From 3404b347b0977810812d00cc8f02f69ef2c3f7a2 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 29 Jan 2024 15:03:23 -0600
Subject: [PATCH 01/33] click, add convert

---
 WrightTools/__main__.py | 74 +++++++++++++++++++++++++++++++++--------
 setup.py                |  3 +-
 2 files changed, 63 insertions(+), 14 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index aedc5dff3..7187b9f95 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -1,29 +1,77 @@
 # --- import --------------------------------------------------------------------------------------
 
 
+import click
 import WrightTools as wt
-import argparse
 
 
 # --- define --------------------------------------------------------------------------------------
 
 
-def wt_tree():
-    parser = argparse.ArgumentParser(description="Print a given data tree.")
+@click.group()
+@click.version_option(wt.__version__)
+def cli():
+    pass
 
-    # Add arguments
-    parser.add_argument("path", type=str)
-    parser.add_argument("--verbose", "-v", action="store_true", help="Verbose? False by default")
-    parser.add_argument("--depth", "-d", "-L", type=int, default=9, help="depth to print (int)")
-    parser.add_argument("internal_path", nargs="?", default="/")
-    args = parser.parse_args()
 
+@cli.command(name="tree", help="Print a given data tree.")
+@click.argument("path", nargs=1)
+@click.option("--internal_path", default="/", help="specify a path internal to the file.  Defaults to root")
+@click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
+@click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
+def tree(path, internal_path, depth=9, verbose=False):
     # Create the data/collection object
-    obj = wt.open(args.path)[args.internal_path]
+    obj = wt.open(path)[internal_path]
 
-    # Print the tree
     # If the object is a data object, it doesn't take depth as a parameter
     if isinstance(obj, wt.Data):
-        obj.print_tree(verbose=args.verbose)
+        obj.print_tree(verbose=verbose)
     else:
-        obj.print_tree(verbose=args.verbose, depth=args.depth)
+        obj.print_tree(verbose=verbose, depth=depth)
+
+
+@cli.command(name="crawl", help="Crawl a directory and report the wt5 objects found.")
+@click.argument("directory", default=".")
+def crawl(directory=None):
+    ...
+
+@cli.command(name="convert", help="Convert numbers to different units.")
+@click.argument("number", type=float, nargs=1)
+@click.argument("unit", nargs=1)
+@click.argument("destination_unit", default=None, nargs=-1)
+def convert(number, unit, destination_unit=None):
+
+    def gen_fmt(ref):
+        sig_figs = len(str(ref))
+        print(str(ref))
+        print(sig_figs)
+
+        def fmt(new):
+            exponent = int(f"{new:e}".split("e")[1])
+            if exponent > 6 or exponent < -3:
+                return f"{new:{sig_figs}e}"
+            else: # a "normal" size number
+                return f"{round(new, sig_figs-exponent)}"
+
+        return fmt
+
+    fmt = gen_fmt(number)
+
+    if len(destination_unit):  # units provided
+        if not wt.units.is_valid_conversion(unit, destination_unit):
+            raise wt.exceptions.UnitsError(
+                wt.units.get_valid_conversions(unit), destination_unit
+            )
+        new = wt.units.convert(number, unit, destination_unit)
+        print(f"{fmt(new)} {destination_unit}")
+    else:
+        valid_units = wt.units.get_valid_conversions(unit)
+        print(valid_units)
+        for d_unit in valid_units:
+            new = wt.units.convert(number, unit, d_unit)
+            print(f"{fmt(new)} {d_unit}")
+
+
+if __name__ == "__main__":
+    cli()
+
diff --git a/setup.py b/setup.py
index 53d512fd9..6c08e3258 100755
--- a/setup.py
+++ b/setup.py
@@ -44,6 +44,7 @@ def read(fname):
         "pint",
         "python-dateutil",
         "scipy",
+        "click",
         "tidy_headers>=1.0.0",
     ],
     extras_require={
@@ -66,7 +67,7 @@ def read(fname):
     license="MIT",
     url="http://wright.tools",
     keywords="spectroscopy science multidimensional visualization",
-    entry_points={"console_scripts": ["wt-tree=WrightTools.__main__:wt_tree"]},
+    entry_points={"console_scripts": ["wt-tree=WrightTools.__main__:cli"]},
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",

From 81d3f3e05de9d6a663414e0448817f7c8268e79d Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 29 Jan 2024 21:20:06 -0600
Subject: [PATCH 02/33] wt-tree crawl

working example
---
 WrightTools/__main__.py | 94 +++++++++++++++++++++++++++++++----------
 1 file changed, 72 insertions(+), 22 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 7187b9f95..9995c8611 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -4,7 +4,6 @@
 import click
 import WrightTools as wt
 
-
 # --- define --------------------------------------------------------------------------------------
 
 
@@ -20,7 +19,7 @@ def cli():
 @click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
 @click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
 def tree(path, internal_path, depth=9, verbose=False):
-    # Create the data/collection object
+    # open the object
     obj = wt.open(path)[internal_path]
 
     # If the object is a data object, it doesn't take depth as a parameter
@@ -30,43 +29,94 @@ def tree(path, internal_path, depth=9, verbose=False):
         obj.print_tree(verbose=verbose, depth=depth)
 
 
-@cli.command(name="crawl", help="Crawl a directory and report the wt5 objects found.")
-@click.argument("directory", default=".")
-def crawl(directory=None):
+@cli.command(name="load", help="Open a python cli with the object pre-loaded.")
+@click.argument("path")
+def load(path):
+    import code
+    d = wt.open(d)
     ...
 
-@cli.command(name="convert", help="Convert numbers to different units.")
+
+@cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
+@click.argument("directory", nargs=-1, default=None)
+@click.option("--recursive", "-r", is_flag=True, help="explore all levels of the directory")
+@click.option("--pausing", "-p", is_flag=True, help="pause at each file and give option to interact.")
+def crawl(directory=(), recursive=False, pausing=False):
+    import glob, os
+
+    if not directory:
+        directory = os.getcwd()
+    else:
+        directory = directory[0]
+
+    if pausing:
+        import code
+        shell = code.InteractiveConsole()
+
+    for pathname in glob.iglob("**/*.wt5", root_dir=directory, recursive=recursive):
+        print(pathname)
+        d = wt.open(os.path.join(directory, pathname))
+        if isinstance(d, wt.Data):
+            d.print_tree(verbose=False)
+        elif isinstance(d, wt.Collection):
+            d.print_tree(depth=1, verbose=False)
+
+        if pausing:
+            msg = shell.raw_input("Continue [y]/n/interact? ")
+            if msg == "n":
+                break
+            elif msg == "interact":
+                lines = ["import WrightTools as wt"]
+                if isinstance(d, wt.Data):
+                    lines += [
+                        "import matplotlib.pyplot as plt",
+                        f"path = r'{os.path.join(directory, pathname)}'",
+                        "d = wt.open(path)",
+                    ]
+                elif isinstance(d, wt.Collection):
+                    lines.append(f"c = wt.open(r'{os.path.join(directory, pathname)}')")
+
+                [shell.push(line) for line in lines]                
+                shell.interact(banner="\n".join([">>> "+line for line in lines]))
+            else:
+                continue
+        print("-"*100)
+        d.close()
+
+
+@cli.command(name="convert")
 @click.argument("number", type=float, nargs=1)
 @click.argument("unit", nargs=1)
 @click.argument("destination_unit", default=None, nargs=-1)
 def convert(number, unit, destination_unit=None):
-
-    def gen_fmt(ref):
-        sig_figs = len(str(ref))
-        print(str(ref))
-        print(sig_figs)
-
-        def fmt(new):
-            exponent = int(f"{new:e}".split("e")[1])
-            if exponent > 6 or exponent < -3:
-                return f"{new:{sig_figs}e}"
-            else: # a "normal" size number
+    """Convert numbers to different units."""
+
+    if int(number) == number:
+        number = int(number)
+    sig_figs = len(str(number))
+    sig_figs -= 1 if "." in str(number) else 0
+
+    def fmt(new):
+        exponent = int(f"{new:e}".split("e")[1])
+        if exponent > 6 or exponent < -3:
+            return f"{new:{sig_figs}e}"
+        else: # if a "normal" size number
+            if sig_figs-exponent <= 0:
+                return f"{int(round(new, sig_figs-exponent))}"
+            else:
                 return f"{round(new, sig_figs-exponent)}"
 
-        return fmt
-
-    fmt = gen_fmt(number)
 
     if len(destination_unit):  # units provided
+        destination_unit = destination_unit[0]
         if not wt.units.is_valid_conversion(unit, destination_unit):
             raise wt.exceptions.UnitsError(
                 wt.units.get_valid_conversions(unit), destination_unit
             )
         new = wt.units.convert(number, unit, destination_unit)
-        print(f"{fmt(new)} {destination_unit}")
+        print(f"{number} {unit} = {fmt(new)} {destination_unit}")
     else:
         valid_units = wt.units.get_valid_conversions(unit)
-        print(valid_units)
         for d_unit in valid_units:
             new = wt.units.convert(number, unit, d_unit)
             print(f"{fmt(new)} {d_unit}")

From 73cd489fadb27595f01f952041c13a5249d6bd52 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 29 Jan 2024 21:20:30 -0600
Subject: [PATCH 03/33] Data.print_tree tweak

---
 WrightTools/data/_data.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/WrightTools/data/_data.py b/WrightTools/data/_data.py
index 86d496d31..5ded034d8 100644
--- a/WrightTools/data/_data.py
+++ b/WrightTools/data/_data.py
@@ -273,30 +273,30 @@ def print_leaves(prefix, lis, vline=True):
 
         if verbose:
             # axes
-            print(prefix + "├── axes")
+            print(prefix + f"├── axes ({len(self.axes)})")
             print_leaves(prefix, self.axes)
             # constants
-            print(prefix + "├── constants")
+            print(prefix + f"├── constants ({len(self.constants)})")
             print_leaves(prefix, self.constants)
             # variables
-            print(prefix + "├── variables")
+            print(prefix + f"├── variables ({len(self.variables)})")
             print_leaves(prefix, self.variables)
             # channels
-            print(prefix + "└── channels")
+            print(prefix + f"└── channels ({len(self.channels)})")
             print_leaves(prefix, self.channels, vline=False)
         else:
             # axes
-            s = "axes: "
+            s = f"axes ({len(self.axes)}): "
             s += ", ".join(["{0} ({1})".format(a.expression, a.units) for a in self.axes])
             print(prefix + "├── " + s)
             # constants
-            s = "constants: "
+            s = f"constants ({len(self.constants)}): "
             s += ", ".join(
                 ["{0} ({1} {2})".format(a.expression, a.value, a.units) for a in self.constants]
             )
             print(prefix + "├── " + s)
             # channels
-            s = "channels: "
+            s = f"channels ({len(self.channels)}): "
             s += ", ".join(self.channel_names)
             print(prefix + "└── " + s)
 
@@ -1444,7 +1444,7 @@ def offset(
 
     def print_tree(self, *, verbose=True):
         """Print a ascii-formatted tree representation of the data contents."""
-        print("{0} ({1})".format(self.natural_name, self.filepath))
+        print("{0} ({1}) {2}".format(self.natural_name, self.filepath, self.shape))
         self._print_branch("", depth=0, verbose=verbose)
 
     def prune(self, keep_channels=True, *, verbose=True):

From ca16c778c9d92207bb58dbc62aae2261265a7cbd Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 29 Jan 2024 21:46:15 -0600
Subject: [PATCH 04/33] wt-tree crawl -p

clean exit
---
 WrightTools/__main__.py | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 9995c8611..90afdc24d 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -40,7 +40,7 @@ def load(path):
 @cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
 @click.argument("directory", nargs=-1, default=None)
 @click.option("--recursive", "-r", is_flag=True, help="explore all levels of the directory")
-@click.option("--pausing", "-p", is_flag=True, help="pause at each file and give option to interact.")
+@click.option("--pausing", "-p", is_flag=True, help="pause at each file readout. Interaction with data is possible.")
 def crawl(directory=(), recursive=False, pausing=False):
     import glob, os
 
@@ -51,8 +51,16 @@ def crawl(directory=(), recursive=False, pausing=False):
 
     if pausing:
         import code
-        shell = code.InteractiveConsole()
 
