💩 Build GMT binary from source, change from gmt-python to PyGMT

Couple of breaking changes. Since GenericMappingTools/pygmt#261, the conda-forge binary package is broken (hence all the recent CI build failures...) and we have to build the GMT binary from source, sigh. The new Dockerfile code for handling this isn't nice but it'll do for now.

Also, the Python `gmt-python` package has been renamed to `pygmt` in GenericMappingTools/pygmt#265, so the Pipfile is updated accordingly here. Also pinning to a newer git version on the upstream branch instead of my personal fork, since GenericMappingTools/pygmt#245 has been merged in!

.env

@@ -1,5 +1,5 @@
 COMET_API_KEY=
 COMET_REST_API_KEY=Wnh3NkQ1aWVNb21XNk1wclM2R28zdDJjQQ==
 LD_LIBRARY_PATH=${CONDA_PREFIX}/lib/
-GMT_LIBRARY_PATH=${CONDA_PREFIX}/lib/
+GMT_LIBRARY_PATH=${PWD}/gmt/lib/
 JUPYTER_CONFIG_DIR=${PWD}/.jupyter

Dockerfile

@@ -48,6 +48,36 @@ RUN conda env create -n deepbedmap -f environment.yml && \
  conda clean -tipsy && \
  conda list -n deepbedmap
 
+# Install Generic Mapping Tools binary from source
+ENV GMT_COMMIT_HASH 9f24c96d09e42d66ddbca4b1505b5c18498e7847
+ENV INSTALLDIR ${HOME}/gmt
+ENV COASTLINEDIR ${INSTALLDIR}/coast
+
+RUN git clone --depth=1 https://github.com/GenericMappingTools/gmt.git && \
+ cd gmt && \
+ git checkout ${GMT_COMMIT_HASH}
+RUN cd gmt && \
+ mkdir -p ${INSTALLDIR} && \
+ mkdir -p ${COASTLINEDIR} && \
+ bash ci/download-coastlines.sh
+USER root
+RUN apt-get -qq update && \
+ apt-get install -y --no-install-recommends \
+ cmake \
+ ninja-build \
+ libcurl4-gnutls-dev \
+ libnetcdf-dev \
+ libgdal-dev \
+ libfftw3-dev \
+ libpcre3-dev \
+ liblapack-dev \
+ ghostscript \
+ curl && \
+ cd gmt && \
+ TEST=false bash ci/build-gmt.sh && \
+ rm -rf /var/lib/apt/lists/*
+USER ${NB_USER}
+
 # Install dependencies in Pipfile.lock using pipenv
 COPY Pipfile* ${HOME}/
 RUN source activate deepbedmap && \

Pipfile

@@ -11,7 +11,7 @@ cupy-cuda92 = "==6.0.0b1"
 cython = "==0.29.2"
 descartes = "==1.1.0"
 geopandas = {editable = true, ref = "0.4.0-26-g9e584cc", git = "https://github.com/geopandas/geopandas.git"}
-gmt = {editable = true, ref = "0.1a3-131-g9772fa3", git = "https://github.com/weiji14/gmt-python.git"}
+gmt = {editable = true, ref = "0.0.1a0-16-g7004aa0", git = "https://github.com/GenericMappingTools/pygmt.git"}
 ipython = "==7.2.0"
 jupyterlab = "==0.35.4"
 jupytext = "==0.8.6"

data_prep.ipynb

@@ -27,11 +27,11 @@
  "text": [
  "Python : 3.6.6 | packaged by conda-forge | (default, Oct 11 2018, 14:33:06) \n",
  "Geopandas : 0.4.0+26.g9e584cc\n",
- "GMT : 0.1a3+131.g9772fa3\n",
+ "GMT : 0.0.1a0+16.g7004aa0\n",
  "Numpy : 1.14.5\n",
- "Rasterio : 1.0.10\n",
- "Scikit-image : 0.14.1\n",
- "Xarray : 0.11.0\n"
+ "Rasterio : 1.0.16\n",
+ "Scikit-image : 0.14.2\n",
+ "Xarray : 0.11.3\n"
  ]
  }
  ],
@@ -49,7 +49,7 @@
  "import yaml\n",
  "\n",
  "import geopandas as gpd\n",
- "import gmt\n",
+ "import pygmt as gmt\n",
  "import IPython.display\n",
  "import matplotlib.pyplot as plt\n",
  "import numpy as np\n",

data_prep.py

@@ -35,7 +35,7 @@
 import yaml
 
 import geopandas as gpd
-import gmt
+import pygmt as gmt
 import IPython.display
 import matplotlib.pyplot as plt
 import numpy as np

environment.yml

@@ -6,7 +6,6 @@ dependencies:
  - defaults::cudnn=7.2.1[md5=6a84069dcf4aca8ba9493d3cb320090e]
  - hcc::cuda_driver=410.73[md5=941787b750b372f4a240287634589d24]
  - defaults::cudatoolkit=9.2[md5=f81c96e01ccb9028800101b35e71b844]
- - gmt=6.0.0a18[md5=3ee3679433e1bf57640d86e4bc8dfc81]
  - pip=18.1[md5=d68c7e5109ba0bf4b1cfe60f0f47870a]
  - conda-forge::python=3.6.6[md5=fe9f54422cdaf8779147b6a02cab2dd1]
  - pip: