use mkdocstrings, add yacman docs

README.md

@@ -11,61 +11,74 @@ Documentation is written using [mkdocs](https://www.mkdocs.org/) and themed with
 
 Each tool gets a `nav` section in `mkdocs.yml`, which maps to its own section/tab in the rendered documentation. So to add a new page, change titles, or change structure, edit `mkdocs.yml`. To edit the documentation itself, edit the `.md` documentation files in the subfolders under `/docs`.
 
-### Prereqs
+### Prerequisites
 
+```bash
+pip install mkdocs-material mkdocstrings[python] mkdocs-jupyter
 ```
-pip install mkdocs-material
+
+You'll also need to install the packages being documented (peppy, looper, pipestat, pypiper, geofetch, eido, yacman) for the API documentation to build correctly:
+
+```bash
+pip install peppy looper pipestat pypiper geofetch eido yacman
 ```
 
 
 ### Building locally for development
 
 I recommend previewing your changes locally before deploying. You can get a hot-reload server going by cloning this repository, and then just running:
 
-```
+```bash
 mkdocs serve
 ```
 
 You can also use `mkdocs build` to build a portable local version of the docs.
 
+The documentation now uses **mkdocstrings** for Python API documentation and **mkdocs-jupyter** for Jupyter notebooks. These plugins automatically generate documentation from the source code and render notebooks, so the build process is now a single step.
+
 
 ### Publishing updates
 
 The documentation is published automatically upon commits to `master` using a GitHub Action, which runs `mkdocs gh-deploy`. This builds the docs, and pushes them to the `gh-pages` branch. This branch is then published with GitHub Pages. There's no need to do this locally, just let the action deploy the updates for you automatically.
 
 ## FAQ
 
+### Python API Documentation
 
-### Updating automatic documentation
-
-In the past, I had a plugin that would auto-document 2 things: 1. Python docs using lucidoc, and 2. Jupyter notebooks. This plugin was neat, but it caused me a lot of maintenance issues as well. So now, I've made it much simpler; now it's no longer a plugin, just a simple Python script. Update all the auto-generated docs (stored in `docs/autodoc_build`) by running the update script manually:
+Python API documentation is now automatically generated using **mkdocstrings** during the build process. No separate script is needed. The API docs are defined in markdown files (e.g., `docs/peppy/code/python-api.md`) using the `:::` syntax:
 
-```console
-python update_python_autodocs.py
+```markdown
+::: peppy.Project
+    options:
+      docstring_style: google
+      show_source: true
 ```
 
-#### Configuring lucidoc rendering
+This syntax tells mkdocstrings to extract and render the documentation for the specified class or function directly from the source code.
 
-Auto-generated Python documentation with `lucidoc` rendering is configured in the `lucidoc`  sections of `mkdocs.yml`.
+### Jupyter Notebooks
+
+Jupyter notebooks are now rendered automatically using the **mkdocs-jupyter** plugin. Configure which notebooks to include in the `plugins` section of `mkdocs.yml`:
 
 ```yaml
-lucidoc:
-  peppy: path/to/output.md
+plugins:
+- mkdocs-jupyter:
+    include:
+      - peppy/notebooks/*.ipynb
+      - looper/notebooks/*.ipynb
 ```
 
-#### Configuring jupyter rendering
+Notebooks are rendered directly from `.ipynb` files during the build - no conversion step is needed.
 
-Configure jupyter notebeeoks in the `jupyter` section, where you specify a list of `in` (for `.ipynb` files) and `out` (for `.md` files) locations.
+### CLI Usage Documentation
 
-```yaml
-jupyter:
-  - in: path/to/notebook_folder1
-    out: path/to/rendered_folder1
-  - in: path/to/notebook_folder2
-    out: path/to/rendered_folder2
-``` 
-
-There, you can specify which folders contain notebooks, and to where they should be rendered as markdown.
+CLI usage documentation for geofetch can be updated manually when needed using the helper script:
+
+```bash
+python scripts/generate_cli_usage_docs.py
+```
+
+This script reads the template at `docs/geofetch/usage-template.md.tpl` and runs `geofetch --help` to generate `docs/geofetch/code/usage.md`. This only needs to be run when the CLI interface changes.
 
 ### Can we version the docs?
 

docs/eido/code/cli.md

@@ -42,7 +42,7 @@ eido inspect peppro_paper.yaml
     Sections: name, pep_version, sample_table, looper, sample_modifiers
 
 
- - To inspect a specific sample, one needs to provide the sample name (via `-n`/`--sample-name` oprional argument)
+ - To inspect a specific sample, one needs to provide the sample name (via `-n`/`--sample-name` optional argument)
 
