From 117186ae57847d7a0b1fdbc5f3b83dea6b801f9e Mon Sep 17 00:00:00 2001
From: Yunmo Chen <yunmo@jhu.edu>
Date: Sat, 16 Sep 2023 05:16:43 -0400
Subject: [PATCH 01/15] Added `ruff`, `black`, `pyright`, and `pytest` to the
 pyproject.toml and updated dependencies.

---
 poetry.lock    | 183 +++++++++++++++++++++++++++++++------------------
 pyproject.toml |  34 ++++++---
 2 files changed, 142 insertions(+), 75 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 44ffc8b..0a0b84b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "colorama"
@@ -36,41 +36,52 @@ files = [
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
 ]
 
+[[package]]
+name = "nodeenv"
+version = "1.8.0"
+description = "Node.js virtual environment builder"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
+files = [
+    {file = "nodeenv-1.8.0-py2.py3-none-any.whl", hash = "sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec"},
+    {file = "nodeenv-1.8.0.tar.gz", hash = "sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2"},
+]
+
+[package.dependencies]
+setuptools = "*"
+
 [[package]]
 name = "numpy"
-version = "1.24.4"
+version = "1.25.2"
 description = "Fundamental package for array computing in Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "numpy-1.25.2-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:1b9735c27cea5d995496f46a8b1cd7b408b3f34b6d50459d9ac8fe3a20cc17bf"},
+    {file = "numpy-1.25.2.tar.gz", hash = "sha256:fd608e19c8d7c55021dffd43bfe5492fab8cc105cc8986f813f8c3c048b38760"},
 ]
 
 [[package]]
@@ -86,28 +97,46 @@ files = [
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
-    {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "pyright"
+version = "1.1.327"
+description = "Command line wrapper for pyright"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pyright-1.1.327-py3-none-any.whl", hash = "sha256:3462cda239e9140276238bbdbd0b59d77406f1c2e14d8cb8c20c8e25639c6b3c"},
+    {file = "pyright-1.1.327.tar.gz", hash = "sha256:ba74148ad64f22020dbbed6781c4bdb38ecb8a7ca90dc3c87a4f08d1c0e11592"},
+]
+
+[package.dependencies]
+nodeenv = ">=1.6.0"
+
+[package.extras]
+all = ["twine (>=3.4.1)"]
+dev = ["twine (>=3.4.1)"]
+
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
-    {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
+    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
+    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
 ]
 
 [package.dependencies]
@@ -123,41 +152,61 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 
 [[package]]
 name = "scipy"
-version = "1.9.3"
+version = "1.11.2"
 description = "Fundamental algorithms for scientific computing in Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = "<3.13,>=3.9"
 files = [
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-    {file = "scipy-1.9.3.tar.gz", hash = "sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027"},
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+    {file = "scipy-1.11.2-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:95763fbda1206bec41157582bea482f50eb3702c85fffcf6d24394b071c0e87a"},
+    {file = "scipy-1.11.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e367904a0fec76433bf3fbf3e85bf60dae8e9e585ffd21898ab1085a29a04d16"},
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+    {file = "scipy-1.11.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:ea932570b1c2a30edafca922345854ff2cd20d43cd9123b6dacfdecebfc1a80b"},
+    {file = "scipy-1.11.2-cp312-cp312-win_amd64.whl", hash = "sha256:4447ad057d7597476f9862ecbd9285bbf13ba9d73ce25acfa4e4b11c6801b4c9"},
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+    {file = "scipy-1.11.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:10eb6af2f751aa3424762948e5352f707b0dece77288206f227864ddf675aca0"},
+    {file = "scipy-1.11.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:0f3261f14b767b316d7137c66cc4f33a80ea05841b9c87ad83a726205b901423"},
+    {file = "scipy-1.11.2-cp39-cp39-win_amd64.whl", hash = "sha256:2c91cf049ffb5575917f2a01da1da082fd24ed48120d08a6e7297dfcac771dcd"},
+    {file = "scipy-1.11.2.tar.gz", hash = "sha256:b29318a5e39bd200ca4381d80b065cdf3076c7d7281c5e36569e99273867f61d"},
 ]
 
 [package.dependencies]
-numpy = ">=1.18.5,<1.26.0"
+numpy = ">=1.21.6,<1.28.0"
+
+[package.extras]
+dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
+doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
+test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
+[[package]]
+name = "setuptools"
+version = "68.2.2"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "setuptools-68.2.2-py3-none-any.whl", hash = "sha256:b454a35605876da60632df1a60f736524eb73cc47bbc9f3f1ef1b644de74fd2a"},
+    {file = "setuptools-68.2.2.tar.gz", hash = "sha256:4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87"},
+]
 
 [package.extras]
-dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"]
-doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"]
-test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "tomli"
@@ -172,5 +221,5 @@ files = [
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "c3754f3a5ef2769b2a4bfe3bec30c0aa8b1b7c0264d37dc15023e02508357f8b"
+python-versions = ">=3.9,<3.13"
+content-hash = "dac26de6ca105acd6c73153c222d74af1526dd74b7d4e5d79c14b2c047d8da96"
diff --git a/pyproject.toml b/pyproject.toml
index 4e06831..770f20c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,19 +1,37 @@
+[tool.ruff]
+line-length = 120
+
+[tool.black]
+line-length = 120
+
+[tool.pyright]
+include = ["src", "tests"]
+
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = ["tests"]
+
 [tool.poetry]
 name = "unified-metric"
 version = "0.1.0"
-description = ""
-authors = ["Tongfei Chen <tongfei@pm.me>"]
-license = "MIT"
+description = "A Unified View of Evaluation Metrics for Information Extraction"
+authors = ["Tongfei Chen <tongfei@pm.me>", "Yunmo Chen <yunmo@jhu.edu>"]
 readme = "README.md"
-packages = [{include = "unimetric"}]
+packages = [{ include = "src/unimetric" }]
 
 [tool.poetry.dependencies]
-python = "^3.8"
-numpy = "^1.19"
-scipy = "^1.9"
+python = ">=3.9,<3.13"
+scipy = "^1.11.2"
+numpy = "^1.25.2"
+pytest = "^7.4.2"
+
+[tool.poetry.group.dev]
+optional = true
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4.0"
+pytest = "^7.4.2"
+pyright = "^1.1.327"
 
 [build-system]
 requires = ["poetry-core"]

From 507f105055826e306aa5f5ee0d0ae09ec87dd8c3 Mon Sep 17 00:00:00 2001
From: Yunmo Chen <yunmo@jhu.edu>
Date: Sat, 16 Sep 2023 05:17:51 -0400
Subject: [PATCH 02/15] Re-arranged the codebase.

---
 {unimetric => src/unimetric}/__init__.py      |  0
 {unimetric => src/unimetric}/alignment.py     | 27 ++++++++++---------
 {unimetric => src/unimetric}/amr.py           |  2 +-
 {unimetric => src/unimetric}/decorator.py     | 21 +++++++--------
 {unimetric => src/unimetric}/ie.py            |  1 +
 .../unimetric}/latent_alignment.py            | 10 +++----
 {unimetric => src/unimetric}/metric.py        |  5 ++--
 tests/__init__.py                             |  0
 tests/test_alignment.py                       | 14 ----------
 tests/unimetric/__init__.py                   |  0
 tests/unimetric/test_alignment.py             | 14 ++++++++++
 .../{test_smatch.py => unimetric/test_amr.py} |  3 ++-
 12 files changed, 50 insertions(+), 47 deletions(-)
 rename {unimetric => src/unimetric}/__init__.py (100%)
 rename {unimetric => src/unimetric}/alignment.py (69%)
 rename {unimetric => src/unimetric}/amr.py (100%)
 rename {unimetric => src/unimetric}/decorator.py (85%)
 rename {unimetric => src/unimetric}/ie.py (99%)
 rename {unimetric => src/unimetric}/latent_alignment.py (95%)
 rename {unimetric => src/unimetric}/metric.py (96%)
 create mode 100644 tests/__init__.py
 delete mode 100644 tests/test_alignment.py
 create mode 100644 tests/unimetric/__init__.py
 create mode 100644 tests/unimetric/test_alignment.py
 rename tests/{test_smatch.py => unimetric/test_amr.py} (91%)

diff --git a/unimetric/__init__.py b/src/unimetric/__init__.py
similarity index 100%
rename from unimetric/__init__.py
rename to src/unimetric/__init__.py
diff --git a/unimetric/alignment.py b/src/unimetric/alignment.py
similarity index 69%
rename from unimetric/alignment.py
rename to src/unimetric/alignment.py
index 16f273d..e94ee2b 100644
--- a/unimetric/alignment.py
+++ b/src/unimetric/alignment.py
@@ -1,10 +1,11 @@
-from typing import Collection, Generic, Mapping, TypeVar, Iterator, Tuple
+import enum
 from enum import Enum
+from typing import Collection, TypeVar
+
 import numpy as np
 import scipy.optimize as spo
 
-from unimetric.metric import Metric, DiscreteMetric
-
+from unimetric.metric import Metric
 
 T = TypeVar('T')
 
@@ -13,14 +14,14 @@ class AlignmentConstraint(Enum):
     """
     Alignment constraints for the alignment metric.
     """
-    ONE_TO_ONE = 0
-    ONE_TO_MANY = 1
-    MANY_TO_ONE = 2
-    MANY_TO_MANY = 3
+    OneToOne = enum.auto()
+    OneToMany = enum.auto()
+    ManyToOne = enum.auto()
+    ManyToMany = enum.auto()
 
 
 class AlignmentMetric(Metric[Collection[T]]):
-    def __init__(self, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.ONE_TO_ONE):
+    def __init__(self, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.OneToOne):
         self.inner = inner
         self.constraint = constraint
 
@@ -32,22 +33,22 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
         )
 
     def score_self(self, x: Collection[T]) -> float:
-        if self.constraint == AlignmentConstraint.MANY_TO_MANY:
+        if self.constraint == AlignmentConstraint.ManyToMany:
             return self.inner.gram_matrix(x, x).sum()
         else:
             return sum(self.inner.score_self(u) for u in x)
 
 
 def solve_alignment(gram_matrix: np.ndarray, constraint: AlignmentConstraint) -> float:
-    if constraint == AlignmentConstraint.ONE_TO_ONE:
+    if constraint == AlignmentConstraint.OneToOne:
         row_idx, col_idx = spo.linear_sum_assignment(
             cost_matrix=gram_matrix,
             maximize=True,
         )
         return gram_matrix[row_idx, col_idx].sum()
-    if constraint == AlignmentConstraint.ONE_TO_MANY:
+    if constraint == AlignmentConstraint.OneToMany:
         return gram_matrix.max(axis=0).sum()
-    if constraint == AlignmentConstraint.MANY_TO_ONE:
+    if constraint == AlignmentConstraint.ManyToOne:
         return gram_matrix.max(axis=1).sum()
-    if constraint == AlignmentConstraint.MANY_TO_MANY:
+    if constraint == AlignmentConstraint.ManyToMany:
         return gram_matrix.sum()
diff --git a/unimetric/amr.py b/src/unimetric/amr.py
similarity index 100%
rename from unimetric/amr.py
rename to src/unimetric/amr.py
index 81ee9a8..c4b9021 100644
--- a/unimetric/amr.py
+++ b/src/unimetric/amr.py
@@ -1,8 +1,8 @@
 from dataclasses import dataclass
 from typing import Collection, Set, Union
 
-from unimetric.latent_alignment import Variable
 from unimetric.decorator import unimetric
+from unimetric.latent_alignment import Variable
 
 
 @unimetric()
diff --git a/unimetric/decorator.py b/src/unimetric/decorator.py
similarity index 85%
rename from unimetric/decorator.py
rename to src/unimetric/decorator.py
index b4756d9..e7cde19 100644
--- a/unimetric/decorator.py
+++ b/src/unimetric/decorator.py
@@ -1,10 +1,9 @@
 from dataclasses import fields, is_dataclass
 from typing import Literal, get_args, get_origin, Collection, Annotated, Union
-from inspect import isclass
 
