forked from pyrocko/pyrocko
parent
befb5a64ec
commit
fa28a350e0
@ -1,5 +0,0 @@
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---
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linters:
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flake8:
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python: 3
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@ -1,93 +0,0 @@
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language: python
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cache:
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pip: true
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directories:
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- $TRAVIS_BUILD_DIR/pyrocko/test/data
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env:
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global:
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- OMP_NUM_THREADS=2
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matrix:
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include:
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- os: linux
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python: 2.7
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virtualenv:
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system_site_packages: true
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dist: precise
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# - os: osx
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# osx_image: xcode7.3
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# language: generic
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# allow_failures:
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# - os: osx
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#
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addons:
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apt:
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packages: [ python-qt4, python-qt4-gl, python-qt4-dev, python-dev,
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gfortran, libatlas-dev, libopenblas-dev,
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python-yaml, python-tk, libyaml-dev,
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poppler-utils, ghostscript, imagemagick, xvfb,
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libssl1.0.0 ]
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before_install:
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew tap homebrew/science; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew tap homebrew/python; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew unlink libyaml; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gcc libyaml; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then pip install matplotlib; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then xcode-select --install || true ; fi
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- pip install --upgrade pip setuptools wheel
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- pip install --only-binary=numpy,scipy,matplotlib scipy numpy matplotlib
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- pip install progressbar setuptools flake8 pyyaml coveralls jinja2 future coverage nose
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- git clone https://github.com/pyrocko/fomosto-qseis
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- cd fomosto-qseis; autoreconf -i; ./configure; make; export PATH=$PATH:`pwd`/src; cd ..
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- git clone https://github.com/pyrocko/fomosto-qseis2d
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- cd fomosto-qseis2d; autoreconf -i; ./configure; make; export PATH=$PATH:`pwd`/src/r:`pwd`/src/s; cd ..
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- git clone https://github.com/pyrocko/fomosto-psgrn-pscmp
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- cd fomosto-psgrn-pscmp; autoreconf -i; ./configure; make; export PATH=$PATH:`pwd`/src/psgrn:`pwd`/src/pscmp; cd ..
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- git clone https://github.com/pyrocko/fomosto-qssp.git
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- cd fomosto-qssp; autoreconf -i; ./configure; make; export PATH=$PATH:`pwd`/src; cd ..
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before_script:
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then flake8 src/ test/ ; fi
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export DISPLAY=:99.0 ; fi
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sh -e /etc/init.d/xvfb start ; fi
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sleep 3 ; fi
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install:
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- pip install .
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script:
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- travis_wait nosetests run --with-coverage --cover-package=pyrocko test/
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after_success:
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then coveralls; fi
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deploy:
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- provider: pypi
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user: pyrocko
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password:
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secure: "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"
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on:
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all_branches: true
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# branch: master
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# tags: true
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distributions: "sdist bdist_wheel"
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server: https://test.pypi.org/legacy/
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- provider: script
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script: maintenance/anaconda_deploy.sh
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on:
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all_branches: true
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# branch: master
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# tags: true
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notifications:
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email: false
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@ -1,5 +0,0 @@
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FROM debian:stable
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RUN apt-get update -y
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RUN apt-get upgrade -y
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RUN apt-get install -y rsync git python3-pip xvfb libgles2-mesa libfontconfig1 libxrender1 libxkbcommon-x11-0 python3-requests
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@ -1,5 +1,5 @@
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#!/bin/bash
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docker build nest -t pyrocko-nest
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docker build docs -t pyrocko-docs
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docker build aux -t pyrocko-aux
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docker build util -t pyrocko-util
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docker build pyrocko -t pyrocko
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@ -0,0 +1,182 @@
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diff -ruN libmseed/libmseed.h libmseed_mod/libmseed.h
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--- libmseed/libmseed.h 2019-06-19 10:59:29.000000000 +0200
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+++ libmseed_mod/libmseed.h 2021-04-09 09:44:41.881346528 +0200
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@@ -511,6 +511,7 @@
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double samprate; /* Nominal sample rate (Hz) */
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int64_t samplecnt; /* Number of samples in trace coverage */
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void *datasamples; /* Data samples, 'numsamples' of type 'sampletype' */
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+ size_t bufsize;
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int64_t numsamples; /* Number of data samples in datasamples */
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char sampletype; /* Sample type code: a, i, f, d */
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void *prvtptr; /* Private pointer for general use, unused by libmseed */
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diff -ruN libmseed/Makefile.win libmseed_mod/Makefile.win
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--- libmseed/Makefile.win 2019-06-19 10:59:29.000000000 +0200
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+++ libmseed_mod/Makefile.win 2021-04-09 09:44:41.881346528 +0200
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@@ -5,9 +5,10 @@
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NODEBUG=1
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INCS = -I.