+        def raise_sys_exit():
+            raise SystemExit
+
+        shell = code.InteractiveConsole(locals={
+            "exit": raise_sys_exit,
+            "quit": raise_sys_exit
+        })
+
+    print("-"*100)
     for pathname in glob.iglob("**/*.wt5", root_dir=directory, recursive=recursive):
         print(pathname)
         d = wt.open(os.path.join(directory, pathname))
@@ -76,8 +84,14 @@ def crawl(directory=(), recursive=False, pausing=False):
                 elif isinstance(d, wt.Collection):
                     lines.append(f"c = wt.open(r'{os.path.join(directory, pathname)}')")
 
-                [shell.push(line) for line in lines]                
-                shell.interact(banner="\n".join([">>> "+line for line in lines]))
+                [shell.push(line) for line in lines]
+                banner = "--- INTERACTING --- (to continue, call exit() or quit())\n"
+                banner += "\n".join([">>> "+line for line in lines])
+                
+                try:
+                    shell.interact(banner=banner)
+                except SystemExit:
+                    pass
             else:
                 continue
         print("-"*100)

From fd9d75c335d723ca7dddb6804b6cbcfa4956bd4b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 30 Jan 2024 03:55:31 +0000
Subject: [PATCH 05/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/__main__.py | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 90afdc24d..8cef6f900 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -15,7 +15,9 @@ def cli():
 
 @cli.command(name="tree", help="Print a given data tree.")
 @click.argument("path", nargs=1)
-@click.option("--internal_path", default="/", help="specify a path internal to the file.  Defaults to root")
+@click.option(
+    "--internal_path", default="/", help="specify a path internal to the file.  Defaults to root"
+)
 @click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
 @click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
 def tree(path, internal_path, depth=9, verbose=False):
@@ -33,6 +35,7 @@ def tree(path, internal_path, depth=9, verbose=False):
 @click.argument("path")
 def load(path):
     import code
+
     d = wt.open(d)
     ...
 
@@ -40,7 +43,12 @@ def load(path):
 @cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
 @click.argument("directory", nargs=-1, default=None)
 @click.option("--recursive", "-r", is_flag=True, help="explore all levels of the directory")
-@click.option("--pausing", "-p", is_flag=True, help="pause at each file readout. Interaction with data is possible.")
+@click.option(
+    "--pausing",
+    "-p",
+    is_flag=True,
+    help="pause at each file readout. Interaction with data is possible.",
+)
 def crawl(directory=(), recursive=False, pausing=False):
     import glob, os
 
@@ -55,12 +63,9 @@ def crawl(directory=(), recursive=False, pausing=False):
         def raise_sys_exit():
             raise SystemExit
 
-        shell = code.InteractiveConsole(locals={
-            "exit": raise_sys_exit,
-            "quit": raise_sys_exit
-        })
+        shell = code.InteractiveConsole(locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
 
-    print("-"*100)
+    print("-" * 100)
     for pathname in glob.iglob("**/*.wt5", root_dir=directory, recursive=recursive):
         print(pathname)
         d = wt.open(os.path.join(directory, pathname))
@@ -86,15 +91,15 @@ def raise_sys_exit():
 
                 [shell.push(line) for line in lines]
                 banner = "--- INTERACTING --- (to continue, call exit() or quit())\n"
-                banner += "\n".join([">>> "+line for line in lines])
-                
+                banner += "\n".join([">>> " + line for line in lines])
+
                 try:
                     shell.interact(banner=banner)
                 except SystemExit:
                     pass
             else:
                 continue
-        print("-"*100)
+        print("-" * 100)
         d.close()
 
 
@@ -114,19 +119,16 @@ def fmt(new):
         exponent = int(f"{new:e}".split("e")[1])
         if exponent > 6 or exponent < -3:
             return f"{new:{sig_figs}e}"
-        else: # if a "normal" size number
-            if sig_figs-exponent <= 0:
+        else:  # if a "normal" size number
+            if sig_figs - exponent <= 0:
                 return f"{int(round(new, sig_figs-exponent))}"
             else:
                 return f"{round(new, sig_figs-exponent)}"
 
-
     if len(destination_unit):  # units provided
         destination_unit = destination_unit[0]
         if not wt.units.is_valid_conversion(unit, destination_unit):
-            raise wt.exceptions.UnitsError(
-                wt.units.get_valid_conversions(unit), destination_unit
-            )
+            raise wt.exceptions.UnitsError(wt.units.get_valid_conversions(unit), destination_unit)
         new = wt.units.convert(number, unit, destination_unit)
         print(f"{number} {unit} = {fmt(new)} {destination_unit}")
     else:
@@ -138,4 +140,3 @@ def fmt(new):
 
 if __name__ == "__main__":
     cli()
-

From 200c557c28bf37ed8858bffcf6388006925da604 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Thu, 1 Feb 2024 11:57:46 -0600
Subject: [PATCH 06/33] removing pause from crawl

---
 WrightTools/__main__.py | 123 ++++++++++++++++++++++++++++------------
 1 file changed, 86 insertions(+), 37 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 8cef6f900..3105c39bb 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -4,6 +4,7 @@
 import click
 import WrightTools as wt
 
+
 # --- define --------------------------------------------------------------------------------------
 
 
@@ -24,7 +25,6 @@ def tree(path, internal_path, depth=9, verbose=False):
     # open the object
     obj = wt.open(path)[internal_path]
 
-    # If the object is a data object, it doesn't take depth as a parameter
     if isinstance(obj, wt.Data):
         obj.print_tree(verbose=verbose)
     else:
@@ -41,21 +41,21 @@ def load(path):
 
 
 @cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
-@click.argument("directory", nargs=-1, default=None)
-@click.option("--recursive", "-r", is_flag=True, help="explore all levels of the directory")
+@click.option("--directory", "-d", default=None, help="Directory to crawl.  Defaults to current directory.")
+@click.option("--recursive", "-r", is_flag=True, help="Explore all levels of the directory")
 @click.option(
     "--pausing",
     "-p",
     is_flag=True,
     help="pause at each file readout. Interaction with data is possible.",
 )
-def crawl(directory=(), recursive=False, pausing=False):
+@click.option("--format", "-f", default=None, help="Formatting keys (default only atm)")
+# TODO: write output as an option
+def crawl(directory=None, recursive=False, pausing=False, format=None):
     import glob, os
 
-    if not directory:
+    if directory is None:
         directory = os.getcwd()
-    else:
-        directory = directory[0]
 
     if pausing:
         import code
@@ -65,44 +65,93 @@ def raise_sys_exit():
 
         shell = code.InteractiveConsole(locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
 
-    print("-" * 100)
-    for pathname in glob.iglob("**/*.wt5", root_dir=directory, recursive=recursive):
-        print(pathname)
-        d = wt.open(os.path.join(directory, pathname))
-        if isinstance(d, wt.Data):
-            d.print_tree(verbose=False)
-        elif isinstance(d, wt.Collection):
-            d.print_tree(depth=1, verbose=False)
+    paths = glob.glob("**/*.wt5", root_dir=directory, recursive=recursive)
+    print(f"{len(paths)} wt5 file{'s' if len(paths) != 1 else None} found in {directory}")
+
+    from rich.console import Console
+    from rich.table import Table
+
+    console = Console()
+
+    table = Table(title=directory)
+    table.add_column("", justify="right")  # index
+    table.add_column("path", max_width=60)
+    table.add_column("size (MB)", justify="center")
+    table.add_column("created", max_width=30)
+    table.add_column("name")
+    table.add_column("shape")
+    table.add_column("axes")
+    table.add_column("variables")
+    table.add_column("channels")
+
+
+    for i, pathname in enumerate(paths):
+        path = os.path.join(directory, pathname)
+        d = wt.open(path)
+        infos = [str(i), pathname, str(int(os.path.getsize(path)/1e6)), *_format_entry(d)]
+        table.add_row(*infos)
 
         if pausing:
-            msg = shell.raw_input("Continue [y]/n/interact? ")
-            if msg == "n":
+            msg = shell.raw_input("Interact ([n=no]/y=yes/q=quit)? ")
+            if msg.lower() in ["q", "quit"]:
                 break
-            elif msg == "interact":
-                lines = ["import WrightTools as wt"]
-                if isinstance(d, wt.Data):
-                    lines += [
-                        "import matplotlib.pyplot as plt",
-                        f"path = r'{os.path.join(directory, pathname)}'",
-                        "d = wt.open(path)",
-                    ]
-                elif isinstance(d, wt.Collection):
-                    lines.append(f"c = wt.open(r'{os.path.join(directory, pathname)}')")
-
-                [shell.push(line) for line in lines]
-                banner = "--- INTERACTING --- (to continue, call exit() or quit())\n"
-                banner += "\n".join([">>> " + line for line in lines])
-
-                try:
-                    shell.interact(banner=banner)
-                except SystemExit:
-                    pass
+            elif msg.lower() in ["y", "yes"]:
+                _interact(shell, os.path.join(directory, pathname), isinstance(d, wt.Collection))
+                print("-" * 100)
             else:
                 continue
-        print("-" * 100)
         d.close()
 
 
+from typing import Tuple, Optional
+class TableEntry:
+    created: str = ""
+    name: str = ""
+    shape: Optional(Tuple(int))
+    axes: Optional(Tuple(str))
+    nvars: Optional(int)
+    nchan: Optional(int)
+    def __init__(self, wt5):
+        self.name = wt5.natural_name
+        self.created = wt5.attrs["created"].date
+        if isinstance(wt5, wt.Data):
+            self.shape = wt5.shape
+            self.axes = wt5.axis_expressions
+            self.nvars = len(wt5.variables)
+            self.nchan = len(wt5.channels)
+
+    
+
+
+
+
+def _format_entry(wt5, format=None):
+    if isinstance(wt5, wt.Data):
+        values = [f"{wt5.attrs['created']}", wt5.natural_name, f"{wt5.shape}", f"{wt5.axis_expressions}", str(len(wt5.variables)), str(len(wt5.channels))]
+    elif isinstance(wt5, wt.Collection):
+        values = ["---"] + [wt5.natural_name] + ["---"] * 4
+    else:
+        values = ["---"] + ["<unknown>"] + ["---"] * 4
+    return values
+
+
+def _interact(shell, path, is_collection):
+    lines = [
+        "import WrightTools as wt",
+        "import matplotlib.pyplot as plt",
+        f"{'c' if is_collection else 'd'} = wt.open(r'{path}')",
+    ]
+
+    [shell.push(line) for line in lines]
+    banner = "--- INTERACTING --- (to continue, call exit() or quit())\n"
+    banner += "\n".join([">>> " + line for line in lines])
+
+    try:
+        shell.interact(banner=banner)
+    except SystemExit:
+        pass
+
+
 @cli.command(name="convert")
 @click.argument("number", type=float, nargs=1)
 @click.argument("unit", nargs=1)

From cce05ef4b84f21d4707b065b585d30e6355cd966 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Thu, 1 Feb 2024 13:04:42 -0600
Subject: [PATCH 07/33] Update __main__.py

interact with crawl after table is made
---
 WrightTools/__main__.py | 126 +++++++++++++++-------------------------
 1 file changed, 48 insertions(+), 78 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 3105c39bb..aa8b56437 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -35,111 +35,81 @@ def tree(path, internal_path, depth=9, verbose=False):
 @click.argument("path")
 def load(path):
     import code
-
-    d = wt.open(d)
-    ...
+    # def raise_sys_exit():
+    #     raise SystemExit
+    shell = code.InteractiveConsole() # locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
+    _interact(shell, path)
 
 
 @cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
 @click.option("--directory", "-d", default=None, help="Directory to crawl.  Defaults to current directory.")
 @click.option("--recursive", "-r", is_flag=True, help="Explore all levels of the directory")
-@click.option(
-    "--pausing",
-    "-p",
-    is_flag=True,
-    help="pause at each file readout. Interaction with data is possible.",
-)
 @click.option("--format", "-f", default=None, help="Formatting keys (default only atm)")
-# TODO: write output as an option
-def crawl(directory=None, recursive=False, pausing=False, format=None):
-    import glob, os
+# TODO: write output as an option; format kwarg?
+def crawl(directory=None, recursive=False, format=None):
+    import glob, os, code
+    # from rich.console import Console
+    from rich.live import Live
+    from rich.table import Table
 
     if directory is None:
         directory = os.getcwd()
 
