mirror of
https://github.com/Stone-Red-Code/dvc.git
synced 2026-11-02 07:18:25 +01:00
test: remove bash functests
We're fully covered by tests/ and no longer need these bash tests. Signed-off-by: Ruslan Kuprieiev <[email protected]>
This commit is contained in:
Ruslan Kuprieiev
@@ -1,5 +0,0 @@
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#!/bin/bash
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source common.sh
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rm -rf $CACHE_DIR $TEST_REPO
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@@ -1,161 +0,0 @@
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#!/bin/bash
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set -e
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SDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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CACHE_DIR=$SDIR/cache
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TEST_REPO=$SDIR/myrepo
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CODE_CACHE=$CACHE_DIR/code
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DATA_CACHE=$CACHE_DIR/data
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DATA="foo bar"
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CODE="code.sh"
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REGION='us-west-2'
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BASE_DIR_S3=https://s3-$REGION.amazonaws.com/dataversioncontrol/functests
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DATA_S3=$BASE_DIR_S3/dummy_data
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CODE_S3=$BASE_DIR_S3/dummy_code
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TEST_REPO_S3="dvc-test/$(uuidgen)"
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TEST_REPO_REGION='us-east-2'
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TEST_REPO_GCP='dvc-test/myrepo'
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TEST_REPO_GCP_PROJECT='dvc-project'
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function is_osx() {
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if [ "$(uname)" == "Darwin" ]; then
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return 0
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else
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return 1
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fi
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}
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function dvc_md5() {
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if is_osx; then
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md5 -r $@
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else
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md5sum $@
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fi
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}
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function dvc_timestamp() {
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if is_osx; then
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stat -f "%m%t%Sm %N" $@
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else
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stat -c %y data/foo $@
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fi
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}
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function dvc_print() {
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echo -e "$1"
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}
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function dvc_info() {
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dvc_print "\e[34m$1\e[0m"
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}
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function dvc_header() {
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dvc_info "=============== DVC test: $1 ==============="
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}
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function dvc_error() {
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dvc_print "\e[31m$1\e[0m"
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}
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function dvc_fail() {
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dvc_error "FAIL"
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exit 1
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}
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function dvc_fatal() {
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dvc_error "$1"
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dvc_fail
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}
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function dvc_pass() {
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dvc_print "\e[32mPASS\e[0m"
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exit 0
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}
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trap 'dvc_fail;' ERR
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function dvc_prepare_cache() {
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if [ -d $CACHE_DIR ]; then
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return
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fi
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mkdir -p $DATA_CACHE
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pushd $DATA_CACHE
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for f in $DATA; do
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wget $DATA_S3/$f
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done
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popd
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mkdir -p $CODE_CACHE
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pushd $CODE_CACHE
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for f in $CODE; do
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wget $CODE_S3/$f
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done
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popd
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}
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function dvc_create_git_repo() {
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dvc_info "Creating git repo"
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dvc_prepare_cache
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rm -rf $TEST_REPO
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mkdir $TEST_REPO
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cd $TEST_REPO
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git init
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git config user.name "DVC tester"
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git config user.email "[email protected]"
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mkdir code
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cp $CODE_CACHE/* code/
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git add code/
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git commit -m 'Add code'
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}
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function dvc_create_repo() {
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dvc_info "Creating dvc repo"
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dvc_create_git_repo
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dvc init
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mkdir data
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cp $DATA_CACHE/* data