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-OPTS = -D_CRT_SECURE_NO_WARNINGS
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+OPTS = -D_CRT_SECURE_NO_WARNINGS -DWIN32
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LIB = libmseed.lib
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DLL = libmseed.dll
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+CFLAGS = /Ox
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OBJS= fileutils.obj \
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genutils.obj \
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diff -ruN libmseed/traceutils.c libmseed_mod/traceutils.c
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--- libmseed/traceutils.c 2019-06-19 10:59:29.000000000 +0200
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+++ libmseed_mod/traceutils.c 2021-04-09 09:44:41.881346528 +0200
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@@ -437,6 +437,7 @@
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mst_addmsr (MSTrace *mst, MSRecord *msr, flag whence)
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{
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int samplesize = 0;
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+ size_t min_size;
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if (!mst || !msr)
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return -1;
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@@ -465,13 +466,16 @@
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return -1;
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}
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- mst->datasamples = realloc (mst->datasamples,
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- (size_t) (mst->numsamples * samplesize + msr->numsamples * samplesize));
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+ min_size = (size_t) (mst->numsamples * samplesize + msr->numsamples * samplesize);
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- if (mst->datasamples == NULL)
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- {
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- ms_log (2, "mst_addmsr(): Cannot allocate memory\n");
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- return -1;
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+ if (min_size > mst->bufsize) {
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+ mst->datasamples = realloc (mst->datasamples, min_size*2);
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+ if (mst->datasamples == NULL)
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+ {
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+ ms_log (2, "mst_addmsr(): Cannot allocate memory\n");
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+ return -1;
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+ }
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+ mst->bufsize = min_size*2;
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}
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}
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@@ -548,6 +552,7 @@
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flag whence)
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{
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int samplesize = 0;
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+ size_t min_size;
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if (!mst)
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return -1;
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@@ -568,13 +573,15 @@
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return -1;
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}
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- mst->datasamples = realloc (mst->datasamples,
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- (size_t) (mst->numsamples * samplesize + numsamples * samplesize));
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-
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- if (mst->datasamples == NULL)
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- {
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- ms_log (2, "mst_addspan(): Cannot allocate memory\n");
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- return -1;
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+ min_size = (size_t) (mst->numsamples * samplesize + numsamples * samplesize);
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+ if (min_size > mst->bufsize) {
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+ mst->datasamples = realloc (mst->datasamples, min_size*2);
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+ if (mst->datasamples == NULL)
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+ {
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+ ms_log (2, "mst_addspan(): Cannot allocate memory\n");
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+ return -1;
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+ }
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+ mst->bufsize = min_size*2;
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}
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}
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@@ -1108,6 +1115,7 @@
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float *fdata;
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double *ddata;
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int64_t idx;
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+ size_t bufsize;
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if (!mst)
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return -1;
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@@ -1160,11 +1168,13 @@
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}
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/* Reallocate buffer for reduced size needed */
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- if (!(mst->datasamples = realloc (mst->datasamples, (size_t) (mst->numsamples * sizeof (int32_t)))))
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+ bufsize = (size_t) (mst->numsamples * sizeof (int32_t));
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+ if (!(mst->datasamples = realloc (mst->datasamples, bufsize)))
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{
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ms_log (2, "mst_convertsamples: cannot re-allocate buffer for sample conversion\n");
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return -1;
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}
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+ mst->bufsize = bufsize;
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}
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mst->sampletype = 'i';
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@@ -1184,11 +1194,13 @@
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fdata[idx] = (float)ddata[idx];
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/* Reallocate buffer for reduced size needed */
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- if (!(mst->datasamples = realloc (mst->datasamples, (size_t) (mst->numsamples * sizeof (float)))))
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+ bufsize = (size_t) (mst->numsamples * sizeof (float));
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+ if (!(mst->datasamples = realloc (mst->datasamples, bufsize)))
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{
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ms_log (2, "mst_convertsamples: cannot re-allocate buffer after sample conversion\n");
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return -1;
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}
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+ mst->bufsize = bufsize;
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}
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mst->sampletype = 'f';
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@@ -1197,7 +1209,8 @@
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/* Convert to 64-bit doubles */
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else if (type == 'd')
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{
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- if (!(ddata = (double *)malloc ((size_t) (mst->numsamples * sizeof (double)))))
