build: Use importlib.metadata for versioning (#195)

* build: Use importlib.metadata for versioning

* docs: Use importlib.metadata for version

bioframe/__init__.py

@@ -1,6 +1,150 @@
-from ._version import __version__
-from .core import *
-from .io import *
-from .ops import *
-from .extras import *
-from .vis import *
+try:
+    from importlib.metadata import PackageNotFoundError, version
+except ImportError:
+    from importlib_metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("bioframe")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+__all__ = [
+    "arrops",
+    "from_any",
+    "from_dict",
+    "from_list",
+    "from_series",
+    "is_bedframe",
+    "is_cataloged",
+    "is_chrom_dtype",
+    "is_complete_ucsc_string",
+    "is_contained",
+    "is_covering",
+    "is_overlapping",
+    "is_sorted",
+    "is_tiling",
+    "is_viewframe",
+    "make_viewframe",
+    "parse_region",
+    "parse_region_string",
+    "sanitize_bedframe",
+    "to_ucsc_string",
+    "update_default_colnames",
+    "binnify",
+    "digest",
+    "frac_gc",
+    "frac_gene_coverage",
+    "frac_mapped",
+    "make_chromarms",
+    "pair_by_distance",
+    "seq_gc",
+    "SCHEMAS",
+    "UCSCClient",
+    "assemblies_available",
+    "assembly_info",
+    "fetch_centromeres",
+    "fetch_chromsizes",
+    "load_fasta",
+    "read_bam",
+    "read_bigbed",
+    "read_bigwig",
+    "read_chromsizes",
+    "read_pairix",
+    "read_tabix",
+    "read_table",
+    "to_bigbed",
+    "to_bigwig",
+    "assign_view",
+    "closest",
+    "cluster",
+    "complement",
+    "count_overlaps",
+    "coverage",
+    "expand",
+    "merge",
+    "overlap",
+    "select",
+    "select_indices",
+    "select_labels",
+    "select_mask",
+    "setdiff",
+    "sort_bedframe",
+    "subtract",
+    "trim",
+    "plot_intervals",
+    "to_ucsc_colorstring",
+]
+
+from .core import (
+    arrops,
+    from_any,
+    from_dict,
+    from_list,
+    from_series,
+    is_bedframe,
+    is_cataloged,
+    is_chrom_dtype,
+    is_complete_ucsc_string,
+    is_contained,
+    is_covering,
+    is_overlapping,
+    is_sorted,
+    is_tiling,
+    is_viewframe,
+    make_viewframe,
+    parse_region,
+    parse_region_string,
+    sanitize_bedframe,
+    to_ucsc_string,
+    update_default_colnames,
+)
+from .extras import (
+    binnify,
+    digest,
+    frac_gc,
+    frac_gene_coverage,
+    frac_mapped,
+    make_chromarms,
+    pair_by_distance,
+    seq_gc,
+)
+from .io import (
+    SCHEMAS,
+    UCSCClient,
+    assemblies_available,
+    assembly_info,
+    fetch_centromeres,
+    fetch_chromsizes,
+    load_fasta,
+    read_bam,
+    read_bigbed,
+    read_bigwig,
+    read_chromsizes,
+    read_pairix,
+    read_tabix,
+    read_table,
+    to_bigbed,
+    to_bigwig,
+)
+from .ops import (
+    assign_view,
+    closest,
+    cluster,
+    complement,
+    count_overlaps,
+    coverage,
+    expand,
+    merge,
+    overlap,
+    select,
+    select_indices,
+    select_labels,
+    select_mask,
+    setdiff,
+    sort_bedframe,
+    subtract,
+    trim,
+)
+from .vis import plot_intervals, to_ucsc_colorstring
+
+del version, PackageNotFoundError

