Rename package to 'indextools' to avoid collision with existing idxto…

…ols package

Makefile

@@ -1,5 +1,5 @@
 repo = dnanexus/IndexTools
-package = idxtools
+package = indextools
 version = 0.1.0
 tests = tests
 
@@ -48,9 +48,7 @@ release:
 	# build
 	$(BUILD)
 	#$(TEST)
-	python setup.py sdist bdist_wheel
-	# release
-	python setup.py sdist upload -r pypi
+	poetry publish
 	# push new tag after successful build
 	git push origin --tags
 	# create release in GitHub
@@ -59,4 +57,3 @@ release:
 		-H "Authorization: token $(token)" \
 		https://api.github.com/repos/$(repo)/releases \
 		-d '{"tag_name":"$(version)","target_commitish": "master","name": "$(version)","body": "$(desc)","draft": false,"prerelease": false}'
-

README.md

@@ -5,7 +5,7 @@ Common index formats, such as BAM Index (BAI) and Tabix (TBI), contain coarse-gr
 ## Installation
 
 ```bash
-pip install idxtools
+pip install indextools
 ```
 
 ## Commands
@@ -16,7 +16,7 @@ The `partition` command processes a BAM index file and generates a file in BED f
 
 ```bash
 # Generate a BED with 10 partitions
-idxtools partition -I tests/data/small.bam.bai \
+indextools partition -I tests/data/small.bam.bai \
   -z tests/data/contig_sizes.txt \
   -n 10 \
   -o small.partitions.bed

idxtools/bed.py → indextools/bed.py

@@ -5,7 +5,7 @@
 import subprocess
 from typing import Callable, Iterable, Iterator, Optional, Sequence, Union, Tuple
 
-from idxtools.intervals import GenomeInterval
+from indextools.intervals import GenomeInterval
 
 from xphyle import STDOUT, open_
 from xphyle.utils import read_delimited

idxtools/console/__init__.py → indextools/console/__init__.py

@@ -1,12 +1,12 @@
 """IndexTools command line interface.
 """
-from idxtools.console import (
+from indextools.console import (
     partition,
     features,
     split,
     commands
 )
-from idxtools.regions import Regions, parse_region
+from indextools.regions import Regions, parse_region
 
 import autoclick as ac
 
@@ -47,13 +47,13 @@ def merge_short_names(d):
 
 
 @ac.group()
-def idxtools():
+def indextools():
     pass
 
 
 # Partition genomic regions based on read density estimated
 # from an index.
-idxtools.command(
+indextools.command(
     decorated=partition.partition,
     types={
         "slop": ac.DelimitedList(int)
@@ -70,14 +70,14 @@ def idxtools():
 
 # Count the features (e.g. reads, variants) in a primary file
 # within partitions (e.g. output by the 'partition' command).
-idxtools.command(
+indextools.command(
     decorated=features.features
 )
 
 
 # Split a primary file (e.g. BAM, VCF) into chunks based on
 # a partition BED file (e.g. output by the 'partition' command).
-idxtools.command(
+indextools.command(
     decorated=split.split,
     types={
         "slop": ac.DelimitedList(int)
@@ -93,12 +93,12 @@ def idxtools():
 
 # Generate a list commands, one per partition, given a template
 # and a partition BED file (e.g. output by the 'partition' command).
-# idxtools.command(
+# indextools.command(
 #    decorated=commands.commands
 # )
 
 
 #
-# idxtools.command(
+# indextools.command(
 #     decorated=run
 # )

idxtools/console/commands.py → indextools/console/commands.py

@@ -3,7 +3,7 @@
 import autoclick as ac
 from xphyle import open_
 
-from idxtools.bed import BedInterval, iter_bed_interval_groups, iter_bed_intervals
+from indextools.bed import BedInterval, iter_bed_interval_groups, iter_bed_intervals
 
 
 def commands(

idxtools/console/features.py → indextools/console/features.py

@@ -3,8 +3,8 @@
 import autoclick as ac
 import pysam
 
-from idxtools.bed import GenomeInterval, iter_bed_intervals, write_intervals_bed
-from idxtools.utils import replace_suffix
+from indextools.bed import GenomeInterval, iter_bed_intervals, write_intervals_bed
+from indextools.utils import replace_suffix
 
 
 def features(

idxtools/console/partition.py → indextools/console/partition.py

@@ -4,11 +4,11 @@
 import pathlib
 from typing import Callable, List, Optional, cast
 
-from idxtools.bed import write_intervals_bed
-from idxtools.index import IntervalGrouping, group_intervals
-from idxtools.intervals import GenomeInterval
-from idxtools.regions import Regions
-from idxtools.utils import References, split_path
+from indextools.bed import write_intervals_bed
+from indextools.index import IntervalGrouping, group_intervals
+from indextools.intervals import GenomeInterval
+from indextools.regions import Regions
+from indextools.utils import References, split_path
 
 import autoclick as ac
 from ngsindex import IndexType, CoordinateIndex, resolve_index_file, parse_index

idxtools/console/split.py → indextools/console/split.py

@@ -6,8 +6,8 @@
 import autoclick as ac
 import pysam
 
-from idxtools.bed import BedInterval, iter_bed_interval_groups
-from idxtools.utils import References, split_path
+from indextools.bed import BedInterval, iter_bed_interval_groups
+from indextools.utils import References, split_path
 
 
 class FeatureInclusion(enum.Enum):

idxtools/index.py → indextools/index.py

@@ -3,9 +3,9 @@
 import statistics
 from typing import Iterator, List, Optional, Sequence, Tuple, Union, Iterable
 
-from idxtools.intervals import GenomeInterval, IVL
-from idxtools.regions import Regions
-from idxtools.utils import References
+from indextools.intervals import GenomeInterval, IVL
+from indextools.regions import Regions
+from indextools.utils import References
 
 from ngsindex import CoordinateIndex, Offset
 

idxtools/intervals.py → indextools/intervals.py

@@ -37,7 +37,7 @@
     cast,
 )
 
-from idxtools.utils import OrderedSet
+from indextools.utils import OrderedSet
 
 from ngsindex.utils import DefaultDict
 

pyproject.toml

@@ -1,5 +1,5 @@
 [tool.poetry]
-name = "idxtools"
+name = "indextools"
 version = "0.1.0"
 description = "A toolkit for accelerating genomics using index files. "
 authors = ["John Didion <jdidion@dnanexus.com>"]
@@ -18,7 +18,7 @@ pytest = "^3.0"
 jinja2 = ["jinja2"]
 
 [tool.poetry.scripts]
-idxtools = "idxtools.console:idxtools"
+indextools = "indextools.console:indextools"
 
 [build-system]
 requires = ["poetry>=0.12"]