bio2zarr 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

bio2zarr/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.2'
-__version_tuple__ = version_tuple = (0, 0, 2)
+__version__ = version = '0.0.4'
+__version_tuple__ = version_tuple = (0, 0, 4)

bio2zarr/cli.py

@@ -1,6 +1,12 @@
+import logging
+import os
+import pathlib
+import shutil
+
 import click
 import tabulate
 import coloredlogs
+import numcodecs
 
 from . import vcf
 from . import vcf_utils
@@ -8,6 +14,9 @@ from . import plink
 from . import provenance
 
 
+logger = logging.getLogger(__name__)
+
+
 class NaturalOrderGroup(click.Group):
     """
     List commands in the order they are provided in the help text.
@@ -18,8 +27,32 @@ class NaturalOrderGroup(click.Group):
 
 
 # Common arguments/options
+vcfs = click.argument(
+    "vcfs", nargs=-1, required=True, type=click.Path(exists=True, dir_okay=False)
+)
+
+new_icf_path = click.argument(
+    "icf_path", type=click.Path(file_okay=False, dir_okay=True)
+)
+
+icf_path = click.argument(
+    "icf_path", type=click.Path(exists=True, file_okay=False, dir_okay=True)
+)
+
+new_zarr_path = click.argument(
+    "zarr_path", type=click.Path(file_okay=False, dir_okay=True)
+)
+
 verbose = click.option("-v", "--verbose", count=True, help="Increase verbosity")
 
+force = click.option(
+    "-f",
+    "--force",
+    is_flag=True,
+    flag_value=True,
+    help="Force overwriting of existing directories",
+)
+
 version = click.version_option(version=f"{provenance.__version__}")
 
 worker_processes = click.option(
@@ -34,6 +67,17 @@ column_chunk_size = click.option(
     help="Approximate uncompressed size of exploded column chunks in MiB",
 )
 
+# We could provide the full flexiblity of numcodecs/Blosc here, but there
+# doesn't seem much point. Can always add more arguments here to control
+# compression level, etc.
+compressor = click.option(
+    "-C",
+    "--compressor",
+    type=click.Choice(["lz4", "zstd"]),
+    default=None,
+    help="Codec to use for compressing column chunks (Default=zstd)."
+)
+
 # Note: -l and -w were chosen when these were called "width" and "length".
 # possibly there are better letters now.
 variants_chunk_size = click.option(
@@ -64,59 +108,101 @@ def setup_logging(verbosity):
     coloredlogs.install(level=level)
 
 
+def check_overwrite_dir(path, force):
+    path = pathlib.Path(path)
+    if path.exists():
+        if not force:
+            click.confirm(
+                f"Do you want to overwrite {path}? (use --force to skip this check)",
+                abort=True,
+            )
+        # These trees can be mondo-big and on slow file systems, so it's entirely
+        # feasible that the delete would fail or be killed. This makes it less likely
+        # that partially deleted paths are mistaken for good paths.
+        tmp_delete_path = path.with_suffix(f"{path.suffix}.{os.getpid()}.DELETING")
+        logger.info(f"Deleting {path} (renamed to {tmp_delete_path} while in progress)")
+        os.rename(path, tmp_delete_path)
+        shutil.rmtree(tmp_delete_path)
+
+
+def get_compressor(cname):
+    if cname is None:
+        return None
+    config = vcf.ICF_DEFAULT_COMPRESSOR.get_config()
+    config["cname"] = cname
+    return numcodecs.get_codec(config)
+
+
 @click.command
-@click.argument("vcfs", nargs=-1, required=True)
-@click.argument("zarr_path", type=click.Path())
+@vcfs
+@new_icf_path
+@force
 @verbose
-@worker_processes
 @column_chunk_size
-def explode(vcfs, zarr_path, verbose, worker_processes, column_chunk_size):
+@compressor
+@worker_processes
+def explode(
+    vcfs, icf_path, force, verbose, column_chunk_size, compressor, worker_processes
+):
     """
     Convert VCF(s) to intermediate columnar format
     """
     setup_logging(verbose)
+    check_overwrite_dir(icf_path, force)
     vcf.explode(
+        icf_path,
         vcfs,
-        zarr_path,
         worker_processes=worker_processes,
         column_chunk_size=column_chunk_size,
+        compressor=get_compressor(compressor),
         show_progress=True,
     )
 