-from unimetric.latent_alignment import Variable, dataclass_has_variable, LatentAlignmentMetric
-from unimetric.metric import Metric, ProductMetric, DiscreteMetric, FScore, Jaccard, Precision, Recall, UnionMetric
 from unimetric.alignment import AlignmentConstraint, AlignmentMetric
+from unimetric.latent_alignment import dataclass_has_variable, LatentAlignmentMetric
+from unimetric.metric import Metric, ProductMetric, DiscreteMetric, FScore, Jaccard, Precision, Recall, UnionMetric
 
 
 def derive_metric(cls: type, constraint: AlignmentConstraint) -> Metric:
@@ -82,14 +81,14 @@ def unimetric(
     """
     def class_decorator(cls):
         alignment_constraint = {
-            '<->': AlignmentConstraint.ONE_TO_ONE,
-            '<-': AlignmentConstraint.ONE_TO_MANY,
-            '->': AlignmentConstraint.MANY_TO_ONE,
-            '~': AlignmentConstraint.MANY_TO_MANY,
-            '1:1': AlignmentConstraint.ONE_TO_ONE,
-            '1:*': AlignmentConstraint.ONE_TO_MANY,
-            '*:1': AlignmentConstraint.MANY_TO_ONE,
-            '*:*': AlignmentConstraint.MANY_TO_MANY,
+            '<->': AlignmentConstraint.OneToOne,
+            '<-': AlignmentConstraint.OneToMany,
+            '->': AlignmentConstraint.ManyToOne,
+            '~': AlignmentConstraint.ManyToMany,
+            '1:1': AlignmentConstraint.OneToOne,
+            '1:*': AlignmentConstraint.OneToMany,
+            '*:1': AlignmentConstraint.ManyToOne,
+            '*:*': AlignmentConstraint.ManyToMany,
         }[constraint]
         metric = derive_metric(cls, constraint=alignment_constraint)
         normalized_metric = {
diff --git a/unimetric/ie.py b/src/unimetric/ie.py
similarity index 99%
rename from unimetric/ie.py
rename to src/unimetric/ie.py
index 4789117..6f8a0bc 100644
--- a/unimetric/ie.py
+++ b/src/unimetric/ie.py
@@ -1,5 +1,6 @@
 from dataclasses import dataclass
 from typing import List
+
 from unimetric.decorator import unimetric
 
 
diff --git a/unimetric/latent_alignment.py b/src/unimetric/latent_alignment.py
similarity index 95%
rename from unimetric/latent_alignment.py
rename to src/unimetric/latent_alignment.py
index a4a63e7..8149f27 100644
--- a/unimetric/latent_alignment.py
+++ b/src/unimetric/latent_alignment.py
@@ -21,7 +21,7 @@ def __hash__(self):
 
 
 class LatentAlignmentMetric(Metric[Collection[T]]):
-    def __init__(self, cls: type, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.ONE_TO_ONE):
+    def __init__(self, cls: type, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.OneToOne):
         if is_dataclass(cls):
             self.fields = fields(cls)
         else:
@@ -71,10 +71,10 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
 
         # each item may be mapped to some other items given the constraint
         item_constraint_matrix_ctor = {
-            AlignmentConstraint.ONE_TO_ONE: _get_one_to_one_constraint_matrix,
-            AlignmentConstraint.ONE_TO_MANY: _get_one_to_many_constraint_matrix,
-            AlignmentConstraint.MANY_TO_ONE: _get_many_to_one_constraint_matrix,
-            AlignmentConstraint.MANY_TO_MANY: lambda _0, _1: None,
+            AlignmentConstraint.OneToOne: _get_one_to_one_constraint_matrix,
+            AlignmentConstraint.OneToMany: _get_one_to_many_constraint_matrix,
+            AlignmentConstraint.ManyToOne: _get_many_to_one_constraint_matrix,
+            AlignmentConstraint.ManyToMany: lambda _0, _1: None,
         }[self.constraint]
         item_constraint_matrix = item_constraint_matrix_ctor(n_x, n_y)
         if item_constraint_matrix is not None:
diff --git a/unimetric/metric.py b/src/unimetric/metric.py
similarity index 96%
rename from unimetric/metric.py
rename to src/unimetric/metric.py
index f2f4d57..2e84f82 100644
--- a/unimetric/metric.py
+++ b/src/unimetric/metric.py
@@ -2,7 +2,8 @@
 from dataclasses import is_dataclass
 from functools import reduce
 from operator import mul
-from typing import Callable, Dict, Generic, Sequence, Set, Type, TypeVar, Collection, Union, get_origin
+from typing import Callable, Dict, Generic, Type, TypeVar, Collection, Union, get_origin
+
 import numpy as np
 
 T = TypeVar('T', contravariant=True)
@@ -142,7 +143,7 @@ def score(self, x: T, y: T) -> float:
 
 class UnionMetric(Metric[T]):
     def __init__(self, cls: type, case_metrics: Dict[type, Metric]):
-        if not get_origin(cls) is Union:
+        if get_origin(cls) is not Union:
             raise ValueError(f"{cls} has to be a union.")
         self.case_metrics = case_metrics
 
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_alignment.py b/tests/test_alignment.py
deleted file mode 100644
index aca147e..0000000
--- a/tests/test_alignment.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from unimetric.alignment import AlignmentConstraint, solve_alignment
-from unimetric.metric import DiscreteMetric
-
-
-def test_alignment():
-    a = [1, 2, 2]
-    b = [1, 1, 1, 2]
-
-    g = DiscreteMetric(int).gram_matrix(a, b)
-
-    assert solve_alignment(g, AlignmentConstraint.ONE_TO_ONE) == 2
-    assert solve_alignment(g, AlignmentConstraint.MANY_TO_ONE) == 3
-    assert solve_alignment(g, AlignmentConstraint.ONE_TO_MANY) == 4
-    assert solve_alignment(g, AlignmentConstraint.MANY_TO_MANY) == 5
diff --git a/tests/unimetric/__init__.py b/tests/unimetric/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/unimetric/test_alignment.py b/tests/unimetric/test_alignment.py
new file mode 100644
index 0000000..24533c4
--- /dev/null
+++ b/tests/unimetric/test_alignment.py
@@ -0,0 +1,14 @@
+from unimetric.alignment import solve_alignment, AlignmentConstraint
+from unimetric.metric import DiscreteMetric
+
+
+def test_solve_alignment():
+    a = [1, 2, 2]
+    b = [1, 1, 1, 2]
+
+    g = DiscreteMetric(int).gram_matrix(a, b)
+
+    assert solve_alignment(g, AlignmentConstraint.OneToOne) == 2
+    assert solve_alignment(g, AlignmentConstraint.ManyToOne) == 3
+    assert solve_alignment(g, AlignmentConstraint.OneToMany) == 4
+    assert solve_alignment(g, AlignmentConstraint.ManyToMany) == 5
diff --git a/tests/test_smatch.py b/tests/unimetric/test_amr.py
similarity index 91%
rename from tests/test_smatch.py
rename to tests/unimetric/test_amr.py
index 5978fac..01e207a 100644
--- a/tests/test_smatch.py
+++ b/tests/unimetric/test_amr.py
@@ -1,6 +1,7 @@
 from pytest import approx
 
-from unimetric.amr import AMR, Variable, Prop
+from unimetric.amr import AMR, Prop
+from unimetric.latent_alignment import Variable
 
 
 def test_smatch():

From 214c716619f96c7070ff9f4c4fe7bc0c042acec8 Mon Sep 17 00:00:00 2001
From: Yunmo Chen <yunmo@jhu.edu>
Date: Sat, 16 Sep 2023 07:22:19 -0400
Subject: [PATCH 03/15] Fixed all pyright errors.

---
 src/unimetric/decorator.py        | 103 +++++++++++++++++++-----------
 src/unimetric/latent_alignment.py |  41 ++++++------
 src/unimetric/metric.py           |   4 +-
 tests/unimetric/test_amr.py       |   7 +-
 4 files changed, 93 insertions(+), 62 deletions(-)

diff --git a/src/unimetric/decorator.py b/src/unimetric/decorator.py
index e7cde19..37538ea 100644
--- a/src/unimetric/decorator.py
+++ b/src/unimetric/decorator.py
@@ -1,12 +1,38 @@
 from dataclasses import fields, is_dataclass
-from typing import Literal, get_args, get_origin, Collection, Annotated, Union
+from typing import (
+    Literal,
+    get_args,
+    get_origin,
+    Collection,
+    Annotated,
+    Union,
+    Protocol,
+    runtime_checkable,
+    Callable,
+    TypeVar,
+)
 
 from unimetric.alignment import AlignmentConstraint, AlignmentMetric
 from unimetric.latent_alignment import dataclass_has_variable, LatentAlignmentMetric
 from unimetric.metric import Metric, ProductMetric, DiscreteMetric, FScore, Jaccard, Precision, Recall, UnionMetric
 
+T = TypeVar("T", covariant=True)
 
-def derive_metric(cls: type, constraint: AlignmentConstraint) -> Metric:
+NormalizerLiteral = Literal["none", "jaccard", "dice", "f1"]
+ConstraintLiteral = Literal["<->", "<-", "->", "~"]
+
+
+@runtime_checkable
+class HasMetric(Protocol):
+    metric: Metric
+
+
+@runtime_checkable
+class HasLatentMetric(Protocol):
+    latent_metric: Metric
+
+
+def derive_metric(cls: object, constraint: AlignmentConstraint) -> Metric:
     """
     Derive a unified metric from any type.
     :param cls: The type to derive a metric from.
@@ -20,34 +46,29 @@ def derive_metric(cls: type, constraint: AlignmentConstraint) -> Metric:
             return metric
 
     # if an explicit metric is defined, use it
-    if getattr(cls, "metric", None) is not None:
+    # if getattr(cls, "metric", None) is not None:
+    if isinstance(cls, HasMetric):
         return cls.metric
 
-    if getattr(cls, "latent_metric", None) is not None:
+    cls_origin = get_origin(cls)
+    # if getattr(cls, "latent_metric", None) is not None:
+    if isinstance(cls, HasLatentMetric):
         return cls.latent_metric
 
     # derive product metric from dataclass
     elif is_dataclass(cls):
         return ProductMetric(
-            cls=cls,
-            field_metrics={
-                fld.name: derive_metric(fld.type, constraint=constraint)
-                for fld in fields(cls)
-            }
+            cls=cls, field_metrics={fld.name: derive_metric(fld.type, constraint=constraint) for fld in fields(cls)}
         )
 
     # derive union metric from unions
-    elif get_origin(cls) is Union:
+    elif cls_origin is Union:
         return UnionMetric(
-            cls=cls,
-            case_metrics={
-                case: derive_metric(case, constraint=constraint)
-                for case in get_args(cls)
-            }
+            cls=cls, case_metrics={case: derive_metric(case, constraint=constraint) for case in get_args(cls)}
         )
 
