Readd CI and fix issues (#148)

* small change to readme

* readd ci

* start fixing tests

* use old typing list or magicgui fails

* use old typing list or magicgui fails

* add headless gui and qt libs

* fix syntax

* ditch 3.8

.github/workflows/ci.yml

@@ -0,0 +1,138 @@
+name: CI
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * 0" # every week (for --pre release tests)
+
+jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Set up QT libraries
+        uses: tlambert03/setup-qt-libs@v1
+
+      # if running a cron job, we add the --pre flag to test against pre-releases
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: Test
+        uses: aganders3/headless-gui@v1
+        with:
+          run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      # If something goes wrong, we can open an issue in the repo
+      - name: Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: '[test-bot] pip install --pre is failing'
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  docs:
+    name: Generate Docs
+    needs: test
+    if: success() && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Install dependencies
+        working-directory: ./docs
+        run: |
+          pip install -U pip
+          pip install -r requirements.txt
+
+      - name: Build the book
+        working-directory: ./docs
+        run: |
+          jupyter-book build .
+
+      - name: GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html
+
+  deploy:
+    name: Deploy
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+
+      - name: Build and publish
+        run: twine upload dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+
+      - uses: softprops/action-gh-release@v1
+        with:
+          generate_release_notes: true

README.md

@@ -8,8 +8,6 @@
 [![CI](https://github.com/brisvag/blik/actions/workflows/ci.yml/badge.svg)](https://github.com/brisvag/blik/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/brisvag/blik/branch/main/graph/badge.svg)](https://codecov.io/gh/brisvag/blik)
 
-*it means glance in Dutch*
-
 ![blik showcase](https://user-images.githubusercontent.com/23482191/161224963-ad746a06-c2e5-46fe-a13b-f356bc4ad72b.png)
 
 **`blik`** is a tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional [napari viewer](https://napari.org) and the scientific python stack.

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 name = "blik"
 description = "Python tool for visualising and interacting with cryo-ET and subtomogram averaging data."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { text = "GPLv3" }
 authors = [
     { email = "[email protected]", name = "Lorenzo Gaifas" },
@@ -18,7 +18,6 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
     "Natural Language :: English",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -48,7 +47,12 @@ all = [
     "napari-properties-viewer",
     "napari-label-interpolator",
 ]
-test = ["pytest>=6.0", "pytest-cov", "napari[all]>=0.4.18"]
+test = [
+    "pytest>=6.0",
+    "pytest-cov",
+    "pytest-qt",
+    "napari[all]>=0.4.18"
+]
 dev = [
     "black",
     "ipython",
@@ -57,6 +61,7 @@ dev = [
     "pre-commit",
     "pytest-cov",
     "pytest",
+    "pytest-qt",
     "rich",
     "ruff",
     "napari[all]>=0.4.18",
@@ -90,7 +95,7 @@ sources = ["src"]
 # https://github.com/charliermarsh/ruff
 [tool.ruff]
 line-length = 120
-target-version = "py38"
+target-version = "py39"
 src = ["src"]
 # https://beta.ruff.rs/docs/rules/
 select = [
@@ -127,7 +132,6 @@ ignore = [
 [tool.pytest.ini_options]
 minversion = "6.0"
 testpaths = ["tests"]
-filterwarnings = ["error"]
 
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]

src/blik/widgets/main_widget.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, List
 
 import numpy as np
 import pandas as pd
@@ -145,7 +145,9 @@ def add_to_exp(layer: napari.layers.Layer):
     call_button="Create",
     l_type={"choices": ["segmentation", "particles", "surface_picking"]},
 )
-def new(l_type) -> list[napari.layers.Layer]:
+def new(
+    l_type,
+) -> List[napari.layers.Layer]:  # noqa. This must be List, not list (magicgui...)
     """create a new layer to add to this experiment."""
     layers = getattr(new._main_widget["experiment"], "current_layers", [])
     if not layers:

tests/test_widget.py

@@ -14,7 +14,9 @@ def test_main_widget(make_napari_viewer):
     viewer = make_napari_viewer()
     with napari.layers._source.layer_source(reader_plugin="blik"):
         viewer.add_image(
-            np.ones((10, 10, 10)), metadata={"experiment_id": "test", "stack": False}
+            np.ones((10, 10, 10)),
+            name="test",
+            metadata={"experiment_id": "test", "stack": False},
         )
     viewer.window.add_dock_widget(wdg)
     assert "test" in wdg[0].experiment_id.choices
@@ -28,6 +30,7 @@ def test_main_widget(make_napari_viewer):
     # add new picking
     wdg[1].l_type.value = "particles"
     wdg[1]()
+    assert viewer.layers[-2].name == "test - particle orientations"
     assert viewer.layers[-1].name == "test - particle positions"
 
     # add layer manually