Merge pull request #33 from NHPatterson/fix-json-pad-issue

fix serialization of numpy to json with encoder

.github/workflows/test_and_deploy.yml

@@ -19,9 +19,10 @@ jobs:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}
     strategy:
+      fail-fast: false
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9"]
+        python-version: [3.8, 3.9, "3.10"]
 
     steps:
       - uses: actions/checkout@v2
@@ -31,37 +32,18 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      # these libraries, along with pytest-xvfb (added in the `deps` in tox.ini),
-      # enable testing on Qt on linux
-      - name: Install Linux libraries
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
-            libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
-            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
-      # strategy borrowed from vispy for installing opengl libs on windows
-      - name: Install Windows OpenGL
-        if: runner.os == 'Windows'
-        run: |
-          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
-          if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools tox tox-gh-actions
-      # this runs the platform-specific tests declared in tox.ini
-      - name: Test with tox
-        run: tox
-        env:
-          PLATFORM: ${{ matrix.platform }}
-
-      - name: Coverage
-        uses: codecov/codecov-action@v2
+          pip install pytest pytest-cookies tox napari-plugin-engine
+          pip install .
+      - name: Test
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: python -m pytest -s -v --color=yes
 
 
   deploy:

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["setuptools", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.setuptools_scm]
+write_to = "src/napari_imsmicrolink/_version.py"

setup.cfg

@@ -1,6 +1,5 @@
 [metadata]
 name = napari-imsmicrolink
-version = 0.1.8
 author = Nathan Heath Patterson
 author_email = heath.patterson@vanderbilt.edu
 license = MIT
@@ -15,7 +14,6 @@ classifiers =
 	Topic :: Software Development :: Testing
 	Programming Language :: Python
 	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3.7
 	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
@@ -29,7 +27,9 @@ project_urls =
 
 [options]
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
+package_dir =
+    =src
 # add your package requirements here
 install_requires = 
 	numpy
@@ -45,7 +45,12 @@ install_requires =
 	opencv-python
 	czifile
 	imagecodecs
+	napari[all]
+setup_requires =
+    setuptools-scm
 
+[options.packages.find]
+where = src
 
 [options.entry_points]
 napari.manifest = 

napari_imsmicrolink/_dock_widget.py → src/napari_imsmicrolink/_dock_widget.py

@@ -37,7 +37,7 @@
 from napari_imsmicrolink.utils.color import COLOR_HEXES
 from napari_imsmicrolink.utils.image import centered_transform, grayscale
 from napari_imsmicrolink.utils.coords import pmap_coords_to_h5
-
+from napari_imsmicrolink.utils.json import NpEncoder
 
 class IMSMicroLink(QWidget):
     def __init__(self, napari_viewer: napari.Viewer):
@@ -833,7 +833,7 @@ def _write_data(
         pmeta_out_fp = Path(output_dir) / f"{project_name}-IMSML-meta.json"
 
         with open(pmeta_out_fp, "w") as json_out:
-            json.dump(project_metadata, json_out, indent=1)
+            json.dump(project_metadata, json_out, indent=1, cls=NpEncoder)
 
         if output_filetype == ".h5":
             if split_by_file_roi:

src/napari_imsmicrolink/utils/json.py

@@ -0,0 +1,12 @@
+import json
+import numpy as np
+
+class NpEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, np.integer):
+            return int(obj)
+        if isinstance(obj, np.floating):
+            return float(obj)
+        if isinstance(obj, np.ndarray):
+            return obj.tolist()
+        return super(NpEncoder, self).default(obj)

tox.ini

@@ -15,26 +15,10 @@ PLATFORM =
     windows-latest: windows
 
 [testenv]
-platform = 
-    macos: darwin
-    linux: linux
-    windows: win32
-passenv = 
-    CI
-    GITHUB_ACTIONS
-    DISPLAY XAUTHORITY
-    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
-    PYVISTA_OFF_SCREEN
-deps = 
-    pytest  # https://docs.pytest.org/en/latest/contents.html
-    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
-    pytest-xvfb ; sys_platform == 'linux'
-    # you can remove these if you don't use them
-    napari
-    pytest-qt
-    qtpy
-    pyqt5
-commands = pytest -v --color=yes --cov=napari_imsmicrolink --cov-report=xml
+deps = pytest
+       pytest-cookies
+       tox
+commands = pytest -v {posargs:tests}
 
 [flake8]
 max-line-length = 88