bioframe/core/__init__.py

@@ -1,21 +1,50 @@
 from . import arrops
-
-from . import specs
-from .specs import *
-
-from . import stringops
-from .stringops import *
-
-from . import checks
-from .checks import *
-
-from . import construction
-from .construction import *
+from .checks import (
+    is_bedframe,
+    is_cataloged,
+    is_contained,
+    is_covering,
+    is_overlapping,
+    is_sorted,
+    is_tiling,
+    is_viewframe,
+)
+from .construction import (
+    from_any,
+    from_dict,
+    from_list,
+    from_series,
+    make_viewframe,
+    sanitize_bedframe,
+)
+from .specs import is_chrom_dtype, update_default_colnames
+from .stringops import (
+    is_complete_ucsc_string,
+    parse_region,
+    parse_region_string,
+    to_ucsc_string,
+)
 
 __all__ = [
     "arrops",
-    *specs.__all__,
-    *stringops.__all__,
-    *checks.__all__,
-    *construction.__all__,
+    "is_bedframe",
+    "is_cataloged",
+    "is_contained",
+    "is_covering",
+    "is_overlapping",
+    "is_sorted",
+    "is_tiling",
+    "is_viewframe",
+    "from_any",
+    "from_dict",
+    "from_list",
+    "from_series",
+    "make_viewframe",
+    "sanitize_bedframe",
+    "is_chrom_dtype",
+    "update_default_colnames",
+    "is_complete_ucsc_string",
+    "parse_region",
+    "parse_region_string",
+    "to_ucsc_string",
 ]

bioframe/io/__init__.py

@@ -1,17 +1,34 @@
+from .assembly import assemblies_available, assembly_info
+from .fileops import (
+    load_fasta,
+    read_bam,
+    read_bigbed,
+    read_bigwig,
+    read_chromsizes,
+    read_pairix,
+    read_tabix,
+    read_table,
+    to_bigbed,
+    to_bigwig,
+)
+from .resources import UCSCClient, fetch_centromeres, fetch_chromsizes
 from .schemas import SCHEMAS
 
-from . import fileops
-from .fileops import *
-
-from . import resources
-from .resources import *
-
-from . import assembly
-from .assembly import *
-
 __all__ = [
+    "assemblies_available",
+    "assembly_info",
+    "read_table",
+    "read_chromsizes",
+    "read_tabix",
+    "read_pairix",
+    "read_bam",
+    "load_fasta",
+    "read_bigwig",
+    "to_bigwig",
+    "read_bigbed",
+    "to_bigbed",
+    "UCSCClient",
+    "fetch_centromeres",
+    "fetch_chromsizes",
     "SCHEMAS",
-    *fileops.__all__,
-    *resources.__all__,
-    *assembly.__all__,
 ]

docs/conf.py

@@ -5,51 +5,25 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath("../"))
-
+# import sys
+from datetime import datetime
+from importlib.metadata import metadata
+from pathlib import Path
 # autodoc_mock_imports = ["numpy", "pandas", "matplotlib", "requests"]
 
 
 # -- Project information -----------------------------------------------------
-
-project = "bioframe"
-copyright = "2020, Open2C"
+# NOTE: If you installed your project in editable mode, this might be stale.
+#       If this is the case, reinstall it to refresh the metadata
+info = metadata("bioframe")
+project_name = info["Name"]
 author = "Open2C"
-
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
 
 # The full version, including alpha/beta/rc tags
-def _read(*parts, **kwargs):
-    import os
-
-    filepath = os.path.join(os.path.dirname(__file__), *parts)
-    encoding = kwargs.pop("encoding", "utf-8")
-    with open(filepath, encoding=encoding) as fh:
-        text = fh.read()
-    return text
-
-
-def get_version():
-    import re
-
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        _read("..", "bioframe", "_version.py"),
-        re.MULTILINE,
-    ).group(1)
-    return version
-
-
-version = get_version()
-# The full version, including alpha/beta/rc tags.
-release = version
+release = info["Version"]
 
 # -- General configuration ---------------------------------------------------