     # derive alignment metric from collections
-    elif get_origin(cls) is not None and isinstance(get_origin(cls), type) and issubclass(get_origin(cls), Collection):
+    elif cls_origin is not None and isinstance(cls_origin, type) and issubclass(cls_origin, Collection):
         elem_type = get_args(cls)[0]
         inner_metric = derive_metric(elem_type, constraint=constraint)
         if dataclass_has_variable(elem_type):
@@ -71,38 +92,46 @@ def derive_metric(cls: type, constraint: AlignmentConstraint) -> Metric:
 
 
 def unimetric(
-        normalizer: Literal['none', 'jaccard', 'dice', 'f1'] = 'none',
-        constraint: Literal['<->', '<-', '->', '~'] = '<->',
-):
+    normalizer: NormalizerLiteral = "none",
+    constraint: ConstraintLiteral = "<->",
+) -> Callable[[T], T]:
     """
     Derive a unified metric from a class.
     :param normalizer:
     :return:
     """
-    def class_decorator(cls):
+
+    def class_decorator(cls: T) -> T:
         alignment_constraint = {
-            '<->': AlignmentConstraint.OneToOne,
-            '<-': AlignmentConstraint.OneToMany,
-            '->': AlignmentConstraint.ManyToOne,
-            '~': AlignmentConstraint.ManyToMany,
-            '1:1': AlignmentConstraint.OneToOne,
-            '1:*': AlignmentConstraint.OneToMany,
-            '*:1': AlignmentConstraint.ManyToOne,
-            '*:*': AlignmentConstraint.ManyToMany,
+            "<->": AlignmentConstraint.OneToOne,
+            "<-": AlignmentConstraint.OneToMany,
+            "->": AlignmentConstraint.ManyToOne,
+            "~": AlignmentConstraint.ManyToMany,
+            "1:1": AlignmentConstraint.OneToOne,
+            "1:*": AlignmentConstraint.OneToMany,
+            "*:1": AlignmentConstraint.ManyToOne,
+            "*:*": AlignmentConstraint.ManyToMany,
         }[constraint]
         metric = derive_metric(cls, constraint=alignment_constraint)
         normalized_metric = {
-            'none': lambda x: x,
-            'jaccard': Jaccard,
-            'dice': FScore,
-            'f1': FScore,
-            'precision': Precision,
-            'recall': Recall,
+            "none": lambda x: x,
+            "jaccard": Jaccard,
+            "dice": FScore,
+            "f1": FScore,
+            "precision": Precision,
+            "recall": Recall,
         }[normalizer](metric)
 
         if dataclass_has_variable(cls):
-            setattr(cls, 'latent_metric', normalized_metric)
+            class LatentMetricWrapper(cls, HasLatentMetric):  # type: ignore
+                latent_metric = normalized_metric
+
+            return LatentMetricWrapper
         else:
-            setattr(cls, 'metric', normalized_metric)
-        return cls
+            class MetricWrapper(cls, HasMetric):  # type: ignore
+                metric = normalized_metric
+
+            return MetricWrapper
+        # return cls
+
     return class_decorator
diff --git a/src/unimetric/latent_alignment.py b/src/unimetric/latent_alignment.py
index 8149f27..3951e33 100644
--- a/src/unimetric/latent_alignment.py
+++ b/src/unimetric/latent_alignment.py
@@ -7,7 +7,7 @@
 from unimetric.alignment import AlignmentConstraint, solve_alignment
 from unimetric.metric import Metric
 
-T = TypeVar('T')
+T = TypeVar("T")
 
 
 @dataclass
@@ -45,28 +45,20 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
 
         # coefficient vector for the objective function
         coef = np.concatenate(
-            [
-                np.zeros(n_x_vars * n_y_vars),
-                gram_matrix.reshape([n_pairs])  # score that x_i matches x_j
-            ],
-            axis=0
+            [np.zeros(n_x_vars * n_y_vars), gram_matrix.reshape([n_pairs])], axis=0  # score that x_i matches x_j
         )
-        
+
         # build the constraint matrix
         n = n_x_vars * n_y_vars + n_pairs
 
         # each variable must be mapped to exactly one variable
         var_constraint_matrix = _get_one_to_one_constraint_matrix(n_x_vars, n_y_vars)
         var_constraint_matrix = np.concatenate(
-            [
-                var_constraint_matrix,
-                np.zeros([var_constraint_matrix.shape[0], n_pairs])
-            ],
-            axis=1
+            [var_constraint_matrix, np.zeros([var_constraint_matrix.shape[0], n_pairs])], axis=1
         )
         var_constraints = spo.LinearConstraint(
             A=var_constraint_matrix,
-            ub=np.ones(var_constraint_matrix.shape[0]),
+            ub=np.ones(var_constraint_matrix.shape[0]),  # type: ignore
         )
 
         # each item may be mapped to some other items given the constraint
@@ -83,11 +75,15 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
                     np.zeros([item_constraint_matrix.shape[0], n_x_vars * n_y_vars]),
                     item_constraint_matrix,
                 ],
-                axis=1
+                axis=1,
+            )
+        item_constraints = (
+            None
+            if item_constraint_matrix is None
+            else spo.LinearConstraint(
+                A=item_constraint_matrix,
+                ub=np.ones(item_constraint_matrix.shape[0]),  # type: ignore
             )
-        item_constraints = None if item_constraint_matrix is None else spo.LinearConstraint(
-            A=item_constraint_matrix,
-            ub=np.ones(item_constraint_matrix.shape[0]),
         )
 
         # constrain the item and their variables
@@ -108,7 +104,7 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
         item_var_constraint_matrix = np.stack(item_var_constraint_vectors, axis=0)  # [PC, N]
         item_var_constraints = spo.LinearConstraint(
             A=item_var_constraint_matrix,
-            ub=np.zeros(item_var_constraint_matrix.shape[0]),
+            ub=np.zeros(item_var_constraint_matrix.shape[0]),  # type: ignore
         )
 
         constraints = [var_constraints, item_var_constraints]
@@ -123,7 +119,7 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
         )
         return -result.fun
 
-    def score_self(self, x: T) -> float:
+    def score_self(self, x: Collection[T]) -> float:
         return solve_alignment(self.inner.gram_matrix(x, x), self.constraint)
 
 
@@ -160,6 +156,7 @@ def _all_variables_iterator(obj: object) -> Iterator[Variable]:
         elif getattr(obj, "__dict__", None) is not None:
             for fld in vars(x).values():
                 yield from _all_variables(fld)
+
     return set(_all_variables_iterator(x))
 
 
@@ -183,7 +180,7 @@ def _get_one_to_one_constraint_matrix(n_x: int, n_y: int) -> np.ndarray:  # [X +
     return np.concatenate([mask_x, mask_y], axis=0)
 
 
-def may_be_variable(cls: type) -> bool:
+def may_be_variable(cls: object) -> bool:
     if cls is Variable:
         return True
     if get_origin(cls) is not None and get_origin(cls) is Union:
@@ -192,10 +189,10 @@ def may_be_variable(cls: type) -> bool:
     return False
 
 
-def dataclass_has_variable(cls: type) -> bool:
+def dataclass_has_variable(cls: object) -> bool:
     if cls is Variable:
         return True
-    if getattr(cls, "__dataclass_fields__", None) is not None:
+    if is_dataclass(cls):
         if any(may_be_variable(t.type) for t in cls.__dataclass_fields__.values()):
             return True
     return False
diff --git a/src/unimetric/metric.py b/src/unimetric/metric.py
index 2e84f82..45033f6 100644
--- a/src/unimetric/metric.py
+++ b/src/unimetric/metric.py
@@ -126,7 +126,7 @@ def score_self(self, x: T) -> float:
 
 
 class ProductMetric(Metric[T]):
-    def __init__(self, cls: type, field_metrics: Dict[str, Metric]):
+    def __init__(self, cls: object, field_metrics: Dict[str, Metric]):
         if not is_dataclass(cls):
             raise ValueError(f"{cls} has to be a dataclass.")
         self.field_metrics = field_metrics
@@ -142,7 +142,7 @@ def score(self, x: T, y: T) -> float:
 
 
 class UnionMetric(Metric[T]):
-    def __init__(self, cls: type, case_metrics: Dict[type, Metric]):
+    def __init__(self, cls: object, case_metrics: Dict[type, Metric]):
         if get_origin(cls) is not Union:
             raise ValueError(f"{cls} has to be a union.")
         self.case_metrics = case_metrics
diff --git a/tests/unimetric/test_amr.py b/tests/unimetric/test_amr.py
index 01e207a..ac3268a 100644
--- a/tests/unimetric/test_amr.py
+++ b/tests/unimetric/test_amr.py
@@ -1,6 +1,7 @@
 from pytest import approx
 
 from unimetric.amr import AMR, Prop
+from unimetric.decorator import HasMetric
 from unimetric.latent_alignment import Variable
 
 
@@ -30,4 +31,8 @@ def test_smatch():
         ]
     )
 
-    assert AMR.metric.score(amr1, amr2) == approx(0.73, abs=0.01)
+    if isinstance(AMR, HasMetric):
+        assert AMR.metric.score(amr1, amr2) == approx(0.73, abs=0.01)
+    else:
+        # In case of failure to derive the metric.
+        assert False

From 2e34bbc5745e378e09a13a956f96cb0b87c23af1 Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sat, 16 Sep 2023 07:33:10 -0400
Subject: [PATCH 04/15] Reformatted codebase.

---
 src/unimetric/alignment.py  |  7 +++----
 src/unimetric/amr.py        |  2 +-
 src/unimetric/decorator.py  | 37 ++++++++++++++++++++++++++++---------
 src/unimetric/ie.py         |  4 ++--
 src/unimetric/metric.py     | 16 ++++------------
 tests/unimetric/test_amr.py | 22 +++++++++++-----------
 6 files changed, 49 insertions(+), 39 deletions(-)

diff --git a/src/unimetric/alignment.py b/src/unimetric/alignment.py
index e94ee2b..47a23f7 100644
--- a/src/unimetric/alignment.py
+++ b/src/unimetric/alignment.py
@@ -7,13 +7,12 @@
 
 from unimetric.metric import Metric
 
-T = TypeVar('T')
+T = TypeVar("T")
 
 
 class AlignmentConstraint(Enum):
-    """
-    Alignment constraints for the alignment metric.
-    """
+    """Alignment constraints for the alignment metric."""
+
     OneToOne = enum.auto()
     OneToMany = enum.auto()
     ManyToOne = enum.auto()
diff --git a/src/unimetric/amr.py b/src/unimetric/amr.py
index c4b9021..7cd3716 100644
--- a/src/unimetric/amr.py
+++ b/src/unimetric/amr.py
@@ -16,7 +16,7 @@ def __hash__(self):
         return hash((self.subj, self.pred, self.obj))
 
 
-@unimetric(normalizer='f1')
+@unimetric(normalizer="f1")
 @dataclass
 class AMR:
     props: Collection[Prop]
diff --git a/src/unimetric/decorator.py b/src/unimetric/decorator.py
index 37538ea..34088fd 100644
--- a/src/unimetric/decorator.py
+++ b/src/unimetric/decorator.py
@@ -33,10 +33,19 @@ class HasLatentMetric(Protocol):
 
 
 def derive_metric(cls: object, constraint: AlignmentConstraint) -> Metric:
-    """
-    Derive a unified metric from any type.
-    :param cls: The type to derive a metric from.
-    :return: A metric object for the given type.
+    """Derive a unified metric from any type.
+
+    Parameters
+    ----------
+    cls : object
+        The dataclass-like class to derive the metric from.
+    constraint : AlignmentConstraint
+        The alignment constraint to use.
+
+    Returns
+    -------
+    Metric
+        The derived metric.
     """
 
     # if the type is annotated with a metric instance, use the metric annotation
@@ -95,10 +104,19 @@ def unimetric(
     normalizer: NormalizerLiteral = "none",
     constraint: ConstraintLiteral = "<->",
 ) -> Callable[[T], T]:
-    """
-    Derive a unified metric from a class.
-    :param normalizer:
-    :return:
+    """Decorator to derive a metric from a dataclass.
+
+    Parameters
+    ----------
+    normalizer : NormalizerLiteral
+        The normalizer to use, by default "none"
+    constraint : ConstraintLiteral
+        The alignment constraint to use, by default "<->"
+
+    Returns
+    -------
+    Callable[[T], T]
+        The decorated new class.
     """
 
     def class_decorator(cls: T) -> T:
@@ -123,15 +141,16 @@ def class_decorator(cls: T) -> T:
         }[normalizer](metric)
 
         if dataclass_has_variable(cls):
+
             class LatentMetricWrapper(cls, HasLatentMetric):  # type: ignore
                 latent_metric = normalized_metric
 
             return LatentMetricWrapper
         else:
+
             class MetricWrapper(cls, HasMetric):  # type: ignore
                 metric = normalized_metric
 
             return MetricWrapper
-        # return cls
 
     return class_decorator
diff --git a/src/unimetric/ie.py b/src/unimetric/ie.py
index 6f8a0bc..78a8202 100644
--- a/src/unimetric/ie.py
+++ b/src/unimetric/ie.py
@@ -50,13 +50,13 @@ class RelationSet:
     relations: List[Relation]
 
