Merge pull request #32 from dartmouth-pbs/enh-dbic2

WiP RF+ENH: further RF to support flexible heuristic to name sequences so they follow BIDS in their naiming

Author: satra

.coveragerc

@@ -0,0 +1,4 @@
+[run]
+include = tests/*
+          bin/*
+          setup.py

.gitignore

@@ -1 +1,4 @@
 *.pyc
+.cache/
+.coverage
+*.egg-info/

.travis.yml

@@ -2,9 +2,9 @@
 language: python
 python:
   - 2.7
-  - 3.3
   - 3.4
   - 3.5
+  - 3.6
 
 cache:
   - apt
@@ -17,17 +17,25 @@ env:
 
 before_install:
   # The ultimate one-liner setup for NeuroDebian repository
-  # which might be needed later for tools
-  #- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-  #- travis_retry sudo apt-get update -qq
-  # for now even remove requirements.txt since dependencies aren't avail
-  - echo '' > requirements.txt
+  - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+  - travis_retry sudo apt-get update -qq
+  - travis_retry sudo apt-get install git-annex-standalone dcm2niix
+  # Install in our own virtualenv
+  - python -m pip install --upgrade pip
+  - pip install --upgrade virtualenv
+  - virtualenv --python=python venv
+  - source venv/bin/activate
+  - python --version # just to check
   - pip install -r dev-requirements.txt
-  - pip install codecov
+  - pip install datalad
+  - pip install codecov pytest
 
+install:
+  - git config --global user.email "[email protected]"
+  - git config --global user.name "Travis Almighty"
 
 script:
-  - nosetests -s -v --with-doctest --doctest-tests --with-cov --cover-package . --logging-level=INFO tests
+  - coverage run `which py.test` -s -v tests heuristics
 
 after_success:
   - codecov

Dockerfile

@@ -3,10 +3,31 @@ FROM continuumio/miniconda
 
 MAINTAINER <[email protected]>
 
-RUN apt-get update && apt-get upgrade -y && apt-get install -y g++ && apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y
-RUN cd /tmp && git clone https://github.com/neurolabusc/dcm2niix.git && cd dcm2niix/console/ && git checkout 60bab318ee738b644ebb1396bbb8cbe1b006218f && g++ -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -DmyDisableJasper && cp dcm2niix /usr/local/bin/
-RUN conda install -y -c conda-forge nipype && pip install https://github.com/moloney/dcmstack/archive/c12d27d2c802d75a33ad70110124500a83e851ee.zip && pip install https://github.com/nipy/nipype/archive/dd1ed4f0d5735c69c1743f29875acf09d23a62e0.zip
-RUN curl -O https://raw.githubusercontent.com/nipy/heudiconv/master/bin/heudiconv && chmod +x heudiconv && cp heudiconv /usr/local/bin/
-RUN curl -O https://raw.githubusercontent.com/nipy/heudiconv/master/heuristics/convertall.py && chmod +x convertall.py
+RUN apt-get update && apt-get upgrade -y && \
+    apt-get install -y g++ pkg-config make && \
+    apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y
+RUN (wget -O- http://neuro.debian.net/lists/jessie.us-nh.full | tee /etc/apt/sources.list.d/neurodebian.sources.list) && \
+    apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
+    apt-get update -qq && apt-get install -y git-annex-standalone && \
+    apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y
+RUN conda install -y -c conda-forge nipype && \
+    conda install cmake && \
+    pip install https://github.com/moloney/dcmstack/archive/c12d27d2c802d75a33ad70110124500a83e851ee.zip && \
+    pip install datalad && \
+    conda clean -tipsy && rm -rf ~/.pip/
+RUN cd /tmp && git clone https://github.com/neurolabusc/dcm2niix.git && \
+    cd dcm2niix && \
+    git checkout 60bab318ee738b644ebb1396bbb8cbe1b006218f && \
+    mkdir build && cd build && cmake -DBATCH_VERSION=ON .. && \
+    make && make install && \
+    cd / && rm -rf /tmp/dcm2niix
+
+COPY bin/heudiconv /usr/local/bin/heudiconv
+RUN chmod +x /usr/local/bin/heudiconv
+RUN mkdir /heuristics
+COPY heuristics/convertall.py /heuristics
+RUN chmod +x /heuristics/convertall.py
+RUN git config --global user.email "[email protected]" && \
+    git config --global user.name "Docker Almighty"
 
 ENTRYPOINT ["/usr/local/bin/heudiconv"]

README.md

@@ -83,7 +83,7 @@ function `infotodict`, which takes a single argument `seqinfo`.
 
 * total_files_till_now
 * example_dcm_file
-* series_number
+* series_id
 * dcm_dir_name
 * unspecified2
 * unspecified3