Fix minimal install and tidy up

.github/workflows/build.yml

@@ -0,0 +1,51 @@
+name: Build
+
+on: [push, pull_request]
+
+jobs:
+  build-and-test:
+    name: Build
+    runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: '3.10'
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+        name: Install Python
+        with:
+          python-version: '3.10'
+
+      - name: Display version
+        run: |
+          python --version
+          pip --version
+
+      - name: Install pypa/build
+        run: |
+          pip install build
+
+      - name: Build a binary wheel and a source tarball
+        run: |
+          python -m build
+
+      - name: Display content dist folder
+        run: |
+          ls dist/
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./dist/*
+
+      - name: Install distribution
+        run: |
+          pip install --pre --find-links dist rosettasciio[all,tests]
+
+      - name: Install HyperSpy (dev)
+        run: |
+          pip install https://github.com/hyperspy/hyperspy/archive/refs/heads/RELEASE_next_major.zip
+
+      - name: Test distribution
+        run: |
+          pytest --pyargs rsciio --reruns 3 -n 2

.github/workflows/tests.yml

@@ -14,26 +14,27 @@ jobs:
       matrix:
         os: [ubuntu, windows, macos]
         PYTHON_VERSION: ['3.8', '3.9']
-        PIP_SELECTOR: ['[all, tests]']
+        LABEL: ['']
         include:
           # test oldest supported version of main dependencies on python 3.6
           - os: ubuntu
             PYTHON_VERSION: '3.7'
-            OLDEST_SUPPORTED_VERSION: true
             DEPENDENCIES: matplotlib==3.1.3 numpy==1.17.1 scipy==1.1 imagecodecs==2020.1.31 tifffile==2020.2.16 dask==2.11.0 distributed==2.11.0 numba==0.52
-            PIP_SELECTOR: '[all, tests]'
-            LABEL: -oldest
+            LABEL: '-oldest'
           # test minimum requirement
           - os: ubuntu
             PYTHON_VERSION: '3.8'
-            PIP_SELECTOR: '[tests]'
-            LABEL: -minimum
+            LABEL: '-minimum'
+          - os: ubuntu
+            PYTHON_VERSION: '3.8'
+            LABEL: '-minimum-wo-hyperspy'
+          - os: ubuntu
+            PYTHON_VERSION: '3.8'
+            LABEL: '-wo-hyperspy'
           - os: ubuntu
             PYTHON_VERSION: '3.7'
-            PIP_SELECTOR: '[all, tests]'
           - os: ubuntu
             PYTHON_VERSION: '3.10'
-            PIP_SELECTOR: '[all, tests]'
 
     steps:
       - uses: actions/checkout@v3
@@ -43,24 +44,35 @@ jobs:
         with:
           python-version: ${{ matrix.PYTHON_VERSION }}
 
+      - name: Set Environment Variable
+        shell: bash
+        # Set PIP_SELECTOR environment variable according to matrix.LABEL
+        run: |
+          if [[ -n "${{ matrix.LABEL }}" && "${{ matrix.LABEL }}" == *"minimum"* ]]; then
+            PIP_SELECTOR="[tests]"
+          else
+            PIP_SELECTOR="[all, tests]"
+          fi
+          echo "PIP_SELECTOR=${PIP_SELECTOR}" >> $GITHUB_ENV
+
       - name: Display version
         run: |
           python --version
           pip --version
 
       - name: Install oldest supported version
-        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        if: contains(matrix.LABEL, 'oldest')
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
       - name: Install
         shell: bash
         run: |
-          pip install --upgrade -e .'${{ matrix.PIP_SELECTOR }}'
+          pip install --upgrade -e .'${{ env.PIP_SELECTOR }}'
 
       - name: Install (HyperSpy dev)
+        if: "!contains(matrix.LABEL, 'wo-hyperspy')"
         # Need to install hyperspy dev until hyperspy 2.0 is released
-        shell: bash
         run: |
           pip install https://github.com/hyperspy/hyperspy/archive/refs/heads/RELEASE_next_major.zip
 

.gitignore

@@ -1,5 +1,6 @@
 /docs/_build/*
 /build/*
+/dist/*
 /RosettaSciIO.egg-info/*
 *__pycache__*
 *test_compilers.obj

MANIFEST.in

@@ -1,6 +1,6 @@
 include *.txt
 include *.rst
-recursive-include rsciio *.pyx
-recursive-include docs *.txt *.rst *.pdf *py *bat makefile
+recursive-include rsciio *.pyx *specifications.yaml
+recursive-include docs *.txt *.rst *.pdf *.py *.bat makefile
 include rsciio/tests/bruker_data/test_compilers.c
 

pyproject.toml

@@ -3,12 +3,12 @@ requires = ["setuptools>=49.0", "wheel", "cython", "pyyaml"]
 build-backend = "setuptools.build_meta:__legacy__"
 
 [tool.pytest.ini_options]
-# Note we may need to use `-n 2` argument for pytest-xdist on CI 
+# Note we may need to use `-n 2` argument for pytest-xdist on CI
 # due to https://github.com/pytest-dev/pytest-xdist/issues/9.
 addopts = "-ra -n auto --dist loadfile"
 minversion = "6.0"
 testpaths = [
-    "rsciio/tests",
+  "rsciio/tests",
 ]
 
 [tool.towncrier]
@@ -62,7 +62,10 @@ testpaths = "rsciio/tests/"
 [tool.coverage.run]
 branch = true
 source = ["rsciio"]
-omit = ["rsciio/tests/*"]
+omit = [
+  "rsciio/tests/*",
+  "setup.py",
+]
 
 [tool.coverage.report]
 precision = 2

rsciio/__init__.py

@@ -34,3 +34,13 @@
             specs = yaml.safe_load(stream)
             specs["api"] = "rsciio.%s.api" % os.path.split(sub)[1]
             IO_PLUGINS.append(specs)
+
+
+__all__ = [
+    "__version__",
+    "IO_PLUGINS",
+]
+
+
+def __dir__():
+    return sorted(__all__)

rsciio/conftest.py

@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+# Copyright 2007-2022 The HyperSpy developers
+#
+# This file is part of RosettaSciIO.
+#
+# RosettaSciIO is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RosettaSciIO is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RosettaSciIO. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+from packaging.version import Version
+
+try:
+    import hyperspy
+
+    if Version(hyperspy.__version__) < Version("2.0.dev"):
+        raise Exception(
+            "To run the test suite using hyperspy, \
+            hyperspy 2.0 or higher is required."
+        )
+except ImportError:
+    pass

rsciio/digital_micrograph/api.py

@@ -26,12 +26,10 @@
 import dateutil.parser
 
 import numpy as np
-import traits.api as t
 from copy import deepcopy
 
 import rsciio.utils.utils_readfile as iou
 from rsciio.exceptions import DM3TagIDError, DM3DataTypeError, DM3TagTypeError
-import rsciio.utils.tools
 from box import Box