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+ bufsize = (size_t) (mst->numsamples * sizeof (double));
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+ if (!(ddata = (double *)malloc (bufsize)))
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{
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ms_log (2, "mst_convertsamples: cannot allocate buffer for sample conversion to doubles\n");
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return -1;
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@@ -1219,6 +1232,7 @@
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}
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mst->datasamples = ddata;
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+ mst->bufsize = bufsize;
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mst->sampletype = 'd';
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} /* Done converting to 64-bit doubles */
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@@ -1659,7 +1673,7 @@
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int trpackedrecords = 0;
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int64_t trpackedsamples = 0;
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int samplesize;
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- int64_t bufsize;
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+ size_t bufsize;
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hptime_t preservestarttime = 0;
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double preservesamprate = 0.0;
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@@ -1745,21 +1759,22 @@
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mst->starttime = msr->starttime;
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samplesize = ms_samplesize (mst->sampletype);
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- bufsize = (mst->numsamples - trpackedsamples) * samplesize;
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+ bufsize = (size_t) (mst->numsamples - trpackedsamples) * samplesize;
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if (bufsize)
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{
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memmove (mst->datasamples,
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(char *)mst->datasamples + (trpackedsamples * samplesize),
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- (size_t)bufsize);
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+ bufsize);
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- mst->datasamples = realloc (mst->datasamples, (size_t)bufsize);
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+ mst->datasamples = realloc (mst->datasamples, bufsize);
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if (mst->datasamples == NULL)
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{
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ms_log (2, "mst_pack(): Cannot (re)allocate datasamples buffer\n");
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return -1;
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}
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+ mst->bufsize = bufsize;
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}
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else
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{
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@ -1,2 +0,0 @@
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# This file is to be called by the conda build process
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$PYTHON setup.py install
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@ -0,0 +1,46 @@
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#!/bin/bash
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set -e
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if [ ! -f "build_packages_windows.sh" ] ; then
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echo 'must be run from inside maintenance/conda'
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exit 1
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fi
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ACTION="$1"
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if [ -z "$ACTION" ] ; then
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echo "usage: build_packages.sh (dryrun|upload)"
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exit 1
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fi
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if [ "$ACTION" == "UPLOAD" ] ; then
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if [ -z "$CONDA_USERNAME" -o -z "$CONDA_PASSWORD" ] ; then
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echo "need anaconda credentials as env variables"
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exit 1
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fi
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fi
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conda install -y conda-build conda-verify anaconda-client numpy
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if [ "$ACTION" == "upload" ] ; then
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anaconda login --username "$CONDA_USERNAME" --password "$CONDA_PASSWORD" --hostname conda-builder-`uname`
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conda config --set anaconda_upload yes
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function anaconda_logout {
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anaconda logout
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}
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trap anaconda_logout EXIT
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else
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conda config --set anaconda_upload no
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fi
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conda-build --python 3.6 build
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conda-build --python 3.7 build
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conda-build --python 3.8 build
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conda-build --python 3.9 build
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|
||||
if [ "$ACTION" == "upload" ] ; then
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trap - EXIT
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anaconda_logout
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fi
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@ -0,0 +1,17 @@
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#!/bin/bash
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destination=$1
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||||
if [ -z "$destination" ] ; then
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echo "usage: upload_wheels.sh (testing|live)"
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fi
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if [ "$destination" == 'live' ] ; then
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twine upload dist/pyrocko-* \
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--username="$PYPI_USERNAME" --password="$PYPI_PASSWORD" \
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--skip-existing --disable-progress-bar
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else
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twine upload --repository-url https://test.pypi.org/legacy/ dist/pyrocko-* \
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--username="$PYPI_USERNAME" --password="$PYPI_PASSWORD" \
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--skip-existing --disable-progress-bar
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fi
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@ -0,0 +1,22 @@
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#!/usr/bin/env python
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|
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import os
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import sys
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from glob import glob
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from nose.core import run_exit
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|
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if len(sys.argv) == 2:
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target = sys.argv[1].split('.')
