Merge pull request #690 from Acellera/newhtmddatamaster

New htmd-data on master
Acellera · May 18, 2018 · 7664265 · 7664265
2 parents 511f14d + e787eed
commit 7664265
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diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "htmd-data"]
+	path = htmd/data
+	url = https://github.com/Acellera/htmd-data.git
+	branch = stable
diff --git a/.travis.yml b/.travis.yml
@@ -61,20 +61,23 @@ install:
   # Install the Conda dependencies HTMD needs
   - df -h
   - conda install --file package/htmd-deps/DEPENDENCIES -y
+  - bash -x continuous-integration/travis/conda_build_htmd-data.sh
+  - conda install $HOME/miniconda/conda-bld/*/htmd-data-[0-9]*.tar.bz2  -y -q
   # Cleaning to reduce amount of space used on disk
   - conda clean --all -y
+
+  # Build and install the HTMD dependencies package
   - python package/htmd-deps/write_meta_yaml.py package/htmd-deps
+  - conda build --python $TRAVIS_PYTHON_VERSION package/htmd-deps --no-include-recipe
+  - conda install $HOME/miniconda/conda-bld/*-64/htmd-deps-[0-9]*.tar.bz2  -y -q
 
   # If not PR, clone the private htmdlib repo,
   - if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then bash -x ./continuous-integration/travis/compile_htmdlib.sh ; fi
 
-  - conda build --python $TRAVIS_PYTHON_VERSION package/htmd-deps --no-include-recipe
-  - conda build package/htmd-data --no-include-recipe
+  # Build and install HTMD
   - conda build --python $TRAVIS_PYTHON_VERSION package/htmd --no-include-recipe
-
-  - conda install $HOME/miniconda/conda-bld/*-64/htmd-deps-[0-9]*.tar.bz2  -y -q
-  - conda install $HOME/miniconda/conda-bld/*/htmd-data-[0-9]*.tar.bz2  -y -q
   - conda install $HOME/miniconda/conda-bld/*-64/htmd-[0-9]*.tar.bz2  -y -q
+
   # Cleaning to reduce amount of space used on disk
   - conda clean --all -y
 

diff --git a/continuous-integration/travis/conda_build_htmd-data.sh b/continuous-integration/travis/conda_build_htmd-data.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+# (c) 2015-2018 Acellera Ltd http://www.acellera.com
+# All Rights Reserved
+# Distributed under HTMD Software License Agreement
+# No redistribution in whole or part
+#
+
+export MAJOR=0
+export MINOR=1
+export SHORTHASH=$(git ls-tree HEAD htmd/data | awk '{print substr($3,0,7)}')
+
+export HTMD_DATA_VERSION="${MAJOR}.${MINOR}.hash${SHORTHASH}"
+
+conda build package/htmd-data --no-include-recipe
diff --git a/htmd/builder/preparationdata.py b/htmd/builder/preparationdata.py
@@ -130,7 +130,7 @@ def _set(self, residue, key, val, append=False):
             self.data.at[pos, key] = val
         else:
             try:
-                ov = self.data.iloc[pos][key]
+                ov = list(self.data.iloc[pos][key])
                 if type(ov) == float and math.isnan(ov):
                     ov = list()
             except:

diff --git a/htmd/data b/htmd/data
diff --git a/htmd/data/1kdx/1kdx.dcd b/htmd/data/1kdx/1kdx.dcd
diff --git a/htmd/data/1kdx/1kdx_0.pdb b/htmd/data/1kdx/1kdx_0.pdb
diff --git a/htmd/data/1kdx/reference.dat b/htmd/data/1kdx/reference.dat
diff --git a/htmd/data/adaptive/data/e1s1_1/output.xtc b/htmd/data/adaptive/data/e1s1_1/output.xtc
diff --git a/htmd/data/adaptive/data/e1s2_1/output.xtc b/htmd/data/adaptive/data/e1s2_1/output.xtc
diff --git a/htmd/data/adaptive/generators/1/input b/htmd/data/adaptive/generators/1/input
diff --git a/htmd/data/adaptive/generators/1/input.coor b/htmd/data/adaptive/generators/1/input.coor
diff --git a/htmd/data/adaptive/generators/1/input.idx b/htmd/data/adaptive/generators/1/input.idx
diff --git a/htmd/data/adaptive/generators/1/input.vel b/htmd/data/adaptive/generators/1/input.vel
diff --git a/htmd/data/adaptive/generators/1/input.xsc b/htmd/data/adaptive/generators/1/input.xsc
diff --git a/htmd/data/adaptive/generators/1/input.xstfile b/htmd/data/adaptive/generators/1/input.xstfile
diff --git a/htmd/data/adaptive/generators/1/parameters b/htmd/data/adaptive/generators/1/parameters
diff --git a/htmd/data/adaptive/generators/1/structure.pdb b/htmd/data/adaptive/generators/1/structure.pdb
diff --git a/htmd/data/adaptive/generators/1/structure.prmtop b/htmd/data/adaptive/generators/1/structure.prmtop
diff --git a/htmd/data/adaptive/input/e1s1_1/FINISH_TIME b/htmd/data/adaptive/input/e1s1_1/FINISH_TIME
diff --git a/htmd/data/adaptive/input/e1s1_1/input b/htmd/data/adaptive/input/e1s1_1/input
diff --git a/htmd/data/adaptive/input/e1s1_1/input.coor b/htmd/data/adaptive/input/e1s1_1/input.coor
diff --git a/htmd/data/adaptive/input/e1s1_1/input.idx b/htmd/data/adaptive/input/e1s1_1/input.idx
diff --git a/htmd/data/adaptive/input/e1s1_1/input.vel b/htmd/data/adaptive/input/e1s1_1/input.vel
diff --git a/htmd/data/adaptive/input/e1s1_1/input.xsc b/htmd/data/adaptive/input/e1s1_1/input.xsc
diff --git a/htmd/data/adaptive/input/e1s1_1/input.xstfile b/htmd/data/adaptive/input/e1s1_1/input.xstfile
diff --git a/htmd/data/adaptive/input/e1s1_1/log.txt b/htmd/data/adaptive/input/e1s1_1/log.txt