From 174036285173e6a66fca0dca115374bfaa88b497 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Fri, 17 May 2024 12:45:43 -0400
Subject: [PATCH 01/11] Add input to specify s3fs open kwargs

---
 algorithm_config.yaml     |  8 ++++++-
 bin/subset.sh             |  3 ++-
 src/gedi_subset/subset.py | 47 ++++++++++++++++++++++++++++++++++-----
 3 files changed, 50 insertions(+), 8 deletions(-)

diff --git a/algorithm_config.yaml b/algorithm_config.yaml
index 7869886..8efa2d9 100644
--- a/algorithm_config.yaml
+++ b/algorithm_config.yaml
@@ -56,7 +56,7 @@ inputs:
       description: Maximum number of GEDI granule data files to download from the CMR,
         regardless of the number of granules within the AOI.
       required: false
-      default: "1000"
+      default: "100_000"
     - name: output
       description: Name of the output file produced by the algorithm.  Defaults to
         using the AOI file name (without the extension) with the suffix "_subset.gpkg".
@@ -67,3 +67,9 @@ inputs:
         provided, Scalene will not be used.
       required: false
       default: ""
+    - name: s3fs_open_kwargs
+      description: 'Python literal dict to pass as keyword arguments to s3fs.open when
+        reading files from S3.  For example: {"block_size": 4194304, "cache_type": "all"}.
+        See https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open.'
+      required: false
+      default: '{"block_size": 4194304, "cache_type": "all"}'
diff --git a/bin/subset.sh b/bin/subset.sh
index eb4d5d8..03766e0 100755
--- a/bin/subset.sh
+++ b/bin/subset.sh
@@ -27,7 +27,7 @@ else
     aoi="$(ls "${input_dir}"/*)"
 
     n_actual=${#}
-    n_expected=10
+    n_expected=11
 
     if test ${n_actual} -ne ${n_expected}; then
         echo "Expected ${n_expected} inputs, but got ${n_actual}:$(printf " '%b'" "$@")" >&2
@@ -46,6 +46,7 @@ else
     [[ -n "${9}" ]] && args+=(--output "${9}")
     # Split the 10th argument into an array of arguments to pass to scalene.
     IFS=' ' read -ra scalene_args <<<"${10}"
+    [[ -n "${11}" ]] && args+=(--s3fs-open-kwargs "${11}")
 
     command=("${subset_py}" "${args[@]}")
 
diff --git a/src/gedi_subset/subset.py b/src/gedi_subset/subset.py
index a684c1b..ab54c8c 100755
--- a/src/gedi_subset/subset.py
+++ b/src/gedi_subset/subset.py
@@ -1,13 +1,24 @@
 #!/usr/bin/env -S python -W ignore::FutureWarning -W ignore::UserWarning
 
+import json
 import logging
 import multiprocessing
 import os
 import os.path
 import time
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Any, Callable, Iterable, Mapping, NoReturn, Optional, Sequence, Tuple
+from typing import (
+    Annotated,
+    Any,
+    Callable,
+    Iterable,
+    Mapping,
+    NoReturn,
+    Optional,
+    Sequence,
+    Tuple,
+)
 
 import geopandas as gpd
 import h5py
@@ -46,7 +57,7 @@
     "L4A": "10.3334/ORNLDAAC/2056",
 }
 
-DEFAULT_LIMIT = 1_000
+DEFAULT_LIMIT = 100_000
 
 LOGGING_FORMAT = "%(asctime)s [%(processName)s:%(name)s] [%(levelname)s] %(message)s"
 
@@ -69,6 +80,7 @@ class SubsetGranuleProps:
     """
 
     fs: s3fs.S3FileSystem | None = None
+    s3fs_open_kwargs: Mapping[str, Any] = field(default_factory=dict)
     granule: Granule
     maap: MAAP
     aoi_gdf: gpd.GeoDataFrame
@@ -166,7 +178,9 @@ def subset_granule(props: SubsetGranuleProps) -> IOResultE[Maybe[str]]:
 
     try:
         with (
-            fs.open(inpath, block_size=4 * 1024 * 1024, cache_type="all") as f,
+            # Force the use of the "rb" mode.  We don't want to allow the mode
+            # to be set by user input.
+            fs.open(inpath, **{**props.s3fs_open_kwargs, "mode": "rb"}) as f,
             h5py.File(f) as hdf5,
         ):
             gdf = subset_hdf5(
@@ -215,6 +229,7 @@ def subset_granules(
     dest: Path,
     init_args: Tuple[Any, ...],
     granules: Iterable[Granule],
+    s3fs_open_kwargs: Mapping[str, Any] = {},
 ) -> IOResultE[Tuple[str, ...]]:
     def subset_saved(path: IOResultE[Maybe[str]]) -> bool:
         """Return `True` if `path`'s value is a `Some`, otherwise `False` if it
@@ -252,6 +267,7 @@ def append_subset(src: str) -> IOResultE[str]:
 
     payloads = (
         SubsetGranuleProps(
+            s3fs_open_kwargs=s3fs_open_kwargs,
             granule=granule,
             maap=maap,
             aoi_gdf=aoi_gdf,
@@ -280,6 +296,7 @@ def append_subset(src: str) -> IOResultE[str]:
 def main(
     aoi: Path = typer.Option(
         ...,
+        show_default=False,
         help="Area of Interest (path to GeoJSON file)",
         exists=True,
         file_okay=True,
@@ -290,6 +307,7 @@ def main(
     ),
     doi=typer.Option(
         ...,
+        show_default=False,
         callback=lambda value: logical_dois.get(value.upper(), value),
         help=(
             "Digital Object Identifier (DOI) of collection to subset"
@@ -298,10 +316,14 @@ def main(
         ),
     ),
     lat: str = typer.Option(
-        ..., help=("Latitude dataset used in the geometry of the dataframe")
+        ...,
+        show_default=False,
+        help=("Latitude dataset used in the geometry of the dataframe"),
     ),
     lon: str = typer.Option(
-        ..., help=("Longitude dataset used in the geometry of the dataframe")
+        ...,
+        show_default=False,
+        help=("Longitude dataset used in the geometry of the dataframe"),
     ),
     beams: str = typer.Option(
         "all",
@@ -314,6 +336,7 @@ def main(
     ),
     columns: str = typer.Option(
         ...,
+        show_default=False,
         help="Comma-separated list of columns to select",
     ),
     query: str = typer.Option(
@@ -344,6 +367,17 @@ def main(
         readable=True,
     ),
     verbose: bool = typer.Option(False, help="Provide verbose output"),
+    s3fs_open_kwargs: Annotated[
+        dict[str, Any],
+        typer.Option(
+            parser=lambda value: json.loads(value) if isinstance(value, str) else value,
+            metavar="JSON",
+            help=(
+                "Keyword arguments (as JSON) to pass to S3FileSystem.open"
+                " for reading HDF5 files"
+            ),
+        ),
+    ] = {"block_size": 4 * 1024 * 1024, "cache_type": "all"},
 ) -> None:
     logging_level = logging.DEBUG if verbose else logging.INFO
     set_logging_level(logging_level)
@@ -393,6 +427,7 @@ def main(
             dest,
             (logging_level,),
             fp.filter(granule_intersects(aoi_gdf.unary_union))(granules),
+            s3fs_open_kwargs,
         )
     ).bind_ioresult(
         lambda subsets: (

From 52c94b45649afaef89261c25aa6dcbd24c50e135 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Fri, 17 May 2024 21:08:12 -0400
Subject: [PATCH 02/11] Add cpus input

---
 algorithm_config.yaml     |  17 ++--
 bin/subset.sh             |  26 ++++--
 src/gedi_subset/subset.py | 183 +++++++++++++++++++++-----------------
 3 files changed, 131 insertions(+), 95 deletions(-)

diff --git a/algorithm_config.yaml b/algorithm_config.yaml
index 8efa2d9..9afd7ef 100644
--- a/algorithm_config.yaml
+++ b/algorithm_config.yaml
@@ -62,14 +62,19 @@ inputs:
         using the AOI file name (without the extension) with the suffix "_subset.gpkg".
       required: false
       default: ""
-    - name: scalene_args
-      description: Arguments to pass to Scalene for memory and CPU profiling.  If not
-        provided, Scalene will not be used.
-      required: false
-      default: ""
     - name: s3fs_open_kwargs
       description: 'Python literal dict to pass as keyword arguments to s3fs.open when
         reading files from S3.  For example: {"block_size": 4194304, "cache_type": "all"}.
         See https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open.'
       required: false
-      default: '{"block_size": 4194304, "cache_type": "all"}'
+      default: ""
+    - name: cpus
+      description: Number of CPUs to use for parallel processing.  If not provided,
+        all available CPUs are used.
+      required: false
+      default: ""
+    - name: scalene_args
+      description: Arguments to pass to Scalene for memory and CPU profiling.  If not
+        provided, Scalene will not be used.
+      required: false
+      default: ""
diff --git a/bin/subset.sh b/bin/subset.sh
index 03766e0..a809095 100755
--- a/bin/subset.sh
+++ b/bin/subset.sh
@@ -27,7 +27,7 @@ else
     aoi="$(ls "${input_dir}"/*)"
 
     n_actual=${#}
-    n_expected=11
+    n_expected=12
 
     if test ${n_actual} -ne ${n_expected}; then
         echo "Expected ${n_expected} inputs, but got ${n_actual}:$(printf " '%b'" "$@")" >&2
@@ -44,23 +44,31 @@ else
     [[ -n "${7}" ]] && args+=(--beams "${7}")
     [[ -n "${8}" ]] && args+=(--limit "${8}")
     [[ -n "${9}" ]] && args+=(--output "${9}")
-    # Split the 10th argument into an array of arguments to pass to scalene.
-    IFS=' ' read -ra scalene_args <<<"${10}"
-    [[ -n "${11}" ]] && args+=(--s3fs-open-kwargs "${11}")
+    [[ -n "${10}" ]] && args+=(--s3fs-open-kwargs "${10}")
+    [[ -n "${11}" ]] && args+=(--cpus "${11}")
+    # Split the last argument into an array of arguments to pass to scalene.
+    IFS=' ' read -ra scalene_args <<<"${12}"
 
     command=("${subset_py}" "${args[@]}")
 
     if [[ ${#scalene_args[@]} -ne 0 ]]; then
+        ext="html"
+
+        for arg in "${scalene_args[@]}"; do
+            if [[ "${arg}" == "--json" ]]; then
+                ext="json"
+            fi
+        done
+
         # Force output to be written to the output directory by adding the
         # `--outfile` argument after any user-provided arguments.  If the user
-        # provides their own `--outfile` argument, it will be ignored.
+        # provides their own `--outfile` argument, it will be ignored.  Also,
+        # add `--cli` to ensure that scalene does not attempt to open a browser.
         command=(
             scalene
             "${scalene_args[@]}"
-            --column-width 165
-            --html
-            --no-browser
-            --outfile "${output_dir}/profile.html"
+            --cli
+            --outfile "${output_dir}/profile.${ext}"
             ---
             "${command[@]}"
         )
diff --git a/src/gedi_subset/subset.py b/src/gedi_subset/subset.py
index ab54c8c..01e7d53 100755
--- a/src/gedi_subset/subset.py
+++ b/src/gedi_subset/subset.py
@@ -229,7 +229,8 @@ def subset_granules(
     dest: Path,
     init_args: Tuple[Any, ...],
     granules: Iterable[Granule],
-    s3fs_open_kwargs: Mapping[str, Any] = {},
+    s3fs_open_kwargs: Optional[Mapping[str, Any]] = None,
+    cpus: Optional[int] = None,
 ) -> IOResultE[Tuple[str, ...]]:
     def subset_saved(path: IOResultE[Maybe[str]]) -> bool:
         """Return `True` if `path`'s value is a `Some`, otherwise `False` if it
@@ -249,11 +250,7 @@ def append_subset(src: str) -> IOResultE[str]:
             map_(fp.always(src)),
         )
 