 
 @click.command
-@click.argument("vcfs", nargs=-1, required=True)
-@click.argument("icf_path", type=click.Path())
-@click.argument("num_partitions", type=int)
+@vcfs
+@new_icf_path
+@click.argument("num_partitions", type=click.IntRange(min=1))
+@force
 @column_chunk_size
+@compressor
 @verbose
 @worker_processes
 def dexplode_init(
-    vcfs, icf_path, num_partitions, column_chunk_size, verbose, worker_processes
+    vcfs,
+    icf_path,
+    num_partitions,
+    force,
+    column_chunk_size,
+    compressor,
+    verbose,
+    worker_processes,
 ):
     """
-    Initial step for parallel conversion of VCF(s) to intermediate columnar format
+    Initial step for distributed conversion of VCF(s) to intermediate columnar format
     over the requested number of paritions.
     """
     setup_logging(verbose)
+    check_overwrite_dir(icf_path, force)
     num_partitions = vcf.explode_init(
         icf_path,
         vcfs,
         target_num_partitions=num_partitions,
         column_chunk_size=column_chunk_size,
         worker_processes=worker_processes,
+        compressor=get_compressor(compressor),
         show_progress=True,
     )
     click.echo(num_partitions)
 
 
 @click.command
-@click.argument("icf_path", type=click.Path())
-@click.argument("partition", type=int)
+@icf_path
+@click.argument("partition", type=click.IntRange(min=0))
 @verbose
 def dexplode_partition(icf_path, partition, verbose):
     """
-    Convert a VCF partition into intermediate columnar format. Must be called *after*
+    Convert a VCF partition to intermediate columnar format. Must be called *after*
     the ICF path has been initialised with dexplode_init. Partition indexes must be
     from 0 (inclusive) to the number of paritions returned by dexplode_init (exclusive).
     """
@@ -129,26 +215,26 @@ def dexplode_partition(icf_path, partition, verbose):
 @verbose
 def dexplode_finalise(path, verbose):
     """
-    Final step for parallel conversion of VCF(s) to intermediate columnar format
+    Final step for distributed conversion of VCF(s) to intermediate columnar format.
     """
     setup_logging(verbose)
     vcf.explode_finalise(path)
 
 
 @click.command
-@click.argument("icf_path", type=click.Path())
+@click.argument("path", type=click.Path())
 @verbose
-def inspect(icf_path, verbose):
+def inspect(path, verbose):
     """
-    Inspect an intermediate format or Zarr path.
+    Inspect an intermediate columnar format or Zarr path.
     """
     setup_logging(verbose)
-    data = vcf.inspect(icf_path)
+    data = vcf.inspect(path)
     click.echo(tabulate.tabulate(data, headers="keys"))
 
 
 @click.command
-@click.argument("icf_path", type=click.Path())
+@icf_path
 def mkschema(icf_path):
     """
     Generate a schema for zarr encoding
@@ -158,8 +244,9 @@ def mkschema(icf_path):
 
 
 @click.command
-@click.argument("icf_path", type=click.Path())
-@click.argument("zarr_path", type=click.Path())
+@icf_path
+@new_zarr_path
+@force
 @verbose
 @click.option("-s", "--schema", default=None, type=click.Path(exists=True))
 @variants_chunk_size
@@ -178,14 +265,14 @@ def mkschema(icf_path):
 @click.option(
     "-M",
     "--max-memory",
-    type=int,
     default=None,
-    help="An approximate bound on overall memory usage in megabytes",
+    help="An approximate bound on overall memory usage (e.g. 10G),",
 )
 @worker_processes
 def encode(
     icf_path,
     zarr_path,
+    force,
     verbose,
     schema,
     variants_chunk_size,
@@ -195,13 +282,14 @@ def encode(
     worker_processes,
 ):
     """
-    Encode intermediate columnar format (see explode) to vcfzarr.
+    Convert intermediate columnar format to vcfzarr.
     """
     setup_logging(verbose)
+    check_overwrite_dir(zarr_path, force)
     vcf.encode(
         icf_path,
         zarr_path,
-        schema,
+        schema_path=schema,
         variants_chunk_size=variants_chunk_size,
         samples_chunk_size=samples_chunk_size,
         max_v_chunks=max_variant_chunks,
@@ -212,8 +300,8 @@ def encode(
 
