Fix alpha shape

.github/workflows/docker.yml

@@ -0,0 +1,51 @@
+name: Docker Image CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "master", "fix-alpha-shape" ]
+
+env:
+  REPO_NAME: ${{ github.repository }}
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        # we need tags for docker version tagging
+        fetch-tags: true
+        fetch-depth: 0
+    - # Activate cache export feature to reduce build time of images
+      name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERIO_USERNAME }}
+        password: ${{ secrets.DOCKERIO_PASSWORD }}
+    - name: define image name from repo name
+      run: echo "IMAGE_NAME=ghcr.io/${REPO_NAME,,}" >> $GITHUB_ENV
+    - name: Build the Docker image
+      # build both tags at the same time
+      run: make docker-build DOCKER_TAG="docker.io/ocrd/cis -t ${{ env.IMAGE_NAME }}"
+    - name: Test the Docker image
+      run: docker run --rm ${{ env.IMAGE_NAME }} ocrd-cis-ocropy-segment -h
+    - name: Push to Dockerhub
+      run: docker push docker.io/ocrd/cis
+    - name: Push to Github Container Registry
+      run: docker push ${{ env.IMAGE_NAME }}
+

.github/workflows/pypi.yml

@@ -0,0 +1,32 @@
+# 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: PyPI CD
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel build twine
+        pip install -r requirements.txt
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+      run: |
+        python -m build .
+        ls -l dist
+        twine upload --verbose dist/ocrd*{tar.gz,whl}

.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: Test ocrd_cis installation and run tests
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        os: [ "ubuntu-22.04" ]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu'
+          java-version: '11'
+      - name: Install ocrd_cis
+        run: make install
+      - name: Test ocrd_cis
+        run: make test V=

.gitignore

@@ -10,3 +10,6 @@ env-dir/*
 /venv*
 /build
 /dist
+TAGS
+*.log
+download/

Dockerfile

@@ -1,7 +1,24 @@
-FROM ocrd/core:latest AS base
-ENV VERSION="Di 12. Mai 13:26:35 CEST 2020"
+ARG DOCKER_BASE_IMAGE
+FROM $DOCKER_BASE_IMAGE AS base
+ARG VCS_REF
+ARG BUILD_DATE
+LABEL \
+    maintainer="https://github.com/cisocrgroup/ocrd_cis/issues" \
+    org.label-schema.vcs-ref=$VCS_REF \
+    org.label-schema.vcs-url="https://github.com/cisocrgroup/ocrd_cis" \
+    org.label-schema.build-date=$BUILD_DATE \
+    org.opencontainers.image.vendor="DFG-Funded Initiative for Optical Character Recognition Development" \
+    org.opencontainers.image.title="ocrd_cis" \
+    org.opencontainers.image.description="Ocropy OCR and CIS post-correction bindings" \
+    org.opencontainers.image.source="https://github.com/cisocrgroup/ocrd_cis" \
+    org.opencontainers.image.documentation="https://github.com/cisocrgroup/ocrd_cis/blob/${VCS_REF}/README.md" \
+    org.opencontainers.image.revision=$VCS_REF \
+    org.opencontainers.image.created=$BUILD_DATE \
+    org.opencontainers.image.base.name=ocrd/core
+
 ENV GITURL="https://github.com/cisocrgroup"
-ENV DOWNLOAD_URL="http://cis.lmu.de/~finkf"
+
+SHELL ["/bin/bash", "-c"]
 
 # deps
 RUN apt-get update \
@@ -16,14 +33,14 @@ RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
 FROM base AS profiler
 RUN apt-get update \
 	&& apt-get -y install --no-install-recommends cmake g++ libcppunit-dev libxerces-c-dev \
-	&& git clone ${GITURL}/Profiler --branch devel --single-branch /build \
-	&& cd /build \
+	&& git clone ${GITURL}/Profiler --branch devel --single-branch /build/Profiler \
+	&& pushd /build/Profiler \
 	&& cmake -DCMAKE_BUILD_TYPE=release . \
 	&& make compileFBDic trainFrequencyList runDictSearch profiler \
 	&& mkdir /apps \
 	&& cp bin/compileFBDic bin/trainFrequencyList bin/profiler bin/runDictSearch /apps/ \
-	&& cd / \
-    && rm -rf /build
+	&& popd \
+    && rm -rf /build/Profiler
 
 FROM profiler AS languagemodel
 # install the profiler's language backend
@@ -32,27 +49,36 @@ COPY --from=profiler /apps/trainFrequencyList /apps/
 COPY --from=profiler /apps/runDictSearch /apps/
 RUN apt-get update \
 	&& apt-get -y install --no-install-recommends icu-devtools \
-	&& git clone ${GITURL}/Resources --branch master --single-branch /build \
-	&& cd /build/lexica \
+	&& git clone ${GITURL}/Resources --branch master --single-branch /build/Resources \
+	&& pushd /build/Resources/lexica \
 	&& PATH=$PATH:/apps make \
 	&& PATH=$PATH:/apps make test \
 	&& PATH=$PATH:/apps make install \
-	&& cd / \
-	&& rm -rf /build
+	&& popd \
+	&& rm -rf /build/Resources
 
