fixes after change to src-layout

.github/workflows/ci.yml

@@ -36,8 +36,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest pytest-mock pytest-cov mypy types-protobuf
-          pip install --use-pep517 -r requirements.txt
+          pip install -r requirements-dev.txt
+          pip install .
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -46,8 +46,8 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=200 --statistics
       - name: Type checking with mypy
         run: |
-          mypy --install-types --non-interactive *.py
-          mypy --strict *.py
+          mypy --install-types --non-interactive src tests
+          mypy --strict src tests
         if: matrix.python-version == '3.x'
       - name: Test with pytest
         run: pytest

.gitignore

@@ -9,8 +9,7 @@ venv/
 !example_output.csv
 !.github/
 !.flake8
-.vscode
-!.vscode/settings.json
+!.vscode/
 !.devcontainer/
 !.devcontainer/*.json
 *.whl
@@ -19,3 +18,4 @@ dist/
 extract_otp_secret_keys.egg-info/
 *.xml
 pytest-coverage.txt
+tests/reports/

Dockerfile

@@ -16,6 +16,6 @@ RUN apt-get update && apt-get install -y libzbar0 libsm6 python3-opencv nano \
 
 WORKDIR /files
 
-ENTRYPOINT ["python", "/extract/extract_otp_secret_keys.py"]
+ENTRYPOINT ["python", "/extract/src/extract_otp_secret_keys.py"]
 
 LABEL org.opencontainers.image.source https://github.com/scito/extract_otp_secret_keys

Dockerfile_no_qr_reader

@@ -15,10 +15,10 @@ RUN apk add --no-cache nano zlib jpeg \
     && if [[ "$(apk --print-arch)" == "aarch64" ]]; then apk add --no-cache --virtual .build-deps gcc libc-dev python3-dev py3-setuptools zlib-dev jpeg-dev; fi \
     && pip install --no-cache-dir protobuf qrcode Pillow \
     && if [[ "$(apk --print-arch)" == "aarch64" ]]; then apk del .build-deps; fi \
-    && if [[ "$RUN_TESTS" == "true" ]]; then /extract/run_pytest.sh test_extract_otp_secret_keys_pytest.py -k "not qreader" --relaxed; else echo "Not running tests..."; fi
+    && if [[ "$RUN_TESTS" == "true" ]]; then /extract/run_pytest.sh tests/test_extract_otp_secret_keys_pytest.py -k "not qreader" --relaxed; else echo "Not running tests..."; fi
 
 WORKDIR /files
 
-ENTRYPOINT ["python", "/extract/extract_otp_secret_keys.py"]
+ENTRYPOINT ["python", "/extract/src/extract_otp_secret_keys.py"]
 
 LABEL org.opencontainers.image.source https://github.com/scito/extract_otp_secret_keys

pyproject.toml

@@ -48,13 +48,13 @@ scripts = {extract_otp_secret_keys = "extract_otp_secret_keys:sys_main"}
 urls = {Project-URL = "https://github.com/scito/extract_otp_secret_keys", Bug-Reports = "https://github.com/scito/extract_otp_secret_keys/issues", Source = "https://github.com/scito/extract_otp_secret_keys" }
 
 [tool.setuptools]
-py-modules = ["extract_otp_secret_keys", "protobuf_generated_python.google_auth_pb2"]
+py-modules = ["extract_otp_secret_keys"]
 
 [tool.setuptools.dynamic]
 # TODO version = {attr = "extract_otp_secret_keys.VERSION"}
 
 [tool.setuptools.package-data]
-"." = ["*.txt", "*.json", "*.csv", "*.png", "*.md"]
+"extract_otp_secret_keys" = ["*.txt", "*.json", "*.csv", "*.png", "*.md"]
 
 # https://blog.ionelmc.ro/2014/05/25/python-packaging/#the-structure%3E
 # https://docs.pytest.org/en/7.1.x/explanation/goodpractices.html#which-import-mode

run_pytest.sh

@@ -1,3 +1,3 @@
 #!/bin/sh
 cd /extract
-pip install -U pytest pytest-mock && pytest "$@"
+pip install -U pytest pytest-mock && pip install --no-deps . && pytest "$@"

tests/utils.py

@@ -39,7 +39,7 @@ Usage:
 with Capturing() as output:
     print("Output")
 '''
-    # TODO remove type ignore when fixed, see https://github.com/python/mypy/issues/11871, https://stackoverflow.com/questions/72174409/type-hinting-the-return-value-of-a-class-method-that-returns-self
+    # TODO remove type ignore if fixed, see https://github.com/python/mypy/issues/11871, https://stackoverflow.com/questions/72174409/type-hinting-the-return-value-of-a-class-method-that-returns-self
     def __enter__(self):  # type: ignore
         self._stdout = sys.stdout
         sys.stdout = self._stringio_std = io.StringIO()

upgrade_deps.sh

@@ -162,7 +162,7 @@ if [ "$OLDVERSION" != "$VERSION" ] || ! $ignore_version_check; then
     if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
     eval "$cmd"
 