-    # https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.Pool.imap
-    # We're dealing with relatively small numbers of granules (dozens, perhaps
-    # hundreds, at most), so we can stick with a chunksize of 1.
-    chunksize = 1
-    processes = min(8, os.cpu_count() or 32)
+    processes = cpus or os.cpu_count()
     found_granules = list(granules)
     # On occasion, a granule is missing a download URL, so the _downloadname
     # attribute is set to None, and attempting to download it throws an
@@ -261,13 +258,16 @@ def append_subset(src: str) -> IOResultE[str]:
     downloadable_granules = [
         granule for granule in found_granules if granule._downloadname
     ]
+    # https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.Pool.imap
+    # If we have at least 10 granules per process, use a chunksize of 10.
+    chunksize = 10 if processes and len(downloadable_granules) >= 10 * processes else 1
 
     logger.info(f"Found {len(found_granules)} in the CMR")
     logger.info(f"Total downloadable granules: {len(downloadable_granules)}")
 
     payloads = (
         SubsetGranuleProps(
-            s3fs_open_kwargs=s3fs_open_kwargs,
+            s3fs_open_kwargs=s3fs_open_kwargs or {},
             granule=granule,
             maap=maap,
             aoi_gdf=aoi_gdf,
@@ -281,7 +281,7 @@ def append_subset(src: str) -> IOResultE[str]:
         for granule in downloadable_granules
     )
 
-    logger.info(f"Subsetting on {processes} processes (chunksize={chunksize})")
+    logger.info(f"Subsetting on {processes} CPUs (chunksize={chunksize})")
 
     with multiprocessing.Pool(processes, init_process, init_args) as pool:
         return flow(
@@ -294,81 +294,100 @@ def append_subset(src: str) -> IOResultE[str]:
 
 
 def main(
-    aoi: Path = typer.Option(
-        ...,
-        show_default=False,
-        help="Area of Interest (path to GeoJSON file)",
-        exists=True,
-        file_okay=True,
-        dir_okay=False,
-        writable=False,
-        readable=True,
-        resolve_path=True,
-    ),
-    doi=typer.Option(
-        ...,
-        show_default=False,
-        callback=lambda value: logical_dois.get(value.upper(), value),
-        help=(
-            "Digital Object Identifier (DOI) of collection to subset"
-            " (https://www.doi.org/), or one of these logical, case-insensitive"
-            f" names: {', '.join(logical_dois)}"
+    aoi: Annotated[
+        Path,
+        typer.Option(
+            show_default=False,
+            help="Area of Interest (path to GeoJSON file)",
+            exists=True,
+            file_okay=True,
+            dir_okay=False,
+            writable=False,
+            readable=True,
+            resolve_path=True,
+        ),
+    ],
+    doi: Annotated[
+        str,
+        typer.Option(
+            show_default=False,
+            callback=lambda value: logical_dois.get(value.upper(), value),
+            help=(
+                "Digital Object Identifier (DOI) of collection to subset"
+                " (https://www.doi.org/), or one of these logical, case-insensitive"
+                f" names: {', '.join(logical_dois)}"
+            ),
+        ),
+    ],
+    lat: Annotated[
+        str,
+        typer.Option(
+            show_default=False,
+            help=("Latitude dataset used in the geometry of the dataframe"),
         ),
-    ),
-    lat: str = typer.Option(
-        ...,
-        show_default=False,
-        help=("Latitude dataset used in the geometry of the dataframe"),
-    ),
-    lon: str = typer.Option(
-        ...,
-        show_default=False,
-        help=("Longitude dataset used in the geometry of the dataframe"),
-    ),
-    beams: str = typer.Option(
-        "all",
-        callback=check_beams_option,
-        help=(
-            "Which beams to include in the subset. Must be 'all', 'coverage', 'power',"
-            " OR a comma-separated list of beam names, with or without the 'BEAM'"
-            " prefix (e.g., 'BEAM0000,BEAM0001' or '0000,0001')"
+    ],
+    lon: Annotated[
+        str,
+        typer.Option(
+            show_default=False,
+            help=("Longitude dataset used in the geometry of the dataframe"),
+        ),
+    ],
+    columns: Annotated[
+        str,
+        typer.Option(
+            show_default=False,
+            help="Comma-separated list of columns to select",
         ),
-    ),
-    columns: str = typer.Option(
-        ...,
-        show_default=False,
-        help="Comma-separated list of columns to select",
-    ),
-    query: str = typer.Option(
-        None,
-        help="Boolean query expression to select rows",
-    ),
-    limit: int = typer.Option(
-        DEFAULT_LIMIT,
-        callback=lambda value: DEFAULT_LIMIT if value < 1 else value,
-        help="Maximum number of granules to subset",
-    ),
-    temporal: str = typer.Option(
-        None,
-        help=(
-            "Temporal range to subset"
-            " (e.g., '2019-01-01T00:00:00Z,2020-01-01T00:00:00Z')"
+    ],
+    beams: Annotated[
+        str,
+        typer.Option(
+            callback=check_beams_option,
+            help=(
+                "Which beams to include in the subset.  Must be 'all', 'coverage',"
+                " 'power', OR a comma-separated list of beam names, with or without the"
+                " 'BEAM' prefix (e.g., 'BEAM0000,BEAM0001' or '0000,0001')"
+            ),
+        ),
+    ] = "all",
+    query: Annotated[
+        Optional[str],
+        typer.Option(help="Boolean query expression to select rows"),
+    ] = None,
+    limit: Annotated[
+        int,
+        typer.Option(
+            callback=lambda value: DEFAULT_LIMIT if value < 1 else value,
+            help="Maximum number of granules to subset",
+        ),
+    ] = DEFAULT_LIMIT,
+    temporal: Annotated[
+        Optional[str],
+        typer.Option(
+            help=(
+                "Temporal range to subset"
+                " (e.g., '2019-01-01T00:00:00Z,2020-01-01T00:00:00Z')"
+            ),
+        ),
+    ] = None,
+    output: Annotated[
+        Optional[Path],
+        typer.Option(
+            ...,
+            "-o",
+            "--output",
+            help="Output file path for generated subset file",
+            exists=False,
+            file_okay=True,
+            dir_okay=False,
+            writable=True,
+            readable=True,
         ),
-    ),
-    output: Path = typer.Option(
-        None,
-        "-o",
-        "--output",
-        help="Output file path for generated subset file",
-        exists=False,
-        file_okay=True,
-        dir_okay=False,
-        writable=True,
-        readable=True,
-    ),
-    verbose: bool = typer.Option(False, help="Provide verbose output"),
+    ] = None,
+    verbose: Annotated[bool, typer.Option(help="Provide verbose output")] = False,
     s3fs_open_kwargs: Annotated[
-        dict[str, Any],
+        Optional[dict[str, Any]],
         typer.Option(
             parser=lambda value: json.loads(value) if isinstance(value, str) else value,
             metavar="JSON",
@@ -377,7 +396,10 @@ def main(
                 " for reading HDF5 files"
             ),
         ),
-    ] = {"block_size": 4 * 1024 * 1024, "cache_type": "all"},
+    ] = None,
+    cpus: Annotated[
+        int, typer.Option(help="Number of CPUs to use for parallel processing")
+    ] = (os.cpu_count() or 1),
 ) -> None:
     logging_level = logging.DEBUG if verbose else logging.INFO
     set_logging_level(logging_level)
@@ -428,6 +450,7 @@ def main(
             (logging_level,),
             fp.filter(granule_intersects(aoi_gdf.unary_union))(granules),
             s3fs_open_kwargs,
+            cpus,
         )
     ).bind_ioresult(
         lambda subsets: (

From 77066de35e05ba339a3a8c16aaf97965495f41c7 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Mon, 20 May 2024 11:37:55 -0400
Subject: [PATCH 03/11] Use txt profile extension for --cli option

---
 bin/subset.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/bin/subset.sh b/bin/subset.sh
index a809095..c599827 100755
--- a/bin/subset.sh
+++ b/bin/subset.sh
@@ -57,17 +57,20 @@ else
         for arg in "${scalene_args[@]}"; do
             if [[ "${arg}" == "--json" ]]; then
                 ext="json"
+            elif [[ "${arg}" == "--cli" ]]; then
+                ext="txt"
             fi
         done
 
         # Force output to be written to the output directory by adding the
         # `--outfile` argument after any user-provided arguments.  If the user
         # provides their own `--outfile` argument, it will be ignored.  Also,
-        # add `--cli` to ensure that scalene does not attempt to open a browser.
+        # add `--no-browser` to ensure that scalene does not attempt to open a
+        # browser.
         command=(
             scalene
             "${scalene_args[@]}"
-            --cli
+            --no-browser
             --outfile "${output_dir}/profile.${ext}"
             ---
             "${command[@]}"

From bebac482b711795ef9b967e1dc15841991d9b571 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Mon, 24 Jun 2024 15:49:55 -0400
Subject: [PATCH 04/11] Set s3fs cache settings for best performance

---
 src/gedi_subset/subset.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/gedi_subset/subset.py b/src/gedi_subset/subset.py
index 01e7d53..1b05c08 100755
--- a/src/gedi_subset/subset.py
+++ b/src/gedi_subset/subset.py
@@ -175,14 +175,19 @@ def subset_granule(props: SubsetGranuleProps) -> IOResultE[Maybe[str]]:
 
     logger.debug(f"Subsetting {inpath}")
     fs = props.fs or s3fs.S3FileSystem()
+    s3fs_open_kwargs = {
+        "cache_type": "all",
+        "block_size": 8 * 1024 * 1024,
+        "fill": True,
+        # Allow the caller to override the default values above.
+        **props.s3fs_open_kwargs,
+        # Force the use of the "rb" mode.  We don't want to allow the mode
+        # to be set by user input.
+        "mode": "rb",
+    }
 
     try:
-        with (
-            # Force the use of the "rb" mode.  We don't want to allow the mode
-            # to be set by user input.
-            fs.open(inpath, **{**props.s3fs_open_kwargs, "mode": "rb"}) as f,
-            h5py.File(f) as hdf5,
-        ):
+        with fs.open(inpath, **s3fs_open_kwargs) as f, h5py.File(f) as hdf5:
             gdf = subset_hdf5(
                 hdf5,
                 aoi=props.aoi_gdf,

From a564cda7100772ccad5417670c2f58aa9cc61a73 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Tue, 25 Jun 2024 12:30:02 -0400
Subject: [PATCH 05/11] Rename `cpu` input to `processes`

---
 algorithm_config.yaml     | 6 +++---
 bin/subset.sh             | 2 +-
 src/gedi_subset/subset.py | 9 ++++-----
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/algorithm_config.yaml b/algorithm_config.yaml
index 9afd7ef..ebe8dfc 100644
--- a/algorithm_config.yaml
+++ b/algorithm_config.yaml
@@ -68,9 +68,9 @@ inputs:
         See https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open.'
       required: false
       default: ""
-    - name: cpus
-      description: Number of CPUs to use for parallel processing.  If not provided,
-        all available CPUs are used.
+    - name: processes
+      description: Number of processes to use for parallel processing.  If not provided,
+        defaults to the number of available CPUs.
       required: false
       default: ""
     - name: scalene_args
diff --git a/bin/subset.sh b/bin/subset.sh
index c599827..6695d24 100755
--- a/bin/subset.sh
+++ b/bin/subset.sh
@@ -45,7 +45,7 @@ else
     [[ -n "${8}" ]] && args+=(--limit "${8}")
     [[ -n "${9}" ]] && args+=(--output "${9}")
     [[ -n "${10}" ]] && args+=(--s3fs-open-kwargs "${10}")
-    [[ -n "${11}" ]] && args+=(--cpus "${11}")
+    [[ -n "${11}" ]] && args+=(--processes "${11}")
     # Split the last argument into an array of arguments to pass to scalene.
     IFS=' ' read -ra scalene_args <<<"${12}"
 
diff --git a/src/gedi_subset/subset.py b/src/gedi_subset/subset.py
index 1b05c08..f0b52a2 100755
--- a/src/gedi_subset/subset.py
+++ b/src/gedi_subset/subset.py
@@ -235,7 +235,7 @@ def subset_granules(
     init_args: Tuple[Any, ...],
     granules: Iterable[Granule],
     s3fs_open_kwargs: Optional[Mapping[str, Any]] = None,
-    cpus: Optional[int] = None,
+    processes: Optional[int] = None,
 ) -> IOResultE[Tuple[str, ...]]:
     def subset_saved(path: IOResultE[Maybe[str]]) -> bool:
         """Return `True` if `path`'s value is a `Some`, otherwise `False` if it
@@ -255,7 +255,6 @@ def append_subset(src: str) -> IOResultE[str]:
             map_(fp.always(src)),
         )
 