 FROM base AS postcorrection
 # install ocrd_cis (python)
-VOLUME ["/data"]
+WORKDIR /build/ocrd_cis
 COPY --from=languagemodel /etc/profiler/languages /etc/profiler/languages
 COPY --from=profiler /apps/profiler /apps/
 COPY --from=profiler /usr/lib/x86_64-linux-gnu/libicuuc.so /usr/lib//x86_64-linux-gnu/
 COPY --from=profiler /usr/lib/x86_64-linux-gnu/libicudata.so /usr/lib//x86_64-linux-gnu/
 COPY --from=profiler /usr/lib//x86_64-linux-gnu/libxerces-c-3.2.so /usr/lib//x86_64-linux-gnu/
-COPY . /build
+COPY . .
+COPY ocrd-tool.json .
+# prepackage ocrd-tool.json as ocrd-all-tool.json
+RUN ocrd ocrd-tool ocrd-tool.json dump-tools > $(dirname $(ocrd bashlib filename))/ocrd-all-tool.json
+# prepackage ocrd-all-module-dir.json
+RUN ocrd ocrd-tool ocrd-tool.json dump-module-dirs > $(dirname $(ocrd bashlib filename))/ocrd-all-module-dir.json
+# install everything and reduce image size
 RUN apt-get update \
 	&& apt-get -y install --no-install-recommends gcc wget default-jre-headless \
-	&& cd /build \
 	&& make install \
-	&& make test \
-	&& cd / \
-	&& rm -rf /build
+	# test always fail, resources not available for download. Resources should be made available
+	# somewhere else, e.g. github.com/OCR-D/assets
+	# && make test \
+	&& rm -rf /build/ocrd_cis
+
+WORKDIR /data
+VOLUME /data

Makefile

@@ -2,23 +2,71 @@ PY ?= python3
 PIP ?= pip3
 V ?= > /dev/null 2>&1
 PKG = ocrd_cis
+DOCKER_TAG ?= ocrd/cis
+DOCKER_BASE_IMAGE ?= docker.io/ocrd/core:latest
+DOCKER ?= docker
+SHELL = bash
+
+help:
+	@echo ""
+	@echo "  Targets"
+	@echo ""
+	@echo "    install          Install ocrd_cis"
+	@echo "    install-dev      Install in editable mode"
+	@echo "    build            Build source and binary distribution"
+	@echo "    docker           Build Docker image"
+	@echo "    test             Run unit tests"
+	@echo ""
+	@echo "  Variables"
+	@echo ""
+	@echo "    DOCKER_TAG   '$(DOCKER_TAG)'"
+	@echo "    PY           '$(PY)'"
+	@echo "    PIP          '$(PIP)'"
 
 install:
-	${PIP} install --upgrade pip .
-install-devel:
-	${PIP} install --upgrade pip -e .
+	${PIP} install .
+
+install-devel install-dev:
+	${PIP} install -e .
+
+build:
+	${PIP} install build
+	${PY} -m build .
+
 uninstall:
 	${PIP} uninstall ${PKG}
 
-docker-build: Dockerfile
-	docker build -t flobar/ocrd_cis:latest .
+docker-build docker: Dockerfile
+	$(DOCKER) build \
+	--build-arg DOCKER_BASE_IMAGE=$(DOCKER_BASE_IMAGE) \
+	--build-arg VCS_REF=$$(git rev-parse --short HEAD) \
+	--build-arg BUILD_DATE=$$(date -u +"%Y-%m-%dT%H:%M:%SZ") \
+	-t $(DOCKER_TAG):latest .
+
 docker-push: docker-build
-	docker push flobar/ocrd_cis:latest
+	$(DOCKER) push $(DOCKER_TAG):latest
+
+TEST_SCRIPTS=$(sort $(filter-out tests/run_training_test.bash, $(wildcard tests/run_*.bash)))
+INDENT != MAX=; for NAME in $(TEST_SCRIPTS:tests/%=%); do if test $${\#MAX} -lt $${\#NAME}; then MAX=$${NAME//?/_}; fi; done; echo $$MAX
+indent = `WHAT=$1; WITH=$(INDENT); echo $$WHAT$${WITH:$${\#WHAT}}`
+format_tr = "$(call indent,$1):\t%U\t%S\t%E\t%P\t(%Mk)"
+format_th = "$(call indent)\tuser\tsystem\telapsed\tCPU\tmaxRSS"
 
-TEST_SCRIPTS=$(sort $(wildcard tests/run_*.bash))
 .PHONY: $(TEST_SCRIPTS)
 $(TEST_SCRIPTS):
-	bash $@ $V
+	OCRD_MAX_PARALLEL_PAGES=1 /usr/bin/time -o test_serially.log -a -f $(call format_tr,$(@F)) bash -x $@ $V
+	OCRD_MAX_PARALLEL_PAGES=4 /usr/bin/time -o test_parallel.log -a -f $(call format_tr,$(@F)) bash -x $@ $V
+
+test: export OCRD_OVERRIDE_LOGLEVEL=DEBUG
+test: export OCRD_MISSING_OUTPUT=ABORT
+test: export OCRD_MAX_MISSING_OUTPUTS=-1
 test: $(TEST_SCRIPTS)
-	echo $^
-.PHONY: install test
+	@echo =====single-processing test results=====
+	@echo -e $(call format_th)
+	@cat test_serially.log
+	@echo =====4-page-parallel test results=====
+	@echo -e $(call format_th)
+	@cat test_parallel.log
+	@$(RM) test_serially.log test_parallel.log
+
+.PHONY: install install-dev install-devel build uninstall test docker docker-build docker-push

ocrd_cis/__init__.py

@@ -1,3 +1,2 @@
 from .javaprocess import JavaAligner
 from .javaprocess import JavaPostCorrector
-from .ocrd_tool import get_ocrd_tool