Merge branch 'yoda2_writer' of github.com:20DM/hepdata-converter into…

… yoda2_writer

.github/workflows/ci.yml

@@ -3,7 +3,7 @@ name: Continuous Integration
 on:
   push:
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
   release:
     types: [ published ]
 
@@ -14,22 +14,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: Install pip dependencies
       run: |
         pip install --upgrade pip
-        pip install --ignore-installed coveralls
+        pip install coveralls
     - name: Run tests
       env:
-        DOCKER_IMAGE: hepdata/hepdata-converter:0.2.0
+        DOCKER_IMAGE: hepdata/hepdata-converter:latest
       run: |
         export CURRENT_PATH=`pwd`
-        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && coverage run -m unittest discover hepdata_converter/testsuite 'test_*'"
-        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && python3 setup.py install && hepdata-converter -v"
+        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && pip install -e '.[tests]' && hepdata-converter -v && coverage run -m unittest discover hepdata_converter/testsuite 'test_*'"
     - name: Run coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -42,14 +41,14 @@ jobs:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Build PyPI package
       env:
-        DOCKER_IMAGE: hepdata/hepdata-converter:0.2.0
+        DOCKER_IMAGE: hepdata/hepdata-converter:latest
       run: |
         export CURRENT_PATH=`pwd`
-        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && pip3 install wheel"
-        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && python3 setup.py sdist bdist_wheel"
+        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && pip install wheel"
+        docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c "cd $CURRENT_PATH && python setup.py sdist bdist_wheel"
     - name: Publish distribution to PyPI
       uses: pypa/gh-action-pypi-publish@master
       with:

.gitignore

@@ -58,4 +58,7 @@ README.html
 target/
 
 .idea
-MANIFEST
+MANIFEST
+
+# venv
+venv/

.readthedocs.yml

@@ -5,18 +5,27 @@
 # Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
+  # Fail on all warnings to avoid broken references
+  fail_on_warning: true
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.7
   install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+  - method: pip
+    path: .
+    extra_requirements:
+    - docs

README.rst

@@ -3,16 +3,16 @@ HEPData Converter
 =================
 
 
-.. image:: https://github.com/HEPData/hepdata-converter/workflows/Continuous%20Integration/badge.svg?branch=master
-   :target: https://github.com/HEPData/hepdata-converter/actions?query=branch%3Amaster
+.. image:: https://github.com/HEPData/hepdata-converter/actions/workflows/ci.yml/badge.svg?branch=main
+   :target: https://github.com/HEPData/hepdata-converter/actions?query=branch%3Amain
    :alt: GitHub Actions Build Status
 
-.. image:: https://coveralls.io/repos/github/HEPData/hepdata-converter/badge.svg?branch=master
-   :target: https://coveralls.io/github/HEPData/hepdata-converter?branch=master
+.. image:: https://coveralls.io/repos/github/HEPData/hepdata-converter/badge.svg?branch=main
+   :target: https://coveralls.io/github/HEPData/hepdata-converter?branch=main
    :alt: Coveralls Status
 
 .. image:: https://img.shields.io/github/license/HEPData/hepdata-converter.svg
-   :target: https://github.com/HEPData/hepdata-converter/blob/master/LICENSE.txt
+   :target: https://github.com/HEPData/hepdata-converter/blob/main/LICENSE.txt
    :alt: License
 
 .. image:: https://img.shields.io/github/release/hepdata/hepdata-converter.svg?maxAge=2592000
@@ -34,11 +34,11 @@ HEPData Converter
 
 This Python 3 library provides support for converting:
 
-* Old HepData input format (`sample <https://github.com/HEPData/hepdata-submission/blob/master/examples/oldhepdata/sample.oldhepdata>`_) to `YAML <https://github.com/HEPData/hepdata-submission>`_
+* Old HepData input format (`sample <https://github.com/HEPData/hepdata-submission/blob/main/examples/oldhepdata/sample.oldhepdata>`_) to `YAML <https://github.com/HEPData/hepdata-submission>`_
 * `YAML <https://github.com/HEPData/hepdata-submission>`_ to:
 
-  * `ROOT <https://root.cern.ch>`_ (tested with v6.22/02)
-  * `YODA <https://yoda.hepforge.org>`_ (tested with v1.8.3)
+  * `ROOT <https://root.cern.ch>`_ (tested with v6.28/04)
+  * `YODA <https://yoda.hepforge.org>`_ (tested with v2.0.0alpha)
   * `CSV <https://en.wikipedia.org/wiki/Comma-separated_values>`_
 
-Documentation: http://hepdata-converter.readthedocs.io
+Documentation: https://hepdata-converter.readthedocs.io

docs/conf.py

@@ -98,7 +98,7 @@ def __getattr__(cls, name):
 #
 # 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:
@@ -340,4 +340,4 @@ def __getattr__(cls, name):
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/2/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/3/', None)}

docs/installation.rst

@@ -33,12 +33,13 @@ alternative output formats via the web interface.
 
