Merge pull request #467 from pepkit/dev

Release 0.40.0

Author: nsheff

.github/workflows/run-pytest.yml

@@ -4,14 +4,14 @@ on:
   push:
     branches: [dev]
   pull_request:
-    branches: [master]
+    branches: [master, dev]
 
 jobs:
   pytest:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-20.04]
 
     steps:
@@ -22,10 +22,10 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dev dependancies
+    - name: Install dev dependencies
       run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
 
-    - name: Install test dependancies
+    - name: Install test dependencies
       run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
 
     - name: Install package

docs/changelog.md

@@ -2,6 +2,21 @@
 
 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.
 
+## [0.40.0] -- 2023-XX-XX
+
+**This version introduced backwards-incompatible changes.**
+
+### Changed
+- Replaced `attmap` with `MutableMapping` (which removes some attributes)
+- Replaced OrderedDict with dict
+- Deprecated support for Python versions <= 3.7
+
+_Due to the changes mentioned above, a few functionalities may be disabled. For example, the `name` and `description` project properties can no longer be accessed with `getitem`; use the `getattr` syntax instead_
+
+### Added
+- Constructor methods: `Project.from_dict`, `Project.from_pandas`, `Project.from_sample_yaml`, `Project.from_pep_config`
+
+
 ## [0.35.7] -- 2023-07-19
 ### Fixed 
 - incorrect setting of sample and subsample indexes using from_dict function (#452)
@@ -17,6 +32,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed
 - Reduced the number of items returned in the to_dict(extended=True) method to 3, with the name and description now stored in the config key.
 
+
 ## [0.35.5] -- 2023-03-27
 ### Fixed
 - A [bug](https://github.com/pepkit/peppy/issues/435) with custom sample ids
@@ -33,8 +49,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [0.35.2] -- 2022-09-13
 ### Fixed
-
 - Returning `NaN` value within `to_dict` method was fixed and method now returns `None` instead
+
 ## [0.35.1] -- 2022-09-07
 ### Changed
 - Organization of test files. Separated unittests from smoketests.
@@ -67,7 +83,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed 
 
 - Way of initialization project from dictionary. Now it's possible as follows: `Project().from_dict()`
-- 
+
 ### Fixed
 
 - Fix error that was raised when duplicated sample in `sample_table` had different read types (single-end mixed with paired-end).

docs/hello-world.md

@@ -40,7 +40,7 @@ project = peppy.Project("example_basic/project_config.yaml") # instantiate in-me
 samples = project.samples # grab the list of Sample objects defined in this Project
 
 # Find the input file for the first sample in the project
-samples[0].file
+samples[0]["file"]
 ```
 
 That's it! You've got `peppy` running on an example project.