 
 @click.command(name="convert")
-@click.argument("vcfs", nargs=-1, required=True)
-@click.argument("zarr_path", type=click.Path())
+@vcfs
+@new_zarr_path
 @variants_chunk_size
 @samples_chunk_size
 @verbose
@@ -235,17 +323,6 @@ def convert_vcf(
     )
 
 
-@click.command
-@click.argument("vcfs", nargs=-1, required=True)
-@click.argument("zarr_path", type=click.Path())
-def validate(vcfs, zarr_path):
-    """
-    Development only, do not use. Will be removed before release.
-    """
-    # FIXME! Will silently not look at remaining VCFs
-    vcf.validate(vcfs[0], zarr_path, show_progress=True)
-
-
 @version
 @click.group(cls=NaturalOrderGroup)
 def vcf2zarr():
@@ -309,7 +386,6 @@ vcf2zarr.add_command(encode)
 vcf2zarr.add_command(dexplode_init)
 vcf2zarr.add_command(dexplode_partition)
 vcf2zarr.add_command(dexplode_finalise)
-vcf2zarr.add_command(validate)
 
 
 @click.command(name="convert")

bio2zarr/core.py

@@ -50,7 +50,8 @@ def wait_on_futures(futures):
             cancel_futures(futures)
             if isinstance(exception, cf.process.BrokenProcessPool):
                 raise RuntimeError(
-                    "Worker process died: you may have run out of memory") from exception
+                    "Worker process died: you may have run out of memory"
+                ) from exception
             else:
                 raise exception
 

bio2zarr/vcf.py

@@ -151,8 +151,8 @@ class VcfPartition:
 
 ICF_METADATA_FORMAT_VERSION = "0.2"
 ICF_DEFAULT_COMPRESSOR = numcodecs.Blosc(
-    cname="lz4", clevel=7, shuffle=numcodecs.Blosc.NOSHUFFLE
-).get_config()
+    cname="zstd", clevel=7, shuffle=numcodecs.Blosc.NOSHUFFLE
+)
 
 
 @dataclasses.dataclass
@@ -284,9 +284,7 @@ def scan_vcf(path, target_num_partitions):
         return metadata, vcf.raw_header
 
 
-def scan_vcfs(
-    paths, show_progress, target_num_partitions, column_chunk_size, worker_processes=1
-):
+def scan_vcfs(paths, show_progress, target_num_partitions, worker_processes=1):
     logger.info(
         f"Scanning {len(paths)} VCFs attempting to split into {target_num_partitions} partitions."
     )
@@ -334,12 +332,6 @@ def scan_vcfs(
         key=lambda x: (contig_index_map[x.region.contig], x.region.start)
     )
     icf_metadata.partitions = all_partitions
-    icf_metadata.format_version = ICF_METADATA_FORMAT_VERSION
-    icf_metadata.compressor = ICF_DEFAULT_COMPRESSOR
-    icf_metadata.column_chunk_size = column_chunk_size
-    # Bare minimum here for provenance - would be nice to include versions of key
-    # dependencies as well.
-    icf_metadata.provenance = {"source": f"bio2zarr-{provenance.__version__}"}
     logger.info(f"Scan complete, resulting in {len(all_partitions)} partitions.")
     return icf_metadata, header
 
@@ -824,13 +816,7 @@ class IcfPartitionWriter(contextlib.AbstractContextManager):
         return False
 