 
-@unimetric(normalizer='f1')
+@unimetric(normalizer="f1")
 @dataclass
 class Entity:
     mentions: List[Mention]
 
 
-@unimetric(normalizer='f1')
+@unimetric(normalizer="f1")
 @dataclass
 class EntitySet:
     entities: List[Entity]
diff --git a/src/unimetric/metric.py b/src/unimetric/metric.py
index 45033f6..2de3b4d 100644
--- a/src/unimetric/metric.py
+++ b/src/unimetric/metric.py
@@ -6,12 +6,11 @@
 
 import numpy as np
 
-T = TypeVar('T', contravariant=True)
-U = TypeVar('U')
+T = TypeVar("T", contravariant=True)
+U = TypeVar("U")
 
 
 class Metric(Generic[T]):
-
     @abstractmethod
     def score(self, x: T, y: T) -> float:
         raise NotImplementedError()
@@ -25,10 +24,7 @@ def score_self(self, x: T) -> float:
         return self.score(x, x)
 
     def gram_matrix(self, xs: Collection[T], ys: Collection[T]) -> np.ndarray:
-        return np.array([
-            [self.score(x, y) for y in ys]
-            for x in xs
-        ])
+        return np.array([[self.score(x, y) for y in ys] for x in xs])
 
     @staticmethod
     def from_function(f: Callable[[T, T], float]) -> "Metric[T]":
@@ -133,11 +129,7 @@ def __init__(self, cls: object, field_metrics: Dict[str, Metric]):
 
     def score(self, x: T, y: T) -> float:
         return reduce(
-            mul,
-            (
-                self.field_metrics[fld].score(getattr(x, fld), getattr(y, fld))
-                for fld in self.field_metrics.keys()
-            )
+            mul, (self.field_metrics[fld].score(getattr(x, fld), getattr(y, fld)) for fld in self.field_metrics.keys())
         )
 
 
diff --git a/tests/unimetric/test_amr.py b/tests/unimetric/test_amr.py
index ac3268a..594a729 100644
--- a/tests/unimetric/test_amr.py
+++ b/tests/unimetric/test_amr.py
@@ -12,22 +12,22 @@ def test_smatch():
 
     amr1 = AMR(
         props=[
-            Prop(Variable('a'), 'instance', 'want-01'),
-            Prop(Variable('b'), 'instance', 'boy'),
-            Prop(Variable('c'), 'instance', 'go-01'),
-            Prop(Variable('a'), 'ARG0', Variable('b')),
-            Prop(Variable('a'), 'ARG1', Variable('c')),
-            Prop(Variable('c'), 'ARG0', Variable('b')),
+            Prop(Variable("a"), "instance", "want-01"),
+            Prop(Variable("b"), "instance", "boy"),
+            Prop(Variable("c"), "instance", "go-01"),
+            Prop(Variable("a"), "ARG0", Variable("b")),
+            Prop(Variable("a"), "ARG1", Variable("c")),
+            Prop(Variable("c"), "ARG0", Variable("b")),
         ]
     )
 
     amr2 = AMR(
         props=[
-            Prop(Variable('x'), 'instance', 'want-01'),
-            Prop(Variable('y'), 'instance', 'boy'),
-            Prop(Variable('z'), 'instance', 'football'),
-            Prop(Variable('x'), 'ARG0', Variable('y')),
-            Prop(Variable('x'), 'ARG1', Variable('z')),
+            Prop(Variable("x"), "instance", "want-01"),
+            Prop(Variable("y"), "instance", "boy"),
+            Prop(Variable("z"), "instance", "football"),
+            Prop(Variable("x"), "ARG0", Variable("y")),
+            Prop(Variable("x"), "ARG1", Variable("z")),
         ]
     )
 

From 980a425486a3785e0430217f675a07bb0b388f4d Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sat, 16 Sep 2023 16:51:05 -0400
Subject: [PATCH 05/15] Configured `ruff` and reformatted codebaes to pass
 checks.

---
 pyproject.toml                    | 17 ++++++++-
 src/unimetric/__init__.py         |  1 +
 src/unimetric/alignment.py        | 30 ++++++++++++++++
 src/unimetric/amr.py              |  6 ++++
 src/unimetric/decorator.py        |  8 +++--
 src/unimetric/ie.py               | 58 ++++++++++++++++++++++++++++++-
 src/unimetric/latent_alignment.py | 13 +++++--
 src/unimetric/metric.py           | 56 +++++++++++++++++++++++++++--
 tests/__init__.py                 |  1 +
 tests/unimetric/__init__.py       |  1 +
 tests/unimetric/test_alignment.py |  2 ++
 tests/unimetric/test_amr.py       |  6 ++--
 12 files changed, 186 insertions(+), 13 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 770f20c..140f11f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,21 @@
 [tool.ruff]
 line-length = 120
+src = ["src", "tests"]
+
+select = [
+  "E", # pycodestyle
+  "F", # pyflakes
+  "UP", # pyupgrade
+  "D", # pydocstyle
+]
+ignore = [
+  "D105", # Missing docstring in magic method
+]
+
+fixable = ["ALL"]
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
 
 [tool.black]
 line-length = 120
@@ -7,7 +23,6 @@ line-length = 120
 [tool.pyright]
 include = ["src", "tests"]
 
-
 [tool.pytest.ini_options]
 minversion = "6.0"
 testpaths = ["tests"]
diff --git a/src/unimetric/__init__.py b/src/unimetric/__init__.py
index e69de29..14dfe1d 100644
--- a/src/unimetric/__init__.py
+++ b/src/unimetric/__init__.py
@@ -0,0 +1 @@
+"""The core functionality of unimetric package."""
diff --git a/src/unimetric/alignment.py b/src/unimetric/alignment.py
index 47a23f7..416d6d1 100644
--- a/src/unimetric/alignment.py
+++ b/src/unimetric/alignment.py
@@ -1,3 +1,4 @@
+"""Metric derivation with alignment constraints."""
 import enum
 from enum import Enum
 from typing import Collection, TypeVar
@@ -20,11 +21,25 @@ class AlignmentConstraint(Enum):
 
 
 class AlignmentMetric(Metric[Collection[T]]):
+    """A metric derived using some alignment constraints."""
+
     def __init__(self, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.OneToOne):
         self.inner = inner
         self.constraint = constraint
 
     def score(self, x: Collection[T], y: Collection[T]) -> float:
+        """Score two collections of objects.
+
+        Parameters
+        ----------
+        x : Collection[T]
+        y : Collection[T]
+
+        Returns
+        -------
+        float
+            The score of the two collections.
+        """
         # TODO: alternative implementation when the inner metric is discrete
         return solve_alignment(
             self.inner.gram_matrix(x, y),
@@ -32,6 +47,7 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
         )
 
     def score_self(self, x: Collection[T]) -> float:
+        """Score a collection of objects with itself."""
         if self.constraint == AlignmentConstraint.ManyToMany:
             return self.inner.gram_matrix(x, x).sum()
         else:
@@ -39,6 +55,20 @@ def score_self(self, x: Collection[T]) -> float:
 
 
 def solve_alignment(gram_matrix: np.ndarray, constraint: AlignmentConstraint) -> float:
+    """Solve the alignment problem.
+
+    Parameters
+    ----------
+    gram_matrix : np.ndarray
+        The gram matrix of the inner metric.
+    constraint : AlignmentConstraint
+        The alignment constraint.
+
+    Returns
+    -------
+    float
+        The score of the alignment.
+    """
     if constraint == AlignmentConstraint.OneToOne:
         row_idx, col_idx = spo.linear_sum_assignment(
             cost_matrix=gram_matrix,
diff --git a/src/unimetric/amr.py b/src/unimetric/amr.py
index 7cd3716..d35d768 100644
--- a/src/unimetric/amr.py
+++ b/src/unimetric/amr.py
@@ -1,3 +1,4 @@
+"""Abstract Meaning Representation (AMR) structure."""
 from dataclasses import dataclass
 from typing import Collection, Set, Union
 
@@ -8,6 +9,8 @@
 @unimetric()
 @dataclass
 class Prop:
+    """A property in an AMR."""
+
     subj: Variable
     pred: str
     obj: Union[Variable, str]
@@ -19,9 +22,12 @@ def __hash__(self):
 @unimetric(normalizer="f1")
 @dataclass
 class AMR:
+    """Abstract Meaning Representation (AMR) structure."""
+
     props: Collection[Prop]
 
     def variables(self) -> Set[Variable]:
+        """Return the set of variables in the AMR."""
         vars = set()
         for p in self.props:
             if isinstance(p.subj, Variable):
diff --git a/src/unimetric/decorator.py b/src/unimetric/decorator.py
index 34088fd..c4cc74e 100644
--- a/src/unimetric/decorator.py
+++ b/src/unimetric/decorator.py
@@ -1,3 +1,4 @@
+"""Decorator for deriving metrics from dataclasses."""
 from dataclasses import fields, is_dataclass
 from typing import (
     Literal,
@@ -24,11 +25,15 @@
 
 @runtime_checkable
 class HasMetric(Protocol):
+    """Protocol for classes that have a metric."""
+
     metric: Metric
 
 
 @runtime_checkable
 class HasLatentMetric(Protocol):
+    """Protocol for classes that have a latent metric."""
+
     latent_metric: Metric
 
 
@@ -47,7 +52,6 @@ def derive_metric(cls: object, constraint: AlignmentConstraint) -> Metric:
     Metric
         The derived metric.
     """
-
     # if the type is annotated with a metric instance, use the metric annotation
     if get_origin(cls) is Annotated:
         metric = get_args(cls)[1]
@@ -104,7 +108,7 @@ def unimetric(
     normalizer: NormalizerLiteral = "none",
     constraint: ConstraintLiteral = "<->",
 ) -> Callable[[T], T]:
-    """Decorator to derive a metric from a dataclass.
+    """Decorate a dataclass to have corresponding metric derived.
 