-    if pausing:
-        import code
-
-        def raise_sys_exit():
-            raise SystemExit
-
-        shell = code.InteractiveConsole(locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
-
     paths = glob.glob("**/*.wt5", root_dir=directory, recursive=recursive)
-    print(f"{len(paths)} wt5 file{'s' if len(paths) != 1 else None} found in {directory}")
-
-    from rich.console import Console
-    from rich.table import Table
 
-    console = Console()
+    def _parse_entry(i, relpath):
+        size = os.path.getsize(os.path.join(directory, relpath)) / 1e6
+        wt5 = wt.open(os.path.join(directory, relpath))
+        name = wt5.natural_name
+        try:
+            created = wt5.created.human
+        except:  # likely an old timestamp that cannot be parsed
+            created = wt5.attrs["created"]
 
-    table = Table(title=directory)
+        if isinstance(wt5, wt.Data):
+            shape = wt5.shape
+            axes = wt5.axis_expressions
+            nvars = len(wt5.variables)
+            nchan = len(wt5.channels)
+        elif isinstance(wt5, wt.Collection):
+            shape = axes = nvars = nchan = "---"            
+        return [
+            str(i), relpath, f"{size:0.1f}", created, name, str(shape), str(axes), str(nvars), str(nchan) 
+        ]
+
+    table = Table(title=directory + f" ({len(paths)} wt5 file{'s' if len(paths) != 1 else None} found)")
     table.add_column("", justify="right")  # index
-    table.add_column("path", max_width=60)
+    table.add_column("path", max_width=60, no_wrap=True)
     table.add_column("size (MB)", justify="center")
     table.add_column("created", max_width=30)
     table.add_column("name")
     table.add_column("shape")
-    table.add_column("axes")
+    table.add_column("axes", max_width=50)
     table.add_column("variables")
     table.add_column("channels")
 
-
-    for i, pathname in enumerate(paths):
-        path = os.path.join(directory, pathname)
-        d = wt.open(path)
-        infos = [str(i), pathname, str(int(os.path.getsize(path)/1e6)), *_format_entry(d)]
-        table.add_row(*infos)
-
-        if pausing:
-            msg = shell.raw_input("Interact ([n=no]/y=yes/q=quit)? ")
-            if msg.lower() in ["q", "quit"]:
-                break
-            elif msg.lower() in ["y", "yes"]:
-                _interact(shell, os.path.join(directory, pathname), isinstance(d, wt.Collection))
-                print("-" * 100)
-            else:
-                continue
-        d.close()
-
-
-from typing import Tuple, Optional
-class TableEntry:
-    created: str = ""
-    name: str = ""
-    shape: Optional(Tuple(int))
-    axes: Optional(Tuple(str))
-    nvars: Optional(int)
-    nchan: Optional(int)
-    def __init__(self, wt5):
-        self.name = wt5.natural_name
-        self.created = wt5.attrs["created"].date
-        if isinstance(wt5, wt.Data):
-            self.shape = wt5.shape
-            self.axes = wt5.axis_expressions
-            self.nvars = len(wt5.variables)
-            self.nchan = len(wt5.channels)
-
+    with Live(table) as live:
+        for i, path in enumerate(paths):
+            table.add_row(*_parse_entry(i, path))
+            live.update(table)
     
+    # give option to interact
+    shell = code.InteractiveConsole()
+    msg = shell.raw_input("Do you wish to load an entry? (specify an index to load, or don't and exit) ")
+    try:
+        valid = 0 < int(msg) + 1 < len(paths)
+    except ValueError:
+        print("invalid index")
+        return    
+    if valid:
+        _interact(shell, os.path.join(directory, paths[int(msg)]))
 
 
-
-
-def _format_entry(wt5, format=None):
-    if isinstance(wt5, wt.Data):
-        values = [f"{wt5.attrs['created']}", wt5.natural_name, f"{wt5.shape}", f"{wt5.axis_expressions}", str(len(wt5.variables)), str(len(wt5.channels))]
-    elif isinstance(wt5, wt.Collection):
-        values = ["---"] + [wt5.natural_name] + ["---"] * 4
-    else:
-        values = ["---"] + ["<unknown>"] + ["---"] * 4
-    return values
-
-
-def _interact(shell, path, is_collection):
+def _interact(shell, path):
     lines = [
         "import WrightTools as wt",
         "import matplotlib.pyplot as plt",
-        f"{'c' if is_collection else 'd'} = wt.open(r'{path}')",
+        f"d = wt.open(r'{path}')",
     ]
 
     [shell.push(line) for line in lines]

From 3af74fa879ad5d85f0a1ee854b5653750cfe0865 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 19:04:58 +0000
Subject: [PATCH 08/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/__main__.py | 32 ++++++++++++++++++++++++--------
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index aa8b56437..c507c3013 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -35,19 +35,23 @@ def tree(path, internal_path, depth=9, verbose=False):
 @click.argument("path")
 def load(path):
     import code
+
     # def raise_sys_exit():
     #     raise SystemExit
-    shell = code.InteractiveConsole() # locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
+    shell = code.InteractiveConsole()  # locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
     _interact(shell, path)
 
 
 @cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
-@click.option("--directory", "-d", default=None, help="Directory to crawl.  Defaults to current directory.")
+@click.option(
+    "--directory", "-d", default=None, help="Directory to crawl.  Defaults to current directory."
+)
 @click.option("--recursive", "-r", is_flag=True, help="Explore all levels of the directory")
 @click.option("--format", "-f", default=None, help="Formatting keys (default only atm)")
 # TODO: write output as an option; format kwarg?
 def crawl(directory=None, recursive=False, format=None):
     import glob, os, code
+
     # from rich.console import Console
     from rich.live import Live
     from rich.table import Table
@@ -72,12 +76,22 @@ def _parse_entry(i, relpath):
             nvars = len(wt5.variables)
             nchan = len(wt5.channels)
         elif isinstance(wt5, wt.Collection):
-            shape = axes = nvars = nchan = "---"            
+            shape = axes = nvars = nchan = "---"
         return [
-            str(i), relpath, f"{size:0.1f}", created, name, str(shape), str(axes), str(nvars), str(nchan) 
+            str(i),
+            relpath,
+            f"{size:0.1f}",
+            created,
+            name,
+            str(shape),
+            str(axes),
+            str(nvars),
+            str(nchan),
         ]
 
-    table = Table(title=directory + f" ({len(paths)} wt5 file{'s' if len(paths) != 1 else None} found)")
+    table = Table(
+        title=directory + f" ({len(paths)} wt5 file{'s' if len(paths) != 1 else None} found)"
+    )
     table.add_column("", justify="right")  # index
     table.add_column("path", max_width=60, no_wrap=True)
     table.add_column("size (MB)", justify="center")
@@ -92,15 +106,17 @@ def _parse_entry(i, relpath):
         for i, path in enumerate(paths):
             table.add_row(*_parse_entry(i, path))
             live.update(table)
-    
+
     # give option to interact
     shell = code.InteractiveConsole()
-    msg = shell.raw_input("Do you wish to load an entry? (specify an index to load, or don't and exit) ")
+    msg = shell.raw_input(
+        "Do you wish to load an entry? (specify an index to load, or don't and exit) "
+    )
     try:
         valid = 0 < int(msg) + 1 < len(paths)
     except ValueError:
         print("invalid index")
-        return    
+        return
     if valid:
         _interact(shell, os.path.join(directory, paths[int(msg)]))
 

From bae841e1c11d88eb7e460d01e85aa23c591159cb Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Thu, 1 Feb 2024 19:13:50 -0600
Subject: [PATCH 09/33] entry point crawl revision

---
 WrightTools/__main__.py     | 62 ++++++++++++-------------------------
 WrightTools/kit/__init__.py |  2 ++
 WrightTools/kit/_glob.py    | 37 ++++++++++++++++++++++
 setup.py                    |  1 +
 4 files changed, 60 insertions(+), 42 deletions(-)
 create mode 100644 WrightTools/kit/_glob.py

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index c507c3013..972a017ce 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -36,9 +36,7 @@ def tree(path, internal_path, depth=9, verbose=False):
 def load(path):
     import code
 
-    # def raise_sys_exit():
-    #     raise SystemExit
-    shell = code.InteractiveConsole()  # locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
+    shell = code.InteractiveConsole()
     _interact(shell, path)
 
 
@@ -46,48 +44,16 @@ def load(path):
 @click.option(
     "--directory", "-d", default=None, help="Directory to crawl.  Defaults to current directory."
 )
-@click.option("--recursive", "-r", is_flag=True, help="Explore all levels of the directory")
-@click.option("--format", "-f", default=None, help="Formatting keys (default only atm)")
-# TODO: write output as an option; format kwarg?
-def crawl(directory=None, recursive=False, format=None):
+# TODO: formatting options (e.g. json)?
+def crawl(directory=None):
     import glob, os, code
-
-    # from rich.console import Console
     from rich.live import Live
     from rich.table import Table
 
     if directory is None:
         directory = os.getcwd()
 
-    paths = glob.glob("**/*.wt5", root_dir=directory, recursive=recursive)
-
-    def _parse_entry(i, relpath):
-        size = os.path.getsize(os.path.join(directory, relpath)) / 1e6
-        wt5 = wt.open(os.path.join(directory, relpath))
-        name = wt5.natural_name
-        try:
-            created = wt5.created.human
-        except:  # likely an old timestamp that cannot be parsed
-            created = wt5.attrs["created"]
-
-        if isinstance(wt5, wt.Data):
-            shape = wt5.shape
-            axes = wt5.axis_expressions
-            nvars = len(wt5.variables)
-            nchan = len(wt5.channels)
-        elif isinstance(wt5, wt.Collection):
-            shape = axes = nvars = nchan = "---"
-        return [
-            str(i),
-            relpath,
-            f"{size:0.1f}",
-            created,
-            name,
-            str(shape),
-            str(axes),
-            str(nvars),
-            str(nchan),
-        ]
+    paths = list(wt.kit.find_wt5s(directory))
 
     table = Table(
         title=directory + f" ({len(paths)} wt5 file{'s' if len(paths) != 1 else None} found)"
@@ -104,7 +70,20 @@ def _parse_entry(i, relpath):
 
     with Live(table) as live:
         for i, path in enumerate(paths):
-            table.add_row(*_parse_entry(i, path))
+            desc = wt.kit.describe_wt5(path)
+            desc["filesize"] = f"{os.path.getsize(path) / 1e6:.1f}"
+            desc["path"] = str(path.relative_to(directory))
+            row = [str(i)] + [str(desc[k]) for k in [
+                "path",
+                "filesize",
+                "created",
+                "name",
+                "shape",
+                "axes",
+                "nvars",
+                "nchan"
+            ]]
+            table.add_row(*row)
             live.update(table)
 
     # give option to interact
@@ -113,12 +92,11 @@ def _parse_entry(i, relpath):
         "Do you wish to load an entry? (specify an index to load, or don't and exit) "
     )
     try:
-        valid = 0 < int(msg) + 1 < len(paths)
+        valid = 0 <= int(msg) < len(paths)
     except ValueError:
-        print("invalid index")
         return
     if valid:
-        _interact(shell, os.path.join(directory, paths[int(msg)]))
+        _interact(shell, str(paths[int(msg)]))
 
 
 def _interact(shell, path):
diff --git a/WrightTools/kit/__init__.py b/WrightTools/kit/__init__.py
index a1966fbe1..0a2978e9c 100644
--- a/WrightTools/kit/__init__.py
+++ b/WrightTools/kit/__init__.py
@@ -13,3 +13,5 @@
 from ._timestamp import *
 from ._unicode import *
 from ._utilities import *
+from ._glob import *
+
diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
new file mode 100644
index 000000000..115cb22a1
--- /dev/null
+++ b/WrightTools/kit/_glob.py
@@ -0,0 +1,37 @@
+import pathlib
+import os
+from typing import Union
+from ..data import Data
+from ..collection import Collection
+from .._open import open
+
+
+__all__ = ["describe_wt5", "find_wt5s"]
+
+
+def describe_wt5(path: Union[str, os.PathLike]):
+    """report useful general information about a wt5 file"""
+    wt5 = open(path)
+    desc = dict()
+    desc["name"] = wt5.natural_name
+    try:
+        desc["created"] = wt5.created.human
+    except:  # likely an old timestamp that cannot be parsed
+        desc["created"] = wt5.attrs["created"]
+
+    if isinstance(wt5, Data):
+        desc["shape"] = wt5.shape
+        desc["axes"] = wt5.axis_expressions
+        desc["nvars"] = len(wt5.variables)
+        desc["nchan"] = len(wt5.channels)
+    elif isinstance(wt5, Collection):
+        for k in ["shape", "axes", "nvars", "nchan"]:
+            desc[k] = "---"
+    wt5.close()
+    return desc
+
+
+def glob_wt5s(directory: Union[str,os.PathLike]):
+    """find all wt5 files in a directory"""
+    return pathlib.Path(directory).glob("**/*.wt5")
+    
diff --git a/setup.py b/setup.py
index 6c08e3258..dba6f42d0 100755
--- a/setup.py
+++ b/setup.py
@@ -46,6 +46,7 @@ def read(fname):
         "scipy",
         "click",
         "tidy_headers>=1.0.0",
+        "rich",
     ],
     extras_require={
         "docs": docs_require,

