From: Benjamin Auder Date: Thu, 16 Mar 2017 15:52:04 +0000 (+0100) Subject: Folder reorganization X-Git-Url: https://git.auder.net/doc/current/app_dev.php?a=commitdiff_plain;h=f87ff0f5116c0c1c59c5608e46563ff0f79e5d43;p=valse.git Folder reorganization --- diff --git a/.git-fat b/.git-fat new file mode 160000 index 0000000..286bcd3 --- /dev/null +++ b/.git-fat @@ -0,0 +1 @@ +Subproject commit 286bcd30cea5f86363a04a9313afaf9e2e7a7b81 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..209bdb1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,6 @@ +*.ipynb filter=nbstripout +*.pdf filter=fat +*.tar.xz filter=fat +*.png filter=fat +*.jpg filter=fat +*.ps filter=fat diff --git a/.gitfat b/.gitfat new file mode 100644 index 0000000..fc5cc54 --- /dev/null +++ b/.gitfat @@ -0,0 +1,2 @@ +[rsync] +remote = gitfat@auder.net:~/files/valse diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..16826ed --- /dev/null +++ b/.gitmodules @@ -0,0 +1,6 @@ +[submodule ".git-fat"] + path = .git-fat + url = https://github.com/yagu0/git-fat.git +[submodule ".nbstripout"] + path = .nbstripout + url = https://github.com/kynan/nbstripout.git diff --git a/.nbstripout b/.nbstripout new file mode 160000 index 0000000..10c80cb --- /dev/null +++ b/.nbstripout @@ -0,0 +1 @@ +Subproject commit 10c80cbd5b6356fa38179ca526ee2894d9b3bd20 diff --git a/biblio/Sparse_Variable_Model_Selection-Devijver2014.pdf b/biblio/Sparse_Variable_Model_Selection-Devijver2014.pdf new file mode 100644 index 0000000..aa2cd4d --- /dev/null +++ b/biblio/Sparse_Variable_Model_Selection-Devijver2014.pdf @@ -0,0 +1 @@ +#$# git-fat cfe2746476d82691a70ac9243b737e0dd6816e4b 284568 diff --git a/biblio/These_Emilie.pdf b/biblio/These_Emilie.pdf new file mode 100644 index 0000000..47bd562 --- /dev/null +++ b/biblio/These_Emilie.pdf @@ -0,0 +1 @@ +#$# git-fat 7f07727d66d742a124d6529eef942c2382d44673 3764608 diff --git a/clean.sh b/clean.sh deleted file mode 100755 index abf77b8..0000000 --- a/clean.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/sh - -rm -f src/*.so -rm -f src/adapters/*.o -rm -f src/sources/*.o -cd src/test && make cclean && cd ../.. diff --git a/initialize.sh b/initialize.sh new file mode 100755 index 0000000..30426f3 --- /dev/null +++ b/initialize.sh @@ -0,0 +1,18 @@ +#!/bin/sh + +#initialize submodules, set-up .git/config and .gitattributes, and pre-push hook +git submodule init && git submodule update --merge +#filter for Jupyter +python .nbstripout/nbstripout.py --install --attributes .gitattributes +#filter for git-fat [TODO: idempotent...] +printf '*.pdf filter=fat\n*.tar.xz filter=fat\n*.png filter=fat\n*.jpg filter=fat\n*.ps filter=fat\n' >> .gitattributes +#pre-push hook: git fat push, submodules update +printf '#!/bin/sh\n./.git-fat/git-fat pull\n./.git-fat/git-fat push\ngit submodule update --merge\n' > .git/hooks/pre-push +chmod 755 .git/hooks/pre-push +#.gitfat file with remote on gitfat@auder.net +printf '[rsync]\nremote = gitfat@auder.net:~/files/valse\n' > .gitfat +#manual git-fat init: with relative path to binary +#1] remove filter if exists http://stackoverflow.com/questions/12179437/replace-3-lines-with-another-line-sed-syntax +sed -i '1N;$!N;s/\[filter "fat"\]\n.*\n.