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}
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function dvc_clean_cloud_aws() {
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dvc_info "Cleaning $TEST_REPO_S3"
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aws s3 rm --recursive "s3://$TEST_REPO_S3/"
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}
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function dvc_clean_cloud_gcp() {
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dvc_info "Cleaning $TEST_REPO_GCP_PROJECT/$TEST_REPO_GCP"
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gsutil rm -rf "gs://$TEST_REPO_GCP/" || true
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}
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function dvc_check_dirs() {
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for d in $1; do
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if [ ! -d "$d" ]; then
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dvc_fatal "Directory $d doesn't exist"
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fi
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done
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}
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function dvc_check_files() {
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for f in $1; do
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if [ ! -f "$f" ]; then
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dvc_fatal "File $f doesn't exist"
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fi
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done
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}
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@@ -1,6 +0,0 @@
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dvc
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pandas
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sklearn
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scipy
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configobj
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networkx
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@@ -1,21 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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TESTS+=" test-init.sh"
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TESTS+=" test-add-remove.sh"
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TESTS+=" test-sync.sh"
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TESTS+=" test-repro-code.sh"
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TESTS+=" test-checkout.sh"
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TESTS+=" test-gc.sh"
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TESTS+=" test-lock.sh"
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for t in $TESTS; do
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rm -rf $TEST_REPO
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dvc_header "$t"
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./$t
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done
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rm -rf $TEST_REPO
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@@ -1,22 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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dvc_create_repo
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dvc add data/foo
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dvc_check_files data/foo.dvc data/foo
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dvc remove data/foo
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if [ -f "data/foo" ]; then
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echo "data/foo was not removed"
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dvc_fail
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fi
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if [ -f "data/foo.dvc" ]; then
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echo "data/foo.dvc was not removed"
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dvc_fail
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fi
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dvc_pass
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@@ -1,14 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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dvc_create_repo
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dvc add data/foo
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rm -f data/foo
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dvc checkout
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dvc_check_files data/foo
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dvc_pass
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@@ -1,39 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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dvc_create_repo
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ORIG_CACHE=$(ls .dvc/cache)
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DUMMY_CACHE+=" .dvc/cache/1"
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DUMMY_CACHE+=" .dvc/cache/2"
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DUMMY_CACHE+=" .dvc/cache/3"
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dvc_info "Create dummy cache files"
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touch $DUMMY_CACHE
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if [ $? -ne 0 ]; then
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dvc_error "Failed to create cache files"
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dvc_fail
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fi
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dvc_info "Run 'dvc gc'"
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dvc gc
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dvc_info "Check that we didn't break good cache"
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dvc_check_dirs ".dvc/cache"
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pushd .dvc/cache
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dvc_check_files $ORIG_CACHE
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popd
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dvc_info "Check that dummy cache files were removed"
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for d in $DUMMY_CACHE; do
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if [ -f $d ]; then
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dvc_error "Dummy cache file $d was not removed by gc"
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dvc_fail
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fi
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done
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dvc_pass
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@@ -1,17 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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dvc_create_git_repo
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dvc init
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DIRS=".dvc/cache .dvc/state"
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FILES=".dvc/config"
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dvc_check_dirs $DIRS
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dvc_check_files $FILES
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dvc_pass
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@@ -1,16 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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dvc_create_repo