From 59984c6d069d99e1d0958ea47b352997bc873330 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 2 Feb 2024 01:14:06 +0000
Subject: [PATCH 10/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/__main__.py     | 14 ++++----------
 WrightTools/kit/__init__.py |  1 -
 WrightTools/kit/_glob.py    |  3 +--
 3 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 972a017ce..656824e63 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -73,16 +73,10 @@ def crawl(directory=None):
             desc = wt.kit.describe_wt5(path)
             desc["filesize"] = f"{os.path.getsize(path) / 1e6:.1f}"
             desc["path"] = str(path.relative_to(directory))
-            row = [str(i)] + [str(desc[k]) for k in [
-                "path",
-                "filesize",
-                "created",
-                "name",
-                "shape",
-                "axes",
-                "nvars",
-                "nchan"
-            ]]
+            row = [str(i)] + [
+                str(desc[k])
+                for k in ["path", "filesize", "created", "name", "shape", "axes", "nvars", "nchan"]
+            ]
             table.add_row(*row)
             live.update(table)
 
diff --git a/WrightTools/kit/__init__.py b/WrightTools/kit/__init__.py
index 0a2978e9c..4144d9074 100644
--- a/WrightTools/kit/__init__.py
+++ b/WrightTools/kit/__init__.py
@@ -14,4 +14,3 @@
 from ._unicode import *
 from ._utilities import *
 from ._glob import *
-
diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index 115cb22a1..01cd3206c 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -31,7 +31,6 @@ def describe_wt5(path: Union[str, os.PathLike]):
     return desc
 
 
-def glob_wt5s(directory: Union[str,os.PathLike]):
+def glob_wt5s(directory: Union[str, os.PathLike]):
     """find all wt5 files in a directory"""
     return pathlib.Path(directory).glob("**/*.wt5")
-    

From ce1a822e4660b49bf652fda19856f9b1f29cbdf8 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Fri, 2 Feb 2024 09:12:09 -0600
Subject: [PATCH 11/33] Update _glob.py

fix typo
---
 WrightTools/kit/_glob.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index 01cd3206c..3d19e7470 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -6,10 +6,10 @@
 from .._open import open
 
 
-__all__ = ["describe_wt5", "find_wt5s"]
+__all__ = ["describe_wt5", "glob_wt5s"]
 
 
-def describe_wt5(path: Union[str, os.PathLike]):
+def describe_wt5(path: Union[str, os.PathLike])->dict:
     """report useful general information about a wt5 file"""
     wt5 = open(path)
     desc = dict()

From b47e82a4f1f4ad8bc8c9757b91c00e5321e6b474 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 2 Feb 2024 15:12:50 +0000
Subject: [PATCH 12/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/kit/_glob.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index 3d19e7470..ca806e45f 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -9,7 +9,7 @@
 __all__ = ["describe_wt5", "glob_wt5s"]
 
 
-def describe_wt5(path: Union[str, os.PathLike])->dict:
+def describe_wt5(path: Union[str, os.PathLike]) -> dict:
     """report useful general information about a wt5 file"""
     wt5 = open(path)
     desc = dict()

From e6953faa30bee5abf2df12cd6897b2e82a0a6ec2 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Fri, 2 Feb 2024 12:36:22 -0600
Subject: [PATCH 13/33] wt-tree -> wtools

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index dba6f42d0..bba80f06a 100755
--- a/setup.py
+++ b/setup.py
@@ -68,7 +68,7 @@ def read(fname):
     license="MIT",
     url="http://wright.tools",
     keywords="spectroscopy science multidimensional visualization",
-    entry_points={"console_scripts": ["wt-tree=WrightTools.__main__:cli"]},
+    entry_points={"console_scripts": ["wtools=WrightTools.__main__:cli"]},
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",

From 82fe3c1afffa1554c7b8aa51e0e83d45b12ef91e Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Fri, 2 Feb 2024 12:36:41 -0600
Subject: [PATCH 14/33] crawl -> scan

---
 WrightTools/__main__.py  | 55 +++++++++++++++++++++++++++-------------
 WrightTools/kit/_glob.py |  6 +++--
 2 files changed, 41 insertions(+), 20 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 656824e63..942648496 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -40,23 +40,22 @@ def load(path):
     _interact(shell, path)
 
 
-@cli.command(name="crawl", help="Crawl a directory and survey the wt5 objects found.")
+@cli.command(name="scan", help="scan a directory and survey the wt5 objects found.")
 @click.option(
-    "--directory", "-d", default=None, help="Directory to crawl.  Defaults to current directory."
+    "--directory", "-d", default=None, help="Directory to scan.  Defaults to current directory."
 )
+@click.option("--no-recursion", is_flag=True, help="Turns recursive scan off.")
 # TODO: formatting options (e.g. json)?
-def crawl(directory=None):
-    import glob, os, code
+def scan(directory=None, no_recursion=False):
+    import os, code
     from rich.live import Live
     from rich.table import Table
 
     if directory is None:
         directory = os.getcwd()
 
-    paths = list(wt.kit.find_wt5s(directory))
-
     table = Table(
-        title=directory + f" ({len(paths)} wt5 file{'s' if len(paths) != 1 else None} found)"
+        title=directory
     )
     table.add_column("", justify="right")  # index
     table.add_column("path", max_width=60, no_wrap=True)
@@ -68,8 +67,12 @@ def crawl(directory=None):
     table.add_column("variables")
     table.add_column("channels")
 
+    update_title = lambda n: directory + f" ({n} wt5 file{'s' if n != 1 else None} found)"
+    paths = []
+
     with Live(table) as live:
-        for i, path in enumerate(paths):
+        for i, path in enumerate(wt.kit.glob_wt5s(directory, not no_recursion)):
+            paths.append(path)
             desc = wt.kit.describe_wt5(path)
             desc["filesize"] = f"{os.path.getsize(path) / 1e6:.1f}"
             desc["path"] = str(path.relative_to(directory))
@@ -77,20 +80,36 @@ def crawl(directory=None):
                 str(desc[k])
                 for k in ["path", "filesize", "created", "name", "shape", "axes", "nvars", "nchan"]
             ]
+            table.title = update_title(i+1)
             table.add_row(*row)
             live.update(table)
 
     # give option to interact
-    shell = code.InteractiveConsole()
-    msg = shell.raw_input(
-        "Do you wish to load an entry? (specify an index to load, or don't and exit) "
-    )
-    try:
-        valid = 0 <= int(msg) < len(paths)
-    except ValueError:
-        return
-    if valid:
-        _interact(shell, str(paths[int(msg)]))
+    def raise_sys_exit():
+        raise SystemExit
+
+    shell = code.InteractiveConsole(locals={
+        "exit": raise_sys_exit,
+        "quit": raise_sys_exit
+    })
+
+    while True:
+        msg = shell.raw_input(" ".join([
+            "Specify an index to load that entry.",
+            "Use 't' to rerender table.",
+            "Use no argument to exit.",
+        ]))
+        if msg == "t":
+            with Live(table) as live:
+                pass
+            continue
+        try:
+            valid = 0 <= int(msg) < len(paths)
+        except ValueError:
+            break
+        if valid:
+            _interact(shell, str(paths[int(msg)]))
+            continue
 
 
 def _interact(shell, path):
diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index ca806e45f..f4b04f87a 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -31,6 +31,8 @@ def describe_wt5(path: Union[str, os.PathLike]) -> dict:
     return desc
 
 
-def glob_wt5s(directory: Union[str, os.PathLike]):
+def glob_wt5s(directory: Union[str, os.PathLike], recursive=True):
     """find all wt5 files in a directory"""
-    return pathlib.Path(directory).glob("**/*.wt5")
+    pattern = "**/*.wt5" if recursive else "*.wt5"
+    print(pattern)
+    return pathlib.Path(directory).glob(pattern)

From 0de18ce50bf7c952b3bfcd02cee26152f4c67227 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 2 Feb 2024 18:36:57 +0000
Subject: [PATCH 15/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/__main__.py | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 942648496..674e7d892 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -54,9 +54,7 @@ def scan(directory=None, no_recursion=False):
     if directory is None:
         directory = os.getcwd()
 
-    table = Table(
-        title=directory
-    )
+    table = Table(title=directory)
     table.add_column("", justify="right")  # index
     table.add_column("path", max_width=60, no_wrap=True)
     table.add_column("size (MB)", justify="center")
@@ -80,7 +78,7 @@ def scan(directory=None, no_recursion=False):
                 str(desc[k])
                 for k in ["path", "filesize", "created", "name", "shape", "axes", "nvars", "nchan"]
             ]
-            table.title = update_title(i+1)
+            table.title = update_title(i + 1)
             table.add_row(*row)
             live.update(table)
 
@@ -88,17 +86,18 @@ def scan(directory=None, no_recursion=False):
     def raise_sys_exit():
         raise SystemExit
 
-    shell = code.InteractiveConsole(locals={
-        "exit": raise_sys_exit,
-        "quit": raise_sys_exit
-    })
+    shell = code.InteractiveConsole(locals={"exit": raise_sys_exit, "quit": raise_sys_exit})
 
     while True:
-        msg = shell.raw_input(" ".join([
-            "Specify an index to load that entry.",
-            "Use 't' to rerender table.",
-            "Use no argument to exit.",
-        ]))
+        msg = shell.raw_input(
+            " ".join(
+                [
+                    "Specify an index to load that entry.",
+                    "Use 't' to rerender table.",
+                    "Use no argument to exit.",
+                ]
+            )
+        )
         if msg == "t":
             with Live(table) as live:
                 pass

From b797ef76b8509f05320ab615e076841166869fc9 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Sat, 17 Feb 2024 12:49:00 -0600
Subject: [PATCH 16/33] change entry points

---
 WrightTools/__main__.py  | 29 ++++++++++++++++-------------
 WrightTools/kit/_glob.py |  3 +--
 setup.py                 |  6 +++++-
 3 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index 674e7d892..d00c9fb94 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -40,7 +40,7 @@ def load(path):
     _interact(shell, path)
 
