dushoff.github.io/Makefile at master · dushoff/dushoff.github.io · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
#### dushoff.github.io
# notebook (gh-pages branch, which is the only one I use)
# http://localhost:4000/
# http://dushoff.github.io/
# make serve

### Hooks for the editor to set the default target

current: target
-include target.mk

##################################################################

# make files

Sources += Makefile .gitignore README.md LICENSE.md

ms = makestuff
Sources += $(ms)
Makefile: $(ms)/Makefile

-include $(ms)/os.mk
-include $(ms)/perl.def

$(ms)/%.mk: $(ms)/Makefile ;
$(ms)/Makefile:
	git submodule update -i

##################################################################

## Content

Sources += $(wildcard *.md) updates.html

Sources += $(wildcard materials/*.*)

######################################################################

## Images

contours.png:
	wget -O $@ "http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0028608.g002"

contours.crop.png: contours.png Makefile
	convert -crop 1245x634+080+0 $< $@

######################################################################

# Posts

# Posts are made from drafts as a side effect of making *.post
Sources += $(wildcard _posts/*.*)
Sources += post.pl

%.post: %.md post.pl
	$(PUSH)
	$(shell_execute)

blog.post: blog.md

######################################################################

# Jekyll

Ignore += *.lock _site
Sources += _config.yml Gemfile
Sources += $(wildcard _includes/* _layouts/* css/* _sass/*)

ggplotExample.Rout: ggplotExample.R

sir.Rout: sir.R

sir.plot.Rout: sir.Rout plot.R
	$(run-R)

Sources += bio.txt

# Accounts

test.sheet = https://docs.google.com/spreadsheets/d/1uTYrqHizf0B8V_s6WWMlyi7de4P5ItTeeBtQmdhvnDU

test.sheet.tsv:

test.sheet.account.txt: test.sheet.tsv

whiteoak.sheet = https://docs.google.com/spreadsheets/d/1fI9i4Gye_SFg0qbcxlExjCjR_gk3dLgdQaTGts51sNo

whiteoak.sheet.account.txt:

######################################################################

# Speed and strength

Sources += phi_notes.tex commands.sty
phi_notes.pdf: phi_notes.tex

Sources += $(wildcard *.R)

EbolaFuns.Rout: EbolaFuns.R
HIVfuns.Rout: HIVfuns.R
kernel.Rout: kernel.R

## Speed and strength talk
hss.Rout: HIVfuns.Rout kernel.Rout hss.R
ess.Rout: EbolaFuns.Rout kernel.Rout ess.R

flat.Rout: hss.Rout flat.R
test.Rout: hss.Rout test.R

test.scen.Rout: HIVscen.R
flat.scen.Rout: HIVscen.R
%.scen.Rout: %.Rout HIVscen.R
	$(run-R)

##################################################################

### Jekyll

jekyll_install:
	bundle install

jekyll_update:
	bundle update github-pages

######################################################################

### Makestuff

-include $(ms)/git.mk
-include $(ms)/visual.mk

-include $(ms)/wrapR.mk
# -include $(ms)/oldlatex.mk
-include $(ms)/accounts.mk