extras] -css = ["tinycss2 (>=1.1.0,<1.5)"] - [[package]] name = "cai2" version = "1.0.5" @@ -485,12 +485,12 @@ version = "8.1.8" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" -groups = ["main", "dev"] +groups = ["main", "dev", "docs"] files = [ {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"}, {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"}, ] -markers = {main = "python_version == \"3.9\" and extra == \"express\"", dev = "python_version == \"3.9\""} +markers = {main = "python_version < \"3.11\" and extra == \"express\"", dev = "python_version < \"3.11\"", docs = "python_version < \"3.11\""} [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} @@ -501,12 +501,12 @@ version = "8.2.1" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.10" -groups = ["main", "dev"] +groups = ["main", "dev", "docs"] files = [ {file = "click-8.2.1-py3-none-any.whl", hash = "sha256:61a3265b914e850b85317d0b3109c7f8cd35a670f963866005d6ef1d5175a12b"}, {file = "click-8.2.1.tar.gz", hash = "sha256:27c491cc05d968d271d5a1db13e3b5a184636d9d930f148c50b038f0d0646202"}, ] -markers = 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check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] @@ -4463,4 +4377,4 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"] [metadata] lock-version = "2.1" python-versions = ">=3.9,<4.0" -content-hash = "d624d3138309950985150a8da5e04ecfa161d2ea3f7f0256f38dee8759a1283b" +content-hash = "ff55198df7ae98e766b3575e330e152dd5995670b2a42034eb3d522b503225eb" diff --git a/pyproject.toml b/pyproject.toml index eff734ad..4f707819 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -87,13 +87,17 @@ requests-mock = ">=1.10.0" [tool.poetry.group.docs.dependencies] numpydoc = "^1.6.0" -sphinx-autobuild = "^2021.3.14" -sphinx-rtd-theme = ">=1.3,<4.0" -nbconvert = "^7.16.4" -myst-parser = [ - { version = ">3.0.0", python = "<3.10" }, - { version = ">=4.0.0", python = ">=3.10" }, -] +sphinx = "*" +# sphinx-rtd-theme = ">=1.3,<4.0" +# nbconvert = "^7.16.4" +# myst-parser = [ +# { version = ">3.0.0", python = "<3.10" }, +# { version = ">=4.0.0", python = ">=3.10" }, +# ] +myst-nb = "*" +sphinx-book-theme = "*" +pandas = "*" +teemi = "*" [tool.poetry.group.dev.dependencies] autopep8 = "^2.1.0"