 To install this package locally, you first need to install `YODA <https://yoda.hepforge.org>`_ and
 `ROOT <https://root.cern.ch>`_ (including `PyROOT <https://root.cern/manual/python/>`_).  Check that you can
-``import yoda`` and ``import ROOT`` from Python.  You might want to install into a dedicated virtual
-environment:
+``import yoda`` and ``import ROOT`` from Python.  You might want to install into a dedicated `virtual environment
+<https://docs.python.org/3/tutorial/venv.html>`_:
 
 .. code-block:: console
 
-    $ mkvirtualenv hepdata-converter
+    $ python3 -m venv hepdata-converter
+    $ source hepdata-converter/bin/activate
     (hepdata-converter)$ pip install hepdata-converter
 
 This will install the latest released version from `PyPI <https://pypi.python.org/pypi/hepdata-converter>`_.
@@ -52,10 +53,11 @@ Developers might want to instead install the project directly from
 
 .. code-block:: console
 
-    $ workon hepdata-converter
-    (hepdata-converter)$ git clone https://github.com/HEPData/hepdata-converter
-    (hepdata-converter)$ cd hepdata-converter
-    (hepdata-converter)$ pip install -e .
+    $ git clone https://github.com/HEPData/hepdata-converter
+    $ cd hepdata-converter
+    $ python3 -m venv venv
+    $ source venv/bin/activate
+    (venv)$ pip install -e '.[tests]'
 
 Developers can then run the tests with the following command:
 
@@ -80,9 +82,9 @@ The ``hepdata-converter`` package can be installed inside the Docker container:
 
 .. code-block:: console
 
-    root@617be04cbab5:/# pip3 install --ignore-installed hepdata-converter
+    root@617be04cbab5:/# pip install hepdata-converter
     root@617be04cbab5:/# hepdata-converter -h
-    root@617be04cbab5:/# python3 -c 'import hepdata_converter'
+    root@617be04cbab5:/# python -c 'import hepdata_converter'
 
 Note that the Docker container will be automatically removed when it exits (if running with the ``--rm`` option).  The
 Python module or CLI can then be used as described in :doc:`Usage <usage>`.  Input and output files can be moved
@@ -105,7 +107,7 @@ mount the current directory of the local filesystem when running the Docker cont
     $ git clone https://github.com/HEPData/hepdata-converter
     $ cd hepdata-converter
     $ docker run -v $PWD:$PWD -w $PWD --rm -it hepdata/hepdata-converter /bin/bash
-    root@2c22e88402d2:/hepdata-converter# python3 -m unittest discover hepdata_converter/testsuite 'test_*'
-    root@2c22e88402d2:/hepdata-converter# pip3 install -e .
+    root@2c22e88402d2:/hepdata-converter# pip install -e '.[tests]'
     root@2c22e88402d2:/hepdata-converter# hepdata-converter -h
-    root@2c22e88402d2:/hepdata-converter# python3 -c 'import hepdata_converter'
+    root@2c22e88402d2:/hepdata-converter# python -c 'import hepdata_converter'
+    root@2c22e88402d2:/hepdata-converter# python -m unittest discover hepdata_converter/testsuite 'test_*'

docs/usage.rst

@@ -26,7 +26,7 @@ Usage
 =====
 
 The library exposes a single function ``convert`` which enables conversion from different input formats
-(``oldhepdata``, ``yaml``) to different output formats (``csv``, ``root``, ``yaml``, ``yoda``), by using a simple in-memory
+(``oldhepdata``, ``yaml``) to different output formats (``csv``, ``root``, ``yaml``, ``yoda``, ``yoda1``), by using a simple in-memory
 intermediary format.
 
 

hepdata_converter/__init__.py

@@ -9,7 +9,7 @@
 
 def convert(input, output=None, options={}):
     """Converts a supported ``input_format`` (*oldhepdata*, *yaml*)
-    to a supported ``output_format`` (*csv*, *root*, *yaml*, *yoda*).
+    to a supported ``output_format`` (*csv*, *root*, *yaml*, *yoda*, *yoda1*).
 
     :param input: location of input file for *oldhepdata* format or input directory for *yaml* format
     :param output: location of output directory to which converted files will be written

run_tests.sh

@@ -4,4 +4,4 @@
 export CURRENT_PATH=`pwd`
 export DOCKER_IMAGE=${DOCKER_IMAGE:-"hepdata/hepdata-converter"}
 docker run -v $CURRENT_PATH:$CURRENT_PATH $DOCKER_IMAGE /bin/bash -c \
-  "cd $CURRENT_PATH && coverage run -m unittest discover hepdata_converter/testsuite 'test_*'"
+  "cd $CURRENT_PATH && pip install -e '.[tests]' && coverage run -m unittest discover hepdata_converter/testsuite 'test_*'"

setup.py

@@ -30,22 +30,19 @@ def get_version():
     long_description = fp.read()
 
 
-extras_require = {'docs': ['Sphinx>=1.4.2', 'mock'],
-                  'all': []}
-
 setup(
     name='hepdata-converter',
     version=get_version(),
-    install_requires=[
-        'pyyaml>=5.3',
-        'hepdata-validator>=0.2.2'
-    ],
+    install_requires=['hepdata-validator>=0.3.5'],
     entry_points={
         'console_scripts': [
             'hepdata-converter = hepdata_converter:main',
         ]
     },
-    extras_require=extras_require,
+    extras_require={
+        'docs': ['Sphinx>=1.4.2', 'mock'],
+        'tests': ['coverage>=5.1'],
+    },
     packages=['hepdata_converter', 'hepdata_converter.parsers', 'hepdata_converter.writers', 'hepdata_converter.testsuite'],
     package_data={'hepdata_converter': get_all_datafiles(package='hepdata_converter/testsuite', path='testdata')},
     include_package_data=True,