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dvc add data/foo
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dvc run -f Dvcfile -d code/code.sh -d data/foo -o data/foo1 bash code/code.sh data/foo data/foo1
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cat Dvcfile | grep 'locked' | grep 'false' || dvc_fatal "stage locked after 'dvc run'"
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dvc lock
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cat Dvcfile | grep 'locked' | grep 'true' || dvc_fatal "stage not locked after 'dvc lock'"
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dvc lock --unlock
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cat Dvcfile | grep 'locked' | grep 'false' || dvc_fatal "stage locked after 'dvc lock --unlock'"
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dvc_pass
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@@ -1,95 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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function test_generic() {
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dvc_info '=== Generic repro test'
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dvc_create_repo
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dvc_info 'Copy foo into foo1'
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dvc add data/foo
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dvc run -d code/code.sh -d data/foo -o data/foo1 bash code/code.sh data/foo data/foo1
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dvc_info 'Modify code'
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echo " " >> code/code.sh
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git commit -am 'Change code'
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dvc_info 'Reproduce foo1'
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dvc repro foo1.dvc
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dvc_check_files data/foo1 data/foo1.dvc
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if [ "$(cat data/foo1)" != "foo" ]; then
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dvc_fail
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fi
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dvc_info 'Modify foo'
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rm -f data/foo
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cp $DATA_CACHE/bar data/foo
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dvc_info 'Reproduce foo1 as default target'
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dvc repro foo1.dvc
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dvc_check_files data/foo1 data/foo1.dvc
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if [ "$(cat data/foo1)" != "bar" ]; then
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dvc_fail
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fi
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}
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function test_partial() {
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dvc_info "=== Partial repro test"
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dvc_create_repo
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cp code/code.sh code/code1.sh
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cp code/code1.sh code/code2.sh
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cp code/code2.sh code/code3.sh
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git add code
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git commit -m "copy code"
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dvc_info "Create repro chain foo -> foo1 -> foo2 -> foo3"
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dvc add data/foo
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dvc run -f copy_foo_foo1.dvc -d code/code1.sh -d data/foo -o data/foo1 cp data/foo data/foo1
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dvc run -f copy_foo1_foo2.dvc -d code/code2.sh -d data/foo1 -o data/foo2 cp data/foo1 data/foo2
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dvc run -f copy_foo2_foo3.dvc -d code/code3.sh -d data/foo2 -o data/foo3 cp data/foo2 data/foo3
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dvc_info "Save original timestamps"
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FOO_TS=$(dvc_timestamp data/foo)
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FOO1_TS=$(dvc_timestamp data/foo1)
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FOO2_TS=$(dvc_timestamp data/foo2)
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FOO3_TS=$(dvc_timestamp data/foo3)
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dvc_info "Modify dependency for data/foo1, that will not result in data/foo1 contents being changed"
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echo " " >> code/code1.sh
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git add code
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git commit -m "modify code1.sh"
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dvc_info "Reproduce data/foo3"
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dvc repro copy_foo2_foo3.dvc
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dvc_info "Check timestamps"
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if [ "$FOO_TS" != "$(dvc_timestamp data/foo)" ]; then
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dvc_error "data/foo timestamp changed"
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dvc_fail
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fi
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if [ "$FOO1_TS" != "$(dvc_timestamp data/foo1)" ]; then
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dvc_error "data/foo1 timestamp changed"
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dvc_fail
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fi
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if [ "$FOO2_TS" != "$(dvc_timestamp data/foo2)" ]; then
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dvc_error "data/foo2 timestamp changed"
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dvc_fail
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fi
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if [ "$FOO3_TS" != "$(dvc_timestamp data/foo3)" ]; then
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dvc_error "data/foo3 timestamp changed"
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dvc_fail
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fi
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}
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test_generic
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test_partial
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dvc_pass
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@@ -1,71 +0,0 @@
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#!/bin/bash
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set -e
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source common.sh
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function test_sync() {
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dvc add data/foo
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dvc run -d code/code.sh -d data/foo -o data/foo1 bash code/code.sh data/foo data/foo1
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dvc_info "Checking status"
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dvc status | grep "new file" || dvc_fail
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dvc_info "Pushing data"
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dvc push
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dvc_info "Checking status"
