From 9fd64224339866154aeb14ca7c0e32561339a424 Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Tue, 21 Oct 2025 10:43:05 -0600 Subject: [PATCH 01/11] cfg: Adding myst-parser as dependency for doc Preparing to use Markdown in the documentation. --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 205ea817..a9f15a4c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -248,6 +248,7 @@ sphinx-click = ">=6.1.0,<7" sphinx-copybutton = ">=0.5.2,<0.6" sphinx-tabs = ">=3.4.1,<4" sphinxcontrib-mermaid = ">=1.2.3,<2" +myst-parser = ">=4.0.1,<5" [tool.pixi.feature.python-anthropic.dependencies] anthropic = ">=0.40.0,<0.41" From 5d03e9af24ce12ff6bc501b1f6af2f0838d37997 Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Tue, 21 Oct 2025 10:44:39 -0600 Subject: [PATCH 02/11] cfg: Adding myst_parser as extension for Sphinx --- docs/source/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index cdc8bd2e..33c3588f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -57,6 +57,7 @@ "sphinx_click.ext", "sphinx_tabs.tabs", "sphinx_copybutton", + "myst_parser", ] intersphinx_mapping = { From aa1ba277849b75aa6612c456ea3b008c1c50d99e Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Tue, 21 Oct 2025 11:44:58 -0600 Subject: [PATCH 03/11] Short name version for Gui --- docs/source/dev/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/dev/README.rst b/docs/source/dev/README.rst index 957e2f2f..1bdd1d8c 100644 --- a/docs/source/dev/README.rst +++ b/docs/source/dev/README.rst @@ -29,7 +29,7 @@ learn how to `create a branch `_. If you are not sure where or how to start contributing to COMPASS, consider reaching out to the -current developer(s): **Paul Pinchuk** ["ppinchuk@nlr.gov"] or **Guilherme Pimenta Castelao** ["gpimenta@nlr.gov"]. +current developer(s): **Paul Pinchuk** ["ppinchuk@nlr.gov"] or **Guilherme Castelao** ["gpimenta@nlr.gov"]. When you are ready to contribute to COMPASS, clone a copy of the COMPASS repository from GitHub, check out your own branch, and make the appropriate changes locally. Ensure that your new code adheres to all of the guidelines From e632210a36130c2d7f214442844004adcebae06e Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Tue, 21 Oct 2025 12:03:44 -0600 Subject: [PATCH 04/11] Note about Ruff on import style --- docs/source/dev/README.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/dev/README.rst b/docs/source/dev/README.rst index 1bdd1d8c..ec36a805 100644 --- a/docs/source/dev/README.rst +++ b/docs/source/dev/README.rst @@ -121,6 +121,7 @@ Use the following import conventions:: import numpy as np import pandas as pd +Note that ``ruff`` will monitor and enforce some style rules such as ordering of imports. Test coverage ------------- From c11986c1c55c2d324b335743ee16bb85625fdb4a Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Tue, 21 Oct 2025 12:07:12 -0600 Subject: [PATCH 05/11] Explicit command to help new users Assuming this guidance will be most useful for anyone new to pixi, let's make it explicit to help them to memorize it, thus `pixi run` instead of `pixi r`. With time they'll learn more efficient ways of doing it. --- docs/source/dev/README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/dev/README.rst b/docs/source/dev/README.rst index ec36a805..68e2ee84 100644 --- a/docs/source/dev/README.rst +++ b/docs/source/dev/README.rst @@ -133,13 +133,13 @@ You can run python COMPASS tests locally using ``pixi``: .. code-block:: shell - pixi r -e ptest tests-p + pixi run -e ptest tests-p To speed up testing, the tests can be run in parallel using ``-n auto``: .. code-block:: shell - pixi r -e ptest tests-p -n auto + pixi run -e ptest tests-p -n auto Tests for a module should ideally cover all code in that module, i.e., statement coverage should be at 100%, though this alone does not ensure that From 6f978c285fc37cf73bb43ae30c50e8bf1a9bc995 Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Tue, 21 Oct 2025 12:56:35 -0600 Subject: [PATCH 06/11] cfg: Extending sufix covered --- docs/source/conf.