Merge pull request #1 from kaczmarj/add/pytests

WIP: Add/pytests

.circleci/config.yml

@@ -4,20 +4,20 @@ jobs:
     machine: true
     steps:
       - checkout
-      - run: docker build -t afni/afni_dev:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} -f Dockerfile.dev .
-      - run: 
+      - run: docker build -t afni/afni_dev:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} --build-arg AFNI_WITH_COVERAGE=1 .
+      - run:
           no_output_timeout: 2h
           command: |
             ci_env=`bash <(curl -s https://codecov.io/env)`
             docker run $ci_env afni/afni_dev:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} /usr/afni_build_dir/tests/run_tests.sh
 
       - run:
           command: |
-            set +o pipefail 
-            if [ $DOCKER_USER == 'afni' ] 
+            set +o pipefail
+            if [ $DOCKER_USER == 'afni' ]
             then
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker build -t afni/afni:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} -f Dockerfile .
+              docker build -t afni/afni:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} .
               docker tag afni/afni_dev:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} afni/afni_dev:latest
               docker push afni/afni_dev
               docker tag afni/afni:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} afni/afni:latest

.dockerignore

@@ -0,0 +1 @@
+Dockerfile

.gitignore

@@ -33,3 +33,11 @@ ___*
 # Octave workspace
 octave-workspace
 /Debug/
+
+# Python
+__pycache__
+*.pyc
+
+# Test and coverage artifacts
+.pytest_cache
+.coverage

Dockerfile

@@ -1,40 +1,70 @@
 FROM ubuntu:bionic-20180526@sha256:c8c275751219dadad8fa56b3ac41ca6cb22219ff117ca98fe82b42f24e1ba64e
-USER root
-RUN apt-get update -y ; apt-get upgrade -y
 
-ENV DEBIAN_FRONTEND=noninteractive
+ARG DEBIAN_FRONTEND=noninteractive
 
-RUN apt-get install -y tcsh vim
-RUN apt-get install -y libxmu-dev libxt-dev libmotif-dev
-RUN apt-get install -y libxpm-dev libxi-dev libxmhtml-dev
-RUN apt-get install -y libglw1-mesa-dev libglu1-mesa-dev
-RUN apt-get install -y libglib2.0-dev libgsl-dev
-RUN apt-get install -y r-base m4
-RUN apt-get install -y python-qt4 git
-RUN apt-get install -yq --no-install-recommends gcc
-RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get update -y -qq \
+    && apt-get install -yq --no-install-recommends \
+          ca-certificates \
+          curl \
+          g++ \
+          gcc \
+          git \
+          libglib2.0-dev \
+          libglu1-mesa-dev \
+          libglw1-mesa-dev \
+          libgsl-dev \
+          libmotif-dev \
+          libxi-dev \
+          libxmhtml-dev \
+          libxmu-dev \
+          libxpm-dev \
+          libxt-dev \
+          m4 \
+          python-matplotlib \
+          python-numpy \
+          python-qt4 \
+          python-rpy2 \
+          python-tk \
+          r-base \
+          tcsh \
+          vim \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-#######################################
-# this copies source code from the host
-# into the image and invalidates the cache
-RUN mkdir /usr/afni_build_dir
-WORKDIR /usr/afni_build_dir
-RUN mkdir src .git
-ADD src src
-ADD .git .git
+# Copy AFNI source code. This can invalidate the build cache.
+ARG AFNI_ROOT=/opt/afni
+COPY [".", "$AFNI_ROOT/"]
 
-ENV PATH=$PATH:/usr/afni_build_dir/src/afni_src/abin
-ARG VERSION
-# RUN git checkout "${VERSION}"
-WORKDIR /usr/afni_build_dir/src
+ARG AFNI_MAKEFILE_SUFFIX=linux_ubuntu_16_64
+ARG AFNI_WITH_COVERAGE="0"
 
-# o files are ignored by the repo but will
-# cause the build to fail.
-RUN make -f  Makefile.linux_ubuntu_16_64  afni_src.tgz \
-    && tar zxvf afni_src.tgz \
-    && cd afni_src \
-    && cp Makefile.linux_ubuntu_16_64 Makefile
-WORKDIR /usr/afni_build_dir/src/afni_src
-# RUN make libmri.so
-RUN make itall && mv linux_ubuntu_16_64 /opt/abin
-WORKDIR /opt/abin
+WORKDIR "$AFNI_ROOT/src"
+RUN \
+    if [ "$AFNI_WITH_COVERAGE" != "0" ]; then \
+      echo "Adding testing and coverage components" \
+      && sed -i 's/# CPROF = /CPROF =  -coverage /' Makefile.$AFNI_MAKEFILE_SUFFIX \
+      && curl -fsSL https://bootstrap.pypa.io/get-pip.py | python3 - --no-cache-dir \
+      && pip3 install --no-cache-dir \
+            codecov \
+            pytest \
+            pytest-cov; \
+    fi \
+    \
+    # Clean AFNI src directory (*.o files can cause build to fail).
+    && make -f  Makefile.$AFNI_MAKEFILE_SUFFIX afni_src.tgz \
+    && mv afni_src.tgz .. \
+    && cd .. \
+    \
+    # Empty the src directory, and replace with the contents of afni_src.tgz
+    && rm -rf src/ && mkdir src \
+    && tar -xzf afni_src.tgz -C $AFNI_ROOT/src --strip-components=1 \
+    && rm afni_src.tgz \
+    \
+    # Build AFNI.
+    && cd src \
+    && cp Makefile.$AFNI_MAKEFILE_SUFFIX Makefile \
+    && make itall \
+    && mv $AFNI_MAKEFILE_SUFFIX $AFNI_ROOT/abin
+
+ENV PATH="$AFNI_ROOT/abin:$PATH"
+WORKDIR "$AFNI_ROOT"

README.rst

@@ -11,13 +11,14 @@ purposes as well.  See https://afni.nimh.nih.gov/afni for more fun.
 AFNI directory
 --------------
 
-Currently top directory contains only two sub-directories
+Currently top directory contains three sub-directories
 
 doc/
     documentation for AFNI
 src/
     source code for AFNI
-
+tests/
+    tests for AFNI
 
 Relevant git-ology for AFNI
 ---------------------------
@@ -90,7 +91,7 @@ To make and install everything do::
     make vastness
 
 The command::
-    
+
     make cleanest
-    
+
 will remove all the *.o files, etc.

src/3dmaxima.c

@@ -3,7 +3,7 @@
    of Wisconsin, 1994-2000, and are released under the Gnu General Public
    License, Version 2.  See the file README.Copyright for details.
 ******************************************************************************/
-   
+
 static char * g_history[] =
 {
     "History:",
@@ -452,4 +452,3 @@ ENTRY("process_args");
 
     RETURN(0);
 }
-