 
 ```bash
@@ -213,6 +213,8 @@ eido convert peppro_paper.yaml --format csv
     H9_treated_PRO-seq_1,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_200nM_romidepsin_rep1_PE1.fastq.gz,PAIRED,H9 treated PRO-seq,H9_treated_PRO-seq_1,H9_200nM_romidepsin_rep1,200 nM romidepsin,8,/Users/mstolarczyk/H9_200nM_romidepsin_rep1_PE2.fastq.gz
     H9_treated_PRO-seq_2,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_200nM_romidepsin_rep2_PE1.fastq.gz,PAIRED,H9 treated PRO-seq,H9_treated_PRO-seq_2,H9_200nM_romidepsin_rep2,200 nM romidepsin,8,/Users/mstolarczyk/H9_200nM_romidepsin_rep2_PE2.fastq.gz
     H9_treated_PRO-seq_3,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_200nM_romidepsin_rep3_PE1.fastq.gz,PAIRED,H9 treated PRO-seq,H9_treated_PRO-seq_3,H9_200nM_romidepsin_rep3,200 nM romidepsin,8,/Users/mstolarczyk/H9_200nM_romidepsin_rep3_PE2.fastq.gz
+
+
     H9_PRO-seq_10,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_PRO-seq_10pct_PE1.fastq.gz,PAIRED,10% subset H9 PRO-seq 2,H9_PRO-seq_10,H9_PRO-seq_10pct,DMSO,8,/Users/mstolarczyk/H9_PRO-seq_10pct_PE2.fastq.gz
     H9_PRO-seq_20,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_PRO-seq_20pct_PE1.fastq.gz,PAIRED,20% subset H9 PRO-seq 2,H9_PRO-seq_20,H9_PRO-seq_20pct,DMSO,8,/Users/mstolarczyk/H9_PRO-seq_20pct_PE2.fastq.gz
     H9_PRO-seq_30,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_PRO-seq_30pct_PE1.fastq.gz,PAIRED,30% subset H9 PRO-seq 2,H9_PRO-seq_30,H9_PRO-seq_30pct,DMSO,8,/Users/mstolarczyk/H9_PRO-seq_30pct_PE2.fastq.gz

docs/eido/code/plugin-api-docs.md

@@ -1,95 +1,42 @@
-<script>
-document.addEventListener('DOMContentLoaded', (event) => {
-  document.querySelectorAll('h3 code').forEach((block) => {
-    hljs.highlightBlock(block);
-  });
-});
-</script>
+# Eido Built-in Filters API
 
-<style>
-h3 .content { 
-    padding-left: 22px;
-    text-indent: -15px;
- }
-h3 .hljs .content {
-    padding-left: 20px;
-    margin-left: 0px;
-    text-indent: -15px;
-    martin-bottom: 0px;
-}
-h4 .content, table .content, p .content, li .content { margin-left: 30px; }
-h4 .content { 
-    font-style: italic;
-    font-size: 1em;
-    margin-bottom: 0px;
-}
+## Overview
 
-</style>
+Eido provides built-in filter functions that can transform PEP projects into different output formats. These filters are useful for converting PEPs to various representations like YAML, CSV, or other formats.
 
+### Available Filters
 
-# Package `eido` Documentation
+Eido includes several built-in filters for converting and exporting PEP data:
 
+- **basic_pep_filter**: Returns the basic PEP representation
+- **yaml_pep_filter**: Converts PEP to YAML format
+- **csv_pep_filter**: Exports sample tables as CSV
+- **yaml_samples_pep_filter**: Exports only sample data as YAML
 
-Project configuration
+## API Reference
 
-```python
-def basic_pep_filter(p, **kwargs) -> Dict[str, str]
-```
+### Filter Functions
 
-Basic PEP filter, that does not convert the Project object.
+::: eido.basic_pep_filter
+    options:
+      docstring_style: google
+      show_source: true
+      show_signature: true
 
-This filter can save the PEP representation to file, if kwargs include `path`.
-#### Parameters:
+::: eido.yaml_pep_filter
+    options:
+      docstring_style: google
+      show_source: true
+      show_signature: true
 
-- `p` (`peppy.Project`):  a Project to run filter on
+::: eido.csv_pep_filter
+    options:
+      docstring_style: google
+      show_source: true
+      show_signature: true
 
-
-
-
-```python
-def yaml_pep_filter(p, **kwargs) -> Dict[str, str]
-```
-
-YAML PEP filter, that returns Project object representation.
-
-This filter can save the YAML to file, if kwargs include `path`.
-#### Parameters:
-
-- `p` (`peppy.Project`):  a Project to run filter on
-
-
-
-
-```python
-def csv_pep_filter(p, **kwargs) -> Dict[str, str]
-```
-
-CSV PEP filter, that returns Sample object representations
-
-This filter can save the CSVs to files, if kwargs include
-`sample_table_path` and/or `subsample_table_path`.
-#### Parameters:
-
-- `p` (`peppy.Project`):  a Project to run filter on
-
-
-
-
-```python
-def yaml_samples_pep_filter(p, **kwargs) -> Dict[str, str]
-```
-
-YAML samples PEP filter, that returns only Sample object representations.
-
-This filter can save the YAML to file, if kwargs include `path`.
-#### Parameters:
-
-- `p` (`peppy.Project`):  a Project to run filter on
-
-
-
-
-
-
-
-*Version Information: `eido` v0.2.2, generated by `lucidoc` v0.4.4*
+::: eido.yaml_samples_pep_filter
+    options:
+      docstring_style: google
+      show_source: true
+      show_signature: true