     Parameters
     ----------
diff --git a/src/unimetric/ie.py b/src/unimetric/ie.py
index 78a8202..a7c13e5 100644
--- a/src/unimetric/ie.py
+++ b/src/unimetric/ie.py
@@ -1,3 +1,7 @@
+"""Data structures commonly used in information extraction.
+
+The data structures defined here can automatically derive commonly used metrics in IE.
+"""
 from dataclasses import dataclass
 from typing import List
 
@@ -7,6 +11,17 @@
 @unimetric()
 @dataclass
 class Mention:
+    """A mention span commonly used for .
+
+    The mention span here does not enforce whether it is right exclusive or not.
+    However, it is a convention that the mention span is right exclusive.
+
+    Attributes
+    ----------
+        left: The left index of the span.
+        right: The right index of the span.
+    """
+
     left: int
     right: int
 
@@ -14,6 +29,16 @@ class Mention:
 @unimetric()
 @dataclass
 class Relation:
+    """A relation between two mentions commonly used in relation extraction.
+
+    Attributes
+    ----------
+        type: The type of the relation.
+        subj: The subject mention.
+        obj: The object mention.
+
+    """
+
     type: str
     subj: Mention
     obj: Mention
@@ -21,12 +46,27 @@ class Relation:
 
 @unimetric()
 class Trigger:
+    """A trigger mention commonly used in event extraction.
+
+    Attributes
+    ----------
+        type: The type of the trigger, commonly used to indicate event type.
+    """
+
     mention: Mention
     type: str
 
 
 @unimetric()
 class Argument:
+    """An argument mention commonly used in event extraction.
+
+    Attributes
+    ----------
+        mention: The mention of the argument.
+        role: The role of the argument.
+    """
+
     mention: Mention
     role: str
 
@@ -34,29 +74,45 @@ class Argument:
 @unimetric()
 @dataclass
 class Event:
-    trig: Trigger
+    """An event commonly used in event extraction.
+
+    Attributes
+    ----------
+        trigger: The trigger of the event.
+        args: The arguments of the event.
+    """
+
+    trigger: Trigger
     args: List[Argument]
 
 
 @unimetric()
 @dataclass
 class EventSet:
+    """A set of events to present predicted or referenced events."""
+
     events: List[Event]
 
 
 @unimetric()
 @dataclass
 class RelationSet:
+    """A set of relations to present predicted or referenced relations."""
+
     relations: List[Relation]
 
 
 @unimetric(normalizer="f1")
 @dataclass
 class Entity:
+    """An entity comprises multiple mentions, commonly used in coreference resolution."""
+
     mentions: List[Mention]
 
 
 @unimetric(normalizer="f1")
 @dataclass
 class EntitySet:
+    """A set of entities to present predicted or referenced entities."""
+
     entities: List[Entity]
diff --git a/src/unimetric/latent_alignment.py b/src/unimetric/latent_alignment.py
index 3951e33..c802527 100644
--- a/src/unimetric/latent_alignment.py
+++ b/src/unimetric/latent_alignment.py
@@ -1,3 +1,4 @@
+"""Metric derivation with latent alignments."""
 from dataclasses import dataclass, fields, is_dataclass
 from typing import ClassVar, Generic, Collection, Mapping, Tuple, TypeVar, Union, Set, Iterator, get_origin, get_args
 
@@ -12,6 +13,8 @@
 
 @dataclass
 class Variable:
+    """A variable in a latent."""
+
     name: str
 
     latent_metric: ClassVar[Metric["Variable"]] = Metric.from_function(lambda x, y: 1.0)
@@ -21,6 +24,8 @@ def __hash__(self):
 
 
 class LatentAlignmentMetric(Metric[Collection[T]]):
+    """A metric derived to support aligning latent variables defined in structures."""
+
     def __init__(self, cls: type, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.OneToOne):
         if is_dataclass(cls):
             self.fields = fields(cls)
@@ -30,6 +35,7 @@ def __init__(self, cls: type, inner: Metric[T], constraint: AlignmentConstraint
         self.constraint = constraint
 
     def score(self, x: Collection[T], y: Collection[T]) -> float:
+        """Score two collections of objects."""
         x = list(x)
         y = list(y)
         x_vars = _all_variables(x)
@@ -120,13 +126,12 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
         return -result.fun
 
     def score_self(self, x: Collection[T]) -> float:
+        """Score a collection of objects with itself."""
         return solve_alignment(self.inner.gram_matrix(x, x), self.constraint)
 
 
 class _PairIndexer(Generic[T], Mapping[Tuple[T, T], int]):
-    """
-    Creates a mapping of a Cartesian product of objects to a single index.
-    """
+    """Creates a mapping of a Cartesian product of objects to a single index."""
 
     def __init__(self, x: Collection[T], y: Collection[T], offset: int = 0):
         self.x = x
@@ -181,6 +186,7 @@ def _get_one_to_one_constraint_matrix(n_x: int, n_y: int) -> np.ndarray:  # [X +
 
 
 def may_be_variable(cls: object) -> bool:
+    """Check if a type may be a `Variable`."""
     if cls is Variable:
         return True
     if get_origin(cls) is not None and get_origin(cls) is Union:
@@ -190,6 +196,7 @@ def may_be_variable(cls: object) -> bool:
 
 
 def dataclass_has_variable(cls: object) -> bool:
+    """Check if a dataclass has a field is in `Variable` type."""
     if cls is Variable:
         return True
     if is_dataclass(cls):
diff --git a/src/unimetric/metric.py b/src/unimetric/metric.py
index 2de3b4d..396e934 100644
--- a/src/unimetric/metric.py
+++ b/src/unimetric/metric.py
@@ -1,3 +1,4 @@
+"""Metric interface and implementations for commonly used metrics."""
 from abc import abstractmethod
 from dataclasses import is_dataclass
 from functools import reduce
@@ -11,103 +12,146 @@
 
 
 class Metric(Generic[T]):
+    """Metric interface."""
+
     @abstractmethod
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         raise NotImplementedError()
 
     def score_self(self, x: T) -> float:
-        """
-        Scores an object against itself.
+        """Scores an object against itself.
+
         In many cases there is a faster way to compute this than the general pair case.
         In such cases, please override this function.
         """
         return self.score(x, x)
 
     def gram_matrix(self, xs: Collection[T], ys: Collection[T]) -> np.ndarray:
+        """Compute the gram matrix of the metric."""
         return np.array([[self.score(x, y) for y in ys] for x in xs])
 
     @staticmethod
     def from_function(f: Callable[[T, T], float]) -> "Metric[T]":
+        """Create a metric from a function.
+
+        Parameters
+        ----------
+        f : Callable[[T, T], float]
+            The function to create the metric from.
+
+
+        Returns
+        -------
+        Metric[T]
+            The metric.
+        """
         return MetricFromFunction(f)
 
 
 class MetricFromFunction(Metric[T]):
+    """A metric wrapped from a function."""
+
     def __init__(self, f: Callable[[T, T], float]):
         self.f = f
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         return self.f(x, y)
 
 
 class ContramappedMetric(Metric[T]):
+    """A metric contramapped by a function."""
+
     def __init__(self, inner: Metric[U], f: Callable[[T], U]):
         self.inner = inner
         self.f = f
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         return self.inner.score(self.f(x), self.f(y))
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return self.inner.score_self(self.f(x))
 
 
 class DiscreteMetric(Metric[T]):
+    """A metric for discrete objects."""
+
     def __init__(self, cls: Type[T]):
         if getattr(cls, "__eq__", None) is None:
             raise ValueError("Class must implement __eq__")
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         return float(x == y)
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return 1.0
 
 
 class Jaccard(Metric[T]):
+    """Jaccard metric."""
+
     def __init__(self, inner: Metric[T]):
         self.inner = inner
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         sxy = self.inner.score(x, y)
         sxx = self.inner.score_self(x)
         syy = self.inner.score_self(y)
         return sxy / (sxx + syy - sxy)
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return 1.0
 
 
 class Precision(Metric[T]):
+    """Precision metric."""
+
     def __init__(self, inner: Metric[T]):
         self.inner = inner
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         sxy = self.inner.score(x, y)
         sxx = self.inner.score_self(x)
         return sxy / sxx
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return 1.0
 
 
 class Recall(Metric[T]):
+    """Recall metric."""
+
     def __init__(self, inner: Metric[T]):
         self.inner = inner
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         sxy = self.inner.score(x, y)
         syy = self.inner.score_self(y)
         return sxy / syy
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return 1.0
 
 
 class FScore(Metric[T]):
+    """F-score metric."""
+
     def __init__(self, inner: Metric[T]):
         self.inner = inner
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         sxy = self.inner.score(x, y)
         sxx = self.inner.score_self(x)
         syy = self.inner.score_self(y)
@@ -118,28 +162,35 @@ def score(self, x: T, y: T) -> float:
         return 2 * p * r / (p + r)
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return 1.0
 
 
 class ProductMetric(Metric[T]):
+    """A metric that is the product of other metrics."""
+
     def __init__(self, cls: object, field_metrics: Dict[str, Metric]):
         if not is_dataclass(cls):
             raise ValueError(f"{cls} has to be a dataclass.")
         self.field_metrics = field_metrics
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         return reduce(
             mul, (self.field_metrics[fld].score(getattr(x, fld), getattr(y, fld)) for fld in self.field_metrics.keys())
         )
 
 
 class UnionMetric(Metric[T]):
+    """A metric that is the union of other metrics."""
+
     def __init__(self, cls: object, case_metrics: Dict[type, Metric]):
         if get_origin(cls) is not Union:
             raise ValueError(f"{cls} has to be a union.")
         self.case_metrics = case_metrics
 
     def score(self, x: T, y: T) -> float:
+        """Score two objects."""
         x_type = type(x)
         y_type = type(y)
         if x_type != y_type:
@@ -147,4 +198,5 @@ def score(self, x: T, y: T) -> float:
         return self.case_metrics[x_type].score(x, y)
 
     def score_self(self, x: T) -> float:
+        """Scores an object against itself."""
         return 1.0
diff --git a/tests/__init__.py b/tests/__init__.py
index e69de29..eb7eff0 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -0,0 +1 @@
+"""Tests for the unimetric project."""
diff --git a/tests/unimetric/__init__.py b/tests/unimetric/__init__.py
index e69de29..313c254 100644
--- a/tests/unimetric/__init__.py
+++ b/tests/unimetric/__init__.py
@@ -0,0 +1 @@
+"""Tests for the unimetric package."""
diff --git a/tests/unimetric/test_alignment.py b/tests/unimetric/test_alignment.py
index 24533c4..244bf2a 100644
--- a/tests/unimetric/test_alignment.py
+++ b/tests/unimetric/test_alignment.py
@@ -1,8 +1,10 @@
+"""Tests for metrics derived with alignments."""
 from unimetric.alignment import solve_alignment, AlignmentConstraint
 from unimetric.metric import DiscreteMetric
 
 
 def test_solve_alignment():
+    """Test the alignment solver."""
     a = [1, 2, 2]
     b = [1, 1, 1, 2]
 
diff --git a/tests/unimetric/test_amr.py b/tests/unimetric/test_amr.py
index 594a729..b74cf6f 100644
--- a/tests/unimetric/test_amr.py
+++ b/tests/unimetric/test_amr.py
@@ -1,3 +1,4 @@
+"""Tests for SMatch derived from the AMR structure."""
 from pytest import approx
 
 from unimetric.amr import AMR, Prop
@@ -6,10 +7,7 @@
 
 
 def test_smatch():
-    """
-    Example from https://aclanthology.org/P13-2131.pdf.
-    """
-
+    """Example from https://aclanthology.org/P13-2131.pdf."""
     amr1 = AMR(
         props=[
             Prop(Variable("a"), "instance", "want-01"),

From 35adc14f4e4cf80d69ea6910420732f3135e75cd Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sat, 16 Sep 2023 16:58:53 -0400
Subject: [PATCH 06/15] Added `ruff` to the dev dependencies.

