Merge pull request #487 from pepkit/dev

Looper v1.8.0 Release

.github/workflows/python-publish.yml

@@ -12,22 +12,18 @@ jobs:
     runs-on: ubuntu-latest
     name: upload release to PyPI
     permissions:
-      # IMPORTANT: this permission is mandatory for trusted publishing
-      id-token: write
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install setuptools wheel twine
       - name: Build and publish
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
           python setup.py sdist bdist_wheel
       - name: Publish package distributions to PyPI

.gitignore

@@ -64,7 +64,7 @@ open_pipelines/
 .coverage*
 .pytest_cache
 .vscode/
-.looper.yaml
+/tests/data/hello_looper-dev/.gitignore
 
 # Reserved files for comparison
 *RESERVE*

.looper.yaml

@@ -0,0 +1,5 @@
+pep_config: example/pep/path
+output_dir: .
+pipeline_interfaces:
+  sample: []
+  project: []

MANIFEST.in

@@ -6,3 +6,4 @@ include looper/default_config/*
 include looper/default_config/divvy_templates/*
 include looper/jinja_templates_old/*
 include looper/schemas/*
+include looper/command_models/*

docs/changelog.md

@@ -2,6 +2,35 @@
 
 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.
 
+
+## [1.8.1] -- 2024-06-06
+
+### Fixed
+- added `-v` and `--version` to the CLI
+- fixed running project level with `--project` argument
+
+## [1.8.0] -- 2024-06-04
+
+### Added
+- looper destroy now destroys individual results when pipestat is configured: https://github.com/pepkit/looper/issues/469
+- comprehensive smoketests: https://github.com/pepkit/looper/issues/464
+- allow rerun to work on both failed or waiting flags: https://github.com/pepkit/looper/issues/463
+
+### Changed
+- Migrated `argparse` CLI definition to a pydantic basis for all commands. See: https://github.com/pepkit/looper/issues/438
+- during project load, check if PEP file path is a file first, then check if it is a registry path: https://github.com/pepkit/looper/issues/456 
+- Looper now uses FutureYamlConfigManager due to the yacman refactor v0.9.3: https://github.com/pepkit/looper/issues/452
+
+### Fixed
+- inferring project name when loading PEP from csv: https://github.com/pepkit/looper/issues/484
+- fix inconsistency resolving pipeline interface paths if multiple paths are supplied: https://github.com/pepkit/looper/issues/474
+- fix bug with checking for completed flags: https://github.com/pepkit/looper/issues/470
+- fix looper destroy not properly destroying all related files: https://github.com/pepkit/looper/issues/468
+- looper rerun now only runs failed jobs as intended: https://github.com/pepkit/looper/issues/467 
+- looper inspect now inspects the looper config: https://github.com/pepkit/looper/issues/462
+- Load PEP from CSV: https://github.com/pepkit/looper/issues/456
+- looper now works with sample_table_index https://github.com/pepkit/looper/issues/458
+
 ## [1.7.1] -- 2024-05-28
 
 ### Fixed

looper/__main__.py

@@ -1,6 +1,6 @@
 import sys
 
-from .cli_looper import main
+from .cli_pydantic import main
 from .cli_divvy import main as divvy_main
 
 if __name__ == "__main__":

looper/_version.py

@@ -1 +1,2 @@
-__version__ = "1.7.1"
+__version__ = "1.8.1"
+# You must change the version in parser = pydantic2_argparse.ArgumentParser in cli_pydantic.py!!!