*//;P;D' .git/config +#2] place new filter +printf '[filter "fat"]\n\tclean = ./.git-fat/git-fat filter-clean\n\tsmudge = ./.git-fat/git-fat filter-smudge\n' >> .git/config diff --git a/DESCRIPTION b/pkg/DESCRIPTION similarity index 100% rename from DESCRIPTION rename to pkg/DESCRIPTION diff --git a/LICENSE b/pkg/LICENSE similarity index 100% rename from LICENSE rename to pkg/LICENSE diff --git a/NAMESPACE b/pkg/NAMESPACE similarity index 100% rename from NAMESPACE rename to pkg/NAMESPACE diff --git a/R/EMGLLF.R b/pkg/R/EMGLLF.R similarity index 100% rename from R/EMGLLF.R rename to pkg/R/EMGLLF.R diff --git a/R/EMGrank.R b/pkg/R/EMGrank.R similarity index 100% rename from R/EMGrank.R rename to pkg/R/EMGrank.R diff --git a/R/constructionModelesLassoMLE.R b/pkg/R/constructionModelesLassoMLE.R similarity index 100% rename from R/constructionModelesLassoMLE.R rename to pkg/R/constructionModelesLassoMLE.R diff --git a/R/constructionModelesLassoRank.R b/pkg/R/constructionModelesLassoRank.R similarity index 100% rename from R/constructionModelesLassoRank.R rename to pkg/R/constructionModelesLassoRank.R diff --git a/R/discardSimilarModels.R b/pkg/R/discardSimilarModels.R similarity index 100% rename from R/discardSimilarModels.R rename to pkg/R/discardSimilarModels.R diff --git a/R/generateSampleInputs.R b/pkg/R/generateSampleInputs.R similarity index 100% rename from R/generateSampleInputs.R rename to pkg/R/generateSampleInputs.R diff --git a/R/gridLambda.R b/pkg/R/gridLambda.R similarity index 100% rename from R/gridLambda.R rename to pkg/R/gridLambda.R diff --git a/R/initSmallEM.R b/pkg/R/initSmallEM.R similarity index 100% rename from R/initSmallEM.R rename to pkg/R/initSmallEM.R diff --git a/R/main.R b/pkg/R/main.R similarity index 100% rename from R/main.R rename to pkg/R/main.R diff --git a/R/modelSelection.R b/pkg/R/modelSelection.R similarity index 100% rename from R/modelSelection.R rename to pkg/R/modelSelection.R diff --git a/R/selectVariables.R b/pkg/R/selectVariables.R similarity index 100% rename from R/selectVariables.R rename to pkg/R/selectVariables.R diff --git a/R/selectiontotale.R b/pkg/R/selectiontotale.R similarity index 100% rename from R/selectiontotale.R rename to pkg/R/selectiontotale.R diff --git a/R/valse.R b/pkg/R/valse.R similarity index 100% rename from R/valse.R rename to pkg/R/valse.R diff --git a/data/TODO b/pkg/data/TODO similarity index 100% rename from data/TODO rename to pkg/data/TODO diff --git a/data/data.RData b/pkg/data/data.RData similarity index 100% rename from data/data.RData rename to pkg/data/data.RData diff --git a/man/basicInitParameters.Rd b/pkg/man/basicInitParameters.Rd similarity index 100% rename from man/basicInitParameters.Rd rename to pkg/man/basicInitParameters.Rd diff --git a/man/discardSimilarModels_EMGLLF.Rd b/pkg/man/discardSimilarModels_EMGLLF.Rd similarity index 100% rename from man/discardSimilarModels_EMGLLF.Rd rename to pkg/man/discardSimilarModels_EMGLLF.Rd diff --git a/man/discardSimilarModels_EMGrank.Rd b/pkg/man/discardSimilarModels_EMGrank.Rd similarity index 100% rename from man/discardSimilarModels_EMGrank.Rd rename to pkg/man/discardSimilarModels_EMGrank.Rd diff --git a/man/generateXY.Rd b/pkg/man/generateXY.Rd similarity index 100% rename from man/generateXY.Rd rename to pkg/man/generateXY.Rd diff --git a/man/generateXYdefault.Rd b/pkg/man/generateXYdefault.Rd similarity index 100% rename from man/generateXYdefault.Rd rename to pkg/man/generateXYdefault.Rd diff --git a/man/gridLambda.Rd b/pkg/man/gridLambda.Rd similarity index 100% rename from man/gridLambda.Rd rename to pkg/man/gridLambda.Rd diff --git a/man/initSmallEM.Rd b/pkg/man/initSmallEM.Rd similarity index 100% rename from man/initSmallEM.Rd rename to pkg/man/initSmallEM.Rd diff --git a/man/modelSelection.Rd b/pkg/man/modelSelection.Rd similarity index 100% rename from man/modelSelection.Rd rename to pkg/man/modelSelection.Rd diff --git a/man/selectVariables.Rd b/pkg/man/selectVariables.Rd similarity index 100% rename from man/selectVariables.Rd rename to pkg/man/selectVariables.Rd diff --git a/man/valse-package.Rd b/pkg/man/valse-package.Rd similarity index 