Merge branch 'master' of auder.net:valse

diff --git a/.git-fat b/.git-fat
new file mode 160000 (submodule)
index 0000000..286bcd3
--- /dev/null
+++ b/.git-fat
@@ -0,0 +1 @@
+Subproject commit 286bcd30cea5f86363a04a9313afaf9e2e7a7b81

diff --git a/.gitattributes b/.gitattributes
new file mode 100644 (file)
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 (file)
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 (file)
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 (submodule)
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 (file)
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 (file)
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 (executable)
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 (executable)
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 (executable)
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