 
-@cli.command(name="scan", help="scan a directory and survey the wt5 objects found.")
+@cli.command(name="glob", help="Scan a directory and survey the wt5 objects found.")
 @click.option(
     "--directory", "-d", default=None, help="Directory to scan.  Defaults to current directory."
 )
@@ -56,25 +56,28 @@ def scan(directory=None, no_recursion=False):
 
     table = Table(title=directory)
     table.add_column("", justify="right")  # index
-    table.add_column("path", max_width=60, no_wrap=True)
-    table.add_column("size (MB)", justify="center")
-    table.add_column("created", max_width=30)
-    table.add_column("name")
-    table.add_column("shape")
-    table.add_column("axes", max_width=50)
-    table.add_column("variables")
-    table.add_column("channels")
+    table.add_column("path", max_width=60, no_wrap=True, style="blue")
+    table.add_column("size (MB)", justify="center", style="blue")
+    table.add_column("created", max_width=30, style="blue")
+    table.add_column("name", style="blue")
+    table.add_column("shape", style="blue")
+    table.add_column("axes", max_width=50, style="blue")
+    table.add_column("variables", style="blue")
+    table.add_column("channels", style="blue")
 
     update_title = lambda n: directory + f" ({n} wt5 file{'s' if n != 1 else None} found)"
     paths = []
 
     with Live(table) as live:
         for i, path in enumerate(wt.kit.glob_wt5s(directory, not no_recursion)):
-            paths.append(path)
             desc = wt.kit.describe_wt5(path)
             desc["filesize"] = f"{os.path.getsize(path) / 1e6:.1f}"
-            desc["path"] = str(path.relative_to(directory))
-            row = [str(i)] + [
+            path = path.relative_to(directory)
+            print(path.parent)
+            desc["path"] = f"[link={path.parent}]{path.parent}[/link]" + r"\\" if str(path.parent) != "." else ""
+            desc["path"] +=  f"[bold]{path.name}[/bold]"
+            # desc["path"] = f"[link={str(path)}]{path}[/link]"
+            row = [f"{i}"] + [
                 str(desc[k])
                 for k in ["path", "filesize", "created", "name", "shape", "axes", "nvars", "nchan"]
             ]
@@ -93,7 +96,7 @@ def raise_sys_exit():
             " ".join(
                 [
                     "Specify an index to load that entry.",
-                    "Use 't' to rerender table.",
+                    "Use `t` to rerender table.",
                     "Use no argument to exit.",
                 ]
             )
diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index f4b04f87a..90c2caadc 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -33,6 +33,5 @@ def describe_wt5(path: Union[str, os.PathLike]) -> dict:
 
 def glob_wt5s(directory: Union[str, os.PathLike], recursive=True):
     """find all wt5 files in a directory"""
-    pattern = "**/*.wt5" if recursive else "*.wt5"
-    print(pattern)
+    pattern = "**/*.wt5" if recursive else f"*.wt5"
     return pathlib.Path(directory).glob(pattern)
diff --git a/setup.py b/setup.py
index bba80f06a..341ae67fe 100755
--- a/setup.py
+++ b/setup.py
@@ -68,7 +68,11 @@ def read(fname):
     license="MIT",
     url="http://wright.tools",
     keywords="spectroscopy science multidimensional visualization",
-    entry_points={"console_scripts": ["wtools=WrightTools.__main__:cli"]},
+    entry_points={"console_scripts": [
+        "wt-tree=WrightTools.__main__:tree", 
+        "wt5=WrightTools.__main__:wt5", 
+        "wt-convert=WrightTools.__main__:convert"
+    ]},
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",

From 6c59e2a5e2b32c92f7550b04370401f6f5509a88 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 17 Feb 2024 18:49:22 +0000
Subject: [PATCH 17/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/__main__.py |  8 ++++++--
 setup.py                | 12 +++++++-----
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/WrightTools/__main__.py b/WrightTools/__main__.py
index d00c9fb94..81c03f19a 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/__main__.py
@@ -74,8 +74,12 @@ def scan(directory=None, no_recursion=False):
             desc["filesize"] = f"{os.path.getsize(path) / 1e6:.1f}"
             path = path.relative_to(directory)
             print(path.parent)
-            desc["path"] = f"[link={path.parent}]{path.parent}[/link]" + r"\\" if str(path.parent) != "." else ""
-            desc["path"] +=  f"[bold]{path.name}[/bold]"
+            desc["path"] = (
+                f"[link={path.parent}]{path.parent}[/link]" + r"\\"
+                if str(path.parent) != "."
+                else ""
+            )
+            desc["path"] += f"[bold]{path.name}[/bold]"
             # desc["path"] = f"[link={str(path)}]{path}[/link]"
             row = [f"{i}"] + [
                 str(desc[k])
diff --git a/setup.py b/setup.py
index 6918a0ee8..8a1fb9739 100755
--- a/setup.py
+++ b/setup.py
@@ -68,11 +68,13 @@ def read(fname):
     license="MIT",
     url="http://wright.tools",
     keywords="spectroscopy science multidimensional visualization",
-    entry_points={"console_scripts": [
-        "wt-tree=WrightTools.__main__:tree", 
-        "wt5=WrightTools.__main__:wt5", 
-        "wt-convert=WrightTools.__main__:convert"
-    ]},
+    entry_points={
+        "console_scripts": [
+            "wt-tree=WrightTools.__main__:tree",
+            "wt5=WrightTools.__main__:wt5",
+            "wt-convert=WrightTools.__main__:convert",
+        ]
+    },
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",

From 28ebbb213b943ab905935be3b7bbe53ea3573f27 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 12:40:08 -0600
Subject: [PATCH 18/33] refactor cli

using multiple entry points
---
 WrightTools/cli/__init__.py              |  3 ++
 WrightTools/cli/_tree.py                 | 36 ++++++++++++++++
 WrightTools/cli/_units.py                | 53 ++++++++++++++++++++++++
 WrightTools/{__main__.py => cli/_wt5.py} | 52 -----------------------
 setup.py                                 |  6 +--
 5 files changed, 95 insertions(+), 55 deletions(-)
 create mode 100644 WrightTools/cli/__init__.py
 create mode 100644 WrightTools/cli/_tree.py
 create mode 100644 WrightTools/cli/_units.py
 rename WrightTools/{__main__.py => cli/_wt5.py} (65%)

diff --git a/WrightTools/cli/__init__.py b/WrightTools/cli/__init__.py
new file mode 100644
index 000000000..b1f623521
--- /dev/null
+++ b/WrightTools/cli/__init__.py
@@ -0,0 +1,3 @@
+from . import _tree
+from . import _units
+from . import _wt5
\ No newline at end of file
diff --git a/WrightTools/cli/_tree.py b/WrightTools/cli/_tree.py
new file mode 100644
index 000000000..5710fe509
--- /dev/null
+++ b/WrightTools/cli/_tree.py
@@ -0,0 +1,36 @@
+# --- import --------------------------------------------------------------------------------------
+
+
+import click
+import WrightTools as wt
+
+
+# --- define --------------------------------------------------------------------------------------
+
+
+@click.group()
+@click.version_option(wt.__version__)
+def cli():
+    pass
+
+
+@cli.command(name="tree", help="Print a given data tree.")
+@click.argument("path", nargs=1)
+@click.option(
+    "--internal_path", default="/", help="specify a path internal to the file.  Defaults to root"
+)
+@click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
+@click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
+def tree(path, internal_path, depth=9, verbose=False):
+    # open the object
+    obj = wt.open(path)[internal_path]
+
+    if isinstance(obj, wt.Data):
+        obj.print_tree(verbose=verbose)
+    else:
+        obj.print_tree(verbose=verbose, depth=depth)
+
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/WrightTools/cli/_units.py b/WrightTools/cli/_units.py
new file mode 100644
index 000000000..14ddd8ea8
--- /dev/null
+++ b/WrightTools/cli/_units.py
@@ -0,0 +1,53 @@
+# --- import --------------------------------------------------------------------------------------
+
+
+import click
+import WrightTools as wt
+
+
+# --- define --------------------------------------------------------------------------------------
+
+
+@click.group()
+@click.version_option(wt.__version__)
+def cli():
+    pass
+
+
+@cli.command(name="convert")
+@click.argument("number", type=float, nargs=1)
+@click.argument("unit", nargs=1)
+@click.argument("destination_unit", default=None, nargs=-1)
+def convert(number, unit, destination_unit=None):
+    """Convert numbers to different units."""
+
+    if int(number) == number:
+        number = int(number)
+    sig_figs = len(str(number))
+    sig_figs -= 1 if "." in str(number) else 0
+
+    def fmt(new):
+        exponent = int(f"{new:e}".split("e")[1])
+        if exponent > 6 or exponent < -3:
+            return f"{new:{sig_figs}e}"
+        else:  # if a "normal" size number
+            if sig_figs - exponent <= 0:
+                return f"{int(round(new, sig_figs-exponent))}"
+            else:
+                return f"{round(new, sig_figs-exponent)}"
+
+    if len(destination_unit):  # units provided
+        destination_unit = destination_unit[0]
+        if not wt.units.is_valid_conversion(unit, destination_unit):
+            raise wt.exceptions.UnitsError(wt.units.get_valid_conversions(unit), destination_unit)
+        new = wt.units.convert(number, unit, destination_unit)
+        print(f"{number} {unit} = {fmt(new)} {destination_unit}")
+    else:
+        valid_units = wt.units.get_valid_conversions(unit)
+        for d_unit in valid_units:
+            new = wt.units.convert(number, unit, d_unit)
+            print(f"{fmt(new)} {d_unit}")
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/WrightTools/__main__.py b/WrightTools/cli/_wt5.py
similarity index 65%
rename from WrightTools/__main__.py
rename to WrightTools/cli/_wt5.py
index 81c03f19a..3aeb30c86 100644
--- a/WrightTools/__main__.py
+++ b/WrightTools/cli/_wt5.py
@@ -14,23 +14,6 @@ def cli():
     pass
 
 
-@cli.command(name="tree", help="Print a given data tree.")
-@click.argument("path", nargs=1)
-@click.option(
-    "--internal_path", default="/", help="specify a path internal to the file.  Defaults to root"
-)
-@click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
-@click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
-def tree(path, internal_path, depth=9, verbose=False):
-    # open the object
-    obj = wt.open(path)[internal_path]
-
-    if isinstance(obj, wt.Data):
-        obj.print_tree(verbose=verbose)
-    else:
-        obj.print_tree(verbose=verbose, depth=depth)
-
-
 @cli.command(name="load", help="Open a python cli with the object pre-loaded.")
 @click.argument("path")
 def load(path):
@@ -135,40 +118,5 @@ def _interact(shell, path):
         pass
 
 
-@cli.command(name="convert")
-@click.argument("number", type=float, nargs=1)
-@click.argument("unit", nargs=1)
-@click.argument("destination_unit", default=None, nargs=-1)
-def convert(number, unit, destination_unit=None):
-    """Convert numbers to different units."""
-
-    if int(number) == number:
-        number = int(number)
-    sig_figs = len(str(number))
-    sig_figs -= 1 if "." in str(number) else 0
-
-    def fmt(new):
-        exponent = int(f"{new:e}".split("e")[1])
-        if exponent > 6 or exponent < -3:
-            return f"{new:{sig_figs}e}"
-        else:  # if a "normal" size number
-            if sig_figs - exponent <= 0:
-                return f"{int(round(new, sig_figs-exponent))}"
-            else:
-                return f"{round(new, sig_figs-exponent)}"
-
-    if len(destination_unit):  # units provided
-        destination_unit = destination_unit[0]
-        if not wt.units.is_valid_conversion(unit, destination_unit):
-            raise wt.exceptions.UnitsError(wt.units.get_valid_conversions(unit), destination_unit)
-        new = wt.units.convert(number, unit, destination_unit)
-        print(f"{number} {unit} = {fmt(new)} {destination_unit}")
-    else:
-        valid_units = wt.units.get_valid_conversions(unit)
-        for d_unit in valid_units:
-            new = wt.units.convert(number, unit, d_unit)
-            print(f"{fmt(new)} {d_unit}")
-
-
 if __name__ == "__main__":
     cli()
diff --git a/setup.py b/setup.py
index 8a1fb9739..53dbb4a4d 100755
--- a/setup.py
+++ b/setup.py
@@ -70,9 +70,9 @@ def read(fname):
     keywords="spectroscopy science multidimensional visualization",
     entry_points={
         "console_scripts": [
-            "wt-tree=WrightTools.__main__:tree",
-            "wt5=WrightTools.__main__:wt5",
-            "wt-convert=WrightTools.__main__:convert",
+            "wt-tree=WrightTools.cli._tree:cli",
+            "wt5=WrightTools.cli._wt5:cli",
+            "wt-convert=WrightTools.cli._units:cli",
         ]
     },
     classifiers=[

From a097b4296572ee85ac629f30368f356a4c536283 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 12:41:04 -0600
Subject: [PATCH 19/33] Update _glob.py

incorporate attrs filter in glob methods
---
 WrightTools/kit/_glob.py | 63 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 57 insertions(+), 6 deletions(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index 90c2caadc..08d411683 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -1,15 +1,15 @@
 import pathlib
-import os
-from typing import Union
+from os import PathLike
+from typing import Union, List, Iterator
 from ..data import Data
 from ..collection import Collection
 from .._open import open
 
