merge

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+extend-ignore = E203,E501,W503
+max-line-length = 99

.github/workflows/linting.yml

@@ -0,0 +1,32 @@
+name: Linters
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 black isort
+      - name: Flake8 Lint
+        run: |
+          flake8 --ignore=E501,W503,E203 .
+      - name: Black Lint
+        run: |
+          black --line-length 99 --check --verbose .
+      - name: isort Lint
+        run: |
+          isort --profile black --check-only --diff .

.gitignore

@@ -105,6 +105,7 @@ celerybeat.pid
 
 # Environments
 .env
+.envrc
 .venv
 env/
 venv/

.travis.yml

@@ -1,20 +1,20 @@
 language: python
 python:
-  - '3.9'
+  - "3.9"
 cache: pip
 install:
   - pip install -r requirements.txt
   # - pip install -r requirements-dev.txt
- 
+
   - pwd
   - cd ..
   - git clone https://github.com/hubmapconsortium/ingest-validation-tools.git
   - cd ingest-validation-tools
   - pwd
-  - git checkout v0.0.15
+  - git checkout v0.0.17
   # - pip install "setuptools==60.9.0"
   - pip install -r requirements.txt
- 
+
   - cd ../ingest-validation-tests # Not sure if this is required, or if it resets between sections.
 script:
   - ./test.sh

README.md

@@ -1,9 +1,58 @@
 # ingest-validation-tests
 
-This repository contains plug-in tests for use during validation of submissions.  It is referenced by ingest-validation-tools.
+This repository contains plug-in tests for use during validation of submissions. It is referenced by ingest-validation-tools.
 
 ## Development process
 
+### Branches
+
 - Make new feature branches from `devel`.
+- Before submitting a PR, make sure your code is black, isort, and flake8 compliant. Run the following from the base `ingest-validation-tests` directory:
+
+  ```
+  black --line-length 99 .
+  isort --profile black --multi-line 3 .
+  flake8
+  ```
+
+  (Integrating black and potentially isort/flake8 with your editor may allow you to skip this step, see Setup section below.)
+
 - Make PRs to `devel`. (This is the default branch.)
-- The last reviewer to approve a PR should merge it.  At the moment that is likely to be @jswelling .
+- The last reviewer to approve a PR should merge it.
+
+### Setup
+
+- Creating and activating a virtual environment is recommended. These instructions assume you are using a virtual environment. Example using venv:
+
+  ```
+  python3.9 -m venv hm-ingest-validation-tests
+  source hm-ingest-validation-tests/bin/activate
+  ```
+
+- Run `pip install -r requirements-dev.txt`
+- (optional) Integrate black with your editor.
+  - [Instructions for black.](https://black.readthedocs.io/en/stable/integrations/editors.html)
+- (optional) Integrate [isort](https://pycqa.github.io/isort/) with your editor.
+- (optional) Integrate [flake8](https://flake8.pycqa.org/en/latest/index.html) with your editor.
+
+### Testing
+
+- If ingest-validation-tools is not already set up:
+
+  ```
+  # Starting from ingest-validation-tests...
+  cd ..
+  git clone https://github.com/hubmapconsortium/ingest-validation-tools.git
+  cd ingest-validation-tests
+  pip install -r ../ingest-validation-tools/requirements.txt
+  pip install -r ../ingest-validation-tools/requirements-dev.txt
+  ```
+
+- If ingest-validation-tools is already set up, add the appropriate ingest-validation-tools path and run:
+
+  ```
+  pip install -r <path-to-ingest-validation-tools>/requirements.txt
+  pip install -r <path-to-ingest-validation-tools>/requirements-dev.txt
+  ```
+
+- Run `test.sh`

pyproject.toml

@@ -0,0 +1,6 @@
+[tool.black]
+line-length = 99
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3

requirements-dev.txt

@@ -0,0 +1,11 @@
+black==23.12.1
+flake8==7.0.0
+git+https://github.com/hubmapconsortium/fastq-utils.git@v0.2.5#egg=hubmap-fastq-utils
+imagecodecs>=2023.3.16
+isort==5.13.2
+jsonschema==4.4.0
+pandas>=1.2.0
+pytest==8.0.0
+python-frontmatter>=1.0.0
+tifffile==2020.10.1
+xmlschema>=1.6

requirements.txt

@@ -1,7 +1,7 @@
-xmlschema>=1.6
-tifffile==2020.10.1
+git+https://github.com/hubmapconsortium/fastq-utils.git@v0.2.5#egg=hubmap-fastq-utils
+imagecodecs>=2023.3.16
 jsonschema==4.4.0
 pandas>=1.2.0
-imagecodecs>=2023.3.16
-python-frontmatter>=1.0.0
-git+https://github.com/hubmapconsortium/fastq-utils.git@v0.2.5#egg=hubmap-fastq-utils
+python-frontmatter>=1.1.0
+tifffile==2020.10.1
+xmlschema>=1.6