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Makefile
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INFILE_DIR=data
INFILE=double_biclique_unambiguous.lp
TEST_CFG_FILE=
SHOW_DURATIONS=--durations=22
FAILED_FIRST=--ff
## Usage and tests
compress:
python -m powergrasp $(INFILE_DIR)/$(INFILE) out/out.bbl
python -m bubbletools validate out/out.bbl
config:
python -m powergrasp --config
test: t
t:
- mv powergrasp.cfg powergrasp.cfg.bak
# try different option sets
$(MAKE) _test_cfg_file TEST_CFG_FILE=default # with default values
$(MAKE) _test_cfg_file TEST_CFG_FILE=oneshot
$(MAKE) _test_cfg_file TEST_CFG_FILE=manyoptions
$(MAKE) _test_cfg_file TEST_CFG_FILE=nostarsearch
rm powergrasp.cfg
- mv powergrasp.cfg.bak powergrasp.cfg
_pure_tests:
pytest powergrasp test -x -vv --doctest-module $(SHOW_DURATIONS) $(FAILED_FIRST)
_test_cfg_file:
cp test/powergrasp.$(TEST_CFG_FILE).cfg powergrasp.cfg
$(MAKE) _pure_tests # with many options tweaked (edges from ASP, integrity,…)
## Packaging
make_dist:
python setup.py sdist
upload:
twine upload --repository pypi dist/PowerGrASP-*.tar.gz
release: fullrelease
fullrelease:
fullrelease
install_deps:
python -c "import configparser; c = configparser.ConfigParser(); c.read('setup.cfg'); print(c['options']['install_requires'])" | xargs pip install -U
.PHONY: test t compress upload
## All real test cases
real-puceron-mi-m-diff:
$(MAKE) compress INFILE_DIR=~/data/puceron/data-playing/output INFILE=miRNA_mRNA_diff.lp
real-puceron-mi-m-diff-no3019:
$(MAKE) compress INFILE_DIR=~/data/puceron/data-playing/output INFILE=miRNA_mRNA_diff-no3019.lp
real-puceron-mi-lnc:
$(MAKE) compress INFILE_DIR=~/data/puceron/data-playing/output INFILE=miRNA_lncRNA.lp
real-puceron-lnc-m:
$(MAKE) compress INFILE_DIR=~/data/puceron/data-playing/output INFILE=lncRNA_mRNA.lp
real-puceron-mi-m-lnc:
$(MAKE) compress INFILE_DIR=~/data/puceron/data-playing/output INFILE=ternary_concepts_mi_m_lnc-edge.lp
real-matrixdb-core27:
$(MAKE) compress INFILE_DIR=~/data/MatrixDb/compmatrixdb/matrixdb_CORE27_example INFILE=matrixdb_CORE27_example.lp
real-matrixdb-90:
$(MAKE) compress INFILE_DIR=~/data/MatrixDb/compmatrixdb/matrixdb_Human_Human_171107_extended INFILE=matrixdb_CORE27_example.lp
real-matrixdb-all:
$(MAKE) compress INFILE_DIR=~/data/MatrixDb/compmatrixdb/matrixdb_Human_Human_171107_extended INFILE=matrixdb_Human_Human_171107_extended_0.0.lp
## All test cases
abnormal:
$(MAKE) compress INFILE=abnormal.lp
bintree:
$(MAKE) compress INFILE=bintree.lp
clique:
$(MAKE) compress INFILE=clique.lp
cliques:
$(MAKE) compress INFILE=cliques.lp
concomp:
$(MAKE) compress INFILE=concomp.lp
concept-loop:
$(MAKE) compress INFILE=concept-loop.lp
ddiam:
$(MAKE) compress INFILE=ddiam.lp
diacli:
$(MAKE) compress INFILE=diacli.lp
diamond:
$(MAKE) compress INFILE=diamond.lp
disjoint-subpnodes:
$(MAKE) compress INFILE=disjoint-subpnodes.lp
double_biclique_unambiguous:
$(MAKE) compress INFILE=double_biclique_unambiguous.lp
double-p-groups:
$(MAKE) compress INFILE=double-p-groups.lp
hanging-bio-notree-cc0:
$(MAKE) compress INFILE=hanging-bio-notree-cc0.lp
horrible_data:
$(MAKE) compress INFILE=horrible_data.lp
inclusions:
$(MAKE) compress INFILE=inclusions.lp
consider-included-nodes:
$(MAKE) compress INFILE=consider-included-nodes.lp
motif-overlapping:
$(MAKE) compress INFILE=motif-overlapping.lp
multiple-optimals:
$(MAKE) compress INFILE=multiple-optimals.lp
n8_d0:
$(MAKE) compress INFILE=n8_d0.7.lp
one_edge:
$(MAKE) compress INFILE=one_edge.lp
order:
$(MAKE) compress INFILE=order.lp
overlapping-bicliques:
$(MAKE) compress INFILE=overlapping-bicliques.lp
partition:
$(MAKE) compress INFILE=partition.lp
perfectfit:
$(MAKE) compress INFILE=perfectfit.lp
phosphatase:
$(MAKE) compress INFILE=phosphatase.lp
pnode-to-clique:
$(MAKE) compress INFILE=pnode-to-clique.lp
prio_deg:
$(MAKE) compress INFILE=prio_deg.lp
quasibiclique:
$(MAKE) compress INFILE=quasibiclique.lp
quoting:
$(MAKE) compress INFILE=quoting.lp
single-node:
$(MAKE) compress INFILE=single-node.lp
star:
$(MAKE) compress INFILE=star.lp
structural-binding:
$(MAKE) compress INFILE=structural-binding.lp
structural-binding-maincc:
$(MAKE) compress INFILE=structural-binding-maincc.lp
structural-binding-nobridge:
$(MAKE) compress INFILE=structural-binding-nobridge.lp
testblocks:
$(MAKE) compress INFILE=testblocks.lp
test-gml:
$(MAKE) compress INFILE=test.gml
test-graphml:
$(MAKE) compress INFILE=test.graphml
thesis:
$(MAKE) compress INFILE=thesis.lp
todel:
$(MAKE) compress INFILE=todel.lp
triplets:
$(MAKE) compress INFILE=triplets.lp
typical:
$(MAKE) compress INFILE=typical-use-case.lp
unclique:
$(MAKE) compress INFILE=unclique.lp
variable-name:
$(MAKE) compress INFILE=variable-name.gml
wiki-tree-decomposition:
$(MAKE) compress INFILE=wiki-tree-decomposition.lp
zorro:
$(MAKE) compress INFILE=zorro.lp