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if len(target) == 3:
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scripts = [sys.argv[1]]
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elif len(target) == 2:
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scripts = glob(os.path.join(*(target + ['test_*.py'])))
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elif len(target) == 1:
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scripts = glob(os.path.join(*(target + ['*', 'test_*.py'])))
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|
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else:
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scripts = glob(os.path.join('test', '*', 'test_*.py'))
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|
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sys.argv[1:] = scripts
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run_exit()
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@ -0,0 +1,15 @@
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VAGRANTFILE_API_VERSION = "2"
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Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
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config.vm.box = "win10"
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config.vm.provider "virtualbox" do |vb|
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vb.customize ["modifyvm", :id, "--memory", "4096"]
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vb.customize ["modifyvm", :id, "--cpus", "2"]
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end
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config.vm.network :private_network, ip: '192.168.115.15'
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config.vm.network :forwarded_port, guest: 22, host: 22015, id: 'ssh'
|
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|
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config.vm.guest = :windows
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config.vm.communicator = "winrm"
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||||
config.winssh.shell = "cmd"
|
||||
end
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@ -0,0 +1,37 @@
|
||||
@echo off
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||||
if not exist "C:\Users\vagrant\miniconda3.exe" (
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||||
echo Downloading conda installer...
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||||
call curl "https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe" -o "C:\Users\vagrant\miniconda3.exe" -s
|
||||
) else (
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||||
echo Conda installer already downloaded.
|
||||
)
|
||||
|
||||
if not exist "%UserProfile%\miniconda3" (
|
||||
echo Installing conda...
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||||
call "C:\Users\vagrant\miniconda3.exe" /InstallationType=JustMe /S /D="%UserProfile%\miniconda3"
|
||||
|
||||
echo Installing conda modules needed by Pyrocko...
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||||
call "%UserProfile%\miniconda3\Scripts\activate.bat"
|
||||
call conda install -y m2-libiconv m2-libintl m2-vim m2-bash m2-patch git
|
||||
call conda install -y setuptools numpy scipy matplotlib pyqt pyyaml progressbar2 requests jinja2 nose
|
||||
) else (
|
||||
echo Conda is already installed, activating...
|
||||
call "%UserProfile%\miniconda3\Scripts\activate.bat"
|
||||
)
|
||||
|
||||
if exist "%UserProfile%\pyrocko" (
|
||||
rmdir /s /q "%UserProfile%\pyrocko"
|
||||
)
|
||||
|
||||
call git clone -b %1 "C:\vagrant\pyrocko.git" "%UserProfile%\pyrocko"
|
||||
|
||||
cd pyrocko
|
||||
|
||||
mklink /d "test\data" "C:\vagrant\pyrocko-test-data"
|
||||
mklink /d "test\example_run_dir" "C:\vagrant\example_run_dir"
|
||||
|
||||
call python setup.py install
|
||||
call python -m pyrocko.print_version deps > "C:\vagrant\test-%1.py3.out"
|
||||
call python maintenance\run_tests_windows.py %2 >> "C:\vagrant\test-%1.py3.out" 2>&1
|
||||
|
||||
exit 0
|
||||
@ -0,0 +1,29 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -e
|
||||
|
||||
branch="$1"
|
||||
|
||||
if [ -z "$branch" ]; then
|
||||
branch=`git rev-parse --abbrev-ref HEAD`
|
||||
fi
|
||||
|
||||
thetest="$2"
|
||||
|
||||
if [ -z "$thetest" ]; then
|
||||
thetest="test"
|
||||
fi
|
||||
|
||||
rm -rf pyrocko.git pyrocko-test-data example_run_dir *.out *.log
|
||||
git clone --bare "../../.." "pyrocko.git"
|
||||
cp -a "../../../test/data" pyrocko-test-data
|
||||
cp -a "../../../test/example_run_dir" example_run_dir
|
||||
|
||||
echo "testing branch: $branch"
|
||||
echo "running test: $thetest"
|
||||
echo "testing branch $branch" >> log.out
|
||||
date -uIseconds >> log.out
|
||||
vagrant up
|
||||
vagrant ssh -- "C:\\vagrant\\inside.bat" "$branch" "$thetest" > >(tee -a "log.out") 2> >(tee -a "log.out" >&2) || /bin/true
|
||||
vagrant halt
|
||||
date -uIseconds >> log.out
|
||||
@ -0,0 +1,9 @@
|
||||
|
||||
:: "c:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvars64.bat"
|
||||
|
||||
IF NOT EXIST "libmseed" (
|
||||
tar -xzf libmseed-2.19.6.tar.gz --exclude=doc --exclude=test --exclude=example
|
||||
patch -s -p0 < libmseed-2.19.6-speedread.patch
|
||||
) ELSE (
|
||||
ECHO libmseed found
|
||||
)
|
||||