<commit_before>PROPINQUITY_OUT_DIR ?= .
export PROPINQUITY_OUT_DIR
CONFIG_FILENAME=$(PROPINQUITY_OUT_DIR)/config

COLLECTIONS_ROOT := $(shell bin/config_checker.py opentree.collections $(CONFIG_FILENAME) $(HOME)/.opentree)
export COLLECTIONS_ROOT

PEYOTL_ROOT := $(shell bin/config_checker.py opentree.peyotl $(CONFIG_FILENAME) $(HOME)/.opentree)
export PEYOTL_ROOT

OTT_DIR := $(shell bin/config_checker.py opentree.ott $(CONFIG_FILENAME) $(HOME)/.opentree)
export OTT_DIR

OTT_FILENAMES=about.json \
	conflicts.tsv \
	deprecated.tsv \
	synonyms.tsv \
	taxonomy.tsv \
	version.txt
export OTT_FILENAMES

OTT_FILEPATHS := $(addprefix $(OTT_DIR)/, $(OTT_FILENAMES))
export OTT_FILEPATHS

PHYLESYSTEM_ROOT := $(shell bin/config_checker.py opentree.phylesystem $(CONFIG_FILENAME) $(HOME)/.opentree)
export PHYLESYSTEM_ROOT

SYNTHESIS_COLLECTIONS := $(shell bin/config_checker.py synthesis.collections $(CONFIG_FILENAME))
export SYNTHESIS_COLLECTIONS

INPUT_PHYLO_ARTIFACTS=$(PROPINQUITY_OUT_DIR)/phylo_input/studies.txt \
                      $(PROPINQUITY_OUT_DIR)/phylo_input/study_tree_pairs.txt

ARTIFACTS=$(PROPINQUITY_OUT_DIR)/cleaned_ott/cleaned_ott.tre \
	  $(PROPINQUITY_OUT_DIR)/cleaned_phylo/phylo_inputs_cleaned.txt \
	  $(PROPINQUITY_OUT_DIR)/exemplified_phylo/nonempty_trees.txt \
	  $(PROPINQUITY_OUT_DIR)/subproblems/subproblem-ids.txt \
	  $(PROPINQUITY_OUT_DIR)/grafted_solution/grafted_solution_ottnames.tre \
	  $(PROPINQUITY_OUT_DIR)/full_supertree/full_supertree.tre \
	  $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree.tre \
	  $(PROPINQUITY_OUT_DIR)/labelled_supertree_ottnames/labelled_supertree_ottnames.tre \
	  $(PROPINQUITY_OUT_DIR)/annotated_supertree/annotations.json

ASSESSMENT_ARTIFACTS = $(PROPINQUITY_OUT_DIR)/assessments/supertree_degree_distribution.txt \
	$(PROPINQUITY_OUT_DIR)/assessments/taxonomy_degree_distribution.txt \
	$(PROPINQUITY_OUT_DIR)/assessments/lost_taxa.txt \
	$(PROPINQUITY_OUT_DIR)/assessments/summary.json

HTML_ARTIFACTS = $(PROPINQUITY_OUT_DIR)/annotated_supertree/index.html \
	$(PROPINQUITY_OUT_DIR)/annotated_supertree/index.json \
	$(PROPINQUITY_OUT_DIR)/assessments/index.html \
	$(PROPINQUITY_OUT_DIR)/cleaned_ott/index.html \
	$(PROPINQUITY_OUT_DIR)/cleaned_ott/index.json \
	$(PROPINQUITY_OUT_DIR)/cleaned_phylo/index.json \
	$(PROPINQUITY_OUT_DIR)/cleaned_phylo/index.html \
	$(PROPINQUITY_OUT_DIR)/exemplified_phylo/index.html \
	$(PROPINQUITY_OUT_DIR)/exemplified_phylo/index.json \
	$(PROPINQUITY_OUT_DIR)/grafted_solution/index.html \
	$(PROPINQUITY_OUT_DIR)/grafted_solution/index.json \
	$(PROPINQUITY_OUT_DIR)/index.html \
	$(PROPINQUITY_OUT_DIR)/index.json \
	$(PROPINQUITY_OUT_DIR)/labelled_supertree/index.html \
	$(PROPINQUITY_OUT_DIR)/labelled_supertree/index.json \
	$(PROPINQUITY_OUT_DIR)/phylo_input/index.json \
	$(PROPINQUITY_OUT_DIR)/phylo_input/index.html \
	$(PROPINQUITY_OUT_DIR)/subproblems/index.html \
	$(PROPINQUITY_OUT_DIR)/subproblems/index.json \
	$(PROPINQUITY_OUT_DIR)/subproblem_solutions/index.html \
	$(PROPINQUITY_OUT_DIR)/subproblem_solutions/index.json \
	$(PROPINQUITY_OUT_DIR)/phylo_snapshot/index.html \
	$(PROPINQUITY_OUT_DIR)/phylo_snapshot/index.json 

all: $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree.tre \
	 $(PROPINQUITY_OUT_DIR)/annotated_supertree/annotations.json

extra: $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree_ottnames.tre \
	   $(PROPINQUITY_OUT_DIR)/grafted_solution/grafted_solution_ottnames.tre

clean: clean1 clean2
	rm -f $(ARTIFACTS)
	rm -f $(INPUT_PHYLO_ARTIFACTS)
	rm -f $(ASSESSMENT_ARTIFACTS)
	rm -f $(HTML_ARTIFACTS)

include Makefile.clean_inputs   # contains clean1: target
include Makefile.subproblems    # contains clean2: target
include Makefile.docs           # contains html: and check: targets
<commit_msg>Fix typo.<commit_after>PROPINQUITY_OUT_DIR ?= .
export PROPINQUITY_OUT_DIR
CONFIG_FILENAME=$(PROPINQUITY_OUT_DIR)/config

