From 0674e10e7188abe2447e8862101cd89abc3de48b Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@sdsc.edu>
Date: Mon, 26 Jun 2023 06:51:07 -0700
Subject: [PATCH 1/5] Switch to lazy obect creation in h5unifrac_all

---
 unifrac/_methods.py | 55 +++++++++++++++++++++++++++++----------------
 1 file changed, 36 insertions(+), 19 deletions(-)

diff --git a/unifrac/_methods.py b/unifrac/_methods.py
index 9c1e616e..77f24d83 100644
--- a/unifrac/_methods.py
+++ b/unifrac/_methods.py
@@ -9,6 +9,7 @@
 from functools import reduce
 from operator import or_
 from typing import Union
+import collections.abc
 
 import numpy as np
 import pandas as pd
@@ -2552,7 +2553,38 @@ def h5unifrac(h5file: str) -> skbio.DistanceMatrix:
     return dm
 
 
-def h5unifrac_all(h5file: str) -> skbio.DistanceMatrix:
+class H5UnifracTuple(collections.abc.Sequence):
+    """Read all UniFrac distance matrices from a hdf5 file"""
+
+    def __init__(self, h5file: str):
+        self.f_u = h5py.File(h5file, "r")
+        self.order = [c.decode('ascii') for c in self.f_u['order'][:]]
+        self.nels = None
+
+    def __getitem__(self, i: int) -> skbio.DistanceMatrix:
+        i_str = 'matrix:%i' % i
+        if i == 0:
+            if 'matrix' in self.f_u.keys():
+                # single format
+                i_str = 'matrix'
+        return skbio.DistanceMatrix(self.f_u[i_str][:, :],
+                                    self.order)
+
+    def __len__(self) -> int:
+        if self.nels is None:
+            i = 0
+            if 'matrix' in self.f_u.keys():
+                # single format
+                i= 1
+            else:
+                # multi format
+                while 'matrix:%i' % i in self.f_u.keys():
+                    i = i + 1
+            self.nels = i
+        return self.nels
+    
+
+def h5unifrac_all(h5file: str) -> H5UnifracTuple:
     """Read all UniFrac distance matrices from a hdf5 file
 
     Parameters
@@ -2562,8 +2594,8 @@ def h5unifrac_all(h5file: str) -> skbio.DistanceMatrix:
 
     Returns
     -------
-    tuple(skbio.DistanceMatrix)
-        The distance matrices.
+    H5UnifracTuple
+        A collection of distance matrices.
 
     Raises
     ------
@@ -2582,22 +2614,7 @@ def h5unifrac_all(h5file: str) -> skbio.DistanceMatrix:
        phylogeny. BMC Bioinformatics 12:118 (2011).
     """
 
-    with h5py.File(h5file, "r") as f_u:
-        order = [c.decode('ascii') for c in f_u['order'][:]]
-        if 'matrix' in f_u.keys():
-            # single format
-            dms = [skbio.DistanceMatrix(
-               f_u['matrix'][:, :], order)]
-        else:
-            # multi format
-            dms = []
-            i = 0
-            while 'matrix:%i' % i in f_u.keys():
-                dms.append(skbio.DistanceMatrix(
-                             f_u['matrix:%i' % i][:, :], order))
-                i = i + 1
-
-    return dms
+    return H5UnifracTuple(h5file)
 
 
 def _build_pcoa(f_u, long_method_name, order_index,

From efcfcc39c6d078a1c141bad1d1010ec87f76520e Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@sdsc.edu>
Date: Mon, 26 Jun 2023 06:52:54 -0700
Subject: [PATCH 2/5] Fix spacing for flake

---
 unifrac/_methods.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/unifrac/_methods.py b/unifrac/_methods.py
index 77f24d83..4677edfa 100644
--- a/unifrac/_methods.py
+++ b/unifrac/_methods.py
@@ -2575,14 +2575,14 @@ def __len__(self) -> int:
             i = 0
             if 'matrix' in self.f_u.keys():
                 # single format
-                i= 1
+                i = 1
             else:
                 # multi format
                 while 'matrix:%i' % i in self.f_u.keys():
                     i = i + 1
             self.nels = i
         return self.nels
-    
+
 
 def h5unifrac_all(h5file: str) -> H5UnifracTuple:
     """Read all UniFrac distance matrices from a hdf5 file