---
 poetry.lock    | 28 +++++++++++++++++++++++++++-
 pyproject.toml |  1 +
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 0a0b84b..f493e18 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -150,6 +150,32 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "ruff"
+version = "0.0.290"
+description = "An extremely fast Python linter, written in Rust."
+optional = false
+python-versions = ">=3.7"
+files = [
+    { file = "ruff-0.0.290-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:0e2b09ac4213b11a3520221083866a5816616f3ae9da123037b8ab275066fbac" },
+    { file = "ruff-0.0.290-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:4ca6285aa77b3d966be32c9a3cd531655b3d4a0171e1f9bf26d66d0372186767" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:35e3550d1d9f2157b0fcc77670f7bb59154f223bff281766e61bdd1dd854e0c5" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:d748c8bd97874f5751aed73e8dde379ce32d16338123d07c18b25c9a2796574a" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:982af5ec67cecd099e2ef5e238650407fb40d56304910102d054c109f390bf3c" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:bbd37352cea4ee007c48a44c9bc45a21f7ba70a57edfe46842e346651e2b995a" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1d9be6351b7889462912e0b8185a260c0219c35dfd920fb490c7f256f1d8313e" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:75cdc7fe32dcf33b7cec306707552dda54632ac29402775b9e212a3c16aad5e6" },
+    { file = "ruff-0.0.290-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eb07f37f7aecdbbc91d759c0c09870ce0fb3eed4025eebedf9c4b98c69abd527" },
+    { file = "ruff-0.0.290-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:2ab41bc0ba359d3f715fc7b705bdeef19c0461351306b70a4e247f836b9350ed" },
+    { file = "ruff-0.0.290-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:150bf8050214cea5b990945b66433bf9a5e0cef395c9bc0f50569e7de7540c86" },
+    { file = "ruff-0.0.290-py3-none-musllinux_1_2_i686.whl", hash = "sha256:75386ebc15fe5467248c039f5bf6a0cfe7bfc619ffbb8cd62406cd8811815fca" },
+    { file = "ruff-0.0.290-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:ac93eadf07bc4ab4c48d8bb4e427bf0f58f3a9c578862eb85d99d704669f5da0" },
+    { file = "ruff-0.0.290-py3-none-win32.whl", hash = "sha256:461fbd1fb9ca806d4e3d5c745a30e185f7cf3ca77293cdc17abb2f2a990ad3f7" },
+    { file = "ruff-0.0.290-py3-none-win_amd64.whl", hash = "sha256:f1f49f5ec967fd5778813780b12a5650ab0ebcb9ddcca28d642c689b36920796" },
+    { file = "ruff-0.0.290-py3-none-win_arm64.whl", hash = "sha256:ae5a92dfbdf1f0c689433c223f8dac0782c2b2584bd502dfdbc76475669f1ba1" },
+    { file = "ruff-0.0.290.tar.gz", hash = "sha256:949fecbc5467bb11b8db810a7fa53c7e02633856ee6bd1302b2f43adcd71b88d" },
+]
+
 [[package]]
 name = "scipy"
 version = "1.11.2"
@@ -222,4 +248,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "dac26de6ca105acd6c73153c222d74af1526dd74b7d4e5d79c14b2c047d8da96"
+content-hash = "63b22b07ccd3415332ad7433c3e384eb28ec462c428b8d57205dd44b6c35836c"
diff --git a/pyproject.toml b/pyproject.toml
index 140f11f..6f98e8c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,6 +47,7 @@ optional = true
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.2"
 pyright = "^1.1.327"
+ruff = "^0.0.290"
 
 [build-system]
 requires = ["poetry-core"]

From 551b08a6c978bd72796ff783f49226b81973a7d4 Mon Sep 17 00:00:00 2001
From: WanMok <16273544+wanmok@users.noreply.github.com>
Date: Sat, 16 Sep 2023 17:12:25 -0400
Subject: [PATCH 07/15] Added GitHub action to run linter and tests.

---
 .github/workflows/python-app.yml | 38 ++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 .github/workflows/python-app.yml

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
new file mode 100644
index 0000000..01008e2
--- /dev/null
+++ b/.github/workflows/python-app.yml
@@ -0,0 +1,38 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.9"
+    - name: Setup Poetry
+      uses: Gr1N/setup-poetry@v8
+      with:
+        poetry-version: 1.6.1
+    - name: Install dependencies
+      run: |
+        poetry install --with dev
+    - uses: chartboost/ruff-action@v1
+      with:
+        version: 0.0.290
+    - name: Test with pytest
+      run: |
+        pytest

From 08fc3cd6266bc56f2f9efe55beeeb7ca08b87c4c Mon Sep 17 00:00:00 2001
From: WanMok <16273544+wanmok@users.noreply.github.com>
Date: Sat, 16 Sep 2023 17:16:20 -0400
Subject: [PATCH 08/15] Update python-app.yml

---
 .github/workflows/python-app.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 01008e2..1b0180c 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -35,4 +35,4 @@ jobs:
         version: 0.0.290
     - name: Test with pytest
       run: |
-        pytest
+        poetry run pytest

From 811ef174e044e704bf21b6c903da0a74dbfbe1ee Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sat, 16 Sep 2023 18:07:22 -0400
Subject: [PATCH 09/15] Modified packages info.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6f98e8c..7e8b0a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ version = "0.1.0"
 description = "A Unified View of Evaluation Metrics for Information Extraction"
 authors = ["Tongfei Chen <tongfei@pm.me>", "Yunmo Chen <yunmo@jhu.edu>"]
 readme = "README.md"
-packages = [{ include = "src/unimetric" }]
+packages = [{ include = "unimetric", from = "src" }]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.13"

From 284f576e963a28a62fa7b4b419a03b231c9bdfa8 Mon Sep 17 00:00:00 2001
From: WanMok <16273544+wanmok@users.noreply.github.com>
Date: Sat, 16 Sep 2023 18:16:16 -0400
Subject: [PATCH 10/15] Added `pyright` actions

---
 .github/workflows/python-app.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 1b0180c..0364f29 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -19,20 +19,22 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.9"
     - name: Setup Poetry
       uses: Gr1N/setup-poetry@v8
       with:
         poetry-version: 1.6.1
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.9"
+        cache: "poetry"
     - name: Install dependencies
       run: |
         poetry install --with dev
     - uses: chartboost/ruff-action@v1
       with:
         version: 0.0.290
+    - uses: jakebailey/pyright-action@v1
     - name: Test with pytest
       run: |
         poetry run pytest

From 52fba8b1be57d7fafbc47ee960ab1675b34bd6c4 Mon Sep 17 00:00:00 2001
From: WanMok <16273544+wanmok@users.noreply.github.com>
Date: Sat, 16 Sep 2023 18:23:09 -0400
Subject: [PATCH 11/15] Update python-app.yml

---
 .github/workflows/python-app.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 0364f29..ed4d5ec 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -31,10 +31,17 @@ jobs:
     - name: Install dependencies
       run: |
         poetry install --with dev
-    - uses: chartboost/ruff-action@v1
+    - name: Ensure Poetry envs
+      run: |
+        echo "$(poetry env info --path)/bin" >> $GITHUB_PATH
+    - name: Run ruff
+      uses: chartboost/ruff-action@v1
       with:
         version: 0.0.290
-    - uses: jakebailey/pyright-action@v1
+    - name: Run pyright
+      uses: jakebailey/pyright-action@v1
+      with:
+        version: "1.1.327"
     - name: Test with pytest
       run: |
         poetry run pytest

From f326364332e3adb2011ddf8c357fae43f740d892 Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sat, 16 Sep 2023 18:32:26 -0400
Subject: [PATCH 12/15] Changed back to `setattr` so that the original class
 name can be kept.

---
 src/unimetric/decorator.py | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/src/unimetric/decorator.py b/src/unimetric/decorator.py
index c4cc74e..e41be45 100644
--- a/src/unimetric/decorator.py
+++ b/src/unimetric/decorator.py
@@ -145,16 +145,9 @@ def class_decorator(cls: T) -> T:
         }[normalizer](metric)
 
         if dataclass_has_variable(cls):
-
-            class LatentMetricWrapper(cls, HasLatentMetric):  # type: ignore
-                latent_metric = normalized_metric
-
-            return LatentMetricWrapper
+            setattr(cls, "latent_metric", normalized_metric)  # type: ignore
         else:
-
-            class MetricWrapper(cls, HasMetric):  # type: ignore
-                metric = normalized_metric
-
-            return MetricWrapper
+            setattr(cls, "metric", normalized_metric)  # type: ignore
+        return cls
 
     return class_decorator

From 8a271f07c5bafe13cda7f44db7d315c371103183 Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sat, 16 Sep 2023 20:27:08 -0400
Subject: [PATCH 13/15] Updated dependencies.

---
 poetry.lock    | 63 ++++++++++++++++++++++++++++----------------------
 pyproject.toml |  1 -
 2 files changed, 35 insertions(+), 29 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f493e18..32c5f5b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -52,36 +52,43 @@ setuptools = "*"
 
