Dockerfile_alpine

FROM alpine:3.8

# ensure local python is preferred over distribution python
ENV PATH /usr/local/bin:$PATH

# http://bugs.python.org/issue19846
# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
ENV LANG C.UTF-8

# install ca-certificates so that HTTPS works consistently
# other runtime dependencies for Python are installed later
RUN apk add --no-cache ca-certificates

ENV GPG_KEY 97FC712E4C024BBEA48A61ED3A5CA953F73C700D
ENV PYTHON_VERSION 3.5.6

RUN set -ex \
	&& apk add --no-cache --virtual .fetch-deps \
		gnupg \
		tar \
		xz \
	\
	&& wget -O python.tar.xz "https://www.python.org/ftp/python/${PYTHON_VERSION%%[a-z]*}/Python-$PYTHON_VERSION.tar.xz" \
	&& wget -O python.tar.xz.asc "https://www.python.org/ftp/python/${PYTHON_VERSION%%[a-z]*}/Python-$PYTHON_VERSION.tar.xz.asc" \
	&& export GNUPGHOME="$(mktemp -d)" \
	&& gpg --batch --keyserver ha.pool.sks-keyservers.net --recv-keys "$GPG_KEY" \
	&& gpg --batch --verify python.tar.xz.asc python.tar.xz \
	&& { command -v gpgconf > /dev/null && gpgconf --kill all || :; } \
	&& rm -rf "$GNUPGHOME" python.tar.xz.asc \
	&& mkdir -p /usr/src/python \
	&& tar -xJC /usr/src/python --strip-components=1 -f python.tar.xz \
	&& rm python.tar.xz \
	\
	&& apk add --no-cache --virtual .build-deps  \
		bzip2-dev \
		coreutils \
		dpkg-dev dpkg \
		expat-dev \
		findutils \
		gcc \
		clang \
		gdbm-dev \
		libc-dev \
		libffi-dev \
		openssl-dev \
		linux-headers \
		make \
		ncurses-dev \
		pax-utils \
		readline-dev \
		sqlite-dev \
		tcl-dev \
		tk \
		tk-dev \
		xz-dev \
		zlib-dev \
# add build deps before removing fetch deps in case there's overlap
	&& apk del .fetch-deps \
	\
	&& cd /usr/src/python \
	&& gnuArch="$(dpkg-architecture --query DEB_BUILD_GNU_TYPE)" \
	&& ./configure \
		--build="$gnuArch" \
		--enable-loadable-sqlite-extensions \
		--enable-shared \
		--with-system-expat \
		--with-system-ffi \
		--without-ensurepip \
	&& make -j "$(nproc)" \
# set thread stack size to 1MB so we don't segfault before we hit sys.getrecursionlimit()
# https://github.com/alpinelinux/aports/commit/2026e1259422d4e0cf92391ca2d3844356c649d0
		EXTRA_CFLAGS="-DTHREAD_STACK_SIZE=0x100000" \
	&& make install \
	\
	&& find /usr/local -type f -executable -not \( -name '*tkinter*' \) -exec scanelf --needed --nobanner --format '%n#p' '{}' ';' \
		| tr ',' '\n' \
		| sort -u \
		| awk 'system("[ -e /usr/local/lib/" $1 " ]") == 0 { next } { print "so:" $1 }' \
		| xargs -rt apk add --no-cache --virtual .python-rundeps \
	&& apk del .build-deps \
	\
	&& find /usr/local -depth \
		\( \
			\( -type d -a \( -name test -o -name tests \) \) \
			-o \
			\( -type f -a \( -name '*.pyc' -o -name '*.pyo' \) \) \
		\) -exec rm -rf '{}' + \
	&& rm -rf /usr/src/python \
	\
	&& python3 --version

# make some useful symlinks that are expected to exist
RUN cd /usr/local/bin \
	&& ln -s idle3 idle \
	&& ln -s pydoc3 pydoc \
	&& ln -s python3 python \
	&& ln -s python3-config python-config

# if this is called "PIP_VERSION", pip explodes with "ValueError: invalid truth value '<VERSION>'"
ENV PYTHON_PIP_VERSION 18.1

RUN set -ex; \
	\
	wget -O get-pip.py 'https://bootstrap.pypa.io/get-pip.py'; \
	\
	python get-pip.py \
		--disable-pip-version-check \
		--no-cache-dir \
		"pip==$PYTHON_PIP_VERSION" \
	; \
	pip --version; \
	\
	find /usr/local -depth \
		\( \
			\( -type d -a \( -name test -o -name tests \) \) \
			-o \
			\( -type f -a \( -name '*.pyc' -o -name '*.pyo' \) \) \
		\) -exec rm -rf '{}' +; \
	rm -f get-pip.py

################################


RUN pip install --upgrade pip
# Install Python packages
RUN pip install --no-cache-dir \
        cython \
        numpy \
    && rm -rf /root/.cache
RUN pip install --no-cache-dir \
        pandas \
        fisher \
        psycopg2-binary \
        retrying \
        Werkzeug \
        WTForms \
        Flask \
        flask-restful \
        networkx \
        lxml \
        pytest \
        pytest-cov \
        markdown \
        flask-markdown \
        requests \
    && rm -rf /root/.cache


RUN mkdir -p /opt/services/flaskapp/src
#VOLUME ["/opt/services/flaskapp/src"]
#RUN echo $PYTHONPATH

# We copy the requirements.txt file first to avoid cache invalidations
COPY ./app/requirements.txt /opt/services/flaskapp/src/
WORKDIR /opt/services/flaskapp/src
RUN pip install -r requirements.txt
RUN rm -rf /root/.cache

COPY ./app /opt/services/flaskapp/src

RUN cd python && python setup.py build_ext --inplace

COPY ./app/.bashrc /root/.bashrc
#COPY . /opt/services/flaskapp/src
#COPY ./data/PostgreSQL/downloads/*.obo /agotool_data/PostgreSQL/downloads/
WORKDIR /opt/services/flaskapp/src
EXPOSE 5912
CMD ["python", "runserver.py"]