Merge pull request #44 from bootphon/packaging-update

Packaging update

.github/workflows/test-pytest.yml

@@ -14,12 +14,12 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

README.md

@@ -23,8 +23,8 @@ Optionally, to allow `pygamma-agreement` to display visual representations of
 our API's objects in Jupyter Notebooks, [Matplotlib](https://matplotlib.org/>) 
 is needed.
 
-pygamma-agreement is a Python 3 package and is currently tested for Python 3.7, 3.8, 3.9 and 3.10. 
-pygamma-agreement does not work with Python 2.7.
+`pygamma-agreement` is a Python 3 package and is currently tested for Python 3.7 to 3.11. 
+`pygamma-agreement` does not work with Python 2.7.
 
 
 ## Installation
@@ -69,6 +69,18 @@ After that, tests are ready to be launched (they take ~2m on a recent laptop) :
 
     $ pytest tests/
 
+## Documentation
+
+The documentation for this package has been written using Sphinx. To build the documentation locally, run:
+
+    $ pip install "pygamma-agreement[docs]"
+    $ cd docs/
+    $ make html
+
+After that, you can view the documentation by running
+
+    $ firefox build/html/index.html
+
 ## Submitting and issue or contributing
 
 Please read `CONTRIBUTING.md` before submitting and issue or writing some contribution 

docs/source/quickstart.rst

@@ -22,8 +22,8 @@ tuple of 3 information:
     * Segment end (at 7.2s)
 
 Obviously, our annotators sometimes disagree on who might be talking,
-or when exactly each person's speech turn is starting or ending. Luckily, the Gamma
-inter-annotator agreement enables us to measure that.
+or when exactly each person's speech turn is starting or ending. The Gamma
+inter-annotator agreement enables us to obtain a measure of that disagreement.
 
 We'll first load the annotation into ``pygamma-agreement``'s base data structure,
 the ``Continuum``, made to store this kind of annotated data.

pygamma_agreement/cst.py

@@ -144,13 +144,15 @@ def category_shuffle(self, continuum: Continuum,
         """
         Shuffles the categories of the annotations in the given continuum using the process described in
         section 3.3.5 of https://hal.archives-ouvertes.fr/hal-00769639/.
+
         Parameters
         ----------
         overlapping_fun:
             gives the "categorical distance" between two annotations, which is taken into account when provided.
             (the lower the distance between categories, the higher the chance one will be changed into the other).
         prevalence:
             specify whether or not to consider the proportion of presence of each category in the reference.
+
         """
         category_weights = self._reference_continuum.category_weights
         # matrix "A"

pygamma_agreement/dissimilarity.py

@@ -73,8 +73,8 @@ def __init__(self, categories: Optional[SortedSet] = None, delta_empty: float =
     @abc.abstractmethod
     def compile_d_mat(self) -> Callable[[np.ndarray, np.ndarray], float]:
         """
-        Must set self.d_mat to the the cfunc (decorated with @dissimilarity_dec) function that corresponds to the
-        unit-to-unit, (in arrays form) disorder given by the dissimilarity.
+        Must set self.d_mat to the cfunc (decorated with @dissimilarity_dec) function that corresponds to the
+        unit-to-unit (in arrays form) disorder given by the dissimilarity.
         """
         raise NotImplemented()
 