 [[package]]
 name = "numpy"
-version = "1.25.2"
+version = "1.26.0"
 description = "Fundamental package for array computing in Python"
 optional = false
-python-versions = ">=3.9"
+python-versions = "<3.13,>=3.9"
 files = [
-    {file = "numpy-1.25.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:db3ccc4e37a6873045580d413fe79b68e47a681af8db2e046f1dacfa11f86eb3"},
-    {file = "numpy-1.25.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:90319e4f002795ccfc9050110bbbaa16c944b1c37c0baeea43c5fb881693ae1f"},
-    {file = "numpy-1.25.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:dfe4a913e29b418d096e696ddd422d8a5d13ffba4ea91f9f60440a3b759b0187"},
-    {file = "numpy-1.25.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f08f2e037bba04e707eebf4bc934f1972a315c883a9e0ebfa8a7756eabf9e357"},
-    {file = "numpy-1.25.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:bec1e7213c7cb00d67093247f8c4db156fd03075f49876957dca4711306d39c9"},
-    {file = "numpy-1.25.2-cp310-cp310-win32.whl", hash = "sha256:7dc869c0c75988e1c693d0e2d5b26034644399dd929bc049db55395b1379e044"},
-    {file = "numpy-1.25.2-cp310-cp310-win_amd64.whl", hash = "sha256:834b386f2b8210dca38c71a6e0f4fd6922f7d3fcff935dbe3a570945acb1b545"},
-    {file = "numpy-1.25.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:c5462d19336db4560041517dbb7759c21d181a67cb01b36ca109b2ae37d32418"},
-    {file = "numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:c5652ea24d33585ea39eb6a6a15dac87a1206a692719ff45d53c5282e66d4a8f"},
-    {file = "numpy-1.25.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0d60fbae8e0019865fc4784745814cff1c421df5afee233db6d88ab4f14655a2"},
-    {file = "numpy-1.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:60e7f0f7f6d0eee8364b9a6304c2845b9c491ac706048c7e8cf47b83123b8dbf"},
-    {file = "numpy-1.25.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:bb33d5a1cf360304754913a350edda36d5b8c5331a8237268c48f91253c3a364"},
-    {file = "numpy-1.25.2-cp311-cp311-win32.whl", hash = "sha256:5883c06bb92f2e6c8181df7b39971a5fb436288db58b5a1c3967702d4278691d"},
-    {file = "numpy-1.25.2-cp311-cp311-win_amd64.whl", hash = "sha256:5c97325a0ba6f9d041feb9390924614b60b99209a71a69c876f71052521d42a4"},
-    {file = "numpy-1.25.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:b79e513d7aac42ae918db3ad1341a015488530d0bb2a6abcbdd10a3a829ccfd3"},
-    {file = "numpy-1.25.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:eb942bfb6f84df5ce05dbf4b46673ffed0d3da59f13635ea9b926af3deb76926"},
-    {file = "numpy-1.25.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3e0746410e73384e70d286f93abf2520035250aad8c5714240b0492a7302fdca"},
-    {file = "numpy-1.25.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d7806500e4f5bdd04095e849265e55de20d8cc4b661b038957354327f6d9b295"},
-    {file = "numpy-1.25.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:8b77775f4b7df768967a7c8b3567e309f617dd5e99aeb886fa14dc1a0791141f"},
-    {file = "numpy-1.25.2-cp39-cp39-win32.whl", hash = "sha256:2792d23d62ec51e50ce4d4b7d73de8f67a2fd3ea710dcbc8563a51a03fb07b01"},
-    {file = "numpy-1.25.2-cp39-cp39-win_amd64.whl", hash = "sha256:76b4115d42a7dfc5d485d358728cdd8719be33cc5ec6ec08632a5d6fca2ed380"},
-    {file = "numpy-1.25.2-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:1a1329e26f46230bf77b02cc19e900db9b52f398d6722ca853349a782d4cff55"},
-    {file = "numpy-1.25.2-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4c3abc71e8b6edba80a01a52e66d83c5d14433cbcd26a40c329ec7ed09f37901"},
-    {file = "numpy-1.25.2-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:1b9735c27cea5d995496f46a8b1cd7b408b3f34b6d50459d9ac8fe3a20cc17bf"},
-    {file = "numpy-1.25.2.tar.gz", hash = "sha256:fd608e19c8d7c55021dffd43bfe5492fab8cc105cc8986f813f8c3c048b38760"},
+    { file = "numpy-1.26.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f8db2f125746e44dce707dd44d4f4efeea8d7e2b43aace3f8d1f235cfa2733dd" },
+    { file = "numpy-1.26.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0621f7daf973d34d18b4e4bafb210bbaf1ef5e0100b5fa750bd9cde84c7ac292" },
+    { file = "numpy-1.26.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:51be5f8c349fdd1a5568e72713a21f518e7d6707bcf8503b528b88d33b57dc68" },
+    { file = "numpy-1.26.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:767254ad364991ccfc4d81b8152912e53e103ec192d1bb4ea6b1f5a7117040be" },
+    { file = "numpy-1.26.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:436c8e9a4bdeeee84e3e59614d38c3dbd3235838a877af8c211cfcac8a80b8d3" },
+    { file = "numpy-1.26.0-cp310-cp310-win32.whl", hash = "sha256:c2e698cb0c6dda9372ea98a0344245ee65bdc1c9dd939cceed6bb91256837896" },
+    { file = "numpy-1.26.0-cp310-cp310-win_amd64.whl", hash = "sha256:09aaee96c2cbdea95de76ecb8a586cb687d281c881f5f17bfc0fb7f5890f6b91" },
+    { file = "numpy-1.26.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:637c58b468a69869258b8ae26f4a4c6ff8abffd4a8334c830ffb63e0feefe99a" },
+    { file = "numpy-1.26.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:306545e234503a24fe9ae95ebf84d25cba1fdc27db971aa2d9f1ab6bba19a9dd" },
+    { file = "numpy-1.26.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8c6adc33561bd1d46f81131d5352348350fc23df4d742bb246cdfca606ea1208" },
+    { file = "numpy-1.26.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e062aa24638bb5018b7841977c360d2f5917268d125c833a686b7cbabbec496c" },
+    { file = "numpy-1.26.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:546b7dd7e22f3c6861463bebb000646fa730e55df5ee4a0224408b5694cc6148" },
+    { file = "numpy-1.26.0-cp311-cp311-win32.whl", hash = "sha256:c0b45c8b65b79337dee5134d038346d30e109e9e2e9d43464a2970e5c0e93229" },
+    { file = "numpy-1.26.0-cp311-cp311-win_amd64.whl", hash = "sha256:eae430ecf5794cb7ae7fa3808740b015aa80747e5266153128ef055975a72b99" },
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+    { file = "numpy-1.26.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:f042f66d0b4ae6d48e70e28d487376204d3cbf43b84c03bac57e28dac6151581" },
+    { file = "numpy-1.26.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e5e18e5b14a7560d8acf1c596688f4dfd19b4f2945b245a71e5af4ddb7422feb" },
+    { file = "numpy-1.26.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7f6bad22a791226d0a5c7c27a80a20e11cfe09ad5ef9084d4d3fc4a299cca505" },
+    { file = "numpy-1.26.0-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:4acc65dd65da28060e206c8f27a573455ed724e6179941edb19f97e58161bb69" },
+    { file = "numpy-1.26.0-cp312-cp312-win32.whl", hash = "sha256:bb0d9a1aaf5f1cb7967320e80690a1d7ff69f1d47ebc5a9bea013e3a21faec95" },
+    { file = "numpy-1.26.0-cp312-cp312-win_amd64.whl", hash = "sha256:ee84ca3c58fe48b8ddafdeb1db87388dce2c3c3f701bf447b05e4cfcc3679112" },
+    { file = "numpy-1.26.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:4a873a8180479bc829313e8d9798d5234dfacfc2e8a7ac188418189bb8eafbd2" },
+    { file = "numpy-1.26.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:914b28d3215e0c721dc75db3ad6d62f51f630cb0c277e6b3bcb39519bed10bd8" },
+    { file = "numpy-1.26.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c78a22e95182fb2e7874712433eaa610478a3caf86f28c621708d35fa4fd6e7f" },
+    { file = "numpy-1.26.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:86f737708b366c36b76e953c46ba5827d8c27b7a8c9d0f471810728e5a2fe57c" },
+    { file = "numpy-1.26.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:b44e6a09afc12952a7d2a58ca0a2429ee0d49a4f89d83a0a11052da696440e49" },
+    { file = "numpy-1.26.0-cp39-cp39-win32.whl", hash = "sha256:5671338034b820c8d58c81ad1dafc0ed5a00771a82fccc71d6438df00302094b" },
+    { file = "numpy-1.26.0-cp39-cp39-win_amd64.whl", hash = "sha256:020cdbee66ed46b671429c7265cf00d8ac91c046901c55684954c3958525dab2" },
+    { file = "numpy-1.26.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:0792824ce2f7ea0c82ed2e4fecc29bb86bee0567a080dacaf2e0a01fe7654369" },
+    { file = "numpy-1.26.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7d484292eaeb3e84a51432a94f53578689ffdea3f90e10c8b203a99be5af57d8" },
+    { file = "numpy-1.26.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:186ba67fad3c60dbe8a3abff3b67a91351100f2661c8e2a80364ae6279720299" },
+    { file = "numpy-1.26.0.tar.gz", hash = "sha256:f93fc78fe8bf15afe2b8d6b6499f1c73953169fad1e9a8dd086cdff3190e7fdf" },
 ]
 
 [[package]]
@@ -248,4 +255,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "63b22b07ccd3415332ad7433c3e384eb28ec462c428b8d57205dd44b6c35836c"
+content-hash = "74ff927924aa7ab530d1ac05f1c0612ebbf90add0eb02affdd427f334db2e8f1"
diff --git a/pyproject.toml b/pyproject.toml
index 7e8b0a2..aeeb78d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,6 @@ packages = [{ include = "unimetric", from = "src" }]
 python = ">=3.9,<3.13"
 scipy = "^1.11.2"
 numpy = "^1.25.2"
-pytest = "^7.4.2"
 
 [tool.poetry.group.dev]
 optional = true

From 48fc6f2685bc839c42d8b9c892701c8b904dff04 Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sun, 17 Sep 2023 03:51:08 -0400
Subject: [PATCH 14/15] Addressed comments.

---
 poetry.lock                                  |  2 +-
 pyproject.toml                               |  1 +
 src/unimetric/amr.py                         | 37 ----------------
 src/unimetric/core/__init__.py               |  0
 src/unimetric/{ => core}/alignment.py        | 22 +++++-----
 src/unimetric/{ => core}/decorator.py        | 27 ++++++------
 src/unimetric/{ => core}/latent_alignment.py | 44 ++++++++++++--------
 src/unimetric/{ => core}/metric.py           |  0
 src/unimetric/metrics/__init__.py            |  0
 src/unimetric/metrics/amr.py                 | 24 +++++++++++
 src/unimetric/{ => metrics}/ie.py            |  2 +-
 tests/unimetric/test_alignment.py            | 12 +++---
 tests/unimetric/test_amr.py                  |  6 +--
 13 files changed, 88 insertions(+), 89 deletions(-)
 delete mode 100644 src/unimetric/amr.py
 create mode 100644 src/unimetric/core/__init__.py
 rename src/unimetric/{ => core}/alignment.py (80%)
 rename src/unimetric/{ => core}/decorator.py (83%)
 rename src/unimetric/{ => core}/latent_alignment.py (88%)
 rename src/unimetric/{ => core}/metric.py (100%)
 create mode 100644 src/unimetric/metrics/__init__.py
 create mode 100644 src/unimetric/metrics/amr.py
 rename src/unimetric/{ => metrics}/ie.py (97%)

diff --git a/poetry.lock b/poetry.lock
index 32c5f5b..31cdb9c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -255,4 +255,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "74ff927924aa7ab530d1ac05f1c0612ebbf90add0eb02affdd427f334db2e8f1"
+content-hash = "63b22b07ccd3415332ad7433c3e384eb28ec462c428b8d57205dd44b6c35836c"
diff --git a/pyproject.toml b/pyproject.toml
index aeeb78d..7e8b0a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,6 +39,7 @@ packages = [{ include = "unimetric", from = "src" }]
 python = ">=3.9,<3.13"
 scipy = "^1.11.2"
 numpy = "^1.25.2"
+pytest = "^7.4.2"
 
 [tool.poetry.group.dev]
 optional = true
diff --git a/src/unimetric/amr.py b/src/unimetric/amr.py
deleted file mode 100644
index d35d768..0000000
--- a/src/unimetric/amr.py
+++ /dev/null
@@ -1,37 +0,0 @@
-"""Abstract Meaning Representation (AMR) structure."""
-from dataclasses import dataclass
-from typing import Collection, Set, Union
-
-from unimetric.decorator import unimetric
-from unimetric.latent_alignment import Variable
-
-
-@unimetric()
-@dataclass
-class Prop:
-    """A property in an AMR."""
-
-    subj: Variable
-    pred: str
-    obj: Union[Variable, str]
-
-    def __hash__(self):
-        return hash((self.subj, self.pred, self.obj))
-
-
-@unimetric(normalizer="f1")
-@dataclass
-class AMR:
-    """Abstract Meaning Representation (AMR) structure."""
-
-    props: Collection[Prop]
-
-    def variables(self) -> Set[Variable]:
-        """Return the set of variables in the AMR."""
-        vars = set()
-        for p in self.props:
-            if isinstance(p.subj, Variable):
-                vars.add(p.subj)
-            if isinstance(p.obj, Variable):
-                vars.add(p.obj)
-        return vars
diff --git a/src/unimetric/core/__init__.py b/src/unimetric/core/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/unimetric/alignment.py b/src/unimetric/core/alignment.py
similarity index 80%
rename from src/unimetric/alignment.py
rename to src/unimetric/core/alignment.py
index 416d6d1..c6b2819 100644
--- a/src/unimetric/alignment.py
+++ b/src/unimetric/core/alignment.py
@@ -6,7 +6,7 @@
 import numpy as np
 import scipy.optimize as spo
 
-from unimetric.metric import Metric
+from unimetric.core.metric import Metric
 
 T = TypeVar("T")
 
@@ -14,16 +14,16 @@
 class AlignmentConstraint(Enum):
     """Alignment constraints for the alignment metric."""
 
-    OneToOne = enum.auto()
-    OneToMany = enum.auto()
-    ManyToOne = enum.auto()
-    ManyToMany = enum.auto()
+    ONE_TO_ONE = enum.auto()
+    ONE_TO_MANY = enum.auto()
+    MANY_TO_ONE = enum.auto()
+    MANY_TO_MANY = enum.auto()
 
 
 class AlignmentMetric(Metric[Collection[T]]):
     """A metric derived using some alignment constraints."""
 
-    def __init__(self, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.OneToOne):
+    def __init__(self, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.ONE_TO_ONE):
         self.inner = inner
         self.constraint = constraint
 
@@ -48,7 +48,7 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
 
     def score_self(self, x: Collection[T]) -> float:
         """Score a collection of objects with itself."""
-        if self.constraint == AlignmentConstraint.ManyToMany:
+        if self.constraint == AlignmentConstraint.MANY_TO_MANY:
             return self.inner.gram_matrix(x, x).sum()
         else:
             return sum(self.inner.score_self(u) for u in x)
@@ -69,15 +69,15 @@ def solve_alignment(gram_matrix: np.ndarray, constraint: AlignmentConstraint) ->
     float
         The score of the alignment.
     """
-    if constraint == AlignmentConstraint.OneToOne:
+    if constraint == AlignmentConstraint.ONE_TO_ONE:
         row_idx, col_idx = spo.linear_sum_assignment(
             cost_matrix=gram_matrix,
             maximize=True,
         )
         return gram_matrix[row_idx, col_idx].sum()
-    if constraint == AlignmentConstraint.OneToMany:
+    if constraint == AlignmentConstraint.ONE_TO_MANY:
         return gram_matrix.max(axis=0).sum()
-    if constraint == AlignmentConstraint.ManyToOne:
+    if constraint == AlignmentConstraint.MANY_TO_ONE:
         return gram_matrix.max(axis=1).sum()
-    if constraint == AlignmentConstraint.ManyToMany:
+    if constraint == AlignmentConstraint.MANY_TO_MANY:
         return gram_matrix.sum()
diff --git a/src/unimetric/decorator.py b/src/unimetric/core/decorator.py
similarity index 83%
rename from src/unimetric/decorator.py
rename to src/unimetric/core/decorator.py
index e41be45..545a0dc 100644
--- a/src/unimetric/decorator.py
+++ b/src/unimetric/core/decorator.py
@@ -11,11 +11,12 @@
     runtime_checkable,
     Callable,
     TypeVar,
+    Any,
 )
 
-from unimetric.alignment import AlignmentConstraint, AlignmentMetric
-from unimetric.latent_alignment import dataclass_has_variable, LatentAlignmentMetric
-from unimetric.metric import Metric, ProductMetric, DiscreteMetric, FScore, Jaccard, Precision, Recall, UnionMetric
+from unimetric.core.alignment import AlignmentConstraint, AlignmentMetric
+from unimetric.core.latent_alignment import dataclass_has_variable, LatentAlignmentMetric
+from unimetric.core.metric import Metric, ProductMetric, DiscreteMetric, FScore, Jaccard, Precision, Recall, UnionMetric
 
 T = TypeVar("T", covariant=True)
 
@@ -37,12 +38,12 @@ class HasLatentMetric(Protocol):
     latent_metric: Metric
 
 
-def derive_metric(cls: object, constraint: AlignmentConstraint) -> Metric:
+def derive_metric(cls: Any, constraint: AlignmentConstraint) -> Metric:
     """Derive a unified metric from any type.
 
