Merge pull request #701 from hed-standard/master

Prepare for release 0.3.0
hed-standard · Jun 20, 2023 · b725048 · b725048
2 parents 6af6b24 + 2f01b91
commit b725048
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -2,9 +2,17 @@ version: 2
 updates:
   - package-ecosystem: "github-actions"
     directory: "/"
+    target-branch: "develop"
     schedule:
       interval: "weekly"
   - package-ecosystem: "pip"
     directory: "/"
+    target-branch: "develop"
     schedule:
       interval: "weekly"
+
+  - package-ecosystem: gitsubmodule
+    schedule:
+        interval: "daily"
+    target-branch: "develop"
+    directory: /
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -104,7 +104,7 @@ jobs:
         with:
           coverageCommand: coverage xml
           debug: true
-        uses: paambaati/codeclimate-action@v3.2.0
+        uses: paambaati/codeclimate-action@v4.0.0
         env:
           CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
 
diff --git a/.github/workflows/spec_tests.yaml b/.github/workflows/spec_tests.yaml
@@ -0,0 +1,43 @@
+name: Spec_tests
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.9]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - name: Checkout hed-python
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade --upgrade-strategy eager pip
+          pip install -r requirements.txt
+
+      - name: Test with unittest
+        run: |
+           python -m unittest spec_tests/test_errors.py > test_results.txt
+
+      - name: Upload spec test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: spec-test-results
+          path: test_results.txt
+
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "spec_tests/hed-specification"]
+	path = spec_tests/hed-specification
+	url = https://github.com/hed-standard/hed-specification/
+	branch = develop
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 HED Standard Working Group
+Copyright (c) 2020+ HED Standard Working Group
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,3 +1,9 @@
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8056010.svg)](https://doi.org/10.5281/zenodo.8056010)
+[![Maintainability](https://api.codeclimate.com/v1/badges/11bf2329590e7b0164ba/maintainability)](https://codeclimate.com/github/hed-standard/hed-python/maintainability)
+[![Test Coverage](https://api.codeclimate.com/v1/badges/11bf2329590e7b0164ba/test_coverage)](https://codeclimate.com/github/hed-standard/hed-python/test_coverage)
+![PyPI - Status](https://img.shields.io/pypi/v/hedtools)
+
+
 # HEDTools - Python
 HED (Hierarchical Event Descriptors) is a framework for systematically describing
 both laboratory and real-world events as well as other experimental metadata.
@@ -11,11 +17,11 @@ Most people will simply annotate their events by creating a spreadsheet
 or a BIDS JSON sidecar that associates HED tags with event codes or the events themselves.
 If you have such a spreadsheet or a JSON, 
 you can use the HED Online Validator currently available at 
-[https://hedtools.ucsd.edu/hed](https://hedtools.ucsd.edu/hed) to validate or transform
+[https://hedtools.org](https://hedtools.org) to validate or transform
 your files without downloading any tools. 
 
 A version of the online tools corresponding to the `develop` branch can be found at:
-[https://hedtools.ucsd.edu/hed_dev](https://hedtools.ucsd.edu/hed_dev).
+[https://hedtools.org/hed_dev](https://hedtools.org/hed_dev).
 
 ### Installation
 Use `pip` to install `hedtools` from PyPI:
@@ -95,7 +101,7 @@ Use `hed.schema.set_cache_directory` to change the location.
 The HED cache can be shared across processes.
 
 Starting with `hedtools 0.2.0` local copies of the most recent schema versions
-are stored within the code modules for easy access.
+are stored within the code modules for easy access.  
 
 ### Other links of interest
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,12 +1,10 @@
 defusedxml>=0.7.1
-inflect>=5.5.1
+inflect>=6.0.2
 myst-parser>=0.18.1
-openpyxl>=3.0.9
+numpy>=1.21.6
+openpyxl>=3.1.0
 pandas>=1.3.5
-portalocker>=2.4.0
-semantic_version>=2.9.0
+portalocker>=2.7.0
+semantic_version>=2.10.0
 Sphinx>=5.2.2
 sphinx_rtd_theme>=1.0.0
-
-# This is just needed for secure_filename and should probably be removed
-Werkzeug>=2.1.2
diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html
@@ -12,7 +12,7 @@
       <li class="toctree-li"><a href="https://www.hed-resources.org/en/latest/">Main resource page</a></li>
       <li class="toctree-li"><a href="https://www.hedtags.org">Project home page</a></li>
       <li class="toctree-li"><a href="https://www.hedtags.org/display_hed.html">Schema viewer</a></li>
-      <li class="toctree-li"><a href="https://www.hedtags.org/display_hed_library.html">Library schema viewer</a></li>
+      <li class="toctree-li"><a href="https://www.hedtags.org/display_hed_prerelease.html">Prerelease schema viewer</a></li>
       <li class="toctree-li"><a href="https://hed-specification.readthedocs.io/en/latest/index.html">Specification</a></li>
       <li class="toctree-li"><a href="https://hed-examples.readthedocs.io/en/latest/">Examples and tutorials</a></li>
       <li class="toctree-li"><a href="https://hedtools.ucsd.edu/hed">Online tools</a></li>

diff --git a/docs/source/api2.rst b/docs/source/api2.rst
@@ -1,5 +1,5 @@
 HED API reference (Auto style)
-========================
+==============================
 
 .. currentmodule:: hed
 

diff --git a/hed/__init__.py b/hed/__init__.py
@@ -7,12 +7,13 @@
 from hed.models.spreadsheet_input import SpreadsheetInput
 from hed.models.tabular_input import TabularInput
 from hed.models.sidecar import Sidecar
+from hed.models.definition_dict import DefinitionDict
+
 
 from hed.schema.hed_schema import HedSchema
 from hed.schema.hed_schema_group import HedSchemaGroup
-from hed.schema.hed_schema_io import get_schema, get_schema_versions, load_schema, load_schema_version
+from hed.schema.hed_schema_io import get_schema, load_schema, load_schema_version
 
-from hed.validator.hed_validator import HedValidator
 
 # from hed import errors, models, schema, tools, validator
 

diff --git a/hed/errors/__init__.py b/hed/errors/__init__.py
@@ -1,4 +1,5 @@
-from .error_reporter import ErrorHandler, get_exception_issue_string, get_printable_issue_string
-from .error_types import DefinitionErrors, OnsetErrors, SchemaErrors, SchemaWarnings,  SidecarErrors, ValidationErrors
+from .error_reporter import ErrorHandler, get_printable_issue_string, sort_issues
+from .error_types import DefinitionErrors, OnsetErrors, SchemaErrors, SchemaWarnings,  SidecarErrors, \
+    ValidationErrors, ColumnErrors
 from .error_types import ErrorContext, ErrorSeverity
 from .exceptions import HedExceptions, HedFileError