100% rename from man/valse-package.Rd rename to pkg/man/valse-package.Rd diff --git a/src/.gitignore b/pkg/src/.gitignore similarity index 100% rename from src/.gitignore rename to pkg/src/.gitignore diff --git a/src/Makevars b/pkg/src/Makevars similarity index 100% rename from src/Makevars rename to pkg/src/Makevars diff --git a/src/adapters/a.EMGLLF.c b/pkg/src/adapters/a.EMGLLF.c similarity index 100% rename from src/adapters/a.EMGLLF.c rename to pkg/src/adapters/a.EMGLLF.c diff --git a/src/adapters/a.EMGrank.c b/pkg/src/adapters/a.EMGrank.c similarity index 100% rename from src/adapters/a.EMGrank.c rename to pkg/src/adapters/a.EMGrank.c diff --git a/src/sources/EMGLLF.c b/pkg/src/sources/EMGLLF.c similarity index 100% rename from src/sources/EMGLLF.c rename to pkg/src/sources/EMGLLF.c diff --git a/src/sources/EMGLLF.h b/pkg/src/sources/EMGLLF.h similarity index 100% rename from src/sources/EMGLLF.h rename to pkg/src/sources/EMGLLF.h diff --git a/src/sources/EMGrank.c b/pkg/src/sources/EMGrank.c similarity index 100% rename from src/sources/EMGrank.c rename to pkg/src/sources/EMGrank.c diff --git a/src/sources/EMGrank.h b/pkg/src/sources/EMGrank.h similarity index 100% rename from src/sources/EMGrank.h rename to pkg/src/sources/EMGrank.h diff --git a/src/sources/utils.h b/pkg/src/sources/utils.h similarity index 100% rename from src/sources/utils.h rename to pkg/src/sources/utils.h diff --git a/R/essai16mars.R b/reports/essai16mars.R similarity index 100% rename from R/essai16mars.R rename to reports/essai16mars.R diff --git a/src/test/.gitignore b/test/.gitignore similarity index 100% rename from src/test/.gitignore rename to test/.gitignore diff --git a/src/test/Makefile b/test/Makefile similarity index 100% rename from src/test/Makefile rename to test/Makefile diff --git a/test/clean.sh b/test/clean.sh new file mode 100755 index 0000000..ad12cce --- /dev/null +++ b/test/clean.sh @@ -0,0 +1,6 @@ +#!/bin/sh + +rm -f ../pkg/src/*.so +rm -f ../pkg/src/adapters/*.o +rm -f ../pkg/src/sources/*.o +make cclean diff --git a/src/test/generate_test_data/EMGLLF.R b/test/generate_test_data/EMGLLF.R similarity index 100% rename from src/test/generate_test_data/EMGLLF.R rename to test/generate_test_data/EMGLLF.R diff --git a/src/test/generate_test_data/EMGrank.R b/test/generate_test_data/EMGrank.R similarity index 100% rename from src/test/generate_test_data/EMGrank.R rename to test/generate_test_data/EMGrank.R diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R b/test/generate_test_data/generateRunSaveTest_EMGLLF.R similarity index 100% rename from src/test/generate_test_data/generateRunSaveTest_EMGLLF.R rename to test/generate_test_data/generateRunSaveTest_EMGLLF.R diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGrank.R b/test/generate_test_data/generateRunSaveTest_EMGrank.R similarity index 100% rename from src/test/generate_test_data/generateRunSaveTest_EMGrank.R rename to test/generate_test_data/generateRunSaveTest_EMGrank.R diff --git a/src/test/sourceAll.R b/test/sourceAll.R similarity index 100% rename from src/test/sourceAll.R rename to test/sourceAll.R diff --git a/src/test/test.EMGLLF.c b/test/test.EMGLLF.c similarity index 100% rename from src/test/test.EMGLLF.c rename to test/test.EMGLLF.c diff --git a/src/test/test.EMGrank.c b/test/test.EMGrank.c similarity index 100% rename from src/test/test.EMGrank.c rename to test/test.EMGrank.c diff --git a/src/test/test_utils.c b/test/test_utils.c similarity index 100% rename from src/test/test_utils.c rename to test/test_utils.c diff --git a/src/test/test_utils.h b/test/test_utils.h similarity index 100% rename from src/test/test_utils.h rename to test/test_utils.h