.gitignore

#Ignore the binary default DB (have SQL dump under tracking)
thapbi_pict/ITS1_DB.sqlite

#Ignore the build directory (and its sub-directories):
build
thapbi_pict.egg-info

#Ignore the distribution directory
dist

#Sphinx temp files and output
docs/api/Makefile
docs/api/conf.py
docs/api/make.bat
docs/api/thapbi_pict.*.rst
docs/_build
docs/_static
docs/_templates

# Python compiled files
*.pyc
*.pyo
*.py{}
*.py-e

#Database: Version stamped local archives, tax-dumps:
database/CURATED.fasta
database/CURATED.sql
database/CURATED.txt
database/CURATED-v*
database/CURATED+NCBI.fasta
database/CURATED+NCBI.sql
database/CURATED+NCBI.txt
database/CURATED+NCBI-v*
# database/ITS1_DB.fasta
database/ITS1_DB.sqlite
database/ITS1_DB.sql
database/ITS1_DB.txt
database/ITS1_DB.tsv
database/ITS1_DB-v*
database/taxdmp_20*
database/new_taxdump_20*
database/Phytophthora_ITS1_DB_sync*.py
database/Phytophthora_ITS1_DB_v*.xlsx
database/Phytophthora_ITS1_DB_v*.tsv
database/Phytophthora_ITS1_DB_v*.txt
# Used when expanding curated DB:
database/unknowns.fasta
# Used in tests
new_taxdump_2019-09-01/

#Examples: Autogenerated symlinks, intermediates, reports, etc
examples/*/expected/
examples/*/taxdmp_20*
examples/*/tmp_merged/
examples/*/intermediate*/
examples/*/summary/
#Notes, papers, etc
examples/NOTES.txt
examples/*/NOTES.txt
examples/*/*.pdf
#Downloads:
examples/woody_hosts/raw_data.tar.gz
#Misc special cases from the worked examples etc:
examples/woody_hosts/DNA15MIX.onebp.tsv
examples/woody_hosts/DNA15MIX.assess.tsv
examples/woody_hosts/DNA10MIX.assess.tsv
examples/recycled_water/P_fallax.fasta
examples/recycled_water/P_fallax.tsv
examples/recycled_water/P_fallax_minimal.fasta
examples/recycled_water/conflicts.tsv
examples/recycled_water/Redekar_et_al_2019_sup_table_3.xgmml
examples/fecal_sequel/COI_430_bats.fasta

#Slurm cluster logs,
slurm-*.out

#Ignore backup files from some editors,
*~
*.swp
*.bak
*#
*/.#*

#Ignore patches and any original files created by patch command
*.diff
*.patch
*.orig
*.rej

#Ignore these hidden files from Mac OS X
.DS_Store

#Ignore random data files
*.fastq
*.fastq.gz
*.sqlite
*.zip

#Ignore any local wheel files
*.whl