Merge pull request #366 from pepkit/dev

v0.31.1

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@stable

.github/workflows/run-pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [2.7, 3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
         os: [ubuntu-latest, macos-latest]
 
     steps:
@@ -32,7 +32,7 @@ jobs:
       run: python -m pip install .
 
     - name: Run pytest tests
-      run: pytest tests --remote-data --cov=./ --cov-report=xml
+      run: pytest tests -x -vv --cov=./ --cov-report=xml --remote-data
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.7.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black

README.md

@@ -3,8 +3,9 @@
 ![Run pytests](https://github.com/pepkit/peppy/workflows/Run%20pytests/badge.svg)
 [![codecov](https://codecov.io/gh/pepkit/peppy/branch/master/graph/badge.svg)](https://codecov.io/gh/pepkit/peppy)
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pep.databio.org)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-`peppy` is the official python package for reading **Portable Encapsulated Projects** or **PEP**s in `python`. 
+`peppy` is the official python package for reading **Portable Encapsulated Projects** or **PEP**s in `python`.
 
 Links to complete documentation:
 

codecov.yml

@@ -0,0 +1,5 @@
+ignore:
+  - "*/argparser.py"
+  - "*/cli.py"
+  - "*/__main__.py"
+  - "setup.py"

docs/changelog.md

@@ -1,6 +1,14 @@
 # Changelog
 
-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. 
+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.
+
+## [0.31.1] -- 2021-04-15
+
+### Added
+- Support for remote URL config files
+
+### Fixed
+- Error when accessing `Project.subsample_table` property when no subsample tables were defined
 
 ## [0.31.0] - 2020-10-07
 
@@ -24,19 +32,19 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [0.30.1] - 2020-05-26
 
-### Changed 
+### Changed
 - Package authors list
 
 ## [0.30.0] - 2020-05-26
 
-**This version introduced backwards-incompatible changes.**  
+**This version introduced backwards-incompatible changes.**
 
 ### Added
 - attribute duplication functionality
 - config importing functionality
 - attribute removal functionality
 - possibility to define multi-attribute rules in attribute implication
-  
+
 ### Changed
 - Project configuration file to follow [PEP2.0.0](http://pep.databio.org/en/2.0.0/specification/) specification. Browse the specification for changes related to config format
 - Do not require `sample_name` attribute in the sample table
@@ -86,19 +94,19 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Added
 - `subsample_table` on a `Project` gives the table of sample subannotation / "units" if applicable.
 ### Changed
-- Add `attribute` parameter to `fetch_samples` function to enable more general applicability. 
+- Add `attribute` parameter to `fetch_samples` function to enable more general applicability.
 Additionally, the attribute value matching is more strict now -- requires perfect match.
 - Remove Python 3.4 support.
 - Use `attmap` for implementation of attribute-style access into a key-value collection.
 - Deprecate `sample_annotation` and `sample_subannotation` in favor of `sample_table` and `subsample_table`, respectively.
 
 ## [0.19.0] -- (2019-01-16)
-### New  
+### New
 - Added `activate_subproject` method to `Project`.
 ### Changed
 - `Project` construction no longer requires sample annotations sheet.
 - Specification of assembly/ies in project config outside of `implied_attributes`  is deprecated.
-- `implied_columns` and `derived_columns` are deprecated in favor of `implied_attributes` and `derived_attributes`.  
+- `implied_columns` and `derived_columns` are deprecated in favor of `implied_attributes` and `derived_attributes`.
 
 ## [0.18.2] -- (2018-07-23)
 ### Fixed
@@ -148,10 +156,10 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 ### New
 - Add `--lump` and `--lumpn` options
 - Catch submission errors from cluster resource managers
-- Implied columns can now be derived  
-- Now protocols can be specified on the command-line `--include-protocols`  
-- Add rudimentary figure summaries    
-- Allow wildcard protocol_mapping for catch-all pipeline assignment  
+- Implied columns can now be derived
+- Now protocols can be specified on the command-line `--include-protocols`
+- Add rudimentary figure summaries
+- Allow wildcard protocol_mapping for catch-all pipeline assignment
 - New sample_subtypes section in pipeline_interface
 ### Changed
 - Sample child classes are now defined explicitly in the pipeline interface. Previously, they were guessed based on presence of a class extending Sample in a pipeline script.
@@ -166,7 +174,7 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 - Merges pipeline interface and protocol mappings. This means we now allow direct pointers to `pipeline_interface.yaml` files, increasing flexibility, so this relaxes the specified folder structure that was previously used for `pipelines_dir` (with `config` subfolder).
 - Allow URLs as paths to sample sheets.
 - Allow tsv format for sample sheets.
-- Checks that the path to a pipeline actually exists before writing the submission script. 
+- Checks that the path to a pipeline actually exists before writing the submission script.
 ### Changed
 - Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models
 - Changed name of `pipelines_dir` to `pipeline_interfaces` (but maintained backwards compatibility for now).