-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMakefile
214 lines (179 loc) · 8.52 KB
/
Makefile
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
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
.ONESHELL:
SHELL=/bin/bash
#################################################################################
# GLOBALS #
#################################################################################
CONDA_BASE=$(shell conda info --base)
PROJECT_NAME = seg_networks
CONDA_ENVIRONMENT = seg_networks
PYTHON_VERSION = 3.9
SRC = draft.md
LASTDRAFT = submitted
#################################################################################
# COMMANDS #
#################################################################################
## Set up python interpreter environment
environment:
mamba env create -f environment.yml
source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT); python setup.py develop -N
## Update the environment in case of changes to dependencies
environment-update:
mamba env update --name $(CONDA_ENVIRONMENT) --file environment.yml
## Install notebook kernel manually
kernel:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
python -m ipykernel install --name $(CONDA_ENVIRONMENT) --user
## Initialize a private git repository
git:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
git init ;\
gh auth login ;\
gh repo create $(PROJECT_NAME) --private
git add .
git commit -m 'init from mandown'
git push --set-upstream origin main
## Build pdf, html, & latex from current draft
paper: clean html tex docx pdf
## Build html file from current draft
html:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc $(SRC) -r markdown+simple_tables+table_captions+yaml_metadata_block+smart --self-contained -w html --resource-path=.:$(PWD) --template=.pandoc/html.template --katex --css=.pandoc/marked/kultiad-serif.css --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/$(PROJECT_NAME).html;
## Build docx from current draft
docx:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc appendix.md --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition \
--citeproc -o compiled/appendix.tex;\
pandoc $(SRC) -r markdown+simple_tables+table_captions+yaml_metadata_block+smart -s --pdf-engine=tectonic \
--template=.pandoc/simple_article.template --filter pandoc-include --filter pandoc-crossref \
--filter pandoc-latex-admonition --citeproc --include-after-body compiled/appendix.tex -o compiled/$(PROJECT_NAME).docx;
## Build latex doc from the current draft
tex:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc $(SRC) -r markdown+simple_tables+table_captions+yaml_metadata_block+smart -w latex -s --pdf-engine=tectonic --template=.pandoc/simple_article.template --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/$(PROJECT_NAME).tex;
appendix:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc appendix.md -r markdown+simple_tables+table_captions+yaml_metadata_block+smart -w latex --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -s -o compiled/appendix.tex;\
pandoc appendix.md --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/appendix.pdf;\
## Build pdf from current draft
pdf:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc appendix.md --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/appendix.tex;\
pandoc $(SRC) -r markdown+simple_tables+table_captions+yaml_metadata_block+smart -s --pdf-engine=tectonic --template=.pandoc/simple_article.template --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/$(PROJECT_NAME).pdf;
## Remove old versions of compiled draft
clean:
rm -f paper/compiled/*.html paper/compiled/*.pdf paper/compiled/*.tex paper/compiled/*.docx;
## Run notebooks
notebooks:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 --ExecutePreprocessor.kernel_name=$(CONDA_ENVIRONMENT) notebooks/*.ipynb;
## Run any necessary scripts
scripts:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);
# python example.py
## Generate draft word count
wordcount:
@source "$(CONDA_BASE)/bin/activate" $(PROJECT_NAME);\
cd paper;\
pandoc $(SRC) -r markdown+simple_tables+table_captions+yaml_metadata_block+smart -s --pdf-engine=tectonic --template=.pandoc/simple_article.template --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc --lua-filter .pandoc/wordcount.lua -o none.pdf;
## Run latex diff on current and previous drafts
diff:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper; \
latexdiff $(LASTDRAFT)/$(PROJECT_NAME).tex compiled/$(PROJECT_NAME).tex > $(PROJECT_NAME)_diff.tex; \
tectonic $(PROJECT_NAME)_diff.tex
mv $(PROJECT_NAME)_diff.tex compiled/$(PROJECT_NAME)_diff.tex
mv $(PROJECT_NAME)_diff.pdf compiled/$(PROJECT_NAME)_diff.pdf
rm $(PROJECT_NAME)_diff.bcf
## Build paper and texdiff with previous draft
revision: paper diff
## Build cover letter
cover:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc cover.md --pdf-engine=tectonic --template=.pandoc/template-letter.tex --data-dir=.:.pandoc -o compiled/cover.pdf
## Build point-by-point pdf responding to reviewers (template in .pandoc/)
response:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc review_response.md --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/review_response.pdf
## Build paper and tag as submitted version
submission:
@echo "Enter submission version number (e.g. v1, v2, v3): "; \
read -r VNO; \
make paper && \
git add . ; \
git commit -m "Version $$VNO for submission"; \
git tag -a $$VNO -m "Version $$VNO for submission"; \
cp -r paper/compiled/ paper/submitted/ ; \
conda env export --name $(CONDA_ENVIRONMENT) > paper/submitted/$(PROJECT_NAME)_env.yml
## Create new submission, diff with prior, & respond to reviewers
resubmission: submission diff response
## Build pdf from current draft
template_pdf:
@source "$(CONDA_BASE)/bin/activate" $(CONDA_ENVIRONMENT);\
cd paper;\
pandoc appendix.md --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc -o compiled/appendix.tex;\
pandoc $(SRC) -r markdown+simple_tables+table_captions+yaml_metadata_block+smart -s --pdf-engine=tectonic --filter pandoc-include --filter pandoc-crossref --filter pandoc-latex-admonition --citeproc --include-after-body compiled/appendix.tex -o compiled/$(PROJECT_NAME).pdf;
#################################################################################
# Self Documenting Commands #
#################################################################################
.DEFAULT_GOAL := show-help
# Inspired by <http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html>
# sed script explained:
# /^##/:
# * save line in hold space
# * purge line
# * Loop:
# * append newline + line to hold space
# * go to next line
# * if line starts with doc comment, strip comment character off and loop
# * remove target prerequisites
# * append hold space (+ newline) to line
# * replace newline plus comments by `---`
# * print line
# Separate expressions are necessary because labels cannot be delimited by
# semicolon; see <http://stackoverflow.com/a/11799865/1968>
.PHONY: show-help notebooks clean
show-help:
@echo "$$(tput bold)Available rules:$$(tput sgr0)"
@echo
@sed -n -e "/^## / { \
h; \
s/.*//; \
:doc" \
-e "H; \
n; \
s/^## //; \
t doc" \
-e "s/:.*//; \
G; \
s/\\n## /---/; \
s/\\n/ /g; \
p; \
}" ${MAKEFILE_LIST} \
| LC_ALL='C' sort --ignore-case \
| awk -F '---' \
-v ncol=$$(tput cols) \
-v indent=19 \
-v col_on="$$(tput setaf 6)" \
-v col_off="$$(tput sgr0)" \
'{ \
printf "%s%*s%s ", col_on, -indent, $$1, col_off; \
n = split($$2, words, " "); \
line_length = ncol - indent; \
for (i = 1; i <= n; i++) { \
line_length -= length(words[i]) + 1; \
if (line_length <= 0) { \
line_length = ncol - indent - length(words[i]) - 1; \
printf "\n%*s ", -indent, " "; \
} \
printf "%s ", words[i]; \
} \
printf "\n"; \
}' \
| more $(shell test $(shell uname) == Darwin && echo '--no-init --raw-control-chars')