     Parameters
     ----------
-    cls : object
+    cls : Any
         The dataclass-like class to derive the metric from.
     constraint : AlignmentConstraint
         The alignment constraint to use.
@@ -125,14 +126,14 @@ def unimetric(
 
     def class_decorator(cls: T) -> T:
         alignment_constraint = {
-            "<->": AlignmentConstraint.OneToOne,
-            "<-": AlignmentConstraint.OneToMany,
-            "->": AlignmentConstraint.ManyToOne,
-            "~": AlignmentConstraint.ManyToMany,
-            "1:1": AlignmentConstraint.OneToOne,
-            "1:*": AlignmentConstraint.OneToMany,
-            "*:1": AlignmentConstraint.ManyToOne,
-            "*:*": AlignmentConstraint.ManyToMany,
+            "<->": AlignmentConstraint.ONE_TO_ONE,
+            "<-": AlignmentConstraint.ONE_TO_MANY,
+            "->": AlignmentConstraint.MANY_TO_ONE,
+            "~": AlignmentConstraint.MANY_TO_MANY,
+            "1:1": AlignmentConstraint.ONE_TO_ONE,
+            "1:*": AlignmentConstraint.ONE_TO_MANY,
+            "*:1": AlignmentConstraint.MANY_TO_ONE,
+            "*:*": AlignmentConstraint.MANY_TO_MANY,
         }[constraint]
         metric = derive_metric(cls, constraint=alignment_constraint)
         normalized_metric = {
diff --git a/src/unimetric/latent_alignment.py b/src/unimetric/core/latent_alignment.py
similarity index 88%
rename from src/unimetric/latent_alignment.py
rename to src/unimetric/core/latent_alignment.py
index c802527..ff095b1 100644
--- a/src/unimetric/latent_alignment.py
+++ b/src/unimetric/core/latent_alignment.py
@@ -1,32 +1,42 @@
 """Metric derivation with latent alignments."""
 from dataclasses import dataclass, fields, is_dataclass
-from typing import ClassVar, Generic, Collection, Mapping, Tuple, TypeVar, Union, Set, Iterator, get_origin, get_args
+from typing import (
+    ClassVar,
+    Generic,
+    Collection,
+    Mapping,
+    Tuple,
+    TypeVar,
+    Union,
+    Set,
+    Iterator,
+    get_origin,
+    get_args,
+    Any,
+)
 
 import numpy as np
 import scipy.optimize as spo
 
-from unimetric.alignment import AlignmentConstraint, solve_alignment
-from unimetric.metric import Metric
+from unimetric.core.alignment import AlignmentConstraint, solve_alignment
+from unimetric.core.metric import Metric
 
 T = TypeVar("T")
 
 
-@dataclass
+@dataclass(eq=True, frozen=True)
 class Variable:
-    """A variable in a latent."""
+    """A variable in latent alignments."""
 
     name: str
 
     latent_metric: ClassVar[Metric["Variable"]] = Metric.from_function(lambda x, y: 1.0)
 
-    def __hash__(self):
-        return hash(self.name)
-
 
 class LatentAlignmentMetric(Metric[Collection[T]]):
     """A metric derived to support aligning latent variables defined in structures."""
 
-    def __init__(self, cls: type, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.OneToOne):
+    def __init__(self, cls: type, inner: Metric[T], constraint: AlignmentConstraint = AlignmentConstraint.ONE_TO_ONE):
         if is_dataclass(cls):
             self.fields = fields(cls)
         else:
@@ -69,10 +79,10 @@ def score(self, x: Collection[T], y: Collection[T]) -> float:
 
         # each item may be mapped to some other items given the constraint
         item_constraint_matrix_ctor = {
-            AlignmentConstraint.OneToOne: _get_one_to_one_constraint_matrix,
-            AlignmentConstraint.OneToMany: _get_one_to_many_constraint_matrix,
-            AlignmentConstraint.ManyToOne: _get_many_to_one_constraint_matrix,
-            AlignmentConstraint.ManyToMany: lambda _0, _1: None,
+            AlignmentConstraint.ONE_TO_ONE: _get_one_to_one_constraint_matrix,
+            AlignmentConstraint.ONE_TO_MANY: _get_one_to_many_constraint_matrix,
+            AlignmentConstraint.MANY_TO_ONE: _get_many_to_one_constraint_matrix,
+            AlignmentConstraint.MANY_TO_MANY: lambda _0, _1: None,
         }[self.constraint]
         item_constraint_matrix = item_constraint_matrix_ctor(n_x, n_y)
         if item_constraint_matrix is not None:
@@ -151,8 +161,8 @@ def __iter__(self) -> Iterator[Tuple[T, T]]:
         return ((x, y) for x in self.x for y in self.y)
 
 
-def _all_variables(x: object) -> Set[Variable]:
-    def _all_variables_iterator(obj: object) -> Iterator[Variable]:
+def _all_variables(x: Any) -> Set[Variable]:
+    def _all_variables_iterator(obj: Any) -> Iterator[Variable]:
         if isinstance(obj, Variable):
             yield obj
         elif isinstance(obj, Collection) and not isinstance(obj, str):
@@ -185,7 +195,7 @@ def _get_one_to_one_constraint_matrix(n_x: int, n_y: int) -> np.ndarray:  # [X +
     return np.concatenate([mask_x, mask_y], axis=0)
 
 
-def may_be_variable(cls: object) -> bool:
+def may_be_variable(cls: Any) -> bool:
     """Check if a type may be a `Variable`."""
     if cls is Variable:
         return True
@@ -195,7 +205,7 @@ def may_be_variable(cls: object) -> bool:
     return False
 
 
-def dataclass_has_variable(cls: object) -> bool:
+def dataclass_has_variable(cls: Any) -> bool:
     """Check if a dataclass has a field is in `Variable` type."""
     if cls is Variable:
         return True
diff --git a/src/unimetric/metric.py b/src/unimetric/core/metric.py
similarity index 100%
rename from src/unimetric/metric.py
rename to src/unimetric/core/metric.py
diff --git a/src/unimetric/metrics/__init__.py b/src/unimetric/metrics/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/unimetric/metrics/amr.py b/src/unimetric/metrics/amr.py
new file mode 100644
index 0000000..fff302f
--- /dev/null
+++ b/src/unimetric/metrics/amr.py
@@ -0,0 +1,24 @@
+"""Abstract Meaning Representation (AMR) structure."""
+from dataclasses import dataclass
+from typing import Collection, Union
+
+from unimetric.core.decorator import unimetric
+from unimetric.core.latent_alignment import Variable
+
+
+@unimetric()
+@dataclass(eq=True, frozen=True)
+class Prop:
+    """A Proposition in an AMR."""
+
+    subj: Variable
+    pred: str
+    obj: Union[Variable, str]
+
+
+@unimetric(normalizer="f1")
+@dataclass
+class AMR:
+    """Abstract Meaning Representation (AMR) structure."""
+
+    props: Collection[Prop]
diff --git a/src/unimetric/ie.py b/src/unimetric/metrics/ie.py
similarity index 97%
rename from src/unimetric/ie.py
rename to src/unimetric/metrics/ie.py
index a7c13e5..407fee4 100644
--- a/src/unimetric/ie.py
+++ b/src/unimetric/metrics/ie.py
@@ -5,7 +5,7 @@
 from dataclasses import dataclass
 from typing import List
 
-from unimetric.decorator import unimetric
+from unimetric.core.decorator import unimetric
 
 
 @unimetric()
diff --git a/tests/unimetric/test_alignment.py b/tests/unimetric/test_alignment.py
index 244bf2a..b08ccfa 100644
--- a/tests/unimetric/test_alignment.py
+++ b/tests/unimetric/test_alignment.py
@@ -1,6 +1,6 @@
 """Tests for metrics derived with alignments."""
-from unimetric.alignment import solve_alignment, AlignmentConstraint
-from unimetric.metric import DiscreteMetric
+from unimetric.core.alignment import solve_alignment, AlignmentConstraint
+from unimetric.core.metric import DiscreteMetric
 
 
 def test_solve_alignment():
@@ -10,7 +10,7 @@ def test_solve_alignment():
 
     g = DiscreteMetric(int).gram_matrix(a, b)
 
-    assert solve_alignment(g, AlignmentConstraint.OneToOne) == 2
-    assert solve_alignment(g, AlignmentConstraint.ManyToOne) == 3
-    assert solve_alignment(g, AlignmentConstraint.OneToMany) == 4
-    assert solve_alignment(g, AlignmentConstraint.ManyToMany) == 5
+    assert solve_alignment(g, AlignmentConstraint.ONE_TO_ONE) == 2
+    assert solve_alignment(g, AlignmentConstraint.MANY_TO_ONE) == 3
+    assert solve_alignment(g, AlignmentConstraint.ONE_TO_MANY) == 4
+    assert solve_alignment(g, AlignmentConstraint.MANY_TO_MANY) == 5
diff --git a/tests/unimetric/test_amr.py b/tests/unimetric/test_amr.py
index b74cf6f..9e1e021 100644
--- a/tests/unimetric/test_amr.py
+++ b/tests/unimetric/test_amr.py
@@ -1,9 +1,9 @@
 """Tests for SMatch derived from the AMR structure."""
 from pytest import approx
 
-from unimetric.amr import AMR, Prop
-from unimetric.decorator import HasMetric
-from unimetric.latent_alignment import Variable
+from unimetric.core.decorator import HasMetric
+from unimetric.core.latent_alignment import Variable
+from unimetric.metrics.amr import AMR, Prop
 
 
 def test_smatch():

From 0bed9790860bfff19d29107d929a6c9c8f2499e8 Mon Sep 17 00:00:00 2001
From: wanmok <chanwanmok@gmail.com>
Date: Sun, 17 Sep 2023 03:56:15 -0400
Subject: [PATCH 15/15] Fixed module docstring.

---
 src/unimetric/core/__init__.py    | 1 +
 src/unimetric/metrics/__init__.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/unimetric/core/__init__.py b/src/unimetric/core/__init__.py
index e69de29..636a954 100644
--- a/src/unimetric/core/__init__.py
+++ b/src/unimetric/core/__init__.py
@@ -0,0 +1 @@
+"""Core functionality for the unimetric package that provides the automatic metric derivation."""
diff --git a/src/unimetric/metrics/__init__.py b/src/unimetric/metrics/__init__.py
index e69de29..41c6818 100644
--- a/src/unimetric/metrics/__init__.py
+++ b/src/unimetric/metrics/__init__.py
@@ -0,0 +1 @@
+"""Metric implementations for specific tasks."""