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dvc status
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dvc_info "Removing all cache"
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rm -rf .dvc/cache/*
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rm -rf data/foo data/bar
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dvc_info "Checking status"
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dvc status | grep "deleted" || dvc_fail
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dvc_info "Pulling data"
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dvc pull
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dvc_check_files data/foo data/bar
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dvc_info "Checking status"
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dvc status
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}
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function test_aws() {
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dvc_create_repo
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dvc_info "Setting up AWS cloud"
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dvc_clean_cloud_aws
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dvc config aws.storagepath $TEST_REPO_S3
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dvc config aws.region $TEST_REPO_REGION
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dvc config global.cloud AWS
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test_sync
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dvc_clean_cloud_aws
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}
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function test_gcp() {
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dvc_create_repo
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dvc_info "Setting up GCP cloud"
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dvc_clean_cloud_gcp
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dvc config gcp.storagepath $TEST_REPO_GCP
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dvc config gcp.projectname $TEST_REPO_GCP_PROJECT
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dvc config global.cloud GCP
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test_sync
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dvc_clean_cloud_gcp
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}
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if [[ "$TRAVIS_PULL_REQUEST" == "false" && "$TRAVIS_SECURE_ENV_VARS" == "true" ]]; then
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test_aws
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# Temporarily disabled for travis
|
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if [[ "$TRAVIS" != "true" ]]; then
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test_gcp
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fi
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fi
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|
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dvc_pass
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@@ -1,146 +0,0 @@
|
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#!/bin/bash
|
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|
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set -e
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|
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# 1. First ML model
|
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|
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mkdir myrepo
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cd myrepo
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|
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git init
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echo "This is an empty readme" > README.md
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git add README.md
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git commit -m 'add readme'
|
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|
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mkdir code
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wget -nv -P code/ https://s3-us-west-2.amazonaws.com/dvc-share/so/code/featurization.py \
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https://s3-us-west-2.amazonaws.com/dvc-share/so/code/evaluate.py \
|
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https://s3-us-west-2.amazonaws.com/dvc-share/so/code/train_model.py \
|
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https://s3-us-west-2.amazonaws.com/dvc-share/so/code/split_train_test.py \
|
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https://s3-us-west-2.amazonaws.com/dvc-share/so/code/xml_to_tsv.py \
|
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https://s3-us-west-2.amazonaws.com/dvc-share/so/code/requirements.txt
|
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#pip install -U -r code/requirements.txt
|
||||
# Edit eval file format
|
||||
git add code/
|
||||
git commit -m 'Download code'
|
||||
|
||||
dvc init
|
||||
|
||||
git checkout -b input_100K
|
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mkdir data
|
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wget https://s3-us-west-2.amazonaws.com/dvc-share/so/100K/Posts.xml.tgz -O data/Posts.xml.tgz
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#cp ../stackoverflow_small_xml/100K/Posts.xml.tgz data/
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dvc add data/Posts.xml.tgz
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dvc run -o data/Posts.xml -d data/Posts.xml.tgz tar zxf data/Posts.xml.tgz -C data/
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dvc run -d code/xml_to_tsv.py -d data/Posts.xml -o data/Posts.tsv python code/xml_to_tsv.py data/Posts.xml data/Posts.tsv python
|
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git add .
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git commit -m 'Extract TSV for 100K dataset'
|
||||
|
||||
git checkout master
|
||||
dvc checkout
|
||||
git checkout -b input_25K
|
||||
dvc checkout
|
||||
mkdir data
|
||||
wget https://s3-us-west-2.amazonaws.com/dvc-share/so/25K/Posts.xml.tgz -O data/Posts.xml.tgz
|
||||
#cp ../stackoverflow_small_xml/25K/Posts.xml.tgz data/
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||||
dvc add data/Posts.xml.tgz
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||||
dvc run -o data/Posts.xml -d data/Posts.xml.tgz tar zxf data/Posts.xml.tgz -C data/
|
||||
|
||||
dvc run -d code/xml_to_tsv.py -d data/Posts.xml -o data/Posts.tsv python code/xml_to_tsv.py data/Posts.xml data/Posts.tsv python
|
||||
dvc run -d code/split_train_test.py -d data/Posts.tsv -o data/Posts-train.tsv -o data/Posts-test.tsv python code/split_train_test.py data/Posts.tsv 0.33 20170426 data/Posts-train.tsv data/Posts-test.tsv
|
||||
dvc run -d code/featurization.py -d data/Posts-train.tsv -d data/Posts-test.tsv -o data/matrix-train.p -o data/matrix-test.p python code/featurization.py data/Posts-train.tsv data/Posts-test.tsv data/matrix-train.p data/matrix-test.p
|
||||
|
||||
dvc run -d code/train_model.py -d data/matrix-train.p -o data/model.p python code/train_model.py data/matrix-train.p 20170426 data/model.p
|
||||
|
||||
dvc run -d code/evaluate.py -d data/model.p -d data/matrix-test.p -O data/eval_auc.txt python code/evaluate.py data/model.p data/matrix-test.p data/eval_auc.txt
|
||||
|
||||
#dvc config Global.Target data/eval_auc.txt
|
||||
#git commit -am 'Set Target'
|
||||
|
||||
cat data/eval_auc.txt
|
||||
# AUC: 0.596182
|
||||
|
||||
git add .