-    processes = cpus or os.cpu_count()
     found_granules = list(granules)
     # On occasion, a granule is missing a download URL, so the _downloadname
     # attribute is set to None, and attempting to download it throws an
@@ -402,8 +401,8 @@ def main(
             ),
         ),
     ] = None,
-    cpus: Annotated[
-        int, typer.Option(help="Number of CPUs to use for parallel processing")
+    processes: Annotated[
+        int, typer.Option(help="Number of processes to use for parallel processing")
     ] = (os.cpu_count() or 1),
 ) -> None:
     logging_level = logging.DEBUG if verbose else logging.INFO
@@ -455,7 +454,7 @@ def main(
             (logging_level,),
             fp.filter(granule_intersects(aoi_gdf.unary_union))(granules),
             s3fs_open_kwargs,
-            cpus,
+            processes,
         )
     ).bind_ioresult(
         lambda subsets: (

From fcb1ca81670bc682d5a06fd753929e14b8a2364a Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Tue, 25 Jun 2024 13:08:03 -0400
Subject: [PATCH 06/11] Set default queue to  maap-dps-worker-32vcpu-64gb

---
 algorithm_config.yaml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/algorithm_config.yaml b/algorithm_config.yaml
index ebe8dfc..724b3dd 100644
--- a/algorithm_config.yaml
+++ b/algorithm_config.yaml
@@ -4,7 +4,7 @@ algorithm_version: 0.7.0
 repository_url: https://github.com/MAAP-Project/gedi-subsetter.git
 docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.1.5
 disk_space: 20GB
-queue: maap-dps-worker-32gb
+queue: maap-dps-worker-32vcpu-64gb
 build_command: gedi-subsetter/bin/build-dps
 run_command: gedi-subsetter/bin/subset.sh
 inputs:
@@ -53,8 +53,8 @@ inputs:
       required: false
       default: all
     - name: limit
-      description: Maximum number of GEDI granule data files to download from the CMR,
-        regardless of the number of granules within the AOI.
+      description: Maximum number of GEDI granules to subset, regardless of the number
+        of granules within the spatio-temporal range.
       required: false
       default: "100_000"
     - name: output
@@ -63,11 +63,11 @@ inputs:
       required: false
       default: ""
     - name: s3fs_open_kwargs
-      description: 'Python literal dict to pass as keyword arguments to s3fs.open when
-        reading files from S3.  For example: {"block_size": 4194304, "cache_type": "all"}.
-        See https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open.'
+      description: JSON object representing keyword arguments to pass to
+        s3fs.S3FileSystem.open when reading files from S3.  See
+        https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open.
       required: false
-      default: ""
+      default: '{"cache_type": "all", "block_size": 8388608, "fill": true}'
     - name: processes
       description: Number of processes to use for parallel processing.  If not provided,
         defaults to the number of available CPUs.

From 1f20e508ae3b4f7472c30e6f3ac3e3c31ce5ab78 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Tue, 25 Jun 2024 13:08:31 -0400
Subject: [PATCH 07/11] Update usage doc and changelog

---
 CHANGELOG.md       |  43 +++++++++++++----
 docs/MAAP_USAGE.md | 116 ++++++++++++++++++++++++++++-----------------
 2 files changed, 106 insertions(+), 53 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 11128a0..4f7b6a1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,13 +9,34 @@ The format is based on [Keep a Changelog], and this project adheres to
 
 ### Changed
 
-- [#14](https://github.com/MAAP-Project/gedi-subsetter/issues/14) AWS S3
-  credentials are no longer obtained via the `maap-py` library.  Instead, they
-  are obtained via a role using the EC2 instance metadata.
-- [#72](https://github.com/MAAP-Project/gedi-subsetter/issues/72) Log messages
-  now use ISO 8601 UTC combined date and time representations with milliseconds.
-- [#54](https://github.com/MAAP-Project/gedi-subsetter/issues/54) Granule files
-  are no longer downloaded.  Instead, they are read directly from AWS S3.
+- Obtain AWS S3 credentials via a role using the EC2 instance metadata rather
+  than via the `maap-py` library
+  ([#14](https://github.com/MAAP-Project/gedi-subsetter/issues/14))
+- Log messages with timestamps in ISO 8601 UTC combined date and time
+  representations with milliseconds
+  ([#72](https://github.com/MAAP-Project/gedi-subsetter/issues/72))
+- Read granule files directly from AWS S3 instead of downloading them
+  ([#54](https://github.com/MAAP-Project/gedi-subsetter/issues/54))
+- Optimize AWS S3 read performance to provide ~10% speed improvement (on
+  average) over downloading files by tuning the `cache_type`, `block_size`, and
+  `fill` keyword arguments to the `s3fs.S3FileSystem.open` method
+  ([#77](https://github.com/MAAP-Project/gedi-subsetter/issues/77))
+- Set default granule `limit` to 100000.  Although this is not unlimited, it
+  effectively behaves as such because all of the supported GEDI collections have
+  fewer granules than this limit.
+  ([#69](https://github.com/MAAP-Project/gedi-subsetter/issues/69))
+- Set default job queue to `maap-dps-worker-32vcpu-64gb` to improve performance
+  by running on 32 CPUs
+  ([#78](https://github.com/MAAP-Project/gedi-subsetter/issues/78))
+
+### Added
+
+- Add `s3fs_open_kwargs` input to allow user to specify keyword arguments to the
+  `s3fs.S3FileSystem.open` method; see [MAAP_USAGE.md] for details.
+  ([#77](https://github.com/MAAP-Project/gedi-subsetter/issues/77))
+- Add `processes` input to allow user to specify the number of processes to use,
+  defaulting to the number of available CPUs
+  ([#77](https://github.com/MAAP-Project/gedi-subsetter/issues/77))
 
 ## 0.7.0 (2024-04-23)
 
@@ -144,8 +165,10 @@ The format is based on [Keep a Changelog], and this project adheres to
 [fine-grained error locations in tracebacks]:
   https://docs.python.org/3/whatsnew/3.11.html#whatsnew311-pep657
 [Keep a Changelog]:
-    https://keepachangelog.com/en/1.0.0/
+  https://keepachangelog.com/en/1.0.0/
 [Semantic Versioning]:
-    https://semver.org/spec/v2.0.0.html
+  https://semver.org/spec/v2.0.0.html
 [MAAP-Project/maap-documentation-examples]:
-    https://github.com/MAAP-Project/maap-documentation-examples
+  https://github.com/MAAP-Project/maap-documentation-examples
+[MAAP_USAGE.md]:
+  docs/MAAP_USAGE.md
diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md
index 083e859..7b78ab7 100644
--- a/docs/MAAP_USAGE.md
+++ b/docs/MAAP_USAGE.md
@@ -31,7 +31,8 @@ At a high level, the GEDI subsetting algorithm does the following:
 
 ## Algorithm Inputs
 
-To run a GEDI subsetting DPS job, you must supply the following inputs:
+To run a GEDI subsetting DPS job, there are a few required inputs and several
+optional inputs:
 
 - `aoi` (_required_): URL to a GeoJSON file representing your area of interest
   (see [Specifying an AOI](#specifying-an-aoi)).  This may contain multiple
@@ -41,16 +42,13 @@ To run a GEDI subsetting DPS job, you must supply the following inputs:
   include in the output file.  These names correspond to the _datasets_ (which
   might also be referred to as _variables_ or _layers_ in the DOI documentation)
   within the data files, and vary from collection to collection.  Consult the
-  documentation for a list of datasets available per collection (see
-  [Specifying a DOI](#specifying-a-doi) for documentation links).
+  documentation for each collection for a list of datasets available per
+  collection (see [Specifying a DOI](#specifying-a-doi) for documentation
+  links).
 
   In addition to the specified columns, the output file will also include a
   `filename` (`str`) column that includes the name of the original `h5` file.
 
-  _Changed in version 0.6.0_: The `beam` column is no longer automatically
-  included.  If you wish to include the `beam` column, you must specify it
-  explicitly in this `columns` value.
-
   **IMPORTANT:** To specify nested datasets (i.e., datasets _not_ at the top of
   a BEAM), you may use a path containing forward slashes (`/`) that is relative
   to the BEAM it appears within.  For example, if a BEAM contains a
@@ -58,6 +56,10 @@ To run a GEDI subsetting DPS job, you must supply the following inputs:
   `sensitivity_a2`, then you would refer to that nested dataset as
   `geolocation/sensitivity_a2`.
 
