Merge pull request #9 from uw-it-aca/pm-update_scipy

added astroalign and fixed build error with biogeme

Author: paulkm

scipy/Dockerfile

@@ -10,7 +10,6 @@ LABEL maintainer="UW-IT AXDD <[email protected]>"
 # bokeh, sqlalchemy, hdf5, vincent, beautifulsoup, protobuf, xlrd, bottleneck,
 # pytables, ipywidgets, ipympl, facets
 
-
 RUN set -ex \
   && conda install --quiet --yes \
   'plotly==4.14.3' \
@@ -52,6 +51,7 @@ RUN set -ex \
 
 # Install Python 3 packages
 RUN pip install \
+  astroalign \
   requests-html \
   joblib \
   tqdm \
@@ -60,7 +60,6 @@ RUN pip install \
   fuzzywuzzy \
   pqdm \
   qgrid \
-  biogeme \
   nbresuse==0.3.3 \
   nbgitpuller && \
   jupyter serverextension enable --py nbresuse --sys-prefix && \
@@ -70,10 +69,14 @@ RUN pip install \
 
 USER root
 
-RUN apt-get update && apt-get install -y vim gcc openssh-client
+RUN apt-get update && apt-get install -y vim gcc openssh-client build-essential
 
 # RUN echo 'export LD_LIBRARY_PATH=/usr/local/nvidia/lib64' >> /etc/profile
 # RUN echo 'export PATH=$PATH:/usr/local/nvidia/bin'>> /etc/profile
 # COPY kernel.json /opt/conda/share/jupyter/kernels/python3/kernel.json
 
 USER $NB_UID
+
+# biogeme failed to install without an interactive bash shell
+SHELL ["/bin/bash", "--login", "-c", "-i"]
+RUN pip install biogeme

