nsheff · Oct 1, 2026 · Sep 25, 2026 · Sep 25, 2026
diff --git a/.github/workflows/notify-docs.yml b/.github/workflows/notify-docs.yml
@@ -0,0 +1,25 @@
+name: Notify pepkit docs
+
+# Tells databio/doc-hubs that this repo's docs changed, so pep.databio.org
+# rebuilds. All the logic is in the reusable workflow; this file only names
+# which site and which spoke. See databio/doc-hubs README, "Add a spoke".
+
+on:
+  push:
+    # Must equal this spoke's `ref` in hubs/pepkit/spokes.toml — the hub builds
+    # that ref, so notifying from any other branch would rebuild the same bytes.
+    branches: [master]
+    paths:
+      - 'docs/**'                       # the spoke's docs tree, docs.yml included
+      - 'peppy/**'                      # the package the hub renders API pages from
+      - '.github/workflows/notify-docs.yml'  # so a notifier fix proves itself
+  workflow_dispatch:
+
+jobs:
+  notify:
+    uses: databio/actions/.github/workflows/notify-doc-hub.yml@master
+    with:
+      site: pepkit
+      spoke: peppy
+    secrets:
+      DOCS_DISPATCH_TOKEN: ${{ secrets.DOCS_DISPATCH_TOKEN }}
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
diff --git a/docs/README.md b/docs/README.md
@@ -1,4 +1,12 @@
-# peppy
+# <img src="img/peppy_logo.svg" alt="peppy" class="img-header"/>
+
+<p align="center">
+<a href="https://pep.databio.org" alt="PEP compatible"><img src="https://pepkit.github.io/img/PEP-compatible-green.svg"/></a>
+<a href="https://github.com/pepkit/peppy/actions/workflows/run-pytest.yml" alt="Run pytests"><img src="https://github.com/pepkit/peppy/workflows/Run%20pytests/badge.svg"/></a>
+<a href="https://codecov.io/gh/pepkit/peppy" alt="codecov"><img src="https://codecov.io/gh/pepkit/peppy/branch/master/graph/badge.svg"/></a>
+<a href="https://pypi.org/project/peppy" alt="PyPI badge"><img src="https://img.shields.io/pypi/v/peppy"/></a>
+<a href="https://github.com/pepkit/peppy" alt="GitHub source code"><img src="https://img.shields.io/badge/source-github-354a75?logo=github"/></a>
+</p>
 
 ## Introduction
 

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,6 +2,41 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.50.0a1] -- 2025-12-22
+### Added
+- Merged [`eido`](https://github.com/pepkit/eido) ([#492](https://github.com/pepkit/peppy/issues/492)) and [`pephubclient`](https://github.com/pepkit/pephubclient) into `peppy`.
+- Command line interface based on `typer` for `eido` and `pephubclient`.
+- Pytest for Windows.
+
+### Fixed
+- Fixed incorrect path expanding from config file URL in Windows.
+- Ambiguity ([#498](https://github.com/pepkit/peppy/issues/498)) and redundancy ([#499](https://github.com/pepkit/peppy/issues/499)) in error messages.
+
+## [0.40.7] -- 2024-09-30
+### Fixed
+- Fixed incorrect sample table index in subtables
+
+## [0.40.6] -- 2024-09-10
+### Changed
+- [#493](https://github.com/pepkit/peppy/issues/493)
+
+## [0.40.5] -- 2024-07-25
+### Fixed
+- Fixed bug in initialization of peppy object from csv
+
+## [0.40.4] -- 2024-07-17
+### Changed
+- minor change, [PR #490](https://github.com/pepkit/peppy/pull/490)
+
+## [0.40.3] -- 2024-07-17
+### Fixed
+- [#393](https://github.com/pepkit/peppy/issues/393)
+- [#480](https://github.com/pepkit/peppy/issues/480)
+- [#369](https://github.com/pepkit/peppy/issues/369)
+- [#399](https://github.com/pepkit/peppy/issues/399)
+- [#476](https://github.com/pepkit/peppy/issues/476)
+- [#471](https://github.com/pepkit/peppy/issues/471)
+
 ## [0.40.2] -- 2024-05-28
 ### Added
 - added `sample_name` property to samples object.
@@ -110,12 +145,12 @@ _Due to the changes mentioned above, a few functionalities may be disabled. For
 ### Fixed
 
 - Performance issues during sample parsing. Two list comprehensions were combined to speed up this functionality.
-- `KeyError` is thrown when attempting to access the `pep_version` of a `peppy.Project` instance instatiated from a sample table (`csv`)
+- `KeyError` is thrown when attempting to access the `pep_version` of a `peppy.Project` instance instantiated from a sample table (`csv`)
 