+  > _Changed in version 0.6.0_: The `beam` column is no longer automatically
+  > included.  If you wish to include the `beam` column, you must specify it
+  > explicitly in this `columns` value.
+
 - `query` (_optional_; default: no query, select all rows): Query expression for
   subsetting the rows in the output file.  This expression selects rows of data
   for which the expression is true.  Again, names in the expression are dataset
@@ -82,35 +84,45 @@ To run a GEDI subsetting DPS job, you must supply the following inputs:
   quality_flag == 1 and `geolocation/sensitivity_a2` > 0.95
   ```
 
-- `limit` (_optional_; default: 1_000): Maximum number of GEDI granule data
-  files to download from the CMR, among those that intersect the specified AOI's
-  bounding box, and fall within the specified temporal range (if supplied).
-
-  _Changed in version 0.6.0_: The default value was reduced from 10000 to 1000.
-  The AOI for most subsetting operations are likely to incur a request for well
-  under 1000 granules for downloading, so a larger default value might only lead
-  to longer CMR query times.
+- `limit` (_optional_; default: 100000): Maximum number of GEDI granule data
+  files to subset, among those that intersect the specified AOI's bounding box,
+  and fall within the specified temporal range (if supplied).  If there are more
+  granules within the spatio-temporal range, only the first `limit` number of
+  granules obtained from the corresponding CMR search are used.
+
+  > _Changed in version 0.6.0_: The default value was reduced from 10000 to 1000.
+  > The AOI for most subsetting operations are likely to incur a request for well
+  > under 1000 granules for downloading, so a larger default value might only lead
+  > to longer CMR query times.
+
+  > _Changed in version 0.8.0_: The default value was increased from 1000 to
+  > 100000 to avoid confusion in cases where a user does _not_ specify a limit,
+  > expecting to subset _all_ granules within the specified spatio-temporal
+  > range, but instead subsetting no more than the default limit of 1000, thus
+  > obtaining an unexpectedly incomplete result.  This new limit should
+  > effectively behave as if it were unlimited because all supported GEDI
+  > collections have fewer granules than this default limit.
 
 - `doi` (_required_): [Digital Object Identifier] (DOI) of the GEDI collection
   to subset, or a logical name representing such a DOI (see
   [Specifying a DOI](#specifying-a-doi))
 
-  _New in version 0.3.0_
+  > _Added in version 0.3.0_
 
-- `lat` (_required_): _Name_ of the dataset used for latitude.
+- `lat` (_required_): _Name_ of the dataset used for latitude values.
 
-  _New in version 0.3.0_
+  > _Added in version 0.3.0_
 
-- `lon` (_required_): _Name_ of the dataset used for longitude.
+- `lon` (_required_): _Name_ of the dataset used for longitude values.
 
-  _New in version 0.3.0_
+  > _Added in version 0.3.0_
 
 - `beams` (_optional_; default: `all`): Which beams to include in the subset.
   If supplied, must be one of logical names `all`, `coverage`, or `power`, _OR_
   a comma-separated list of specific beam names, with or without the `BEAM`
   prefix (e.g., `BEAM0000,BEAM0001` or `0000,0001`)
 
-  _New in version 0.4.0_
+  > _Added in version 0.4.0_
 
 - `temporal` (_optional_; default: full temporal range available): Temporal
   range to subset.  You may specify either a closed range, with start and end
@@ -118,7 +130,7 @@ To run a GEDI subsetting DPS job, you must supply the following inputs:
   full details on the valid formats, see the NASA CMR's documentation on
   [temporal range searches](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html#temporal-range-searches).
 
-  _New in version 0.6.0_
+  > _Added in version 0.6.0_
 
 - `output` (_optional_): Name to use for the output file.  This can also include
   a path, which will be relative to the standard DPS output directory for a job.
@@ -139,35 +151,51 @@ To run a GEDI subsetting DPS job, you must supply the following inputs:
   - `myoutput.h5` -> `myoutput.gpkg`
   - `mypath/myoutput` -> `mypath/myoutput.gpkg`
 
-  _New in version 0.6.0_
+  > _Added in version 0.6.0_
+
+- `s3fs_open_kwargs` (_optional_; default:
+  `'{"cache_type": "all", "block_size": 8388608, "fill": true}'`): JSON string
+  to pass as keyword arguments to [s3fs.S3FileSystem.open] when reading granule
+  files from S3.  The default value was chosen to provide optimal speed, after
+  conducting performance profiling for various combinations of possible values,
+  so it should be unnecessary to supply this input.
 
-- `scalene_args` (_optional_): Arguments to pass to [Scalene] for performance
-  profiling.  Normal usage should leave this argument blank.
+  > _Added in version 0.8.0_
 
-  Fill this in if you want to collect performance metrics (i.e.  CPU and RAM
-  usage).  The recommended value for this input is `--reduced-profile` (see
-  below for more advanced usage).  When used, you will find `profile.html` in
-  your algorithm output folder.
+- `processes` (_optional_; default: number of available CPUs): Number of
+  processes to use for parallel processing.
+
+  > _Added in version 0.8.0_
+
+- `scalene_args` (_optional_; default: none): Arguments to pass to [Scalene] for
+  performance profiling.  Normal usage should leave this argument blank, meaning
+  that Scalene will _not_ be used.
 
   When this input is supplied, the algorithm will be run via the `scalene`
-  command, and the value of this input will be passed as arguments to the
-  command.  For a list of the available command-line options, see
+  command for collecting performance metrics (i.e.  CPU and RAM usage), and the
+  value of this input will be passed as arguments to the command.  For a list of
+  available command-line options, see
   <https://github.com/plasma-umass/scalene?tab=readme-ov-file#scalene>.
 
-  Starting with `--reduced-profile` produces a relatively brief report that may
-  aid in more quickly identifying hotspots than a full profile would.  However,
-  to produce a full profile where you want to use all of Scalene's default
-  values, you must supply _some_ value for this input, so the simplest valid
-  Scalene option is `--on`.  Otherwise, as mentioned above, when no value is
-  supplied for this input, Scalene will not be used at all.
+  By default, the name of the profile output file is `profile.html` (placed in
+  your job's output folder).  If you specify the `--json` flag, it will be named
+  `profile.json`.  If you specify the `--cli` flag, it will be named
+  `profile.txt`.
+
+  If you want to use all of Scalene's default values (i.e.  not specify any
+  override values), you cannot leave this input blank, otherwise Scalene will
+  not be used at all (as mentioned above).  In this case, you must supply _some_
+  value for this input, so the simplest valid Scalene option is `--on`.
+
+  **Note:** Since no browser is available in DPS, when any value is supplied for
+  this input, the `--no-browser` option will be included to prevent Scalene from
+  attempting to open a browser.
 
-  > **Note:** Since no browser is available in DPS, when any value is
-  > supplied for this input, the `--no-browser` option will be included to
-  > prevent Scalene from attempting to open a browser.  However, the `--web`
-  > option will also be included, which will produce HTML output to a file named
-  > `profile.html`.
+  > _Added in version 0.7.0_
 
-  _New in version 0.7.0_
+  > _Changed in version 0.8.0_: Specifying the `--json` flag changes the name of
+  > the profile output file to `profile.json` and specifying `--cli` changes it
+  > to `profile.txt`.
 
 ### Specifying an AOI
 
@@ -463,3 +491,5 @@ administrative boundaries.  PLoS ONE 15(4): e0231866.
   https://www.geoboundaries.org/api.html
 [Scalene]:
   https://github.com/plasma-umass/scalene
+[s3fs.S3FileSystem.open]:
+  https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open

From 5fd3433493802e0aba8e72737185650a4b4523cf Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Fri, 28 Jun 2024 19:03:53 -0400
Subject: [PATCH 08/11] Upgrade s3fs to version with cache stats

---
 conda-lock.yml            | 5226 +++++++++++++++++++------------------
 environment.yml           |    2 +-
 src/gedi_subset/subset.py |    9 +-
 3 files changed, 2703 insertions(+), 2534 deletions(-)

diff --git a/conda-lock.yml b/conda-lock.yml
index f9804e8..e216090 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -15,9 +15,9 @@
 version: 1
 metadata:
   content_hash:
-    linux-64: dd32ff7f4b18fe2421677c430b28a1b488a36635e70638bf3dd60ded3fd95b2d
-    osx-64: 5b5a70d458f34e28a4c7c5552ff8d11b44eaf72be6ad91e3af68bb895a632751
-    osx-arm64: d131dcf1b3882514580e58daac9e328d9b0497c3185e5ceac37eec85ad219643
+    linux-64: cfc05d4f35432e186dc1f491a88ecc8b65aa0b60431c23b7a47265ce97cc8020
+    osx-64: 214b44d82d275e379fd22b71f033e5c8db994d3890f3f8000d639578b6028d9a
+    osx-arm64: c7fcb0ada1be94e9b00e03ddbc71079ab770da28a86617bcd396c695b16ef7ad
   channels:
   - url: conda-forge
     used_env_vars: []
@@ -92,51 +92,51 @@ package:
   category: dev
   optional: true
 - name: aiobotocore
-  version: 2.12.3
+  version: 2.13.1
   manager: conda
   platform: linux-64
   dependencies:
-    aiohttp: '>=3.7.4.post0,<4.0.0'
+    aiohttp: '>=3.9.2,<4.0.0'
     aioitertools: '>=0.5.1,<1.0.0'
-    botocore: '>=1.34.41,<1.34.70'
-    python: '>=3.11,<3.12.0a0'
+    botocore: '>=1.34.70,<1.34.132'
+    python: '>=3.8'
     wrapt: '>=1.10.10,<2.0.0'
-  url: https://repo.anaconda.com/pkgs/main/linux-64/aiobotocore-2.12.3-py311h06a4308_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/aiobotocore-2.13.1-pyhd8ed1ab_0.conda
   hash:
-    md5: 6fc6216ad68ce98048f300b60dc57f59
-    sha256: e04e2fd6d3259330a50ef1e413c19ed8a94a41bdb6325c68fd79947781561bc9
+    md5: 64ebb883a6c94f2a18aafedecc215351
+    sha256: 8eacb10e5877fb743d75ae2c50eaaa89ece85479e557e693db8275bd96740ef3
   category: main
   optional: false
 - name: aiobotocore
-  version: 2.12.3
+  version: 2.13.1
   manager: conda
   platform: osx-64
   dependencies:
-    aiohttp: '>=3.7.4.post0,<4.0.0'
+    aiohttp: '>=3.9.2,<4.0.0'
     aioitertools: '>=0.5.1,<1.0.0'
-    botocore: '>=1.34.41,<1.34.70'
-    python: '>=3.11,<3.12.0a0'
+    botocore: '>=1.34.70,<1.34.132'
+    python: '>=3.8'
     wrapt: '>=1.10.10,<2.0.0'
-  url: https://repo.anaconda.com/pkgs/main/osx-64/aiobotocore-2.12.3-py311hecd8cb5_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/aiobotocore-2.13.1-pyhd8ed1ab_0.conda
   hash:
-    md5: c3e5c71b60197dbaf34e4d2152aa1361
-    sha256: 53a6c8646dc6da425cd93d46e83e33f3592b084881e041bd1e714cba6c700a94
+    md5: 64ebb883a6c94f2a18aafedecc215351
+    sha256: 8eacb10e5877fb743d75ae2c50eaaa89ece85479e557e693db8275bd96740ef3
   category: main
   optional: false
 - name: aiobotocore
-  version: 2.12.3
+  version: 2.13.1
   manager: conda
   platform: osx-arm64