scipy/README.md

@@ -16,15 +16,16 @@ via `pip list`
 
 | Package | Version |
 | ----------------------------- | ------------------- |
-| absl-py | 0.12.0 |
-| aiohttp | 3.7.4 |
+| absl-py | 0.13.0 |
+| aiohttp | 3.7.4.post0 |
 | alembic | 1.6.0 |
 | anyio | 2.2.0 |
 | appdirs | 1.4.4 |
 | argon2-cffi | 20.1.0 |
 | arviz | 0.11.2 |
-| asdf | 2.8.0 |
+| asdf | 2.8.1 |
 | asteval | 0.9.23 |
+| astroalign | 2.4 |
 | astroML | 0.4.1 |
 | astroplan | 0.8 |
 | astropy | 4.2.1 |
@@ -39,14 +40,14 @@ via `pip list`
 | backports.functools-lru-cache | 1.6.4 |
 | beautifulsoup4 | 4.9.3 |
 | biogeme | 3.2.6 |
-| black | 21.5b1 |
+| black | 21.5b2 |
 | bleach | 3.3.0 |
 | blinker | 1.4 |
 | blis | 0.7.4 |
 | bokeh | 2.3.1 |
 | boto | 2.49.0 |
-| boto3 | 1.17.79 |
-| botocore | 1.20.79 |
+| boto3 | 1.17.99 |
+| botocore | 1.20.100 |
 | Bottleneck | 1.3.2 |
 | bounded-pool-executor | 0.0.3 |
 | brotlipy | 0.7.0 |
@@ -56,7 +57,7 @@ via `pip list`
 | cachetools | 4.2.2 |
 | catalogue | 2.0.4 |
 | ccdproc | 2.2.0 |
-| certifi | 2020.12.5 |
+| certifi | 2021.5.30 |
 | certipy | 0.1.3 |
 | cffi | 1.14.5 |
 | cftime | 1.5.0 |
@@ -95,21 +96,21 @@ via `pip list`
 | gatspy | 0.3 |
 | gensim | 4.0.1 |
 | gmpy2 | 2.1.0b1 |
-| google-api-core | 1.26.3 |
-| google-auth | 1.30.0 |
-| google-cloud-core | 1.5.0 |
-| google-cloud-storage | 1.19.0 |
+| google-api-core | 1.30.0 |
+| google-auth | 1.30.2 |
+| google-cloud-core | 1.7.0 |
+| google-cloud-storage | 1.38.0 |
 | google-crc32c | 1.1.2 |
-| google-resumable-media | 1.2.0 |
+| google-resumable-media | 1.3.0 |
 | googleapis-common-protos | 1.53.0 |
 | greenlet | 1.0.0 |
-| grpcio | 1.38.0 |
+| grpcio | 1.38.1 |
 | gwcs | 0.16.1 |
 | h5py | 3.1.0 |
 | HeapDict | 1.0.1 |
 | hickle | 3.4.5 |
 | html5lib | 1.1 |
-| hypothesis | 6.13.5 |
+| hypothesis | 6.14.0 |
 | idna | 2.10 |
 | imagecodecs | 2021.3.31 |
 | imageio | 2.9.0 |
@@ -121,7 +122,7 @@ via `pip list`
 | ipython | 7.23.0 |
 | ipython-genutils | 0.2.0 |
 | ipywidgets | 7.6.3 |
-| jax | 0.2.13 |
+| jax | 0.2.16 |
 | jaxlib | 0.1.67 |
 | jdcal | 1.4.1 |
 | jedi | 0.18.0 |
@@ -141,7 +142,7 @@ via `pip list`
 | jupyterlab-pygments | 0.1.2 |
 | jupyterlab-server | 2.5.0 |
 | jupyterlab-widgets | 1.0.0 |
-| keyring | 23.0.1 |
+| keyring | 22.3.0 |
 | kiwisolver | 1.3.1 |
 | llvmlite | 0.36.0 |
 | lmfit | 1.0.2 |
@@ -167,10 +168,10 @@ via `pip list`
 | nbclient | 0.5.3 |
 | nbconvert | 6.0.7 |
 | nbformat | 5.1.3 |
-| nbgitpuller | 0.9.0 |
+| nbgitpuller | 0.10.1 |
 | nbresuse | 0.3.3 |
 | nest-asyncio | 1.5.1 |
-| netCDF4 | 1.5.6 |
+| netCDF4 | 1.5.7 |
 | networkx | 2.5 |
 | nltk | 3.6.2 |
 | notebook | 6.3.0 |
@@ -216,7 +217,7 @@ via `pip list`
 | pycurl | 7.43.0.6 |
 | pydantic | 1.7.3 |
 | pyee | 8.1.0 |
-| pyerfa | 1.7.3 |
+| pyerfa | 2.0.0 |
 | Pygments | 2.8.1 |
 | pygpu | 0.7.6 |
 | PyJWT | 2.1.0 |
@@ -233,7 +234,7 @@ via `pip list`
 | pytest-arraydiff | 0.3 |
 | pytest-astropy | 0.8.0 |
 | pytest-astropy-header | 0.1.2 |
-| pytest-cov | 2.12.0 |
+| pytest-cov | 2.12.1 |
 | pytest-doctestplus | 0.9.0 |
 | pytest-filter-subpackage | 0.1.1 |
 | pytest-mock | 3.6.1 |
@@ -244,6 +245,7 @@ via `pip list`
 | python-json-logger | 2.0.1 |
 | python-mimeparse | 1.6.0 |
 | pytz | 2021.1 |
+| pyu2f | 0.1.5 |
 | pyvo | 1.1 |
 | PyWavelets | 1.1.1 |
 | PyYAML | 5.4.1 |
@@ -269,6 +271,7 @@ via `pip list`
 | semantic-version | 2.8.5 |
 | semver | 2.13.0 |
 | Send2Trash | 1.5.0 |
+| sep | 1.2.0 |
 | setuptools | 49.6.0.post20210108 |
 | shellingham | 1.4.0 |
 | six | 1.15.0 |
@@ -278,7 +281,7 @@ via `pip list`
 | sortedcontainers | 2.3.0 |
 | soupsieve | 2.0.1 |
 | spacy | 3.0.6 |
-| spacy-legacy | 3.0.5 |
+| spacy-legacy | 3.0.6 |
 | SQLAlchemy | 1.4.13 |
 | srsly | 2.4.1 |
 | statsmodels | 0.12.2 |
@@ -315,7 +318,7 @@ via `pip list`
 | widgetsnbextension | 3.5.1 |
 | xarray | 0.18.2 |
 | xlrd | 2.0.1 |
-| yarl | 1.6.3 |
+| yarl | 1.5.1 |
 | zict | 2.0.0 |
 | zipp | 3.4.1 |