From b2e92efd32687be1b790f40f9621e071d7276938 Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@sdsc.edu>
Date: Mon, 26 Jun 2023 07:19:42 -0700
Subject: [PATCH 3/5] Cache last accessed value to make it more use friendly

---
 unifrac/_methods.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/unifrac/_methods.py b/unifrac/_methods.py
index 4677edfa..784a6769 100644
--- a/unifrac/_methods.py
+++ b/unifrac/_methods.py
@@ -2559,16 +2559,25 @@ class H5UnifracTuple(collections.abc.Sequence):
     def __init__(self, h5file: str):
         self.f_u = h5py.File(h5file, "r")
         self.order = [c.decode('ascii') for c in self.f_u['order'][:]]
+        # cache some often used values
         self.nels = None
+        self.cached_idx = None
+        self.cached_el = None
 
     def __getitem__(self, i: int) -> skbio.DistanceMatrix:
+        if i == self.cached_idx:
+            return self.cached_el
         i_str = 'matrix:%i' % i
         if i == 0:
             if 'matrix' in self.f_u.keys():
                 # single format
                 i_str = 'matrix'
-        return skbio.DistanceMatrix(self.f_u[i_str][:, :],
-                                    self.order)
+        el = skbio.DistanceMatrix(self.f_u[i_str][:, :],
+                                  self.order)
+        # if it did not throw, cache
+        self.cached_idx = i
+        self.cached_el = el
+        return self.cached_el
 
     def __len__(self) -> int:
         if self.nels is None:

From 4654fe6767139ba95651c7930abb87b48479fa67 Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@sdsc.edu>
Date: Mon, 26 Jun 2023 07:29:10 -0700
Subject: [PATCH 4/5] Add close method

---
 unifrac/_methods.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/unifrac/_methods.py b/unifrac/_methods.py
index 784a6769..9f711195 100644
--- a/unifrac/_methods.py
+++ b/unifrac/_methods.py
@@ -2592,6 +2592,15 @@ def __len__(self) -> int:
             self.nels = i
         return self.nels
 
+    def close(self):
+        """Explicitly close the underlying file descriptor"""
+        self.f_u.close()
+        # invalidate all other cache values
+        self.order = None
+        self.nels = 0
+        self.cached_idx = None
+        self.cached_el = None
+
 
 def h5unifrac_all(h5file: str) -> H5UnifracTuple:
     """Read all UniFrac distance matrices from a hdf5 file

From 7d5f03483c069d0f3735251652b480f1f97ece72 Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@sdsc.edu>
Date: Mon, 26 Jun 2023 09:15:15 -0700
Subject: [PATCH 5/5] Add proper h5unifrac_all tests

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4b5c7655..0e5569fa 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -121,6 +121,8 @@ jobs:
         python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac('ci/test2.dm.h5'); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1"
         python -c "import unifrac; st_l=unifrac.h5permanova_dict('ci/test2.dm.h5'); assert len(st_l) == 1"
         python -c "import unifrac; pc=unifrac.h5pcoa('ci/test3.dm.h5'); print(pc); assert len(pc.eigvals) == 2"
+        ssu -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre --pcoa 3 --mode multi --subsample-depth 2 --n-subsamples 10 -r hdf5 -o ci/test4.dm.h5 -m unweighted
+        python -c "import unifrac; dm_u=unifrac.h5unifrac_all('ci/test4.dm.h5'); assert len(dm_u) == 10; print(dm_u[0]); print(dm_u[4]); print(dm_u[9]); dm_u.close(); assert len(dm_u) == 0"
         if [[ "$(uname -s)" == "Linux" ]]; 
         then
           MD5=md5sum