   dependencies:
-    aiohttp: '>=3.7.4.post0,<4.0.0'
+    aiohttp: '>=3.9.2,<4.0.0'
     aioitertools: '>=0.5.1,<1.0.0'
-    botocore: '>=1.34.41,<1.34.70'
-    python: '>=3.11,<3.12.0a0'
+    botocore: '>=1.34.70,<1.34.132'
+    python: '>=3.8'
     wrapt: '>=1.10.10,<2.0.0'
-  url: https://repo.anaconda.com/pkgs/main/osx-arm64/aiobotocore-2.12.3-py311hca03da5_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/aiobotocore-2.13.1-pyhd8ed1ab_0.conda
   hash:
-    md5: 78b5240f7363dc1a62c2c214a32b6be9
-    sha256: 3cd836bada2aa9405360a2815e3aad9075a5228eabb59fdc7fb853d958afa743
+    md5: 64ebb883a6c94f2a18aafedecc215351
+    sha256: 8eacb10e5877fb743d75ae2c50eaaa89ece85479e557e693db8275bd96740ef3
   category: main
   optional: false
 - name: aiohttp
@@ -273,42 +273,42 @@ package:
   category: main
   optional: false
 - name: annotated-types
-  version: 0.6.0
+  version: 0.7.0
   manager: conda
   platform: linux-64
   dependencies:
     python: '>=3.7'
     typing-extensions: '>=4.0.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.6.0-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_0.conda
   hash:
-    md5: 997c29372bdbe2afee073dff71f35923
-    sha256: 3a2c98154d95cfd54daba6b7d507d31f5ba07ac2ad955c44eb041b66563193cd
+    md5: 7e9f4612544c8edbfd6afad17f1bd045
+    sha256: 668f0825b6c18e4012ca24a0070562b6ec801ebc7008228a428eb52b4038873f
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     python: '>=3.8'
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+    zstd: '>=1.5.6,<1.6.0a0'
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+    md5: 3ac9ef8975965f9698dbedd2a4cc5894
+    sha256: 41bd5fef28b2755d637e3a8ea5c84010628392fbcf80c7e3d7370aaced7ee4fe
   category: main
   optional: false
 - name: zlib
-  version: 1.2.13
+  version: 1.3.1
   manager: conda
   platform: osx-arm64
   dependencies:
-    libzlib: 1.2.13
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.2.13-h53f4e23_5.conda
+    __osx: '>=11.0'
+    libzlib: 1.3.1
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.1-hfb2fe0b_1.conda
   hash:
-    md5: a08383f223b10b71492d27566fafbf6c
-    sha256: de0ee1e24aa6867058d3b852a15c8d7f49f262f5828772700c647186d4a96bbe
+    md5: f27e021db7862b6ddbc1d3578f10d883
+    sha256: 87360c2dc662916aac37cf01e53324b4f4f78db6f399220818076752b093ede5
   category: main
   optional: false
 - name: zstandard
-  version: 0.19.0
+  version: 0.22.0
   manager: conda
   platform: linux-64
   dependencies:
-    cffi: '>=1.8'
+    cffi: '>=1.11'
     libgcc-ng: '>=12'
     python: '>=3.11,<3.12.0a0'
     python_abi: 3.11.*
-  url: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.19.0-py311hd4cff14_0.tar.bz2
+    zstd: '>=1.5.6,<1.6.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.22.0-py311hb6f056b_1.conda
   hash:
-    md5: 056b3271f46abaa4673c8c6783283a07
-    sha256: 8aac43cc4fbdcc420fe8a22c764b67f6ac9168b103bfd10d79a82b748304ddf6
+    md5: 72e84ef20a510ab5fca1f3d80a16e9e2
+    sha256: 9980740f9b5f9028288c71b750d6a6691d0676ae50db97866d9ee34ab51e8b16
   category: main
   optional: false
 - name: zstandard
-  version: 0.19.0
+  version: 0.22.0
   manager: conda
   platform: osx-64
   dependencies:
-    cffi: '>=1.8'
+    __osx: '>=10.13'
+    cffi: '>=1.11'
     python: '>=3.11,<3.12.0a0'
     python_abi: 3.11.*
-  url: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.19.0-py311h5547dcb_0.tar.bz2
+    zstd: '>=1.5.6,<1.6.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.22.0-py311h51fa951_1.conda
   hash:
-    md5: 96e4e2aa960398abbe5c4a6cf22269b8
-    sha256: b470229c05df4d96d27904def00660b5dfa7ad57bf2b9dfd826325233f9e8510
+    md5: d6c3e7fc0b4eb316556974d0381d9cc7
+    sha256: cc6e7268e2a22b32bb14ff00786e69d113fff043916705c4671c26613d29973f
   category: main
   optional: false
 - name: zstandard
-  version: 0.19.0
+  version: 0.22.0
   manager: conda
   platform: osx-arm64
   dependencies:
-    cffi: '>=1.8'
+    __osx: '>=11.0'
+    cffi: '>=1.11'
     python: '>=3.11,<3.12.0a0'
     python_abi: 3.11.*
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.19.0-py311he2be06e_0.tar.bz2
+    zstd: '>=1.5.6,<1.6.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.22.0-py311h4a6b76e_1.conda
   hash:
-    md5: ece21cb47a93c985aa4b44219c4c8c8b
-    sha256: 43eaee70cd406468d96d1643b75d16e0da3955a9c1d37056767134b91b61d515
+    md5: 34b2bd2270fd11f9926e0498c0c87a05
+    sha256: b7b86382936a604d58af2706933c743c124bd9078054e13e6b76d57807596613
   category: main
   optional: false
 - name: zstd
@@ -18311,7 +18477,7 @@ package:
   dependencies:
     libgcc-ng: '>=12'
     libstdcxx-ng: '>=12'
-    libzlib: '>=1.2.13,<1.3.0a0'
+    libzlib: '>=1.2.13,<2.0.0a0'
   url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
   hash:
     md5: 4d056880988120e29d75bfff282e0f45
@@ -18324,7 +18490,7 @@ package:
   platform: osx-64
   dependencies:
     __osx: '>=10.9'
-    libzlib: '>=1.2.13,<1.3.0a0'
+    libzlib: '>=1.2.13,<2.0.0a0'
   url: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
   hash:
     md5: 4cb2cd56f039b129bb0e491c1164167e
@@ -18337,7 +18503,7 @@ package:
   platform: osx-arm64
   dependencies:
     __osx: '>=11.0'
-    libzlib: '>=1.2.13,<1.3.0a0'
+    libzlib: '>=1.2.13,<2.0.0a0'
   url: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda
   hash:
     md5: d96942c06c3e84bfcc5efb038724a7fd
diff --git a/environment.yml b/environment.yml
index a6b4dd9..a923166 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,7 +23,7 @@ dependencies:
   - pyarrow~=14.0  # parquet support in pandas
   - pydantic~=2.0
   - returns~=0.20
-  - s3fs~=2024.3
+  - s3fs~=2024.6
   - scalene~=1.5  # CPU+mem profiling
   - shapely~=2.0
   - typer~=0.9  # CLI
diff --git a/src/gedi_subset/subset.py b/src/gedi_subset/subset.py
index f0b52a2..d224840 100755
--- a/src/gedi_subset/subset.py
+++ b/src/gedi_subset/subset.py
@@ -20,9 +20,9 @@
     Tuple,
 )
 
+import fsspec
 import geopandas as gpd
 import h5py
-import s3fs
 import typer
 from maap.maap import MAAP
 from maap.Result import Collection, Granule
@@ -79,7 +79,7 @@ class SubsetGranuleProps:
     single argument.
     """
 
-    fs: s3fs.S3FileSystem | None = None
+    fs: fsspec.AbstractFileSystem | None = None
     s3fs_open_kwargs: Mapping[str, Any] = field(default_factory=dict)
     granule: Granule
     maap: MAAP
@@ -174,7 +174,7 @@ def subset_granule(props: SubsetGranuleProps) -> IOResultE[Maybe[str]]:
         return IOSuccess(Nothing)
 
     logger.debug(f"Subsetting {inpath}")
-    fs = props.fs or s3fs.S3FileSystem()
+    fs = props.fs or fsspec
     s3fs_open_kwargs = {
         "cache_type": "all",
         "block_size": 8 * 1024 * 1024,
@@ -197,6 +197,9 @@ def subset_granule(props: SubsetGranuleProps) -> IOResultE[Maybe[str]]:
                 columns=props.columns,
                 query=props.query,
             )
+
+            if isinstance(f, fsspec.spec.AbstractBufferedFile):
+                logger.debug(f"{f.cache!r}")
     except Exception as e:
         granule_ur = props.granule["Granule"]["GranuleUR"]
         logger.warning(f"Skipping granule {granule_ur} [failed to read {inpath}: {e}]")

From 350a11327d4156fd5be307da28e5d7bbd104fcca Mon Sep 17 00:00:00 2001
From: Chuck Daniels <cjdaniels4@gmail.com>
Date: Wed, 3 Jul 2024 10:53:34 -0400
Subject: [PATCH 09/11] Directly import fsspec, not s3fs

---
 .gitignore                | 24 ++++++++++++
 .vscode/settings.json     | 14 -------
 CHANGELOG.md              |  9 +++--
 algorithm_config.yaml     | 10 ++---
 conda-lock.yml            | 82 +++++++++++++++++++--------------------
 docs/MAAP_USAGE.md        | 25 ++++++------
 environment.yml           | 17 ++++----
 pyproject.toml            |  1 +
 src/gedi_subset/subset.py | 30 +++++++-------
 tests/test_subset.py      | 22 ++++-------
 10 files changed, 120 insertions(+), 114 deletions(-)
 delete mode 100644 .vscode/settings.json

diff --git a/.gitignore b/.gitignore
index 553fe07..0c88bde 100644
--- a/.gitignore
+++ b/.gitignore
@@ -134,3 +134,27 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode
+
+### VisualStudioCode ###
+.vscode/*
+#!.vscode/settings.json
+#!.vscode/tasks.json
+#!.vscode/launch.json
+#!.vscode/extensions.json
+#!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode
diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index 391d878..0000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "python.analysis.stubPath": "./gedi-subset/typings",
-    "python.analysis.extraPaths": [
-        "./gedi-subset/src"
-    ],
-    "mypy-type-checker.importStrategy": "fromEnvironment",
-    "mypy-type-checker.preferDaemon": true,
-    "mypy-type-checker.reportingScope": "workspace",
-    "editor.formatOnSave": true,
-    "editor.defaultFormatter": "ms-python.black-formatter",
-    "[shellscript]": {
-        "editor.defaultFormatter": "foxundermoon.shell-format"
-    }
-}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4f7b6a1..07a3ba3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,8 +18,9 @@ The format is based on [Keep a Changelog], and this project adheres to
 - Read granule files directly from AWS S3 instead of downloading them
   ([#54](https://github.com/MAAP-Project/gedi-subsetter/issues/54))
 - Optimize AWS S3 read performance to provide ~10% speed improvement (on
-  average) over downloading files by tuning the `cache_type`, `block_size`, and
-  `fill` keyword arguments to the `s3fs.S3FileSystem.open` method
+  average) over downloading files by tuning the `default_cache_type`,
+  `default_block_size`, and `default_fill_cache` keyword arguments to the
+  `fsspec.url_to_fs` function
   ([#77](https://github.com/MAAP-Project/gedi-subsetter/issues/77))
 - Set default granule `limit` to 100000.  Although this is not unlimited, it
   effectively behaves as such because all of the supported GEDI collections have
@@ -31,8 +32,8 @@ The format is based on [Keep a Changelog], and this project adheres to
 
 ### Added
 
-- Add `s3fs_open_kwargs` input to allow user to specify keyword arguments to the
-  `s3fs.S3FileSystem.open` method; see [MAAP_USAGE.md] for details.
+- Add `fsspec_kwargs` input to allow user to specify keyword arguments to the
+  `fsspec.url_to_fs` method; see [MAAP_USAGE.md] for details.
   ([#77](https://github.com/MAAP-Project/gedi-subsetter/issues/77))
 - Add `processes` input to allow user to specify the number of processes to use,
   defaulting to the number of available CPUs
diff --git a/algorithm_config.yaml b/algorithm_config.yaml
index 724b3dd..f7113c4 100644
--- a/algorithm_config.yaml
+++ b/algorithm_config.yaml
@@ -62,12 +62,12 @@ inputs:
         using the AOI file name (without the extension) with the suffix "_subset.gpkg".
       required: false
       default: ""
-    - name: s3fs_open_kwargs
-      description: JSON object representing keyword arguments to pass to
-        s3fs.S3FileSystem.open when reading files from S3.  See
-        https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open.