|
||||
git commit -m 'Full pipeline'
|
||||
|
||||
|
||||
git checkout input_100K
|
||||
dvc checkout
|
||||
git merge -X theirs input_25K # git merge -X theirs input_25K
|
||||
## Resolve conflicts by hands!!!
|
||||
#git add .
|
||||
#git commit -m 'Merge conflicts'
|
||||
dvc merge
|
||||
dvc repro # <-- Error. Reproducng Posts.xml and Posts.tsv
|
||||
|
||||
|
||||
# Improve the model:
|
||||
git checkout input_25K
|
||||
dvc checkout
|
||||
vi code/train_model.py # Change: estimators=500
|
||||
git commit -am 'estimators=500'
|
||||
vi code/train_model.py # Change: n_jobs=6
|
||||
git commit -am 'n_jobs=6'
|
||||
dvc repro
|
||||
cat data/eval_auc.txt
|
||||
# 0.619262
|
||||
vi code/featurization.py # Change: add ngram_range=(1, 2) to CountVectorizer
|
||||
git commit -am 'Add bigrams'
|
||||
dvc repro
|
||||
cat data/eval_auc.txt
|
||||
# 0.628989
|
||||
vi code/featurization.py
|
||||
git commit -am 'Add three-grams' # Change: ngram_range=(1, 3)
|
||||
dvc repro
|
||||
cat data/eval_auc.txt
|
||||
# 0.630682
|
||||
vi code/featurization.py
|
||||
git commit -am 'Add 4-grams' # Change: ngram_range=(1, 4)
|
||||
dvc repro
|
||||
cat data/eval_auc.txt
|
||||
# 0.621002
|
||||
|
||||
# Create a branch for unsuccessful commit
|
||||
git checkout -b four_grams
|
||||
dvc checkout
|
||||
# The last successful commit which is the second last humman-created commit
|
||||
git log --pretty=oneline | grep -v "DVC repro-run: " | head -n 2 | tail -n 1
|
||||
# Move the current HEAD to the last successful commit
|
||||
git branch -f input_25K `git log --pretty=oneline | grep -v "DVC repro-run: " | head -n 2 | tail -n 1 | cut -d" " -f1`
|
||||
git checkout input_25K
|
||||
dvc checkout
|
||||
|
||||
# Continue to optimize the target metrics
|
||||
vi code/train_model.py # Change: min_samples_split=5
|
||||
git commit -am 'min_samples_split=5'
|
||||
dvc repro
|
||||
|
||||
git checkout input_100K
|
||||
dvc checkout
|
||||
git merge -X theirs input_25K
|
||||
git add data/
|
||||
git commit -am "After merge"
|
||||
dvc repro
|
||||
|
||||
##
|
||||
|
||||
vi code/featurization.py
|
||||
# 0.578447
|
||||
|
||||
# 2. Reproduce: change input dataset
|
||||
|
||||
dvc remove data/Posts.xml.tgz
|
||||
#dvc import https://s3-us-west-2.amazonaws.com/dvc-share/so/100K/Posts.xml.tgz data/
|
||||
dvc import https://s3-us-west-2.amazonaws.com/dvc-share/so/25K/Posts.xml.tgz data/
|
||||
dvc repro data/evaluation.txt
|
||||
cat data/evaluation.txt
|
||||
# AUC: 0.639861
|
||||
|
||||
# 3. Share your research
|
||||
|
||||
# Improve features
|
||||
echo " " >> code/featurization.py
|
||||
git add code/featurization.py
|
||||
git commit -m 'Include bigram'
|
||||
dvc repro data/evaluation.txt
|
||||
cat data/evaluation.txt
|
||||
@@ -1,61 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
set -e
|
||||
|
||||
# 1. First ML model
|
||||
|
||||
rm -rf myrepo
|
||||
mkdir myrepo
|
||||
cd myrepo
|
||||
mkdir data
|
||||
mkdir code
|
||||
