vmenger · vmenger · Dec 20, 2023 · Nov 30, 2023 · Nov 30, 2023 · Dec 1, 2023
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -2,6 +2,8 @@ name: build
 
 on:
   workflow_dispatch:
+  release:
+    types: [published]
 
 jobs:
 
@@ -34,7 +36,7 @@ jobs:
         poetry install --only dev
 
     - name: Test build
-      run: make test
+      run: python -m pytest .
 
     - name: Set up Pypi credentials
       run: poetry config pypi-token.pypi ${{ SECRETS.PYPI_TOKEN }}

diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml
@@ -30,8 +30,20 @@ jobs:
     - name: Install dependencies
       run: poetry install
 
-    - name: Check formatting
-      run: make format CHECK=1
+    - name: black
+      run: python -m black . --check
 
-    - name: Check linting
-      run: make lint CHECK=1
+    - name: isort
+      run: python -m isort . -c
+
+    - name: docformatter
+      run: python -m docformatter . --check
+
+    - name: flake8
+      run: python -m flake8 .
+
+    - name: pylint
+      run: python -m pylint docdeid/
+
+    - name: mypy
+      run: python -m mypy docdeid/
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -36,33 +36,15 @@ jobs:
       run: poetry install
 
     - name: Test with pytest
-      run: make test
+      run: python -m pytest --cov-report xml
 
-    - name: Extract git branch name
-      id: git-branch-name
-      uses: EthanSK/git-branch-name-action@v1
-
-    - name: Coveralls parallel
-      uses: coverallsapp/github-action@1.1.3
+    - name: Code Coverage Summary Report
+      uses: irongut/CodeCoverageSummary@v1.3.0
       with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        flag-name: py-${{ matrix.python-version }}
-        git-branch: ${{ env.GIT_BRANCH_NAME }}
-        path-to-lcov: coverage.lcov
-        parallel: true
-
-  finalize-coverage:
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-
-    - name: Git branch name
-      id: git-branch-name
-      uses: EthanSK/git-branch-name-action@v1
+        filename: coverage.xml
+        badge: true
+        format: 'markdown'
+        output: 'both'
 
-    - name: Coveralls finish
-      uses: coverallsapp/github-action@1.1.3
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        git-branch: ${{ env.GIT_BRANCH_NAME }}
-        parallel-finished: true
+    - name: Write to Job Summary
+      run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,32 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 1.0.0 (2023-12-20)
+
+### Added 
+* some internal speedups for `SingleTokenLooupAnnotator`, `MultiTokenLookupAnnotator` and `LookupTrie`
+* caching for sorting annotations, which helps with speed
+* the `pre_match_words` attribute for `RegexpAnnotator`
+* the option to provide a `LookupTrie` to a `MultiTokenAnnotator` directly
+* a method for getting all words or, for looking up tokens with specific text values in a `TokenList`, with options for `matching_pipeline`
+* automated build/publish on merge to main
+
+### Changed
+* sorting `Annotation` and `AnnotationSet` now requires sort key to be provided as a `tuple`, and callbacks as a `frozendict`
+* renamed `docdeid.tokenize` to `docdeid.tokenizer`
+* renamed `docdeid.process.doc` to `docdeid.process.doc_processor`
+* renamed `docdeid.process.annotation_set` to `docdeid.process.annotation_processor`
+* `Annotation` and `Token` now only include `int`/`str` fields when serializing
+* formatting and linting settings
+* moved the logic for linking tokens to `TokenList` rather than `Tokenizer`
+* use `casefold()` instead of `lower()` for lowercasing
+
+### Fixed
+* a bug with overlapping annotations in `MultiTokenLookupAnnotator`
+
+### Removed
+* automated coverage reporting
+
 ## 0.1.10 (2023-11-28) 
 
 ### Added

diff --git a/Makefile b/Makefile
@@ -1,60 +1,12 @@
-MAX_LINE_LENGTH := 120
-CHECK ?= 0
+format:
+	python -m black .
+	python -m isort .
+	python -m docformatter .
 
-format_dirs := docdeid/ tests/
-lint_dirs := docdeid/
-
-black_args := --line-length $(MAX_LINE_LENGTH)
-isort_args := --profile black
-docformatter_args := --recursive --wrap-summaries $(MAX_LINE_LENGTH) --wrap-descriptions $(MAX_LINE_LENGTH) --pre-summary-newline
-
-typehints_args := --select ANN001,ANN2,ANN3 --max-line-length $(MAX_LINE_LENGTH)
-doclint_args := --disable=all --enable C0112,C0115,C0116
-pylint_args := --disable=C0112,C0114,C0115,C0116 --max-line-length=$(MAX_LINE_LENGTH)
-mypy_args :=
-
-ifeq ($(CHECK), 1)
-	black_args += --check
-	isort_args += -c
-	docformatter_args := --check $(docformatter_args)
-	doclint_args += --fail-under 10.0
-	pylint_args += --fail-under 9.0
-
-else
-	docformatter_args := --in-place $(docformatter_args)
-	typehints_args += --exit-zero
-	doclint_args += --exit-zero
-	pylint_args += --exit-zero
-
-endif
-
-format: black isort docformat
-
-lint: typehints doclint pylint mypy
-
-black:
-	python -m black $(black_args) $(format_dirs)
-
-isort:
-	python -m isort $(isort_args)  $(format_dirs)
-
-docformat:
-	python -m docformatter $(docformatter_args) $(format_dirs)
-
-typehints:
-	python -m flake8 $(typehints_args) $(lint_dirs)
-
-doclint:
-	python -m pylint $(doclint_args) $(lint_dirs)
-
-pylint:
-	python -m pylint $(pylint_args) $(lint_dirs)
-
-mypy:
-	python -m mypy $(mypy_args) $(lint_dirs)
-
-test:
-	python -m pytest --cov-report html --cov-report lcov --cov=docdeid --cov-fail-under=80 tests/
+lint:
+	python -m flake8 .
+	python -m pylint docdeid/
+	python -m mypy docdeid/
 
 build-docs:
 	sphinx-apidoc --module-first --force --templatedir=docs/templates -o docs/source/api docdeid
@@ -67,9 +19,7 @@ clean:
 	rm -rf .pytest_cache
 	rm -rf .mypy_cache
 	rm -rf dist
-
-clean-docs:
 	rm -rf docs/_build
 	rm -rf docs/source/api
 
-.PHONY: format lint black isort docformat typehints doclint pylint mypy test clean
+.PHONY: format lint clean
diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
 # docdeid
 
 [![tests](https://github.com/vmenger/docdeid/actions/workflows/test.yml/badge.svg)](https://github.com/vmenger/docdeid/actions/workflows/test.yml)
-[![coverage](https://coveralls.io/repos/github/vmenger/docdeid/badge.svg)](https://coveralls.io/github/vmenger/docdeid)
 [![build](https://github.com/vmenger/docdeid/actions/workflows/build.yml/badge.svg)](https://github.com/vmenger/docdeid/actions/workflows/build.yml)
 [![Documentation Status](https://readthedocs.org/projects/docdeid/badge/?version=latest)](https://docdeid.readthedocs.io/en/latest/)
 [![pypy version](https://img.shields.io/pypi/v/docdeid)](https://pypi.org/project/docdeid/)

diff --git a/docdeid/__init__.py b/docdeid/__init__.py
@@ -7,4 +7,4 @@
 from .deidentifier import DocDeid
 from .document import Document, MetaData
 from .pattern import TokenPattern
-from .tokenize import Token, Tokenizer, TokenList
+from .tokenizer import Token, Tokenizer, TokenList