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appveyor.yml
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environment:
# See README for information on the token
ANACONDA_TOKEN:
secure: AaDohlZ5kwkG4ymSAkUVvTIzL1SDr1WMl/0A/07mnOWqcxOTDMqaMTSeDSvlOEZV
FTP_USER:
secure: wuDqH0Ne8+H5LLA13XOnJc2JhOOAHuCJD0hq8n1Sm0c=
FTP_PASSWORD:
secure: Xonq2cmbnVHxH70z4WD+BDiq/WClXiOYbuKSzaaLzts=
global:
# SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
# /E:ON and /V:ON options are not enabled in the batch script intepreter
# See: http://stackoverflow.com/a/13751649/163740
CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\ci\\appveyor\\run_with_env.cmd"
matrix:
# - PYTHON: "C:\\Python27_32"
# PYTHON_VERSION: "2.7"
# PYTHON_ARCH: "32"
# CONDA_PY: "27"
- PYTHON: "C:\\Python27_64"
PYTHON_VERSION: "2.7"
PYTHON_ARCH: "64"
CONDA_PY: "27"
#- PYTHON: "C:\\Python34_32"
# PYTHON_VERSION: "3.4"
# PYTHON_ARCH: "32"
# CONDA_PY: "34"
# - PYTHON: "C:\\Python34_64"
# PYTHON_VERSION: "3.4"
# PYTHON_ARCH: "64"
# CONDA_PY: "34"
#- PYTHON: "C:\\Python35_32"
# PYTHON_VERSION: "3.5"
# PYTHON_ARCH: "32"
# CONDA_PY: "35"
# - PYTHON: "C:\\Python35_64"
# PYTHON_VERSION: "3.5"
# PYTHON_ARCH: "64"
# CONDA_PY: "35"
install:
# https://www.appveyor.com/docs/installed-software#python
- if "%PYTHON_VERSION%" == "3.4" set "BASE_PYTHON_VERSION=3"
- if "%PYTHON_VERSION%" == "3.5" set "BASE_PYTHON_VERSION=35"
- if "%PYTHON_ARCH%" == "64" set "ARCH_LABEL=-x64"
# These are already installed on appveyor. Update them.
- set "CONDA_ROOT=C:\Miniconda%BASE_PYTHON_VERSION%%ARCH_LABEL%"
- set "PATH=%CONDA_ROOT%;%CONDA_ROOT%\Scripts;%CONDA_ROOT%\Library\bin;%PATH%"
- set "CXX=gcc -pthread"
#- set "PATH=C:\MinGW\bin;%PATH%"
- conda config --set always_yes yes
- conda update -q conda
- conda info
- conda update -q --all
- python -c "import sys; print(sys.version)"
- python -c "import sys; print(sys.executable)"
- python -c "import sys; print(sys.prefix)"
- conda create --yes --name oddt_env python=%PYTHON_VERSION%
- activate oddt_env
- conda install -q six
- conda install -q -c openbabel openbabel
# temp
- conda install -q numpy scipy scikit-learn joblib
- pip install --no-deps git+https://github.com/oddt/oddt.git@experimental-windows
# Use commit pre-MKL
- pip install git+https://github.com/pyinstaller/pyinstaller.git@feb0d271263ca884b91033fd588b79fadf3a3a7f
# Remove buggy numpy hook instead of @feb0d271263ca884b91033fd588b79fadf3a3a7f
- python -c "import PyInstaller;print(PyInstaller.__file__)"
#- del /F %CONDA_PREFIX%\Lib\site-packages\PyInstaller\hooks\hook-numpy.core.py
# dlfcn
- conda install -q -c conda-forge mingwpy git make
- git clone https://github.com/dlfcn-win32/dlfcn-win32.git
- cd dlfcn-win32
- bash configure --prefix=%CONDA_PREFIX%/Library --enable-shared --enable-static
- make
- copy libdl.dll %CONDA_PREFIX%/libdl.dll
- cd ..
# compiledtrees
- gcc -v
# - pip install git+https://github.com/mwojcikowski/sklearn-compiledtrees.git@windows-compilation
- git clone -b windows-compiling https://github.com/mwojcikowski/sklearn-compiledtrees.git
- cd sklearn-compiledtrees
- python setup.py build_ext --compiler=mingw32 --libraries=libdl -L ../dlfcn-win32 -I ../dlfcn-win32
- python setup.py install
- cd ..
- curl -L -o upx.zip http://libgd.blob.core.windows.net/upx/upx391w.zip && 7z e upx.zip *.exe -r
- curl -L -o RFScoreVS_v2_vina.pickle http://wojcikowski.pl/rfscorevs/RFScoreVS_v2_vina_win.pickle
# Convert molecules to all supported formats
- obabel test\xiap\actives_docked.sdf -O test\xiap\actives_docked.mol2
- obabel test\xiap\actives_docked.sdf -O test\xiap\actives_docked.pdbqt
- obabel test\xiap\actives_docked.sdf -O test\xiap\actives_docked.pdb
build: false
test_script:
- 'pyinstaller --clean ^
--additional-hooks-dir . ^
--hidden-import="sklearn.tree._utils" ^
--hidden-import=sklearn.neighbors.typedefs ^
--hidden-import=six ^
--hidden-import=compiledtrees ^
--runtime-hook pyi_rth_obdata.py ^
--add-data "./RFScoreVS_v2_vina.pickle;." ^
--add-binary "%CONDA_PREFIX%\Library\bin\mkl_def.dll;." ^
--add-binary "%CONDA_PREFIX%\Library\bin\formats_*.obf;." ^
--add-binary "%CONDA_PREFIX%\Library\bin\plugin_*.obf;." ^
--add-binary "%CONDA_PREFIX%\Library\bin\libxml2.dll;." ^
--add-binary "%CONDA_PREFIX%\Library\bin\iconv.dll;." ^
--add-binary "%CONDA_PREFIX%\Library\bin\charset.dll;." ^
--add-data "%CONDA_PREFIX%\share\openbabel\*;data" ^
--exclude-module=rdkit ^
--exclude-module tcl ^
--exclude-module Tkinter ^
--noupx ^
--nowindow ^
-y -n rf-score-vs --onefile .\rf-score-vs'
- deactivate
- dist\rf-score-vs.exe --help
- dist\rf-score-vs.exe --receptor test/xiap/receptor_rdkit.pdb test/xiap/actives_docked.sdf -ocsv --field "name" --field "RFScoreVS_v2"
- dist\rf-score-vs.exe --receptor test/xiap/receptor_rdkit.pdb test/xiap/actives_docked.mol2 -ocsv --field "name" --field "RFScoreVS_v2"
- dist\rf-score-vs.exe --receptor test/xiap/receptor_rdkit.pdb test/xiap/actives_docked.pdbqt -ocsv --field "name" --field "RFScoreVS_v2"
- dist\rf-score-vs.exe --receptor test/xiap/receptor_rdkit.pdb test/xiap/actives_docked.pdb -ocsv --field "name" --field "RFScoreVS_v2"
# Setup bundle
- mkdir dist\test\
- xcopy test\xiap\* dist\test\ /y
- copy README.md .\dist\
- 7z a rf-score-vs_v1.0_win_%PYTHON_VERSION%.zip .\dist\*
- curl --ftp-create-dirs -T rf-score-vs_v1.0_win_%PYTHON_VERSION%.zip -u %FTP_USER%:%FTP_PASSWORD% ftp://wojcikowski.pl
artifacts:
# Archive the generated conda package in the ci.appveyor.com build report.
- path: .\dist\rf-score-vs.exe