+    - name: fsspec_kwargs
+      description: "JSON object representing keyword arguments to pass to the
+        fsspec.core.url_to_fs function when reading granule data files.  See
+        https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.core.url_to_fs."
       required: false
-      default: '{"cache_type": "all", "block_size": 8388608, "fill": true}'
+      default: '{"default_cache_type": "all", "default_block_size": 8388608}'
     - name: processes
       description: Number of processes to use for parallel processing.  If not provided,
         defaults to the number of available CPUs.
diff --git a/conda-lock.yml b/conda-lock.yml
index e216090..fd06a8a 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -5,9 +5,9 @@
 # available, unless you explicitly update the lock file.
 #
 # Install this environment as "YOURENV" with:
-#     conda-lock install -n YOURENV conda-lock.yml
+#     conda-lock install -n YOURENV --file conda-lock.yml
 # This lock contains optional development dependencies. Include them in the installed environment with:
-#     conda-lock install --dev-dependencies -n YOURENV conda-lock.yml
+#     conda-lock install --dev-dependencies -n YOURENV --file conda-lock.yml
 # To update a single package to the latest version compatible with the version constraints in the source:
 #     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
 # To re-solve the entire environment, e.g. after changing a version constraint in the source file:
@@ -1740,53 +1740,53 @@ package:
   category: main
   optional: false
 - name: boto3-stubs
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: linux-64
   dependencies:
     boto3: ''
     python: ''
     typing_extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.135-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.136-pyhd8ed1ab_0.conda
   hash:
-    md5: e8668d449763f1e91f400e654ccac114
-    sha256: 2e455588d6358dbc8b83fae092edc18541e14398876ed92a8bb9bd52169f4fc4
+    md5: 26d6ab84e689a1f9009829361c84fff5
+    sha256: e888390282d6f5334e1dbe77500c10d4bfa7d9cc8c85081dd12d6f7c6faa967b
   category: dev
   optional: true
 - name: boto3-stubs
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: osx-64
   dependencies:
     boto3: ''
     python: ''
     typing_extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.135-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.136-pyhd8ed1ab_0.conda
   hash:
-    md5: e8668d449763f1e91f400e654ccac114
-    sha256: 2e455588d6358dbc8b83fae092edc18541e14398876ed92a8bb9bd52169f4fc4
+    md5: 26d6ab84e689a1f9009829361c84fff5
+    sha256: e888390282d6f5334e1dbe77500c10d4bfa7d9cc8c85081dd12d6f7c6faa967b
   category: dev
   optional: true
 - name: boto3-stubs
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: osx-arm64
   dependencies:
     boto3: ''
     python: ''
     typing_extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.135-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.136-pyhd8ed1ab_0.conda
   hash:
-    md5: e8668d449763f1e91f400e654ccac114
-    sha256: 2e455588d6358dbc8b83fae092edc18541e14398876ed92a8bb9bd52169f4fc4
+    md5: 26d6ab84e689a1f9009829361c84fff5
+    sha256: e888390282d6f5334e1dbe77500c10d4bfa7d9cc8c85081dd12d6f7c6faa967b
   category: dev
   optional: true
 - name: boto3-stubs-essential
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: linux-64
   dependencies:
-    boto3-stubs: 1.34.135
+    boto3-stubs: 1.34.136
     mypy-boto3-s3: ''
     mypy_boto3_cloudformation: ''
     mypy_boto3_dynamodb: ''
@@ -1794,18 +1794,18 @@ package:
     mypy_boto3_lambda: ''
     mypy_boto3_rds: ''
     mypy_boto3_sqs: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.135-hd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.136-hd8ed1ab_0.conda
   hash:
-    md5: 7252c9f0819769faea98b88d08ad5313
-    sha256: e70791c81cc48980a3db1f264beda9238b8eda3c651f40c89750dde153dfd537
+    md5: 78f5a7c53b27388e150dff4d23c74806
+    sha256: 4c6629b759ed226b817b6f319b3d85506fad601da50d1675a037257110e74042
   category: dev
   optional: true
 - name: boto3-stubs-essential
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: osx-64
   dependencies:
-    boto3-stubs: 1.34.135
+    boto3-stubs: 1.34.136
     mypy-boto3-s3: ''
     mypy_boto3_cloudformation: ''
     mypy_boto3_dynamodb: ''
@@ -1813,18 +1813,18 @@ package:
     mypy_boto3_lambda: ''
     mypy_boto3_rds: ''
     mypy_boto3_sqs: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.135-hd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.136-hd8ed1ab_0.conda
   hash:
-    md5: 7252c9f0819769faea98b88d08ad5313
-    sha256: e70791c81cc48980a3db1f264beda9238b8eda3c651f40c89750dde153dfd537
+    md5: 78f5a7c53b27388e150dff4d23c74806
+    sha256: 4c6629b759ed226b817b6f319b3d85506fad601da50d1675a037257110e74042
   category: dev
   optional: true
 - name: boto3-stubs-essential
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: osx-arm64
   dependencies:
-    boto3-stubs: 1.34.135
+    boto3-stubs: 1.34.136
     mypy-boto3-s3: ''
     mypy_boto3_cloudformation: ''
     mypy_boto3_dynamodb: ''
@@ -1832,10 +1832,10 @@ package:
     mypy_boto3_lambda: ''
     mypy_boto3_rds: ''
     mypy_boto3_sqs: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.135-hd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.136-hd8ed1ab_0.conda
   hash:
-    md5: 7252c9f0819769faea98b88d08ad5313
-    sha256: e70791c81cc48980a3db1f264beda9238b8eda3c651f40c89750dde153dfd537
+    md5: 78f5a7c53b27388e150dff4d23c74806
+    sha256: 4c6629b759ed226b817b6f319b3d85506fad601da50d1675a037257110e74042
   category: dev
   optional: true
 - name: botocore
@@ -1884,45 +1884,45 @@ package:
   category: main
   optional: false
 - name: botocore-stubs
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: linux-64
   dependencies:
     python: '>=3.8,<4.0'
     types-awscrt: ''
     typing_extensions: '>=4.1.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.135-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.136-pyhd8ed1ab_0.conda
   hash:
-    md5: 6ac67bb969054466e4047fa630a53f47
-    sha256: 77a71f86e2cb7cb42007aa58ec8a8f1b3a7279e1212b16a50a9cf63ce4646bfb
+    md5: e799bd0a8d9b687e60f7ab9ba6248144
+    sha256: 68ec2fc18144aa58520e8f59a29a8137f1d4c0c445fcac95763e5dd4fffa15de
   category: dev
   optional: true
 - name: botocore-stubs
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: osx-64
   dependencies:
     python: '>=3.8,<4.0'
     types-awscrt: ''
     typing_extensions: '>=4.1.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.135-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.136-pyhd8ed1ab_0.conda
   hash:
-    md5: 6ac67bb969054466e4047fa630a53f47
-    sha256: 77a71f86e2cb7cb42007aa58ec8a8f1b3a7279e1212b16a50a9cf63ce4646bfb
+    md5: e799bd0a8d9b687e60f7ab9ba6248144
+    sha256: 68ec2fc18144aa58520e8f59a29a8137f1d4c0c445fcac95763e5dd4fffa15de
   category: dev
   optional: true
 - name: botocore-stubs
-  version: 1.34.135
+  version: 1.34.136
   manager: conda
   platform: osx-arm64
   dependencies:
     python: '>=3.8,<4.0'
     types-awscrt: ''
     typing_extensions: '>=4.1.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.135-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.136-pyhd8ed1ab_0.conda
   hash:
-    md5: 6ac67bb969054466e4047fa630a53f47
-    sha256: 77a71f86e2cb7cb42007aa58ec8a8f1b3a7279e1212b16a50a9cf63ce4646bfb
+    md5: e799bd0a8d9b687e60f7ab9ba6248144
+    sha256: 68ec2fc18144aa58520e8f59a29a8137f1d4c0c445fcac95763e5dd4fffa15de
   category: dev
   optional: true
 - name: bottleneck
diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md
index 7b78ab7..eeb3af8 100644
--- a/docs/MAAP_USAGE.md
+++ b/docs/MAAP_USAGE.md
@@ -153,23 +153,26 @@ optional inputs:
 
   > _Added in version 0.6.0_
 
-- `s3fs_open_kwargs` (_optional_; default:
-  `'{"cache_type": "all", "block_size": 8388608, "fill": true}'`): JSON string
-  to pass as keyword arguments to [s3fs.S3FileSystem.open] when reading granule
-  files from S3.  The default value was chosen to provide optimal speed, after
-  conducting performance profiling for various combinations of possible values,
-  so it should be unnecessary to supply this input.
+- `fsspec_kwargs` (_optional_; default:
+  `'{"default_cache_type": "all", "default_block_size": 8388608`): JSON object
+  representing keyword arguments to pass to the [fsspec.url_to_fs] function when
+  reading granule files.  **ADVANCED:** Normal usage should leave this input
+  blank, meaning that the default value will be used, which prioritizes
+  algorithm speed over minimizing data transfer volume.
 
   > _Added in version 0.8.0_
 
 - `processes` (_optional_; default: number of available CPUs): Number of
-  processes to use for parallel processing.
+  processes to use for parallel processing.  **ADVANCED:** Normal usage should
+  leave this input blank, meaning that the algorithm will use all available
+  CPUs.  This input is intended only for performance profiling purposes.
 
   > _Added in version 0.8.0_
 
 - `scalene_args` (_optional_; default: none): Arguments to pass to [Scalene] for
-  performance profiling.  Normal usage should leave this argument blank, meaning
-  that Scalene will _not_ be used.
+  performance profiling.  **ADVANCED:** Normal usage should leave this argument
+  blank, meaning that Scalene will _not_ be used.  This input is intended only
+  for performance profiling purposes.
 
   When this input is supplied, the algorithm will be run via the `scalene`
   command for collecting performance metrics (i.e.  CPU and RAM usage), and the
@@ -485,11 +488,11 @@ administrative boundaries.  PLoS ONE 15(4): e0231866.
 
 [Digital Object Identifier]:
    https://doi.org
+[fsspec.url_to_fs]:
+  https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.core.url_to_fs."
 [geoBoundaries]:
   https://www.geoboundaries.org
 [geoBoundaries API]:
   https://www.geoboundaries.org/api.html
 [Scalene]:
   https://github.com/plasma-umass/scalene
-[s3fs.S3FileSystem.open]:
-  https://filesystem-spec.readthedocs.io/en/latest/api.html#s3fs.S3FileSystem.open
diff --git a/environment.yml b/environment.yml
index a923166..171ad6e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,26 +10,27 @@ dependencies:
   - python~=3.11.0
 
   - boto3~=1.33
-  - bottleneck~=1.3  # pandas performance
+  - bottleneck~=1.3 # pandas performance
   - cachetools~=5.3
   - conda~=24.0
   - conda-lock~=2.0
+  - fsspec~=2024.6 # keep in sync w/s3fs version
   - geopandas~=0.14
   - h5py~=3.9
-  - numba~=0.56  # pandas performance
-  - numexpr~=2.8  # pandas performance
+  - numba~=0.56 # pandas performance
+  - numexpr~=2.8 # pandas performance
   - pandas~=2.0
   - pip~=23.1
-  - pyarrow~=14.0  # parquet support in pandas
+  - pyarrow~=14.0 # parquet support in pandas
   - pydantic~=2.0
   - returns~=0.20
-  - s3fs~=2024.6
-  - scalene~=1.5  # CPU+mem profiling
+  - s3fs~=2024.6 # keep in sync w/fsspec
+  - scalene~=1.5 # CPU+mem profiling
   - shapely~=2.0