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 33c3588f..4bb90511 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -78,7 +78,11 @@ # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # -source_suffix = ".rst" +source_suffix = { + '.rst': 'restructuredtext', + '.txt': 'markdown', + '.md': 'markdown', +} # source_parsers = {'.md': MarkdownParser} From 05ee7af99411ecd1a9f214aa7ff4681ac2ba8930 Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Fri, 10 Apr 2026 14:47:11 -0600 Subject: [PATCH 07/11] cfg: Adding dependency on myst-parser for optional docs --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a9f15a4c..8325bab7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -79,6 +79,7 @@ doc = [ "sphinx-copybutton>=0.5", "sphinx-tabs>=3.4", "sphinxcontrib-mermaid>=1.2.3,<2", + "myst-parser>=5.0.0,<6", ] anthropic = [ "anthropic>=0.40.0,<0.41", @@ -248,7 +249,7 @@ sphinx-click = ">=6.1.0,<7" sphinx-copybutton = ">=0.5.2,<0.6" sphinx-tabs = ">=3.4.1,<4" sphinxcontrib-mermaid = ">=1.2.3,<2" -myst-parser = ">=4.0.1,<5" +myst-parser = ">=5.0.0,<6" [tool.pixi.feature.python-anthropic.dependencies] anthropic = ">=0.40.0,<0.41" From 9e4e916c2ef9d710372daef056c2b2791a6a7bfb Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Fri, 10 Apr 2026 14:49:38 -0600 Subject: [PATCH 08/11] Removing txt as markdown Following Copilot suggestion to avoid unintentional behavior. --- docs/source/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 4bb90511..11874848 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -80,7 +80,6 @@ # source_suffix = { '.rst': 'restructuredtext', - '.txt': 'markdown', '.md': 'markdown', } From d4e645ed664e287e18208e2e9aa9e36ac70eac45 Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Sun, 12 Apr 2026 09:10:47 -0600 Subject: [PATCH 09/11] fix: Reference to a readme, not an implicit index --- examples/parse_existing_docs/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/parse_existing_docs/README.md b/examples/parse_existing_docs/README.md index 98813816..cd8a2faf 100644 --- a/examples/parse_existing_docs/README.md +++ b/examples/parse_existing_docs/README.md @@ -2,9 +2,9 @@ This directory contains examples/tutorials to help you parse local documents using ``COMPASS``. -- [`Parsing via CLI`](./CLI): Example showing how to parse local documents via the CLI +- [`Parsing via CLI`](./CLI/README.rst): Example showing how to parse local documents via the CLI using a typical ``COMPASS`` configuration file. -- [`Parsing via Code`](./code): Tutorial using the ``COMPASS`` Python API to write code that +- [`Parsing via Code`](./code/README.rst): Tutorial using the ``COMPASS`` Python API to write code that parses a local PDF file. For rendered versions of these guides, see the From f162d3b5f5d0978a183a37ce380679b7bff70751 Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Sun, 12 Apr 2026 09:34:06 -0600 Subject: [PATCH 10/11] fix: Linking documents md -> rst using Markdown style --- examples/parse_existing_docs/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/parse_existing_docs/README.md b/examples/parse_existing_docs/README.md index cd8a2faf..f039d14a 100644 --- a/examples/parse_existing_docs/README.md +++ b/examples/parse_existing_docs/README.md @@ -2,9 +2,9 @@ This directory contains examples/tutorials to help you parse local documents using ``COMPASS``. -- [`Parsing via CLI`](./CLI/README.rst): Example showing how to parse local documents via the CLI +- {doc}`Parsing via CLI <./CLI/README>`: Example showing how to parse local documents via the CLI using a typical ``COMPASS`` configuration file. -- [`Parsing via Code`](./code/README.rst): Tutorial using the ``COMPASS`` Python API to write code that +- {doc}`Parsing via Code <./code/README>`: Tutorial using the ``COMPASS`` Python API to write code that parses a local PDF file. For rendered versions of these guides, see the From a22948762282146e6798129683f10075963fdd2c Mon Sep 17 00:00:00 2001 From: Gui Castelao Date: Sun, 12 Apr 2026 17:35:22 -0600 Subject: [PATCH 11/11] cfg: Updating pixi.lock after rebasing --- pixi.lock | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 52 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index f7a6fcf8..c39df66c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3258,12 +3258,14 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py313h3dea7bd_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.8-py313h683a580_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/minizip-4.0.10-h05a5f5f_0.conda - 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