merge conflict in readme solved

elpaco-escience · Jan 5, 2024 · 180c4f6 · 180c4f6
2 parents 95d6db5 + 540f89f
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.0
+current_version = 0.1.1
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved

diff --git a/.githooks/pre-commit b/.githooks/pre-commit
@@ -2,6 +2,8 @@
 
 ### To enable this githook, run:
 ### git config --local core.hooksPath .githooks
+### to disable:
+### git config --unset core.hooksPath
 
 echo "Script $0 triggered ..."
 

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'windows-latest']
-        python-version: ['3.7', '3.10']
+        python-version: ['3.9', '3.12']
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -16,10 +16,10 @@ jobs:
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Python info
         shell: bash -l {0}
         run: |
@@ -30,7 +30,7 @@ jobs:
           python3 -m pip install --upgrade pip setuptools
           python3 -m pip install .[dev,publishing]
       - name: Install pandoc using apt
-        run: sudo apt install pandoc        
+        run: sudo apt install pandoc
       - name: Build documentation
         run: make coverage doctest html
         working-directory: docs
diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
@@ -0,0 +1,73 @@
+name: Publish Python distributions to PyPI and TestPyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 🐍
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/') && !contains(github.ref, 'rc')  # only publish to PyPI on tag pushes that do not contain 'rc'
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scikit-talk
+    permissions:
+      id-token: write
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    if: startsWith(github.ref, 'refs/tags') && contains(github.ref, 'rc') # only publish to PyPI on tag pushes with 'rc' (release candidate) label
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/sktalk # the testpypi url is different as scikit-talk is still in use
+    permissions:
+      id-token: write
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,4 +1,14 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
 version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 python:
   install:
     - method: pip

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,18 +1,33 @@
 # Changelog
+
 All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.1.1] - 2024-01-05
+
+### Added
+
+- DOI links to the Zenodo archive
 
-## [0.0.1] - 1900-12-31
+## [0.1.0] - 2024-01-05
 
 ### Added
 
+- Initial release
+- main modules `Corpus`, `Conversation` and `Utterance`
+- parsers for `.eaf` and `.cha` files
+- read and write `.json` files
+- write `.csv` files
+- calculate FTO in a Conversation object
+
 ### Removed
 
+N/A
+
 ### Changed
 
-[Unreleased]: https://github.com/olivierlacan/keep-a-changelog/compare/v1.0.0...HEAD
-[0.0.1]: https://github.com/olivierlacan/keep-a-changelog/releases/tag/v0.0.1
+N/A
+
+[0.1.0]: https://github.com/elpaco-escience/scikit-talk/releases/tag/v0.1.0
diff --git a/CITATION.cff b/CITATION.cff
@@ -14,21 +14,28 @@ authors:
   -
     family-names: Gabor
     given-names: Parti
-  -
-    family-names: Viviani
-    given-names: Eva
-    orcid: "https://orcid.org/0000-0002-1330-0585"
   -
     family-names: Dingemanse
     given-names: Mark
     orcid: "https://orcid.org/0000-0002-3290-5723"
-date-released: 2023-03-03
-doi: 10.0000/FIXME
-version: "0.1.0"
+  -
+    family-names: Schnober
+    given-names: Carsten
+    orcid: "https://orcid.org/0000-0001-9139-1577"
+  -
+    family-names: De Kleijn
+    given-names: Maurice
+  -
+    family-names: Qi
+    given-names: Ji
+    orcid: "https://orcid.org/0000-0001-8074-2730"
+date-released: 2024-01-05
+doi: 10.5281/zenodo.10462997
+version: "0.1.1"
 repository-code: "https://github.com/elpaco-escience/scikit-talk"
 keywords:
     - conversation
     - language corpora
     - turn-taking
-message: "If you use this software, please cite it using these metadata."
+message: "If you use this software, please cite the original paper DOI:10.18653/v1/2021.sigdial-1.26"
 license: Apache-2.0
diff --git a/README.dev.md b/README.dev.md
@@ -134,81 +134,43 @@ bumpversion patch
 This section describes how to make a release in 3 parts:
 
