Preparation for 0.3.5 release

.codespell_ignore_list

@@ -0,0 +1,4 @@
+punctuations
+Bellow
+Coo
+Patter

.github/environment-ci.yml

@@ -0,0 +1,18 @@
+name: test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pip
+  - numpy >=1.20.0
+  - jsonschema >=4.0.1
+  - pandas >=1.2.0
+  - mir_eval >=0.8.2
+  - matplotlib-base>=3.4.1
+  - sortedcontainers >=2.1.0
+  - six
+  - decorator
+  - pytest
+  - coverage
+  - pytest-cov
+  - pytest-mpl

.github/environment-lint.yml

@@ -0,0 +1,21 @@
+name: lint
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # required
+  - pip
+  - bandit
+  - codespell
+  - flake8
+  - pytest
+  - pydocstyle
+
+  # Dependencies for velin
+  - numpydoc>=1.1.0
+  - sphinx>=5.1.0
+  - pygments
+  - black
+
+  - pip:
+    - velin

.github/environment-minimal.yml

@@ -0,0 +1,18 @@
+name: test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pip
+  - numpy ==1.20.0
+  - jsonschema ==4.0.1
+  - pandas ==1.2.0
+  - mir_eval ==0.8.2
+  - matplotlib-base ==3.4.1
+  - sortedcontainers ==2.1.0
+  - six
+  - decorator
+  - pytest
+  - coverage
+  - pytest-cov
+  - pytest-mpl

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: JSON Annotated Music Specification for Reproducible MIR Research
+name: CI Testing
 
 on:
   push:
@@ -8,25 +8,91 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: True
+
 jobs:
-  install:
-    runs-on: ubuntu-latest
+  test:
+    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version:
-        - "3.9"
-        - "3.10"
-        - "3.11"
-        - "3.12"
-    timeout-minutes: 5
+        include:
+          - os: ubuntu-latest
+            python-version: "3.9"
+            channel-priority: "strict"
+            envfile: ".github/environment-ci.yml"
+
+          - os: ubuntu-latest
+            python-version: "3.10"
+            channel-priority: "strict"
+            envfile: ".github/environment-ci.yml"
+
+          - os: ubuntu-latest
+            python-version: "3.11"
+            channel-priority: "strict"
+            envfile: ".github/environment-ci.yml"
+
+          - os: ubuntu-latest
+            python-version: "3.12"
+            channel-priority: "strict"
+            envfile: ".github/environment-ci.yml"
+
+          - os: ubuntu-latest
+            python-version: "3.13"
+            channel-priority: "strict"
+            envfile: ".github/environment-ci.yml"
+
+          - python-version: "3.13"
+            os: macos-latest
+            channel-priority: "strict"
+            envfile: ".github/environment-ci.yml"
+
+          - python-version: "3.13"
+            os: windows-latest
+            envfile: ".github/environment-ci.yml"
+
+          - os: ubuntu-latest
+            python-version: "3.9"
+            envfile: ".github/environment-minimal.yml"
+            channel-priority: "flexible"
+            name: "Minimal dependencies"
+
     steps:
     - uses: actions/checkout@v4
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - name: Create conda environment
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+        channel-priority: ${{ matrix.channel-priority }}
+        environment-file: ${{ matrix.envfile }}
+        # Disabling bz2 to get more recent dependencies.
+        # NOTE: this breaks cache support, so CI will be slower.
+        use-only-tar-bz2: False # IMPORTANT: This needs to be set for caching to work properly!
     - name: Install jams
-      run: pip install -e .[display,tests]
-    - name: Run tests
+      shell: bash -l {0}
+      run: python -m pip install --upgrade-strategy=only-if-needed -e .[display,tests]
+    - name: Log installed packages for debugging
+      shell: bash -l {0}
       run: |
-        pytest -v --cov-report term-missing --cov jams
+        python -c "import sys; print(sys.version)"
+        conda info -a
+        conda list
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: pytest
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: true
+        verbose: true

.github/workflows/lint_python.yml

@@ -0,0 +1,71 @@
+name: lint_python
+on: [pull_request, push]
+jobs:
+  lint_python:
+    name: "Lint and code analysis"
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: "3.11"
+            channel-priority: "flexible"
+            envfile: ".github/environment-lint.yml"
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Cache conda
+      uses: actions/cache@v4
+      env:
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles( matrix.envfile ) }}
+    - name: Install conda environmnent
+      uses: conda-incubator/setup-miniconda@v3
+      with: 
+        auto-update-conda: false
+        python-version: ${{ matrix.python-version }}
+        add-pip-as-python-dependency: true
+        auto-activate-base: false
+        activate-environment: lint
+        # mamba-version: "*"
+        channel-priority: ${{ matrix.channel-priority }}
+        environment-file: ${{ matrix.envfile }}
+        use-only-tar-bz2: false 
+
+    - name: Conda info
+      shell: bash -l {0}
+      run: |
+        conda info -a
+        conda list
+
+    - name: Spell check package
+      shell: bash -l {0}
+      run: codespell --ignore-words .codespell_ignore_list jams
+
+    - name: Security check
+      shell: bash -l {0}
+      run: bandit --recursive --skip B101,B110 .
+
+    - name: Style check package
+      shell: bash -l {0}
+      run: python -m flake8 jams
+
+    - name: Format check package
+      shell: bash -l {0}
+      run: python -m black --check jams
+
+    - name: Format check tests
+      shell: bash -l {0}
+      run: python -m black --check tests
+
+    - name: Docstring check
+      shell: bash -l {0}
+      run: python -m velin --check jams
+
+    - name: Docstring style check
+      shell: bash -l {0}
+      run: python -m pydocstyle jams

