From 6bdce6a5a657ef9d7eea1fbeec36eb0b88518d45 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alexander=20F=20R=C3=B8dseth?= <rodseth@gmail.com>
Date: Thu, 11 Jan 2018 12:48:57 +0100
Subject: [PATCH 1/3] Use pymake instead of GNU Make

---
 .gitmodules     |  3 +++
 Makefile        | 34 +++++++++++++++++++++++++---------
 src/Makefile.in |  6 ++++--
 src/pymake      |  1 +
 src/sakemake.in |  2 +-
 5 files changed, 34 insertions(+), 12 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 src/pymake

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..18ef2b7
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "pymake"]
+	path = src/pymake
+	url = https://github.com/mozilla/pymake
diff --git a/Makefile b/Makefile
index 8df5c9b..82e0aa9 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean generate uninstall src/Makefile src/sakemake
+.PHONY: clean generate install_pymake src/Makefile src/pymake/make.py src/sakemake uninstall uninstall_pymake
 
 NAME := sakemake
 ALIAS := sm
@@ -10,15 +10,16 @@ SRCDIR := ${ROOTDIR}/src
 
 # macOS detection
 UNAME_S := $(shell uname -s)
+PYMAKE ?= ${SRCDIR}/pymake/make.py
 ifeq ($(UNAME_S),Darwin)
   PREFIX ?= /usr/local
-  MAKE ?= make
+  PYMAKE ?= ${PREFIX}/pymake/make.py
 else ifeq ($(UNAME_S),FreeBSD)
   PREFIX ?= /usr/local
-  MAKE ?= gmake
+  PYMAKE ?= ${PREFIX}/pymake/make.py
 else
   PREFIX ?= /usr
-  MAKE ?= make
+  PYMAKE ?= ${PREFIX}/pymake/make.py
 endif
 
 VERSION := $(shell grep -F '* Version: ' README.md | cut -d' ' -f3)
@@ -30,15 +31,30 @@ else
   pkgdir ?= ${PWD}/pkg
 endif
 
-generate: src/Makefile src/sakemake
+generate: src/Makefile src/sakemake src/pymake/make.py
 
 src/Makefile: src/Makefile.in
-	@sed "s,@@PREFIX@@,${PREFIX},g;s,@@MAKE@@,${MAKE},g;s,@@VERSION@@,${VERSION},g" $< > $@
+	@sed "s,@@PREFIX@@,${PREFIX},g;s,@@PYMAKE@@,${PYMAKE},g;s,@@VERSION@@,${VERSION},g" $< > $@
 
 src/sakemake: src/sakemake.in
-	@sed "s,@@PREFIX@@,${PREFIX},g;s,@@MAKE@@,${MAKE},g;s,@@VERSION@@,${VERSION},g" $< > $@
+	@sed "s,@@PREFIX@@,${PREFIX},g;s,@@PYMAKE@@,${PYMAKE},g;s,@@VERSION@@,${VERSION},g" $< > $@
 
-install: generate
+src/pymake/make.py:
+	@sed 's/env python$$/env python2/g' -i $@
+
+install_pymake:
+	@cp -r "${SRCDIR}/pymake" "${DESTDIR}${PREFIX}/share/${NAME}/"
+	@rm -rf "${DESTDIR}${PREFIX}/share/${NAME}/pymake/tests"
+	@find "${DESTDIR}${PREFIX}/share/${NAME}" -type d -exec chmod 755 {} \;
+	@find "${DESTDIR}${PREFIX}/share/${NAME}" -type f -exec chmod 644 {} \;
+	@chmod 755 "${DESTDIR}${PREFIX}/share/${NAME}/pymake/make.py"
+	@find "${DESTDIR}${PREFIX}/share/${NAME}" -type d -name .git -delete
+	@find "${DESTDIR}${PREFIX}/share/${NAME}" -type f -name ".*ignore" -delete
+
+uninstall_pymake:
+	@rm -rf "${DESTDIR}${PREFIX}/share/${NAME}/pymake"
+
+install: generate install_pymake
 	@install -d "${DESTDIR}${PREFIX}/bin"
 	@install -m755 "${SRCDIR}/${NAME}" "${DESTDIR}${PREFIX}/bin/${NAME}"
 	@ln -sf "${PREFIX}/bin/${NAME}" "${DESTDIR}${PREFIX}/bin/${ALIAS}"
@@ -48,7 +64,7 @@ install: generate
 	@install -d "${DESTDIR}${PREFIX}/share/licenses/${NAME}"
 	@install -m644 "${ROOTDIR}/LICENSE" "${DESTDIR}${PREFIX}/share/licenses/${NAME}/LICENSE"
 