 1. preparation
-1. making a release on PyPI
 1. making a release on GitHub
+1. verification
 
 ### (1/3) Preparation
 
 1. Update the <CHANGELOG.md> (don't forget to update links at bottom of page)
-2. Verify that the information in `CITATION.cff` is correct, and that `.zenodo.json` contains equivalent data
-3. Make sure the [version has been updated](#versioning).
-4. Run the unit tests with `pytest -v`
+1. Verify that the information in `CITATION.cff` is correct
+1. Make sure the [version has been updated](#versioning).
+1. Run the unit tests with `pytest -v`
+
+### (2/3) Release on GitHub
+
+Releases start on GitHub.
+Open [releases](https://github.com/elpaco-escience/scikit-talk/releases/new) and draft a new release.
+Copy the changelog for this version into the description.
+Tag the release according to [semantic versioning guidelines](https://semver.org/), preceded with a `v` (e.g.: v1.0.0).
+The release title is the tag and the release date together (e.g.: v1.0.0 (2019-07-25)).
+
+The Zenodo integration will take care of updating the Zenodo record with a new release.
+Releasing on GitHub will also automatically trigger the publication of the release to PyPI, through a Github Action.
+To verify that everything works as expected, it is recommended to first publish a release candidate (see [below](#release-candidates)).
+
+> [!NOTE]
+>
+> #### Release candidates
+>
+> When releasing a release candidate on Github, tick the pre-release box, and amend the version tag with `-rc` and the candidate number (e.g. v1.0.0-rc1).
+> Ensure the release candidate version is accurate in `CITATION.cff`.
+> Versions with "rc" (release candidate) in their version tag will only be published to [test.PyPI](https://test.pypi.org/project/test-scikit-talk/).
+> Other version tags will trigger a [PyPI release](https://pypi.org/project/scikit-talk/).
+> Inspect `.github/workflows/publish-pypi.yml` for more information.
+
+### (3/3) Verification
+
+1. Verify the publication to [testPyPI](https://test.pypi.org/project/test-scikit-talk/) or [PyPI](https://pypi.org/project/scikit-talk/) (depending on the version tag).
+1. Confirm that the released package can be installed
+    - from PyPI with `pip install scikit-talk`
+    - from test.PyPI with `pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/test-scikit-talk`
+1. The release should have triggered a [Zenodo upload](https://zenodo.org/doi/10.5281/zenodo.10462997). Confirm that the Zenodo record has been updated.
 