.github/workflows/release.yml

@@ -0,0 +1,43 @@
+name: Publish Python 🐍 distributions 📦 to PyPI
+
+on: 
+  release:
+    types: [created] 
+
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/jams
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+
+    - name: Publish package distributions to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -22,6 +22,7 @@ pip-log.txt
 
 # Unit test / coverage reports
 .coverage
+coverage.xml
 .tox
 
 #Translations

CONTRIBUTING.md

@@ -41,48 +41,6 @@ review. This will send an email to the committers.
 (If any of the above seems like magic to you, then look up the 
 [Git documentation](http://git-scm.com/documentation) on the web.)
 
-It is recommended to check that your contribution complies with the
-following rules before submitting a pull request:
-
--  All public methods should have informative docstrings with sample
-   usage presented.
-
-You can also check for common programming errors with the following
-tools:
-
--  Code with good unittest coverage (at least 80%), check with:
-
-          $ pip install nose coverage
-          $ nosetests --with-coverage --cover-package=jams -w jams/tests/
-
--  No pyflakes warnings, check with:
-
-           $ pip install pyflakes
-           $ pyflakes path/to/module.py
-
--  No PEP8 warnings, check with:
-
-           $ pip install pep8
-           $ pep8 path/to/module.py
-
--  AutoPEP8 can help you fix some of the easy redundant errors:
-
-           $ pip install autopep8
-           $ autopep8 path/to/pep8.py
-
-
-Documentation
--------------
-
-You can edit the documentation using any text editor and then generate
-the HTML output by typing ``make html`` from the docs/ directory.
-The resulting HTML files will be placed in _build/html/ and are viewable 
-in a web browser. See the README file in the doc/ directory for more information.
-
-For building the documentation, you will need
-[sphinx](http://sphinx.pocoo.org/),
-[matplotlib](http://matplotlib.sourceforge.net/), and [scikit-learn](http://scikit-learn.org/).
-
 
 Note
 ----

README.md

@@ -2,8 +2,8 @@ jams
 ====
 [![PyPI](https://img.shields.io/pypi/v/jams.svg)](https://pypi.python.org/pypi/jams)
 [![License](https://img.shields.io/pypi/l/jams.svg)](https://github.com/marl/jams/blob/master/LICENSE.md)
-[![Build Status](https://travis-ci.org/marl/jams.svg?branch=master)](https://travis-ci.org/marl/jams)
-[![Coverage Status](https://coveralls.io/repos/marl/jams/badge.svg?branch=master)](https://coveralls.io/r/marl/jams?branch=master)
+[![Tests](https://github.com/marl/jams/actions/workflows/ci.yml/badge.svg)](https://github.com/marl/jams/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/marl/jams/graph/badge.svg?token=dRCLnaNTTO)](https://codecov.io/gh/marl/jams)
 [![Dependency Status](https://dependencyci.com/github/marl/jams/badge)](https://dependencyci.com/github/marl/jams)
 
 A JSON Annotated Music Specification for Reproducible MIR Research.
@@ -20,7 +20,7 @@ We provide:
 * The ability to store multiple annotations per file
 * Schema definitions for a wide range of annotation types (beats, chords, segments, tags, etc.)
 * Error detection and validation for annotations
-* A translation layer to interface with [mir eval](https://craffel.github.io/mir_eval)
+* A translation layer to interface with [mir eval](https://mir-eval.readthedocs.io/latest/)
     for evaluating annotations
 
 Why

jams/__init__.py

@@ -23,14 +23,21 @@
 if sys.version_info < (3, 10):
     from pkg_resources import resource_filename
 
-    for _ in util.find_with_extension(resource_filename(__name__, schema.NS_SCHEMA_DIR), 'json'):
+    for _ in util.find_with_extension(
+        resource_filename(__name__, schema.NS_SCHEMA_DIR), "json"
+    ):
         schema.add_namespace(_)
 
 else:
-    for ns in chain(*map(lambda p: p.rglob('*.json'), resources.files('jams.schemata.namespaces').iterdir())):
+    for ns in chain(
+        *map(
+            lambda p: p.rglob("*.json"),
+            resources.files("jams.schemata.namespaces").iterdir(),
+        )
+    ):
         schema.add_namespace(ns)
 
 # Populate local namespaces
-if 'JAMS_SCHEMA_DIR' in os.environ:
-    for ns in util.find_with_extension(os.environ['JAMS_SCHEMA_DIR'], 'json'):
+if "JAMS_SCHEMA_DIR" in os.environ:
+    for ns in util.find_with_extension(os.environ["JAMS_SCHEMA_DIR"], "json"):
         schema.add_namespace(ns)