Merge branch 'main' into submission-linking

HEPData · Jul 6, 2023 · 85458d6 · 85458d6
2 parents 6e0619c + 8a56cb8
commit 85458d6
Show file tree

Hide file tree

Showing 9 changed files with 211 additions and 34 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,7 +3,7 @@ name: Continuous Integration
 on:
   push:
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
   release:
     types: [ published ]
   schedule:
@@ -16,12 +16,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.6', '3.7', '3.8', '3.9' ]
+        python-version: [ '3.7', '3.8', '3.9' ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install pip dependencies
@@ -39,7 +39,7 @@ jobs:
       env:
         COVERAGE_FILE: '.coverage_libyaml'
     - name: Run coveralls
-      if: startsWith(matrix.python-version, '3.8')
+      if: startsWith(matrix.python-version, '3.9')
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         COVERALLS_SERVICE_NAME: github
@@ -52,17 +52,17 @@ jobs:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.7'
+        python-version: '3.9'
     - name: Build PyPI package
       run: |
         pip install wheel
         python setup.py sdist bdist_wheel
     - name: Publish distribution to PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+     - method: pip
+       path: .
+       extra_requirements:
+         - docs
diff --git a/README.rst b/README.rst
@@ -2,16 +2,16 @@
  HEPData Validator
 ==================
 
-.. image:: https://github.com/HEPData/hepdata-validator/workflows/Continuous%20Integration/badge.svg?branch=master
-   :target: https://github.com/HEPData/hepdata-validator/actions?query=branch%3Amaster
+.. image:: https://github.com/HEPData/hepdata-validator/workflows/Continuous%20Integration/badge.svg?branch=main
+   :target: https://github.com/HEPData/hepdata-validator/actions?query=branch%3Amain
    :alt: GitHub Actions Build Status
 
-.. image:: https://coveralls.io/repos/github/HEPData/hepdata-validator/badge.svg?branch=master
-   :target: https://coveralls.io/github/HEPData/hepdata-validator?branch=master
+.. image:: https://coveralls.io/repos/github/HEPData/hepdata-validator/badge.svg?branch=main
+   :target: https://coveralls.io/github/HEPData/hepdata-validator?branch=main
    :alt: Coveralls Status
 
 .. image:: https://img.shields.io/github/license/HEPData/hepdata-validator.svg
-   :target: https://github.com/HEPData/hepdata-validator/blob/master/LICENSE.txt
+   :target: https://github.com/HEPData/hepdata-validator/blob/main/LICENSE.txt
    :alt: License
 
 .. image:: https://img.shields.io/github/release/hepdata/hepdata-validator.svg?maxAge=2592000
@@ -27,12 +27,12 @@
    :alt: GitHub Issues
 
 .. image:: https://readthedocs.org/projects/hepdata-validator/badge/?version=latest
-   :target: http://hepdata-validator.readthedocs.io/en/latest/?badge=latest
+   :target: https://hepdata-validator.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 
 JSON schema and validation code (in Python 3) for HEPData submissions
 
-* Documentation: http://hepdata-validator.readthedocs.io
+* Documentation: https://hepdata-validator.readthedocs.io
 
 
 Installation
@@ -65,16 +65,17 @@ Developers should install from GitHub in a `virtual environment <https://docs.py
 
    $ git clone https://github.com/HEPData/hepdata-validator
    $ cd hepdata-validator
-   $ python3 -m venv ~/venv/hepdata-validator
-   $ source ~/venv/hepdata-validator/bin/activate
-   (hepdata-validator) $ pip install --upgrade -e ".[tests]"
+   $ python3.9 -m venv venv
+   $ source venv/bin/activate
+   (venv)$ pip install --upgrade pip
+   (venv)$ pip install --upgrade -e ".[all]"
 
 Tests should be run both with and without LibYAML, as error messages from the different YAML parsers vary:
 
 .. code:: bash
 
-   (hepdata-validator) $ USE_LIBYAML=True pytest testsuite
-   (hepdata-validator) $ USE_LIBYAML=False pytest testsuite
+   (venv) $ USE_LIBYAML=True pytest testsuite
+   (venv) $ USE_LIBYAML=False pytest testsuite
 
 Usage
 -----
@@ -266,7 +267,7 @@ Schema Versions
 ---------------
 
 When considering **native HEPData JSON schemas**, there are multiple `versions
-<https://github.com/HEPData/hepdata-validator/tree/master/hepdata_validator/schemas>`_.
+<https://github.com/HEPData/hepdata-validator/tree/main/hepdata_validator/schemas>`_.
 In most cases you should use the **latest** version (the default). If you need to use a different version,
 you can pass a keyword argument ``schema_version`` when initialising the validator:
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -57,8 +57,8 @@
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
 
-# The master toctree document.
-master_doc = 'index'
+# The root toctree document.
+root_doc = 'index'
 
 # General information about the project.
 project = u''
@@ -85,7 +85,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -265,7 +265,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  (master_doc, 'HEPData-Validator.tex', u'HEPData Documentation',
+  (root_doc, 'HEPData-Validator.tex', u'HEPData Documentation',
    u'CERN', 'manual'),
 ]
 
@@ -295,7 +295,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'HEPData Validator', u'HEPData Validator Documentation',
+    (root_doc, 'HEPData Validator', u'HEPData Validator Documentation',
      [author], 1)
 ]
 