-### (2/3) PyPI
-
-In a new terminal, without an activated virtual environment or an env directory:
-
-```shell
-# prepare a new directory
-cd $(mktemp -d scikit-talk.XXXXXX)
-
-# fresh git clone ensures the release has the state of origin/main branch
-git clone git@github.com:elpaco-escience/scikit-talk .
-
-# prepare a clean virtual environment and activate it
-python3 -m venv env
-source env/bin/activate
-
-# make sure to have a recent version of pip and setuptools
-python3 -m pip install --upgrade pip setuptools
-
-# install runtime dependencies and publishing dependencies
-python3 -m pip install --no-cache-dir .
-python3 -m pip install --no-cache-dir .[publishing]
-
-# clean up any previously generated artefacts
-rm -rf scikit-talk.egg-info
-rm -rf dist
-
-# create the source distribution and the wheel
-python3 setup.py sdist bdist_wheel
-
-# upload to test pypi instance (requires credentials)
-twine upload --repository-url https://test.pypi.org/legacy/ dist/*
-```
-
-Visit
-[https://test.pypi.org/project/scikit-talk](https://test.pypi.org/project/scikit-talk)
-and verify that your package was uploaded successfully. Keep the terminal open, we'll need it later.
-
-In a new terminal, without an activated virtual environment or an env directory:
-
-```shell
-cd $(mktemp -d scikit-talk-test.XXXXXX)
-
-# prepare a clean virtual environment and activate it
-python3 -m venv env
-source env/bin/activate
-
-# make sure to have a recent version of pip and setuptools
-pip install --upgrade pip setuptools
-
-# install from test pypi instance:
-python3 -m pip -v install --no-cache-dir \
---index-url https://test.pypi.org/simple/ \
---extra-index-url https://pypi.org/simple scikit-talk
-```
-
-Check that the package works as it should when installed from pypitest.
-
-Then upload to pypi.org with:
-
-```shell
-# Back to the first terminal,
-# FINAL STEP: upload to PyPI (requires credentials)
-twine upload dist/*
-```
-
-### (3/3) GitHub
-
-Don't forget to also make a [release on GitHub](git@github.com:elpaco-escience/scikit-talk/releases/new). If your repository uses the GitHub-Zenodo integration this will also trigger Zenodo into making a snapshot of your repository and sticking a DOI on it.
diff --git a/README.md b/README.md
@@ -7,13 +7,13 @@
 | (1/5) code repository              | [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](git@github.com:elpaco-escience/scikit-talk) |
 | (2/5) license                      | [![github license badge](https://img.shields.io/github/license/elpaco-escience/scikit-talk)](git@github.com:elpaco-escience/scikit-talk) |
 | (3/5) community registry           | [![RSD](https://img.shields.io/badge/rsd-diversity-aware.svg)](https://www.research-software.nl/projects/diversity-aware) [![workflow pypi badge](https://img.shields.io/pypi/v/scikit-talk.svg?colorB=blue)](https://pypi.python.org/project/scikit-talk/) |
-| (4/5) citation                     | [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>) |
+| (4/5) citation                     | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10462997.svg)](https://doi.org/10.5281/zenodo.10462997) |
 | (5/5) checklist                    | [![workflow cii badge](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>/badge)](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
 | howfairis                          | [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) |
 | **Other best practices**           | &nbsp; |
 | Static analysis                    | [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project=elpaco-escience_scikit-talk&metric=alert_status)](https://sonarcloud.io/dashboard?id=elpaco-escience_scikit-talk) |
 | Coverage                           | [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=elpaco-escience_scikit-talk&metric=coverage)](https://sonarcloud.io/dashboard?id=elpaco-escience_scikit-talk) |
-| Documentation                      | [![Documentation Status](https://readthedocs.org/projects/scikit-talk/badge/?version=latest)](https://scikit-talk.readthedocs.io/en/latest/?badge=latest) |
+| Documentation                      | [![Documentation Status](https://readthedocs.org/projects/sktalk/badge/?version=latest)](https://sktalk.readthedocs.io/en/latest/?badge=latest) |
 | **GitHub Actions**                 | &nbsp; |
 | Build                              | [![build](https://github.com/elpaco-escience/scikit-talk/actions/workflows/build.yml/badge.svg)](https://github.com/elpaco-escience/scikit-talk/actions/workflows/build.yml) |
 | SonarCloud                         | [![sonarcloud](https://github.com/elpaco-escience/scikit-talk/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/elpaco-escience/scikit-talk/actions/workflows/sonarcloud.yml) |
@@ -38,7 +38,8 @@ python3 -m pip install .
 
 ## Documentation
 
-Include a link to your project's full documentation here.
+The user documentation can be found [here](https://sktalk.readthedocs.io/en/latest/?badge=latest).
+To read more about the aims of this software, [this paper](https://aclanthology.org/2021.sigdial-1.26/) by Liesenfeld _et al._ (2021) describes the project in detail.
 
 ## Contributing
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = "0.1.0"
+version = "0.1.1"
 # The full version, including alpha/beta/rc tags.
 release = version
 
@@ -46,6 +46,7 @@
     "sphinx.ext.viewcode",
     "autoapi.extension",
     "myst_parser",
+    "nbsphinx",
 ]
 
 # Add any paths that contain templates here, relative to this directory.