-  - typer~=0.9  # CLI
+  - typer~=0.9 # CLI
 
   - pip:
-    - git+https://github.com/MAAP-Project/maap-py.git@v3.1.5
+      - git+https://github.com/MAAP-Project/maap-py.git@v3.1.5
 
 platforms:
   - linux-64
diff --git a/pyproject.toml b/pyproject.toml
index 44dceab..bc208ff 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,6 +37,7 @@ warn_unused_ignores = true
 
 [[tool.mypy.overrides]]
 module = [
+  "fsspec",
   "geopandas",
   "h5py",
   "moto",
diff --git a/src/gedi_subset/subset.py b/src/gedi_subset/subset.py
index d224840..01c06d1 100755
--- a/src/gedi_subset/subset.py
+++ b/src/gedi_subset/subset.py
@@ -79,8 +79,7 @@ class SubsetGranuleProps:
     single argument.
     """
 
-    fs: fsspec.AbstractFileSystem | None = None
-    s3fs_open_kwargs: Mapping[str, Any] = field(default_factory=dict)
+    fsspec_kwargs: Mapping[str, Any] = field(default_factory=dict)
     granule: Granule
     maap: MAAP
     aoi_gdf: gpd.GeoDataFrame
@@ -174,20 +173,17 @@ def subset_granule(props: SubsetGranuleProps) -> IOResultE[Maybe[str]]:
         return IOSuccess(Nothing)
 
     logger.debug(f"Subsetting {inpath}")
-    fs = props.fs or fsspec
-    s3fs_open_kwargs = {
-        "cache_type": "all",
-        "block_size": 8 * 1024 * 1024,
-        "fill": True,
+    fsspec_kwargs = {
+        "default_cache_type": "all",
+        "default_block_size": 8 * 1024 * 1024,
+        "default_fill_cache": True,
         # Allow the caller to override the default values above.
-        **props.s3fs_open_kwargs,
-        # Force the use of the "rb" mode.  We don't want to allow the mode
-        # to be set by user input.
-        "mode": "rb",
+        **props.fsspec_kwargs,
     }
+    fs, urlpath = fsspec.url_to_fs(inpath, **fsspec_kwargs)
 
     try:
-        with fs.open(inpath, **s3fs_open_kwargs) as f, h5py.File(f) as hdf5:
+        with fs.open(urlpath, mode="rb") as f, h5py.File(f) as hdf5:
             gdf = subset_hdf5(
                 hdf5,
                 aoi=props.aoi_gdf,
@@ -237,7 +233,7 @@ def subset_granules(
     dest: Path,
     init_args: Tuple[Any, ...],
     granules: Iterable[Granule],
-    s3fs_open_kwargs: Optional[Mapping[str, Any]] = None,
+    fsspec_kwargs: Optional[Mapping[str, Any]] = None,
     processes: Optional[int] = None,
 ) -> IOResultE[Tuple[str, ...]]:
     def subset_saved(path: IOResultE[Maybe[str]]) -> bool:
@@ -274,7 +270,7 @@ def append_subset(src: str) -> IOResultE[str]:
 
     payloads = (
         SubsetGranuleProps(
-            s3fs_open_kwargs=s3fs_open_kwargs or {},
+            fsspec_kwargs=fsspec_kwargs or {},
             granule=granule,
             maap=maap,
             aoi_gdf=aoi_gdf,
@@ -393,13 +389,13 @@ def main(
         ),
     ] = None,
     verbose: Annotated[bool, typer.Option(help="Provide verbose output")] = False,
-    s3fs_open_kwargs: Annotated[
+    fsspec_kwargs: Annotated[
         Optional[dict[str, Any]],
         typer.Option(
             parser=lambda value: json.loads(value) if isinstance(value, str) else value,
             metavar="JSON",
             help=(
-                "Keyword arguments (as JSON) to pass to S3FileSystem.open"
+                "Keyword arguments (as JSON object) to pass to fsspec.url_to_fs"
                 " for reading HDF5 files"
             ),
         ),
@@ -456,7 +452,7 @@ def main(
             dest,
             (logging_level,),
             fp.filter(granule_intersects(aoi_gdf.unary_union))(granules),
-            s3fs_open_kwargs,
+            fsspec_kwargs,
             processes,
         )
     ).bind_ioresult(
diff --git a/tests/test_subset.py b/tests/test_subset.py
index 8bc121b..862618f 100644
--- a/tests/test_subset.py
+++ b/tests/test_subset.py
@@ -12,7 +12,6 @@
 from mypy_boto3_s3.client import S3Client
 from returns.io import IOSuccess
 from returns.maybe import Some
-from s3fs import S3FileSystem
 from typer import BadParameter
 
 from gedi_subset.subset import SubsetGranuleProps, check_beams_option, subset_granule
@@ -39,22 +38,17 @@ def reset_s3_fixture():
     requests.post(f"{endpoint_uri}/moto-api/reset")
 
 
-@pytest.fixture()
-def fs(moto_server, h5_path: str):
+def test_subset_granule(
+    moto_server,
+    h5_path: str,
+    maap: MAAP,
+    aoi_gdf: gpd.GeoDataFrame,
+    tmp_path: Path,
+):
     client = cast(S3Client, Session().create_client("s3", endpoint_url=endpoint_uri))
     client.create_bucket(Bucket="mybucket")
     client.put_object(Bucket="mybucket", Key="temp.h5", Body=Path(h5_path).read_bytes())
 
-    S3FileSystem.clear_instance_cache()
-    fs = S3FileSystem(client_kwargs={"endpoint_url": endpoint_uri})
-    fs.invalidate_cache()
-
-    yield fs
-
-
-def test_subset_granule(
-    fs: S3FileSystem, maap: MAAP, aoi_gdf: gpd.GeoDataFrame, tmp_path: Path
-):
     granule = Granule(
         {
             "Granule": {
@@ -80,7 +74,7 @@ def test_subset_granule(
     expected_path = os.path.join(tmp_path, "temp.gpq")
     io_result = subset_granule(
         SubsetGranuleProps(
-            fs=fs,
+            fsspec_kwargs={"endpoint_url": endpoint_uri, "skip_instance_cache": True},
             granule=granule,
             maap=maap,
             aoi_gdf=aoi_gdf,

From a8d4f19d3676ec692e724c88c725c521bf6dac3b Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Wed, 3 Jul 2024 11:43:48 -0400
Subject: [PATCH 10/11] Update conda lock file

---
 conda-lock.yml | 383 +++++++++++++++++++++++++++----------------------
 1 file changed, 213 insertions(+), 170 deletions(-)

diff --git a/conda-lock.yml b/conda-lock.yml
index fd06a8a..88911ce 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -5,9 +5,9 @@
 # available, unless you explicitly update the lock file.
 #
 # Install this environment as "YOURENV" with:
-#     conda-lock install -n YOURENV --file conda-lock.yml
+#     conda-lock install -n YOURENV conda-lock.yml
 # This lock contains optional development dependencies. Include them in the installed environment with:
-#     conda-lock install --dev-dependencies -n YOURENV --file conda-lock.yml
+#     conda-lock install --dev-dependencies -n YOURENV conda-lock.yml
 # To update a single package to the latest version compatible with the version constraints in the source:
 #     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
 # To re-solve the entire environment, e.g. after changing a version constraint in the source file:
@@ -15,9 +15,9 @@
 version: 1
 metadata:
   content_hash:
-    linux-64: cfc05d4f35432e186dc1f491a88ecc8b65aa0b60431c23b7a47265ce97cc8020
-    osx-64: 214b44d82d275e379fd22b71f033e5c8db994d3890f3f8000d639578b6028d9a
-    osx-arm64: c7fcb0ada1be94e9b00e03ddbc71079ab770da28a86617bcd396c695b16ef7ad
+    linux-64: 78ed939631437d21d332567b95b57a781d6c5d3483494e5804eef44a99758d03
+    osx-64: 73f899ce85cd59a17f5770e48f508ee1da3da8b62d6c18899973ce71c6aa75a4
+    osx-arm64: 8b23417a31456423573189af43ec716ee9a2c63c31aca4ace776e38ad0794e3b
   channels:
   - url: conda-forge
     used_env_vars: []
@@ -1740,53 +1740,53 @@ package:
   category: main
   optional: false
 - name: boto3-stubs
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: linux-64
   dependencies:
     boto3: ''
     python: ''
     typing_extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.136-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.138-pyhd8ed1ab_0.conda
   hash:
-    md5: 26d6ab84e689a1f9009829361c84fff5
-    sha256: e888390282d6f5334e1dbe77500c10d4bfa7d9cc8c85081dd12d6f7c6faa967b
+    md5: f280947d39f7920e683a314ab5190d1c
+    sha256: dddfe813a1018184c5da009c605a2c86240677e10e5be8cc3c72cf7ea718f526
   category: dev
   optional: true
 - name: boto3-stubs
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: osx-64
   dependencies:
     boto3: ''
     python: ''
     typing_extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.136-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.138-pyhd8ed1ab_0.conda
   hash:
-    md5: 26d6ab84e689a1f9009829361c84fff5
-    sha256: e888390282d6f5334e1dbe77500c10d4bfa7d9cc8c85081dd12d6f7c6faa967b
+    md5: f280947d39f7920e683a314ab5190d1c
+    sha256: dddfe813a1018184c5da009c605a2c86240677e10e5be8cc3c72cf7ea718f526
   category: dev
   optional: true
 - name: boto3-stubs
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: osx-arm64
   dependencies:
     boto3: ''
     python: ''
     typing_extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.136-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-1.34.138-pyhd8ed1ab_0.conda
   hash:
-    md5: 26d6ab84e689a1f9009829361c84fff5
-    sha256: e888390282d6f5334e1dbe77500c10d4bfa7d9cc8c85081dd12d6f7c6faa967b
+    md5: f280947d39f7920e683a314ab5190d1c
+    sha256: dddfe813a1018184c5da009c605a2c86240677e10e5be8cc3c72cf7ea718f526
   category: dev
   optional: true
 - name: boto3-stubs-essential
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: linux-64
   dependencies:
-    boto3-stubs: 1.34.136
+    boto3-stubs: 1.34.138
     mypy-boto3-s3: ''
     mypy_boto3_cloudformation: ''
     mypy_boto3_dynamodb: ''
@@ -1794,18 +1794,18 @@ package:
     mypy_boto3_lambda: ''
     mypy_boto3_rds: ''
     mypy_boto3_sqs: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.136-hd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.138-hd8ed1ab_0.conda
   hash:
-    md5: 78f5a7c53b27388e150dff4d23c74806
-    sha256: 4c6629b759ed226b817b6f319b3d85506fad601da50d1675a037257110e74042
+    md5: 4aaee4181a3ac6e8b91ad0f30b182743
+    sha256: 1e992b97f9bccde3f53e08cfa8d519909d810a6cc1636ec7d253fde897c98587
   category: dev
   optional: true
 - name: boto3-stubs-essential
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: osx-64
   dependencies:
-    boto3-stubs: 1.34.136
+    boto3-stubs: 1.34.138
     mypy-boto3-s3: ''
     mypy_boto3_cloudformation: ''
     mypy_boto3_dynamodb: ''
@@ -1813,18 +1813,18 @@ package:
     mypy_boto3_lambda: ''
     mypy_boto3_rds: ''
     mypy_boto3_sqs: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.136-hd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.138-hd8ed1ab_0.conda
   hash:
-    md5: 78f5a7c53b27388e150dff4d23c74806
-    sha256: 4c6629b759ed226b817b6f319b3d85506fad601da50d1675a037257110e74042
+    md5: 4aaee4181a3ac6e8b91ad0f30b182743
+    sha256: 1e992b97f9bccde3f53e08cfa8d519909d810a6cc1636ec7d253fde897c98587
   category: dev
   optional: true
 - name: boto3-stubs-essential
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: osx-arm64
   dependencies:
-    boto3-stubs: 1.34.136
+    boto3-stubs: 1.34.138
     mypy-boto3-s3: ''
     mypy_boto3_cloudformation: ''
     mypy_boto3_dynamodb: ''
@@ -1832,10 +1832,10 @@ package:
     mypy_boto3_lambda: ''
     mypy_boto3_rds: ''
     mypy_boto3_sqs: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.136-hd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/boto3-stubs-essential-1.34.138-hd8ed1ab_0.conda
   hash:
-    md5: 78f5a7c53b27388e150dff4d23c74806
-    sha256: 4c6629b759ed226b817b6f319b3d85506fad601da50d1675a037257110e74042