@@ -309,7 +309,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'HEPData Validator', u'HEPData Validator Documentation',
+  (root_doc, 'HEPData Validator', u'HEPData Validator Documentation',
    author, 'HEPData Validator', 'Submission schemas and validation for HEPData.',
    'Miscellaneous'),
 ]
@@ -328,4 +328,4 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/3/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/3/', None)}
diff --git a/hepdata_validator/__init__.py b/hepdata_validator/__init__.py
@@ -25,7 +25,6 @@
 import abc
 import os
 
-from jsonschema import validate as json_validate, ValidationError
 from jsonschema.validators import validator_for
 from jsonschema.exceptions import by_relevance
 from packaging import version as packaging_version

diff --git a/hepdata_validator/data_file_validator.py b/hepdata_validator/data_file_validator.py
@@ -247,7 +247,7 @@ def check_length_values(self, file_path, data):
         """
         Check that the length of the 'values' list is consistent for
         each of the independent_variables and dependent_variables.
-        Adds validation error if uncertainties are all zero.
+        Invalidate only independent_variables but no dependent_variables.
 
         :param data: data table in YAML format
         """
@@ -260,6 +260,14 @@ def check_length_values(self, file_path, data):
                 instance=data
             )
             self.add_validation_error(file_path, error)
+        if indep_count and not dep_count:  # only independent_variables
+            error = ValidationError(
+                "Case of only independent_variables but no dependent_variables is not supported: " +
+                "independent_variables %s, dependent_variables %s" % (str(indep_count), str(dep_count)),
+                instance=data
+            )
+            self.add_validation_error(file_path, error)
+
 
     def convert_to_float(self, error, file_path, path, instance):
         """

diff --git a/setup.py b/setup.py
@@ -18,10 +18,12 @@
 
 extras_require = {
     'all': [],
-    'docs': ['Sphinx>=1.4.2'],
+    'docs': ['Sphinx>7'],
     'tests': test_requirements,
 }
 
+for name, reqs in extras_require.items():
+    extras_require['all'].extend(reqs)
 
 class PyTest(TestCommand):
     """PyTest Test."""
@@ -92,7 +94,7 @@ def run_tests(self):
     test_suite='hepdata_validator.testsuite',
     tests_require=test_requirements,
     cmdclass={'test': PyTest},
-    python_requires='>=3.6',
+    python_requires='>=3.7',
     entry_points={
         'console_scripts': ['hepdata-validate=hepdata_validator.cli:validate'],
     }

diff --git a/testsuite/test_data/binning_average.yaml b/testsuite/test_data/binning_average.yaml
@@ -0,0 +1,128 @@
+dependent_variables: []
+independent_variables:
+- header:
+    name: Bin
+  values:
+  - value: 0
+  - value: 1
+  - value: 2
+  - value: 3
+  - value: 4
+  - value: 5
+  - value: 6
+  - value: 7
+  - value: 8
+  - value: 9
+  - value: 10
+  - value: 11
+  - value: 12
+  - value: 13
+  - value: 14
+  - value: 15
+  - value: 16
+  - value: 17
+  - value: 18
+  - value: 19
+  - value: 20
+  - value: 21
+  - value: 22
+  - value: 23
+  - value: 24
+  - value: 25
+  - value: 26
+  - value: 27
+  - value: 28
+  - value: 29
+  - value: 30
+  - value: 31
+  - value: 32
+  - value: 33
+  - value: 34
+  - value: 35
+  - value: 36
+  - value: 37
+  - value: 38
+  - value: 39
+- header:
+    name: Bin
+  values:
+  - high: 1.05
+    low: 1.0
+  - high: 1.1
+    low: 1.05
+  - high: 1.15
+    low: 1.1
+  - high: 1.2
+    low: 1.15
+  - high: 1.25
+    low: 1.2
+  - high: 1.3
+    low: 1.25
+  - high: 1.35
+    low: 1.3
+  - high: 1.4
+    low: 1.35
+  - high: 1.45
+    low: 1.4
+  - high: 1.5035
+    low: 1.45
+  - high: -0.8
+    low: -1.0
+  - high: -0.6
+    low: -0.8
+  - high: -0.4
+    low: -0.6
+  - high: -0.2
+    low: -0.4
+  - high: 0.0
+    low: -0.2
+  - high: 0.2
+    low: 0.0
+  - high: 0.4
+    low: 0.2
+  - high: 0.6
+    low: 0.4
+  - high: 0.8
+    low: 0.6
+  - high: 1.0
+    low: 0.8
+  - high: -0.8
+    low: -1.0
+  - high: -0.6
+    low: -0.8
+  - high: -0.4
+    low: -0.6
+  - high: -0.2
+    low: -0.4
+  - high: 0.0
+    low: -0.2
+  - high: 0.2
+    low: 0.0
+  - high: 0.4
+    low: 0.2
+  - high: 0.6
+    low: 0.4
+  - high: 0.8
+    low: 0.6
+  - high: 1.0
+    low: 0.8
+  - high: 0.62832
+    low: 0.0
+  - high: 1.2566
+    low: 0.62832
+  - high: 1.885
+    low: 1.2566
+  - high: 2.5133
+    low: 1.885
+  - high: 3.1416
+    low: 2.5133
+  - high: 3.7699
+    low: 3.1416
+  - high: 4.3982
+    low: 3.7699
+  - high: 5.0265
+    low: 4.3982
+  - high: 5.6549
+    low: 5.0265
+  - high: 6.2832
+    low: 5.6549