-    cmd="$BIN/$DEST/bin/protoc --plugin=protoc-gen-mypy=/home/rkurmann/.local/bin/protoc-gen-mypy --python_out=protobuf_generated_python --mypy_out=protobuf_generated_python google_auth.proto"
+    cmd="$BIN/$DEST/bin/protoc --plugin=protoc-gen-mypy=$HOME/.local/bin/protoc-gen-mypy --python_out=protobuf_generated_python --mypy_out=protobuf_generated_python src/google_auth.proto"
     if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
     eval "$cmd"
 
@@ -232,17 +232,42 @@ cmd="$MYPY --install-types --non-interactive *.py"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
-cmd="$MYPY --strict *.py"
+# change to src as python -m mypy adds the current dir Python sys.path
+# execute in a subshell in order not to loose the exit code and not to change the dir in the currrent shell
+cmd="(cd src && $MYPY --strict *.py ../tests)"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+# pip install
+
+cmd="$PIP install -e ."
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+cmd="extract_otp_secret_keys example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+cmd="extract_otp_secret_keys - < example_export.txt"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
 # Test
 
-cmd="pytest --cov=test_extract_otp_secret_keys_pytest --junitxml=pytest.xml --cov-report=term-missing | tee pytest-coverage.txt"
+cmd="$PYTHON src/extract_otp_secret_keys.py example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+cmd="$PYTHON src/extract_otp_secret_keys.py - < example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+COVERAGE_OUT="tests/reports/pytest-coverage.txt"
+cmd="pytest --cov=test_extract_otp_secret_keys_pytest --junitxml=tests/reports/pytest.xml --cov-report html:tests/reports/html --cov-report=term-missing tests/ | tee $COVERAGE_OUT"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
-cmd="$PIPENV run pytest --cov=test_extract_otp_secret_keys_pytest"
+cmd="$PIPENV run pytest --cov=test_extract_otp_secret_keys_pytest tests/"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
@@ -250,7 +275,8 @@ eval "$cmd"
 
 # https://github.com/marketplace/actions/pytest-coverage-comment
 # Coverage-95%25-yellowgreen
-TOTAL_COVERAGE=$(cat pytest-coverage.txt | grep 'TOTAL' | perl -ne 'print "$&" if /\b(\d{1,3})%/') && perl -i -pe "s/coverage-(\d{1,3}%)25-/coverage-${TOTAL_COVERAGE}25-/" README.md
+echo -e "Upgrade code coverage in README.md"
+TOTAL_COVERAGE=$(cat $COVERAGE_OUT | grep 'TOTAL' | perl -ne 'print "$&" if /\b(\d{1,3})%/') && perl -i -pe "s/coverage-(\d{1,3}%)25-/coverage-${TOTAL_COVERAGE}25-/" README.md
 
 # Build docker
 
@@ -258,7 +284,15 @@ cmd="docker build . -t extract_otp_secret_keys_no_qr_reader -f Dockerfile_no_qr_
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
-cmd="docker run --entrypoint /extract/run_pytest.sh --rm -v \"$(pwd)\":/files:ro extract_otp_secret_keys_no_qr_reader test_extract_otp_secret_keys_pytest.py -k 'not qreader' -vvv --relaxed"
+cmd="docker run --rm -v \"$(pwd)\":/files:ro extract_otp_secret_keys_no_qr_reader example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+cmd="docker run --rm -i -v \"$(pwd)\":/files:ro extract_otp_secret_keys_no_qr_reader - < example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+cmd="docker run --entrypoint /extract/run_pytest.sh --rm -v \"$(pwd)\":/files:ro extract_otp_secret_keys_no_qr_reader tests/test_extract_otp_secret_keys_pytest.py -k 'not qreader' -vvv --relaxed"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
@@ -266,15 +300,23 @@ cmd="docker build . -t extract_otp_secret_keys --pull"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
+cmd="docker run --rm -v \"$(pwd)\":/files:ro extract_otp_secret_keys example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
+cmd="docker run --rm -i -v \"$(pwd)\":/files:ro extract_otp_secret_keys - < example_export.txt"
+if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
+eval "$cmd"
+
 cmd="docker run --entrypoint /extract/run_pytest.sh --rm -v \"$(pwd)\":/files:ro extract_otp_secret_keys"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
-cmd="docker image prune"
+cmd="docker image prune || echo 'No docker image pruning'"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"
 
-cmd="$PYTHON extract_otp_secret_keys.py &"
+cmd="$PYTHON src/extract_otp_secret_keys.py &"
 if $interactive ; then askContinueYn "$cmd"; else echo -e "${cyan}$cmd${reset}";fi
 eval "$cmd"