 
-# TODO rename to IntermediateColumnarFormat and move to icf.py
-
-
 class IntermediateColumnarFormat(collections.abc.Mapping):
-    # TODO Check if other compressors would give reasonable compression
-    # with significantly faster times
-
     def __init__(self, path):
         self.path = pathlib.Path(path)
         # TODO raise a more informative error here telling people this
@@ -904,6 +890,15 @@ class IntermediateColumnarFormat(collections.abc.Mapping):
         return len(self.columns)
 
 
+
+def mkdir_with_progress(path):
+    logger.debug(f"mkdir f{path}")
+    # NOTE we may have race-conditions here, I'm not sure. Hopefully allowing
+    # parents=True will take care of it.
+    path.mkdir(parents=True)
+    core.update_progress(1)
+
+
 class IntermediateColumnarFormatWriter:
     def __init__(self, path):
         self.path = pathlib.Path(path)
@@ -922,9 +917,12 @@ class IntermediateColumnarFormatWriter:
         worker_processes=1,
         target_num_partitions=None,
         show_progress=False,
+        compressor=None,
     ):
         if self.path.exists():
-            shutil.rmtree(self.path)
+            raise ValueError("ICF path already exists")
+        if compressor is None:
+            compressor = ICF_DEFAULT_COMPRESSOR
         vcfs = [pathlib.Path(vcf) for vcf in vcfs]
         target_num_partitions = max(target_num_partitions, len(vcfs))
 
@@ -934,14 +932,19 @@ class IntermediateColumnarFormatWriter:
             worker_processes=worker_processes,
             show_progress=show_progress,
             target_num_partitions=target_num_partitions,
-            column_chunk_size=column_chunk_size,
         )
         self.metadata = icf_metadata
+        self.metadata.format_version = ICF_METADATA_FORMAT_VERSION
+        self.metadata.compressor = compressor.get_config()
+        self.metadata.column_chunk_size = column_chunk_size
+        # Bare minimum here for provenance - would be nice to include versions of key
+        # dependencies as well.
+        self.metadata.provenance = {"source": f"bio2zarr-{provenance.__version__}"}
 
-        self.mkdirs()
+        self.mkdirs(worker_processes, show_progress=show_progress)
 
         # Note: this is needed for the current version of the vcfzarr spec, but it's
-        # probably goint to be dropped.
+        # probably going to be dropped.
         # https://github.com/pystatgen/vcf-zarr-spec/issues/15
         # May be useful to keep lying around still though?
         logger.info(f"Writing VCF header")
@@ -953,20 +956,30 @@ class IntermediateColumnarFormatWriter:
             json.dump(self.metadata.asdict(), f, indent=4)
         return self.num_partitions
 
-    def mkdirs(self):
-        # TODO add worker_processes here and do this with the ParallelWorkManager
-        logger.info(
-            f"Creating {len(self.metadata.fields) * self.num_partitions} directories"
-        )
+    def mkdirs(self, worker_processes=1, show_progress=False):
+        num_dirs = len(self.metadata.fields) * self.num_partitions
+        logger.info(f"Creating {num_dirs} directories")
         self.path.mkdir()
         self.wip_path.mkdir()
-        for field in self.metadata.fields:
-            col_path = get_vcf_field_path(self.path, field)
-            logger.debug(f"Make directories for {field.full_name} at {col_path}")
-            col_path.mkdir(parents=True)
-            for j in range(self.num_partitions):
-                part_path = col_path / f"p{j}"
-                part_path.mkdir()
+        # Due to high latency batch system filesystems, we create all the directories in
+        # parallel
+        progress_config = core.ProgressConfig(
+            total=num_dirs,
+            units="dirs",
+            title="Mkdirs",
+            show=show_progress,
+        )
+        with core.ParallelWorkManager(
+            worker_processes=worker_processes, progress_config=progress_config
+        ) as manager:
+            for field in self.metadata.fields:
+                col_path = get_vcf_field_path(self.path, field)
+                # Don't bother trying to count the intermediate directories towards
+                # progress
+                manager.submit(col_path.mkdir, parents=True)
+                for j in range(self.num_partitions):
+                    part_path = col_path / f"p{j}"
+                    manager.submit(mkdir_with_progress, part_path)
 