 
-__all__ = ["describe_wt5", "glob_wt5s"]
+__all__ = ["describe_wt5", "filter_wt5s", "glob_wt5s", "search_for_attrs",]
 
 
-def describe_wt5(path: Union[str, os.PathLike]) -> dict:
+def describe_wt5(path: Union[str, PathLike]) -> dict:
     """report useful general information about a wt5 file"""
     wt5 = open(path)
     desc = dict()
@@ -31,7 +31,58 @@ def describe_wt5(path: Union[str, os.PathLike]) -> dict:
     return desc
 
 
-def glob_wt5s(directory: Union[str, os.PathLike], recursive=True):
-    """find all wt5 files in a directory"""
+def glob_wt5s(directory: Union[str, PathLike], recursive=True) -> Iterator:
+    """glob all wt5 files in a directory"""
     pattern = "**/*.wt5" if recursive else f"*.wt5"
     return pathlib.Path(directory).glob(pattern)
+
+
+def search_for_attrs(
+        directory: Union[str, PathLike],
+        recursive=True,
+        **kwargs
+    ) -> List[pathlib.Path]:
+    """
+    Find wt5 file(s) by matching data attrs items.  
+
+    Parameters
+    ----------
+    directory : path-like
+        directory to search
+    recursive : boolean (default True)
+        whether or not recursively search the directory
+
+    kwargs
+    ------
+    key value pairs to filter the attrs with
+
+    Returns
+    -------
+    paths : list
+        list of pathlib.Path objects that match
+    
+    Example
+    -------
+    To find a scan based on scan parameters in the bluesky-cmds:
+    >>> search_wt5_by_attr(os.environ["WT5_DATA_DIR"], name="primary", shape=[136,101], )
+    """
+    return filter_wt5s(glob_wt5s(directory, recursive), **kwargs)
+
+
+def filter_wt5s(
+        paths:List[Union[str, PathLike]],
+        **kwargs
+    ) -> List[Union[str, PathLike]]:
+    """fillter wt5s by attrs
+    """
+    return [p for p in filter(_gen_filter_by_attrs(**kwargs), paths)]
+
+
+def _gen_filter_by_attrs(**kwargs):
+    def fil(x):
+        attrs = open(x).attrs
+        if all([key in attrs for key in kwargs.keys()]):
+            return all([attrs[key] == kwargs[key] for key in kwargs])
+        else:
+            return False
+    return fil

From b8e93a9dd284e63e0017e5faa859cf5530cae6d0 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 13:44:08 -0600
Subject: [PATCH 20/33] refactor kit path/glob utils

try to use pathlib over os
---
 WrightTools/kit/_glob.py | 28 +++++++++++++++--
 WrightTools/kit/_path.py | 65 +++++++++-------------------------------
 2 files changed, 40 insertions(+), 53 deletions(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index 08d411683..a1e91ff6e 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -6,7 +6,7 @@
 from .._open import open
 
 
-__all__ = ["describe_wt5", "filter_wt5s", "glob_wt5s", "search_for_attrs",]
+__all__ = ["describe_wt5", "filter_wt5s", "glob_handler", "glob_wt5s", "search_for_attrs",]
 
 
 def describe_wt5(path: Union[str, PathLike]) -> dict:
@@ -37,6 +37,30 @@ def glob_wt5s(directory: Union[str, PathLike], recursive=True) -> Iterator:
     return pathlib.Path(directory).glob(pattern)
 
 
+def glob_handler(extension, folder=None, identifier=None, recursive=True) -> List[pathlib.Path]:
+    """Return a list of all files matching specified inputs.
+
+    Parameters
+    ----------
+    extension : string
+        File extension.
+    folder : string (optional)
+        Folder to search within. Default is None (current working
+        directory).
+    identifier : string
+        Unique identifier. Default is None.
+    recursive : bool
+        When true, searches folder and all subfolders for identifier
+
+    Returns
+    -------
+    list of pathlib.Path objects
+        path objects for matching files.
+    """
+    pattern = f"**/*.{extension}" if recursive else f"*.{extension}"
+    return [x for x in filter(lambda x: identifier in str(x), pathlib.Path(folder).glob(pattern))]
+
+
 def search_for_attrs(
         directory: Union[str, PathLike],
         recursive=True,
@@ -63,7 +87,7 @@ def search_for_attrs(
     
     Example
     -------
-    To find a scan based on scan parameters in the bluesky-cmds:
+    To find a scan from scan parameters in the bluesky-cmds:
     >>> search_wt5_by_attr(os.environ["WT5_DATA_DIR"], name="primary", shape=[136,101], )
     """
     return filter_wt5s(glob_wt5s(directory, recursive), **kwargs)
diff --git a/WrightTools/kit/_path.py b/WrightTools/kit/_path.py
index 9e386b615..cf3def9c0 100644
--- a/WrightTools/kit/_path.py
+++ b/WrightTools/kit/_path.py
@@ -3,78 +3,41 @@
 # --- import --------------------------------------------------------------------------------------
 
 
-import os
-import glob
+import pathlib
 
 
 # --- define --------------------------------------------------------------------------------------
 
 
-__all__ = ["get_path_matching", "glob_handler"]
+__all__ = ["get_path_matching"]
 
 
 # --- functions -----------------------------------------------------------------------------------
 
 
-def get_path_matching(name):
-    """Get path matching a name.
+def get_path_matching(name:str) -> pathlib.Path:
+    """
+    Non-recursive search for path to the folder "name".
+    Searches the user directory, then looks up the cwd for a parent folder that matches.
 
     Parameters
     ----------
     name : string
-        Name to search for.
+        name of directory to search for.
 
     Returns
     -------
-    string
-        Full filepath.
+    pathlib.Path
+        Full filepath to directory name.
+
     """
     # first try looking in the user folder
-    p = os.path.join(os.path.expanduser("~"), name)
+    p = pathlib.Path.home() / name
     # then try expanding upwards from cwd
-    if not os.path.isdir(p):
+    if not p.is_dir():
         p = None
-        drive, folders = os.path.splitdrive(os.getcwd())
-        folders = folders.split(os.sep)
-        folders.insert(0, os.sep)
+        drive, *folders = pathlib.Path.cwd().parts
         if name in folders:
-            p = os.path.join(drive, *folders[: folders.index(name) + 1])
+            p = pathlib.Path(drive).joinpath(*folders[:folders.index(name)+1])
     # TODO: something more robust to catch the rest of the cases?
     return p
-
-
-def glob_handler(extension, folder=None, identifier=None):
-    """Return a list of all files matching specified inputs.
-
-    Parameters
-    ----------
-    extension : string
-        File extension.
-    folder : string (optional)
-        Folder to search within. Default is None (current working
-        directory).
-    identifier : string
-        Unique identifier. Default is None.
-
-    Returns
-    -------
-    list of strings
-        Full path of matching files.
-    """
-    filepaths = []
-    if folder:
-        # comment out [ and ]...
-        folder = folder.replace("[", "?")
-        folder = folder.replace("]", "*")
-        folder = folder.replace("?", "[[]")
-        folder = folder.replace("*", "[]]")
-        glob_str = os.path.join(folder, "*" + extension)
-    else:
-        glob_str = "*" + extension + "*"
-    for filepath in glob.glob(glob_str):
-        if identifier:
-            if identifier in filepath:
-                filepaths.append(filepath)
-        else:
-            filepaths.append(filepath)
-    return filepaths

From 8e4fbc2d5db65ad12623bf2e88ae31a22099bdf5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Feb 2024 19:44:23 +0000
Subject: [PATCH 21/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/cli/__init__.py |  2 +-
 WrightTools/cli/_tree.py    |  1 -
 WrightTools/kit/_glob.py    | 27 ++++++++++++++-------------
 WrightTools/kit/_path.py    |  4 ++--
 4 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/WrightTools/cli/__init__.py b/WrightTools/cli/__init__.py
index b1f623521..c8efc90b5 100644
--- a/WrightTools/cli/__init__.py
+++ b/WrightTools/cli/__init__.py
@@ -1,3 +1,3 @@
 from . import _tree
 from . import _units
-from . import _wt5
\ No newline at end of file
+from . import _wt5
diff --git a/WrightTools/cli/_tree.py b/WrightTools/cli/_tree.py
index 5710fe509..e52d51dee 100644
--- a/WrightTools/cli/_tree.py
+++ b/WrightTools/cli/_tree.py
@@ -31,6 +31,5 @@ def tree(path, internal_path, depth=9, verbose=False):
         obj.print_tree(verbose=verbose, depth=depth)
 
 
-
 if __name__ == "__main__":
     cli()
diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index a1e91ff6e..c0d051b14 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -6,7 +6,13 @@
 from .._open import open
 
 
-__all__ = ["describe_wt5", "filter_wt5s", "glob_handler", "glob_wt5s", "search_for_attrs",]
+__all__ = [
+    "describe_wt5",
+    "filter_wt5s",
+    "glob_handler",
+    "glob_wt5s",
+    "search_for_attrs",
+]
 
 
 def describe_wt5(path: Union[str, PathLike]) -> dict:
@@ -62,12 +68,10 @@ def glob_handler(extension, folder=None, identifier=None, recursive=True) -> Lis
 
 
 def search_for_attrs(
-        directory: Union[str, PathLike],
-        recursive=True,
-        **kwargs
-    ) -> List[pathlib.Path]:
+    directory: Union[str, PathLike], recursive=True, **kwargs
+) -> List[pathlib.Path]:
     """
-    Find wt5 file(s) by matching data attrs items.  
+    Find wt5 file(s) by matching data attrs items.
 
     Parameters
     ----------
@@ -84,7 +88,7 @@ def search_for_attrs(
     -------
     paths : list
         list of pathlib.Path objects that match
-    
+
     Example
     -------
     To find a scan from scan parameters in the bluesky-cmds:
@@ -93,12 +97,8 @@ def search_for_attrs(
     return filter_wt5s(glob_wt5s(directory, recursive), **kwargs)
 
 
-def filter_wt5s(
-        paths:List[Union[str, PathLike]],
-        **kwargs
-    ) -> List[Union[str, PathLike]]:
-    """fillter wt5s by attrs
-    """
+def filter_wt5s(paths: List[Union[str, PathLike]], **kwargs) -> List[Union[str, PathLike]]:
+    """fillter wt5s by attrs"""
     return [p for p in filter(_gen_filter_by_attrs(**kwargs), paths)]
 
 
@@ -109,4 +109,5 @@ def fil(x):
             return all([attrs[key] == kwargs[key] for key in kwargs])
         else:
             return False
+
     return fil
diff --git a/WrightTools/kit/_path.py b/WrightTools/kit/_path.py
index cf3def9c0..d7c558bea 100644
--- a/WrightTools/kit/_path.py
+++ b/WrightTools/kit/_path.py
@@ -15,7 +15,7 @@
 # --- functions -----------------------------------------------------------------------------------
 
 
-def get_path_matching(name:str) -> pathlib.Path:
+def get_path_matching(name: str) -> pathlib.Path:
     """
     Non-recursive search for path to the folder "name".
     Searches the user directory, then looks up the cwd for a parent folder that matches.
@@ -38,6 +38,6 @@ def get_path_matching(name:str) -> pathlib.Path:
         p = None
         drive, *folders = pathlib.Path.cwd().parts
         if name in folders:
-            p = pathlib.Path(drive).joinpath(*folders[:folders.index(name)+1])
+            p = pathlib.Path(drive).joinpath(*folders[: folders.index(name) + 1])
     # TODO: something more robust to catch the rest of the cases?
     return p

From 7757bbbd84ced93e264739a382df6f0f3b1744dc Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 14:24:31 -0600
Subject: [PATCH 22/33] Update _wt5.py

---
 WrightTools/cli/_wt5.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/WrightTools/cli/_wt5.py b/WrightTools/cli/_wt5.py
index 3aeb30c86..a8473c060 100644
--- a/WrightTools/cli/_wt5.py
+++ b/WrightTools/cli/_wt5.py
@@ -56,7 +56,7 @@ def scan(directory=None, no_recursion=False):
             desc = wt.kit.describe_wt5(path)
             desc["filesize"] = f"{os.path.getsize(path) / 1e6:.1f}"
             path = path.relative_to(directory)
-            print(path.parent)
+            paths.append(path)
             desc["path"] = (
                 f"[link={path.parent}]{path.parent}[/link]" + r"\\"
                 if str(path.parent) != "."
@@ -97,6 +97,7 @@ def raise_sys_exit():
         except ValueError:
             break
         if valid:
+            print("interacting...")
             _interact(shell, str(paths[int(msg)]))
             continue
 