@@ -283,9 +283,11 @@ class PositionalSporadicDissimilarity(AbstractDissimilarity):
     """
     Positional-sporadic dissimilarity. Takes only the position of annotations into account.
     This distance is :
+
     * 0 when segments are equal
-    * < delta_empty when segments completely overlap :math:`A \cup B = A` or :math:`B`)
+    * < delta_empty when segments completely overlap (:math:`A \cup B = A` or :math:`B`)
     * > delta_empty when segments are separated (:math:`A \cap B = \emptyset`)
+
     """
     def __init__(self, delta_empty: float = 1.0):
         super().__init__(delta_empty=delta_empty)
@@ -415,7 +417,7 @@ def cat_dissim_func(str1: str, str2: str) -> float:
 class OrdinalCategoricalDissimilarity(PrecomputedCategoricalDissimilarity):
     """
     Categorical dissimilarity where each label is given a position on the real axis, and the disorder between
-    categories of positions 'a' and 'b' being |a - b|/m * delta_empty with m the maximum position. If not provided,
+    categories of positions 'a' and 'b' being \|a - b\|/m * delta_empty with m the maximum position. If not provided,
     positions are 0, 1, 2...
     """
     def __init__(self, labels: Iterable[str], p: Iterable[float] = None, delta_empty=1.0):
@@ -453,7 +455,7 @@ def __init__(self, labels: Iterable[str], p: Iterable[float] = None, delta_empty
 class NumericalCategoricalDissimilarity(OrdinalCategoricalDissimilarity):
     """
     Categorical dissimilarity made for numerical categories (i.e a category is a float or int literal).
-    The disorder between categories 'a' and 'b' being |a - b|/m * delta_empty with m the maximum category.
+    The disorder between categories 'a' and 'b' being \|a - b\|/m * delta_empty with m the maximum category.
     """
     def __init__(self, labels: Iterable[str], delta_empty: float = 1.0):
         try:
@@ -468,6 +470,7 @@ class CombinedCategoricalDissimilarity(AbstractDissimilarity):
     """
     This dissimilarity takes both positioning and categorizing of annotations into account.
     Combined categorical dissimilarity constructor.
+
     Parameters
     ----------
     delta_empty : optional, float
@@ -479,6 +482,7 @@ class CombinedCategoricalDissimilarity(AbstractDissimilarity):
         coefficient weighting the categorical dissimilarity value. Defaults to 1.
     cat_dissim : optional, CategoricalDissimilarity
         Categorical-only dissimilarity to be used. If not set, defaults to the absolute categorical dissimilarity.
+
     """
     def __init__(self,
                  alpha: float = 1.0,

pygamma_agreement/sampler.py

@@ -198,6 +198,7 @@ class StatisticalContinuumSampler(AbstractContinuumSampler):
     - The number of annotations per annotator
     - The gap between two of an annotator's annotations
     - The duration of the annotations' segments
+
     The sample is thus created by computing normal distributions using these parameters.
 
     It also requires the probability of occurence of each annotations category. You can either initalize sampling with

pyproject.toml

@@ -0,0 +1,63 @@
+[project]
+name = "pygamma-agreement"
+readme = "README.md"
+version = "0.5.7"
+description = 'Inter-annotator agreement measure and alignment written in python'
+
+authors = [
+    { name = "Hadrien Titeux", email = "[email protected]" },
+    { name = "Rachid Riad", email = "[email protected]" },
+    { name = "Léopold Favre", email = "[email protected]" },
+]
+maintainers = [
+    { name = "Hadrien Titeux", email = "[email protected]" },
+]
+
+
+license = { text = "MIT" }
+requires-python = ">=3.7"
+keywords = []
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Text Processing :: Linguistic",
+    "Topic :: Multimedia :: Sound/Audio :: Speech",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dynamic = ["dependencies"]
+
+[project.urls]
+Documentation = "https://pygamma-agreement.readthedocs.io/en/latest/"
+Homepage = "https://github.com/bootphon/pygamma-agreement"
+Repository = "https://github.com/bootphon/pygamma-agreement"
+
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements.txt"] }
+
+[project.optional-dependencies]
+notebook = ["matplotlib"]
+CBC = ["cylp"]
+testing = ["pytest", "cylp"]
+docs = ["sphinx", "sphinx_rtd_theme"]
+
+[build-system]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project.scripts]
+pygamma-agreement = "pygamma_agreement.cli_apps:pygamma_cmd"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["adfluo*"]
+exclude = ["docs*", "tests*"]
+

requirements.txt

@@ -2,7 +2,7 @@ sortedcontainers>= 2.0.4
 numpy>= 1.10.4
 pyannote.core>=4.1
 cvxpy>= 1.0.25
-cvxopt== 1.2.7
+cvxopt== 1.3.2
 tqdm>= 4.46.0
 numba>= 0.54.0
 typing_extensions>= 3.7.4.3