wget -nv -P code/ https://s3-us-west-2.amazonaws.com/dvc-share/so/code/featurization.py \
|
||||
https://s3-us-west-2.amazonaws.com/dvc-share/so/code/evaluate.py \
|
||||
https://s3-us-west-2.amazonaws.com/dvc-share/so/code/train_model.py \
|
||||
https://s3-us-west-2.amazonaws.com/dvc-share/so/code/split_train_test.py \
|
||||
https://s3-us-west-2.amazonaws.com/dvc-share/so/code/xml_to_tsv.py \
|
||||
https://s3-us-west-2.amazonaws.com/dvc-share/so/code/requirements.txt
|
||||
pip install -U -r code/requirements.txt
|
||||
|
||||
git init
|
||||
git add code/
|
||||
git commit -m 'Download code'
|
||||
|
||||
|
||||
dvc init
|
||||
wget -P data/ https://s3-us-west-2.amazonaws.com/dvc-share/so/10K/Posts.xml.tgz
|
||||
dvc add data/Posts.xml.tgz
|
||||
dvc run -d data/Posts.xml.tgz -o data/Posts.xml tar zxf data/Posts.xml.tgz -C data/
|
||||
|
||||
dvc run -d code/xml_to_tsv.py -d data/Posts.xml -o data/Posts.tsv python code/xml_to_tsv.py data/Posts.xml data/Posts.tsv python
|
||||
dvc run -d code/split_train_test.py -d data/Posts.tsv -o data/Posts-test.tsv python code/split_train_test.py data/Posts.tsv 0.33 20170426 data/Posts-train.tsv data/Posts-test.tsv
|
||||
dvc run -d code/featurization.py -d data/Posts-train.tsv -d data/Posts-test.tsv -o data/matrix-train.p -o data/matrix-test.p python code/featurization.py data/Posts-train.tsv data/Posts-test.tsv data/matrix-train.p data/matrix-test.p
|
||||
|
||||
dvc run -d code/train_model.py -d data/matrix-train.p -o data/model.p python code/train_model.py data/matrix-train.p 20170426 data/model.p
|
||||
|
||||
dvc run -d code/evaluate.py -d data/model.p -d data/matrix-test.p -o data/evaluation.txt python code/evaluate.py data/model.p data/matrix-test.p data/evaluation.txt
|
||||
|
||||
cat data/evaluation.txt
|
||||
# AUC: 0.552980
|
||||
|
||||
exit 0
|
||||
|
||||
# 2. Reproduce: change input dataset
|
||||
|
||||
dvc remove data/Posts.xml.tgz
|
||||
#dvc import https://s3-us-west-2.amazonaws.com/dvc-share/so/100K/Posts.xml.tgz data/
|
||||
|
||||
wget -P data/ https://s3-us-west-2.amazonaws.com/dvc-share/so/25K/Posts.xml.tgz
|
||||
dvc add data/Posts.xml.tgz
|
||||
dvc repro -v data/evaluation.txt
|
||||
cat data/evaluation.txt
|
||||
# AUC: 0.639861
|
||||
|
||||
# 3. Share your research
|
||||
|
||||
# Improve features
|
||||
echo " " >> code/featurization.py
|
||||
git add code/featurization.py
|
||||
git commit -m 'Include bigram'
|
||||
dvc repro data/evaluation.txt
|
||||
cat data/evaluation.txt
|
||||
@@ -1,11 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
|
||||
BIN=$DIR/bin
|
||||
DVC_HOME=$DIR
|
||||
|
||||
export PATH=$BIN:$PATH
|
||||
export DVC_HOME=$DIR
|
||||
|
||||
cd functest
|
||||
./run.sh
|
||||
@@ -4,7 +4,6 @@ set -x
|
||||
set -e
|
||||
|
||||
./unittests.sh
|
||||
./functests.sh
|
||||
|
||||
if [[ ! -z "$TRAVIS_TAG" ]]; then
|
||||
if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
|
||||
|
||||
Reference in New Issue
Block a user