-uninstall:
+uninstall: uninstall_pymake
 	@-rm -f "${DESTDIR}${PREFIX}/bin/${NAME}"
 	@-rm -f "${DESTDIR}${PREFIX}/bin/${ALIAS}"
 	@-rmdir "${DESTDIR}${PREFIX}/bin" 2>/dev/null || true
diff --git a/src/Makefile.in b/src/Makefile.in
index 6ffc280..14ae884 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -10,10 +10,12 @@ patch_paths ?= 0
 run ?= 0
 
 std ?= c++17
-MAKE ?= @@MAKE@@
+PYMAKE ?= @@PYMAKE@@
 PREFIX ?= @@PREFIX@@
 system_include_dir ?= ${PREFIX}/include
 
+CXX ?= c++
+
 # the name of the installed executable and related directories
 NAME ?= $(shell basename $(CURDIR))
 
@@ -55,7 +57,7 @@ all: build
 
 version:
 	@echo sakemake @@VERSION@@
-	@${MAKE} --version | head -1
+	@${PYMAKE} --version | head -1
 	@echo '   SCons '$$(scons --version | grep ": v" | head -1 | cut -d: -f2 | cut -dv -f2 | cut -b-5)
 
 build:
diff --git a/src/pymake b/src/pymake
new file mode 160000
index 0000000..034ae9e
--- /dev/null
+++ b/src/pymake
@@ -0,0 +1 @@
+Subproject commit 034ae9ea5b726e03647d049147c5dbf688e94aaf
diff --git a/src/sakemake.in b/src/sakemake.in
index 6847448..f9b55b1 100644
--- a/src/sakemake.in
+++ b/src/sakemake.in
@@ -25,4 +25,4 @@ sm small        - build a smaller executable
 
 dog
 fi
-@@MAKE@@ --no-print-directory -f "$SAKEMAKE_DIR/Makefile" "$@"
+@@PYMAKE@@ --no-print-directory -f "$SAKEMAKE_DIR/Makefile" "$@"

From e933344136f74f26a52893bb58e014da5e6a3584 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alexander=20F=20R=C3=B8dseth?= <rodseth@gmail.com>
Date: Thu, 11 Jan 2018 12:53:04 +0100
Subject: [PATCH 2/3] Undo changes to pymake after installation

---
 Makefile | 7 +++++--
 install  | 2 ++
 2 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100755 install

diff --git a/Makefile b/Makefile
index 82e0aa9..e735b51 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean generate install_pymake src/Makefile src/pymake/make.py src/sakemake uninstall uninstall_pymake
+.PHONY: clean generate install_pymake src/Makefile src/pymake/make.py src/sakemake uninstall uninstall_pymake unpatch
 
 NAME := sakemake
 ALIAS := sm
@@ -42,6 +42,9 @@ src/sakemake: src/sakemake.in
 src/pymake/make.py:
 	@sed 's/env python$$/env python2/g' -i $@
 
+unpatch:
+	@sed 's/env python2$$/env python/g' -i src/pymake/make.py
+
 install_pymake:
 	@cp -r "${SRCDIR}/pymake" "${DESTDIR}${PREFIX}/share/${NAME}/"
 	@rm -rf "${DESTDIR}${PREFIX}/share/${NAME}/pymake/tests"
@@ -54,7 +57,7 @@ install_pymake:
 uninstall_pymake:
 	@rm -rf "${DESTDIR}${PREFIX}/share/${NAME}/pymake"
 
