From f87ff0f5116c0c1c59c5608e46563ff0f79e5d43 Mon Sep 17 00:00:00 2001
From: Benjamin Auder <benjamin.auder@somewhere>
Date: Thu, 16 Mar 2017 16:52:04 +0100
Subject: [PATCH] Folder reorganization

---
 .git-fat                                      |   1 +
 .gitattributes                                |   6 ++++++
 .gitfat                                       |   2 ++
 .gitmodules                                   |   6 ++++++
 .nbstripout                                   |   1 +
 ..._Variable_Model_Selection-Devijver2014.pdf |   1 +
 biblio/These_Emilie.pdf                       |   1 +
 clean.sh                                      |   6 ------
 initialize.sh                                 |  18 ++++++++++++++++++
 DESCRIPTION => pkg/DESCRIPTION                |   0
 LICENSE => pkg/LICENSE                        |   0
 NAMESPACE => pkg/NAMESPACE                    |   0
 {R => pkg/R}/EMGLLF.R                         |   0
 {R => pkg/R}/EMGrank.R                        |   0
 {R => pkg/R}/constructionModelesLassoMLE.R    |   0
 {R => pkg/R}/constructionModelesLassoRank.R   |   0
 {R => pkg/R}/discardSimilarModels.R           |   0
 {R => pkg/R}/generateSampleInputs.R           |   0
 {R => pkg/R}/gridLambda.R                     |   0
 {R => pkg/R}/initSmallEM.R                    |   0
 {R => pkg/R}/main.R                           |   0
 {R => pkg/R}/modelSelection.R                 |   0
 {R => pkg/R}/selectVariables.R                |   0
 {R => pkg/R}/selectiontotale.R                |   0
 {R => pkg/R}/valse.R                          |   0
 {data => pkg/data}/TODO                       |   0
 {data => pkg/data}/data.RData                 | Bin
 {man => pkg/man}/basicInitParameters.Rd       |   0
 .../man}/discardSimilarModels_EMGLLF.Rd       |   0
 .../man}/discardSimilarModels_EMGrank.Rd      |   0
 {man => pkg/man}/generateXY.Rd                |   0
 {man => pkg/man}/generateXYdefault.Rd         |   0
 {man => pkg/man}/gridLambda.Rd                |   0
 {man => pkg/man}/initSmallEM.Rd               |   0
 {man => pkg/man}/modelSelection.Rd            |   0
 {man => pkg/man}/selectVariables.Rd           |   0
 {man => pkg/man}/valse-package.Rd             |   0
 {src => pkg/src}/.gitignore                   |   0
 {src => pkg/src}/Makevars                     |   0
 {src => pkg/src}/adapters/a.EMGLLF.c          |   0
 {src => pkg/src}/adapters/a.EMGrank.c         |   0
 {src => pkg/src}/sources/EMGLLF.c             |   0
 {src => pkg/src}/sources/EMGLLF.h             |   0
 {src => pkg/src}/sources/EMGrank.c            |   0
 {src => pkg/src}/sources/EMGrank.h            |   0
 {src => pkg/src}/sources/utils.h              |   0
 {R => reports}/essai16mars.R                  |   0
 {src/test => test}/.gitignore                 |   0
 {src/test => test}/Makefile                   |   0
 test/clean.sh                                 |   6 ++++++
 .../test => test}/generate_test_data/EMGLLF.R |   0
 .../generate_test_data/EMGrank.R              |   0
 .../generateRunSaveTest_EMGLLF.R              |   0
 .../generateRunSaveTest_EMGrank.R             |   0
 {src/test => test}/sourceAll.R                |   0
 {src/test => test}/test.EMGLLF.c              |   0
 {src/test => test}/test.EMGrank.c             |   0
 {src/test => test}/test_utils.c               |   0
 {src/test => test}/test_utils.h               |   0
 59 files changed, 42 insertions(+), 6 deletions(-)
 create mode 160000 .git-fat
 create mode 100644 .gitattributes
 create mode 100644 .gitfat
 create mode 100644 .gitmodules
 create mode 160000 .nbstripout
 create mode 100644 biblio/Sparse_Variable_Model_Selection-Devijver2014.pdf
 create mode 100644 biblio/These_Emilie.pdf
 delete mode 100755 clean.sh
 create mode 100755 initialize.sh
 rename DESCRIPTION => pkg/DESCRIPTION (100%)
 rename LICENSE => pkg/LICENSE (100%)
 rename NAMESPACE => pkg/NAMESPACE (100%)
 rename {R => pkg/R}/EMGLLF.R (100%)
 rename {R => pkg/R}/EMGrank.R (100%)
 rename {R => pkg/R}/constructionModelesLassoMLE.R (100%)
 rename {R => pkg/R}/constructionModelesLassoRank.R (100%)
 rename {R => pkg/R}/discardSimilarModels.R (100%)
 rename {R => pkg/R}/generateSampleInputs.R (100%)
 rename {R => pkg/R}/gridLambda.R (100%)
 rename {R => pkg/R}/initSmallEM.R (100%)
 rename {R => pkg/R}/main.R (100%)
 rename {R => pkg/R}/modelSelection.R (100%)
 rename {R => pkg/R}/selectVariables.R (100%)
 rename {R => pkg/R}/selectiontotale.R (100%)
 rename {R => pkg/R}/valse.R (100%)
 rename {data => pkg/data}/TODO (100%)
 rename {data => pkg/data}/data.RData (100%)
 rename {man => pkg/man}/basicInitParameters.Rd (100%)
 rename {man => pkg/man}/discardSimilarModels_EMGLLF.Rd (100%)
 rename {man => pkg/man}/discardSimilarModels_EMGrank.Rd (100%)
 rename {man => pkg/man}/generateXY.Rd (100%)
 rename {man => pkg/man}/generateXYdefault.Rd (100%)
 rename {man => pkg/man}/gridLambda.Rd (100%)
 rename {man => pkg/man}/initSmallEM.Rd (100%)
 rename {man => pkg/man}/modelSelection.Rd (100%)
 rename {man => pkg/man}/selectVariables.Rd (100%)
 rename {man => pkg/man}/valse-package.Rd (100%)
 rename {src => pkg/src}/.gitignore (100%)
 rename {src => pkg/src}/Makevars (100%)
 rename {src => pkg/src}/adapters/a.EMGLLF.c (100%)
 rename {src => pkg/src}/adapters/a.EMGrank.c (100%)
 rename {src => pkg/src}/sources/EMGLLF.c (100%)
 rename {src => pkg/src}/sources/EMGLLF.h (100%)
 rename {src => pkg/src}/sources/EMGrank.c (100%)
 rename {src => pkg/src}/sources/EMGrank.h (100%)
 rename {src => pkg/src}/sources/utils.h (100%)
 rename {R => reports}/essai16mars.R (100%)
 rename {src/test => test}/.gitignore (100%)
 rename {src/test => test}/Makefile (100%)
 create mode 100755 test/clean.sh
 rename {src/test => test}/generate_test_data/EMGLLF.R (100%)
 rename {src/test => test}/generate_test_data/EMGrank.R (100%)
 rename {src/test => test}/generate_test_data/generateRunSaveTest_EMGLLF.R (100%)
 rename {src/test => test}/generate_test_data/generateRunSaveTest_EMGrank.R (100%)
 rename {src/test => test}/sourceAll.R (100%)
 rename {src/test => test}/test.EMGLLF.c (100%)
 rename {src/test => test}/test.EMGrank.c (100%)
 rename {src/test => test}/test_utils.c (100%)
 rename {src/test => test}/test_utils.h (100%)

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
-- 
2.44.0