Merge pull request #12 from hed-standard/dev_tests

Try to get tests working

.github/workflows/run_single_test.yml

@@ -0,0 +1,158 @@
+name: Run one test
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  run-all-tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+
+    steps:
+      - name: Cancel non-latest runs
+        uses: styfle/[email protected]
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip list
+          python -m pip check
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        if: ${{ matrix.os != 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_hed"
+
+      - name: Test installation from a wheel (windows)
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          test-wheel-env/Scripts/activate.bat
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_hed"
+
+  run-all-tests-on-conda:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    defaults:
+     run:
+       shell: bash -l {0}  # needed for conda environment to work
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: conda-linux-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: true
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_hed"

pyproject.toml

@@ -37,6 +37,7 @@ keywords = [
 dependencies = [
     "pynwb>=2.5.0",
     "hdmf>=3.10.0",
+    "hedtools>=0.4.0"
 ]
 
 # TODO: add URLs before release

setup.py

@@ -1,64 +1,69 @@
 # -*- coding: utf-8 -*-
 
-import os
+from setuptools import setup
 
-from setuptools import setup, find_packages
-from shutil import copy2
+if __name__ == "__main__":
+    setup()
 
-# load README.md/README.rst file
-try:
-    if os.path.exists('README.md'):
-        with open('README.md', 'r') as fp:
-            readme = fp.read()
-            readme_type = 'text/markdown; charset=UTF-8'
-    elif os.path.exists('README.rst'):
-        with open('README.rst', 'r') as fp:
-            readme = fp.read()
-            readme_type = 'text/x-rst; charset=UTF-8'
-    else:
-        readme = ""
-except Exception:
-    readme = ""
-
-setup_args = {
-    'name': 'ndx-hed',
-    'version': '0.1.0',
-    'description': 'NWB extension for storing HED annotations in VectorData format.',
-    'long_description': readme,
-    'long_description_content_type': readme_type,
-    'author': 'Ryan Ly, Kay Robbins',
-    'author_email': '[email protected], [email protected]',
-    'url': 'https://github.com/hed-standard/ndx-hed',
-    'license': 'BSD 3-Clause',
-    'install_requires': [
-        'pynwb>=1.1.2'
-    ],
-    'packages': find_packages('src/pynwb'),
-    'package_dir': {'': 'src/pynwb'},
-    'package_data': {'ndx_hed': [
-        'spec/ndx-hed.namespace.yaml',
-        'spec/ndx-hed.extensions.yaml',
-    ]},
-    'classifiers': [
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-    ],
-    'zip_safe': False
-}
-
-
-def _copy_spec_files(project_dir):
-    ns_path = os.path.join(project_dir, 'spec', 'ndx-hed.namespace.yaml')
-    ext_path = os.path.join(project_dir, 'spec', 'ndx-hed.extensions.yaml')
-
-    dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_hed', 'spec')
-    if not os.path.exists(dst_dir):
-        os.mkdir(dst_dir)
-
-    copy2(ns_path, dst_dir)
-    copy2(ext_path, dst_dir)
-
-
-if __name__ == '__main__':
-    _copy_spec_files(os.path.dirname(__file__))
-    setup(**setup_args)
+# import os
+#
+# from setuptools import setup, find_packages
+# from shutil import copy2
+#
+# # load README.md/README.rst file
+# try:
+#     if os.path.exists('README.md'):
+#         with open('README.md', 'r') as fp:
+#             readme = fp.read()
+#             readme_type = 'text/markdown; charset=UTF-8'
+#     elif os.path.exists('README.rst'):
+#         with open('README.rst', 'r') as fp:
+#             readme = fp.read()
+#             readme_type = 'text/x-rst; charset=UTF-8'
+#     else:
+#         readme = ""
+# except Exception:
+#     readme = ""
+#
+# setup_args = {
+#     'name': 'ndx-hed',
+#     'version': '0.1.0',
+#     'description': 'NWB extension for storing HED annotations in VectorData format.',
+#     'long_description': readme,
+#     'long_description_content_type': readme_type,
+#     'author': 'Ryan Ly, Kay Robbins',
+#     'author_email': '[email protected], [email protected]',
+#     'url': 'https://github.com/hed-standard/ndx-hed',
+#     'license': 'BSD 3-Clause',
+#     'install_requires': [
+#         'pynwb>=1.1.2'
+#     ],
+#     'packages': find_packages('src/pynwb'),
+#     'package_dir': {'': 'src/pynwb'},
+#     'package_data': {'ndx_hed': [
+#         'spec/ndx-hed.namespace.yaml',
+#         'spec/ndx-hed.extensions.yaml',
+#     ]},
+#     'classifiers': [
+#         "Intended Audience :: Developers",
+#         "Intended Audience :: Science/Research",
+#     ],
+#     'zip_safe': False
+# }
+#
+#
+# def _copy_spec_files(project_dir):
+#     ns_path = os.path.join(project_dir, 'spec', 'ndx-hed.namespace.yaml')
+#     ext_path = os.path.join(project_dir, 'spec', 'ndx-hed.extensions.yaml')
+#
+#     dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_hed', 'spec')
+#     if not os.path.exists(dst_dir):
+#         os.mkdir(dst_dir)
+#
+#     copy2(ns_path, dst_dir)
+#     copy2(ext_path, dst_dir)
+#
+#
+# if __name__ == '__main__':
+#     _copy_spec_files(os.path.dirname(__file__))
+#     setup(**setup_args)

src/pynwb/ndx_hed/__init__.py

@@ -5,7 +5,7 @@
 ndx_hed_specpath = os.path.join(
     os.path.dirname(__file__),
     'spec',
-    'ndx-events.namespace.yaml'
+    'ndx-hed.namespace.yaml'
 )
 
 # If the extension has not been installed yet but we are running directly from