     def load_partition_summaries(self):
         summaries = []
@@ -1133,12 +1146,13 @@ class IntermediateColumnarFormatWriter:
 
 
 def explode(
-    vcfs,
     icf_path,
+    vcfs,
     *,
     column_chunk_size=16,
     worker_processes=1,
     show_progress=False,
+    compressor=None,
 ):
     writer = IntermediateColumnarFormatWriter(icf_path)
     num_partitions = writer.init(
@@ -1148,6 +1162,7 @@ def explode(
         worker_processes=worker_processes,
         show_progress=show_progress,
         column_chunk_size=column_chunk_size,
+        compressor=compressor,
     )
     writer.explode(worker_processes=worker_processes, show_progress=show_progress)
     writer.finalise()
@@ -1162,6 +1177,7 @@ def explode_init(
     target_num_partitions=1,
     worker_processes=1,
     show_progress=False,
+    compressor=None,
 ):
     writer = IntermediateColumnarFormatWriter(icf_path)
     return writer.init(
@@ -1170,6 +1186,7 @@ def explode_init(
         worker_processes=worker_processes,
         show_progress=show_progress,
         column_chunk_size=column_chunk_size,
+        compressor=compressor,
     )
 
 
@@ -1480,16 +1497,28 @@ class EncodingWork:
     memory: int = 0
 
 
+def parse_max_memory(max_memory):
+    if max_memory is None:
+        # Effectively unbounded
+        return 2**63
+    if isinstance(max_memory, str):
+        max_memory = humanfriendly.parse_size(max_memory)
+    logger.info(f"Set memory budget to {display_size(max_memory)}")
+    return max_memory
+
+
 class VcfZarrWriter:
-    def __init__(self, path, icf, schema):
+    def __init__(self, path, icf, schema, dimension_separator=None):
         self.path = pathlib.Path(path)
         self.icf = icf
         self.schema = schema
+        # Default to using nested directories following the Zarr v3 default.
+        # This seems to require version 2.17+ to work properly
+        self.dimension_separator = "/" if dimension_separator is None else dimension_separator
         store = zarr.DirectoryStore(self.path)
         self.root = zarr.group(store=store)
 
     def init_array(self, variable):
-        # print("CREATE", variable)
         object_codec = None
         if variable.dtype == "O":
             object_codec = numcodecs.VLenUTF8()
@@ -1501,7 +1530,9 @@ class VcfZarrWriter:
             compressor=numcodecs.get_codec(variable.compressor),
             filters=[numcodecs.get_codec(filt) for filt in variable.filters],
             object_codec=object_codec,
+            dimension_separator=self.dimension_separator,
         )
+        # Dimension names are part of the spec in Zarr v3
         a.attrs["_ARRAY_DIMENSIONS"] = variable.dimensions
 
     def get_array(self, name):
@@ -1639,6 +1670,7 @@ class VcfZarrWriter:
                 "contig_length",
                 self.schema.contig_length,
                 dtype=np.int64,
+                compressor=DEFAULT_ZARR_COMPRESSOR,
             )
             array.attrs["_ARRAY_DIMENSIONS"] = ["contigs"]
         return {v: j for j, v in enumerate(self.schema.contig_id)}
@@ -1661,8 +1693,6 @@ class VcfZarrWriter:
             self.init_array(column)
 
     def finalise(self):
-        # for column in self.schema.columns.values():
-        #     self.finalise_array(column)
         zarr.consolidate_metadata(self.path)
 
     def encode(
@@ -1672,12 +1702,7 @@ class VcfZarrWriter:
         show_progress=False,
         max_memory=None,
     ):
-        if max_memory is None:
-            # Unbounded
-            max_memory = 2**63
-        else:
-            # Value is specified in Mibibytes
-            max_memory *= 2**20  # NEEDS TEST
+        max_memory = parse_max_memory(max_memory)
 
         # TODO this will move into the setup logic later when we're making it possible
         # to split the work by slice
@@ -1764,8 +1789,8 @@ class VcfZarrWriter:
 