 ### Added
 
 - Implementation of `__eq__` for the `peppy.Project` class such that two instances of the class can be compared using python's equality operators (`==`, `!=`).
-- New `from_dict` function that lets a user instatiate a new `peppy.Project` object using an in-memory representation of a PEP (a `dict`). This supports database storage of PEPs.
+- New `from_dict` function that lets a user instantiate a new `peppy.Project` object using an in-memory representation of a PEP (a `dict`). This supports database storage of PEPs.
 - New `extended` flag for the `to_dict` method on `peppy.Project` objects. This creates a **richer** dictionary representation of PEPs.
 - Better sample parsing
 

diff --git a/docs/code/feature1_append.md b/docs/code/feature1_append.md
@@ -0,0 +1,143 @@
+# Learn append sample modifier in `peppy`
+
+This vignette will show you how and why to use the append functionality of the `pepr` package. 
+
+ - basic information about this concept on the [specification website](http://pep.databio.org/en/2.0.0/specification/#sample_modifiersappend).
+
+## Problem/Goal
+The example below demonstrates how to use the constant attributes to **define the samples attributes in the `read_type` column** of the `sample_table.csv` file. This functionality is extremely useful when there are many samples that are characterized by identical values of certain attribute (here: value `SINGLE` in `read_type` attribute). Please consider the example below for reference:
+
+
+```python
+examples_dir = "../tests/data/example_peps-cfg2/example_append/"
+sample_table_ori = examples_dir + "sample_table_pre.csv"
+%cat $sample_table_ori | column -t -s, | cat
+```
+
+    sample_name  organism  time  read_type
+
+    pig_0h       pig       0     SINGLE
+
+    pig_1h       pig       1     SINGLE
+
+    frog_0h      frog      0     SINGLE
+
+    frog_1h      frog      1     SINGLE
+
+
+## Solution
+As the name suggests the attributes in the specified attributes (here: `read_type`) can be defined as constant ones. The way how this process is carried out is indicated explicitly in the `project_config.yaml` file (presented below). The name of the column is determined in the `sample_modifiers.append` key-value pair. Note that definition of more than one constant attribute is possible.
+
+
+
+```python
+project_config_file = examples_dir + "project_config.yaml"
+%cat $project_config_file
+```
+
+    pep_version: "2.0.0"
+    sample_table: sample_table.csv
+
+    sample_modifiers:
+      append:
+        read_type: SINGLE
+
+
+
+Let's introduce a few modifications to the original `sample_table.csv` file to use the `sample_modifiers.append` section of the config. Simply skip the attributes that are set constant and let the `pepr` do the work for you.
+
+
+```python
+sample_table = examples_dir + "sample_table.csv"
+%cat $sample_table | column -t -s, | cat
+```
+
+    sample_name  organism  time 
+
+    pig_0h       pig       0
+
+    pig_1h       pig       1
+
+    frog_0h      frog      0
+
+    frog_1h      frog      1
+
+
+
+## Code
+Import `peppy` and read in the project metadata by specifying the path to the `project_config.yaml`:
+
+
+```python
+from peppy import Project
+p = Project(project_config_file)
+```
+
+And inspect it:
+
+
+```python
+print(p)
+p.sample_table
+```
+
+    Project 'example_append' (/Users/mstolarczyk/Uczelnia/UVA/code/peppy/tests/data/example_peps-cfg2/example_append/project_config.yaml)
+    4 samples: pig_0h, pig_1h, frog_0h, frog_1h
+    Sections: pep_version, sample_table, sample_modifiers
+
+
+
+
+
+<table border="1" class="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>organism</th>
+      <th>read_type</th>
+      <th>sample_name</th>
+      <th>time</th>
+    </tr>
+    <tr>
+      <th>sample_name</th>
+      <th></th>
+      <th></th>
+      <th></th>
+      <th></th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>pig_0h</th>
+      <td>pig</td>
+      <td>SINGLE</td>
+      <td>pig_0h</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <th>pig_1h</th>
+      <td>pig</td>
+      <td>SINGLE</td>
+      <td>pig_1h</td>
+      <td>1</td>
+    </tr>
+    <tr>
+      <th>frog_0h</th>
+      <td>frog</td>
+      <td>SINGLE</td>
+      <td>frog_0h</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <th>frog_1h</th>
+      <td>frog</td>
+      <td>SINGLE</td>
+      <td>frog_1h</td>
+      <td>1</td>
+    </tr>
+  </tbody>
+</table>
+
+
+
+As you can see, the resulting samples are annotated the same way as if they were read from the original annotations file with attributes in the last column manually determined.