+    md5: 4aaee4181a3ac6e8b91ad0f30b182743
+    sha256: 1e992b97f9bccde3f53e08cfa8d519909d810a6cc1636ec7d253fde897c98587
   category: dev
   optional: true
 - name: botocore
@@ -1884,45 +1884,45 @@ package:
   category: main
   optional: false
 - name: botocore-stubs
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: linux-64
   dependencies:
     python: '>=3.8,<4.0'
     types-awscrt: ''
     typing_extensions: '>=4.1.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.136-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.138-pyhd8ed1ab_0.conda
   hash:
-    md5: e799bd0a8d9b687e60f7ab9ba6248144
-    sha256: 68ec2fc18144aa58520e8f59a29a8137f1d4c0c445fcac95763e5dd4fffa15de
+    md5: 4cf2403f69d36d8f83fd5c142b8a1a96
+    sha256: f1576f7966d639863aa4a0c2286c075ef1a0115d6b9c5d98b766abeafff21443
   category: dev
   optional: true
 - name: botocore-stubs
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: osx-64
   dependencies:
     python: '>=3.8,<4.0'
     types-awscrt: ''
     typing_extensions: '>=4.1.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.136-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.138-pyhd8ed1ab_0.conda
   hash:
-    md5: e799bd0a8d9b687e60f7ab9ba6248144
-    sha256: 68ec2fc18144aa58520e8f59a29a8137f1d4c0c445fcac95763e5dd4fffa15de
+    md5: 4cf2403f69d36d8f83fd5c142b8a1a96
+    sha256: f1576f7966d639863aa4a0c2286c075ef1a0115d6b9c5d98b766abeafff21443
   category: dev
   optional: true
 - name: botocore-stubs
-  version: 1.34.136
+  version: 1.34.138
   manager: conda
   platform: osx-arm64
   dependencies:
     python: '>=3.8,<4.0'
     types-awscrt: ''
     typing_extensions: '>=4.1.0'
-  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.136-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/botocore-stubs-1.34.138-pyhd8ed1ab_0.conda
   hash:
-    md5: e799bd0a8d9b687e60f7ab9ba6248144
-    sha256: 68ec2fc18144aa58520e8f59a29a8137f1d4c0c445fcac95763e5dd4fffa15de
+    md5: 4cf2403f69d36d8f83fd5c142b8a1a96
+    sha256: f1576f7966d639863aa4a0c2286c075ef1a0115d6b9c5d98b766abeafff21443
   category: dev
   optional: true
 - name: bottleneck
@@ -2706,7 +2706,7 @@ package:
   category: main
   optional: false
 - name: cfn-lint
-  version: 1.4.2
+  version: 1.5.0
   manager: conda
   platform: linux-64
   dependencies:
@@ -2722,14 +2722,14 @@ package:
     sarif-om: '>=1.0.4,<1.1.dev0'
     sympy: '>=1.0.0'
     typing-extensions: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/cfn-lint-1.4.2-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/cfn-lint-1.5.0-pyhd8ed1ab_0.conda
   hash:
-    md5: 05764d5ce613381431231df269dc5591
-    sha256: 629255bcb16a7d5bce011712f6261f3e4b77df15c261db00cb6182985eb24e31
+    md5: f71363d2131dd302419ccfc7a6d942a2
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+  url: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.20.0-py311h5ecf98a_0.conda
   hash:
-    md5: c4de9699f095e3049dc02bcf811497b7
-    sha256: 2c34d272a1afe39afbf4713a7f96366a579cb628a0321159e3015695b1e54913
+    md5: 357e4ea089cacaf208a06e619463240c
+    sha256: 4b3c0e2c8131cbf7372e63492bc485bf3b12d68acd0ddc073b7fd7b81a6148a1
   category: main
   optional: false
 - name: pydantic-core
-  version: 2.18.4
+  version: 2.20.0
   manager: conda
   platform: osx-64
   dependencies:
@@ -14026,14 +14029,14 @@ package:
     python: '>=3.11,<3.12.0a0'
     python_abi: 3.11.*
     typing-extensions: '>=4.6.0,!=4.7.0'
-  url: https://conda.anaconda.org/conda-forge/osx-64/pydantic-core-2.18.4-py311h295b1db_0.conda
+  url: https://conda.anaconda.org/conda-forge/osx-64/pydantic-core-2.20.0-py311h295b1db_0.conda
   hash:
-    md5: 48eeeced53f0a9e3ccb95ff414714f9b
-    sha256: 1fa07bf5f4f1f2685ee01de43c037800eb2fa4228e70a8dfac60b98912463565
+    md5: 231062bb6857cba8b2f2386846610d03
+    sha256: d9b1e604ca8c90573f2f3f097f621229a90bff2479cdc20100823ae3a83c1795
   category: main
   optional: false
 - name: pydantic-core
-  version: 2.18.4
+  version: 2.20.0
   manager: conda
   platform: osx-arm64
   dependencies:
@@ -14041,10 +14044,10 @@ package:
     python: '>=3.11,<3.12.0a0'
     python_abi: 3.11.*
     typing-extensions: '>=4.6.0,!=4.7.0'
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/pydantic-core-2.18.4-py311h98c6a39_0.conda
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/pydantic-core-2.20.0-py311h98c6a39_0.conda
   hash:
-    md5: d7a6b069772e61897ab8ade15d268dde
-    sha256: ca8342ba184e1e9ce1367c7225cbd837516b3d69381a17fc53c434bb2a2a1f0f
+    md5: 097fe8a69713c1c5c90cdfd98136fbd3
+    sha256: 25285138f550875285101504d98d2ce23522f9da51f4b55dc4dba42b93e9a2c4
   category: main
   optional: false
 - name: pyflakes
@@ -14860,6 +14863,43 @@ package:
     sha256: 03b787e5d09ebd7c8e5a359d21ed264c4f0c473e7421be48d339fabddd43ffea
   category: dev
   optional: true
+- name: qhull
+  version: '2020.2'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=9.4.0'
+    libstdcxx-ng: '>=9.4.0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/qhull-2020.2-h4bd325d_2.tar.bz2
+  hash:
+    md5: 5acb8407fefa1c1929c11c167237e776
+    sha256: e1d6e4e74486ce4844c4bbdc7198bb4d8191b70881f6415d1f4b5fd8d98f18d7
+  category: main
+  optional: false
+- name: qhull
+  version: '2020.2'
+  manager: conda
+  platform: osx-64
+  dependencies:
+    libcxx: '>=11.1.0'
+  url: https://conda.anaconda.org/conda-forge/osx-64/qhull-2020.2-h940c156_2.tar.bz2
+  hash:
+    md5: 031bd4afafd89fff7bef4fb6c9f49058
+    sha256: a1dff011b3f314ee417a7bd626eecbc44d536b20e51884d378cfc89cc8e90a45
+  category: main
+  optional: false
+- name: qhull
+  version: '2020.2'
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    libcxx: '>=11.1.0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/qhull-2020.2-hc021e02_2.tar.bz2
+  hash:
+    md5: 3a085cac271088b14b68c34d50576fe4
+    sha256: dc423d80d1e36c0250a796f578ac1d090b76b1a5ba9de7a2a8c90388d284224e
+  category: main
+  optional: false
 - name: rasterio
   version: 1.3.10
   manager: conda
@@ -15817,10 +15857,11 @@ package:
   category: main
   optional: false
 - name: scikit-learn
-  version: 1.5.0
+  version: 1.5.1
   manager: conda
   platform: linux-64
   dependencies:
+    __glibc: '>=2.17,<3.0.a0'
     _openmp_mutex: '>=4.5'
     joblib: '>=1.2.0'
     libgcc-ng: '>=12'
@@ -15830,14 +15871,14 @@ package:
     python_abi: 3.11.*
     scipy: ''
     threadpoolctl: '>=3.1.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.5.0-py311he08f58d_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.5.1-py311hd632256_0.conda
   hash:
-    md5: d55e4dde3b30272090f33ddd367c580b
-    sha256: 8f4150216761b2dcd5d55066c74c46fd3a2bc823178c730acd18bf050f85ef8a
+    md5: f3928b428ad924ecb8f0e9b71124ed7f
+    sha256: 855a322daff2d64c9a75b1fea560d2f6f4dd02685220519c9a3ce25bbdd92f7d
   category: main
   optional: false
 - name: scikit-learn
-  version: 1.5.0
+  version: 1.5.1
   manager: conda
   platform: osx-64
   dependencies:
@@ -15850,14 +15891,14 @@ package:
     python_abi: 3.11.*
     scipy: ''
     threadpoolctl: '>=3.1.0'
-  url: https://conda.anaconda.org/conda-forge/osx-64/scikit-learn-1.5.0-py311h3c3ac6d_1.conda
+  url: https://conda.anaconda.org/conda-forge/osx-64/scikit-learn-1.5.1-py311h3c3ac6d_0.conda
   hash:
-    md5: d8edd327c45efef9fb9319c85c08226d
-    sha256: b056a9cc59711b2f86d114289a3d8800e9057ebc15a2bd0659f4c8326b8a89fe
+    md5: 209cc9f21aced058dfe783848c7a13d9
+    sha256: 9484c7f5c686252e7dd5e180537f35bf7518bae2ba0f5970f849313a427b4a4f
   category: main
   optional: false
 - name: scikit-learn
-  version: 1.5.0
+  version: 1.5.1
   manager: conda
   platform: osx-arm64
   dependencies:
@@ -15870,10 +15911,10 @@ package:
     python_abi: 3.11.*
     scipy: ''
     threadpoolctl: '>=3.1.0'
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/scikit-learn-1.5.0-py311hbfb48bc_1.conda
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/scikit-learn-1.5.1-py311hbfb48bc_0.conda
   hash:
-    md5: f80b6aacea4b2e164efeb011e619015d
-    sha256: 95fe4cf505effa93a734508b77fef4bba0e6d396f8d0a077b10d4f5873fca561
+    md5: c0859c6e5ce3b8f341fca34a52433925
+    sha256: 750975969130d3cf01d211a1efc8455aaab747040bc1bea48f3da767e5b1fd0a
   category: main
   optional: false
 - name: scipy
@@ -16183,40 +16224,42 @@ package:
   category: main
   optional: false
 - name: snappy
-  version: 1.2.0
+  version: 1.2.1
   manager: conda
   platform: linux-64
   dependencies:
     libgcc-ng: '>=12'
     libstdcxx-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/snappy-1.2.0-hdb0a2a9_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/snappy-1.2.1-ha2e4443_0.conda
   hash:
-    md5: 843bbb8ace1d64ac50d64639ff38b014
-    sha256: bb87116b8c6198f6979b3d212e9af12e08e12f2bf09970d0f9b4582607648b22
+    md5: 6b7dcc7349efd123d493d2dbe85a045f
+    sha256: dc7c8e0e8c3e8702aae81c52d940bfaabe756953ee51b1f1757e891bab62cf7f
   category: main
   optional: false
 - name: snappy
-  version: 1.2.0
+  version: 1.2.1
   manager: conda
   platform: osx-64
   dependencies:
+    __osx: '>=10.13'
     libcxx: '>=16'
-  url: https://conda.anaconda.org/conda-forge/osx-64/snappy-1.2.0-h6dc393e_1.conda
+  url: https://conda.anaconda.org/conda-forge/osx-64/snappy-1.2.1-he1e6707_0.conda
   hash:
-    md5: 9c322ec36340610fcf213b72999b049e
-    sha256: dc2abe5f45859263c36d287d0d6212e83a3552ef19faf98194d32e70d755d648
+    md5: ddceef5df973c8ff7d6b32353c0cb358
+    sha256: a979319cd4916f0e7450aa92bb3cf4c2518afa80be50de99f31d075e693a6dd9
   category: main
   optional: false
 - name: snappy
-  version: 1.2.0
+  version: 1.2.1
   manager: conda
   platform: osx-arm64
   dependencies:
+    __osx: '>=11.0'
     libcxx: '>=16'
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/snappy-1.2.0-hd04f947_1.conda
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/snappy-1.2.1-hd02b534_0.conda
   hash:
-    md5: 32cf833d440ee18d3c4c04ec38cf2b01
-    sha256: 88afe00f550e1e2d66326516e5372aa1834c51fb6b53afa7a3636c65cd75ce42
+    md5: 69d0f9694f3294418ee935da3d5f7272
+    sha256: cb7a9440241c6092e0f1c795fdca149c4767023e783eaf9cfebc501f906b4897
   category: main
   optional: false
 - name: snuggs

From 0ab8e8375c70796865d2db16fdaa578872069b05 Mon Sep 17 00:00:00 2001
From: Chuck Daniels <chuck@developmentseed.org>
Date: Wed, 3 Jul 2024 11:52:23 -0400
Subject: [PATCH 11/11] Change s3fs-open-kwargs CLI option to fsspec-kwargs

---
 bin/subset.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/subset.sh b/bin/subset.sh
index 6695d24..21c12ae 100755
--- a/bin/subset.sh
+++ b/bin/subset.sh
@@ -44,7 +44,7 @@ else
     [[ -n "${7}" ]] && args+=(--beams "${7}")
     [[ -n "${8}" ]] && args+=(--limit "${8}")
     [[ -n "${9}" ]] && args+=(--output "${9}")
-    [[ -n "${10}" ]] && args+=(--s3fs-open-kwargs "${10}")
+    [[ -n "${10}" ]] && args+=(--fsspec-kwargs "${10}")
     [[ -n "${11}" ]] && args+=(--processes "${11}")
     # Split the last argument into an array of arguments to pass to scalene.
     IFS=' ' read -ra scalene_args <<<"${12}"