-install: generate install_pymake
+install: generate install_pymake unpatch
 	@install -d "${DESTDIR}${PREFIX}/bin"
 	@install -m755 "${SRCDIR}/${NAME}" "${DESTDIR}${PREFIX}/bin/${NAME}"
 	@ln -sf "${PREFIX}/bin/${NAME}" "${DESTDIR}${PREFIX}/bin/${ALIAS}"
diff --git a/install b/install
new file mode 100755
index 0000000..8749b33
--- /dev/null
+++ b/install
@@ -0,0 +1,2 @@
+#!/bin/sh
+python2 src/pymake/make.py -f Makefile install

From f07cf3f8e612a93cd32cbc18c64d78d911883b80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alexander=20F=20R=C3=B8dseth?= <rodseth@gmail.com>
Date: Thu, 11 Jan 2018 13:30:49 +0100
Subject: [PATCH 3/3] Not a good direction, abandoning branch

---
 Makefile | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index e735b51..1cde9bb 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean generate install_pymake src/Makefile src/pymake/make.py src/sakemake uninstall uninstall_pymake unpatch
+.PHONY: clean generate install_pymake install_sakemake src/Makefile src/pymake/make.py src/sakemake uninstall uninstall_pymake install
 
 NAME := sakemake
 ALIAS := sm
@@ -31,7 +31,7 @@ else
   pkgdir ?= ${PWD}/pkg
 endif
 
-generate: src/Makefile src/sakemake src/pymake/make.py
+generate: src/Makefile src/sakemake
 
 src/Makefile: src/Makefile.in
 	@sed "s,@@PREFIX@@,${PREFIX},g;s,@@PYMAKE@@,${PYMAKE},g;s,@@VERSION@@,${VERSION},g" $< > $@
@@ -39,12 +39,6 @@ src/Makefile: src/Makefile.in
 src/sakemake: src/sakemake.in
 	@sed "s,@@PREFIX@@,${PREFIX},g;s,@@PYMAKE@@,${PYMAKE},g;s,@@VERSION@@,${VERSION},g" $< > $@
 
-src/pymake/make.py:
-	@sed 's/env python$$/env python2/g' -i $@
-
-unpatch:
-	@sed 's/env python2$$/env python/g' -i src/pymake/make.py
-
 install_pymake:
 	@cp -r "${SRCDIR}/pymake" "${DESTDIR}${PREFIX}/share/${NAME}/"
 	@rm -rf "${DESTDIR}${PREFIX}/share/${NAME}/pymake/tests"
@@ -53,11 +47,12 @@ install_pymake:
 	@chmod 755 "${DESTDIR}${PREFIX}/share/${NAME}/pymake/make.py"
 	@find "${DESTDIR}${PREFIX}/share/${NAME}" -type d -name .git -delete
 	@find "${DESTDIR}${PREFIX}/share/${NAME}" -type f -name ".*ignore" -delete
+	@sed 's/env python$$/env python2/g' -i "${DESTDIR}${PREFIX}/share/${NAME}/pymake/make.py"
 
 uninstall_pymake:
 	@rm -rf "${DESTDIR}${PREFIX}/share/${NAME}/pymake"
 
-install: generate install_pymake unpatch
+install_sakemake: generate
 	@install -d "${DESTDIR}${PREFIX}/bin"
 	@install -m755 "${SRCDIR}/${NAME}" "${DESTDIR}${PREFIX}/bin/${NAME}"
 	@ln -sf "${PREFIX}/bin/${NAME}" "${DESTDIR}${PREFIX}/bin/${ALIAS}"
@@ -67,6 +62,8 @@ install: generate install_pymake unpatch
 	@install -d "${DESTDIR}${PREFIX}/share/licenses/${NAME}"
 	@install -m644 "${ROOTDIR}/LICENSE" "${DESTDIR}${PREFIX}/share/licenses/${NAME}/LICENSE"
 
+install: install_sakemake install_pymake
+
 uninstall: uninstall_pymake
 	@-rm -f "${DESTDIR}${PREFIX}/bin/${NAME}"
 	@-rm -f "${DESTDIR}${PREFIX}/bin/${ALIAS}"