         # Fail early if we can't fit a particular column into memory
         for wp in work:
-            if wp.memory >= max_memory:
-                raise ValueError(  # NEEDS TEST
+            if wp.memory > max_memory:
+                raise ValueError(
                     f"Insufficient memory for {wp.columns}: "
                     f"{display_size(wp.memory)} > {display_size(max_memory)}"
                 )
@@ -1778,6 +1803,8 @@ class VcfZarrWriter:
         )
 
         used_memory = 0
+        # We need to keep some bounds on the queue size or the memory bounds algorithm
+        # below doesn't really work.
         max_queued = 4 * max(1, worker_processes)
         encoded_slices = collections.Counter()
 
@@ -1804,10 +1831,14 @@ class VcfZarrWriter:
                             self.finalise_array(column)
 
             for wp in work:
-                if (
+                while (
                     used_memory + wp.memory > max_memory
                     or len(future_to_work) > max_queued
                 ):
+                    logger.debug(
+                        f"Wait: mem_required={used_memory + wp.memory} max_mem={max_memory} "
+                        f"queued={len(future_to_work)} max_queued={max_queued}"
+                    )
                     service_completed_futures()
                 future = pwm.submit(wp.func, wp.start, wp.stop)
                 used_memory += wp.memory
@@ -1832,6 +1863,7 @@ def encode(
     variants_chunk_size=None,
     samples_chunk_size=None,
     max_v_chunks=None,
+    dimension_separator=None,
     max_memory=None,
     worker_processes=1,
     show_progress=False,
@@ -1855,7 +1887,7 @@ def encode(
     if zarr_path.exists():
         logger.warning(f"Deleting existing {zarr_path}")
         shutil.rmtree(zarr_path)
-    vzw = VcfZarrWriter(zarr_path, icf, schema)
+    vzw = VcfZarrWriter(zarr_path, icf, schema, dimension_separator=dimension_separator)
     vzw.init()
     vzw.encode(
         max_v_chunks=max_v_chunks,
@@ -1876,10 +1908,11 @@ def convert(
     show_progress=False,
     # TODO add arguments to control location of tmpdir
 ):
-    with tempfile.TemporaryDirectory(prefix="vcf2zarr_if_") as if_dir:
+    with tempfile.TemporaryDirectory(prefix="vcf2zarr") as tmp:
+        if_dir = pathlib.Path(tmp) / "if"
         explode(
-            vcfs,
             if_dir,
+            vcfs,
             worker_processes=worker_processes,
             show_progress=show_progress,
         )

{bio2zarr-0.0.2.dist-info → bio2zarr-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bio2zarr
-Version: 0.0.2
+Version: 0.0.4
 Summary: Convert bioinformatics data to Zarr
 Home-page: https://github.com/pystatgen/bio2zarr
 Author: sgkit Developers
@@ -20,7 +20,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: zarr !=2.11.0,!=2.11.1,!=2.11.2,>=2.10.0
+Requires-Dist: zarr >=2.17
 Requires-Dist: click
 Requires-Dist: tabulate
 Requires-Dist: tqdm

bio2zarr-0.0.4.dist-info/RECORD

@@ -0,0 +1,16 @@
+bio2zarr/__init__.py,sha256=yIJYx4GyKtOLOtODOX0kGCeGPYgQ-TBbsRdT1NwBpQQ,37
+bio2zarr/__main__.py,sha256=3cgaQ4x8YKXt-9xC2GLrHnS6UA38y1GXqttwZiBZJg4,525
+bio2zarr/_version.py,sha256=yBVOKdXLEcTVc7YV7ZPqRXhRDRt-pKrfXxcgHkgPY5g,411
+bio2zarr/cli.py,sha256=QE0DfoZHbBbxq9K_im9y4tJ49_Wss0zzavSjjz-85Xw,11484
+bio2zarr/core.py,sha256=tZb9exfFmuzbA8tUpPY8avSm9YvfH31-vUCTM4fpj78,8128
+bio2zarr/plink.py,sha256=llhfP-v44BVPvgCcwXktk0YrKaJSII63U_PTtpHlGtM,6755
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