From acc6b366b5d5a9e23d1681c698636a27346ecb44 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 15:50:52 -0600
Subject: [PATCH 23/33] Update _glob.py

---
 WrightTools/kit/_glob.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index c0d051b14..01be2a54e 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -98,16 +98,16 @@ def search_for_attrs(
 
 
 def filter_wt5s(paths: List[Union[str, PathLike]], **kwargs) -> List[Union[str, PathLike]]:
-    """fillter wt5s by attrs"""
+    """fillter a list of wt5 paths by attrs"""
     return [p for p in filter(_gen_filter_by_attrs(**kwargs), paths)]
 
 
 def _gen_filter_by_attrs(**kwargs):
-    def fil(x):
+    def filter(x):
         attrs = open(x).attrs
         if all([key in attrs for key in kwargs.keys()]):
             return all([attrs[key] == kwargs[key] for key in kwargs])
         else:
             return False
 
-    return fil
+    return filter

From 2c4de2cdb20b84692d98c7f683a5e1dfc5e2d79f Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 16:01:43 -0600
Subject: [PATCH 24/33] tree and convert work

---
 WrightTools/cli/_tree.py  | 9 ++-------
 WrightTools/cli/_units.py | 9 ++-------
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/WrightTools/cli/_tree.py b/WrightTools/cli/_tree.py
index e52d51dee..15114333c 100644
--- a/WrightTools/cli/_tree.py
+++ b/WrightTools/cli/_tree.py
@@ -8,20 +8,15 @@
 # --- define --------------------------------------------------------------------------------------
 
 
-@click.group()
+@click.command(name="tree", help="Print a given data tree.")
 @click.version_option(wt.__version__)
-def cli():
-    pass
-
-
-@cli.command(name="tree", help="Print a given data tree.")
 @click.argument("path", nargs=1)
 @click.option(
     "--internal_path", default="/", help="specify a path internal to the file.  Defaults to root"
 )
 @click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
 @click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
-def tree(path, internal_path, depth=9, verbose=False):
+def cli(path, internal_path, depth=9, verbose=False):
     # open the object
     obj = wt.open(path)[internal_path]
 
diff --git a/WrightTools/cli/_units.py b/WrightTools/cli/_units.py
index 14ddd8ea8..20b021411 100644
--- a/WrightTools/cli/_units.py
+++ b/WrightTools/cli/_units.py
@@ -8,17 +8,12 @@
 # --- define --------------------------------------------------------------------------------------
 
 
-@click.group()
+@click.command()
 @click.version_option(wt.__version__)
-def cli():
-    pass
-
-
-@cli.command(name="convert")
 @click.argument("number", type=float, nargs=1)
 @click.argument("unit", nargs=1)
 @click.argument("destination_unit", default=None, nargs=-1)
-def convert(number, unit, destination_unit=None):
+def cli(number, unit, destination_unit=None):
     """Convert numbers to different units."""
 
     if int(number) == number:

From fd0ddc5c25c3f746d2c068670a9363870fd6961f Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 16:57:19 -0600
Subject: [PATCH 25/33] cleanup

---
 WrightTools/cli/__init__.py |  1 -
 WrightTools/cli/_tree.py    | 30 ------------------------------
 WrightTools/cli/_units.py   | 18 ++++++++++--------
 WrightTools/cli/_wt5.py     | 20 +++++++++++++++++++-
 setup.py                    |  1 -
 5 files changed, 29 insertions(+), 41 deletions(-)
 delete mode 100644 WrightTools/cli/_tree.py

diff --git a/WrightTools/cli/__init__.py b/WrightTools/cli/__init__.py
index c8efc90b5..c534ccce2 100644
--- a/WrightTools/cli/__init__.py
+++ b/WrightTools/cli/__init__.py
@@ -1,3 +1,2 @@
-from . import _tree
 from . import _units
 from . import _wt5
diff --git a/WrightTools/cli/_tree.py b/WrightTools/cli/_tree.py
deleted file mode 100644
index 15114333c..000000000
--- a/WrightTools/cli/_tree.py
+++ /dev/null
@@ -1,30 +0,0 @@
-# --- import --------------------------------------------------------------------------------------
-
-
-import click
-import WrightTools as wt
-
-
-# --- define --------------------------------------------------------------------------------------
-
-
-@click.command(name="tree", help="Print a given data tree.")
-@click.version_option(wt.__version__)
-@click.argument("path", nargs=1)
-@click.option(
-    "--internal_path", default="/", help="specify a path internal to the file.  Defaults to root"
-)
-@click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
-@click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
-def cli(path, internal_path, depth=9, verbose=False):
-    # open the object
-    obj = wt.open(path)[internal_path]
-
-    if isinstance(obj, wt.Data):
-        obj.print_tree(verbose=verbose)
-    else:
-        obj.print_tree(verbose=verbose, depth=depth)
-
-
-if __name__ == "__main__":
-    cli()
diff --git a/WrightTools/cli/_units.py b/WrightTools/cli/_units.py
index 20b021411..fd5f8eb2d 100644
--- a/WrightTools/cli/_units.py
+++ b/WrightTools/cli/_units.py
@@ -2,14 +2,16 @@
 
 
 import click
-import WrightTools as wt
+from WrightTools import __version__ as __wt_version__
+from WrightTools.units import is_valid_conversion, get_valid_conversions, convert
+from WrightTools.exceptions import UnitsError
 
 
 # --- define --------------------------------------------------------------------------------------
 
 
-@click.command()
-@click.version_option(wt.__version__)
+@click.command(name="convert", help="convert numbers to different units.")
+@click.version_option(__wt_version__, package_name="WrightTools")
 @click.argument("number", type=float, nargs=1)
 @click.argument("unit", nargs=1)
 @click.argument("destination_unit", default=None, nargs=-1)
@@ -33,14 +35,14 @@ def fmt(new):
 
     if len(destination_unit):  # units provided
         destination_unit = destination_unit[0]
-        if not wt.units.is_valid_conversion(unit, destination_unit):
-            raise wt.exceptions.UnitsError(wt.units.get_valid_conversions(unit), destination_unit)
-        new = wt.units.convert(number, unit, destination_unit)
+        if not is_valid_conversion(unit, destination_unit):
+            raise UnitsError(get_valid_conversions(unit), destination_unit)
+        new = convert(number, unit, destination_unit)
         print(f"{number} {unit} = {fmt(new)} {destination_unit}")
     else:
-        valid_units = wt.units.get_valid_conversions(unit)
+        valid_units = get_valid_conversions(unit)
         for d_unit in valid_units:
-            new = wt.units.convert(number, unit, d_unit)
+            new = convert(number, unit, d_unit)
             print(f"{fmt(new)} {d_unit}")
 
 
diff --git a/WrightTools/cli/_wt5.py b/WrightTools/cli/_wt5.py
index a8473c060..75fe8ed2c 100644
--- a/WrightTools/cli/_wt5.py
+++ b/WrightTools/cli/_wt5.py
@@ -9,11 +9,29 @@
 
 
 @click.group()
-@click.version_option(wt.__version__)
+@click.version_option(wt.__version__, prog_name="WrightTools")
 def cli():
     pass
 
 
+@cli.command(name="tree", help="Print a given data tree.")
+@click.argument("path", nargs=1)
+@click.option(
+    "--internal_path", default="/", help="specify a path internal to the file.  Defaults to root"
+)
+@click.option("--depth", "-d", "-L", type=int, default=9, help="Depth to print.")
+@click.option("--verbose", "-v", is_flag=True, default=False, help="Print a more detailed tree.")
+def tree(path, internal_path, depth=9, verbose=False):
+    # open the object
+    obj = wt.open(path)[internal_path]
+
+    if isinstance(obj, wt.Data):
+        obj.print_tree(verbose=verbose)
+    else:
+        obj.print_tree(verbose=verbose, depth=depth)
+
+
+
 @cli.command(name="load", help="Open a python cli with the object pre-loaded.")
 @click.argument("path")
 def load(path):
diff --git a/setup.py b/setup.py
index 53dbb4a4d..d4fe3588a 100755
--- a/setup.py
+++ b/setup.py
@@ -70,7 +70,6 @@ def read(fname):
     keywords="spectroscopy science multidimensional visualization",
     entry_points={
         "console_scripts": [
-            "wt-tree=WrightTools.cli._tree:cli",
             "wt5=WrightTools.cli._wt5:cli",
             "wt-convert=WrightTools.cli._units:cli",
         ]

From b380fcd1e0512e64e9c5a9a1f2b23966e9e580ac Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 16:57:31 -0600
Subject: [PATCH 26/33] docs

---
 docs/cli.rst   | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++
 docs/index.rst |  1 +
 2 files changed, 59 insertions(+)
 create mode 100644 docs/cli.rst

diff --git a/docs/cli.rst b/docs/cli.rst
new file mode 100644
index 000000000..ea5d5db84
--- /dev/null
+++ b/docs/cli.rst
@@ -0,0 +1,58 @@
+.. _cli:
+
+Command Line Interface (CLI)
+============================
+
+Most of the CLI interface is new as of v3.5.2 and under active depelopment.
+The commands here may change.
+Currently, there are two supported CLI calls to use:  `wt-units`, and `wt5`.
+For usage hints, use the `--help` argument.
+
+wt-units
+----------
+
+Use wt-units to explore the WrightTools units system and the conversions of units.
+
+.. code-block:: shell
+    > wt-units 1330 nm wn
+    7692.3 wn
+    0.95372 eV
+    953.72 meV
+    2.306096e+14 Hz
+    230.61 THz
+    230610 GHz
+
+wt5
+---
+
+The wt5 command is meant to provide easy access to wt5 files and some basic wt5 properties.
+
+Use `wt5 glob` to quickly probe a folder for wt5s contained inside
+
+.. code-block:: shell
+
+    > wt5 glob -d path/to/datasets
+    "
+    ┏━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━┓
+    ┃   ┃ path                                                ┃ size (MB) ┃ created             ┃ name          ┃ shape        ┃ axes                  ┃ variables ┃ channels ┃
+    ┡━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━┩
+    │ 0 │ tests\dataset\max_cached.wt5                        │    0.0    │ 2020-11-16 23:49:27 │ data          │ (3,)         │ ()                    │ 1         │ 0        │
+    │ 1 │ WrightTools\datasets\wt5\v1.0.0\perovskite_TA.wt5   │    3.4    │ 2016.03.28 21_15_20 │ perovskite_TA │ (52, 52, 13) │ ('w1=wm', 'w2', 'd2') │ 27        │ 10       │
+    │ 2 │ WrightTools\datasets\wt5\v1.0.1\MoS2_TrEE_movie.wt5 │    2.3    │ 2018-06-11 16:41:47 │ _001_dat      │ (41, 41, 23) │ ('w2', 'w1=wm', 'd2') │ 7         │ 6        │
+    └───┴─────────────────────────────────────────────────────┴───────────┴─────────────────────┴───────────────┴──────────────┴───────────────────────┴───────────┴──────────┘
+    Specify an index to load that entry. Use `t` to rerender table. Use no argument to exit.
+    "
+
+Use `wt5 load` to quickly open an interactive python console with your wt5 data pre-loaded. 
+
+Use `wt5 tree` to see a quick tree structure of a wt5 file.
+
+.. code-block:: shell
+    > wt5 tree path\to\data
+    "
+    / (...\felu75fe.wt5) (25, 256)
+    ├── axes (2): w2 (wn), w2-wa (wn)
+    ├── constants (0):
+    └── channels (1): array_signal
+    "
+
diff --git a/docs/index.rst b/docs/index.rst
index 82c408986..89b9a2568 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -55,6 +55,7 @@ Contents
    datasets
    contributing
    wt5
+   cli
    api/modules
    auto_examples/index
    citation

From f7d44a62066f95535b72706ec9f8fa4009899d9d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Feb 2024 22:57:48 +0000
Subject: [PATCH 27/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/cli/_wt5.py | 1 -
 docs/cli.rst            | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/WrightTools/cli/_wt5.py b/WrightTools/cli/_wt5.py
index 75fe8ed2c..f1d9e1e38 100644
--- a/WrightTools/cli/_wt5.py
+++ b/WrightTools/cli/_wt5.py
@@ -31,7 +31,6 @@ def tree(path, internal_path, depth=9, verbose=False):
         obj.print_tree(verbose=verbose, depth=depth)
 
 
-
 @cli.command(name="load", help="Open a python cli with the object pre-loaded.")
 @click.argument("path")
 def load(path):
diff --git a/docs/cli.rst b/docs/cli.rst
index ea5d5db84..d103d2caa 100644
--- a/docs/cli.rst
+++ b/docs/cli.rst
@@ -43,7 +43,7 @@ Use `wt5 glob` to quickly probe a folder for wt5s contained inside
     Specify an index to load that entry. Use `t` to rerender table. Use no argument to exit.
     "
 
-Use `wt5 load` to quickly open an interactive python console with your wt5 data pre-loaded. 
+Use `wt5 load` to quickly open an interactive python console with your wt5 data pre-loaded.
 