COLLECTIONS_ROOT := $(shell bin/config_checker.py opentree.collections $(CONFIG_FILENAME) $(HOME)/.opentree)
export COLLECTIONS_ROOT

PEYOTL_ROOT := $(shell bin/config_checker.py opentree.peyotl $(CONFIG_FILENAME) $(HOME)/.opentree)
export PEYOTL_ROOT

OTT_DIR := $(shell bin/config_checker.py opentree.ott $(CONFIG_FILENAME) $(HOME)/.opentree)
export OTT_DIR

OTT_FILENAMES=about.json \
	conflicts.tsv \
	deprecated.tsv \
	synonyms.tsv \
	taxonomy.tsv \
	version.txt
export OTT_FILENAMES

OTT_FILEPATHS := $(addprefix $(OTT_DIR)/, $(OTT_FILENAMES))
export OTT_FILEPATHS

PHYLESYSTEM_ROOT := $(shell bin/config_checker.py opentree.phylesystem $(CONFIG_FILENAME) $(HOME)/.opentree)
export PHYLESYSTEM_ROOT

SYNTHESIS_COLLECTIONS := $(shell bin/config_checker.py synthesis.collections $(CONFIG_FILENAME))
export SYNTHESIS_COLLECTIONS

INPUT_PHYLO_ARTIFACTS=$(PROPINQUITY_OUT_DIR)/phylo_input/studies.txt \
                      $(PROPINQUITY_OUT_DIR)/phylo_input/study_tree_pairs.txt

ARTIFACTS=$(PROPINQUITY_OUT_DIR)/cleaned_ott/cleaned_ott.tre \
	  $(PROPINQUITY_OUT_DIR)/cleaned_phylo/phylo_inputs_cleaned.txt \
	  $(PROPINQUITY_OUT_DIR)/exemplified_phylo/nonempty_trees.txt \
	  $(PROPINQUITY_OUT_DIR)/subproblems/subproblem-ids.txt \
	  $(PROPINQUITY_OUT_DIR)/grafted_solution/grafted_solution_ottnames.tre \
	  $(PROPINQUITY_OUT_DIR)/full_supertree/full_supertree.tre \
	  $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree.tre \
	  $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree_ottnames.tre \
	  $(PROPINQUITY_OUT_DIR)/annotated_supertree/annotations.json

ASSESSMENT_ARTIFACTS = $(PROPINQUITY_OUT_DIR)/assessments/supertree_degree_distribution.txt \
	$(PROPINQUITY_OUT_DIR)/assessments/taxonomy_degree_distribution.txt \
	$(PROPINQUITY_OUT_DIR)/assessments/lost_taxa.txt \
	$(PROPINQUITY_OUT_DIR)/assessments/summary.json

HTML_ARTIFACTS = $(PROPINQUITY_OUT_DIR)/annotated_supertree/index.html \
	$(PROPINQUITY_OUT_DIR)/annotated_supertree/index.json \
	$(PROPINQUITY_OUT_DIR)/assessments/index.html \
	$(PROPINQUITY_OUT_DIR)/cleaned_ott/index.html \
	$(PROPINQUITY_OUT_DIR)/cleaned_ott/index.json \
	$(PROPINQUITY_OUT_DIR)/cleaned_phylo/index.json \
	$(PROPINQUITY_OUT_DIR)/cleaned_phylo/index.html \
	$(PROPINQUITY_OUT_DIR)/exemplified_phylo/index.html \
	$(PROPINQUITY_OUT_DIR)/exemplified_phylo/index.json \
	$(PROPINQUITY_OUT_DIR)/grafted_solution/index.html \
	$(PROPINQUITY_OUT_DIR)/grafted_solution/index.json \
	$(PROPINQUITY_OUT_DIR)/index.html \
	$(PROPINQUITY_OUT_DIR)/index.json \
	$(PROPINQUITY_OUT_DIR)/labelled_supertree/index.html \
	$(PROPINQUITY_OUT_DIR)/labelled_supertree/index.json \
	$(PROPINQUITY_OUT_DIR)/phylo_input/index.json \
	$(PROPINQUITY_OUT_DIR)/phylo_input/index.html \
	$(PROPINQUITY_OUT_DIR)/subproblems/index.html \
	$(PROPINQUITY_OUT_DIR)/subproblems/index.json \
	$(PROPINQUITY_OUT_DIR)/subproblem_solutions/index.html \
	$(PROPINQUITY_OUT_DIR)/subproblem_solutions/index.json \
	$(PROPINQUITY_OUT_DIR)/phylo_snapshot/index.html \
	$(PROPINQUITY_OUT_DIR)/phylo_snapshot/index.json 

all: $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree.tre \
	 $(PROPINQUITY_OUT_DIR)/annotated_supertree/annotations.json

extra: $(PROPINQUITY_OUT_DIR)/labelled_supertree/labelled_supertree_ottnames.tre \
	   $(PROPINQUITY_OUT_DIR)/grafted_solution/grafted_solution_ottnames.tre

clean: clean1 clean2
	rm -f $(ARTIFACTS)
	rm -f $(INPUT_PHYLO_ARTIFACTS)
	rm -f $(ASSESSMENT_ARTIFACTS)
	rm -f $(HTML_ARTIFACTS)

include Makefile.clean_inputs   # contains clean1: target
include Makefile.subproblems    # contains clean2: target
include Makefile.docs           # contains html: and check: targets

{'fraction_non_alphanumeric': 0.11389732083938234, 'fraction_numerical': 0.0010558268443975189, 'mean_word_length': 6.393170731707317, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7399193', 'n_tokens_mistral': 3074, 'n_tokens_neox': 2943, 'n_words': 271}