Merge pull request #152 from pepkit/dev

v0.8.1 release

.github/workflows/python-publish.yml

@@ -12,12 +12,11 @@ jobs:
     name: upload release to PyPI
     runs-on: ubuntu-latest
     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@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.pre-commit-config.yaml

@@ -9,13 +9,14 @@ repos:
       - id: trailing-whitespace
       - id: check-ast
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.9.1
-    hooks:
-      - id: isort
-        args: ["--profile", "black"]
+#  - repo: https://github.com/PyCQA/isort
+#    rev: 5.9.1
+#    hooks:
+#      - id: isort
+#        args: ["--profile", "black"]
 
   - repo: https://github.com/psf/black
     rev: 21.6b0
     hooks:
       - id: black
+        args : ["--line-length", "99"]

README.md

@@ -9,20 +9,33 @@
 
 Pipestat standardizes reporting of pipeline results. It provides 1) a standard specification for how pipeline outputs should be stored; and 2) an implementation to easily write results to that format from within Python or from the command line. A pipeline author defines all the outputs produced by a pipeline by writing a JSON-schema. The pipeline then uses pipestat to report pipeline outputs as the pipeline runs, either via the Python API or command line interface. The user configures results to be stored either in a [YAML-formatted file](https://yaml.org/spec/1.2/spec.html) or a [PostgreSQL database](https://www.postgresql.org/).
 
-See [Pipestat documentation](https://pipestat.databio.org) for complete details.
+See [Pipestat documentation](https://pep.databio.org/pipestat/) for complete details.
 
 
 ## Developer tests
 
-First you need a local demo instance of posgres running to test the database back-end. you can get one using docker matching the included config file like this:
+###  Optional Dependencies
 
-```
-docker run --rm -it -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pipestat-password -e POSTGRES_DB=pipestat-test -p 5432:5432 postgres
-```
+Note: to run the pytest suite locally, you will need to install the related requirements:
+
+```bash
+cd pipestat
 
-Then, run tests:
+pip install -r requirements/requirements-test.txt
 
 ```
-pytest
+
+### Database Backend Configuration for Tests
+
+Many of the tests require a postgres database to be set up otherwise many of the tests will skip.
+
+We recommend using docker:
+```bash
+docker run --rm -it --name pipestat_test_db \
+    -e POSTGRES_USER=postgres \
+    -e POSTGRES_PASSWORD=pipestat-password \
+    -e POSTGRES_DB=pipestat-test \
+    -p 5432:5432 \
+    postgres
 ```