 Use `wt5 tree` to see a quick tree structure of a wt5 file.
 

From ba91121ff4247f9daf98db16a8fe617348a5a656 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 18:40:17 -0600
Subject: [PATCH 28/33] Update wt_tree.py

---
 tests/entry_points/wt_tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/entry_points/wt_tree.py b/tests/entry_points/wt_tree.py
index 6ab6bf221..f9a3f5e02 100644
--- a/tests/entry_points/wt_tree.py
+++ b/tests/entry_points/wt_tree.py
@@ -11,7 +11,7 @@ def test_no_change():
     before = hashlib.sha1()
     with open("test_no_change.wt5", "rb") as f:
         before.update(f.read())
-    subprocess.call(["wt-tree", "test_no_change.wt5"])
+    subprocess.call(["wt5", "tree", "test_no_change.wt5"])
     after = hashlib.sha1()
     with open("test_no_change.wt5", "rb") as f:
         after.update(f.read())

From f6c2b00c683d4d0ad551f13537be851a0708326c Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 19 Feb 2024 18:41:38 -0600
Subject: [PATCH 29/33] Update _units.py

---
 WrightTools/cli/_units.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/WrightTools/cli/_units.py b/WrightTools/cli/_units.py
index fd5f8eb2d..93044877a 100644
--- a/WrightTools/cli/_units.py
+++ b/WrightTools/cli/_units.py
@@ -11,7 +11,7 @@
 
 
 @click.command(name="convert", help="convert numbers to different units.")
-@click.version_option(__wt_version__, package_name="WrightTools")
+@click.version_option(__wt_version__, prog_name="WrightTools")
 @click.argument("number", type=float, nargs=1)
 @click.argument("unit", nargs=1)
 @click.argument("destination_unit", default=None, nargs=-1)

From 28a6befe707071bcf4775aae575ec85c0003d1d4 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Tue, 20 Feb 2024 10:42:36 -0600
Subject: [PATCH 30/33] Update _glob.py

directory is optional argument for most methods
---
 WrightTools/kit/_glob.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index 01be2a54e..dd2b1a359 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -37,20 +37,22 @@ def describe_wt5(path: Union[str, PathLike]) -> dict:
     return desc
 
 
-def glob_wt5s(directory: Union[str, PathLike], recursive=True) -> Iterator:
+def glob_wt5s(directory: Union[str, PathLike, None]=None, recursive=True) -> Iterator:
     """glob all wt5 files in a directory"""
+    if directory is None:
+        directory = pathlib.Path.cwd()
     pattern = "**/*.wt5" if recursive else f"*.wt5"
     return pathlib.Path(directory).glob(pattern)
 
 
-def glob_handler(extension, folder=None, identifier=None, recursive=True) -> List[pathlib.Path]:
+def glob_handler(extension, directory=None, identifier=None, recursive=True) -> List[pathlib.Path]:
     """Return a list of all files matching specified inputs.
 
     Parameters
     ----------
     extension : string
         File extension.
-    folder : string (optional)
+    directory : string (optional)
         Folder to search within. Default is None (current working
         directory).
     identifier : string
@@ -63,12 +65,14 @@ def glob_handler(extension, folder=None, identifier=None, recursive=True) -> Lis
     list of pathlib.Path objects
         path objects for matching files.
     """
+    if directory is None:
+        directory = pathlib.Path.cwd()
     pattern = f"**/*.{extension}" if recursive else f"*.{extension}"
-    return [x for x in filter(lambda x: identifier in str(x), pathlib.Path(folder).glob(pattern))]
+    return [x for x in filter(lambda x: identifier in str(x), pathlib.Path(directory).glob(pattern))]
 
 
 def search_for_attrs(
-    directory: Union[str, PathLike], recursive=True, **kwargs
+    directory: Union[str, PathLike, None]=None, recursive=True, **kwargs
 ) -> List[pathlib.Path]:
     """
     Find wt5 file(s) by matching data attrs items.
@@ -76,7 +80,7 @@ def search_for_attrs(
     Parameters
     ----------
     directory : path-like
-        directory to search
+        directory to search.  Defaults to cwd.
     recursive : boolean (default True)
         whether or not recursively search the directory
 

From fae48aed283ce3d84443cc334b822fac7a95e29d Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Tue, 20 Feb 2024 12:55:03 -0600
Subject: [PATCH 31/33] wt5 glob and explore

---
 WrightTools/cli/_wt5.py | 12 +++++++++++-
 docs/cli.rst            | 23 +++++++++++++++++++----
 2 files changed, 30 insertions(+), 5 deletions(-)

diff --git a/WrightTools/cli/_wt5.py b/WrightTools/cli/_wt5.py
index f1d9e1e38..9cd94b351 100644
--- a/WrightTools/cli/_wt5.py
+++ b/WrightTools/cli/_wt5.py
@@ -40,7 +40,17 @@ def load(path):
     _interact(shell, path)
 
 
-@cli.command(name="glob", help="Scan a directory and survey the wt5 objects found.")
+@cli.command(name="glob", help="Find paths to all wt5 files within a directory.")
+@click.option(
+    "--directory", "-d", default=None, help="Directory to scan.  Defaults to current directory."
+)
+@click.option("--no-recursion", is_flag=True, help="Turns recursive scan off.")
+def glob(directory=None, no_recursion=False):
+    for path in wt.kit.glob_wt5s(directory, not no_recursion):
+        print(str(path))
+
+
+@cli.command(name="explore", help="Scan a directory and survey the wt5 objects found.")
 @click.option(
     "--directory", "-d", default=None, help="Directory to scan.  Defaults to current directory."
 )
diff --git a/docs/cli.rst b/docs/cli.rst
index d103d2caa..2ef596a2a 100644
--- a/docs/cli.rst
+++ b/docs/cli.rst
@@ -5,13 +5,13 @@ Command Line Interface (CLI)
 
 Most of the CLI interface is new as of v3.5.2 and under active depelopment.
 The commands here may change.
-Currently, there are two supported CLI calls to use:  `wt-units`, and `wt5`.
+Currently, there are two supported CLI calls to use:  `wt-convert`, and `wt5`.
 For usage hints, use the `--help` argument.
 
-wt-units
+wt-convert
 ----------
 
-Use wt-units to explore the WrightTools units system and the conversions of units.
+Use `wt-convert`` to explore the WrightTools units system and the conversions of units.
 
 .. code-block:: shell
     > wt-units 1330 nm wn
@@ -28,10 +28,17 @@ wt5
 The wt5 command is meant to provide easy access to wt5 files and some basic wt5 properties.
 
 Use `wt5 glob` to quickly probe a folder for wt5s contained inside
-
 .. code-block:: shell
 
     > wt5 glob -d path/to/datasets
+    tests\dataset\max_cached.wt5
+    WrightTools\datasets\wt5\v1.0.0\perovskite_TA.wt5  
+    WrightTools\datasets\wt5\v1.0.1\MoS2_TrEE_movie.wt5
+
+Use `wt5 explore` to see details of wt5s within a folder, as the option of quick load a wt5.
+.. code-block:: shell
+
+    > wt5 explore -d path/to/data/folders
     "
     ┏━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━┓
     ┃   ┃ path                                                ┃ size (MB) ┃ created             ┃ name          ┃ shape        ┃ axes                  ┃ variables ┃ channels ┃
@@ -44,6 +51,14 @@ Use `wt5 glob` to quickly probe a folder for wt5s contained inside
     "
 
 Use `wt5 load` to quickly open an interactive python console with your wt5 data pre-loaded.
+.. code-block:: shell
+    > wt5 load path\to\data_file.wt5
+    --- INTERACTING --- (to continue, call exit() or quit())
+    >>> import WrightTools as wt
+    >>> import matplotlib.pyplot as plt
+    >>> d = wt.open(r'path/to/data_file.wt5')
+    >>> 
+
 
 Use `wt5 tree` to see a quick tree structure of a wt5 file.
 

From a1f118d2f011dd7588d6e7ff8dae781c2d8ca597 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Tue, 20 Feb 2024 12:56:15 -0600
Subject: [PATCH 32/33] Update CHANGELOG.md

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c295dfdbf..34ec9f87b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 
 ## [Unreleased]
 
+### Added
+- `wt5` entry point: methods `load`, `explore`, `glob`, `tree`
+- `wt-convert` entry point: convert a number to different units
+- new glob utilities in `kit`
+
+### Changed
+- `wt-tree` entry point removed.  Use `wt5 tree` instead.
+
 ## [3.5.1]
 
 ### Added

From a05f6b32dc89c44f727e308dbf43093ccda0e7de Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 20 Feb 2024 18:57:49 +0000
Subject: [PATCH 33/33] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/kit/_glob.py | 8 +++++---
 docs/cli.rst             | 4 ++--
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/WrightTools/kit/_glob.py b/WrightTools/kit/_glob.py
index dd2b1a359..1f6bbdc17 100644
--- a/WrightTools/kit/_glob.py
+++ b/WrightTools/kit/_glob.py
@@ -37,7 +37,7 @@ def describe_wt5(path: Union[str, PathLike]) -> dict:
     return desc
 
 
-def glob_wt5s(directory: Union[str, PathLike, None]=None, recursive=True) -> Iterator:
+def glob_wt5s(directory: Union[str, PathLike, None] = None, recursive=True) -> Iterator:
     """glob all wt5 files in a directory"""
     if directory is None:
         directory = pathlib.Path.cwd()
@@ -68,11 +68,13 @@ def glob_handler(extension, directory=None, identifier=None, recursive=True) ->
     if directory is None:
         directory = pathlib.Path.cwd()
     pattern = f"**/*.{extension}" if recursive else f"*.{extension}"
-    return [x for x in filter(lambda x: identifier in str(x), pathlib.Path(directory).glob(pattern))]
+    return [
+        x for x in filter(lambda x: identifier in str(x), pathlib.Path(directory).glob(pattern))
+    ]
 
 
 def search_for_attrs(
-    directory: Union[str, PathLike, None]=None, recursive=True, **kwargs
+    directory: Union[str, PathLike, None] = None, recursive=True, **kwargs
 ) -> List[pathlib.Path]:
     """
     Find wt5 file(s) by matching data attrs items.
diff --git a/docs/cli.rst b/docs/cli.rst
index 2ef596a2a..1b576ff15 100644
--- a/docs/cli.rst
+++ b/docs/cli.rst
@@ -32,7 +32,7 @@ Use `wt5 glob` to quickly probe a folder for wt5s contained inside
 
     > wt5 glob -d path/to/datasets
     tests\dataset\max_cached.wt5
-    WrightTools\datasets\wt5\v1.0.0\perovskite_TA.wt5  
+    WrightTools\datasets\wt5\v1.0.0\perovskite_TA.wt5
     WrightTools\datasets\wt5\v1.0.1\MoS2_TrEE_movie.wt5
 
 Use `wt5 explore` to see details of wt5s within a folder, as the option of quick load a wt5.
@@ -57,7 +57,7 @@ Use `wt5 load` to quickly open an interactive python console with your wt5 data
     >>> import WrightTools as wt
     >>> import matplotlib.pyplot as plt
     >>> d = wt.open(r'path/to/data_file.wt5')
-    >>> 
+    >>>
 
 
 Use `wt5 tree` to see a quick tree structure of a wt5 file.